WorldWideScience

Sample records for human domain expert

  1. Computers Simulate Human Experts.

    Science.gov (United States)

    Roberts, Steven K.

    1983-01-01

    Discusses recent progress in artificial intelligence in such narrowly defined areas as medical and electronic diagnosis. Also discusses use of expert systems, man-machine communication problems, novel programing environments (including comments on LISP and LISP machines), and types of knowledge used (factual, heuristic, and meta-knowledge). (JN)

  2. Computers Simulate Human Experts.

    Science.gov (United States)

    Roberts, Steven K.

    1983-01-01

    Discusses recent progress in artificial intelligence in such narrowly defined areas as medical and electronic diagnosis. Also discusses use of expert systems, man-machine communication problems, novel programing environments (including comments on LISP and LISP machines), and types of knowledge used (factual, heuristic, and meta-knowledge). (JN)

  3. The genomic CDS sandbox: An assessment among domain experts.

    Science.gov (United States)

    Aziz, Ayesha; Kawamoto, Kensaku; Eilbeck, Karen; Williams, Marc S; Freimuth, Robert R; Hoffman, Mark A; Rasmussen, Luke V; Overby, Casey L; Shirts, Brian H; Hoffman, James M; Welch, Brandon M

    2016-04-01

    Genomics is a promising tool that is becoming more widely available to improve the care and treatment of individuals. While there is much assertion, genomics will most certainly require the use of clinical decision support (CDS) to be fully realized in the routine clinical setting. The National Human Genome Research Institute (NHGRI) of the National Institutes of Health recently convened an in-person, multi-day meeting on this topic. It was widely recognized that there is a need to promote the innovation and development of resources for genomic CDS such as a CDS sandbox. The purpose of this study was to evaluate a proposed approach for such a genomic CDS sandbox among domain experts and potential users. Survey results indicate a significant interest and desire for a genomic CDS sandbox environment among domain experts. These results will be used to guide the development of a genomic CDS sandbox.

  4. Outlier Detection and Explanation for Domain Experts

    DEFF Research Database (Denmark)

    Micenková, Barbora

    to poor overall performance. Furthermore, in many applications some labeled examples of outliers are available but not sufficient enough in number as training data for standard supervised learning methods. As such, this valuable information is typically ignored. We introduce a new paradigm for outlier...... to a supervised classifier. The resulting method is robust to parameters and as such it can be easily applied to data by non-experts in data mining. We also consider the case where computational resources at test time are limited and introduce a feature selection technique that respects a computational budget...

  5. Expert System Models in the Companies' Financial and Accounting Domain

    CERN Document Server

    Mates, D; Bostan, I; Grosu, V

    2010-01-01

    The present paper is based on studying, analyzing and implementing the expert systems in the financial and accounting domain of the companies, describing the use method of the informational systems that can be used in the multi-national companies, public interest institutions, and medium and small dimension economical entities, in order to optimize the managerial decisions and render efficient the financial-accounting functionality. The purpose of this paper is aimed to identifying the economical exigencies of the entities, based on the already used accounting instruments and the management software that could consent the control of the economical processes and patrimonial assets.

  6. A Novel Web-based Human Advisor Fuzzy Expert System

    Directory of Open Access Journals (Sweden)

    Vahid Rafe

    2013-02-01

    Full Text Available The applications of the Internet-based technologies and the concepts of fuzzy expert systems (FES have created new methods for sharing and distributing knowledge. However, there has been a general lack of investigation in the area of web-based fuzzy expert systems. In this paper, the issues associated with the design, development, and use of web-based applications from a standpoint of the benefits and challenges of development and utilization are investigated. The original theory and concepts in conventional FES are reviewed and a knowledge engineering framework for developing such systems is revised. For a human advisor to have a satisfying performance, expertise is a must. In addition, some of advisory rules are subject to change because of domain knowledge update. The human requests may have linguistic or crisp forms and a conventional expert system (ES is not able to overcome the fuzziness in the problem nature. In this research, a Web-based fuzzy expert system for Common Human Advisor (FES-CHA is developed and implemented to be used as a student advisor at the department‘s web portal. The system is implemented by using Microsoft Visual Studio .NET 2010, MVC and Microsoft SQL Server 2012.

  7. Expert Assessment of Human-Human Stigmergy

    Science.gov (United States)

    2005-10-01

    environments can be viewed as digital libraries (a domain with an extensive research literature [23], organizational infrastructure [22, 43], and public...266, 2004. http://www.cs.drexel.edu/~cicirello/jaamas-8-3.pdf. [17] CIDL. Canadian Initiative on Digital Libraries / Initiative Canadienne sur les...Society. 2005. http://www.ewh.ieee.org/tc/its/trans.html. [43] IFLA. Digital Libraries : Resources and Projects. 2003. Web site, http://www.ifla.org/II

  8. A Novel Web-based Human Advisor Fuzzy Expert System

    Directory of Open Access Journals (Sweden)

    Vahid Rafe

    2013-01-01

    Full Text Available The applications of the Internet-based technologies and the concepts of fuzzy expert systems (FES have creatednew methods for sharing and distributing knowledge. However, there has been a general lack of investigation in thearea of web-based fuzzy expert systems. In this paper, the issues associated with the design, development, and useof web-based applications from a standpoint of the benefits and challenges of development and utilization areinvestigated. The original theory and concepts in conventional FES are reviewed and a knowledge engineeringframework for developing such systems is revised. For a human advisor to have a satisfying performance, expertise isa must. In addition, some of advisory rules are subject to change because of domain knowledge update. The humanrequests may have linguistic or crisp forms and a conventional expert system (ES is not able to overcome thefuzziness in the problem nature. In this research, a Web-based fuzzy expert system for Common Human Advisor(FES-CHA is developed and implemented to be used as a student advisor at the department's web portal. Thesystem is implemented by using Microsoft Visual Studio .NET 2010, MVC and Microsoft SQL Server 2012.

  9. Expanding the domain of a prototype expert system with an eye on future maintenance - The FIESTA case study

    Science.gov (United States)

    Happell, Nadine; Miksell, Steven G.

    1989-01-01

    The methods by which an expert system architecture can support such key elements of domain expansion and maintenance as knowledge acquisition, representation, addition, and modification, are presently illustrated by the Fault Isolation Expert System for TDRSS Applications (FIESTA). FIESTA highlights such similarities between conventional software engineering and expert system development as the benefits that accrue to loose coupling, modularity, and documentation. A major difference, however, is the set of opportunities afforded automated end-user maintenance by expert system technology.

  10. Clinic expert information extraction based on domain model and block importance model.

    Science.gov (United States)

    Zhang, Yuanpeng; Wang, Li; Qian, Danmin; Geng, Xingyun; Yao, Dengfu; Dong, Jiancheng

    2015-11-01

    To extract expert clinic information from the Deep Web, there are two challenges to face. The first one is to make a judgment on forms. A novel method based on a domain model, which is a tree structure constructed by the attributes of query interfaces is proposed. With this model, query interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from response Web pages indexed by query interfaces. To filter the noisy information on a Web page, a block importance model is proposed, both content and spatial features are taken into account in this model. The experimental results indicate that the domain model yields a precision 4.89% higher than that of the rule-based method, whereas the block importance model yields an F1 measure 10.5% higher than that of the XPath method.

  11. Human Disease Diagnosis Using a Fuzzy Expert System

    CERN Document Server

    Hasan, Mir Anamul; Chowdhury, Ahsan Raja

    2010-01-01

    Human disease diagnosis is a complicated process and requires high level of expertise. Any attempt of developing a web-based expert system dealing with human disease diagnosis has to overcome various difficulties. This paper describes a project work aiming to develop a web-based fuzzy expert system for diagnosing human diseases. Now a days fuzzy systems are being used successfully in an increasing number of application areas; they use linguistic rules to describe systems. This research project focuses on the research and development of a web-based clinical tool designed to improve the quality of the exchange of health information between health care professionals and patients. Practitioners can also use this web-based tool to corroborate diagnosis. The proposed system is experimented on various scenarios in order to evaluate it's performance. In all the cases, proposed system exhibits satisfactory results.

  12. An Expert System Approach to Global Fault Detection and Isolation Design

    Science.gov (United States)

    1990-01-01

    problem solving skill of a human expert in a narrow domain. The development of the expert systen design assistant is feasible since the domain...technology. An expert system is a computer program that mimics the problem solving skill of a human expert in a narrow domain. The development of the expert

  13. Human Reliability for the Next Generation of Nuclear Experts

    Energy Technology Data Exchange (ETDEWEB)

    Coates, Cameron W [ORNL; Eisele, Gerhard R [ORNL

    2010-01-01

    As the nuclear renaissance progresses and today s nuclear and radiological experts retire, a new generation of experts will ultimately be recruited, trained, and replace the old guard. Selecting individuals who have the attitudes and values appropriate to work in the nuclear industry and who have the best qualifications for the position will be a key to the success of this renaissance. In a world with deep divisions on political and social issues; how a State, agency, or company assures that those hired can be trusted with the access to, and responsibilities for, nuclear and/or radiological materials is an important consideration. Human interactions invariably rely on the offering of assurance and the receipt of trust. A fundamental element in any human relationship is knowing when to trust and when to doubt. When are assurances to be believed or questioned? Human reliability programs (HRP) are used to assure a person s truthfulness and loyalty to the State. An HRP program has a number of elements and may not fit all cultures in the same form. An HRP can vary in scope from simple background checks of readily available data to full field investigations and testing. This presentation discusses possible elements for an HRP from regulation to implementation and the issues related to each element. The effects of an HRP on potential recruits will be discussed.

  14. Embedding Human Expert Cognition Into Autonomous UAS Trajectory Planning.

    Science.gov (United States)

    Narayan, Pritesh; Meyer, Patrick; Campbell, Duncan

    2013-04-01

    This paper presents a new approach for the inclusion of human expert cognition into autonomous trajectory planning for unmanned aerial systems (UASs) operating in low-altitude environments. During typical UAS operations, multiple objectives may exist; therefore, the use of multicriteria decision aid techniques can potentially allow for convergence to trajectory solutions which better reflect overall mission requirements. In that context, additive multiattribute value theory has been applied to optimize trajectories with respect to multiple objectives. A graphical user interface was developed to allow for knowledge capture from a human decision maker (HDM) through simulated decision scenarios. The expert decision data gathered are converted into value functions and corresponding criteria weightings using utility additive theory. The inclusion of preferences elicited from HDM data within an automated decision system allows for the generation of trajectories which more closely represent the candidate HDM decision preferences. This approach has been demonstrated in this paper through simulation using a fixed-wing UAS operating in low-altitude environments.

  15. Expert System Shells: Tools to Aid Human Performance.

    Science.gov (United States)

    Welsh, Jack R.; Wilson, Brent G.

    1987-01-01

    Examines expert system shells and the role a microcomputer-based expert system can play as an intelligent job aid. Characteristics of traditional and automated job aids techniques are described, and the role of instructional designers in developing expert systems within organizations is discussed. (Author/LRW)

  16. Optimizing predictive performance of CASE Ultra expert system models using the applicability domains of individual toxicity alerts.

    Science.gov (United States)

    Chakravarti, Suman K; Saiakhov, Roustem D; Klopman, Gilles

    2012-10-22

    Fragment based expert system models of toxicological end points are primarily comprised of a set of substructures that are statistically related to the toxic property in question. These special substructures are often referred to as toxicity alerts, toxicophores, or biophores. They are the main building blocks/classifying units of the model, and it is important to define the chemical structural space within which the alerts are expected to produce reliable predictions. Furthermore, defining an appropriate applicability domain is required as part of the OECD guidelines for the validation of quantitative structure-activity relationships (QSARs). In this respect, this paper describes a method to construct applicability domains for individual toxicity alerts that are part of the CASE Ultra expert system models. Defining applicability domain for individual alerts was necessary because each CASE Ultra model is comprised of multiple alerts, and different alerts of a model usually represent different toxicity mechanisms and cover different structural space; the use of an applicability domain for the overall model is often not adequate. The domain for each alert was constructed using a set of fragments that were found to be statistically related to the end point in question as opposed to using overall structural similarity or physicochemical properties. Use of the applicability domains in reducing false positive predictions is demonstrated. It is now possible to obtain ROC (receiver operating characteristic) profiles of CASE Ultra models by applying domain adherence cutoffs on the alerts identified in test chemicals. This helps in optimizing the performance of a model based on their true positive-false positive prediction trade-offs and reduce drastic effects on the predictive performance caused by the active/inactive ratio of the model's training set. None of the major currently available commercial expert systems for toxicity prediction offer the possibility to explore a

  17. Changing domains in human capital measurement

    Directory of Open Access Journals (Sweden)

    Pharny D. Chrysler-Fox

    2014-02-01

    Full Text Available Orientation: The management context is dynamic; this is especially evident in human capital as the primary source of value creation as opposed to physical and natural resources. In response, measurement methodologies have moved from a transactional approach (strategy implementation to a transformational approach (human capital contribution paradigm, as well as diverging into different purposes. To date, there has been little overlap on recent domains to consider in managing and measuring the contribution of the human resource function and employees, and how to unlock and add value.Research purpose: The aim of the study was to explore and describe changing domains within human capital management to be managed and measured.Motivation for the study: The motivation was to advance the understanding of changing measurement domains to aid practitioners to manage and measure the contribution of the human resource function and employees, in order to unlock and add value and ultimately contribute to the success of an organisation.Research design, approach and method: Unstructured, in-depth interview data of purposively selected cases from a selected panel of human resource practitioners specialising in human capital measurement was thematically analysed in this exploratory-descriptive investigation.Main findings: Findings suggested that seven domains should be managed and measured. These domains highlight new areas of impact and levels of management. In addition, crossdomain relationships in measurement allow for an understanding of the impact and potential value on which to capitalise.Practical/managerial implications: New domains to manage and measure focus the attention of practitioners beyond the transactional performance management paradigm to a transformational approach to influence the business strategy. Higher education institutions need to develop students’ cognitive skills to facilitate systems thinking.Contribution: This study suggests a new

  18. Expert Seeker

    Science.gov (United States)

    Fernandez, Becerra

    2003-01-01

    Expert Seeker is a computer program of the knowledge-management-system (KMS) type that falls within the category of expertise-locator systems. The main goal of the KMS system implemented by Expert Seeker is to organize and distribute knowledge of who are the domain experts within and without a given institution, company, or other organization. The intent in developing this KMS was to enable the re-use of organizational knowledge and provide a methodology for querying existing information (including structured, semistructured, and unstructured information) in a way that could help identify organizational experts. More specifically, Expert Seeker was developed to make it possible, by use of an intranet, to do any or all of the following: Assist an employee in identifying who has the skills needed for specific projects and to determine whether the experts so identified are available. Assist managers in identifying employees who may need training opportunities. Assist managers in determining what expertise is lost when employees retire or otherwise leave. Facilitate the development of new ways of identifying opportunities for innovation and minimization of duplicated efforts. Assist employees in achieving competitive advantages through the application of knowledge-management concepts and related systems. Assist external organizations in requesting speakers for specific engagements or determining from whom they might be able to request help via electronic mail. Help foster an environment of collaboration for rapid development in today's environment, in which it is increasingly necessary to assemble teams of experts from government, universities, research laboratories, and industries, to quickly solve problems anytime, anywhere. Make experts more visible. Provide a central repository of information about employees, including information that, heretofore, has typically not been captured by the human-resources systems (e.g., information about past projects, patents, or

  19. Experts' memory superiority for domain-specific random material generalizes across fields of expertise: A meta-analysis.

    Science.gov (United States)

    Sala, Giovanni; Gobet, Fernand

    2017-02-01

    Experts' remarkable ability to recall meaningful domain-specific material is a classic result in cognitive psychology. Influential explanations for this ability have focused on the acquisition of high-level structures (e.g., schemata) or experts' capability to process information holistically. However, research on chess players suggests that experts maintain some reliable memory advantage over novices when random stimuli (e.g., shuffled chess positions) are presented. This skill effect cannot be explained by theories emphasizing high-level memory structures or holistic processing of stimuli, because random material does not contain large structures nor wholes. By contrast, theories hypothesizing the presence of small memory structures-such as chunks-predict this outcome, because some chunks still occur by chance in the stimuli, even after randomization. The current meta-analysis assessed the correlation between level of expertise and recall of random material in diverse domains. The overall correlation was moderate but statistically significant ([Formula: see text]), and the effect was observed in nearly every study. This outcome suggests that experts partly base their superiority on a vaster amount of small memory structures, in addition to high-level structures or holistic processing.

  20. Computer-Aided Decisions in Human Services: Expert Systems and Multivariate Models.

    Science.gov (United States)

    Sicoly, Fiore

    1989-01-01

    This comparison of two approaches to the development of computerized supports for decision making--expert systems and multivariate models--focuses on computerized systems that assist professionals with tasks related to diagnosis or classification in human services. Validation of both expert systems and statistical models is emphasized. (39…

  1. Domain Expert-Directed Program Optimizations for Accelerated Performance on Heterogeneous Multi-core Processors

    Science.gov (United States)

    2013-12-01

    modulo ) operation as used in Ed25519 ( A←A+BC2255−19 ) in the radix- 251 redundant representation, and will complete the verification of the same...Taiwan University this year. He is a young up-and-coming expert on formal verification and languages, and his impressive resumè include joint work

  2. Dog experts' brains distinguish socially relevant body postures similarly in dogs and humans.

    Science.gov (United States)

    Kujala, Miiamaaria V; Kujala, Jan; Carlson, Synnöve; Hari, Riitta

    2012-01-01

    We read conspecifics' social cues effortlessly, but little is known about our abilities to understand social gestures of other species. To investigate the neural underpinnings of such skills, we used functional magnetic resonance imaging to study the brain activity of experts and non-experts of dog behavior while they observed humans or dogs either interacting with, or facing away from a conspecific. The posterior superior temporal sulcus (pSTS) of both subject groups dissociated humans facing toward each other from humans facing away, and in dog experts, a distinction also occurred for dogs facing toward vs. away in a bilateral area extending from the pSTS to the inferior temporo-occipital cortex: the dissociation of dog behavior was significantly stronger in expert than control group. Furthermore, the control group had stronger pSTS responses to humans than dogs facing toward a conspecific, whereas in dog experts, the responses were of similar magnitude. These findings suggest that dog experts' brains distinguish socially relevant body postures similarly in dogs and humans.

  3. Research Workshop on Expert Judgment, Human Error, and Intelligent Systems

    OpenAIRE

    Silverman, Barry G.

    1993-01-01

    This workshop brought together 20 computer scientists, psychologists, and human-computer interaction (HCI) researchers to exchange results and views on human error and judgment bias. Human error is typically studied when operators undertake actions, but judgment bias is an issue in thinking rather than acting. Both topics are generally ignored by the HCI community, which is interested in designs that eliminate human error and bias tendencies. As a result, almost no one at the workshop had met...

  4. Becoming an Expert in the Musical Domain: It Takes More than Just Practice

    Science.gov (United States)

    Ruthsatz, Joanne; Detterman, Douglas; Griscom, William S.; Cirullo, Britney A.

    2008-01-01

    Previous research has supported the theory that acquisition of expertise in any domain is possible for healthy individuals with sufficient deliberate practice, but such an extreme environmental position brings the existence of innate talent into question. The present study investigates the effects of both environmental factors and talent on expert…

  5. Application of social domain of human mind in water management

    Science.gov (United States)

    Piirimäe, Kristjan

    2010-05-01

    , and NGOs. These people were randomly divided to two working groups and asked to criticize the proposed plan. One group was encouraged to detect cheating behind the plan. Later, a group of independent experts evaluated the criticism of both groups and each individual person. The resulting assignements rated the group of cheater detectors as significantly more adequate decision-supporters. The results confirmed that simulation of the 'cheater detection module' of human mind might improve the performance of an EDSS. The study calls for the development of special methodologies for the stimulation and application of social domain in water management. References Buchner, A., Bell, R., Mehl, B., & Musch, J., (2009). No enhanced recognition memory, but better source memory for faces of cheaters. Evolution and Human Behaviour, 30(3), 212 - 224. Byrne, R., Bates, L. (2009). Sociality, evolution and cognition. Current Biology, 17(16), R714 - R723. Cosmides, L. (1989). The logic of social exchange: Has natural selection shaped how humans reason? Studies with the Wason selection task. Cognition, 31(3), 187-276. Fiddick, L. (2004). Domains of deontic reasoning: Resolving the discrepancy between the cognitive and moral reasoning literatures. The Quartlerly Journal of Experimental Psychology, 57A(3), 447 - 474.

  6. Human-computer interface incorporating personal and application domains

    Science.gov (United States)

    Anderson, Thomas G.

    2011-03-29

    The present invention provides a human-computer interface. The interface includes provision of an application domain, for example corresponding to a three-dimensional application. The user is allowed to navigate and interact with the application domain. The interface also includes a personal domain, offering the user controls and interaction distinct from the application domain. The separation into two domains allows the most suitable interface methods in each: for example, three-dimensional navigation in the application domain, and two- or three-dimensional controls in the personal domain. Transitions between the application domain and the personal domain are under control of the user, and the transition method is substantially independent of the navigation in the application domain. For example, the user can fly through a three-dimensional application domain, and always move to the personal domain by moving a cursor near one extreme of the display.

  7. Expert judgment in analysis of human and organizational behaviour at nuclear power plants

    Energy Technology Data Exchange (ETDEWEB)

    Reiman, L. [Finnish Centre for Radiation and Nuclear Safety, Helsinki (Finland). Dept. of Nuclear Safety

    1994-12-01

    Probabilistic safety assessment (PSA) of a nuclear power plant includes an assessment of the probability of each event sequence that can lead to a reactor core damage and of their consequences. Despite increasing maturity of PSA methods, there are still several problems in their use. These include the assessment of human reliability and the impact of organizational factors on plant safety. The assessment of both these issues is based on expert judgment. Therefore, the use of expert judgment in analysis of human and organizational behaviour was studied theoretically and in practical case studies in this thesis. Human errors were analysed in two case studies. In the first study cognitive actions of control room operators were analysed. For this purpose methods were developed for the qualitative and quantitative phases of the analysis. Errors of test and maintenance personnel were analysed in the second case study. Especially the dependence of errors between sequential tasks performed in redundant subsystems of a safety system was studied. A method to assess organizational behaviour was developed and applied in the third case study. The three case studies demonstrated that expert judgment can be used in the analysis of human reliability and organizational behaviour taking into account the observations made and the remarks presented in the study. However, significant uncertainties are related with expert judgment. Recommendations are presented concerning the use of different methods. Also, some insights are presented into how reliance on expert judgment could be reduced. (241 refs., 20 figs., 36 tabs.).

  8. [Domains in the clinical practice of Clinical Nursing Experts in Germany and their correspondence with the internationally described "Advanced Nursing Practice"].

    Science.gov (United States)

    Mendel, Simon; Feuchtinger, Johanna

    2009-06-01

    In spite of a growing trend toward academic education and increasing numbers of "nursing experts" functioning as change agents in Germany, actual nursing experts as in the internationally described Advanced Nursing Practice (ANP) are scarce. Drawing from a ten-year experience in implementing the international concept, the University Hospital Freiburg (UKF), Germany, constitutes a notable exception, as it presently employs ten clinically practicing nursing experts. Based on this background of educating nursing experts, this presentation aims at describing the implementation of the nursing expert's role and its fit and conformance with the international ANP. A 3-stage Delphi design was used for interviewing all the nursing experts at the hospital (n = 10) about their expert opinions; in addition, all nursing managers (n = 7) as well as unit and team leaders (n = 49) were asked about their opinion to relevant functions and domains of nursing experts. The following clinical practice domains of nursing experts were identified: Direct patient care, patient education, support and supervision of nurses, maintenance and expansion of professional skills and knowledge of the nursing staff, counselling of managers, quality assurance and organizational development, theory to practice transfer, nursing research, maintenance of own professional skills and knowledge and continuing education, and publicity work. Additionally, a three-year nursing education, a longer lasting professional experience, a degree in nursing science or nursing education, and specialist skills in the respective area of expertise were identified as credentials for nursing expert practice. The nursing expert concept at UKF shows elements of the international ANP with similarities to the role of a Clinical Nurse Specialist.

  9. An Expert Distributed Robotics System with Comprehension and Learning Abilities in the Aircraft Flight Domain.

    Science.gov (United States)

    1982-07-01

    basket of the crowded Pompidou Center in ex- change for the girl. Asking that the police not intervene, Boul- lard arranged for the delivery of the money...Rumelhart, "An Interactive Activation Model of the Effect of Context in Perception", Technical reports 91 & 95, Center for Human Information

  10. Analyses of domains and domain fusions in human proto-oncogenes

    Directory of Open Access Journals (Sweden)

    Wan Ping

    2009-03-01

    Full Text Available Abstract Background Understanding the constituent domains of oncogenes, their origins and their fusions may shed new light about the initiation and the development of cancers. Results We have developed a computational pipeline for identification of functional domains of human genes, prediction of the origins of these domains and their major fusion events during evolution through integration of existing and new tools of our own. An application of the pipeline to 124 well-characterized human oncogenes has led to the identification of a collection of domains and domain pairs that occur substantially more frequently in oncogenes than in human genes on average. Most of these enriched domains and domain pairs are related to tyrosine kinase activities. In addition, our analyses indicate that a substantial portion of the domain-fusion events of oncogenes took place in metazoans during evolution. Conclusion We expect that the computational pipeline for domain identification, domain origin and domain fusion prediction will prove to be useful for studying other groups of genes.

  11. Expert System

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas Troels; Cattani, Gian Luca

    2016-01-01

    An expert system is a computer system for inferring knowledge from a knowledge base, typically by using a set of inference rules. When the concept of expert systems was introduced at Stanford University in the early 1970s, the knowledge base was an unstructured set of facts. Today the knowledge...... base of expert systems is often given in terms of an ontology, extracted and built from various data sources by employing natural language-processing and statistics. To emphasize such capabilities, the term “expert” is now often replaced by “cognitive,” “knowledge,” “knowledge-based,” or “intelligent......” system. With very few exceptions, general-purpose expert systems have failed to emerge so far. However, expert systems are applied in specialized domains, particularly in healthcare. The increasing availability of large quantities of data to organizations today provides a valuable opportunity...

  12. Human motion tracking by temporal-spatial local gaussian process experts.

    Science.gov (United States)

    Zhao, Xu; Fu, Yun; Liu, Yuncai

    2011-04-01

    Human pose estimation via motion tracking systems can be considered as a regression problem within a discriminative framework. It is always a challenging task to model the mapping from observation space to state space because of the high-dimensional characteristic in the multimodal conditional distribution. In order to build the mapping, existing techniques usually involve a large set of training samples in the learning process which are limited in their capability to deal with multimodality. We propose, in this work, a novel online sparse Gaussian Process (GP) regression model to recover 3-D human motion in monocular videos. Particularly, we investigate the fact that for a given test input, its output is mainly determined by the training samples potentially residing in its local neighborhood and defined in the unified input-output space. This leads to a local mixture GP experts system composed of different local GP experts, each of which dominates a mapping behavior with the specific covariance function adapting to a local region. To handle the multimodality, we combine both temporal and spatial information therefore to obtain two categories of local experts. The temporal and spatial experts are integrated into a seamless hybrid system, which is automatically self-initialized and robust for visual tracking of nonlinear human motion. Learning and inference are extremely efficient as all the local experts are defined online within very small neighborhoods. Extensive experiments on two real-world databases, HumanEva and PEAR, demonstrate the effectiveness of our proposed model, which significantly improve the performance of existing models.

  13. Human experts' and a fuzzy model's predictions of outcomes of scoliosis treatment: a comparative analysis.

    Science.gov (United States)

    Chalmers, Eric; Pedrycz, Witold; Lou, Edmond

    2015-03-01

    Brace treatment is the most commonly used nonsurgical treatment for adolescents with idiopathic scoliosis. However, brace treatment is not always successful and the factors influencing its success are not completely clear. This makes treatment outcome difficult to predict. A computer model which can accurately predict treatment outcomes could potentially provide valuable treatment recommendations. This paper describes a fuzzy system that includes a prediction model and a decision support engine. The model was constructed using conditional fuzzy c-means clustering to discover patterns in retrospective patient data. The model's ability to predict treatment outcome was compared to the ability of eight Scoliosis experts. The model and experts each predicted treatment outcome retrospectively for 28 braced patients, and these predictions were compared to the actual outcomes. The model outperformed all but one expert individually and performed similarly to the experts as a group. These results suggest that the fuzzy model is capable of providing meaningful treatment recommendations. This study offers the first model for this application whose performance has been shown to be at or above the human expert level.

  14. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong (Toronto); (Penn)

    2013-09-25

    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  15. Discoidin Domain Receptors Role in Human Diseases

    Directory of Open Access Journals (Sweden)

    Iker BADIOLA

    2011-11-01

    Full Text Available Discoidin Domain Receptor 1 and Discodin Domain Receptor 2 are the two only members of the DDR family. The DDR family is a Tyrosine Kinase Receptor (TKR family with some peculiarities compared with other Tyrosine Kinase Receptors such as their natural ligand; which in this case is the fibrillar collagen; or the slow phosphorylation pattern. These peculiarities confer a special role to the receptors present in many diseases development processes as cancer, cirrhosis or lung fibrosis. In this review it is described the overview of the DDRs structure and their role in the different disease development and the possibility to consider them as therapeutic targets.

  16. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.

    Directory of Open Access Journals (Sweden)

    Oscar Beijbom

    Full Text Available Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys.

  17. Generating human reliability estimates using expert judgment. Volume 1. Main report

    Energy Technology Data Exchange (ETDEWEB)

    Comer, M.K.; Seaver, D.A.; Stillwell, W.G.; Gaddy, C.D.

    1984-11-01

    The US Nuclear Regulatory Commission is conducting a research program to determine the practicality, acceptability, and usefulness of several different methods for obtaining human reliability data and estimates that can be used in nuclear power plant probabilistic risk assessment (PRA). One method, investigated as part of this overall research program, uses expert judgment to generate human error probability (HEP) estimates and associated uncertainty bounds. The project described in this document evaluated two techniques for using expert judgment: paired comparisons and direct numerical estimation. Volume 1 of this report provides a brief overview of the background of the project, the procedure for using psychological scaling techniques to generate HEP estimates and conclusions from evaluation of the techniques. Results of the evaluation indicate that techniques using expert judgment should be given strong consideration for use in developing HEP estimates. In addition, HEP estimates for 35 tasks related to boiling water reactors (BMRs) were obtained as part of the evaluation. These HEP estimates are also included in the report.

  18. Generating human reliability estimates using expert judgment. Volume 2. Appendices. [PWR; BWR

    Energy Technology Data Exchange (ETDEWEB)

    Comer, M.K.; Seaver, D.A.; Stillwell, W.G.; Gaddy, C.D.

    1984-11-01

    The US Nuclear Regulatory Commission is conducting a research program to determine the practicality, acceptability, and usefulness of several different methods for obtaining human reliability data and estimates that can be used in nuclear power plant probabilistic risk assessments (PRA). One method, investigated as part of this overall research program, uses expert judgment to generate human error probability (HEP) estimates and associated uncertainty bounds. The project described in this document evaluated two techniques for using expert judgment: paired comparisons and direct numerical estimation. Volume 2 provides detailed procedures for using the techniques, detailed descriptions of the analyses performed to evaluate the techniques, and HEP estimates generated as part of this project. The results of the evaluation indicate that techniques using expert judgment should be given strong consideration for use in developing HEP estimates. Judgments were shown to be consistent and to provide HEP estimates with a good degree of convergent validity. Of the two techniques tested, direct numerical estimation appears to be preferable in terms of ease of application and quality of results.

  19. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.

    Science.gov (United States)

    Beijbom, Oscar; Edmunds, Peter J; Roelfsema, Chris; Smith, Jennifer; Kline, David I; Neal, Benjamin P; Dunlap, Matthew J; Moriarty, Vincent; Fan, Tung-Yung; Tan, Chih-Jui; Chan, Stephen; Treibitz, Tali; Gamst, Anthony; Mitchell, B Greg; Kriegman, David

    2015-01-01

    Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys.

  20. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation

    Science.gov (United States)

    Beijbom, Oscar; Edmunds, Peter J.; Roelfsema, Chris; Smith, Jennifer; Kline, David I.; Neal, Benjamin P.; Dunlap, Matthew J.; Moriarty, Vincent; Fan, Tung-Yung; Tan, Chih-Jui; Chan, Stephen; Treibitz, Tali; Gamst, Anthony; Mitchell, B. Greg; Kriegman, David

    2015-01-01

    Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys. PMID:26154157

  1. Structural and histone binding ability characterizations of human PWWP domains.

    Directory of Open Access Journals (Sweden)

    Hong Wu

    Full Text Available BACKGROUND: The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. METHODOLOGY/PRINCIPAL FINDINGS: The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. CONCLUSIONS: PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical β-barrel core, an insertion motif between the second and third β-strands and a C-terminal α-helix bundle. Both the canonical β-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones. ENHANCED VERSION: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web

  2. [Expert consensus on induction of human embryonic stem cells into tenocytes].

    Science.gov (United States)

    Chen, Xiao; Zou, Xiaohui; Yu, Guangyan; Fu, Xin; Cao, Tong; Xiao, Yin; Ouyang, Hongwei

    2016-03-01

    Embryonic stem cells have unlimited proliferative capacity, which may provide a source of tendon stem/progenitor cells for tissue engineering. Experts of International Science and Technology Collaborative Program of Ministry of Science and Technology have developed a protocol consensus on differentiation of human embryonic stem cells into the tendon cells. The consensus recommends a protocol of two-step generation of human embryonic stem cells into tendon cells: the human embryonic stem cells are first differentiated into mesenchymal stem cells on different material surfaces; then with the scaffold-free tissue engineering tendon formed by high-density planting, the mesenchymal stem cells are induced into tendon cells under static or dynamic mechanical stimulation in vivo and in vitro. Tissue engineering tendon established in vitro by the protocol can be used as a model in toxicological analysis and safety evaluation of tendon-relevant small molecule compounds, medical materials and drugs.

  3. Structure of the first PDZ domain of human PSD-93

    DEFF Research Database (Denmark)

    Fiorentini, Monica; Nielsen, Ann Kallehauge; Kristensen, Ole

    2009-01-01

    The crystal structure of the PDZ1 domain of human PSD-93 has been determined to 2.0 A resolution. The PDZ1 domain forms a crystallographic trimer that is also predicted to be stable in solution. The main contributions to the stabilization of the trimer seem to arise from interactions involving th...... as well as of the closely related human PSD-95 PDZ1 shows that they are very similar in terms of amino-acid composition. However, the cleft is significantly narrower in PSD-95. This could be part of the basis of peptide selectivity between PSD-93 PDZ1 and PSD-95 PDZ1....

  4. The role of human-at-work systems in business sustainability: perspectives based on expert and qualified production workers in a manufacturing enterprise.

    Science.gov (United States)

    Genaidy, Ash M; Rinder, Maria M; Sequeira, Reynold; A-Rehim, Amal

    2010-04-01

    and enterprise levels, in terms of organisational/social/technological environment. This is particularly noted for the organisational environment. The compatibility values obtained for the experienced domains mirror those obtained for acting domains. The overall workload was assessed as requiring major redesign during the day shift and needing added responsibilities for the night shift according to both expert and qualified workers. The assessment of qualified workers is comparable with that of expert workers for the job content and immediate surroundings. Differences are more observed for process- and enterprise-based factors; thereby, providing company management different perspectives in order to devise organisational strategies conducive for optimum human and corporate health and pointing to the probable interactions of the different systems impacting individual and enterprise performance. STATEMENT OF RELEVANCE: This research examines similarities and differences between qualified and expert workers in their assessment of the worker-work environment interface. The contribution to improved understanding of the complex interactions of human-at-work and enterprise systems should be beneficial to organisations in their quest to remain competitive in a global economy.

  5. Modeling human response errors in synthetic flight simulator domain

    Science.gov (United States)

    Ntuen, Celestine A.

    1992-01-01

    This paper presents a control theoretic approach to modeling human response errors (HRE) in the flight simulation domain. The human pilot is modeled as a supervisor of a highly automated system. The synthesis uses the theory of optimal control pilot modeling for integrating the pilot's observation error and the error due to the simulation model (experimental error). Methods for solving the HRE problem are suggested. Experimental verification of the models will be tested in a flight quality handling simulation.

  6. Neural correlates of natural human echolocation in early and late blind echolocation experts.

    Directory of Open Access Journals (Sweden)

    Lore Thaler

    Full Text Available BACKGROUND: A small number of blind people are adept at echolocating silent objects simply by producing mouth clicks and listening to the returning echoes. Yet the neural architecture underlying this type of aid-free human echolocation has not been investigated. To tackle this question, we recruited echolocation experts, one early- and one late-blind, and measured functional brain activity in each of them while they listened to their own echolocation sounds. RESULTS: When we compared brain activity for sounds that contained both clicks and the returning echoes with brain activity for control sounds that did not contain the echoes, but were otherwise acoustically matched, we found activity in calcarine cortex in both individuals. Importantly, for the same comparison, we did not observe a difference in activity in auditory cortex. In the early-blind, but not the late-blind participant, we also found that the calcarine activity was greater for echoes reflected from surfaces located in contralateral space. Finally, in both individuals, we found activation in middle temporal and nearby cortical regions when they listened to echoes reflected from moving targets. CONCLUSIONS: These findings suggest that processing of click-echoes recruits brain regions typically devoted to vision rather than audition in both early and late blind echolocation experts.

  7. DUF1220 domains, cognitive disease, and human brain evolution.

    Science.gov (United States)

    Dumas, L; Sikela, J M

    2009-01-01

    We have established that human genome sequences encoding a novel protein domain, DUF1220, show a dramatically elevated copy number in the human lineage (>200 copies in humans vs. 1 in mouse/rat) and may be important to human evolutionary adaptation. Copy-number variations (CNVs) in the 1q21.1 region, where most DUF1220 sequences map, have now been implicated in numerous diseases associated with cognitive dysfunction, including autism, autism spectrum disorder, mental retardation, schizophrenia, microcephaly, and macrocephaly. We report here that these disease-related 1q21.1 CNVs either encompass or are directly flanked by DUF1220 sequences and exhibit a dosage-related correlation with human brain size. Microcephaly-producing 1q21.1 CNVs are deletions, whereas macrocephaly-producing 1q21.1 CNVs are duplications. Similarly, 1q21.1 deletions and smaller brain size are linked with schizophrenia, whereas 1q21.1 duplications and larger brain size are associated with autism. Interestingly, these two diseases are thought to be phenotypic opposites. These data suggest a model which proposes that (1) DUF1220 domain copy number may be involved in influencing human brain size and (2) the evolutionary advantage of rapidly increasing DUF1220 copy number in the human lineage has resulted in favoring retention of the high genomic instability of the 1q21.1 region, which, in turn, has precipitated a spectrum of recurrent human brain and developmental disorders.

  8. Mouth-clicks used by blind expert human echolocators - signal description and model based signal synthesis.

    Directory of Open Access Journals (Sweden)

    Lore Thaler

    2017-08-01

    Full Text Available Echolocation is the ability to use sound-echoes to infer spatial information about the environment. Some blind people have developed extraordinary proficiency in echolocation using mouth-clicks. The first step of human biosonar is the transmission (mouth click and subsequent reception of the resultant sound through the ear. Existing head-related transfer function (HRTF data bases provide descriptions of reception of the resultant sound. For the current report, we collected a large database of click emissions with three blind people expertly trained in echolocation, which allowed us to perform unprecedented analyses. Specifically, the current report provides the first ever description of the spatial distribution (i.e. beam pattern of human expert echolocation transmissions, as well as spectro-temporal descriptions at a level of detail not available before. Our data show that transmission levels are fairly constant within a 60° cone emanating from the mouth, but levels drop gradually at further angles, more than for speech. In terms of spectro-temporal features, our data show that emissions are consistently very brief (~3ms duration with peak frequencies 2-4kHz, but with energy also at 10kHz. This differs from previous reports of durations 3-15ms and peak frequencies 2-8kHz, which were based on less detailed measurements. Based on our measurements we propose to model transmissions as sum of monotones modulated by a decaying exponential, with angular attenuation by a modified cardioid. We provide model parameters for each echolocator. These results are a step towards developing computational models of human biosonar. For example, in bats, spatial and spectro-temporal features of emissions have been used to derive and test model based hypotheses about behaviour. The data we present here suggest similar research opportunities within the context of human echolocation. Relatedly, the data are a basis to develop synthetic models of human echolocation

  9. Expert judgment on markers to deter inadvertent human intrusion into the Waste Isolation Pilot Plant

    Energy Technology Data Exchange (ETDEWEB)

    Trauth, K.M. [Sandia National Labs., Albuquerque, NM (United States); Hora, S.C. [Hawaii Univ., Hilo, HI (United States); Guzowski, R.V. [Science Applications International Corp., San Diego, CA (United States)

    1993-11-01

    The expert panel identified basic principles to guide current and future marker development efforts: (1) the site must be marked, (2) message(s) must be truthful and informative, (3) multiple components within a marker system, (4) multiple means of communication (e.g., language, pictographs, scientific diagrams), (5) multiple levels of complexity within individual messages on individual marker system elements, (6) use of materials with little recycle value, and (7) international effort to maintain knowledge of the locations and contents of nuclear waste repositories. The efficacy of the markers in deterring inadvertent human intrusion was estimated to decrease with time, with the probability function varying with the mode of intrusion (who is intruding and for what purpose) and the level of technological development of the society. The development of a permanent, passive marker system capable of surviving and remaining interpretable for 10,000 years will require further study prior to implementation.

  10. Procedures for using expert judgment to estimate human-error probabilities in nuclear power plant operations. [PWR; BWR

    Energy Technology Data Exchange (ETDEWEB)

    Seaver, D.A.; Stillwell, W.G.

    1983-03-01

    This report describes and evaluates several procedures for using expert judgment to estimate human-error probabilities (HEPs) in nuclear power plant operations. These HEPs are currently needed for several purposes, particularly for probabilistic risk assessments. Data do not exist for estimating these HEPs, so expert judgment can provide these estimates in a timely manner. Five judgmental procedures are described here: paired comparisons, ranking and rating, direct numerical estimation, indirect numerical estimation and multiattribute utility measurement. These procedures are evaluated in terms of several criteria: quality of judgments, difficulty of data collection, empirical support, acceptability, theoretical justification, and data processing. Situational constraints such as the number of experts available, the number of HEPs to be estimated, the time available, the location of the experts, and the resources available are discussed in regard to their implications for selecting a procedure for use.

  11. The Human-Computer Domain Relation in UX Models

    DEFF Research Database (Denmark)

    Clemmensen, Torkil

    This paper argues that the conceptualization of the human, the computer and the domain of use in competing lines of UX research have problematic similarities and superficial differences. The paper qualitatively analyses concepts and models in five research papers that together represent two...... influential lines of UX research: aesthetics and temporal UX, and two use situations: using a website and starting to use a smartphone. The results suggest that the two lines of UX research share a focus on users’ evaluative judgments of technology, both focuses on product qualities rather than activity...... domains, give little details about users, and treat human-computer interaction as perception. The conclusion gives similarities and differences between the approaches to UX. The implications for theory building are indicated....

  12. Speech spectrogram expert

    Energy Technology Data Exchange (ETDEWEB)

    Johannsen, J.; Macallister, J.; Michalek, T.; Ross, S.

    1983-01-01

    Various authors have pointed out that humans can become quite adept at deriving phonetic transcriptions from speech spectrograms (as good as 90percent accuracy at the phoneme level). The authors describe an expert system which attempts to simulate this performance. The speech spectrogram expert (spex) is actually a society made up of three experts: a 2-dimensional vision expert, an acoustic-phonetic expert, and a phonetics expert. The visual reasoning expert finds important visual features of the spectrogram. The acoustic-phonetic expert reasons about how visual features relates to phonemes, and about how phonemes change visually in different contexts. The phonetics expert reasons about allowable phoneme sequences and transformations, and deduces an english spelling for phoneme strings. The speech spectrogram expert is highly interactive, allowing users to investigate hypotheses and edit rules. 10 references.

  13. Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge

    Directory of Open Access Journals (Sweden)

    Mayordomo Elvira

    2011-05-01

    Full Text Available Abstract Background Mitochondrial DNA is an ideal source of information to conduct evolutionary and phylogenetic studies due to its extraordinary properties and abundance. Many insights can be gained from these, including but not limited to screening genetic variation to identify potentially deleterious mutations. However, such advances require efficient solutions to very difficult computational problems, a need that is hampered by the very plenty of data that confers strength to the analysis. Results We develop a systematic, automated methodology to overcome these difficulties, building from readily available, public sequence databases to high-quality alignments and phylogenetic trees. Within each stage in an autonomous workflow, outputs are carefully evaluated and outlier detection rules defined to integrate expert knowledge and automated curation, hence avoiding the manual bottleneck found in past approaches to the problem. Using these techniques, we have performed exhaustive updates to the human mitochondrial phylogeny, illustrating the power and computational scalability of our approach, and we have conducted some initial analyses on the resulting phylogenies. Conclusions The problem at hand demands careful definition of inputs and adequate algorithmic treatment for its solutions to be realistic and useful. It is possible to define formal rules to address the former requirement by refining inputs directly and through their combination as outputs, and the latter are also of help to ascertain the performance of chosen algorithms. Rules can exploit known or inferred properties of datasets to simplify inputs through partitioning, therefore cutting computational costs and affording work on rapidly growing, otherwise intractable datasets. Although expert guidance may be necessary to assist the learning process, low-risk results can be fully automated and have proved themselves convenient and valuable.

  14. Being Human Beings: The Domains and a Human Realm

    Science.gov (United States)

    2013-03-01

    evolutionary step to highlight the human component in conflict. As Francis Bacon said, “It would be an unused fancy and self-contradictory to expect that...Special Operations Command, Special Operations White Paper, 1. 50 Francis Bacon , “The New Organon or True Directions Concerning the Interpretation of...Nature,” 1620, http://www.constitution.org/ bacon /nov_org.htm, (accessed February 24, 2013). 51 Mark E. Redden and Michael P. Hughes, “Global

  15. [Social engineers--providers--bioethicists. Human genetics experts in West-Germany and Denmark between 1950 and 1990].

    Science.gov (United States)

    Thomaschke, Dirk

    2013-01-01

    The author compares the history of human genetics in the Federal Republic of Germany and Denmark from the 1950s to the 1980s. The paper combines a discourse analysis with the exploration of human genetics experts' subject forms along the lines of current considerations within cultural studies. In the 1950s and 1960s, human geneticists acted in close cooperation with other political, judicial and administrative expert groups. They monitored the 'overall genetic development' of the population and cautioned about 'genetic crises'. Laypersons were supposed to submit to 'objectively reasonable' behavioral patterns--to their own as well as society's benefit. In the 1970s, the experts turned into 'providers' of a 'precise, purely medical, diagnostic service'. The patients mainly appeared as 'de-personalized' sources of a common human demand for 'safe eugenic information'. In the 1980s, the demand and supply paradigm manifested psychological and ethical side effects. Human geneticists became aware of the social and historical interrelations of their research and practices. The results of this study contribute to a more complex understanding of the dominant 'individualization narrative' of human genetics history. In this context, the development in Germany and Denmark displays two complementary forms of a transnational discourse.

  16. How do physicians become medical experts? A test of three competing theories: distinct domains, independent influence and encapsulation models.

    Science.gov (United States)

    Violato, Claudio; Gao, Hong; O'Brien, Mary Claire; Grier, David; Shen, E

    2017-07-12

    The distinction between basic sciences and clinical knowledge which has led to a theoretical debate on how medical expertise is developed has implications for medical school and lifelong medical education. This longitudinal, population based observational study was conducted to test the fit of three theories-knowledge encapsulation, independent influence, distinct domains-of the development of medical expertise employing structural equation modelling. Data were collected from 548 physicians (292 men-53.3%; 256 women-46.7%; mean age = 24.2 years on admission) who had graduated from medical school 2009-2014. They included (1) Admissions data of undergraduate grade point average and Medical College Admission Test sub-test scores, (2) Course performance data from years 1, 2, and 3 of medical school, and (3) Performance on the NBME exams (i.e., Step 1, Step 2 CK, and Step 3). Statistical fit indices (Goodness of Fit Index-GFI; standardized root mean squared residual-SRMR; root mean squared error of approximation-RSMEA) and comparative fit [Formula: see text] of three theories of cognitive development of medical expertise were used to assess model fit. There is support for the knowledge encapsulation three factor model of clinical competency (GFI = 0.973, SRMR = 0.043, RSMEA = 0.063) which had superior fit indices to both the independent influence and distinct domains theories ([Formula: see text] vs [Formula: see text] [[Formula: see text

  17. Estimating Production Potentials: Expert Bias in Applied Decision Making

    Energy Technology Data Exchange (ETDEWEB)

    L. J. Matthews; L. K. Burggraf (ISU); W. J. Reece (INEEL)

    1998-10-01

    A study was conducted to evaluate how workers predict manufacturing production potentials given positively and negatively framed information. Findings indicate the existence of a bias toward positive information and suggest that this bias may be reduced with experience but is never the less maintained. Experts err in the same way non experts do in differentially processing negative and positive information. Additionally, both experts and non experts tend to overestimate production potentials in a positive direction. The authors propose that these biases should be addressed with further research including cross domain analyses and consideration in training, workplace design, and human performance modeling.

  18. MERS-CoV at the Animal-Human interface: inputs on exposure pathways from an Expert-Opinion elicitation

    Directory of Open Access Journals (Sweden)

    Anna Funk

    2016-10-01

    Full Text Available Nearly four years after the first report of the emergence of Middle-East respiratory syndrome Coronavirus (MERS-CoV and nearly 1800 human cases later, the ecology of MERS-CoV, its epidemiology, and risk factors of MERS-CoV transmission between camels are poorly understood. Knowledge about the pathways and mechanisms of transmission from animals to humans is limited; as of yet, transmission risks have not been quantified. Moreover the divergent sanitary situations and exposures to animals among populations in the Arabian Peninsula, where human primary cases appear to dominate, vs. other regions in the Middle East and Africa, with no reported human clinical cases and where the virus has been detected only in dromedaries, represents huge scientific and health challenges. Here, we have used expert opinion elicitation in order to obtain ideas on relative importance of MERS-CoV risk factors and estimates of transmission risks from various types of contact between humans and dromedaries. Fourteen (14 experts with diverse and extensive experience in MERS-CoV relevant fields were enrolled and completed an online questionnaire that examined pathways based on several scenarios e.g. camels-camels, camels-human, bats/other species to camels/humans and the role of diverse biological substances (milk, urine etc. and potential fomites.Experts believed that dromedary camels play the largest role in MERS-CoV infection of other dromedaries; however, they also indicated a significant influence of the season (i.e. calving or weaning periods on transmission risk. All experts thought that MERS-CoV infected dromedaries and asymptomatic humans play the most important role in infection of humans, with bats and other species presenting a possible, but yet undefined, risk. Direct and indirect contact of humans with dromedary camels were identified as the most risky types of contact, when compared to consumption of various camel products, with estimated 'most

  19. Crystal Structures of the BAR-PH and PTB Domains of Human APPL1

    Energy Technology Data Exchange (ETDEWEB)

    Li,J.; Mao, X.; Dong, L.; Liu, F.; Tong, L.

    2007-01-01

    APPL1 interacts with adiponectin receptors and other important signaling molecules. It contains a BAR and a PH domain near its N terminus, and the two domains may function as a unit (BAR-PH domain). We report here the crystal structures of the BAR-PH and PTB domains of human APPL1. The structures reveal novel features for BAR domain dimerization and for the interactions between the BAR and PH domains. The BAR domain dimer of APPL1 contains two four-helical bundles, whereas other BAR domain dimers have only three helices in each bundle. The PH domain is located at the opposite ends of the BAR domain dimer. Yeast two-hybrid assays confirm the interactions between the BAR and PH domains. Lipid binding assays show that the BAR, PH, and PTB domains can bind phospholipids. The ability of APPL1 to interact with multiple signaling molecules and phospholipids supports an important role for this adaptor in cell signaling.

  20. PedExpert: a computer program for the application of Bayesian networks to human paternity testing.

    Science.gov (United States)

    Gomes, R R; Campos, S V A; Pena, S D J

    2009-01-01

    PedExpert is a Windows-based Bayesian network software, especially constructed to solve problems in parentage testing that are complex because of missing genetic information on the alleged father and/or because they involve genetic mutations. PedExpert automates the creation and manipulation of Bayesian networks, implementing algorithms that convert pedigrees and sets of indispensable information (genotypes, allele frequencies, mutation rates) into Bayesian networks. This program has a novel feature that can incorporate information about gene mutations into tables of conditional probabilities of transmission of alleles from the alleged father to the child, without adding new nodes to the network. This permits using the same Bayesian network in different modes, for analysis of cases that include mutations or not. PedExpert is user-friendly and greatly reduces the time of analysis for complex cases of paternity testing, eliminating most sources of logical and operational error.

  1. [Fluorescent fusion proteins with 10th human fibronectin domain].

    Science.gov (United States)

    Petrovskaia, L E; Gapizov, S Sh; Shingarova, L N; Kriukova, E A; Boldyreva, E F; Iakimov, S A; Svirshchevskaia, E V; Lukashev, E P; Dolgikh, D A; Kirpichnikov, M P

    2014-01-01

    In the current paper we describe a new type of hybrid molecules including red fluorescent protein mCherry and 10th type III human fibronectin domain (10Fn3) - one of the alternative scaffold proteins which can be used for the construction of antibody mimics with various binding specificity. We have constructed different gene variants encoding for the hybrid fluorescent protein and studied their expression in Escherichia coli cells. It was shown that N-terminal position of mCherry and modification of its N-terminal amino acid sequence promotes efficientbacterial expression of the hybrid protein in the soluble form. On the basis of the proposed construction we have obtained the hybrid fluorescent protein ChIBF, containing alphaVbeta3-integrin binding vari- ant of 10Fn3, and demonstrated the possibility of its utilization for the visualization of alphaVbeta3-integrin at the surface of MDCK epithelial cells by confocal microscopy.

  2. Fully Human VH Single Domains That Rival the Stability and Cleft Recognition of Camelid Antibodies.

    Science.gov (United States)

    Rouet, Romain; Dudgeon, Kip; Christie, Mary; Langley, David; Christ, Daniel

    2015-05-01

    Human VH single domains represent a promising class of antibody fragments with applications as therapeutic modalities. Unfortunately, isolated human VH domains also generally display poor biophysical properties and a propensity to aggregate. This has encouraged the development of non-human antibody domains as alternative means of antigen recognition and, in particular, camelid (VHH) domains. Naturally devoid of light chain partners, these domains are characterized by favorable biophysical properties and propensity for cleft binding, a highly desirable characteristic, allowing the targeting of cryptic epitopes. In contrast, previously reported structures of human VH single domains had failed to recapitulate this property. Here we report the engineering and characterization of phage display libraries of stable human VH domains and the selection of binders against a diverse set of antigens. Unlike "camelized" human domains, the domains do not rely on potentially immunogenic framework mutations and maintain the structure of the VH/VL interface. Structure determination in complex with hen egg white lysozyme revealed an extended VH binding interface, with complementarity-determining region 3 deeply penetrating into the active site cleft, highly reminiscent of what has been observed for camelid domains. Taken together, our results demonstrate that fully human VH domains can be constructed that are not only stable and well expressed but also rival the cleft binding properties of camelid antibodies.

  3. Terahertz time-domain spectroscopy combined with fuzzy rule-building expert system and fuzzy optimal associative memory applied to diagnosis of cervical carcinoma.

    Science.gov (United States)

    Qi, Na; Zhang, Zhuoyong; Xiang, Yuhong; Yang, Yuping; Harrington, Peter de B

    2015-01-01

    Combined with terahertz time-domain spectroscopy, the feasibility of fast and reliable diagnosis of cervical carcinoma by a fuzzy rule-building expert system (FuRES) and a fuzzy optimal associative memory (FOAM) had been studied. The terahertz spectra of 52 specimens of cervix were collected in the work. The original data of samples were preprocessed by Savitzky-Golay first derivative (χderivative), principal component orthogonal signal correction (PC-OSC) and emphatic orthogonal signal correction to improve the performance of FuRES and FOAM models. The effect of the different pretreating methods to improve prediction accuracy was evaluated. The FuRES and FOAM models were validated using bootstrapped Latin-partition method. The obtained results showed that the FuRES and FOAM model optimized with the combination S-G first derivative and PC-OSC method had the better predictive ability with classification rates of 92.9 ± 0.4 and 92.5 ± 0.4 %, respectively. The proposed procedure proved that terahertz spectroscopy combined with fuzzy classifiers could supply a technology which has potential for diagnosis of cancerous tissue.

  4. Expanding the landscape of chromatin modification (CM-related functional domains and genes in human.

    Directory of Open Access Journals (Sweden)

    Shuye Pu

    Full Text Available Chromatin modification (CM plays a key role in regulating transcription, DNA replication, repair and recombination. However, our knowledge of these processes in humans remains very limited. Here we use computational approaches to study proteins and functional domains involved in CM in humans. We analyze the abundance and the pair-wise domain-domain co-occurrences of 25 well-documented CM domains in 5 model organisms: yeast, worm, fly, mouse and human. Results show that domains involved in histone methylation, DNA methylation, and histone variants are remarkably expanded in metazoan, reflecting the increased demand for cell type-specific gene regulation. We find that CM domains tend to co-occur with a limited number of partner domains and are hence not promiscuous. This property is exploited to identify 47 potentially novel CM domains, including 24 DNA-binding domains, whose role in CM has received little attention so far. Lastly, we use a consensus Machine Learning approach to predict 379 novel CM genes (coding for 329 proteins in humans based on domain compositions. Several of these predictions are supported by very recent experimental studies and others are slated for experimental verification. Identification of novel CM genes and domains in humans will aid our understanding of fundamental epigenetic processes that are important for stem cell differentiation and cancer biology. Information on all the candidate CM domains and genes reported here is publicly available.

  5. Structure of the human Nac1 POZ domain.

    Science.gov (United States)

    Stead, Mark A; Carr, Stephen B; Wright, Stephanie C

    2009-05-01

    Nac1 is a POZ-domain transcription factor that is involved in the self-renewal of embryonic stem cells. It is overexpressed in ovarian serous carcinoma and targeting the interactions of its POZ domain is a potential therapeutic strategy. Nac1 lacks a zinc-finger DNA-binding domain and thereby differs from most other POZ-domain transcription factors. Here, the crystal structure of the Nac1 POZ domain at 2.1 A resolution is reported. The Nac1 POZ domain crystallized as a dimer in which the interaction interfaces between subunits resemble those found in the POZ-zinc finger transcription factors. The organization of the Nac1 POZ-domain core resembles reported POZ-domain structures, whereas the C-terminus differs markedly. The C-terminal alpha-helix of the Nac1 POZ domain is shorter than that observed in most other POZ-domain transcription factors; variation in the organization of this region may be a general feature of POZ-domain structures.

  6. Development of knowledge Base Expert System for Natural treatment of Diabetes disease

    CERN Document Server

    Jha, Sanjeev Kumar

    2012-01-01

    The development of expert system for treatment of Diabetes disease by using natural methods is new information technology derived from Artificial Intelligent research using ESTA (Expert System Text Animation) System. The proposed expert system contains knowledge about various methods of natural treatment methods (Massage, Herbal/Proper Nutrition, Acupuncture, Gems) for Diabetes diseases of Human Beings. The system is developed in the ESTA (Expert System shell for Text Animation) which is Visual Prolog 7.3 Application. The knowledge for the said system will be acquired from domain experts, texts and other related sources.

  7. Development of knowledge Base Expert System for Natural treatment of Diabetes disease

    Directory of Open Access Journals (Sweden)

    Sanjeev Kumar Jha

    2012-03-01

    Full Text Available The development of expert system for treatment of Diabetes disease by using natural methods is new information technology derived from Artificial Intelligent research using ESTA (Expert System Text Animation System. The proposed expert system contains knowledge about various methods of natural treatment methods (Massage, Herbal/Proper Nutrition, Acupuncture, Gems for Diabetes diseases of Human Beings. The system is developed in the ESTA (Expert System shell for Text Animation which is Visual Prolog 7.3 Application. The knowledge for the said system will be acquired from domain experts, texts and other related sources

  8. Recombinant expression and purification of L2 domain of human ...

    African Journals Online (AJOL)

    USER

    2010-08-16

    Aug 16, 2010 ... and plays an important role in some malignant processes. L2 domain of ..... production of monoclonal antibodies, screening for specific ligands and studies on ... Isolation and characterization of. A-431 cells that retain high ...

  9. A viral-human interactome based on structural motif-domain interactions captures the human infectome.

    Directory of Open Access Journals (Sweden)

    Aldo Segura-Cabrera

    Full Text Available Protein interactions between a pathogen and its host are fundamental in the establishment of the pathogen and underline the infection mechanism. In the present work, we developed a single predictive model for building a host-viral interactome based on the identification of structural descriptors from motif-domain interactions of protein complexes deposited in the Protein Data Bank (PDB. The structural descriptors were used for searching, in a database of protein sequences of human and five clinically important viruses; therefore, viral and human proteins sharing a descriptor were predicted as interacting proteins. The analysis of the host-viral interactome allowed to identify a set of new interactions that further explain molecular mechanism associated with viral infections and showed that it was able to capture human proteins already associated to viral infections (human infectome and non-infectious diseases (human diseasome. The analysis of human proteins targeted by viral proteins in the context of a human interactome showed that their neighbors are enriched in proteins reported with differential expression under infection and disease conditions. It is expected that the findings of this work will contribute to the development of systems biology for infectious diseases, and help guide the rational identification and prioritization of novel drug targets.

  10. Expert System Design Aid for Applications of Human Factors in Robotics.

    Science.gov (United States)

    1986-06-12

    Publishers B.V., Amsterdam, 1984. Parsons, H.M., ERGONOMIE ET ROBOTIQUE (Human Factors and Robotics), Paper presented at The International Conference on...Amsterdam, 1984. Parsons, H.M., ERGONOMIE ET ROBOTIQUE (Human Factors and Robotics), Paper presented at The International Conference on Occupational

  11. Automatic Bibliography Integration System for Domain Experts%一种领域专家文献自动收集系统

    Institute of Scientific and Technical Information of China (English)

    廖晓锋; 王永吉; 周津慧; 关贝

    2012-01-01

    We designed and implemented a system called BibCollector which can automatically collect the bibliography information from different databases. This system is targeted at experts in Information Technology (IT) domain. The databases covered include the most used ones such as SpringerLink, IEEE Xplore, ACM Digital Library, Elsevier ScienceDirect Two main Chinese databases CNK1 and Wanfang are also included. The citation databases that are covered include: Science Citation Index, El, ISTP, CSCD. Besides these, the Derwent patent database is also included. We presented a method by using the name and affiliation/address of a person to accurately query from these databases. We also developed some algorithms to exclude the unrelated records and identify the duplicate ones. Comparing to the overseas and domestic counterparts, our system has advantages of richer record sources and more accurate results.%设计并实现了一种自动专家文献信息收集系统(BibCollector).收录对象针对计算机科学技术领域的专家学者,收集范围涵盖国内外主要的全文数据库(SpringerLink,IEEE Xplore,ACM Digital Library,Elsevier Science Direct,中国知网CNKI和万方数据)和常用的引文数据库(SCI,EI,ISTP,CSCD)及专利数据库(Derwent).该系统使用专家姓名和工作单位作为标识,判断记录相关性和去除重复项,生成的文献列表具有较高的准确度.该系统同时收集专家所发表的中文和外文文献,因此无论相比国外和国内的类似系统,该系统都具有数据来源更丰富的优势.该系统能为相关的文献收集工作节省大量人力.

  12. Proposed human stratum corneum water domain in chemical absorption.

    Science.gov (United States)

    Zhu, Hanjiang; Jung, Eui-Chang; Hui, Xiaoying; Maibach, Howard

    2016-08-01

    Compounds with varying physical and chemical properties may have different affinities to the stratum corneum (SC) and/or its intercellular lipids, keratin protein, and possible water domains. To better understand the mechanism of percutaneous absorption, we utilized 21 carbon-14 labeled chemicals, with wide hydrophilicity (log P = -0.05 to 6.17), and quantified their absorption/adsorption properties for a short incubation time (15 min) with regards to intact SC membrane, delipidized SC membrane and SC lipid. A facile method was developed for SC/lipid absorption, providing a more equivalent procedure and comparable data. SC lipid absorption of chemical solutes positively correlated with the octanol/water partition coefficient (log P). Differences between the percent dose of chemical absorption to intact SC and the total percent dose contributed by the protein and lipid domains suggest the possibility and significance of a water domain. Absorption rate experiments showed a longer lag time for intact SC than for delipidized SC or SC lipid, suggesting that the water domain may delay chemical binding to protein and lipid domains, and may be a factor in the resistance of many chemicals to current decontamination methods. Copyright © 2015 John Wiley & Sons, Ltd.

  13. Expert views on critical success and failure factors for nutrigenomics

    NARCIS (Netherlands)

    Ronteltap, A.; Trijp, van J.C.M.; Renes, R.J.

    2007-01-01

    Public adoption of new technologies is an important determinant for their success. In this paper we examined a specific case of new technology in the nutrition domain ¿ nutrigenomics ¿ the interaction between nutrition and human genes. From 29 semi-structured interviews with Dutch experts in the fie

  14. Expert Systems and Special Education.

    Science.gov (United States)

    Hofmeister, Alan M.; Ferrara, Joseph M.

    1986-01-01

    The article discusses the characteristics of expert systems (computer programs designed to replicate human expertise in a variety of areas), describes recently available expert system development tools, suggests applications within the field of special education, and reviews recent efforts to apply expert systems technology to special education…

  15. Human-Robot Interaction in High Vulnerability Domains

    Science.gov (United States)

    Gore, Brian F.

    2016-01-01

    Future NASA missions will require successful integration of the human with highly complex systems. Highly complex systems are likely to involve humans, automation, and some level of robotic assistance. The complex environments will require successful integration of the human with automation, with robots, and with human-automation-robot teams to accomplish mission critical goals. Many challenges exist for the human performing in these types of operational environments with these kinds of systems. Systems must be designed to optimally integrate various levels of inputs and outputs based on the roles and responsibilities of the human, the automation, and the robots; from direct manual control, shared human-robotic control, or no active human control (i.e. human supervisory control). It is assumed that the human will remain involved at some level. Technologies that vary based on contextual demands and on operator characteristics (workload, situation awareness) will be needed when the human integrates into these systems. Predictive models that estimate the impact of the technologies on the system performance and the on the human operator are also needed to meet the challenges associated with such future complex human-automation-robot systems in extreme environments.

  16. inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO.

    Science.gov (United States)

    Taminau, Jonatan; Steenhoff, David; Coletta, Alain; Meganck, Stijn; Lazar, Cosmin; de Schaetzen, Virginie; Duque, Robin; Molter, Colin; Bersini, Hugues; Nowé, Ann; Weiss Solís, David Y

    2011-11-15

    Microarray technology has become an integral part of biomedical research and increasing amounts of datasets become available through public repositories. However, re-use of these datasets is severely hindered by unstructured, missing or incorrect biological samples information; as well as the wide variety of preprocessing methods in use. The inSilicoDb R/Bioconductor package is a command-line front-end to the InSilico DB, a web-based database currently containing 86 104 expert-curated human Affymetrix expression profiles compiled from 1937 GEO repository series. The use of this package builds on the Bioconductor project's focus on reproducibility by enabling a clear workflow in which not only analysis, but also the retrieval of verified data is supported.

  17. Matching simulated antemortem and post-mortem dental radiographs from human skulls by dental students and experts: testing skills for pattern recognition.

    Science.gov (United States)

    Wenzel, A; Richards, A; Heidmann, J

    2010-12-01

    The aim of this study was to evaluate the ability of undergraduate dental students to match simulated ante- and post-mortem radiographs in human skulls with experts as controls for the 1)number of post-mortem images needed for a match, 2)accuracy of the matches, and 3)time spent for a match. A film bitewing was recorded in each side of 51 dentate dry human skulls (a.m.-images) and digital images of the teeth were recorded using a sensor (p.m.-images). 102 correctly matching and 102 non-matching image pairs were constructed. Ten students and three experts scored the image pairs as: certain match, certain non-match, or uncertain. None of the experts but half of the students made false positive scores. Half of the students performed just as accurately as the experts. All students (except one who made 8 FPs) asked for more p.m.-images than did the experts before deciding on a match, however, all students, but one, also spent less time per image pair than did the experts before deciding on a match (Ppattern recognition and thus help in the decision on who might be included as part of a forensic dental team when extra help is needed.

  18. A highly conserved pericentromeric domain in human and gorilla chromosomes.

    Science.gov (United States)

    Pita, M; Gosálvez, J; Gosálvez, A; Nieddu, M; López-Fernández, C; Mezzanotte, R

    2009-01-01

    Significant similarity between human and gorilla genomes has been found in all chromosome arms, but not in centromeres, using whole-comparative genomic hybridization (W-CGH). In human chromosomes, centromeric regions, generally containing highly repetitive DNAs, are characterized by the presence of specific human DNA sequences and an absence of homology with gorilla DNA sequences. The only exception is the pericentromeric area of human chromosome 9, which, in addition to a large block of human DNA, also contains a region of homology with gorilla DNA sequences; the localization of these sequences coincides with that of human satellite III. Since highly repetitive DNAs are known for their high mutation frequency, we hypothesized that the chromosome 9 pericentromeric DNA conserved in human chromosomes and deriving from the gorilla genome may thus play some important functional role.

  19. The transducer domain is important for clamp operation in human DNA topoisomerase IIalpha

    DEFF Research Database (Denmark)

    Oestergaard, Vibe H; Bjergbaek, Lotte; Skouboe, Camilla

    2003-01-01

    the clamp to the enzyme core. Although structurally conserved, it is unclear whether the transducer domain is involved in clamp mechanism. We have purified and characterized a human topoisomerase II alpha enzyme with a two-amino acid insertion at position 408 in the transducer domain. The enzyme retains...

  20. The impact of human-technology cooperation and distributed cognition in forensic science: biasing effects of AFIS contextual information on human experts.

    Science.gov (United States)

    Dror, Itiel E; Wertheim, Kasey; Fraser-Mackenzie, Peter; Walajtys, Jeff

    2012-03-01

    Experts play a critical role in forensic decision making, even when cognition is offloaded and distributed between human and machine. In this paper, we investigated the impact of using Automated Fingerprint Identification Systems (AFIS) on human decision makers. We provided 3680 AFIS lists (a total of 55,200 comparisons) to 23 latent fingerprint examiners as part of their normal casework. We manipulated the position of the matching print in the AFIS list. The data showed that latent fingerprint examiners were affected by the position of the matching print in terms of false exclusions and false inconclusives. Furthermore, the data showed that false identification errors were more likely at the top of the list and that such errors occurred even when the correct match was present further down the list. These effects need to be studied and considered carefully, so as to optimize human decision making when using technologies such as AFIS.

  1. Philippine Counterinsurgency Success: Implications for the Human Domain of Warfare

    Science.gov (United States)

    2013-03-01

    And if it is indeed new and distinct from the land domain, inanimate and geographic, we in our Nation’s Army should be preparing ourselves to...different ethnic, cultural, and religious backgrounds. The post-World War II Philippine government has been no stranger to internal conflict...environments. We must identify how we get ourselves to where we need to be in order to best influence outcomes, to include better applying the tools we

  2. Genome-wide genetic interaction analysis of glaucoma using expert knowledge derived from human phenotype networks.

    Science.gov (United States)

    Hu, Ting; Darabos, Christian; Cricco, Maria E; Kong, Emily; Moore, Jason H

    2015-01-01

    The large volume of GWAS data poses great computational challenges for analyzing genetic interactions associated with common human diseases. We propose a computational framework for characterizing epistatic interactions among large sets of genetic attributes in GWAS data. We build the human phenotype network (HPN) and focus around a disease of interest. In this study, we use the GLAUGEN glaucoma GWAS dataset and apply the HPN as a biological knowledge-based filter to prioritize genetic variants. Then, we use the statistical epistasis network (SEN) to identify a significant connected network of pairwise epistatic interactions among the prioritized SNPs. These clearly highlight the complex genetic basis of glaucoma. Furthermore, we identify key SNPs by quantifying structural network characteristics. Through functional annotation of these key SNPs using Biofilter, a software accessing multiple publicly available human genetic data sources, we find supporting biomedical evidences linking glaucoma to an array of genetic diseases, proving our concept. We conclude by suggesting hypotheses for a better understanding of the disease.

  3. Production of Slit2 LRR domains in mammalian cells for structural studies and the structure of human Slit2 domain 3.

    Science.gov (United States)

    Morlot, Cecile; Hemrika, Wieger; Romijn, Roland A; Gros, Piet; Cusack, Stephen; McCarthy, Andrew A

    2007-09-01

    Slit2 and Roundabout 1 (Robo1) provide a key ligand-receptor interaction for the navigation of commissural neurons during the development of the central nervous system. Slit2 is a large multidomain protein containing an unusual domain organization of four tandem leucine-rich repeat (LRR) domains at its N-terminus. These domains are well known to mediate protein-protein interactions; indeed, the Robo1-binding region has been mapped to the concave face of the second LRR domain. It has also been shown that the fourth LRR domain may mediate Slit dimerization and that both the first and second domains can bind heparin. Thus, while roles have been ascribed for three of the LRR domains, there is still no known role for the third domain. Each of the four LRR domains from human Slit2 have now been successfully expressed in milligram quantities using expression in mammalian cells. Here, the crystallization of the second and third LRR domains and the structure of the third LRR domain are presented. This is the first structure of an LRR domain from human Slit2, which has an extra repeat compared with the Drosophila homologue. It is proposed that a highly conserved patch of surface residues on the concave face may mediate any protein-protein interactions involving this LRR domain, a result that will be useful in guiding further studies on Slit2.

  4. Activities of human RRP6 and structure of the human RRP6 catalytic domain

    Energy Technology Data Exchange (ETDEWEB)

    Januszyk, Kurt; Liu, Quansheng; Lima, Christopher D. (SKI)

    2011-08-29

    The eukaryotic RNA exosome is a highly conserved multi-subunit complex that catalyzes degradation and processing of coding and noncoding RNA. A noncatalytic nine-subunit exosome core interacts with Rrp44 and Rrp6, two subunits that possess processive and distributive 3'-to-5' exoribonuclease activity, respectively. While both Rrp6 and Rrp44 are responsible for RNA processing in budding yeast, Rrp6 may play a more prominent role in processing, as it has been demonstrated to be inhibited by stable RNA secondary structure in vitro and because the null allele in budding yeast leads to the buildup of specific structured RNA substrates. Human RRP6, otherwise known as PM/SCL-100 or EXOSC10, shares sequence similarity to budding yeast Rrp6 and is proposed to catalyze 3'-to-5' exoribonuclease activity on a variety of nuclear transcripts including ribosomal RNA subunits, RNA that has been poly-adenylated by TRAMP, as well as other nuclear RNA transcripts destined for processing and/or destruction. To characterize human RRP6, we expressed the full-length enzyme as well as truncation mutants that retain catalytic activity, compared their activities to analogous constructs for Saccharomyces cerevisiae Rrp6, and determined the X-ray structure of a human construct containing the exoribonuclease and HRDC domains that retains catalytic activity. Structural data show that the human active site is more exposed when compared to the yeast structure, and biochemical data suggest that this feature may play a role in the ability of human RRP6 to productively engage and degrade structured RNA substrates more effectively than the analogous budding yeast enzyme.

  5. Replacement of the human topoisomerase linker domain with the plasmodial counterpart renders the enzyme camptothecin resistant

    DEFF Research Database (Denmark)

    Arnò, Barbara; D'Annessa, Ilda; Tesauro, Cinzia;

    2013-01-01

    , but it is characterized by a much faster religation rate. The hybrid enzyme is also camptothecin resistant. A 3D structure of the hybrid enzyme has been built and its structural-dynamical properties have been analyzed by molecular dynamics simulation. The analysis indicates that the swapped plasmodial linker samples......A human/plasmodial hybrid enzyme, generated by swapping the human topoisomerase IB linker domain with the corresponding domain of the Plasmodium falciparum enzyme, has been produced and characterized. The hybrid enzyme displays a relaxation activity comparable to the human enzyme...... in the modulation of the topoisomerase IB activity....

  6. The human insulin gene is part of a large open chromatin domain specific for human islets.

    Science.gov (United States)

    Mutskov, Vesco; Felsenfeld, Gary

    2009-10-13

    Knowledge of how insulin (INS) gene expression is regulated will lead to better understanding of normal and abnormal pancreatic beta cell function. We have mapped histone modifications over the INS region, coupled with an expression profile, in freshly isolated islets from multiple human donors. Unlike many other human genes, in which active modifications tend to be concentrated within 1 kb around the transcription start site, these marks are distributed over the entire coding region of INS as well. Moreover, a region of approximately 80 kb around the INS gene, which contains the {tyrosine hydroxylase (TH)-(INS)-insulin-like growth factor 2 antisense (IGF2AS)-insulin-like growth factor 2 (IGF2)} gene cluster, unusually is marked by almost uniformly elevated levels of histone acetylation and H3K4 dimethylation, extending both downstream into IGF2 and upstream beyond the TH gene. This is accompanied by islet specific coordinate expression with INS of the neighboring TH and IGF2 genes. The presence of islet specific intergenic transcripts suggests their possible function in the maintenance of this unusual large open chromatin domain.

  7. EXPERT DISCOVERY AND KNOWLEDGE MINING IN COMPLEX MULTI-AGENT SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    Minjie ZHANG; Xijin TANG; Quan BAI; Jifa GU

    2007-01-01

    Complex problem solving requires diverse expertise and multiple techniques. In order to solve such problems, complex multi-agent systems that include both of human experts and autonomous agents are required in many application domains. Most complex multi-agent systems work in open domains and include various heterogeneous agents. Due to the heterogeneity of agents and dynamic features of working environments, expertise and capabilities of agents might not be well estimated and presented in these systems. Therefore, how to discover useful knowledge from human and autonomous experts,make more accurate estimation for experts' capabilities and find out suitable expert(s) to solve incoming problems ("Expert Mining") are important research issues in the area of multi-agent system.In this paper, we introduce an ontology-based approach for knowledge and expert mining in hybrid multi-agent systems. In this research, ontologies are hired to describe knowledge of the system.Knowledge and expert mining processes are executed as the system handles incoming problems. In this approach, we embed more self-learning and self-adjusting abilities in multi-agent systems, so as to help in discovering knowledge of heterogeneous experts of multi-agent systems.

  8. Escherichia coli lipoprotein binds human plasminogen via an intramolecular domain

    Directory of Open Access Journals (Sweden)

    Tammy eGonzalez

    2015-10-01

    Full Text Available Escherichia coli lipoprotein (Lpp is a major cellular component that exists in two distinct states, bound-form and free-form. Bound-form Lpp is known to interact with the periplasmic bacterial cell wall, while free-form Lpp is localized to the bacterial cell surface. A function for surface-exposed Lpp has yet to be determined. We hypothesized that the presence of C-terminal lysines in the surface-exposed region of Lpp would facilitate binding to the host zymogen plasminogen, a protease commandeered by a number of clinically important bacteria. Recombinant Lpp was synthesized and the binding of Lpp to plasminogen, the effect of various inhibitors on this binding, and the effects of various mutations of Lpp on Lpp-plasminogen interactions were examined. Additionally, the ability of Lpp-bound plasminogen to be converted to active plasmin was analyzed. We determined that Lpp binds plasminogen via an atypical domain located near the center of mature Lpp that may not be exposed on the surface of intact E. coli according to the current localization model. Finally, we found that plasminogen bound by Lpp can be converted to active plasmin. While the consequences of Lpp binding plasminogen are unclear, these results prompt further investigation of the ability of surface exposed Lpp to interact with host molecules such as extracellular matrix components and complement regulators, and the role of these interactions in infections caused by E. coli and other bacteria.

  9. Expert Systems: What Is an Expert System?

    Science.gov (United States)

    Duval, Beverly K.; Main, Linda

    1994-01-01

    Describes expert systems and discusses their use in libraries. Highlights include parts of an expert system; expert system shells; an example of how to build an expert system; a bibliography of 34 sources of information on expert systems in libraries; and a list of 10 expert system shells used in libraries. (Contains five references.) (LRW)

  10. Expert Systems: What Is an Expert System?

    Science.gov (United States)

    Duval, Beverly K.; Main, Linda

    1994-01-01

    Describes expert systems and discusses their use in libraries. Highlights include parts of an expert system; expert system shells; an example of how to build an expert system; a bibliography of 34 sources of information on expert systems in libraries; and a list of 10 expert system shells used in libraries. (Contains five references.) (LRW)

  11. Expert Systems and Intelligent Information Retrieval.

    Science.gov (United States)

    Brooks, H. M.

    1987-01-01

    Explores what an intelligent information retrieval system involves and why expert system techniques might interest system designers. Expert systems research is reviewed with emphasis on components, architecture, and computer interaction, and it is concluded that information retrieval is not an ideal problem domain for expert system application at…

  12. Human Systems Integration (HSI) in Acquisition. HSI Domain Guide

    Science.gov (United States)

    2009-08-01

    Activities boxes correspond to the numbers In the Inputs and Outputs boxes. Tools: ● CATIA ● HSI Requirements Guide ● IMPRINT Activities for Each Output...Tools: ● IMPRINT ● CATIA ● IPME References: ● DODI 5000.02 & DODD 5000.01 ● DAG ● CJCSI 3170.01 ● AFPD 63-1/AFPD 20-1 ● AFI 63-101 & AFI 63...correspond to the numbers In the Inputs and Outputs boxes. Technology Development Phase (Outputs) Human Systems Integration Tools: ● IMPRINT ● CATIA

  13. Solution structure of the RecQ C-terminal domain of human Bloom syndrome protein.

    Science.gov (United States)

    Park, Chin-Ju; Ko, Junsang; Ryu, Kyoung-Seok; Choi, Byong-Seok

    2014-02-01

    RecQ C-terminal (RQC) domain is known as the main DNA binding module of RecQ helicases such as Bloom syndrome protein (BLM) and Werner syndrome protein (WRN) that recognizes various DNA structures. Even though BLM is able to resolve various DNA structures similarly to WRN, BLM has different binding preferences for DNA substrates from WRN. In this study, we determined the solution structure of the RQC domain of human BLM. The structure shares the common winged-helix motif with other RQC domains. However, half of the N-terminal has unstructured regions (α1-α2 loop and α3 region), and the aromatic side chain on the top of the β-hairpin, which is important for DNA duplex strand separation in other RQC domains, is substituted with a negatively charged residue (D1165) followed by the polar residue (Q1166). The structurally distinctive features of the RQC domain of human BLM suggest that the DNA binding modes of the BLM RQC domain may be different from those of other RQC domains.

  14. Definition of the applicability domains of knowledge-based predictive toxicology expert systems by using a structural fragment-based approach.

    Science.gov (United States)

    Ellison, Claire M; Enoch, Steven J; Cronin, Mark Td; Madden, Judith C; Judson, Philip

    2009-11-01

    The applicability domain of a (quantitative) structure-activity relationship ([Q]SAR) must be defined, if a model is to be used successfully for toxicity prediction, particularly for regulatory purposes. Previous efforts to set guidelines on the definition of applicability domains have often been biased toward quantitative, rather than qualitative, models. As a result, novel techniques are still required to define the applicability domains of structural alert models and knowledge-based systems. By using Derek for Windows as an example, this study defined the domain for the skin sensitisation structural alert rule-base. This was achieved by fragmenting the molecules within a training set of compounds, then searching the fragments for those created from a test compound. This novel method was able to highlight test chemicals which differed from those in the training set. The information was then used to designate chemicals as being either within or outside the domain of applicability for the structural alert on which that training set was based.

  15. Structure and function of the regulatory HRDC domain from human Bloom syndrome protein.

    Science.gov (United States)

    Kim, Young Mee; Choi, Byong-Seok

    2010-11-01

    The helicase and RNaseD C-terminal (HRDC) domain, conserved among members of the RecQ helicase family, regulates helicase activity by virtue of variations in its surface residues. The HRDC domain of Bloom syndrome protein (BLM) is known as a critical determinant of the dissolution function of double Holliday junctions by the BLM-Topoisomerase IIIα complex. In this study, we determined the solution structure of the human BLM HRDC domain and characterized its DNA-binding activity. The BLM HRDC domain consists of five α-helices with a hydrophobic 3(10)-helical loop between helices 1 and 2 and an extended acidic surface comprising residues in helices 3-5. The BLM HRDC domain preferentially binds to ssDNA, though with a markedly low binding affinity (K(d) ∼100 μM). NMR chemical shift perturbation studies suggested that the critical DNA-binding residues of the BLM HRDC domain are located in the hydrophobic loop and the N-terminus of helix 2. Interestingly, the isolated BLM HRDC domain had quite different DNA-binding modes between ssDNA and Holliday junctions in electrophoretic mobility shift assay experiments. Based on its surface charge separation and DNA-binding properties, we suggest that the HRDC domain of BLM may be adapted for a unique function among RecQ helicases--that of bridging protein and DNA interactions.

  16. ExpertFOAF recommends experts

    DEFF Research Database (Denmark)

    Iofcu, Tereza; Diederich, Joerg; Dolog, Peter

    2007-01-01

    the GrowBag approach [1]. The main assumption is that such user profiles can provide good hints about users' expertise. Such extended FOAF files (called ExpertFOAF) can be published on a user's home page, on web pages of institutions or conferences to characterize them. They can be crawled by distributed...

  17. Structural Basis for Ubiquitin Recognition by the Human ESCRT-II EAP45 GLUE Domain

    Energy Technology Data Exchange (ETDEWEB)

    Alam,S.; Langelier, C.; Whitby, F.; Koirala, S.; Robinson, H.; Hill, C.; Sundquist, W.

    2006-01-01

    ESCRT-IESCRT-IIGLUEEAP45VPS36The ESCRT-I and ESCRT-II complexes help sort ubiquitinated proteins into vesicles that accumulate within multivesicular bodies (MVBs). Crystallographic and biochemical analyses reveal that the GLUE domain of the human ESCRT-II EAP45 (also called VPS36) subunit is a split pleckstrin-homology domain that binds ubiquitin along one edge of the {beta}-sandwich. The structure suggests how human ESCRT-II can couple recognition of ubiquitinated cargoes and endosomal phospholipids during MVB protein sorting.

  18. Expert Systems Research.

    Science.gov (United States)

    Duda, Richard O.; Shortliffe, Edward H.

    1983-01-01

    Discusses a class of artificial intelligence computer programs (often called "expert systems" because they address problems normally thought to require human specialists for their solution) intended to serve as consultants for decision making. Also discusses accomplishments (including information systematization in medical diagnosis and…

  19. Working to define professionalism in pediatric anesthesiology: a qualitative study of domains of the expert pediatric anesthesiologist as valued by interdisciplinary stakeholders.

    Science.gov (United States)

    Lockman, Justin L; Schwartz, Alan Jay; Cronholm, Peter F

    2017-02-01

    Unprofessional behavior is a significant problem throughout graduate medical education programs and medical centers. Some authors have suggested that professionalism curricula should be focused toward faculty, not trainees, to interrupt the modeling of unprofessionalism. Developing such curricula requires a needs assessment and is challenging given data indicating that the definition of professionalism varies based on medical specialty. Thus, a specialty-specific definition of professionalism is needed as a first step in any curriculum development. The aim of this study was to define professionalism in pediatric anesthesiology. This is a qualitative study using focus groups for data collection and a grounded theory approach for analysis. Four relevant stakeholder groups, pediatric surgeons and endoscopists, perioperative nurses, pediatric anesthesiologists, and parents of children who had undergone surgery at our facility, were recruited for participation. De-identified transcripts were analyzed and coded to derive major domains and component themes relevant to the definition of professionalism for pediatric anesthesiology. Member checking with participants from our stakeholder groups was used to validate thematic development and increase the trustworthiness of our findings. Focus group participants included 20 individuals, 14 of whom were female. Analysis of transcripts identified 11 major domains across the four groups: Patient Ownership, Specialty Expertise, Continuous Team Improvement, Expressive Communication, Active Listening, Care Coordination, Medical Hierarchy, Leadership, Teamwork, Personality Traits, and Physical Image. The data uncovered several controversies for future study. A composite of these 11 domains may give a more complete image of what surgical and nursing colleagues, patient families, and anesthesiologist partners expect of the pediatric anesthesiologist. Despite some overlap and interdependence between domains, this research may contribute

  20. Construction of Powerful Online Search Expert System Based on Semantic Web

    Directory of Open Access Journals (Sweden)

    Yasser A. Nada

    2013-01-01

    Full Text Available In this paper we intends to build an expert system based on semantic web for online search using XML, to help users to find the desired software, and read about its features and specifications. The expert system saves user's time and effort of web searching or buying software from available libraries. Building online search expert system is ideal for capturing support knowledge to produce interactive on-line systems that provide searching details, situation-specific advice exactly like setting a session with an expert. Any person can access this interactive system from his web browser and get some questions answer in addition to precise advice which was provided by an expert. The system can provide some troubleshooting diagnose, find the right products; … Etc. The proposed system further combines aspects of three research topics (Semantic Web, Expert System and XML. Semantic web Ontology will be considered as a set of directed graphs where each node represents an item and the edges denote a term which is related to another term. Organizations can now optimize their most valuable expert knowledge through powerful interactive Web-enabled knowledge automation expert system. Online sessions emulate a conversation with a human expert asking focused questions and producing customized recommendations and advice. Hence, the main powerful point of the proposed expert system is that the skills of any domain expert will be available to everyone.

  1. Defining the specificity space of the human SRC homology 2 domain.

    Science.gov (United States)

    Huang, Haiming; Li, Lei; Wu, Chenggang; Schibli, David; Colwill, Karen; Ma, Sucan; Li, Chengjun; Roy, Protiva; Ho, Krystina; Songyang, Zhou; Pawson, Tony; Gao, Youhe; Li, Shawn S-C

    2008-04-01

    Src homology 2 (SH2) domains are the largest family of interaction modules encoded by the human genome to recognize tyrosine-phosphorylated sequences and thereby play pivotal roles in transducing and controlling cellular signals emanating from protein-tyrosine kinases. Different SH2 domains select for distinct phosphopeptides, and the function of a given SH2 domain is often dictated by the specific motifs that it recognizes. Therefore, deciphering the phosphotyrosyl peptide motif recognized by an SH2 domain is the key to understanding its cellular function. Here we cloned all 120 SH2 domains identified in the human genome and determined the phosphotyrosyl peptide binding properties of 76 SH2 domains by screening an oriented peptide array library. Of these 76, we defined the selectivity for 43 SH2 domains and refined the binding motifs for another 33 SH2 domains. We identified a number of novel binding motifs, which are exemplified by the BRDG1 SH2 domain that selects specifically for a bulky, hydrophobic residue at P + 4 relative to the Tyr(P) residue. Based on the oriented peptide array library data, we developed scoring matrix-assisted ligand identification (or SMALI), a Web-based program for predicting binding partners for SH2-containing proteins. When applied to SH2D1A/SAP (SLAM-associated protein), a protein whose mutation or deletion underlies the X-linked lymphoproliferative syndrome, SMALI not only recapitulated known interactions but also identified a number of novel interacting proteins for this disease-associated protein. SMALI also identified a number of potential interactors for BRDG1, a protein whose function is largely unknown. Peptide in-solution binding analysis demonstrated that a SMALI score correlates well with the binding energy of a peptide to a given SH2 domain. The definition of the specificity space of the human SH2 domain provides both the necessary molecular basis and a platform for future exploration of the functions for SH2-containing

  2. Structure of the human histone chaperone FACT Spt16 N-terminal domain

    Energy Technology Data Exchange (ETDEWEB)

    Marcianò, G.; Huang, D. T., E-mail: d.huang@beatson.gla.ac.uk [Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland (United Kingdom)

    2016-01-22

    The Spt16–SSRP1 heterodimer is a histone chaperone that plays an important role in regulating chromatin assembly. Here, a crystal structure of the N-terminal domain of human Spt16 is presented and it is shown that this domain may contribute to histone binding. The histone chaperone FACT plays an important role in facilitating nucleosome assembly and disassembly during transcription. FACT is a heterodimeric complex consisting of Spt16 and SSRP1. The N-terminal domain of Spt16 resembles an inactive aminopeptidase. How this domain contributes to the histone chaperone activity of FACT remains elusive. Here, the crystal structure of the N-terminal domain (NTD) of human Spt16 is reported at a resolution of 1.84 Å. The structure adopts an aminopeptidase-like fold similar to those of the Saccharomyces cerevisiae and Schizosaccharomyces pombe Spt16 NTDs. Isothermal titration calorimetry analyses show that human Spt16 NTD binds histones H3/H4 with low-micromolar affinity, suggesting that Spt16 NTD may contribute to histone binding in the FACT complex. Surface-residue conservation and electrostatic analysis reveal a conserved acidic patch that may be involved in histone binding.

  3. Identification of novel human WW domain-containing proteins by cloning of ligand targets.

    Science.gov (United States)

    Pirozzi, G; McConnell, S J; Uveges, A J; Carter, J M; Sparks, A B; Kay, B K; Fowlkes, D M

    1997-06-06

    A recently described protein module consisting of 35-40 semiconserved residues, termed the WW domain, has been identified in a number of diverse proteins including dystrophin and Yes-associated protein (YAP). Two putative ligands of YAP, termed WBP-1 and WBP-2, have been found previously to contain several short peptide regions consisting of PPPPY residues (PY motif) that mediate binding to the WW domain of YAP. Although the function(s) of the WW domain remain to be elucidated, these observations strongly support a role for the WW domain in protein-protein interactions. Here we report the isolation of three novel human cDNAs encoding a total of nine WW domains, using a newly developed approach termed COLT (cloning of ligand targets), in which the rapid cloning of modular protein domains is accomplished by screening cDNA expression libraries with specific peptide ligands. Two of the new genes identified appear to be members of a family of proteins, including Rsp5 and Nedd-4, which have ubiquitin-protein ligase activity. In addition, we demonstrate that peptides corresponding to PY and PY-like motifs present in several known signaling or regulatory proteins, including RasGAP, AP-2, p53BP-2 (p53-binding protein-2), interleukin-6 receptor-alpha, chloride channel CLCN5, and epithelial sodium channel ENaC, can selectively bind to certain of these novel WW domains.

  4. Structurally Similar but Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin

    Energy Technology Data Exchange (ETDEWEB)

    Yasunaga, Mai; Ipsaro, Jonathan J.; Mondragón, Alfonso (NWU)

    2014-10-02

    The metazoan cell membrane is highly organized. Maintaining such organization and preserving membrane integrity under different conditions are accomplished through intracellular tethering to an extensive, flexible protein network. Spectrin, the principal component of this network, is attached to the membrane through the adaptor protein ankyrin, which directly bridges the interaction between {beta}-spectrin and membrane proteins. Ankyrins have a modular structure that includes two tandem ZU5 domains. The first domain, ZU5A, is directly responsible for binding {beta}-spectrin. Here, we present a structure of the tandem ZU5 repeats of human erythrocyte ankyrin. Structural and biophysical experiments show that the second ZU5 domain, ZU5B, does not participate in spectrin binding. ZU5B is structurally similar to the ZU5 domain found in the netrin receptor UNC5b supramodule, suggesting that it could interact with other domains in ankyrin. Comparison of several ZU5 domains demonstrates that the ZU5 domain represents a compact and versatile protein interaction module.

  5. Recombinant expression in E. coli of human FGFR2 with its transmembrane and extracellular domains

    Directory of Open Access Journals (Sweden)

    Adam Bajinting

    2017-06-01

    Full Text Available Fibroblast growth factor receptors (FGFRs are a family of receptor tyrosine kinases containing three domains: an extracellular receptor domain, a single transmembrane helix, and an intracellular tyrosine kinase domain. FGFRs are activated by fibroblast growth factors (FGFs as part of complex signal transduction cascades regulating angiogenesis, skeletal formation, cell differentiation, proliferation, cell survival, and cancer. We have developed the first recombinant expression system in E. coli to produce a construct of human FGFR2 containing its transmembrane and extracellular receptor domains. We demonstrate that the expressed construct is functional in binding heparin and dimerizing. Size exclusion chromatography demonstrates that the purified FGFR2 does not form a complex with FGF1 or adopts an inactive dimer conformation. Progress towards the successful recombinant production of intact FGFRs will facilitate further biochemical experiments and structure determination that will provide insight into how extracellular FGF binding activates intracellular kinase activity.

  6. Structure of the human histone chaperone FACT Spt16 N-terminal domain.

    Science.gov (United States)

    Marcianò, G; Huang, D T

    2016-02-01

    The histone chaperone FACT plays an important role in facilitating nucleosome assembly and disassembly during transcription. FACT is a heterodimeric complex consisting of Spt16 and SSRP1. The N-terminal domain of Spt16 resembles an inactive aminopeptidase. How this domain contributes to the histone chaperone activity of FACT remains elusive. Here, the crystal structure of the N-terminal domain (NTD) of human Spt16 is reported at a resolution of 1.84 Å. The structure adopts an aminopeptidase-like fold similar to those of the Saccharomyces cerevisiae and Schizosaccharomyces pombe Spt16 NTDs. Isothermal titration calorimetry analyses show that human Spt16 NTD binds histones H3/H4 with low-micromolar affinity, suggesting that Spt16 NTD may contribute to histone binding in the FACT complex. Surface-residue conservation and electrostatic analysis reveal a conserved acidic patch that may be involved in histone binding.

  7. Structure of the C-type lectin carbohydrate recognition domain of human tetranectin

    DEFF Research Database (Denmark)

    Kastrup, J S; Nielsen, B B; Rasmussen, H

    1998-01-01

    of certain human carcinomas, whereas none or little is present in the corresponding normal tissue. The crystal structure of full-length trimeric TN (2.8 A resolution) has recently been published [Nielsen et al. (1997). FEBS Lett. 412, 388-396]. The crystal structure of the carbohydrate recognition domain...

  8. CRITERIA FOR AN UPDATED CLASSIFICATION OF HUMAN TRANSCRIPTION FACTOR DNA-BINDING DOMAINS

    NARCIS (Netherlands)

    Wingender, Edgar

    2013-01-01

    By binding to cis-regulatory elements in a sequence-specific manner, transcription factors regulate the activity of nearby genes. Here, we discuss the criteria for a comprehensive classification of human TFs based on their DNA-binding domains. In particular, classification of basic leucine zipper (b

  9. CRITERIA FOR AN UPDATED CLASSIFICATION OF HUMAN TRANSCRIPTION FACTOR DNA-BINDING DOMAINS

    NARCIS (Netherlands)

    Wingender, Edgar

    By binding to cis-regulatory elements in a sequence-specific manner, transcription factors regulate the activity of nearby genes. Here, we discuss the criteria for a comprehensive classification of human TFs based on their DNA-binding domains. In particular, classification of basic leucine zipper

  10. Identification of a minimal functional linker in human topoisomerase I by domain swapping with Cre recombinase

    DEFF Research Database (Denmark)

    Hougaard, Rikke Frøhlich; Juul, Sissel; Vinther, Maria

    2008-01-01

    . In this study we replace 86 amino acids including the linker domain of the cellular type IB topoisomerase, human topoisomerase I, with four, six, or eight amino acids from the corresponding short loop region in Cre recombinase. In vitro characterization of the resulting chimeras, denoted Cropos, reveals...

  11. Expression, purification and enzymatic characterization of the catalytic domains of human tryptophan hydroxylase isoforms

    DEFF Research Database (Denmark)

    Windahl, Michael Skovbo; Boesen, Jane; Karlsen, Pernille Efferbach;

    2009-01-01

    Tryptophan hydroxylase exists in two isoforms: Isoform 1 catalyses the first and rate-limiting step in the synthesis of serotonin in the peripheral parts of the body while isoform 2 catalyses this step in the brain. The catalytic domains of human tryptophan hydroxylase 1 and 2 have been expressed...

  12. Getting CAD in shape: the atomic structure of human dihydroorotase domain.

    Science.gov (United States)

    Hermoso, Juan A

    2014-02-04

    CAD is a large multifunctional polypeptide that initiates and controls the de novo biosynthesis of pyrimidines in animals. In this issue of Structure, Grande-García and colleagues provide the first atomic information of this antitumoral target by reporting the crystal structure of the dihydroorotase domain of human CAD.

  13. An evaluation of an expert system for detecting critical events during anesthesia in a human patient simulator: a prospective randomized controlled study.

    Science.gov (United States)

    Görges, Matthias; Winton, Pamela; Koval, Valentyna; Lim, Joanne; Stinson, Jonathan; Choi, Peter T; Schwarz, Stephan K W; Dumont, Guy A; Ansermino, J Mark

    2013-08-01

    Perioperative monitoring systems produce a large amount of uninterpreted data, use threshold alarms prone to artifacts, and rely on the clinician to continuously visually track changes in physiological data. To address these deficiencies, we developed an expert system that provides real-time clinical decisions for the identification of critical events. We evaluated the efficacy of the expert system for enhancing critical event detection in a simulated environment. We hypothesized that anesthesiologists would identify critical ventilatory events more rapidly and accurately with the expert system. We used a high-fidelity human patient simulator to simulate an operating room environment. Participants managed 4 scenarios (anesthetic vapor overdose, tension pneumothorax, anaphylaxis, and endotracheal tube cuff leak) in random order. In 2 of their 4 scenarios, participants were randomly assigned to the expert system, which provided trend-based alerts and potential differential diagnoses. Time to detection and time to treatment were measured. Workload questionnaires and structured debriefings were completed after each scenario, and a usability questionnaire at the conclusion of the session. Data were analyzed using a mixed-effects linear regression model; Fisher exact test was used for workload scores. Twenty anesthesiology trainees and 15 staff anesthesiologists with a combined median (range) of 36 (29-66) years of age and 6 (1-38) years of anesthesia experience participated. For the endotracheal tube cuff leak, the expert system caused mean reductions of 128 (99% confidence interval [CI], 54-202) seconds in time to detection and 140 (99% CI, 79-200) seconds in time to treatment. In the other 3 scenarios, a best-case decrease of 97 seconds (lower 99% CI) in time to diagnosis for anaphylaxis and a worst-case increase of 63 seconds (upper 99% CI) in time to treatment for anesthetic vapor overdose were found. Participants were highly satisfied with the expert system (median

  14. The impact of the human DNA topoisomerase II C-terminal domain on activity.

    Directory of Open Access Journals (Sweden)

    Emma L Meczes

    Full Text Available BACKGROUND: Type II DNA topoisomerases (topos are essential enzymes needed for the resolution of topological problems that occur during DNA metabolic processes. Topos carry out an ATP-dependent strand passage reaction whereby one double helix is passed through a transient break in another. Humans have two topoII isoforms, alpha and beta, which while enzymatically similar are differentially expressed and regulated, and are thought to have different cellular roles. The C-terminal domain (CTD of the enzyme has the most diversity, and has been implicated in regulation. We sought to investigate the impact of the CTD domain on activity. METHODOLOGY/PRINCIPLE FINDINGS: We have investigated the role of the human topoII C-terminal domain by creating constructs encoding C-terminally truncated recombinant topoIIalpha and beta and topoIIalpha+beta-tail and topoIIbeta+alpha-tail chimeric proteins. We then investigated function in vivo in a yeast system, and in vitro in activity assays. We find that the C-terminal domain of human topoII isoforms is needed for in vivo function of the enzyme, but not needed for cleavage activity. C-terminally truncated enzymes had similar strand passage activity to full length enzymes, but the presence of the opposite C-terminal domain had a large effect, with the topoIIalpha-CTD increasing activity, and the topoIIbeta-CTD decreasing activity. CONCLUSIONS/SIGNIFICANCE: In vivo complementation data show that the topoIIalpha C-terminal domain is needed for growth, but the topoIIbeta isoform is able to support low levels of growth without a C-terminal domain. This may indicate that topoIIbeta has an additional localisation signal. In vitro data suggest that, while the lack of any C-terminal domain has little effect on activity, the presence of either the topoIIalpha or beta C-terminal domain can affect strand passage activity. Data indicates that the topoIIbeta-CTD may be a negative regulator. This is the first report of in vitro

  15. Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

    Science.gov (United States)

    Pal, Lipika R; Guda, Chittibabu

    2006-11-07

    The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome.

  16. Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2008-12-01

    Full Text Available Abstract Background Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. Result The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Conclusion Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.

  17. Crystal structure of the first WW domain of human YAP2 isoform.

    Science.gov (United States)

    Martinez-Rodriguez, Sergio; Bacarizo, Julio; Luque, Irene; Camara-Artigas, Ana

    2015-09-01

    The WW domains are the smallest modular domains known. The study of the structural basis of their stability is important to understand their physiological role. These domains are intrinsically flexible, which makes them difficult to crystallize. The first WW domain of the human Yes tyrosine kinase Associated Protein (YAP) has been crystallized and its structure has been solved by X-ray diffraction at 1.6 Å resolution. Crystals belong to the orthorhombic space group P21212 with unit cell parameters a=42.67, b=43.10 and c=21.30. The addition of proline and other small-molecule additives improves drastically the quality of the crystals. The interactions that stabilize this minimal modular domain have been analysed. This crystal structure reveals that, besides the stabilization of the hydrophobic core of the protein by the aromatic cluster formed by Trp177-Phe189-Pro202, some salt-bridges interactions might affect the stability of the domain. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis.

    Science.gov (United States)

    Xiong, Zi-Jian; Huang, Jingjing; Poda, Gennady; Pomès, Régis; Privé, Gilbert G

    2016-07-31

    Acid sphingomyelinase (ASM) is a lysosomal phosphodiesterase that catalyzes the hydrolysis of sphingomyelin to produce ceramide and phosphocholine. While other lysosomal sphingolipid hydrolases require a saposin activator protein for full activity, the ASM polypeptide incorporates a built-in N-terminal saposin domain and does not require an external activator protein. Here, we report the crystal structure of human ASM and describe the organization of the three main regions of the enzyme: the N-terminal saposin domain, the proline-rich connector, and the catalytic domain. The saposin domain is tightly associated along an edge of the large, bowl-shaped catalytic domain and adopts an open form that exposes a hydrophobic concave surface approximately 30Å from the catalytic center. The calculated electrostatic potential of the enzyme is electropositive at the acidic pH of the lysosome, consistent with the strict requirement for the presence of acidic lipids in target membranes. Docking studies indicate that sphingomyelin binds with the ceramide-phosphate group positioned at the binuclear zinc center and molecular dynamic simulations indicate that the intrinsic flexibility of the saposin domain is important for monomer-dimer exchange and for membrane interactions. Overall, ASM uses a combination of electrostatic and hydrophobic interactions to cause local disruptions of target bilayers in order to bring the lipid headgroup to the catalytic center in a membrane-bound reaction.

  19. Structural and functional analysis of the YAP-binding domain of human TEAD2

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Wei; Yu, Jianzhong; Tomchick, Diana R.; Pan, Duojia; Luo, Xuelian (JHU-MED); (UTSMC)

    2010-06-15

    The Hippo pathway controls organ size and suppresses tumorigenesis in metazoans by blocking cell proliferation and promoting apoptosis. The TEAD1-4 proteins (which contain a DNA-binding domain but lack an activation domain) interact with YAP (which lacks a DNA-binding domain but contains an activation domain) to form functional heterodimeric transcription factors that activate proliferative and prosurvival gene expression programs. The Hippo pathway inhibits the YAP-TEAD hybrid transcription factors by phosphorylating and promoting cytoplasmic retention of YAP. Here we report the crystal structure of the YAP-binding domain (YBD) of human TEAD2. TEAD2 YBD adopts an immunoglobulin-like {beta}-sandwich fold with two extra helix-turn-helix inserts. NMR studies reveal that the TEAD-binding domain of YAP is natively unfolded and that TEAD binding causes localized conformational changes in YAP. In vitro binding and in vivo functional assays define an extensive conserved surface of TEAD2 YBD as the YAP-binding site. Therefore, our studies suggest that a short segment of YAP adopts an extended conformation and forms extensive contacts with a rigid surface of TEAD. Targeting a surface-exposed pocket of TEAD might be an effective strategy to disrupt the YAP-TEAD interaction and to reduce the oncogenic potential of YAP.

  20. Structural and functional analysis of the YAP-binding domain of human TEAD2.

    Science.gov (United States)

    Tian, Wei; Yu, Jianzhong; Tomchick, Diana R; Pan, Duojia; Luo, Xuelian

    2010-04-20

    The Hippo pathway controls organ size and suppresses tumorigenesis in metazoans by blocking cell proliferation and promoting apoptosis. The TEAD1-4 proteins (which contain a DNA-binding domain but lack an activation domain) interact with YAP (which lacks a DNA-binding domain but contains an activation domain) to form functional heterodimeric transcription factors that activate proliferative and prosurvival gene expression programs. The Hippo pathway inhibits the YAP-TEAD hybrid transcription factors by phosphorylating and promoting cytoplasmic retention of YAP. Here we report the crystal structure of the YAP-binding domain (YBD) of human TEAD2. TEAD2 YBD adopts an immunoglobulin-like beta-sandwich fold with two extra helix-turn-helix inserts. NMR studies reveal that the TEAD-binding domain of YAP is natively unfolded and that TEAD binding causes localized conformational changes in YAP. In vitro binding and in vivo functional assays define an extensive conserved surface of TEAD2 YBD as the YAP-binding site. Therefore, our studies suggest that a short segment of YAP adopts an extended conformation and forms extensive contacts with a rigid surface of TEAD. Targeting a surface-exposed pocket of TEAD might be an effective strategy to disrupt the YAP-TEAD interaction and to reduce the oncogenic potential of YAP.

  1. The canalicular system and the osteoblast domain in human secondary osteons.

    Science.gov (United States)

    Pazzaglia, U E; Congiu, T; Marchese, M; Zarattini, G; Dell'Orbo, C

    2012-12-01

    The lacunar-canalicular system in human secondary osteons was examined by two complementary techniques: light microscopy analysis of undecalcified thick sections and the SEM cortex-fractured surface technique. Unlike the earlier definitions of 'osteoblastic domain' presented as the matrix volume produced by osteoblasts in the process of osteon infilling, this study measured the domain by the length of osteoblast dendritic processes. The domain extension was defined along radial vectors advancing from the reversal line towards the central canal. According to their lengths, domains were divided into three classes: peripheral, intermediate and internal. The mean length of peripheral domains was significantly shorter than those of the intermediate and internal domains. This suggests that the infilling process is modulated by an initial preparatory phase characterised by osteoblast adhesion to the wall of the cutting cone, and a limited matrix synthesis, followed by a regular matrix volume apposition organised in concentric layers. In addition to the radial canaliculae arranged along converging vectors in planes perpendicular to the central canal, we distinguished a further class of canaliculae, the equatorial canaliculae originating from the major perimeter of the lacuna and spreading out radially in the plane of the same lacuna (therefore, perpendicularly to the radial canaliculae). The whole lacunar-canalicular network was structured as a closed system around the vascular axis of the central canal with very few canaliculae crossing the reversal line and connecting the neighbouring osteons. These anatomical observations contribute to our knowledge of lacunar-canalicular system development. © 2012 Blackwell Verlag GmbH.

  2. Replication domains are self-interacting structural chromatin units of human chromosomes

    Science.gov (United States)

    Arneodo, Alain

    2011-03-01

    In higher eukaryotes, the absence of specific sequence motifs marking the origins of replication has been a serious hindrance to the understanding of the mechanisms that regulate the initiation and the maintenance of the replication program in different cell types. In silico analysis of nucleotide compositional skew has predicted the existence, in the germline, of replication N-domains bordered by putative replication origins and where the skew decreases rather linearly as the signature of a progressive inversion of the average fork polarity. Here, from the demonstration that the average fork polarity can be directly extracted from the derivative of replication timing profiles, we develop a wavelet-based pattern recognition methodology to delineate replication U-domains where the replication timing profile is shaped as a U and its derivative as a N. Replication U-domains are robustly found in seven cell lines as covering a significant portion (40-50%) of the human genome where the replication timing data actually displays some plasticity between cell lines. The early replication initiation zones at U-domains borders are found to be hypersensitive to DNase I cleavage, to be associated with transcriptional activity and to present a significant enrichment in insular-binding proteins CTCF, the hallmark of an open chromatin structure. A comparative analysis of genome-wide chromatin interaction (HiC) data shows that replication-U domains correspond to self-interacting structural high order chromatin units of megabase characteristic size. Taken together, these findings provide evidence that the epigenetic compartmentalization of the human genome into autonomous replication U-domains comes along with an extensive remodelling of the threedimensional chromosome architecture during development or in specific diseases. The observed cell specific conservation of the replication timing between the human and mouse genomes strongly suggests that this chromosome organization into

  3. Structure of the single-strand annealing domain of human RAD52 protein

    OpenAIRE

    Singleton, Martin R.; Wentzell, Lois M.; Liu, Yilun; West, Stephen C.; Wigley, Dale B.

    2002-01-01

    In eukaryotic cells, RAD52 protein plays a central role in genetic recombination and DNA repair by (i) promoting the annealing of complementary single-stranded DNA and (ii) stimulation of the RAD51 recombinase. The single-strand annealing domain resides in the N-terminal region of the protein and is highly conserved, whereas the nonconserved RAD51-interaction domain is located in the C-terminal region. An N-terminal fragment of human RAD52 (residues 1–209) has been purified to homogeneity and...

  4. Large-Scale Brain Networks in Board Game Experts: Insights from a Domain-Related Task and Task-Free Resting State

    Science.gov (United States)

    Duan, Xujun; Liao, Wei; Liang, Dongmei; Qiu, Lihua; Gao, Qing; Liu, Chengyi; Gong, Qiyong; Chen, Huafu

    2012-01-01

    Cognitive performance relies on the coordination of large-scale networks of brain regions that are not only temporally correlated during different tasks, but also networks that show highly correlated spontaneous activity during a task-free state. Both task-related and task-free network activity has been associated with individual differences in cognitive performance. Therefore, we aimed to examine the influence of cognitive expertise on four networks associated with cognitive task performance: the default mode network (DMN) and three other cognitive networks (central-executive network, dorsal attention network, and salience network). During fMRI scanning, fifteen grandmaster and master level Chinese chess players (GM/M) and fifteen novice players carried out a Chinese chess task and a task-free resting state. Modulations of network activity during task were assessed, as well as resting-state functional connectivity of those networks. Relative to novices, GM/Ms showed a broader task-induced deactivation of DMN in the chess problem-solving task, and intrinsic functional connectivity of DMN was increased with a connectivity pattern associated with the caudate nucleus in GM/Ms. The three other cognitive networks did not exhibit any difference in task-evoked activation or intrinsic functional connectivity between the two groups. These findings demonstrate the effect of long-term learning and practice in cognitive expertise on large-scale brain networks, suggesting the important role of DMN deactivation in expert performance and enhanced functional integration of spontaneous activity within widely distributed DMN-caudate circuitry, which might better support high-level cognitive control of behavior. PMID:22427852

  5. Improved Ant Colony Optimization Algorithm based Expert System on Nephrology

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    Sri.N.V.Ramana Murty

    2010-07-01

    Full Text Available Expert system Nephrology is a computer program that exhibits, within a specific domain, a degree of expertise in problem solving that is comparable to that of a human expert. The knowledge base consistsof information about a particular problem area. This information is collected from domain experts (doctors. This system mainly contains two modules one is Information System and the other is Expert Advisory system. The Information System contains the static information about different diseases and drugs in the field of Nephrology. This information system helps the patients /users to know about the problems related to kidneys. The Nephrology Advisory system helps the Patients /users to get the required and suitable advice depending on their queries. This medical expert system is developedusing Java Server Pages (JSP as front-end and MYSQL database as Backend in such a way that all the activities are carried out in a user-friendly manner. Improved Ant Colony Optimization Algorithm (ACO along with RETE algorithm is also used for better results.

  6. Knowledge acquisition from natural language for expert systems based on classification problem-solving methods

    Science.gov (United States)

    Gomez, Fernando

    1989-01-01

    It is shown how certain kinds of domain independent expert systems based on classification problem-solving methods can be constructed directly from natural language descriptions by a human expert. The expert knowledge is not translated into production rules. Rather, it is mapped into conceptual structures which are integrated into long-term memory (LTM). The resulting system is one in which problem-solving, retrieval and memory organization are integrated processes. In other words, the same algorithm and knowledge representation structures are shared by these processes. As a result of this, the system can answer questions, solve problems or reorganize LTM.

  7. Stereoselective binding of mexiletine and ketoprofen enantiomers with human serum albumin domains

    Institute of Scientific and Technical Information of China (English)

    Da SHI; Yin-xiu JIN; Yi-hong TANG; Hai-hong HU; Si-yun XU; Lu-shanYU; Hui-di JIANG; Su ZENG

    2012-01-01

    To investigate the stereoselective binding of mexiletine or ketoprofen enantiomers with different recombinant domains of human serum albumin (HSA).Methods:Three domains (HSA DOM Ⅰ,Ⅱ and Ⅲ) were expressed in Pichia pastoris GS115 cells.Blue Sepharose 6 Fast Flow was employed to purify the recombinant HSA domains.The binding properties of the standard ligands,digitoxin,phenylbutazone and diazepam,and the chiral drugs to HSA domains were investigated using ultrafiltration.The concentrations of the standard ligands,ketoprofen and mexiletine were analyzed with HPLC.Results:The recombinant HSA domains were highly purified as shown by SDS-PAGE and Western blotting analyses,The standard HSA ligands digitoxin,phenylbutazone and diazepam selectively binds to DOM Ⅰ,DOM Ⅱ and DOM Ⅲ,respectively.For the chiral drugs,R-ketoprofen showed a higher binding affinity toward DOM Ⅲ than S-ketoprofen,whereas S-mexiletine bound to DOM Ⅱ with a greater affinity than R-mexiletine.Conclusion:The results demonstrate that HSA DOM Ⅲ possesses the chiral recognition ability for the ketoprofen enantiomers,whereas HSA DOM Ⅱ possesses that for the mexiletine enantiomers.

  8. Self-assembly of human plasma fibrinogens on binary organosilane monolayers with micro domains

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S.H. [Faculty of Engineering, Shinshu Universuty, 4-17-1 Wakasato, Nagano 380 8553 (Japan); Saito, N., E-mail: hiro@eco-t.esi.nagoya-u.ac.jp [Department of Materials, Physics and Energy Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464 8603 (Japan); Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464 8603 (Japan); Takai, O. [EcoTopia Science Institute, Nagoya University, Furo-cho, Chikusa, Nagoya 464 8603 (Japan)

    2009-06-30

    The adsorption behavior and self-assembly of human plasma fibrinogen (HPF) on binary methyl- and amino-terminated self-assembled monolayers (SAMs) were investigated by atomic force microscopy (AFM). The binary SAMs were fabricated through self-assembly mechanism of organosilane molecules. The height of domains is the domain height is 0.8 {+-} 0.2 nm from the AFM topographic image. It corresponds to the domain height is 0.8 {+-} 0.2 nm from the AFM topographic image. It corresponds to the difference between the length of the alkyl chain of octadecyltrichlorosilane (OTS) and that of n-(6-aminohexyl)aminopropyltrimethoxysilane (AHAPS). The fibrinogen solution used ultrapure water as the solvent and its pH was adjusted at 3 and 10. From the AFM results at pH 3, HPF only formed network structures on the OTS domains of the binary SAM at early immersion times, and then the network structures expanded and connected between OTS domains through the AHAPS surface at long immersion times. In this case, a few HPFs are discretely adsorbed on the AHAPS surface. However, HPF is uniformly adsorbed on the binary SAM under the other conditions of pH.

  9. The HhH domain of the human DNA repair protein XPF forms stable homodimers.

    Science.gov (United States)

    Das, Devashish; Tripsianes, Konstantinos; Jaspers, Nicolaas G J; Hoeijmakers, Jan H J; Kaptein, Robert; Boelens, Rolf; Folkers, Gert E

    2008-03-01

    The human XPF-ERCC1 protein complex plays an essential role in nucleotide excision repair by catalysing positioned nicking of a DNA strand at the 5' side of the damage. We have recently solved the structure of the heterodimeric complex of the C-terminal domains of XPF and ERCC1 (Tripsianes et al., Structure 2005;13:1849-1858). We found that this complex comprises a pseudo twofold symmetry axis and that the helix-hairpin-helix motif of ERCC1 is required for DNA binding, whereas the corresponding domain of XPF is functioning as a scaffold for complex formation with ERCC1. Despite the functional importance of heterodimerization, the C-terminal domain of XPF can also form homodimers in vitro. We here compare the stabilities of homodimeric and heterodimeric complexes of the C-terminal domains of XPF and ERCC1. The higher stability of the XPF HhH complexes under various experimental conditions, determined using CD and NMR spectroscopy and mass spectrometry, is well explained by the structural differences that exist between the HhH domains of the two complexes. The XPF HhH homodimer has a larger interaction interface, aromatic stacking interactions, and additional hydrogen bond contacts as compared to the XPF/ERCC1 HhH complex, which accounts for its higher stability.

  10. Crystal Structure of the Central Coiled-Coil Domain from Human Liprin-[beta]2

    Energy Technology Data Exchange (ETDEWEB)

    Stafford, Ryan L.; Tang, Ming-Yun; Sawaya, Michael R.; Phillips, Martin L.; Bowie, James U. (UCLA)

    2012-02-07

    Liprins are a conserved family of scaffolding proteins important for the proper regulation and development of neuronal synapses. Humans have four liprin-{alpha}s and two liprin-{beta}s which all contain long coiled-coil domains followed by three tandem SAM domains. Complex interactions between the coiled-coil and SAM domains are thought to create liprin scaffolds, but the structural and biochemical properties of these domains remain largely uncharacterized. In this study we find that the human liprin-{beta}2 coiled-coil forms an extended dimer. Several protease-resistant subdomains within the liprin-{beta}1 and liprin-{beta}2 coiled-coils were also identified. A 2.0 {angstrom} crystal structure of the central, protease-resistant core of the liprin-{beta}2 coiled-coil reveals a parallel helix orientation. These studies represent an initial step toward determining the overall architecture of liprin scaffolds and understanding the molecular basis for their synaptic functions.

  11. Interpretation of p16(INK4a) /Ki-67 dual immunostaining for the triage of human papillomavirus-positive women by experts and nonexperts in cervical cytology.

    Science.gov (United States)

    Allia, Elena; Ronco, Guglielmo; Coccia, Anna; Luparia, Patrizia; Macrì, Luigia; Fiorito, Corinna; Maletta, Francesca; Deambrogio, Cristina; Tunesi, Sara; De Marco, Laura; Gillio-Tos, Anna; Sapino, Anna; Ghiringhello, Bruno

    2015-04-01

    The triage of human papillomavirus (HPV)-positive women is needed to avoid overreferral to colposcopy. p16(INK4a) immunostaining is an efficient triage method. p16(INK4a) /Ki-67 dual staining was introduced mainly to increase reproducibility and specificity compared with stand-alone p16(INK4a) staining. Within a pilot project, HPV-positive women were referred to colposcopy if cytology was abnormal or unsatisfactory or HPV testing was still positive after 1 year. For 500 consecutive women, a slide obtained during colposcopy was immunostained for p16(INK4a) /Ki-67 and independently interpreted by 7 readers without previous experience with dual staining. Four of these readers were experts in cervical pathology and 3 were not. Kappa values for multiple raters, sensitivity, and specificity for cervical intraepithelial neoplasia type 2-positive histology were computed. Because women with normal cytology were underrepresented, estimates for all HPV-positive women were obtained as weighted means of cytology-specific estimates. The overall kappa for HPV-positive women was 0.70 (95% confidence interval [95% CI], 0.60-0.77). Kappa values were not found to be significantly different between expert and nonexpert readers with regard to cervical cytology but were significantly increased (P =. 0066) after consensus discussion. The overall specificity estimate for HPV-positive women was 64.0% (95% CI, 57.4%-70.2%): 66.7% (95% CI, 59.8%-73.0%) for experts and 60.5% (95% CI, 59.8%-73.0%) for nonexperts. Among women with abnormal cytology, the sensitivity was 85.5% (95% CI, 77.9%-90.8%): 85.8% (95% CI, 77.9%-91.2%) for experts and 85.1% (95% CI, 76.6%-90.9%) for nonexperts. p16(INK4a) /Ki-67 immunostaining demonstrated good reproducibility and specificity when triaging HPV-positive women. Dual-staining interpretation can be performed, after short training, even by staff who are not experts in cervical cytology. This allows HPV-based screening with triage to be performed in settings in

  12. Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level

    OpenAIRE

    Guda Chittibabu; Pal Lipika R

    2006-01-01

    Abstract Background The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. Results This stu...

  13. Recovery of a human natural antibody against the noncollagenous-1 domain of type IV collagen using humanized models.

    Science.gov (United States)

    Worni-Schudel, Inge M; Clark, Amy G; Chien, Tiffany; Hwang, Kwan-Ki; Chen, Benny J; Foster, Mary H

    2015-06-06

    Anti-glomerular basement membrane nephritis and Goodpasture syndrome result from autoantibody (Ab)-mediated destruction of kidney and lung. Ab target the noncollagenous 1 (NC1) domain of alpha3(IV) collagen, but little is known about Ab origins or structure. This ignorance is due in part to the inability to recover monoclonal Ab by transformation of patients' blood cells. The aim of this study was to assess the suitability of two humanized models for this purpose. NOD-scid-gamma immunodeficient mice were engrafted either with human CD34+ hematopoietic stem cells (HSC) (Hu-HSC mice) and immunized with alpha3(IV)NC1 collagen containing the Goodpasture epitopes or with nephritis patients' peripheral blood leukocytes (PBL) (Hu-PBL mice). After in vivo immune cell development and/or expansion, recovered human B cells were Epstein Barr virus (EBV)-transformed, screened for antigen (Ag) binding, electrofused with a mouse-human heterohybridoma, subcloned, and human Ab RNA sequenced by PCR after reverse transcription to cDNA. Flow cytometry was used to assess human B cell markers and differentiation in Hu-PBL mice. Sequence analysis of a human Ab derived from an immunized Hu-HSC mouse and reactive with alpha3(IV)NC1 collagen reveals that it is encoded by unmutated heavy and light chain genes. The heavy chain complementarity determining region 3, a major determinant of Ag binding, contains uncommon motifs, including an N-region somatically-introduced highly hydrophobic tetrapeptide and dual cysteines encoded by a uniquely human IGHD2-2 Ab gene segment that lacks a murine counterpart. Comparison of human and mouse autoantibodies suggests that structurally similar murine Ab may arise by convergent selection. In contrast to the Hu-HSC model, transformed human B cells are rarely recovered from Hu-PBL mice, in which human B cells terminally differentiate and lose expression of EBV receptor CD21, thus precluding their transformation and recovery. Hu-HSC mice reveal that

  14. Structural and biophysical characterization of the cytoplasmic domains of human BAP29 and BAP31.

    Science.gov (United States)

    Quistgaard, Esben M; Löw, Christian; Moberg, Per; Guettou, Fatma; Maddi, Karthik; Nordlund, Pär

    2013-01-01

    Two members of the B-cell associated 31 (BAP31) family are found in humans; BAP29 and BAP31. These are ubiquitously expressed receptors residing in the endoplasmic reticulum. BAP31 functions in sorting of membrane proteins and in caspase-8 mediated apoptosis, while BAP29 appears to mainly corroborate with BAP31 in sorting. The N-terminal half of these proteins is membrane-bound while the C-terminal half is cytoplasmic. The latter include the so called variant of death effector domain (vDED), which shares weak sequence homology with DED domains. Here we present two structures of BAP31 vDED determined from a single and a twinned crystal, grown at pH 8.0 and pH 4.2, respectively. These structures show that BAP31 vDED forms a dimeric parallel coiled coil with no structural similarity to DED domains. Solution studies support this conclusion and strongly suggest that an additional α-helical domain is present in the C-terminal cytoplasmic region, probably forming a second coiled coil. The thermal stability of BAP31 vDED is quite modest at neutral pH, suggesting that it may assemble in a dynamic fashion in vivo. Surprisingly, BAP29 vDED is partially unfolded at pH 7, while a coiled coil is formed at pH 4.2 in vitro. It is however likely that folding of the domain is triggered by other factors than low pH in vivo. We found no evidence for direct interaction of the cytoplasmic domains of BAP29 and BAP31.

  15. Structural and biophysical characterization of the cytoplasmic domains of human BAP29 and BAP31.

    Directory of Open Access Journals (Sweden)

    Esben M Quistgaard

    Full Text Available Two members of the B-cell associated 31 (BAP31 family are found in humans; BAP29 and BAP31. These are ubiquitously expressed receptors residing in the endoplasmic reticulum. BAP31 functions in sorting of membrane proteins and in caspase-8 mediated apoptosis, while BAP29 appears to mainly corroborate with BAP31 in sorting. The N-terminal half of these proteins is membrane-bound while the C-terminal half is cytoplasmic. The latter include the so called variant of death effector domain (vDED, which shares weak sequence homology with DED domains. Here we present two structures of BAP31 vDED determined from a single and a twinned crystal, grown at pH 8.0 and pH 4.2, respectively. These structures show that BAP31 vDED forms a dimeric parallel coiled coil with no structural similarity to DED domains. Solution studies support this conclusion and strongly suggest that an additional α-helical domain is present in the C-terminal cytoplasmic region, probably forming a second coiled coil. The thermal stability of BAP31 vDED is quite modest at neutral pH, suggesting that it may assemble in a dynamic fashion in vivo. Surprisingly, BAP29 vDED is partially unfolded at pH 7, while a coiled coil is formed at pH 4.2 in vitro. It is however likely that folding of the domain is triggered by other factors than low pH in vivo. We found no evidence for direct interaction of the cytoplasmic domains of BAP29 and BAP31.

  16. How does domain replacement affect fibril formation of the rabbit/human prion proteins.

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    Xu Yan

    Full Text Available It is known that in vivo human prion protein (PrP have the tendency to form fibril deposits and are associated with infectious fatal prion diseases, while the rabbit PrP does not readily form fibrils and is unlikely to cause prion diseases. Although we have previously demonstrated that amyloid fibrils formed by the rabbit PrP and the human PrP have different secondary structures and macromolecular crowding has different effects on fibril formation of the rabbit/human PrPs, we do not know which domains of PrPs cause such differences. In this study, we have constructed two PrP chimeras, rabbit chimera and human chimera, and investigated how domain replacement affects fibril formation of the rabbit/human PrPs.As revealed by thioflavin T binding assays and Sarkosyl-soluble SDS-PAGE, the presence of a strong crowding agent dramatically promotes fibril formation of both chimeras. As evidenced by circular dichroism, Fourier transform infrared spectroscopy, and proteinase K digestion assays, amyloid fibrils formed by human chimera have secondary structures and proteinase K-resistant features similar to those formed by the human PrP. However, amyloid fibrils formed by rabbit chimera have proteinase K-resistant features and secondary structures in crowded physiological environments different from those formed by the rabbit PrP, and secondary structures in dilute solutions similar to the rabbit PrP. The results from transmission electron microscopy show that macromolecular crowding caused human chimera but not rabbit chimera to form short fibrils and non-fibrillar particles.We demonstrate for the first time that the domains beyond PrP-H2H3 (β-strand 1, α-helix 1, and β-strand 2 have a remarkable effect on fibrillization of the rabbit PrP but almost no effect on the human PrP. Our findings can help to explain why amyloid fibrils formed by the rabbit PrP and the human PrP have different secondary structures and why macromolecular crowding has different

  17. Interpretation of the margin of exposure for genotoxic carcinogens - elicitation of expert knowledge about the form of the dose response curve at human relevant exposures.

    Science.gov (United States)

    Boobis, Alan; Flari, Villie; Gosling, John Paul; Hart, Andy; Craig, Peter; Rushton, Lesley; Idahosa-Taylor, Ehi

    2013-07-01

    The general approach to risk assessment of genotoxic carcinogens has been to advise reduction of exposure to "as low as reasonably achievable/practicable" (ALARA/P). However, whilst this remains the preferred risk management option, it does not provide guidance on the urgency or extent of risk management actions necessary. To address this, the "Margin of Exposure" (MOE) approach has been proposed. The MOE is the ratio between the point of departure for carcinogenesis and estimated human exposure. However, interpretation of the MOE requires implicit or explicit consideration of the shape of the dose-response curve at human relevant exposures. In a structured elicitation exercise, we captured expert opinion on available scientific evidence for low dose-response relationships for genotoxic carcinogens. This allowed assessment of: available evidence for the nature of dose-response relationships at human relevant exposures; the generality of judgments about such dose-response relationships; uncertainties affecting judgments on the nature of such dose-response relationships; and whether this last should differ for different classes of genotoxic carcinogens. Elicitation results reflected the variability in experts' views on the form of the dose-response curve for low dose exposure and major sources of uncertainty affecting the assumption of a linear relationship.

  18. Research Approaches and Methods for Evaluating the Protein Quality of Human Foods Proposed by an FAO Expert Working Group in 2014.

    Science.gov (United States)

    Lee, Warren Tk; Weisell, Robert; Albert, Janice; Tomé, Daniel; Kurpad, Anura V; Uauy, Ricardo

    2016-05-01

    The Protein Digestibility Corrected Amino Acid Score (PDCAAS) has been adopted for assessing protein quality in human foods since 1991, and the shortcomings of using the PDCAAS have been recognized since its adoption. The 2011 FAO Expert Consultation recognized that the Digestible Indispensable Amino Acid Score (DIAAS) was superior to the PDCAAS for determining protein quality. However, there were insufficient human data on amino acid digestibility before adopting the DIAAS. More human data were needed before DIAAS could be implemented. In 2014, FAO convened an expert working group to propose and agree on research protocols using both human-based assays and animal models to study ileal amino acid digestibility (metabolic availability) of human foods. The working group identified 5 research protocols for further research and development. A robust database of protein digestibility of foods commonly consumed worldwide, including those consumed in low-income countries, is needed for an informed decision on adopting the DIAAS. A review on the impacts of using the DIAAS on public health policies is necessary. It would be advantageous to have a global coordinating effort to advance research and data collection. Collaboration with international and national agriculture institutes is desirable. Opportunities should be provided for young researchers, particularly those from developing countries, to engage in protein-quality research for sustainable implementation of DIAAS. To conclude, the DIAAS is a conceptually preferable method compared with the PDCAAS for protein and amino acid quality evaluation. However, the complete value of the DIAAS and its impact on public health nutrition cannot be realized until there are sufficient accumulated ileal amino acid digestibility data on human foods that are consumed in different nutritional and environmental conditions, measured by competent authorities. A future meeting may be needed to evaluate the size and quality of the data set

  19. Solution structure of the HRDC domain of human Bloom syndrome protein BLM.

    Science.gov (United States)

    Sato, Akiko; Mishima, Masaki; Nagai, Aki; Kim, Sun-Yong; Ito, Yutaka; Hakoshima, Toshio; Jee, Jun-Goo; Kitano, Ken

    2010-10-01

    Bloom syndrome is a rare genetic disorder characterized by severe growth retardation and cancer predisposition. The disease is caused by a loss of function of the Bloom syndrome protein (BLM), a member of the RecQ family of DNA helicases. Here we report on the first 3D structure of a BLM fragment, a solution structure of the C-terminal helicase-and-ribonuclease D-C-terminal (HRDC) domain from human BLM. The structure reveals unique features of BLM HRDC that are distinct from the HRDC domain of Werner syndrome protein. In particular, BLM HRDC retains many acidic residues exposed to the solvent, which makes the domain surface extensively electronegative. Consistent with this, fluorescence polarization assays showed an inability of isolated BLM HRDC to interact with DNA substrates. Analyses employing ultracentrifugation, gel-filtration, CD spectroscopy and dynamic light scattering showed that the BLM HRDC domain exists as a stable monomer in solution. The results show that BLM HRDC is a compact, robust and acidic motif which may play a distinct role apart from DNA binding.

  20. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

    Directory of Open Access Journals (Sweden)

    Schlegel Brigitte

    2004-03-01

    Full Text Available Abstract Background High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. Results 88 different E. coli expression constructs for 17 human protein domains were analysed using high-throughput cloning, purification and folding analysis to obtain candidates suitable for structural analysis. After 96 deep-well microplate expression and automated protein purification, protein domains were directly analysed using 1D 1H-NMR spectroscopy. In addition, analytical hydrophobic interaction chromatography (HIC was used to detect natively folded protein. With these two analytical methods, six constructs (representing two domains were quickly identified as being well folded and suitable for structural analysis. Conclusion The described approach facilitates high-throughput structural analysis. Clones expressing natively folded proteins suitable for NMR structure determination were quickly identified upon small scale expression screening using 1D 1H-NMR and/or analytical HIC. This procedure is especially effective as a fast and inexpensive screen for the 'low hanging fruits' in structural genomics.

  1. Crystal structure of a coiled-coil domain from human ROCK I.

    Directory of Open Access Journals (Sweden)

    Daqi Tu

    Full Text Available The small GTPase Rho and one of its targets, Rho-associated kinase (ROCK, participate in a variety of actin-based cellular processes including smooth muscle contraction, cell migration, and stress fiber formation. The ROCK protein consists of an N-terminal kinase domain, a central coiled-coil domain containing a Rho binding site, and a C-terminal pleckstrin homology domain. Here we present the crystal structure of a large section of the central coiled-coil domain of human ROCK I (amino acids 535-700. The structure forms a parallel α-helical coiled-coil dimer that is structurally similar to tropomyosin, an actin filament binding protein. There is an unusual discontinuity in the coiled-coil; three charged residues (E613, R617 and D620 are positioned at what is normally the hydrophobic core of coiled-coil packing. We speculate that this conserved irregularity could function as a hinge that allows ROCK to adopt its autoinhibited conformation.

  2. Functional mapping of human dynamin-1-like GTPase domain based on x-ray structure analyses.

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    Julia Wenger

    Full Text Available Human dynamin-1-like protein (DNM1L is a GTP-driven molecular machine that segregates mitochondria and peroxisomes. To obtain insights into its catalytic mechanism, we determined crystal structures of a construct comprising the GTPase domain and the bundle signaling element (BSE in the nucleotide-free and GTP-analogue-bound states. The GTPase domain of DNM1L is structurally related to that of dynamin and binds the nucleotide 5'-Guanylyl-imidodiphosphate (GMP-PNP via five highly conserved motifs, whereas the BSE folds into a pocket at the opposite side. Based on these structures, the GTPase center was systematically mapped by alanine mutagenesis and kinetic measurements. Thus, residues essential for the GTPase reaction were characterized, among them Lys38, Ser39 and Ser40 in the phosphate binding loop, Thr59 from switch I, Asp146 and Gly149 from switch II, Lys216 and Asp218 in the G4 element, as well as Asn246 in the G5 element. Also, mutated Glu81 and Glu82 in the unique 16-residue insertion of DNM1L influence the activity significantly. Mutations of Gln34, Ser35, and Asp190 in the predicted assembly interface interfered with dimerization of the GTPase domain induced by a transition state analogue and led to a loss of the lipid-stimulated GTPase activity. Our data point to related catalytic mechanisms of DNM1L and dynamin involving dimerization of their GTPase domains.

  3. Isoform-specific targeting and interaction domains in human nicotinamide mononucleotide adenylyltransferases.

    Science.gov (United States)

    Lau, Corinna; Dölle, Christian; Gossmann, Toni I; Agledal, Line; Niere, Marc; Ziegler, Mathias

    2010-06-11

    Several important signaling pathways require NAD as substrate, thereby leading to significant consumption of the molecule. Because NAD is also an essential redox carrier, its continuous resynthesis is vital. In higher eukaryotes, maintenance of compartmentalized NAD pools is critical, but so far rather little is known about the regulation and subcellular distribution of NAD biosynthetic enzymes. The key step in NAD biosynthesis is the formation of the dinucleotide by nicotinamide/nicotinic acid mononucleotide adenylyltransferases (NMNATs). The three human isoforms were localized to the nucleus, the Golgi complex, and mitochondria. Here, we show that their genes contain unique exons that encode isoform-specific domains to mediate subcellular targeting and post-translational modifications. These domains are dispensable for catalytic activity, consistent with their absence from NMNATs of lower organisms. We further demonstrate that the Golgi-associated NMNAT is palmitoylated at two adjacent cysteine residues of its isoform-specific domain and thereby anchored at the cytoplasmic surface, a potential mechanism to regulate the cytosolic NAD pool. Insertion of unique domains thus provides a yet unrecognized enzyme targeting mode, which has also been adapted to modulate subcellular NAD supply.

  4. Human fixation detection model in video compressed domain based on Markov random field

    Science.gov (United States)

    Li, Yongjun; Li, Yunsong; Liu, Weijia; Hu, Jing; Ge, Chiru

    2017-01-01

    Recently, research on and applications of human fixation detection in video compressed domain have gained increasing attention. However, prediction accuracy and computational complexity still remain a challenge. This paper addresses the problem of compressed domain fixations detection in the videos based on residual discrete cosine transform coefficients norm (RDCN) and Markov random field (MRF). RDCN feature is directly extracted from the compressed video with partial decoding and is normalized. After spatial-temporal filtering, the normalized map [Smoothed RDCN (SRDCN) map] is taken to the MRF model, and the optimal binary label map is obtained. Based on the label map and the center saliency map, saliency enhancement and nonsaliency inhibition are done for the SRDCN map, and the final SRDCN-MRF salient map is obtained. Compared with the similar models, we enhance the available energy functions and introduce an energy function that indicates the positional information of the saliency. The procedure is advantageous for improving prediction accuracy and reducing computational complexity. The validation and comparison are made by several accuracy metrics on two ground truth datasets. Experimental results show that the proposed saliency detection model achieves superior performances over several state-of-the-art compressed-domain and pixel-domain algorithms on evaluation metrics. Computationally, our algorithm reduces 26% more computational complexity with comparison to similar algorithms.

  5. ALICE Expert System

    CERN Document Server

    Ionita, C

    2014-01-01

    The ALICE experiment at CERN employs a number of human operators (shifters), who have to make sure that the experiment is always in a state compatible with taking Physics data. Given the complexity of the system and the myriad of errors that can arise, this is not always a trivial task. The aim of this paper is to describe an expert system that is capable of assisting human shifters in the ALICE control room. The system diagnoses potential issues and attempts to make smart recommendations for troubleshooting. At its core, a Prolog engine infers whether a Physics or a technical run can be started based on the current state of the underlying sub-systems. A separate C++ component queries certain SMI objects and stores their state as facts in a Prolog knowledge base. By mining the data stored in dierent system logs, the expert system can also diagnose errors arising during a run. Currently the system is used by the on-call experts for faster response times, but we expect it to be adopted as a standard tool by reg...

  6. Mapping cis-Regulatory Domains in the Human Genome UsingMulti-Species Conservation of Synteny

    Energy Technology Data Exchange (ETDEWEB)

    Ahituv, Nadav; Prabhakar, Shyam; Poulin, Francis; Rubin, EdwardM.; Couronne, Olivier

    2005-06-13

    Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries we used whole-genome human-mouse-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synteny (CBS), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes that they regulate. A total of 2,116 and 1,942 CBS>200 kb were assembled for HMC and HMF respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBS we analyzed the prevalence and distribution of chromosomal aberrations leading to position effects (disruption of a genes regulatory environment), observing a clear bias not only for mapping onto CBS but also for longer CBS size. Our results provide a genome wide data set characterizing the regulatory domains of genes and the conserved regulatory elements within them.

  7. Expert Systems: An Overview.

    Science.gov (United States)

    Adiga, Sadashiv

    1984-01-01

    Discusses: (1) the architecture of expert systems; (2) features that distinguish expert systems from conventional programs; (3) conditions necessary to select a particular application for the development of successful expert systems; (4) issues to be resolved when building expert systems; and (5) limitations. Examples of selected expert systems…

  8. Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level

    Directory of Open Access Journals (Sweden)

    Guda Chittibabu

    2006-11-01

    Full Text Available Abstract Background The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. Results This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. Conclusion This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome.

  9. Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology.

    Science.gov (United States)

    Belsom, Adam; Schneider, Michael; Fischer, Lutz; Brock, Oliver; Rappsilber, Juri

    2016-03-01

    Chemical cross-linking combined with mass spectrometry has proven useful for studying protein-protein interactions and protein structure, however the low density of cross-link data has so far precluded its use in determining structures de novo. Cross-linking density has been typically limited by the chemical selectivity of the standard cross-linking reagents that are commonly used for protein cross-linking. We have implemented the use of a heterobifunctional cross-linking reagent, sulfosuccinimidyl 4,4'-azipentanoate (sulfo-SDA), combining a traditional sulfo-N-hydroxysuccinimide (sulfo-NHS) ester and a UV photoactivatable diazirine group. This diazirine yields a highly reactive and promiscuous carbene species, the net result being a greatly increased number of cross-links compared with homobifunctional, NHS-based cross-linkers. We present a novel methodology that combines the use of this high density photo-cross-linking data with conformational space search to investigate the structure of human serum albumin domains, from purified samples, and in its native environment, human blood serum. Our approach is able to determine human serum albumin domain structures with good accuracy: root-mean-square deviation to crystal structure are 2.8/5.6/2.9 Å (purified samples) and 4.5/5.9/4.8Å (serum samples) for domains A/B/C for the first selected structure; 2.5/4.9/2.9 Å (purified samples) and 3.5/5.2/3.8 Å (serum samples) for the best out of top five selected structures. Our proof-of-concept study on human serum albumin demonstrates initial potential of our approach for determining the structures of more proteins in the complex biological contexts in which they function and which they may require for correct folding. Data are available via ProteomeXchange with identifier PXD001692.

  10. Structural analysis of 5'-mRNA-cap interactions with the human AGO2 MID domain.

    Science.gov (United States)

    Frank, Filipp; Fabian, Marc R; Stepinski, Janusz; Jemielity, Jacek; Darzynkiewicz, Edward; Sonenberg, Nahum; Nagar, Bhushan

    2011-05-01

    In RNA silencing, microRNA (miRNA)-mediated translational repression occurs through mechanisms that do not invoke messenger-RNA (mRNA) target cleavage by Argonaute proteins. The nature of these mechanisms is unclear, but several recent studies have proposed that a direct interaction between the mRNA-cap and the middle (MID) domain of Argonautes is involved. Here, we present crystallographic and NMR data demonstrating that cap analogues do not bind significantly to the isolated MID domain of human Argonaute 2 (hAGO2) and are found in the miRNA 5'-nucleotide binding site in an implausible binding mode. Additionally, in vitro pull-down experiments with full-length hAGO2 indicate that the interaction with cap analogues is nonspecific.

  11. Role of the intracellular receptor domain of gp130 (exon 17) in human inflammatory bowel disease

    Institute of Scientific and Technical Information of China (English)

    Christoph J. Auernhammer; Thomas Ochsenkühn; Kathrin Zitzmann; Fabian Schnitzler; Julia Seiderer; Peter Lohse; George Vlotides; Dieter Engelhardt; Michael Sackmann; Burkhard G(o)ke

    2005-01-01

    AIM: To study the role of the intracellular receptor domain of gp130 in human inflammatory bowel disease (IBD).METHODS: We amplified and sequenced the complete exon 17 of the human gp130 gene in 146 patients with IBD. According to clinical and histopathological signs,the 146 patients with IBD were classified as having Crohn's disease (n = 73) or ulcerative colitis (n = 63),or as indeterminate status (n = 10).RESULTS: No mutations in exon 17 of the gp130 gene could be detected in any of the 146 patients with IBD examined.CONCLUSION: There is no evidence that mutations in exon 17 of the gp130 gene are involved in the pathogenesis of human IBD.

  12. Towards a Fuzzy Expert System on Toxicological Data Quality Assessment.

    Science.gov (United States)

    Yang, Longzhi; Neagu, Daniel; Cronin, Mark T D; Hewitt, Mark; Enoch, Steven J; Madden, Judith C; Przybylak, Katarzyna

    2013-01-01

    Quality assessment (QA) requires high levels of domain-specific experience and knowledge. QA tasks for toxicological data are usually performed by human experts manually, although a number of quality evaluation schemes have been proposed in the literature. For instance, the most widely utilised Klimisch scheme1 defines four data quality categories in order to tag data instances with respect to their qualities; ToxRTool2 is an extension of the Klimisch approach aiming to increase the transparency and harmonisation of the approach. Note that the processes of QA in many other areas have been automatised by employing expert systems. Briefly, an expert system is a computer program that uses a knowledge base built upon human expertise, and an inference engine that mimics the reasoning processes of human experts to infer new statements from incoming data. In particular, expert systems have been extended to deal with the uncertainty of information by representing uncertain information (such as linguistic terms) as fuzzy sets under the framework of fuzzy set theory and performing inferences upon fuzzy sets according to fuzzy arithmetic. This paper presents an experimental fuzzy expert system for toxicological data QA which is developed on the basis of the Klimisch approach and the ToxRTool in an effort to illustrate the power of expert systems to toxicologists, and to examine if fuzzy expert systems are a viable solution for QA of toxicological data. Such direction still faces great difficulties due to the well-known common challenge of toxicological data QA that "five toxicologists may have six opinions". In the meantime, this challenge may offer an opportunity for expert systems because the construction and refinement of the knowledge base could be a converging process of different opinions which is of significant importance for regulatory policy making under the regulation of REACH, though a consensus may never be reached. Also, in order to facilitate the implementation

  13. Proteolytic dissection of Zab, the Z-DNA-binding domain of human ADAR1

    Science.gov (United States)

    Schwartz, T.; Lowenhaupt, K.; Kim, Y. G.; Li, L.; Brown, B. A. 2nd; Herbert, A.; Rich, A.

    1999-01-01

    Zalpha is a peptide motif that binds to Z-DNA with high affinity. This motif binds to alternating dC-dG sequences stabilized in the Z-conformation by means of bromination or supercoiling, but not to B-DNA. Zalpha is part of the N-terminal region of double-stranded RNA adenosine deaminase (ADAR1), a candidate enzyme for nuclear pre-mRNA editing in mammals. Zalpha is conserved in ADAR1 from many species; in each case, there is a second similar motif, Zbeta, separated from Zalpha by a more divergent linker. To investigate the structure-function relationship of Zalpha, its domain structure was studied by limited proteolysis. Proteolytic profiles indicated that Zalpha is part of a domain, Zab, of 229 amino acids (residues 133-361 in human ADAR1). This domain contains both Zalpha and Zbeta as well as a tandem repeat of a 49-amino acid linker module. Prolonged proteolysis revealed a minimal core domain of 77 amino acids (positions 133-209), containing only Zalpha, which is sufficient to bind left-handed Z-DNA; however, the substrate binding is strikingly different from that of Zab. The second motif, Zbeta, retains its structural integrity only in the context of Zab and does not bind Z-DNA as a separate entity. These results suggest that Zalpha and Zbeta act as a single bipartite domain. In the presence of substrate DNA, Zab becomes more resistant to proteases, suggesting that it adopts a more rigid structure when bound to its substrate, possibly with conformational changes in parts of the protein.

  14. The human insulin gene is part of a large open chromatin domain specific for human islets

    OpenAIRE

    Mutskov, Vesco; Felsenfeld, Gary

    2009-01-01

    Knowledge of how insulin (INS) gene expression is regulated will lead to better understanding of normal and abnormal pancreatic β cell function. We have mapped histone modifications over the INS region, coupled with an expression profile, in freshly isolated islets from multiple human donors. Unlike many other human genes, in which active modifications tend to be concentrated within 1 kb around the transcription start site, these marks are distributed over the entire coding region of INS as w...

  15. Expert system for compressor maintenance support; Sistema especialista para apoio a manutencao de compressores

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Jonny Carlos da [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Dept. de Engenharia Mecanica; Caletti, Luciano [KEOHPS - Knowledge Engineering on Hydraulic and Pneumatic System, SC (Brazil); Luna, Paulo de T.M. [Universidade Regional de Blumenau - FURB, SC (Brazil)

    2004-07-01

    The performance of critical machines in industrial processes, such as compressors used in industrial plants, is fundamental for overall company operation. In this context, it becomes strategic the application of methods and tools to support the operation and maintenance of the most relevant process equipment. Among these computational tools are the Expert Systems, which aim to emulate the decision making process of human experts in a specific knowledge domain. In Oil and Gas domain, an example of such tools is the SEGRED project, which combines expert system techniques with dynamic simulation of transport and distribution natural gas networks. The SECOMP project, Expert System for Compressor Maintenance, is considered a spin-off of the SEGRED. Its objective is to develop an expert system to support maintenance activities, aiming to increase reliability, improve performance and reduce maintenance and operational costs. This article presents the first phase of the SECOMP project, which is related to the development of an expert system prototype for corrective maintenance of natural gas reciprocating compressors. The paper discusses the context of this knowledge domain, the prototype development and its potential contribution in an industrial environment. (author)

  16. The contribution of research on expertise to understanding of expert thinking

    Directory of Open Access Journals (Sweden)

    Krnjaić Zora

    2013-01-01

    Full Text Available Expertise is determined based on the high level of mastery of knowledge and skills in different areas of human activities (science, art, sports and other less formal domains. This paper explores the contribution of empirical research on expertise to understanding of the nature of expert thinking. For that purpose we have compiled an overview and performed an analysis of the findings of relevant research on expertise based on different approaches and paradigms. We have included the studies that researched experts singled out based on their exceptional performances in different domains (absolute expertise and the studies based on comparing experts with novices (relative expertise. We have analyzed the studies using different paradigms: psychometric and cognitive paradigms, as well as the new offshoot, the paradigm based on viewing giftedness as developing expertise. Research results provide empirically grounded findings on the characteristics of expert thinking and consistently point to the fact that knowledge is the core of expertise. The characteristics of expert knowledge are operationalized via the quantity and organization of knowledge and the mastery of deep contents and knowledge systems, which enables the recognition of rules, models and information sets, as well as the use of knowledge in further studying, detecting and solving different problems. It can be concluded that research findings on expertise are one of the foundations in the conceptualization of expert thinking. They significantly contribute to obtaining an insight into the way in which knowledge shapes thought and into understanding the mechanisms of demonstrating knowledge in the mental processes of experts.

  17. Functional Domains of Autoimmune Regulator (AIRE) Modulate INS-VNTR Transcription in Human Thymic Epithelial Cells*

    Science.gov (United States)

    Sparks, Avis E.; Chen, Chiachen; Breslin, Mary B.; Lan, Michael S.

    2016-01-01

    INS-VNTR (insulin-variable number of tandem repeats) and AIRE (autoimmune regulator) have been associated with the modulation of insulin gene expression in thymus, which is essential to induce either insulin tolerance or the development of insulin autoimmunity and type 1 diabetes. We sought to analyze whether each functional domain of AIRE is critical for the activation of INS-VNTR in human thymic epithelial cells. Twelve missense or nonsense mutations in AIRE and two chimeric AIRE constructs were generated. A luciferase reporter assay and a pulldown assay using biotinylated INS-class I VNTR probe were performed to examine the transactivation and binding activities of WT, mutant, and chimeric AIREs on the INS-VNTR promoter. Confocal microscopy analysis was performed for WT or mutant AIRE cellular localization. We found that all of the AIRE mutations resulted in loss of transcriptional activation of INS-VNTR except mutant P252L. Using WT/mutant AIRE heterozygous forms to modulate the INS-VNTR target revealed five mutations (R257X, G228W, C311fsX376, L397fsX478, and R433fsX502) that functioned in a dominant negative fashion. The LXXLL-3 motif is identified for the first time to be essential for DNA binding to INS-VNTR, whereas the intact PHD1, PHD2, LXXLL-3, and LXXLL-4 motifs were important for successful transcriptional activation. AIRE nuclear localization in the human thymic epithelial cell line was disrupted by mutations in the homogenously staining region domain and the R257X mutation in the PHD1 domain. This study supports the notion that AIRE mutation could specifically affect human insulin gene expression in thymic epithelial cells through INS-VNTR and subsequently induce either insulin tolerance or autoimmunity. PMID:27048654

  18. Functional Domains of Autoimmune Regulator (AIRE) Modulate INS-VNTR Transcription in Human Thymic Epithelial Cells.

    Science.gov (United States)

    Sparks, Avis E; Chen, Chiachen; Breslin, Mary B; Lan, Michael S

    2016-05-20

    INS-VNTR (insulin-variable number of tandem repeats) and AIRE (autoimmune regulator) have been associated with the modulation of insulin gene expression in thymus, which is essential to induce either insulin tolerance or the development of insulin autoimmunity and type 1 diabetes. We sought to analyze whether each functional domain of AIRE is critical for the activation of INS-VNTR in human thymic epithelial cells. Twelve missense or nonsense mutations in AIRE and two chimeric AIRE constructs were generated. A luciferase reporter assay and a pulldown assay using biotinylated INS-class I VNTR probe were performed to examine the transactivation and binding activities of WT, mutant, and chimeric AIREs on the INS-VNTR promoter. Confocal microscopy analysis was performed for WT or mutant AIRE cellular localization. We found that all of the AIRE mutations resulted in loss of transcriptional activation of INS-VNTR except mutant P252L. Using WT/mutant AIRE heterozygous forms to modulate the INS-VNTR target revealed five mutations (R257X, G228W, C311fsX376, L397fsX478, and R433fsX502) that functioned in a dominant negative fashion. The LXXLL-3 motif is identified for the first time to be essential for DNA binding to INS-VNTR, whereas the intact PHD1, PHD2, LXXLL-3, and LXXLL-4 motifs were important for successful transcriptional activation. AIRE nuclear localization in the human thymic epithelial cell line was disrupted by mutations in the homogenously staining region domain and the R257X mutation in the PHD1 domain. This study supports the notion that AIRE mutation could specifically affect human insulin gene expression in thymic epithelial cells through INS-VNTR and subsequently induce either insulin tolerance or autoimmunity.

  19. Iron-sulfur cluster biosynthesis: functional characterization of the N- and C-terminal domains of human NFU.

    Science.gov (United States)

    Liu, Yushi; Qi, Wenbin; Cowan, J A

    2009-02-10

    Human NFU (also known as HIRIP5) has been implicated in cellular iron-sulfur cluster biosynthesis. Bacterial and yeast forms are smaller than the human protein and are homologous to the C-terminal domain of the latter. This C-terminal domain contains a pair of redox active cysteines and demonstrates thioredoxin-like activity by mediating persulfide bond cleavage of sulfur-loaded NifS (an IscS-type protein), the sulfide donor for [2Fe-2S] cluster assembly on ISU-type scaffold proteins. Herein, the affinity of full-length human NFU and the individual N- and C-terminal domains for sulfide donor and cluster scaffold proteins is assessed. The influence of the N-terminal domain on C-terminal NFU binding to NifS and persulfide reductase activity is also examined. Only the C-terminal domain is required for persulfide reductase activity, while complex formation of NifS with full-length NFU is similar to that of the C-terminal domain alone (K(D) approximately 9.7 +/- 0.7 and 10.1 +/- 0.6 microM, respectively). There is negligible affinity between the isolated C- and N-terminal domains, while the N-terminal domain has negligible affinity for either sulfide donor or cluster scaffold proteins. The temperature dependence of the binding enthalpy for formation of the complex between NifS and the C-terminal domain of NFU yields a change in molar heat capacity (DeltaC(p) approximately 138 cal mol(-1) K(-1)) that suggests bonding at the protein-protein interface is dominated by electrostatic interactions. This is consistent with electrostatic potential maps for bacterial homologues of the N- and C-terminal domains of human NFU, which most likely reflect the structural characteristics expected for full-length human NFU.

  20. Characteristic spectral features of the polarized fluorescence of human breast cancer in the wavelet domain

    CERN Document Server

    Gharekhan, Anita H; Gupta, Sharad; Panigrahi, Prasanta K; Pradhan, Asima

    2012-01-01

    Wavelet transform of polarized fluorescence spectra of human breast tissues is found to localize spectral features that can reliably differentiate normal and malignant tissue types. The intensity differences of parallel and perpendicularly polarized fluorescence spectra are subjected to investigation, since the same is relatively free of the diffusive background. A number of parameters, capturing spectral variations and subtle changes in the diseased tissues in the visible wavelength regime, are clearly identifiable in the wavelet domain. These manifest both in the average low pass and high frequency high pass wavelet coefficients.

  1. Improvements and Limitations of Humanized Mouse Models for HIV Research: NIH/NIAID "Meet the Experts" 2015 Workshop Summary.

    Science.gov (United States)

    Akkina, Ramesh; Allam, Atef; Balazs, Alejandro B; Blankson, Joel N; Burnett, John C; Casares, Sofia; Garcia, J Victor; Hasenkrug, Kim J; Kashanchi, Fatah; Kitchen, Scott G; Klein, Florian; Kumar, Priti; Luster, Andrew D; Poluektova, Larisa Y; Rao, Mangala; Sanders-Beer, Brigitte E; Shultz, Leonard D; Zack, Jerome A

    2016-02-01

    The number of humanized mouse models for the human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) and other infectious diseases has expanded rapidly over the past 8 years. Highly immunodeficient mouse strains, such as NOD/SCID/gamma chain(null) (NSG, NOG), support better human hematopoietic cell engraftment. Another improvement is the derivation of highly immunodeficient mice, transgenic with human leukocyte antigens (HLAs) and cytokines that supported development of HLA-restricted human T cells and heightened human myeloid cell engraftment. Humanized mice are also used to study the HIV reservoir using new imaging techniques. Despite these advances, there are still limitations in HIV immune responses and deficits in lymphoid structures in these models in addition to xenogeneic graft-versus-host responses. To understand and disseminate the improvements and limitations of humanized mouse models to the scientific community, the NIH sponsored and convened a meeting on April 15, 2015 to discuss the state of knowledge concerning these questions and best practices for selecting a humanized mouse model for a particular scientific investigation. This report summarizes the findings of the NIH meeting.

  2. Structure of the RecQ C-terminal domain of human Bloom syndrome protein.

    Science.gov (United States)

    Kim, Sun-Yong; Hakoshima, Toshio; Kitano, Ken

    2013-11-21

    Bloom syndrome is a rare genetic disorder characterized by genomic instability and cancer predisposition. The disease is caused by mutations of the Bloom syndrome protein (BLM). Here we report the crystal structure of a RecQ C-terminal (RQC) domain from human BLM. The structure reveals three novel features of BLM RQC which distinguish it from the previous structures of the Werner syndrome protein (WRN) and RECQ1. First, BLM RQC lacks an aromatic residue at the tip of the β-wing, a key element of the RecQ-family helicases used for DNA-strand separation. Second, a BLM-specific insertion between the N-terminal helices exhibits a looping-out structure that extends at right angles to the β-wing. Deletion mutagenesis of this insertion interfered with binding to Holliday junction. Third, the C-terminal region of BLM RQC adopts an extended structure running along the domain surface, which may facilitate the spatial positioning of an HRDC domain in the full-length protein.

  3. Zn-binding AZUL domain of human ubiquitin protein ligase Ube3A

    Energy Technology Data Exchange (ETDEWEB)

    Lemak, Alexander; Yee, Adelinda [University of Toronto, and Northeast Structural Genomics Consortium, Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics (Canada); Bezsonova, Irina, E-mail: bezsonova@uchc.edu [University of Connecticut Health Center, Department of Molecular Microbial and Structural Biology (United States); Dhe-Paganon, Sirano, E-mail: sirano.dhepaganon@utoronto.ca [University of Toronto, Structural Genomics Consortium (Canada); Arrowsmith, Cheryl H., E-mail: carrow@uhnresearch.ca [University of Toronto, and Northeast Structural Genomics Consortium, Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics (Canada)

    2011-09-15

    Ube3A (also referred to as E6AP for E6 Associated Protein) is a E3 ubiquitin-protein ligase implicated in the development of Angelman syndrome by controlling degradation of synaptic protein Arc and oncogenic papilloma virus infection by controlling degradation of p53. This article describe the solution NMR structure of the conserved N-terminal domain of human Ube3A (residues 24-87) that contains two residues (Cys44 and Arg62) found to be mutated in patients with Angelman syndrome. The structure of this domain adopts a novel Zn-binding fold we called AZUL (Amino-terminal Zn-finger of Ube3a Ligase). The AZUL domain has a helix-loop-helix architecture with a Zn ion coordinated by four Cys residues arranged in Cys-X{sub 4}-Cys-X{sub 4}-Cys-X{sub 28}-Cys motif. Three of the Zn-bound residues are located in a 23-residue long and well structured loop that connects two {alpha}-helicies.

  4. Structural stability of human protein tyrosine phosphatase ρ catalytic domain: effect of point mutations.

    Directory of Open Access Journals (Sweden)

    Alessandra Pasquo

    Full Text Available Protein tyrosine phosphatase ρ (PTPρ belongs to the classical receptor type IIB family of protein tyrosine phosphatase, the most frequently mutated tyrosine phosphatase in human cancer. There are evidences to suggest that PTPρ may act as a tumor suppressor gene and dysregulation of Tyr phosphorylation can be observed in diverse diseases, such as diabetes, immune deficiencies and cancer. PTPρ variants in the catalytic domain have been identified in cancer tissues. These natural variants are nonsynonymous single nucleotide polymorphisms, variations of a single nucleotide occurring in the coding region and leading to amino acid substitutions. In this study we investigated the effect of amino acid substitution on the structural stability and on the activity of the membrane-proximal catalytic domain of PTPρ. We expressed and purified as soluble recombinant proteins some of the mutants of the membrane-proximal catalytic domain of PTPρ identified in colorectal cancer and in the single nucleotide polymorphisms database. The mutants show a decreased thermal and thermodynamic stability and decreased activation energy relative to phosphatase activity, when compared to wild- type. All the variants show three-state equilibrium unfolding transitions similar to that of the wild- type, with the accumulation of a folding intermediate populated at ~4.0 M urea.

  5. Characterization of the regulatory domains of the human skn-1a/Epoc-1/Oct-11 POU transcription factor.

    Science.gov (United States)

    Hildesheim, J; Foster, R A; Chamberlin, M E; Vogel, J C

    1999-09-10

    The Skn-1a POU transcription factor is primarily expressed in keratinocytes of murine embryonic and adult epidermis. Although some POU factors expressed in a tissue-specific manner are important for normal differentiation, the biological function of Skn-1a remains unknown. Previous in vitro studies indicate that Skn-1a has the ability to transactivate markers of keratinocyte differentiation. In this study, we have characterized Skn-1a's transactivation domain(s) and engineered a dominant negative protein that lacked this transactivation domain. Deletional analysis of the human homologue of Skn-1a with three target promoters revealed the presence of two functional domains: a primary C-terminal transactivation domain and a combined N-terminal inhibitory domain and transactivation domain. Skn-1a lacking the C-terminal region completely lost transactivation ability, irrespective of the promoter tested, and was able to block transactivation by normal Skn-1a in competition assays. Compared with full-length, Skn-1a lacking the N-terminal region demonstrated either increased transactivation (bovine cytokeratin 6 promoter), comparable transactivation (human papillomavirus type 1a long control region), or loss of transactivation (human papillomavirus type 18 long control region). The identification of a primary C-terminal transactivation domain enabled us to generate a dominant negative Skn-1a factor, which will be useful in the quest for a better understanding of this keratinocyte-specific gene regulator.

  6. Nucleic acid sequences encoding D1 and D1/D2 domains of human coxsackievirus and adenovirus receptor (CAR)

    Science.gov (United States)

    Freimuth, Paul I.

    2010-04-06

    The invention provides recombinant human CAR (coxsackievirus and adenovirus receptor) polypeptides which bind adenovirus. Specifically, polypeptides corresponding to adenovirus binding domain D1 and the entire extracellular domain of human CAR protein comprising D1 and D2 are provided. In another aspect, the invention provides nucleic acid sequences encoding these domains and expression vectors for producing the domains and bacterial cells containing such vectors. The invention also includes an isolated fusion protein comprised of the D1 polypeptide fused to a polypeptide which facilitates folding of D1 when expressed in bacteria. The functional D1 domain finds application in a therapeutic method for treating a patient infected with a CAR D1-binding virus, and also in a method for identifying an antiviral compound which interferes with viral attachment. The invention also provides a method for specifically targeting a cell for infection by a virus which binds to D1.

  7. Structure of the SH3 domain of human osteoclast-stimulating factor at atomic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Liqing, E-mail: chenlq@uah.edu; Wang, Yujun [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Wells, David; Toh, Diana; Harold, Hunt [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Zhou, Jing [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); DiGiammarino, Enrico [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Meehan, Edward J. [Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States); Graduate Program of Biotechnology, University of Alabama in Huntsville, Huntsville, Alabama 35899 (United States)

    2006-09-01

    The crystal structure of the SH3 domain of human osteoclast-stimulating factor has been determined and refined to the ultrahigh resolution of 1.07 Å. The structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors. Osteoclast-stimulating factor (OSF) is an intracellular signaling protein, produced by osteoclasts themselves, that enhances osteoclast formation and bone resorption. It is thought to act via an Src-related signaling pathway and contains SH3 and ankyrin-repeat domains which are involved in protein–protein interactions. As part of a structure-based anti-bone-loss drug-design program, the atomic resolution X-ray structure of the recombinant human OSF SH3 domain (hOSF-SH3) has been determined. The domain, residues 12–72, yielded crystals that diffracted to the ultrahigh resolution of 1.07 Å. The overall structure shows a characteristic SH3 fold consisting of two perpendicular β-sheets that form a β-barrel. Structure-based sequence alignment reveals that the putative proline-rich peptide-binding site of hOSF-SH3 consists of (i) residues that are highly conserved in the SH3-domain family, including residues Tyr21, Phe23, Trp49, Pro62, Asn64 and Tyr65, and (ii) residues that are less conserved and/or even specific to hOSF, including Thr22, Arg26, Thr27, Glu30, Asp46, Thr47, Asn48 and Leu60, which might be key to designing specific inhibitors for hOSF to fight osteoporosis and related bone-loss diseases. There are a total of 13 well defined water molecules forming hydrogen bonds with the above residues in and around the peptide-binding pocket. Some of those water molecules might be important for drug-design approaches. The hOSF-SH3 structure at atomic resolution provides an accurate framework for structure-based design of its inhibitors.

  8. Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF

    Energy Technology Data Exchange (ETDEWEB)

    Kamada, Katsuhiko; De Angelis, Jacqueline; Roeder, Robert G.; Burley, Stephen K. (Rockefeller)

    2012-12-13

    The x-ray structure of a C-terminal fragment of the RAP74 subunit of human transcription factor (TF) IIF has been determined at 1.02-{angstrom} resolution. The {alpha}/{beta} structure is strikingly similar to the globular domain of linker histone H5 and the DNA-binding domain of hepatocyte nuclear factor 3{gamma} (HNF-3{gamma}), making it a winged-helix protein. The surface electrostatic properties of this compact domain differ significantly from those of bona fide winged-helix transcription factors (HNF-3{gamma} and RFX1) and from the winged-helix domains found within the RAP30 subunit of TFIIF and the {beta} subunit of TFIIE. RAP74 has been shown to interact with the TFIIF-associated C-terminal domain phosphatase FCP1, and a putative phosphatase binding site has been identified within the RAP74 winged-helix domain.

  9. Fluorescence study of domain structure and lipid interaction of human apolipoproteins E3 and E4.

    Science.gov (United States)

    Mizuguchi, Chiharu; Hata, Mami; Dhanasekaran, Padmaja; Nickel, Margaret; Okuhira, Keiichiro; Phillips, Michael C; Lund-Katz, Sissel; Saito, Hiroyuki

    2014-12-01

    Human apolipoprotein E (apoE) isoforms exhibit different conformational stabilities and lipid-binding properties that give rise to altered cholesterol metabolism among the isoforms. Using Trp-substituted mutations and site- directed fluorescence labeling, we made a comprehensive comparison of the conformational organization of the N- and C-terminal domains and lipid interactions between the apoE3 and apoE4 isoforms. Trp fluorescence measurements for selectively Trp-substituted variants of apoE isoforms demonstrated that apoE4 adopts less stable conformations in both the N- and C-terminal domains compared to apoE3. Consistent with this, the conformational reorganization of the N-terminal helix bundle occurs at lower guanidine hydrochloride concentration in apoE4 than in apoE3 as monitored by fluorescence resonance energy transfer (FRET) from Trp residues to acrylodan attached at the N-terminal helix. Upon binding of apoE3 and apoE4 variants to egg phosphatidylcholine small unilamellar vesicles, similar changes in Trp fluorescence or FRET efficiency were observed for the isoforms, indi- cating that the opening of the N-terminal helix bundle occurs similarly in apoE3 and apoE4. Introduction of mutations into the C-terminal domain of the apoE isoforms to prevent self-association and maintain the monomeric state resulted in great increase in the rate of binding of the C-terminal helices to a lipid surface. Overall, our results demonstrate that the different conformational organizations of the N- and C-terminal domains have a minor effect on the steady-state lipid-binding behavior of apoE3 and apoE4: rather, self-association property is a critical determinant in the kinetics of lipid binding through the C-terminal helices of apoE isoforms.

  10. Construction of a Semisynthetic Human VH Single-Domain Antibody Library and Selection of Domain Antibodies against α-Crystalline of Mycobacterium tuberculosis.

    Science.gov (United States)

    Hairul Bahara, Nur Hidayah; Chin, Siang Tean; Choong, Yee Siew; Lim, Theam Soon

    2016-01-01

    The use of human variable heavy (VH) domain antibodies has been on the rise due to their small scaffold size and simple folding mechanism. A highly diverse library is largely dependent on the diversity introduced within the complementarity-determining region (CDR) cassettes. Here we introduced diversity with the use of a single framework diversifying all three CDRs using tailored codons consisting of degenerate trinucleotides (NNK). The length of the degeneracy in the CDRs was also taken into consideration based on the most frequently occurring length of CDRs and the canonical confirmation for each antibody subfamily. The semisynthetic human VH domain genes were assembled in a single pot using a temperature cascading process. The affinity selection process with Mycobacterium tuberculosis (MTb) α-crystalline was done using a semiautomated process. Enrichment of target-specific clones was observed with successful identification of monoclonal VH domain antibodies for MTb α-crystalline. In short, the semisynthetic library generated was able to select monoclonal VH domain antibodies against full MTb α-crystalline protein with complete semisynthetic CDRs displayed on a single scaffold. The library has the potential to be applied for the isolation of antibodies against other pathogenic proteins.

  11. The Cytoplasmic Domain of CD4 Is Sufficient for Its Down-Regulation from the Cell Surface by Human Immunodeficiency Virus Type 1 Nef

    OpenAIRE

    S. J. Anderson; Lenburg, M; Landau, N R; Garcia, J. V.

    1994-01-01

    Human immunodeficiency virus type 1 Nef down-regulates surface expression of murine and human CD4 but not human CD8. We recently reported that the cytoplasmic domain of CD4 is required for its down-regulation by Nef. Using a chimeric molecule composed of the extracellular and transmembrane domains of human CD8 fused to the cytoplasmic domain of human CD4, we show here that the cytoplasmic domain of CD4 is sufficient for down-regulation by Nef. Since the cytoplasmic domain of CD4 is also the s...

  12. Domain of dentine sialoprotein mediates proliferation and differentiation of human periodontal ligament stem cells.

    Directory of Open Access Journals (Sweden)

    Alkan Ozer

    Full Text Available Classic embryological studies have documented the inductive role of root dentin on adjacent periodontal ligament differentiation.  The biochemical composition of root dentin includes collagens and cleavage products of dentin sialophosphoprotein (DSPP, such as dentin sialoprotein (DSP.  The high abundance of DSP in root dentin prompted us to ask the question whether DSP or peptides derived thereof would serve as potent biological matrix components to induce periodontal progenitors to further differentiate into periodontal ligament cells. Here, we test the hypothesis that domain of DSP influences cell fate. In situ hybridization and immunohistochemical analyses showed that the COOH-terminal DSP domain is expressed in mouse periodontium at various stages of root development. The recombinant COOH-terminal DSP fragment (rC-DSP enhanced attachment and migration of human periodontal ligament stem cells (PDLSC, human primary PDL cells without cell toxicity. rC-DSP induced PDLSC cell proliferation as well as differentiation and mineralization of PDLSC and PDL cells by formation of mineralized tissue and ALPase activity. Effect of rC-DSP on cell proliferation and differentiation was to promote gene expression of tooth/bone-relate markers, transcription factors and growth factors. The results for the first time showed that rC-DSP may be one of the components of cell niche for stimulating stem/progenitor cell proliferation and differentiation and a natural scaffold for periodontal regeneration application.

  13. Crystal structure of the extracellular domain of human myelin protein zero

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhigang; Wang, Yong; Yedidi, Ravikiran S.; Brunzelle, Joseph S.; Kovari, Iulia A.; Sohi, Jasloveleen; Kamholz, John; Kovari, Ladislau C. (WSU-MED); (NWU)

    2012-03-27

    Charcot-Marie-Tooth disease (CMT), a hereditary motor and sensory neuropathy, is the most common genetic neuropathy with an incidence of 1 in 2600. Several forms of CMT have been identified arising from different genomic abnormalities such as CMT1 including CMT1A, CMT1B, and CMTX. CMT1 with associated peripheral nervous system (PNS) demyelination, the most frequent diagnosis, demonstrates slowed nerve conduction velocities and segmental demyelination upon nerve biopsy. One of its subtypes, CMT1A, presents a 1.5-Mb duplication in the p11-p12 region of the human chromosome 17 which encodes peripheral myelin protein 22 (PMP22). CMT1B, a less common form, arises from the mutations in the myelin protein zero (MPZ) gene on chromosome 1, region q22-q23, which encodes the major structural component of the peripheral myelin. A rare type of CMT1 has been found recently and is caused by point mutations in early growth response gene 2 (EGR2), encoding a zinc finger transcription factor in Schwann cells. In addition, CMTX, an X-linked form of CMT, arises from a mutation in the connexin-32 gene. Myelin protein zero, associated with CMT1B, is a transmembrane protein of 219 amino acid residues. Human MPZ consists of three domains: 125 residues constitute the glycosylated immunoglobulin-like extracellular domain; 27 residues span the membrane; and 67 residues comprise the highly basic intracellular domain. MPZ makes up approximately 50% of the protein content of myelin, and is expressed predominantly in Schwann cells, the myelinating cell of the PNS. Myelin protein zero, a homophilic adhesion molecule, is a member of the immunoglobulin super-family and is essential for normal myelin structure and function. In addition, MPZ knockout mice displayed abnormal myelin that severely affects the myelination pathway, and overexpression of MPZ causes congenital hypomyelination of peripheral nerves. Myelin protein zero mutations account for {approx}5% of patients with CMT. To date, over 125

  14. Extending NGOMSL Model for Human-Humanoid Robot Interaction in the Soccer Robotics Domain

    Directory of Open Access Journals (Sweden)

    Rajesh Elara Mohan

    2008-01-01

    Full Text Available In the field of human-computer interaction, the Natural Goals, Operators, Methods, and Selection rules Language (NGOMSL model is one of the most popular methods for modelling knowledge and cognitive processes for rapid usability evaluation. The NGOMSL model is a description of the knowledge that a user must possess to operate the system represented as elementary actions for effective usability evaluations. In the last few years, mobile robots have been exhibiting a stronger presence in commercial markets and very little work has been done with NGOMSL modelling for usability evaluations in the human-robot interaction discipline. This paper focuses on extending the NGOMSL model for usability evaluation of human-humanoid robot interaction in the soccer robotics domain. The NGOMSL modelled human-humanoid interaction design of Robo-Erectus Junior was evaluated and the results of the experiments showed that the interaction design was able to find faults in an average time of 23.84 s. Also, the interaction design was able to detect the fault within the 60 s in 100% of the cases. The Evaluated Interaction design was adopted by our Robo-Erectus Junior version of humanoid robots in the RoboCup 2007 humanoid soccer league.

  15. Characterization of Human and Murine T-Cell Immunoglobulin Mucin Domain 4 (TIM-4) IgV Domain Residues Critical for Ebola Virus Entry.

    Science.gov (United States)

    Rhein, Bethany A; Brouillette, Rachel B; Schaack, Grace A; Chiorini, John A; Maury, Wendy

    2016-07-01

    Phosphatidylserine (PtdSer) receptors that are responsible for the clearance of dying cells have recently been found to mediate enveloped virus entry. Ebola virus (EBOV), a member of the Filoviridae family of viruses, utilizes PtdSer receptors for entry into target cells. The PtdSer receptors human and murine T-cell immunoglobulin mucin (TIM) domain proteins TIM-1 and TIM-4 mediate filovirus entry by binding to PtdSer on the virion surface via a conserved PtdSer binding pocket within the amino-terminal IgV domain. While the residues within the TIM-1 IgV domain that are important for EBOV entry are characterized, the molecular details of virion-TIM-4 interactions have yet to be investigated. As sequences and structural alignments of the TIM proteins suggest distinct differences in the TIM-1 and TIM-4 IgV domain structures, we sought to characterize TIM-4 IgV domain residues required for EBOV entry. Using vesicular stomatitis virus pseudovirions bearing EBOV glycoprotein (EBOV GP/VSVΔG), we evaluated virus binding and entry into cells expressing TIM-4 molecules mutated within the IgV domain, allowing us to identify residues important for entry. Similar to TIM-1, residues in the PtdSer binding pocket of murine and human TIM-4 (mTIM-4 and hTIM-4) were found to be important for EBOV entry. However, additional TIM-4-specific residues were also found to impact EBOV entry, with a total of 8 mTIM-4 and 14 hTIM-4 IgV domain residues being critical for virion binding and internalization. Together, these findings provide a greater understanding of the interaction of TIM-4 with EBOV virions. With more than 28,000 cases and over 11,000 deaths during the largest and most recent Ebola virus (EBOV) outbreak, there has been increased emphasis on the development of therapeutics against filoviruses. Many therapies under investigation target EBOV cell entry. T-cell immunoglobulin mucin (TIM) domain proteins are cell surface factors important for the entry of many enveloped viruses

  16. Influence of domain stability on the properties of human apolipoprotein E3 and E4 and mouse apolipoprotein E.

    Science.gov (United States)

    Nguyen, David; Dhanasekaran, Padmaja; Nickel, Margaret; Mizuguchi, Chiharu; Watanabe, Mayu; Saito, Hiroyuki; Phillips, Michael C; Lund-Katz, Sissel

    2014-06-24

    The human apolipoprotein (apo) E4 isoform, which differs from wild-type apoE3 by the single amino acid substitution C112R, is associated with elevated risk of cardiovascular and Alzheimer’s diseases, but the molecular basis for this variation between isoforms is not understood. Human apoE is a two-domain protein comprising an N-terminal helix bundle and a separately folded C-terminal region. Here, we examine the concept that the ability of the protein to bind to lipid surfaces is influenced by the stability (or readiness to unfold) of these domains. The lipid-free structures and abilities to bind to lipid and lipoprotein particles of a series of human and mouse apoE variants with varying domain stabilities and domain–domain interactions are compared. As assessed by urea denaturation, the two domains are more unstable in apoE4 than in apoE3. To distinguish the contributions of the destabilization of each domain to the greater lipid-binding ability of apoE4, the properties of the apoE4 R61T and E255A variants, which have the same helix bundle stabilities but altered C-terminal domain stabilities, are compared. In these cases, the effects on lipid-binding properties are relatively minor, indicating that the destabilization of the helix bundle domain is primarily responsible for the enhanced lipid-binding ability of apoE4. Unlike human apoE, mouse apoE behaves essentially as a single domain, and its lipid-binding characteristics are more similar to those of apoE4. Together, the results show that the overall stability of the entire apoE molecule exerts a major influence on its lipid- and lipoprotein-binding properties.

  17. DUF1220-domain copy number implicated in human brain-size pathology and evolution.

    Science.gov (United States)

    Dumas, Laura J; O'Bleness, Majesta S; Davis, Jonathan M; Dickens, C Michael; Anderson, Nathan; Keeney, J G; Jackson, Jay; Sikela, Megan; Raznahan, Armin; Giedd, Jay; Rapoport, Judith; Nagamani, Sandesh S C; Erez, Ayelet; Brunetti-Pierri, Nicola; Sugalski, Rachel; Lupski, James R; Fingerlin, Tasha; Cheung, Sau Wai; Sikela, James M

    2012-09-07

    DUF1220 domains show the largest human-lineage-specific increase in copy number of any protein-coding region in the human genome and map primarily to 1q21, where deletions and reciprocal duplications have been associated with microcephaly and macrocephaly, respectively. Given these findings and the high correlation between DUF1220 copy number and brain size across primate lineages (R(2) = 0.98; p = 1.8 × 10(-6)), DUF1220 sequences represent plausible candidates for underlying 1q21-associated brain-size pathologies. To investigate this possibility, we used specialized bioinformatics tools developed for scoring highly duplicated DUF1220 sequences to implement targeted 1q21 array comparative genomic hybridization on individuals (n = 42) with 1q21-associated microcephaly and macrocephaly. We show that of all the 1q21 genes examined (n = 53), DUF1220 copy number shows the strongest association with brain size among individuals with 1q21-associated microcephaly, particularly with respect to the three evolutionarily conserved DUF1220 clades CON1(p = 0.0079), CON2 (p = 0.0134), and CON3 (p = 0.0116). Interestingly, all 1q21 DUF1220-encoding genes belonging to the NBPF family show significant correlations with frontal-occipital-circumference Z scores in the deletion group. In a similar survey of a nondisease population, we show that DUF1220 copy number exhibits the strongest correlation with brain gray-matter volume (CON1, p = 0.0246; and CON2, p = 0.0334). Notably, only DUF1220 sequences are consistently significant in both disease and nondisease populations. Taken together, these data strongly implicate the loss of DUF1220 copy number in the etiology of 1q21-associated microcephaly and support the view that DUF1220 domains function as general effectors of evolutionary, pathological, and normal variation in brain size. Copyright © 2012 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  18. Characterization of the transcriptional activation domains of human TEF3-1 (transcription enhancer factor 3 isoform 1).

    Science.gov (United States)

    Qiao, Cheng; Jiang, Yajie; Deng, Cuilan; Huang, Zebo; Teng, Kaixuan; Chen, Lan; Liu, Xin

    2015-03-01

    TEF3-1 (transcription enhancer factor 3 isoform 1) is a human transcriptional factor, which has a N-terminal TEA/ATTS domain supposedly for DNA binding and C-terminal PRD and STY domains for transcriptional activation. Taking advantage of the efficient reporter design of yeast two-hybrid system, we characterized the TEF3-1 domains in activating gene expression. Previously study usually mentioned that the C-terminal domain of TEF3-1 has the transcriptional activity, however, our data shows that the peptides TEF3-11-66 and TEF3-1197-434 functioned as two independent activation domains, suggesting that N-terminal domain of TEF3-1 also has transcriptional activation capacity. Additionally, more deletions of amino acids 197-434 showed that only the peptides TEF3-1197-265 contained the minimum sequences for the C-terminal transcriptional activation domain. The protein structure is predicted to contain a helix-turn-helix structure in TEF3-11-66 and four β sheets in TEF3-1197-265. Finally, after the truncated fragments of TEF3-1 were expressed in HUVEC cells, the whole TEF3-1 and the two activation domains could increase F-actin stress fiber, cell proliferation, migration and targeted gene expression. Further analysis and characterization of the activation domains in TEF3-1 may broaden our understanding of the gene involved in angiogenesis and other pathological processes.

  19. Expert systems for electric power system operation. Denryoku keito un[prime]yo expert system

    Energy Technology Data Exchange (ETDEWEB)

    Kunugi, M.; Shimada, K.; Nagata, J. (Toshiba Corp., Tokyo (Japan))

    1992-07-01

    This review article describes recent noteworthy technological trends in the expert systems for electric power system operation. These technological trends include the development of domain shell for the purpose of facilitating and insuring system development, the integration of expert systems with a conventional energy management system and a SCADA (supervisory control and data acquisition) system, and the integration of an expert system with fuzzy-logic applications and a neural network. This paper also introduces two recent expert systems for electric power system operation. One is the integrated expert system for emergency operations delivered to the Miyagi Load-Dispatching Office of Tohoku Electric Power Company, which consists of the accident reasoning expert system, the inteligent alarm processing, and the accident restoration procedure expert system. Another one is the voltage reactive power control system delivered to Chubu Electric Power Company. 4 refs., 3 figs., 1 tab.

  20. Expert System Techniques and Applications in AEC-Design

    DEFF Research Database (Denmark)

    Andersen, Tom

    This part of a book presents expert system techniques applicable to building design and construction, and it reports and evaluates on systems developed in thar domain.......This part of a book presents expert system techniques applicable to building design and construction, and it reports and evaluates on systems developed in thar domain....

  1. Crystal structures of the coil 2B fragment and the globular tail domain of human lamin B1

    Energy Technology Data Exchange (ETDEWEB)

    Ruan, Jianbin; Xu, Chao; Bian, Chuanbing; Lam, Robert; Wang, Jia-Pey; Kania, Joanna; Min, Jinrong; Zang, Jianye (Toronto); (UST - China)

    2012-07-18

    We present here the crystal structures of human lamin B1 globular tail domain and coiled 2B domain, which adopt similar folds to Ig-like domain and coiled-coil domain of lamin A, respectively. Despite the overall similarity, we found an extra intermolecular disulfide bond in the lamin B1 coil 2B domain, which does not exist in lamin A/C. In addition, the structural analysis indicates that interactions at the lamin B1 homodimer interface are quite different from those of lamin A/C. Thus our research not only reveals the diversely formed homodimers among lamin family members, but also sheds light on understanding the important roles of lamin B1 in forming the nuclear lamina matrix.

  2. Contextual Factors for Finding Similar Experts

    DEFF Research Database (Denmark)

    Hofmann, Katja; Balog, Krisztian; Bogers, Toine;

    2010-01-01

    Expertise-seeking research studies how people search for expertise and choose whom to contact in the context of a specific task. An important outcome are models that identify factors that influence expert finding. Expertise retrieval addresses the same problem, expert finding, but from a system......-seeking models, are rarely taken into account. In this article, we extend content-based expert-finding approaches with contextual factors that have been found to influence human expert finding. We focus on a task of science communicators in a knowledge-intensive environment, the task of finding similar experts......, given an example expert. Our approach combines expertise-seeking and retrieval research. First, we conduct a user study to identify contextual factors that may play a role in the studied task and environment. Then, we design expert retrieval models to capture these factors. We combine these with content...

  3. Novel Mutations in the Transcriptional Activator Domain of the Human TBX20 in Patients with Atrial Septal Defect

    Directory of Open Access Journals (Sweden)

    Irma Eloisa Monroy-Muñoz

    2015-01-01

    Full Text Available Background. The relevance of TBX20 gene in heart development has been demonstrated in many animal models, but there are few works that try to elucidate the effect of TBX20 mutations in human congenital heart diseases. In these studies, all missense mutations associated with atrial septal defect (ASD were found in the DNA-binding T-box domain, none in the transcriptional activator domain. Methods. We search for TBX20 mutations in a group of patients with ASD or ventricular septal defect (VSD using the High Resolution Melting (HRM method and DNA sequencing. Results. We report three missense mutations (Y309D, T370O, and M395R within the transcriptional activator domain of human TBX20 that were associated with ASD. Conclusions. This is the first association of TBX20 transcriptional activator domain missense mutations with ASD. These findings could have implications for diagnosis, genetic screening, and patient follow-up.

  4. Structure of FGFR3 transmembrane domain dimer: implications for signaling and human pathologies.

    Science.gov (United States)

    Bocharov, Eduard V; Lesovoy, Dmitry M; Goncharuk, Sergey A; Goncharuk, Marina V; Hristova, Kalina; Arseniev, Alexander S

    2013-11-05

    Fibroblast growth factor receptor 3 (FGFR3) transduces biochemical signals via lateral dimerization in the plasma membrane, and plays an important role in human development and disease. Eight different pathogenic mutations, implicated in cancers and growth disorders, have been identified in the FGFR3 transmembrane segment. Here, we describe the dimerization of the FGFR3 transmembrane domain in membrane-mimicking DPC/SDS (9/1) micelles. In the solved NMR structure, the two transmembrane helices pack into a symmetric left-handed dimer, with intermolecular stacking interactions occurring in the dimer central region. Some pathogenic mutations fall within the helix-helix interface, whereas others are located within a putative alternative interface. This implies that although the observed dimer structure is important for FGFR3 signaling, the mechanism of FGFR3-mediated transduction across the membrane is complex. We propose an FGFR3 signaling mechanism that is based on the solved structure, available structures of isolated soluble FGFR domains, and published biochemical and biophysical data.

  5. NMR backbone dynamics of VEK-30 bound to the human plasminogen kringle 2 domain.

    Science.gov (United States)

    Wang, Min; Prorok, Mary; Castellino, Francis J

    2010-07-07

    To gain insights into the mechanisms for the tight and highly specific interaction of the kringle 2 domain of human plasminogen (K2(Pg)) with a 30-residue internal peptide (VEK-30) from a group A streptococcal M-like protein, the dynamic properties of free and bound K2(Pg) and VEK-30 were investigated using backbone amide (15)N-NMR relaxation measurements. Dynamic parameters, namely the generalized order parameter, S(2), the local correlation time, tau(e), and the conformational exchange contribution, R(ex), were obtained for this complex by Lipari-Szabo model-free analysis. The results show that VEK-30 displays distinctly different dynamic behavior as a consequence of binding to K2(Pg), manifest by decreased backbone flexibility, particularly at the binding region of the peptide. In contrast, the backbone dynamics parameters of K2(Pg) displayed similar patterns in the free and bound forms, but, nonetheless, showed interesting differences. Based on our previous structure-function studies of this interaction, we also made comparisons of the VEK-30/K2(Pg) dynamics results from different kringle modules complexed with small lysine analogs. The differences in dynamics observed for kringles with different ligands provide what we believe to be new insights into the interactions responsible for protein-ligand recognition and a better understanding of the differences in binding affinity and binding specificity of kringle domains with various ligands.

  6. Construction of human Fab library and screening of a single-domain antibody of amyloid-beta 42 oligomers

    Institute of Scientific and Technical Information of China (English)

    Zuanning Yuan; Minge Du; Yiwen Chen; Fei Dou

    2013-01-01

    Screening humanized antibodies from a human Fab phage display library is an effective and quick method to obtain beta-amyloid oligomers. Thus, the present study prepared amyloid-beta 42 oli-gomers and constructed a naïve human Fab phage display library based on blood samples from six healthy people. After three rounds of biopanning in vitro, a human single-domain antibody that spe-cifical y recognized amyloid-beta 42 oligomers was identified. Western blot and enzyme-linked immunosorbent assay demonstrated this antibody bound specifical y to human amyloid-beta 42 te-tramer and nonamer, but not the monomer or high molecular weight oligomers. This study suc-cessful y constructed a human phage display library and screened a single-domain antibody that specifical y recognized amyloid-beta 42 oligomers.

  7. Discoidin domain receptor 1: isoform expression and potential functions in cirrhotic human liver.

    Science.gov (United States)

    Song, Sunmi; Shackel, Nicholas A; Wang, Xin M; Ajami, Katerina; McCaughan, Geoffrey W; Gorrell, Mark D

    2011-03-01

    Discoidin domain receptor 1 (DDR1) is a receptor tyrosine kinase that binds and is activated by collagens. Transcriptional profiling of cirrhosis in human liver using a DNA array and quantitative PCR detected elevated mRNA expression of DDR1 compared with that in nondiseased liver. The present study characterized DDR1 expression in cirrhotic and nondiseased human liver and examined the cellular effects of DDR1 expression. mRNA expression of all five isoforms of DDR1 was detected in human liver, whereas DDR1a demonstrated differential expression in liver with hepatitis C virus and primary biliary cirrhosis compared with nondiseased liver. In addition, immunoblot analysis detected shed fragments of DDR1 more readily in cirrhotic liver than in nondiseased liver. Inasmuch as DDR1 is subject to protease-mediated cleavage after prolonged interaction with collagen, this differential expression may indicate more intense activation of DDR1 protein in cirrhotic compared with nondiseased liver. In situ hybridization and immunofluorescence localized intense DDR1 mRNA and protein expression to epithelial cells including hepatocytes at the portal-parenchymal interface and the luminal aspect of the biliary epithelium. Overexpression of DDR1a altered hepatocyte behavior including increased adhesion and less migration on extracelular matrix substrates. DDR1a regulated extracellular expression of matrix metalloproteinases 1 and 2. These data elucidate DDR1 function pertinent to cirrhosis and indicate the importance of epithelial cell-collagen interactions in chronic liver injury.

  8. Prediction on the binding domain between human interleukin-6 and its receptor

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Based on the spatial conformations of human interleukin-6 (hIL-6) derived from nuclear magnetic resonance analysis and human interleukin-6 receptor (hIL-6R) modeled with homology modeling method using human growth hormone receptor as template, the interaction between hIL-6 and its receptor (hIL-6R) is studied with docking program according to the surface electrostatic potential analysis and spatial conformation complement. The stable region structure composed of hIL-6 and hIL-6R is obtained on the basis of molecular mechanism optimization and molecular dynamics simulation. The binding domain between hIL-6 and hIL-6R is predicted theoretically. Furthermore, the especial binding sites that influence the interaction between hIL-6 and hIL-6R are confirmed. The results lay a theoretical foundation for confirming the active regions of hIL-6 and designing novel antagonist with computer-guided techniques.

  9. Prediction on the binding domain between human interleukin-6 and its receptor

    Institute of Scientific and Technical Information of China (English)

    冯健男; 任蕴芳; 沈倍奋

    2000-01-01

    Based on the spatial conformations of human interleukin-6 (hlL-6) derived from nuclear magnetic resonance analysis and human interleukin-6 receptor (hlL-6R) modeled with homology modeling method using human growth hormone receptor as template, the interaction between hlL-6 and its receptor (hIL-6R) is studied with docking program according to the surface electrostatic potential analysis and spatial conformation complement. The stable region structure composed of hlL-6 and hlL-6R is obtained on the basis of molecular mechanism optimization and molecular dynamics simulation. The binding domain between hIL-6 and hIL-6R is predicted theoretically. Furthermore, the especial binding sites that influence the interaction between hlL-6 and hlL-6R are confirmed. The results lay a theoretical foundation for confirming the active regions of hlL-6 and designing novel antagonist with computer-guided techniques.

  10. Similarity of recombinant human perlecan domain 1 by alternative expression systems bioactive heterogenous recombinant human perlecan D1

    DEFF Research Database (Denmark)

    Ellis, April L; Pan, Wensheng; Yang, Guang

    2010-01-01

    BACKGROUND: Heparan sulfate glycosaminoglycans are diverse components of certain proteoglycans and are known to interact with growth factors as a co-receptor necessary to induce signalling and growth factor activity. In this report we characterize heterogeneously glycosylated recombinant human...... perlecan domain 1 (HSPG2 abbreviated as rhPln.D1) synthesized in either HEK 293 cells or HUVECs by transient gene delivery using either adenoviral or expression plasmid technology. RESULTS: By SDS-PAGE analysis following anion exchange chromatography, the recombinant proteoglycans appeared to possess...... glycosaminoglycan chains ranging, in total, from 6 kDa to >90 kDa per recombinant. Immunoblot analysis of enzyme-digested high Mr rhPln.D1 demonstrated that the rhPln.D1 was synthesized as either a chondroitin sulfate or heparan sulfate proteoglycan, in an approximately 2:1 ratio, with negligible hybrids. Secondary...

  11. A novel role for fibronectin type I domain in the regulation of human hematopoietic cell adhesiveness through binding to follistatin domains of FLRG and follistatin.

    Science.gov (United States)

    Maguer-Satta, Véronique; Forissier, Stéphanie; Bartholin, Laurent; Martel, Sylvie; Jeanpierre, Sandrine; Bachelard, Elodie; Rimokh, Ruth

    2006-02-15

    FLRG and follistatin belong to the family of follistatin proteins involved in the regulation of various biological effects, such as hematopoiesis, mediated by their binding to activin and BMP, both members of the TGFbeta family. To further characterize the function of FLRG, we searched for other possible functional partners using a yeast two-hybrid screen. We identified human fibronectin as a new partner for both FLRG and follistatin. We also demonstrated that their physical interaction is mediated by type I motifs of fibronectin and follistatin domains. We then analyzed the biological consequences of these protein interactions on the regulation of hematopoiesis. For the first time, we associated a biological effect with the regulation of human hematopoietic cell adhesiveness of both the type I motifs of fibronectin and the follistatin domains of FLRG and follistatin. Indeed, we observed a significant and specific dose-dependent increase of cell adhesion to fibronectin in the presence of FLRG or follistatin, using either a human hematopoietic cell line or primary cells. In particular, we observed a significantly increased adhesion of immature hematopoietic precursors (CFC, LTC-IC). Altogether these results highlight a new mechanism by which FLRG and follistatin regulate human hematopoiesis.

  12. Extensive inter-domain lateral gene transfer in the evolution of the human commensal Methanosphaera stadtmanae

    Directory of Open Access Journals (Sweden)

    Mor Nadia Lurie-Weinberger

    2012-09-01

    Full Text Available Methanosphaera stadtmanae is a commensal methanogenic archaeon found in the human gut. As most of its niche-neighbors are bacteria, it is expected that lateral gene transfer (LGT from bacteria might have contributed to the evolutionary history of this organism. We performed a phylogenomic survey of putative lateral gene transfer events in M. stadtmanae, using a phylogenetic pipeline. Our analysis indicates that a substantial fraction of the proteins of M. stadtmanae are inferred to have been involved in inter-domain LGT. Laterally acquired genes have had a large contribution to surface functions, by providing novel glycosyltransferase functions. In addition, several ABC transporters seem to be of bacterial origin, including the molybdate transporter. Thus, bacterial genes contributed to the adaptation of M. stadtmanae to a host dependent lifestyle by allowing a larger variation in surface structures and increasing transport efficiency in the gut niche which is diverse and competitive

  13. Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter.

    Science.gov (United States)

    Kim, Dong-Sik; Song, Hyung-Nam; Nam, Hyo Jung; Kim, Sung-Geun; Park, Young-Seoub; Park, Jae-Chan; Woo, Eui-Jeon; Lim, Hyung-Kwon

    2014-01-01

    Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.

  14. Systematic analysis of FKBP inducible degradation domain tagging strategies for the human malaria parasite Plasmodium falciparum.

    Directory of Open Access Journals (Sweden)

    Mauro Ferreira de Azevedo

    Full Text Available Targeted regulation of protein levels is an important tool to gain insights into the role of proteins essential to cell function and development. In recent years, a method based on mutated forms of the human FKBP12 has been established and used to great effect in various cell types to explore protein function. The mutated FKBP protein, referred to as destabilization domain (DD tag when fused with a native protein at the N- or C-terminus targets the protein for proteosomal degradation. Regulated expression is achieved via addition of a compound, Shld-1, that stabilizes the protein and prevents degradation. A limited number of studies have used this system to provide powerful insight into protein function in the human malaria parasite Plasmodium falciparum. In order to better understand the DD inducible system in P. falciparum, we studied the effect of Shld-1 on parasite growth, demonstrating that although development is not impaired, it is delayed, requiring the appropriate controls for phenotype interpretation. We explored the quantified regulation of reporter Green Fluorescent Protein (GFP and luciferase constructs fused to three DD variants in parasite cells either via transient or stable transfection. The regulation obtained with the original FKBP derived DD domain was compared to two triple mutants DD24 and DD29, which had been described to provide better regulation for C-terminal tagging in other cell types. When cloned to the C-terminal of reporter proteins, DD24 provided the strongest regulation allowing reporter activity to be reduced to lower levels than DD and to restore the activity of stabilised proteins to higher levels than DD29. Importantly, DD24 has not previously been applied to regulate proteins in P. falciparum. The possibility of regulating an exported protein was addressed by targeting the Ring-Infected Erythrocyte Surface Antigen (RESA at its C-terminus. The tagged protein demonstrated an important modulation of its

  15. Identification of a novel human islet amyloid polypeptide beta-sheet domain and factors influencing fibrillogenesis.

    Science.gov (United States)

    Jaikaran, E T; Higham, C E; Serpell, L C; Zurdo, J; Gross, M; Clark, A; Fraser, P E

    2001-05-04

    Human islet amyloid polypeptide (hIAPP) accumulates as pancreatic amyloid in type 2 diabetes and readily forms fibrils in vitro. Investigations into the mechanism of hIAPP fibril formation have focused largely on residues 20 to 29, which are considered to comprise a primary amyloidogenic domain. In rodents, proline substitutions within this region and the subsequent beta-sheet disruption, prevents fibril formation. An additional amyloidogenic fragment within the C-terminal sequence, residues 30 to 37, has been identified recently. We have extended these observations by examining a series of overlapping peptide fragments from the human and rodent sequences. Using protein spectroscopy (CD/FTIR), electron microscopy and X-ray diffraction, a previously unrecognised amyloidogenic domain was localised within residues 8 to 20. Synthetic peptides corresponding to this region exhibited a transition from random coil to beta-sheet conformation and assembled into fibrils having a typical amyloid-like morphology. The comparable rat 8-20 sequence, which contains a single His18Arg substitution, was also capable of assembling into amyloid-like fibrils. Examination of peptide fragments corresponding to residues 1 to 13 revealed that the immediate N-terminal region is likely to have only a modulating influence on fibril formation or conformational conversion. The contributions of charged residues as they relate to the amyloid-forming 8-20 sequence were also investigated using IAPP fragments and by assessing the effects of pH and counterions. The identification of these principal amyloidogenic sequences and the effects of associated factors provide details on the IAPP aggregation pathway and structure of the peptide in its fibrillar state. Copyright 2001 Academic Press.

  16. Expert System for Data Security Risk Management for SMEs

    Directory of Open Access Journals (Sweden)

    Justinas Janulevičius

    2013-05-01

    Full Text Available Accessibility of expertise and expert inferences is one of the key factors for appropriate expert evaluation. Appropriate and timely expert information allows a smooth process of expertise. Small and medium enterprises (SMEs have limited possibilities to acquire professional expertise for data security risk analysis due to limited finances. A risk management expert system is developed for SMEs with the ability to adapt to various subject domains using ontologies of the field.Article in Lithuanian

  17. Impact of the [delta]F508 Mutation in First Nucleotide-binding Domain of Human Cystic Fibrosis Transmembrane Conductance Regulator on Domain Folding and Structure

    Energy Technology Data Exchange (ETDEWEB)

    Lewis, Hal A.; Zhao, Xun; Wang, Chi; Sauder, J. Michael; Rooney, Isabelle; Noland, Brian W.; Lorimer, Don; Kearins, Margaret C.; Conners, Kris; Condon, Brad; Maloney, Peter C.; Guggino, William B.; Hunt, John F.; Emtage, Spencer (SG); (Columbia); (JHU)

    2010-07-19

    Cystic fibrosis is caused by defects in the cystic fibrosis transmembrane conductance regulator (CFTR), commonly the deletion of residue Phe-508 (DeltaF508) in the first nucleotide-binding domain (NBD1), which results in a severe reduction in the population of functional channels at the epithelial cell surface. Previous studies employing incomplete NBD1 domains have attributed this to aberrant folding of DeltaF508 NBD1. We report structural and biophysical studies on complete human NBD1 domains, which fail to demonstrate significant changes of in vitro stability or folding kinetics in the presence or absence of the DeltaF508 mutation. Crystal structures show minimal changes in protein conformation but substantial changes in local surface topography at the site of the mutation, which is located in the region of NBD1 believed to interact with the first membrane spanning domain of CFTR. These results raise the possibility that the primary effect of DeltaF508 is a disruption of proper interdomain interactions at this site in CFTR rather than interference with the folding of NBD1. Interestingly, increases in the stability of NBD1 constructs are observed upon introduction of second-site mutations that suppress the trafficking defect caused by the DeltaF508 mutation, suggesting that these suppressors might function indirectly by improving the folding efficiency of NBD1 in the context of the full-length protein. The human NBD1 structures also solidify the understanding of CFTR regulation by showing that its two protein segments that can be phosphorylated both adopt multiple conformations that modulate access to the ATPase active site and functional interdomain interfaces.

  18. EXPERT SYSTEMS - DEVELOPMENT OF AGRICULTURAL INSURANCE TOOL

    OpenAIRE

    2013-01-01

    Because of the fact that specialty agricultural assistance is not always available when the farmers need it, we identified expert systems as a strong instrument with an extended potential in agriculture. This started to grow in scale recently, including all socially-economic activity fields, having the role of collecting data regarding different aspects from human experts with the purpose of assisting the user in the necessary steps for solving problems, at the performance level of the expert...

  19. Expert systems in treating substance abuse.

    OpenAIRE

    Wesson, D R; Hink, R H

    1990-01-01

    Computer programs can assist humans in solving complex problems that cannot be solved by traditional computational techniques using mathematic formulas. These programs, or "expert systems," are commonly used in finance, engineering, and computer design. Although not routinely used in medicine at present, medical expert systems have been developed to assist physicians in solving many kinds of medical problems that traditionally require consultation from a physician specialist. No expert system...

  20. What Are Expert Systems?

    Science.gov (United States)

    d'Agapeyeff, A.

    1986-01-01

    Intended for potential business users, this paper describes the main characteristics of expert systems; discusses practical use considerations; presents a taxonomy of the systems; and reviews several expert system development projects in business and industry. (MBR)

  1. Robot learning from human teachers

    CERN Document Server

    Chernova, Sonia

    2014-01-01

    Learning from Demonstration (LfD) explores techniques for learning a task policy from examples provided by a human teacher. The field of LfD has grown into an extensive body of literature over the past 30 years, with a wide variety of approaches for encoding human demonstrations and modeling skills and tasks. Additionally, we have recently seen a focus on gathering data from non-expert human teachers (i.e., domain experts but not robotics experts). In this book, we provide an introduction to the field with a focus on the unique technical challenges associated with designing robots that learn f

  2. Expert auditors’ services classification

    OpenAIRE

    Jolanta Wisniewska

    2013-01-01

    The profession of an expert auditor is a public trust occupation with a distinctive feature of taking responsibility for actions in the public interest. The main responsibility of expert auditors is performing financial auditing; however, expert auditors are prepared to carry out different tasks which encompass a wide plethora of financial and auditing services for different kinds of institutions and companies. The aim of the article is first of all the description of expert auditors’ service...

  3. Tactical Weather Expert System.

    Science.gov (United States)

    The objective of this project was to assess the feasibility of developing an expert system for tactical weather prediction. Using WILLARD, an expert ...indicate that intelligent interpretations of cloud formations can be made. These inferences can then be automatically passed to the expert system for...processing as another piece of information. It is anticipated that this technology will significantly reduce the dependence of the expert system on a

  4. i-bodies, Human Single Domain Antibodies That Antagonize Chemokine Receptor CXCR4.

    Science.gov (United States)

    Griffiths, Katherine; Dolezal, Olan; Cao, Benjamin; Nilsson, Susan K; See, Heng B; Pfleger, Kevin D G; Roche, Michael; Gorry, Paul R; Pow, Andrew; Viduka, Katerina; Lim, Kevin; Lu, Bernadine G C; Chang, Denison H C; Murray-Rust, Thomas; Kvansakul, Marc; Perugini, Matthew A; Dogovski, Con; Doerflinger, Marcel; Zhang, Yuan; Parisi, Kathy; Casey, Joanne L; Nuttall, Stewart D; Foley, Michael

    2016-06-10

    CXCR4 is a G protein-coupled receptor with excellent potential as a therapeutic target for a range of clinical conditions, including stem cell mobilization, cancer prognosis and treatment, fibrosis therapy, and HIV infection. We report here the development of a fully human single-domain antibody-like scaffold termed an "i-body," the engineering of which produces an i-body library possessing a long complementarity determining region binding loop, and the isolation and characterization of a panel of i-bodies with activity against human CXCR4. The CXCR4-specific i-bodies show antagonistic activity in a range of in vitro and in vivo assays, including inhibition of HIV infection, cell migration, and leukocyte recruitment but, importantly, not the mobilization of hematopoietic stem cells. Epitope mapping of the three CXCR4 i-bodies AM3-114, AM4-272, and AM3-523 revealed binding deep in the binding pocket of the receptor.

  5. Application of Fourier Domain OCT Imaging Technology to the Anterior Segment of the Human Eye

    Science.gov (United States)

    Wojtkowski, Maciej; Marcos, Susana; Ortiz, Sergio; Grulkowski, Ireneusz

    The anterior segment is the front part of the human eye, which forms the optical system and hence directly impacts vision. Traumatic or pathological changes in the anterior segment may lead to vision loss and, in some cases, even blindness. Since the eighteenth century, optical instrumentation for measuring and imaging the anterior segment of the human eye has been developing along with modern ophthalmology. The application of OCT to the anterior segment imaging is particularly of interest, since this could potentially provide substantial complementary information regarding the large-scale architecture of the cornea and the crystalline lens, or on small portions of tissue imaged with high spatial resolutions comparable to regular microscopy. Especially an introduction of Fourier domain detection in OCT has opened new frontiers in OCT ophthalmic applications. The resultant substantial speed improvement enables rapid image acquisition, helping to reduce artifacts due to patient motion. Thus, it is currently possible to perform high-speed, in vivo, three-dimensional volumetric imaging over large scales within a reasonable time limit and without reducing system sensitivity. This chapter describes the state-of the art OCT technology dedicated to anterior segment imaging and indicates all important parameters which are required for optimization of the performance of OCT instrument.

  6. Direct injection of functional single-domain antibodies from E. coli into human cells.

    Directory of Open Access Journals (Sweden)

    Ana Blanco-Toribio

    Full Text Available Intracellular proteins have a great potential as targets for therapeutic antibodies (Abs but the plasma membrane prevents access to these antigens. Ab fragments and IgGs are selected and engineered in E. coli and this microorganism may be also an ideal vector for their intracellular delivery. In this work we demonstrate that single-domain Ab (sdAbs can be engineered to be injected into human cells by E. coli bacteria carrying molecular syringes assembled by a type III protein secretion system (T3SS. The injected sdAbs accumulate in the cytoplasm of HeLa cells at levels ca. 10⁵-10⁶ molecules per cell and their functionality is shown by the isolation of sdAb-antigen complexes. Injection of sdAbs does not require bacterial invasion or the transfer of genetic material. These results are proof-of-principle for the capacity of E. coli bacteria to directly deliver intracellular sdAbs (intrabodies into human cells for analytical and therapeutic purposes.

  7. Persuasiveness of expert systems

    NARCIS (Netherlands)

    Dijkstra, JJ; Liebrand, WBG; Timminga, E; Liebrand, Wim B.G.

    1998-01-01

    Expert system advice is not always evaluated by examining its contents. Users can be persuaded by expert system advice because they have certain beliefs about advice given by a computer. The experiment in this paper shows that subjects (n = 84) thought that, given the same argumentation, expert syst

  8. Development Expert System

    Institute of Scientific and Technical Information of China (English)

    CAI Heng

    2010-01-01

    The expert system is a high-level technology.It is a sub-field of artificial intelligence.We demonstrated the character and software evaluation,carrying out an initial study of expert system.A good development expert system was developed.

  9. Structural and functional analysis of the YAP-binding domain of human TEAD2

    OpenAIRE

    Tian, Wei; Yu,Jianzhong; Tomchick, Diana R.; Pan, Duojia; Luo, Xuelian

    2010-01-01

    The Hippo pathway controls organ size and suppresses tumorigenesis in metazoans by blocking cell proliferation and promoting apoptosis. The TEAD1-4 proteins (which contain a DNA-binding domain but lack an activation domain) interact with YAP (which lacks a DNA-binding domain but contains an activation domain) to form functional heterodimeric transcription factors that activate proliferative and prosurvival gene expression programs. The Hippo pathway inhibits the YAP-TEAD hybrid transcription ...

  10. From the chromatin interaction network to the organization of the human genome into replication N/U-domains

    Science.gov (United States)

    Boulos, Rasha E.; Julienne, Hanna; Baker, Antoine; Chen, Chun-Long; Petryk, Nataliya; Kahli, Malik; dʼAubenton-Carafa, Yves; Goldar, Arach; Jensen, Pablo; Hyrien, Olivier; Thermes, Claude; Arneodo, Alain; Audit, Benjamin

    2014-11-01

    The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to the recent development of chromatin conformation capture (3C) technologies. Here we report the results of a combined multiscale analysis of genome-wide mean replication timing and chromatin conformation data that reveal some intimate relationships between chromatin folding and human DNA replication. We previously described megabase replication N/U-domains as mammalian multiorigin replication units, and showed that their borders are ‘master’ replication initiation zones that likely initiate cascades of origin firing responsible for the stereotypic replication of these domains. Here, we demonstrate that replication N/U-domains correspond to the structural domains of self-interacting chromatin, and that their borders act as insulating regions both in high-throughput 3C (Hi-C) data and high-resolution 3C (4C) experiments. Further analyses of Hi-C data using a graph-theoretical approach reveal that N/U-domain borders are long-distance, interconnected hubs of the chromatin interaction network. Overall, these results and the observation that a well-defined ordering of chromatin states exists from N/U-domain borders to centers suggest that ‘master’ replication initiation zones are at the heart of a high-order, epigenetically controlled 3D organization of the human genome.

  11. Evidence for a lectin activity for human interleukin 3 and modeling of its carbohydrate recognition domain.

    Science.gov (United States)

    Zanetta, Jean-Pierre; Bindeus, Roland; Normand, Guy; Durier, Viviane; Lagant, Philippe; Maes, Emmanuel; Vergoten, Gérard

    2002-10-11

    We demonstrate that human interleukin 3 (IL-3) is a lectin recognizing specifically the glycosaminoglycan part of a chondroitin sulfate proteoglycan (PGS3; Normand, G., Kuchler, S., Meyer, A., Vincendon, G., and Zanetta, J. P. (1988) J. Neurochem. 51, 665-676) isolated from the adult rat brain. The specificity of the interaction of this particular proteoglycan with IL-3 is due to the abundance of GlcA(2S)beta 1,3GalNAc(4S)beta 1 disaccharide units as suggested by (1)H NMR. Computational docking experiments of the lower energy conformers of the different disaccharides from chondroitin sulfates reveal a privileged binding site for GlcA(2S)beta 1,3GalNAc(4S)beta 1 (involving His-26, Arg-29, Asn-70, and Trp-104) localized in an area of IL-3 different from the receptor-binding domain previously identified by others (Bagley, C. J., Phillips, J., Cambareri, B., Vadas, M. A., and Lopez, A. F. (1996) J. Biol. Chem. 271, 31922-31928). Molecular modeling of the mutation P33G, described as increasing the biological activity of IL-3 without affecting its receptor binding (Lokker, N. A., Movva, N. R., Strittmatter, U., Fagg, B., and Zenke, G. (1991) J. Biol. Chem. 266, 10624-10631) provokes a change of the three-dimensional structure of IL-3, especially in the area of the putative carbohydrate recognition domain defined above. Computational docking experiments of the different disaccharides of chondroitin sulfates indicate a loss of affinity for the previous ligand but a higher affinity for the classic disaccharide of chondroitin-4-sulfate. This change from a rare and specific ligand to a more abundant constituent of proteoglycans could induce an increased quantitative association between the IL-3 receptors and its ligands and, consequently, an increased signaling.

  12. X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1 Reveals Features of Its Chitin Binding Domain.

    Directory of Open Access Journals (Sweden)

    Firas Fadel

    Full Text Available Chitinases are enzymes that catalyze the hydrolysis of chitin. Human chitotriosidase (CHIT1 is one of the two active human chitinases, involved in the innate immune response and highly expressed in a variety of diseases. CHIT1 is composed of a catalytic domain linked by a hinge to its chitin binding domain (ChBD. This latter domain belongs to the carbohydrate-binding module family 14 (CBM14 family and facilitates binding to chitin. So far, the available crystal structures of the human chitinase CHIT1 and the Acidic Mammalian Chitinase (AMCase comprise only their catalytic domain. Here, we report a crystallization strategy combining cross-seeding and micro-seeding cycles which allowed us to obtain the first crystal structure of the full length CHIT1 (CHIT1-FL at 1.95 Å resolution. The CHIT1 chitin binding domain (ChBDCHIT1 structure shows a distorted β-sandwich 3D fold, typical of CBM14 family members. Accordingly, ChBDCHIT1 presents six conserved cysteine residues forming three disulfide bridges and several exposed aromatic residues that probably are involved in chitin binding, including the highly conserved Trp465 in a surface- exposed conformation. Furthermore, ChBDCHIT1 presents a positively charged surface which may be involved in electrostatic interactions. Our data highlight the strong structural conservation of CBM14 family members and uncover the structural similarity between the human ChBDCHIT1, tachycitin and house mite dust allergens. Overall, our new CHIT1-FL structure, determined with an adapted crystallization approach, is one of the few complete bi-modular chitinase structures available and reveals the structural features of a human CBM14 domain.

  13. X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain

    Science.gov (United States)

    Fadel, Firas; Zhao, Yuguang; Cousido-Siah, Alexandra; Ruiz, Francesc X.; Mitschler, André; Podjarny, Alberto

    2016-01-01

    Chitinases are enzymes that catalyze the hydrolysis of chitin. Human chitotriosidase (CHIT1) is one of the two active human chitinases, involved in the innate immune response and highly expressed in a variety of diseases. CHIT1 is composed of a catalytic domain linked by a hinge to its chitin binding domain (ChBD). This latter domain belongs to the carbohydrate-binding module family 14 (CBM14 family) and facilitates binding to chitin. So far, the available crystal structures of the human chitinase CHIT1 and the Acidic Mammalian Chitinase (AMCase) comprise only their catalytic domain. Here, we report a crystallization strategy combining cross-seeding and micro-seeding cycles which allowed us to obtain the first crystal structure of the full length CHIT1 (CHIT1-FL) at 1.95 Å resolution. The CHIT1 chitin binding domain (ChBDCHIT1) structure shows a distorted β-sandwich 3D fold, typical of CBM14 family members. Accordingly, ChBDCHIT1 presents six conserved cysteine residues forming three disulfide bridges and several exposed aromatic residues that probably are involved in chitin binding, including the highly conserved Trp465 in a surface- exposed conformation. Furthermore, ChBDCHIT1 presents a positively charged surface which may be involved in electrostatic interactions. Our data highlight the strong structural conservation of CBM14 family members and uncover the structural similarity between the human ChBDCHIT1, tachycitin and house mite dust allergens. Overall, our new CHIT1-FL structure, determined with an adapted crystallization approach, is one of the few complete bi-modular chitinase structures available and reveals the structural features of a human CBM14 domain. PMID:27111557

  14. Expert system for traffic signal setting assistance

    Energy Technology Data Exchange (ETDEWEB)

    Zozaya-Gorostiza, C.; Hendrickson, C.

    1987-03-01

    An experimental knowledge-based expert system to assist in traffic signal setting for isolated intersections is presented. In contrast to existing computer aids, the system can be applied to intersections of highly irregular geometries. Algorithmic processes to evaluate signal settings and decision tables to identify traffic flow conflicts are invoked by the expert system; phase distribution of flows is performed by applying heuristic rules. The system was written in the OPS5 export system environment. Advantages and disadvantages of the expert system programming approach relative to conventional algorithmic processes in the traffic engineering domain are described.

  15. Kinase domain insert containing receptor promotor controlled suicide gene system kills human umbilical vein endothelial cells

    Institute of Scientific and Technical Information of China (English)

    Zong-Hai Huang; Wen-Yu Yang; Qi Cheng; Jing-Long Yu; Zhou Li; Zong-Yan Tong; Hui-Juan Song; Xiao-Yan Che

    2005-01-01

    AIM: To evaluate the killing effect of double suicide gene mediated by adenovirus and regulated under kinase domain insert containing receptor (KDR) promoter on human umbilical vein endothelial cells. METHODS: By PCR technology, human KDR promoter gene, Escherichia coli(E. coli) cytosine deaminase (CD) gene and the herpes simple virus-thymidine kinase (TK) gene were cloned. Plasmid pKDR-CDglyTK was constructed with them. Then, a recombinant adenoviral plasmid pAdKDRCDglyTK was constructed in a "two-step transformation protocol". The newly constructed plasmids were transfected to 293 packaging cells to grow adenoviruses, which were further propagated and purified. Human umbilical vein endothelial cells (HUVEC) were infected with a different multiplicity of infection (MOI) of resultant recombinant adenovirus, the infection rate was measured with the aid of (GFP) expression. Infected cells were cultured in culture media containing different concentrations of (GCV) and/or 5-(FC), and the killing effects were measured.RESULTS: Recombinant adenoviruses AdKDR-CDglyTK were successfully constructed, and they infected HUVEC cells efficiently. Our data indicated that the infection rate was relevant to MOI of recombinant adenoviruses. HUVEC cells infected with AdKDR-CDglyTK were highly sensitive to the prodrugs, their survival rate correlated to both the concentration of the prodrugs and the MOI of recombinant adenoviruses. Our data also indicated that the two prodrugs used in combination were much more effective on killing transgeneic cells than GCV or 5-FC used alone. CONCLUSION: Prodrug/KDR-CDglyTK system is effective on killing HUVEC cells, its killing effect correlates to the concentration of prodrugs and recombinant adenovirus' MOI. Combined use of the two prodrugs confers better killing effects on transgeneic cells.

  16. Popeye domain-containing 1 is down-regulated in failing human hearts.

    Science.gov (United States)

    Gingold-Belfer, Rachel; Bergman, Michael; Alcalay, Yifat; Schlesinger, Hadassa; Aravot, Dan; Berman, Marius; Salman, Hertzel; Brand, Thomas; Kessler-Icekson, Gania

    2011-01-01

    Congestive heart failure, a complex disease of heterogeneous etiology, involves alterations in the expression of multiple genes. The Popeye domain-containing (POPDC) family of three novel muscle-restricted genes (POPDC1-3) is evolutionarily conserved and developmentally regulated. In mice, POPDC1 has been shown to play an important role in skeletal and cardiac muscles subjected to injury or stress. However, it has never been explored in human hearts. In biopsies from non-failing and failing human hearts, we examined the cellular distribution of POPDC1 as well as the expression patterns of POPDC1-3 mRNAs. POPDC1 was visualized by immunohistochemistry and estimated by Western immunoblotting. The mRNA levels of POPDC1-3 and ß myosin heavy chain (MYHC7) were assessed using reverse transcription/quantitative polymerase chain reaction. POPDC1 was predominantly localized in the sarcolemma with an enhanced expression in the intercalated discs. In failing hearts, many cardiomyocytes appeared deformed and POPDC1 labeling was deranged. The three POPDC mRNAs were expressed in the four heart chambers with higher transcript levels in the ventricles compared to the atria. Heart failure concurred with reduced levels of POPDC1 mRNA and protein in the left ventricle. Correlation analyses of mRNA levels among the failing heart specimens indicated the coordinated regulation of POPDC1 with POPDC3 and of POPDC2 with MYHC7. It can be concluded that POPDC gene expression is modified in end-stage heart failure in humans in a manner suggesting regulatory and/or functional differences between the three family members and that POPDC1 is particularly susceptible to this condition.

  17. Epidemiology of environmental exposures and human autoimmune diseases: findings from a National Institute of Environmental Health Sciences Expert Panel Workshop.

    Science.gov (United States)

    Miller, Frederick W; Alfredsson, Lars; Costenbader, Karen H; Kamen, Diane L; Nelson, Lorene M; Norris, Jill M; De Roos, Anneclaire J

    2012-12-01

    Autoimmune diseases (AID) are a collection of many complex disorders of unknown etiology resulting in immune responses to self-antigens and are thought to result from interactions between genetic and environmental factors. Here we review the epidemiologic evidence for the role of environmental factors in the development of human AID, the conclusions that can be drawn from the existing data, critical knowledge gaps, and research needed to fill these gaps and to resolve uncertainties. We specifically summarize the state of knowledge and our levels of confidence in the role of specific agents in the development of autoimmune diseases, and we define the areas of greatest impact for future investigations. Among our consensus findings we are confident that: 1) crystalline silica exposure can contribute to the development of several AID; 2) solvent exposure can contribute to the development of systemic sclerosis; 3) smoking can contribute to the development of seropositive rheumatoid arthritis; and 4) an inverse association exists between ultraviolet radiation exposure and the risk of development of multiple sclerosis. We suggest that more studies of phenotypes, genotypes, and multiple exposures are needed. Additional knowledge gaps needing investigation include: defining important windows in the timing of exposures and latencies relating to age, developmental state, and hormonal changes; understanding dose-response relationships; and elucidating mechanisms for disease development. Addressing these essential issues will require more resources to support research, particularly of rare AID, but knowledge of the risks conferred by environmental factors in specific genetic contexts could pave the way for prevention of AID in the future.

  18. Expert witness and Jungian archetypes.

    Science.gov (United States)

    Lallave, Juan Antonio; Gutheil, Thomas Gordon

    2012-01-01

    Jung's theories of archetype, shadow, and the personal and collective unconscious provide a postmodern framework in which to consider the role of the expert witness in judicial proceedings. Archetypal themes, motifs, and influences help to illuminate the shadow of the judicial system and projections and behaviors among the cast of the court in pursuing justice. This article speaks to archetypal influences and dialectical tensions encountered by the expert witness in this judicial drama. The archetype of Justice is born from the human need for order and relational fairness in a world of chaos. The persona of justice is the promise of truth in the drama. The shadow of justice is untruth, the need to win by any means. The dynamics of the trickster archetype serve and promote injustice. These influences are examined by means of a case example. This approach will deepen understanding of court proceedings and the role of the expert witness in the heroic quest for justice.

  19. Human CTP:phosphoethanolamine cytidylyltransferase: enzymatic properties and unequal catalytic roles of CTP-binding motifs in two cytidylyltransferase domains.

    Science.gov (United States)

    Tian, Siqi; Ohtsuka, Jun; Wang, Shipeng; Nagata, Koji; Tanokura, Masaru; Ohta, Akinori; Horiuchi, Hiroyuki; Fukuda, Ryouichi

    2014-06-20

    CTP:phosphoethanolamine cytidylyltransferase (ECT) is a key enzyme in the CDP-ethanolamine branch of the Kennedy pathway, which is the primary pathway of phosphatidylethanolamine (PE) synthesis in mammalian cells. Here, the enzymatic properties of recombinant human ECT (hECT) were characterized. The catalytic reaction of hECT obeyed Michaelis-Menten kinetics with respect to both CTP and phosphoethanolamine. hECT is composed of two tandem cytidylyltransferase (CT) domains as ECTs of other organisms. The histidines, especially the first histidine, in the CTP-binding motif HxGH in the N-terminal CT domain were critical for its catalytic activity in vitro, while those in the C-terminal CT domain were not. Overexpression of the wild-type hECT and hECT mutants containing amino acid substitutions in the HxGH motif in the C-terminal CT domain suppressed the growth defect of the Saccharomyces cerevisiae mutant of ECT1 encoding ECT in the absence of a PE supply via the decarboxylation of phosphatidylserine, but overexpression of hECT mutants of the N-terminal CT domain did not. These results suggest that the N-terminal CT domain of hECT contributes to its catalytic reaction, but C-terminal CT domain does not. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Human FAD synthase is a bi-functional enzyme with a FAD hydrolase activity in the molybdopterin binding domain.

    Science.gov (United States)

    Giancaspero, Teresa Anna; Galluccio, Michele; Miccolis, Angelica; Leone, Piero; Eberini, Ivano; Iametti, Stefania; Indiveri, Cesare; Barile, Maria

    2015-09-25

    FAD synthase (FMN:ATP adenylyl transferase, FMNAT or FADS, EC 2.7.7.2) is involved in the biochemical pathway for converting riboflavin into FAD. Human FADS exists in different isoforms. Two of these have been characterized and are localized in different subcellular compartments. hFADS2 containing 490 amino acids shows a two domain organization: the 3'-phosphoadenosine-5'-phosphosulfate (PAPS) reductase domain, that is the FAD-forming catalytic domain, and a resembling molybdopterin-binding (MPTb) domain. By a multialignment of hFADS2 with other MPTb containing proteins of various organisms from bacteria to plants, the critical residues for hydrolytic function were identified. A homology model of the MPTb domain of hFADS2 was built, using as template the solved structure of a T. acidophilum enzyme. The capacity of hFADS2 to catalyse FAD hydrolysis was revealed. The recombinant hFADS2 was able to hydrolyse added FAD in a Co(2+) and mersalyl dependent reaction. The recombinant PAPS reductase domain is not able to perform the same function. The mutant C440A catalyses the same hydrolytic function of WT with no essential requirement for mersalyl, thus indicating the involvement of C440 in the control of hydrolysis switch. The enzyme C440A is also able to catalyse hydrolysis of FAD bound to the PAPS reductase domain, which is quantitatively converted into FMN.

  1. Expert System Detects Power-Distribution Faults

    Science.gov (United States)

    Walters, Jerry L.; Quinn, Todd M.

    1994-01-01

    Autonomous Power Expert (APEX) computer program is prototype expert-system program detecting faults in electrical-power-distribution system. Assists human operators in diagnosing faults and deciding what adjustments or repairs needed for immediate recovery from faults or for maintenance to correct initially nonthreatening conditions that could develop into faults. Written in Lisp.

  2. Bifunctional homodimeric triokinase/FMN cyclase: contribution of protein domains to the activities of the human enzyme and molecular dynamics simulation of domain movements.

    Science.gov (United States)

    Rodrigues, Joaquim Rui; Couto, Ana; Cabezas, Alicia; Pinto, Rosa María; Ribeiro, João Meireles; Canales, José; Costas, María Jesús; Cameselle, José Carlos

    2014-04-11

    Mammalian triokinase, which phosphorylates exogenous dihydroxyacetone and fructose-derived glyceraldehyde, is neither molecularly identified nor firmly associated to an encoding gene. Human FMN cyclase, which splits FAD and other ribonucleoside diphosphate-X compounds to ribonucleoside monophosphate and cyclic X-phosphodiester, is identical to a DAK-encoded dihydroxyacetone kinase. This bifunctional protein was identified as triokinase. It was modeled as a homodimer of two-domain (K and L) subunits. Active centers lie between K1 and L2 or K2 and L1: dihydroxyacetone binds K and ATP binds L in different subunits too distant (≈ 14 Å) for phosphoryl transfer. FAD docked to the ATP site with ribityl 4'-OH in a possible near-attack conformation for cyclase activity. Reciprocal inhibition between kinase and cyclase reactants confirmed substrate site locations. The differential roles of protein domains were supported by their individual expression: K was inactive, and L displayed cyclase but not kinase activity. The importance of domain mobility for the kinase activity of dimeric triokinase was highlighted by molecular dynamics simulations: ATP approached dihydroxyacetone at distances below 5 Å in near-attack conformation. Based upon structure, docking, and molecular dynamics simulations, relevant residues were mutated to alanine, and kcat and Km were assayed whenever kinase and/or cyclase activity was conserved. The results supported the roles of Thr(112) (hydrogen bonding of ATP adenine to K in the closed active center), His(221) (covalent anchoring of dihydroxyacetone to K), Asp(401) and Asp(403) (metal coordination to L), and Asp(556) (hydrogen bonding of ATP or FAD ribose to L domain). Interestingly, the His(221) point mutant acted specifically as a cyclase without kinase activity.

  3. Expert status and performance.

    Directory of Open Access Journals (Sweden)

    Mark A Burgman

    Full Text Available Expert judgements are essential when time and resources are stretched or we face novel dilemmas requiring fast solutions. Good advice can save lives and large sums of money. Typically, experts are defined by their qualifications, track record and experience. The social expectation hypothesis argues that more highly regarded and more experienced experts will give better advice. We asked experts to predict how they will perform, and how their peers will perform, on sets of questions. The results indicate that the way experts regard each other is consistent, but unfortunately, ranks are a poor guide to actual performance. Expert advice will be more accurate if technical decisions routinely use broadly-defined expert groups, structured question protocols and feedback.

  4. Regulation of deleted in liver cancer-1 gene domains on the proliferation of human colon cancer HT29 cell

    Institute of Scientific and Technical Information of China (English)

    吴平平

    2013-01-01

    Objective To study the role of deleted in liver cancer-1(DLC-1) gene main domains on the regulation of hu-man colon cancer HT29 cell proliferation. Methods Subcloning recombinant plasmid vectors with Rho GTPase activating protein(RhoGAP),sterile alpha motif(SAM)

  5. The human ACC2 CT-domain C-terminus is required for full functionality and has a novel twist

    Energy Technology Data Exchange (ETDEWEB)

    Madauss, Kevin P. [Department of Computational and Structural Chemistry, GlaxoSmithKline Inc., Five Moore Drive, Research Triangle Park, NC 27709 (United States); Burkhart, William A.; Consler, Thomas G. [Department of Biochemical Reagents and Assay Development, GlaxoSmithKline Inc., Five Moore Drive, Research Triangle Park, NC 27709 (United States); Cowan, David J. [Department of Chemistry in the Center for Excellence in Metabolic Pathways Drug Discovery, GlaxoSmithKline Inc., Five Moore Drive, Research Triangle Park, NC 27709 (United States); Gottschalk, William K. [Institute for Genome Sciences and Policy and Department of Medicine, Division of Neurology, Duke University, Durham, NC 27708 (United States); Miller, Aaron B. [Department of Computational and Structural Chemistry, GlaxoSmithKline Inc., Five Moore Drive, Research Triangle Park, NC 27709 (United States); Short, Steven A. [Department of Biochemical Reagents and Assay Development, GlaxoSmithKline Inc., Five Moore Drive, Research Triangle Park, NC 27709 (United States); Tran, Thuy B. [Department of Physiology, UNC School of Medicine, University of North Carolina, Chapel Hill, NC 27515 (United States); Williams, Shawn P., E-mail: shawn.p.williams@gsk.com [Department of Computational and Structural Chemistry, GlaxoSmithKline Inc., Five Moore Drive, Research Triangle Park, NC 27709 (United States)

    2009-05-01

    The use of biophysical assays permitted the identification of a specific human ACC2 carboxyl transferase (CT) domain mutant that binds inhibitors and crystallizes in their presence. This mutant led to determination of the human ACC2 CT domain–CP-640186 complex crystal structure, which revealed differences in the inhibitor conformation from the yeast protein complex that are caused by differing residues in the binding pocket. Inhibition of acetyl-CoA carboxylase (ACC) may prevent lipid-induced insulin resistance and type 2 diabetes, making the enzyme an attractive pharmaceutical target. Although the enzyme is highly conserved amongst animals, only the yeast enzyme structure is available for rational drug design. The use of biophysical assays has permitted the identification of a specific C-terminal truncation of the 826-residue human ACC2 carboxyl transferase (CT) domain that is both functionally competent to bind inhibitors and crystallizes in their presence. This C-terminal truncation led to the determination of the human ACC2 CT domain–CP-640186 complex crystal structure, which revealed distinctions from the yeast-enzyme complex. The human ACC2 CT-domain C-terminus is comprised of three intertwined α-helices that extend outwards from the enzyme on the opposite side to the ligand-binding site. Differences in the observed inhibitor conformation between the yeast and human structures are caused by differing residues in the binding pocket.

  6. KASER: Knowledge Amplification by Structured Expert Randomization.

    Science.gov (United States)

    Rubin, Stuart H; Murthy, S N Jayaram; Smith, Michael H; Trajković, Ljiljana

    2004-12-01

    In this paper and attached video, we present a third-generation expert system named Knowledge Amplification by Structured Expert Randomization (KASER) for which a patent has been filed by the U.S. Navy's SPAWAR Systems Center, San Diego, CA (SSC SD). KASER is a creative expert system. It is capable of deductive, inductive, and mixed derivations. Its qualitative creativity is realized by using a tree-search mechanism. The system achieves creative reasoning by using a declarative representation of knowledge consisting of object trees and inheritance. KASER computes with words and phrases. It possesses a capability for metaphor-based explanations. This capability is useful in explaining its creative suggestions and serves to augment the capabilities provided by the explanation subsystems of conventional expert systems. KASER also exhibits an accelerated capability to learn. However, this capability depends on the particulars of the selected application domain. For example, application domains such as the game of chess exhibit a high degree of geometric symmetry. Conversely, application domains such as the game of craps played with two dice exhibit no predictable pattern, unless the dice are loaded. More generally, we say that domains whose informative content can be compressed to a significant degree without loss (or with relatively little loss) are symmetric. Incompressible domains are said to be asymmetric or random. The measure of symmetry plus the measure of randomness must always sum to unity.

  7. Discoidin domain receptors regulate the migration of primary human lung fibroblasts through collagen matrices

    Directory of Open Access Journals (Sweden)

    Ruiz Pedro A

    2012-02-01

    Full Text Available Abstract Background The two discoidin domain receptors (DDRs, DDR1 and DDR2 are receptor tyrosine kinases (RTKs with the unique ability among RTKs to respond to collagen. We have previously shown that collagen I induces DDR1 and matrix metalloproteinase (MMP-10 expression through DDR2 activation and a Janus kinase (JAK2 and extracellular signal-regulated kinase (ERK1/2-mediated mechanism in primary human lung fibroblasts suggesting that these signaling pathways play a role in fibroblast function. Fibroblasts can traverse basement membrane barriers during development, wound healing and pathological conditions such as cancer and fibrosis by activating tissue-invasive programs, the identity of which remain largely undefined. In the present work, we investigated the role of DDRs and DDR-associated signal transduction in these processes. Results Transwell migration experiments showed that normal human lung fibroblast (NHLF transmigration through collagen I-coated inserts is mediated by DDR2 and the DDR2-associated signaling kinases JAK2 and ERK1/2, but not DDR1. Additionally, experiments with specific small interfering (siRNAs revealed that collagen I-induced expression of MMP-10 and MMP-2 is DDR2 but not DDR1 dependent in NHLFs. Our data showed that collagen I increases NHLF migration through collagen IV, the main component of basement membranes. Furthermore, basal and collagen I-induced NHLF migration through collagen IV-coated inserts was both DDR2 and DDR1 dependent. Finally, DDR2, but not DDR1 was shown to be involved in fibroblast proliferation. Conclusions Our results suggest a mechanism by which the presence of collagen I in situations of excessive matrix deposition could induce fibroblast migration through basement membranes through DDR2 activation and subsequent DDR1 and MMP-2 gene expression. This work provides new insights into the role of DDRs in fibroblast function.

  8. INCA, a novel human caspase recruitment domain protein that inhibits interleukin-1beta generation.

    Science.gov (United States)

    Lamkanfi, Mohamed; Denecker, Geertrui; Kalai, Michael; D'hondt, Kathleen; Meeus, Ann; Declercq, Wim; Saelens, Xavier; Vandenabeele, Peter

    2004-12-10

    Using in silico methods for screening the human genome for new caspase recruitment domain (CARD) proteins, we have identified INCA (Inhibitory CARD) as a protein that shares 81% identity with the prodomain of caspase-1. The INCA gene is located on chromosome 11q22 between the genes of COP/Pseudo-ICE and ICEBERG, two other CARD proteins that arose from caspase-1 gene duplications. We show that INCA mRNA is expressed in many tissues. INCA is specifically upregulated by interferon-gamma in the monocytic cell lines THP-1 and U937. INCA physically interacts with procaspase-1 and blocks the release of mature IL-1beta from LPS-stimulated macrophages. Unlike COP/Pseudo-ICE and procaspase-1, INCA does not interact with RIP2 and does not induce NF-kappaB activation. Our data show that INCA is a novel intracellular regulator of procaspase-1 activation, involved in the regulation of pro-IL-1beta processing and its release during inflammation.

  9. The complex regulation of HIC (Human I-mfa domain containing protein) expression.

    Science.gov (United States)

    Reiss-Sklan, Ella; Levitzki, Alexander; Naveh-Many, Tally

    2009-07-07

    Human I-mfa domain containing protein (HIC) differentially regulates transcription from viral promoters. HIC affects the Wnt pathway, the JNK/SAPK pathway and the activity of positive transcription elongation factor-b (P-TEFb). Studies exploring HIC function in mammalian cells used ectopically expressed HIC due to undetected endogenous HIC protein. HIC mRNA contains exceptionally long 5' and 3' untranslated regions (UTRs) compared to the average length of mRNA UTRs. Here we show that HIC protein is subject to strict repression at multiple levels. The HIC mRNA UTRs reduce the expression of HIC or of a reporter protein: The HIC 3'-UTR decreases both HIC and reporter mRNA levels, whereas upstream open reading frames located in the 5'-UTR repress the translation of HIC or of the reporter protein. In addition, ectopically expressed HIC protein is degraded by the proteasome, with a half-life of approximately 1 h, suggesting that upon activation, HIC expression in cells may be transient. The strict regulation of HIC expression at the levels of mRNA stability, translation efficiency and protein stability suggests that expression of the HIC protein and its involvement in the various pathways is required only under specific cellular conditions.

  10. The complex regulation of HIC (Human I-mfa domain containing protein expression.

    Directory of Open Access Journals (Sweden)

    Ella Reiss-Sklan

    Full Text Available Human I-mfa domain containing protein (HIC differentially regulates transcription from viral promoters. HIC affects the Wnt pathway, the JNK/SAPK pathway and the activity of positive transcription elongation factor-b (P-TEFb. Studies exploring HIC function in mammalian cells used ectopically expressed HIC due to undetected endogenous HIC protein. HIC mRNA contains exceptionally long 5' and 3' untranslated regions (UTRs compared to the average length of mRNA UTRs. Here we show that HIC protein is subject to strict repression at multiple levels. The HIC mRNA UTRs reduce the expression of HIC or of a reporter protein: The HIC 3'-UTR decreases both HIC and reporter mRNA levels, whereas upstream open reading frames located in the 5'-UTR repress the translation of HIC or of the reporter protein. In addition, ectopically expressed HIC protein is degraded by the proteasome, with a half-life of approximately 1 h, suggesting that upon activation, HIC expression in cells may be transient. The strict regulation of HIC expression at the levels of mRNA stability, translation efficiency and protein stability suggests that expression of the HIC protein and its involvement in the various pathways is required only under specific cellular conditions.

  11. ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Iwase, Shigeki; Xiang, Bin; Ghosh, Sharmistha; Ren, Ting; Lewis, Peter W.; Cochrane, Jesse C.; Allis, C. David; Picketts, David J.; Patel, Dinshaw J.; Li, Haitao; Shi, Yang (Harvard-Med); (Ottawa Hosp.); (MSKCC); (Rockefeller); (CH-Boston); (Tsinghua); (Mass. Gen. Hosp.)

    2011-07-19

    ATR-X (alpha-thalassemia/mental retardation, X-linked) syndrome is a human congenital disorder that causes severe intellectual disabilities. Mutations in the ATRX gene, which encodes an ATP-dependent chromatin-remodeler, are responsible for the syndrome. Approximately 50% of the missense mutations in affected persons are clustered in a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, ADD{sub ATRX}), whose function has remained elusive. Here we identify ADD{sub ATRX} as a previously unknown histone H3-binding module, whose binding is promoted by lysine 9 trimethylation (H3K9me3) but inhibited by lysine 4 trimethylation (H3K4me3). The cocrystal structure of ADD{sub ATRX} bound to H3{sub 1-15}K9me3 peptide reveals an atypical composite H3K9me3-binding pocket, which is distinct from the conventional trimethyllysine-binding aromatic cage. Notably, H3K9me3-pocket mutants and ATR-X syndrome mutants are defective in both H3K9me3 binding and localization at pericentromeric heterochromatin; thus, we have discovered a unique histone-recognition mechanism underlying the ATR-X etiology.

  12. ATRX ADD Domain Links an Atypical Histone Methylation Recognition Mechanism to Human Mental-Retardation Syndrome

    Energy Technology Data Exchange (ETDEWEB)

    S Iwase; B Xiang; S Ghosh; T Ren; P Lewis; J Cochrane; C Allis; D Picketts; D Patel; et al.

    2011-12-31

    ATR-X (alpha-thalassemia/mental retardation, X-linked) syndrome is a human congenital disorder that causes severe intellectual disabilities. Mutations in the ATRX gene, which encodes an ATP-dependent chromatin-remodeler, are responsible for the syndrome. Approximately 50% of the missense mutations in affected persons are clustered in a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, ADD{sub ATRX}), whose function has remained elusive. Here we identify ADD{sub ATRX} as a previously unknown histone H3-binding module, whose binding is promoted by lysine 9 trimethylation (H3K9me3) but inhibited by lysine 4 trimethylation (H3K4me3). The cocrystal structure of ADD{sub ATRX} bound to H3{sub 1-15}K9me3 peptide reveals an atypical composite H3K9me3-binding pocket, which is distinct from the conventional trimethyllysine-binding aromatic cage. Notably, H3K9me3-pocket mutants and ATR-X syndrome mutants are defective in both H3K9me3 binding and localization at pericentromeric heterochromatin; thus, we have discovered a unique histone-recognition mechanism underlying the ATR-X etiology.

  13. Role of a Putative gp41 Dimerization Domain in Human Immunodeficiency Virus Type 1 Membrane Fusion

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.; Deng, Y; Li, Q; Dey, A; Moore, J; Lu, M

    2010-01-01

    The entry of human immunodeficiency virus type 1 (HIV-1) into a target cell entails a series of conformational changes in the gp41 transmembrane glycoprotein that mediates the fusion of the viral and target cell membranes. A trimer-of-hairpins structure formed by the association of two heptad repeat (HR) regions of the gp41 ectodomain has been implicated in a late step of the fusion pathway. Earlier native and intermediate states of the protein are postulated to mediate the antiviral activity of the fusion inhibitor enfuvirtide and of broadly neutralizing monoclonal antibodies (NAbs), but the details of these structures remain unknown. Here, we report the identification and crystal structure of a dimerization domain in the C-terminal ectodomain of gp41 (residues 630 to 683, or C54). Two C54 monomers associate to form an asymmetric, antiparallel coiled coil with two distinct C-terminal {alpha}-helical overhangs. This dimer structure is conferred largely by interactions within a central core that corresponds to the sequence of enfuvirtide. The mutagenic alteration of the dimer interface severely impairs the infectivity of Env-pseudotyped viruses. Moreover, the C54 structure binds tightly to both the 2F5 and 4E10 NAbs and likely represents a potential intermediate conformation of gp41. These results should enhance our understanding of the molecular basis of the gp41 fusogenic structural transitions and thereby guide rational, structure-based efforts to design new fusion inhibitors and vaccine candidates intended to induce broadly neutralizing antibodies.

  14. The 5' binding MID domain of human Argonaute2 tolerates chemically modified nucleotide analogues.

    Science.gov (United States)

    Deleavey, Glen F; Frank, Filipp; Hassler, Matthew; Wisnovsky, Simon; Nagar, Bhushan; Damha, Masad J

    2013-02-01

    Small interfering RNAs (siRNAs) can trigger potent gene silencing through the RNA interference (RNAi) pathway. The RNA-induced silencing complex (RISC) is key to this targeted mRNA degradation, and the human Argonaute2 (hAGO2) endonuclease component of RISC is responsible for the actual mRNA cleavage event. During RNAi, hAGO2 becomes loaded with the siRNA guide strand, making several key nucleic acid-enzyme interactions. Chemically modified siRNAs are now widely used in place of natural double-stranded RNAs, and understanding the effects chemical modifications have on guide strand-hAGO2 interactions has become particularly important. Here, interactions between the 5' nucleotide binding domain of hAGO2, MID, and chemically modified nucleotide analogues are investigated. Measured dissociation constants reveal that hAGO2 does not discriminate between nucleotide analogues during binding, regardless of the preferred sugar conformation of the nucleotide analogues. These results correlate well with cell-based gene silencing results employing siRNAs with 5'-modified guide strands. Additionally, chemical modification with 2'-deoxy-2'-fluoroarabino nucleic acid (2'F-ANA) and 2'-deoxy-2'-fluororibonucleic acid (2'F-RNA) at the passenger strand cleavage site of siRNAs has been shown to prevent hAGO2-mediated strand cleavage, an observation that appears to have little impact on overall gene silencing potency.

  15. Human Protein-disulfide Isomerase Is a Redox-regulated Chaperone Activated by Oxidation of Domain a′*

    Science.gov (United States)

    Wang, Chao; Yu, Jiang; Huo, Lin; Wang, Lei; Feng, Wei; Wang, Chih-chen

    2012-01-01

    Protein-disulfide isomerase (PDI), with domains arranged as abb′xa′c, is a key enzyme and chaperone localized in the endoplasmic reticulum (ER) catalyzing oxidative folding and preventing misfolding/aggregation of proteins. It has been controversial whether the chaperone activity of PDI is redox-regulated, and the molecular basis is unclear. Here, we show that both the chaperone activity and the overall conformation of human PDI are redox-regulated. We further demonstrate that the conformational changes are triggered by the active site of domain a′, and the minimum redox-regulated cassette is located in b′xa′. The structure of the reduced bb′xa′ reveals for the first time that domain a′ packs tightly with both domain b′ and linker x to form one compact structural module. Oxidation of domain a′ releases the compact conformation and exposes the shielded hydrophobic areas to facilitate its high chaperone activity. Thus, the study unequivocally provides mechanistic insights into the redox-regulated chaperone activity of human PDI. PMID:22090031

  16. Definition of the transcriptional activation domains of three human HOX proteins depends on the DNA-binding context.

    Science.gov (United States)

    Viganò, M A; Di Rocco, G; Zappavigna, V; Mavilio, F

    1998-11-01

    Hox proteins control developmental patterns and cell differentiation in vertebrates by acting as positive or negative regulators of still unidentified downstream target genes. The homeodomain and other small accessory sequences encode the DNA-protein and protein-protein interaction functions which ultimately dictate target recognition and functional specificity in vivo. The effector domains responsible for either positive or negative interactions with the cell transcriptional machinery are unknown for most Hox proteins, largely due to a lack of physiological targets on which to carry out functional analysis. We report the identification of the transcriptional activation domains of three human Hox proteins, HOXB1, HOXB3, and HOXD9, which interact in vivo with the autoregulatory and cross-regulatory enhancers of the murine Hoxb-1 and human HOXD9 genes. Activation domains have been defined both in a homologous context, i.e., within a HOX protein binding as a monomer or as a HOX-PBX heterodimer to the specific target, and in a heterologous context, after translocation to the yeast Gal4 DNA-binding domain. Transfection analysis indicates that activation domains can be identified in different regions of the three HOX proteins depending on the context in which they interact with the DNA target. These results suggest that Hox proteins may be multifunctional transcriptional regulators, interacting with different cofactors and/or components of the transcriptional machinery depending on the structure of their target regulatory elements.

  17. An Expert System Approach for Garden Designing

    Directory of Open Access Journals (Sweden)

    NiloofarMozafari

    2012-10-01

    Full Text Available In the recent years, the quality of human life is improved by artificial intelligencetechniques. In artificial intelligence, an expert system is a computer system that emulates thedecision-making ability of a human expert. Expert systems are designed to solve complexproblems by reasoning about knowledge, like an expert. In this paper, we propose an expertsystem with the aim of designing the garden with considering the different taste of thepeople. The proposed system can help people to design their garden themselves. Indeed, it isable to use by architectures to provide decision support system, interactive training tool andexpert advice. The system constitutes part of intelligent system of designing the garden. Aninitial evaluation of the expert system was carried out and a positive feedback was receivedfrom the users.

  18. Contextual Factors for Finding Similar Experts

    DEFF Research Database (Denmark)

    Hofmann, Katja; Balog, Krisztian; Bogers, Toine

    2010-01-01

    -seeking models, are rarely taken into account. In this article, we extend content-based expert-finding approaches with contextual factors that have been found to influence human expert finding. We focus on a task of science communicators in a knowledge-intensive environment, the task of finding similar experts......, given an example expert. Our approach combines expertise-seeking and retrieval research. First, we conduct a user study to identify contextual factors that may play a role in the studied task and environment. Then, we design expert retrieval models to capture these factors. We combine these with content......-based retrieval models and evaluate them in a retrieval experiment. Our main finding is that while content-based features are the most important, human participants also take contextual factors into account, such as media experience and organizational structure. We develop two principled ways of modeling...

  19. Implications of Human Transient Receptor Potential Melastatin 8 (TRPM8) Channel Gating from Menthol Binding Studies of the Sensing Domain.

    Science.gov (United States)

    Rath, Parthasarathi; Hilton, Jacob K; Sisco, Nicholas J; Van Horn, Wade D

    2016-01-12

    The transient receptor potential melastatin 8 (TRPM8) ion channel is the primary cold sensor in humans. TRPM8 is gated by physiologically relevant cold temperatures and chemical ligands that induce cold sensations, such as the analgesic compound menthol. Characterization of TRPM8 ligand-gated channel activation will lead to a better understanding of the fundamental mechanisms that underlie TRPM8 function. Here, the direct binding of menthol to the isolated hTRPM8 sensing domain (transmembrane helices S1-S4) is investigated. These data are compared with two mutant sensing domain proteins, Y745H (S2 helix) and R842H (S4 helix), which have been previously identified in full length TRPM8 to be menthol insensitive. The data presented herein show that menthol specifically binds to the wild type, Y745H, and R842H TRPM8 sensing domain proteins. These results are the first to show that menthol directly binds to the TRPM8 sensing domain and indicates that Y745 and R842 residues, previously identified in functional studies as crucial to menthol sensitivity, do not affect menthol binding but instead alter coupling between the sensing domain and the pore domain.

  20. A novel expression system of domain I of human beta2 glycoprotein I in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Pearl Laurence H

    2006-02-01

    Full Text Available Abstract Background The antiphospholipid syndrome (APS, characterised by recurrent miscarriage and thrombosis, is a significant cause of morbidity and mortality. Domain I (DI of human beta 2 glycoprotein I (β2GPI is thought to contain crucial antibody binding epitopes for antiphospholipid antibodies (aPL, which are critical to the pathogenesis of APS. Expressing this protein in bacteria could facilitate studies investigating how this molecule interacts with aPL. Methods Using a computer programme called Juniper, sequentially overlapping primers were designed to be used in a recursive polymerase chain reaction (PCR to produce a synthetic DI gene. Specifically Juniper incorporates 'major' codons preferred by bacteria altering 41 codons out of 61. This was cloned into the expression plasmid pET(26b and expressed in BL21(DE3 Escherichia coli (E. coli. By virtue of a pelB leader sequence, periplasmic localisation of DI aided disulphide bond formation and toxicity was addressed by tightly regulating expression through the high stringency T7lac promoter. Results Purified, soluble his-tagged DI in yields of 750 μg/L bacterial culture was obtained and confirmed on Western blot. Expression using the native human cDNA sequence of DI in the same construct under identical conditions yielded significantly less DI compared to the recombinant optimised sequence. This constitutes the first description of prokaryotic expression of soluble DI of β2GPI. Binding to murine monoclonal antibodies that recognise conformationally restricted epitopes on the surface of DI and pathogenic human monoclonal IgG aPL was confirmed by direct and indirect immunoassay. Recombinant DI also bound a series of 21 polyclonal IgG samples derived from patients with APS. Conclusion By producing a synthetic gene globally optimised for expression in E. coli, tightly regulating expression and utilising periplasmic product translocation, efficient, soluble E. coli expression of the

  1. Chemical enhancer solubility in human stratum corneum lipids and enhancer mechanism of action on stratum corneum lipid domain.

    Science.gov (United States)

    Ibrahim, Sarah A; Li, S Kevin

    2010-01-04

    Previously, chemical enhancer-induced permeation enhancement on human stratum corneum (SC) lipoidal pathway at enhancer thermodynamic activities approaching unity in the absence of cosolvents (defined as Emax) was determined and hypothesized to be related to the enhancer solubilities in the SC lipid domain. The objectives of the present study were to (a) quantify enhancer uptake into SC lipid domain at saturation, (b) elucidate enhancer mechanism(s) of action, and (c) study the SC lipid phase behavior at Emax. It was concluded that direct quantification of enhancer uptake into SC lipid domain using intact SC was complicated. Therefore a liposomal model of extracted human SC lipids was used. In the liposome study, enhancer uptake into extracted human SC lipid liposomes (EHSCLL) was shown to correlate with Emax. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) and differential scanning calorimetry (DSC) were used to evaluate lipid phase alterations in enhancer-treated intact SC. IR spectra demonstrated an increase in the lipid domain fluidity and DSC thermograms indicated a decrease in the phase transition temperature with increasing Emax. These results suggest that the enhancer mechanism of action is through enhancer intercalation into SC intercellular lipids and subsequent lipid lamellae fluidization related to enhancer lipid concentration.

  2. Structure of Human J-type Co-chaperone HscB Reveals a Tetracysteine Metal-binding Domain

    Energy Technology Data Exchange (ETDEWEB)

    Bitto, Eduard; Bingman, Craig A.; Bittova, Lenka; Kondrashov, Dmitry A.; Bannen, Ryan M.; Fox, Brian G.; Markley, John L.; Phillips, Jr., George N. (UW); (UC)

    2008-11-24

    Iron-sulfur proteins play indispensable roles in a broad range of biochemical processes. The biogenesis of iron-sulfur proteins is a complex process that has become a subject of extensive research. The final step of iron-sulfur protein assembly involves transfer of an iron-sulfur cluster from a cluster-donor to a cluster-acceptor protein. This process is facilitated by a specialized chaperone system, which consists of a molecular chaperone from the Hsc70 family and a co-chaperone of the J-domain family. The 3.0 A crystal structure of a human mitochondrial J-type co-chaperone HscB revealed an L-shaped protein that resembles Escherichia coli HscB. The important difference between the two homologs is the presence of an auxiliary metal-binding domain at the N terminus of human HscB that coordinates a metal via the tetracysteine consensus motif CWXCX(9-13)FCXXCXXXQ. The domain is found in HscB homologs from animals and plants as well as in magnetotactic bacteria. The metal-binding site of the domain is structurally similar to that of rubredoxin and several zinc finger proteins containing rubredoxin-like knuckles. The normal mode analysis of HscB revealed that this L-shaped protein preferentially undergoes a scissors-like motion that correlates well with the conformational changes of human HscB observed in the crystals.

  3. Functional interactions of the AF-2 activation domain core region of the human androgen receptor with the amino-terminal domain and with the transcriptional coactivator TIF2 (transcriptional intermediary factor2)

    NARCIS (Netherlands)

    C.A. Berrevoets (Cor); P. Doesburg (Paul); K. Steketee (Karine); J. Trapman (Jan); A.O. Brinkmann (Albert)

    1998-01-01

    textabstractPrevious studies in yeast and mammalian cells showed a functional interaction between the amino-terminal domain and the carboxy-terminal, ligand-binding domain (LBD) of the human androgen receptor (AR). In the present study, the AR subdomains involved in thi

  4. Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup Repeat Specificity

    DEFF Research Database (Denmark)

    Vognsen, Tina Reinholdt; Möller, Ingvar Rúnar; Kristensen, Ole

    2013-01-01

    Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat...... crystal form might indicate a novel ligand binding site that, however, remains to be validated. The crystal structures give insight into the nuclear transportation mechanisms of G3BP and provide a basis for future structure based drug design....

  5. SELF LEARNING COMPUTER TROUBLESHOOTING EXPERT SYSTEM

    OpenAIRE

    Amanuel Ayde Ergado

    2016-01-01

    In computer domain the professionals were limited in number but the numbers of institutions looking for computer professionals were high. The aim of this study is developing self learning expert system which is providing troubleshooting information about problems occurred in the computer system for the information and communication technology technicians and computer users to solve problems effectively and efficiently to utilize computer and computer related resources. Domain know...

  6. Mapping the transcription repressive domain in the highly conserved human gene hnulp1

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    HNULP1,a new member of the basic helixloop-helix transcription factors,contains a DUF654 domain in its C-terminus and is highly conserved from Drosophilae,yeast,zebrafish to mouse.The function of this motif,however,is currently unknown.In this research,we fused five deletion fragments of the DUF654 domain to the GAL4 DNA-binding domain and then co-transfected with plasmids L8G5-Luc and VP-16.The analysis of the GAL4 luciferase reporter gene indicated that fragments from 228 to 407 amino acids in the DUF654 domain had a strong transcription repression activity.Therefore,this study lays a solid foundation for research on the mechanism of hnulp1 transcriptional regulation and the function of the DUF654 domain.

  7. Domain of the Gods: Do traditional beliefs hinder public acceptance of the human role in climate change?

    Science.gov (United States)

    Donner, S.

    2008-12-01

    Public acceptance of new scientific discoveries like natural selection, plate tectonics, or the human role in climate change naturally lags behind the pace of the discoveries. In the case of climate change, unease or outright rejection of the scientific evidence for the role of human activity in climate change has been a hindrance to mitigation and adaptation efforts. This skepticism is normally attributed to everything from the quality of science education, to disinformation campaigns by representatives of the coal and gas industry, to individual resistance to behavioral change, to the nature of the modern information culture. This skepticism of scientific evidence for climate change, though often inspired by politics, economics and the particular dynamics of climate change, may actually be rooted in ancient beliefs that the climate is beyond the influence of humans. In this presentation, I will outline how the notion that humans control or influence the weather runs contrary to thousands of years of belief in a separation between the earth - the domain of man - and sky - the domain of the gods. Evidence from religious history, traditional villages in the Pacific (Fjij and Kiribati) and from public discourse in North America all indicates that the millennia-old belief in an earth-sky separation hinders people's acceptance that human activity is affecting the climate. The human role in climate change therefore represents a substantial paradigm shift, similar to the role of natural selection in human evolution. These deep roots of climate change skepticism must be factored into public climate change education efforts.

  8. Far-infrared in vivo signature of human skin by terahertz time-domain spectroscopy using waveform rebuilding technology

    Science.gov (United States)

    Li, Xiangjun; Liu, Jianjun; Hong, Zhi

    2010-11-01

    We present terahertz time-domain spectroscopy characterization of human thumb skin in reflection measurement mode with waveform rebuilding technology. The thumb skin contacts one side of a high resistive silicon wafer with 3 mm thick, and here is an orthogonal incidence of the THz pulse putting on the other side of the wafer. We rebuild the time domain signal from silicon-skin interface as a sample signal by the signal from the air-silicon interface as a reference and a Fresnel transform function between them. Material parameters were calculated by minimizing the difference between the measured sample waveform and a rebuilt one in time domain. The double Debye model parameters for the thumb skin were fitted. The method has potential to research complex layer-structures in skin if a precise model is built.

  9. Expression,purification,crystallization,and preliminary X-ray diffraction analysis of the human TLE1 Q domain

    Institute of Scientific and Technical Information of China (English)

    Su Wang; Jiamu Du; Hua Tang; Xinyu Ding; Manwu Zha; Zhifei Xu

    2011-01-01

    Human transducin-like enhancer of split 1(TLE1)plays crucial roles in a number of developmental processes and is involved in pathogenesis of malignancy tumors.The N-terminal glutamine-rich domain(Q domain)of TLEI mediates its tetramerization and interactions with different DNA-binding transcription factors to regulate Notch and Wnt signaling pathways.To better understand the molecular mechanism of TLEI's functions in these pathways,we cloned,purified,and crystallized the TLE1 Q domain(TLEI-Q).The crystals belong to space group C2221,with the complete diffraction data of the native and Se-Met TLEI-Q collected to 3.5 and 4.1 A resolutions,respectively.The phasing-solving and model building are in progress.

  10. ANKRD54 preferentially selects Bruton's Tyrosine Kinase (BTK) from a Human Src-Homology 3 (SH3) domain library.

    Science.gov (United States)

    Gustafsson, Manuela O; Mohammad, Dara K; Ylösmäki, Erkko; Choi, Hyunseok; Shrestha, Subhash; Wang, Qing; Nore, Beston F; Saksela, Kalle; Smith, C I Edvard

    2017-01-01

    Bruton's Tyrosine Kinase (BTK) is a cytoplasmic protein tyrosine kinase with a fundamental role in B-lymphocyte development and activation. The nucleocytoplasmic shuttling of BTK is specifically modulated by the Ankyrin Repeat Domain 54 (ANKRD54) protein and the interaction is known to be exclusively SH3-dependent. To identify the spectrum of the ANKRD54 SH3-interactome, we applied phage-display screening of a library containing all the 296 human SH3 domains. The BTK-SH3 domain was the prime interactor. Quantitative western blotting analysis demonstrated the accuracy of the screening procedure. Revealing the spectrum and specificity of ANKRD54-interactome is a critical step toward functional analysis in cells and tissues.

  11. The human ACC2 CT-domain C-terminus is required for full functionality and has a novel twist

    Energy Technology Data Exchange (ETDEWEB)

    Madauss, Kevin P.; Burkhart, William A.; Consler, Thomas G.; Cowan, David J.; Gottschalk, William K.; Miller, Aaron B; Short, Steven A.; Tran, Thuy B.; Williams, Shawn P.; (GSKNC); (Duke); (UNC)

    2009-06-15

    Inhibition of acetyl-CoA carboxylase (ACC) may prevent lipid-induced insulin resistance and type 2 diabetes, making the enzyme an attractive pharmaceutical target. Although the enzyme is highly conserved amongst animals, only the yeast enzyme structure is available for rational drug design. The use of biophysical assays has permitted the identification of a specific C-terminal truncation of the 826-residue human ACC2 carboxyl transferase (CT) domain that is both functionally competent to bind inhibitors and crystallizes in their presence. This C-terminal truncation led to the determination of the human ACC2 CT domain-CP-640186 complex crystal structure, which revealed distinctions from the yeast-enzyme complex. The human ACC2 CT-domain C-terminus is comprised of three intertwined -helices that extend outwards from the enzyme on the opposite side to the ligand-binding site. Differences in the observed inhibitor conformation between the yeast and human structures are caused by differing residues in the binding pocket.

  12. Connecting art and science: An interdisciplinary strategy and its impact on the affective domain of community college human anatomy students

    Science.gov (United States)

    Petti, Kevin

    Educational objectives are often described within the framework of a three-domain taxonomy: cognitive, affective and psychomotor. While most of the research on educational objectives has focused on the cognitive domain, the research that has been conducted on the affective domain, which speaks to emotions, attitudes, and values, has identified a number of positive outcomes. One approach to enhancing the affective domain is that of interdisciplinary education. Science education research in the realm of interdisciplinary education and affective outcomes is limited; especially research conducted on community college students of human anatomy. This project investigated the relationship between an interdisciplinary teaching strategy and the affective domain in science education by utilizing an interdisciplinary lecture in a human anatomy class. Subjects were anatomy students in a California community college who listened to a one-hour lecture describing the cultural, historical and scientific significance of selected pieces of art depicting human dissection in European medieval and Renaissance universities. The focus was on how these renderings represent the state of anatomy education during their respective eras. After listening to the lecture, subjects were administered a 35-question survey that was composed of 14 demographic questions and 21 Likert-style statements that asked respondents to rate the extent to which the intervention influenced their affective domain. Descriptive statistics were then used to determine which component of the affective domain was most influenced, and multiple regression analysis was used to examine the extent to which individual differences along the affective continuum were explained by select demographic measures such as gender, race/ethnicity, education level, and previous exposure to science courses. Results indicate that the interdisciplinary intervention had a positive impact on every component of the affective domain hierarchy

  13. Expert analogy use in a naturalistic setting

    Science.gov (United States)

    Kretz, Donald R.; Krawczyk, Daniel C.

    2014-01-01

    The use of analogy is an important component of human cognition. The type of analogy we produce and communicate depends heavily on a number of factors, such as the setting, the level of domain expertise present, and the speaker's goal or intent. In this observational study, we recorded economics experts during scientific discussion and examined the categorical distance and structural depth of the analogies they produced. We also sought to characterize the purpose of the analogies that were generated. Our results supported previous conclusions about the infrequency of superficial similarity in subject-generated analogs, but also showed that distance and depth characteristics were more evenly balanced than in previous observational studies. This finding was likely due to the nature of the goals of the participants, as well as the broader nature of their expertise. An analysis of analogical purpose indicated that the generation of concrete source examples of more general target concepts was most prevalent. We also noted frequent instances of analogies intended to form visual images of source concepts. Other common purposes for analogies were the addition of colorful speech, inclusion (i.e., subsumption) of a target into a source concept, or differentiation between source and target concepts. We found no association between depth and either of the other two characteristics, but our findings suggest a relationship between purpose and distance; i.e., that visual imagery typically entailed an outside-domain source whereas exemplification was most frequently accomplished using within-domain analogies. Overall, we observed a rich and diverse set of spontaneously produced analogical comparisons. The high degree of expertise within the observed group along with the richly comparative nature of the economics discipline likely contributed to this analogical abundance. PMID:25505437

  14. Recombinant domain V of human perlecan is a bioactive vascular proteoglycan.

    Science.gov (United States)

    Rnjak-Kovacina, Jelena; Tang, Fengying; Lin, Xiaoting; Whitelock, John M; Lord, Megan S

    2017-08-28

    The C-terminal domain V of the extracellular matrix proteoglycan perlecan plays unique and often divergent roles in a number of biological processes, including angiogenesis, vascular cell interactions, wound healing and autophagy. Recombinant forms of this domain (domain V) have been proposed as therapeutic agents for the treatment of cancer, stroke and the development of cardiovascular devices and bioartificial tissues. However, the effect of domain V appears to be related to the differences in domain V structure and function observed in different expression systems and environments and exactly how this occurs is not well understood. In this study, the sequence from amino acid 3626 to 4391 of the perlecan protein core, which includes domain V, was expressed in HEK-293 cells and purified as a secreted product from conditioned media. This recombinant domain V (rDV) was expressed as a proteoglycan decorated with heparan sulfate and chondroitin sulfate chains and supported endothelial cell interactions to the same extent as full-length perlecan. This expression system serves as an important model of recombinant proteoglycan expression, as well as a source of biologically active rDV for therapeutic applications. This article is protected by copyright. All rights reserved.

  15. Solution NMR structure and histone binding of the PHD domain of human MLL5.

    Directory of Open Access Journals (Sweden)

    Alexander Lemak

    Full Text Available Mixed Lineage Leukemia 5 (MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. In addition to its catalytic domain, MLL5 contains a PHD finger domain, a protein module that is often involved in binding to the N-terminus of histone H3. Here we report the NMR solution structure of the MLL5 PHD domain showing a variant of the canonical PHD fold that combines conserved H3 binding features from several classes of other PHD domains (including an aromatic cage along with a novel C-terminal α-helix, not previously seen. We further demonstrate that the PHD domain binds with similar affinity to histone H3 tail peptides di- and tri-methylated at lysine 4 (H3K4me2 and H3K4me3, the former being the putative product of the MLL5 catalytic reaction. This work establishes the PHD domain of MLL5 as a bone fide 'reader' domain of H3K4 methyl marks suggesting that it may guide the spreading or further methylation of this site on chromatin.

  16. Sherlock Holmes: an expert's view of expertise.

    Science.gov (United States)

    André, Didierjean; Fernand, Gobet

    2008-02-01

    In recent years, there has been an intense research effort to understand the cognitive processes and structures underlying expert behaviour. Work in different fields, including scientific domains, sports, games and mnemonics, has shown that there are vast differences in perceptual abilities between experts and novices, and that these differences may underpin other cognitive differences in learning, memory and problem solving. In this article, we evaluate the progress made in the last years through the eyes of an outstanding, albeit fictional, expert: Sherlock Holmes. We first use the Sherlock Holmes character to illustrate expert processes as described by current research and theories. In particular, the role of perception, as well as the nature and influence of expert knowledge, are all present in the description of Conan Doyle's hero. In the second part of the article, we discuss a number of issues that current research on expertise has barely addressed. These gaps include, for example, several forms of reasoning, the influence of emotions on cognition, and the effect of age on experts' knowledge and cognitive processes. Thus, although nearly 120-year-old, Conan Doyle's books show remarkable illustrations of expert behaviour, including the coverage of themes that have mostly been overlooked by current research.

  17. WATERS Expert Query Tool

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Expert Query Tool is a web-based reporting tool using the EPA’s WATERS database.There are just three steps to using Expert Query:1. View Selection – Choose what...

  18. How Expert Designers Design

    NARCIS (Netherlands)

    C. Carr; Dr. Peter Sloep; P. Kirschner; J. van Merrienboer

    2003-01-01

    This paper discusses two studies - the one in a business context, the other in a university context - carried out with expert educational designers. The studies aimed to determine the priorities experts claim to employ when designing competence-based learning environments. Designers in both contexts

  19. CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells.

    Directory of Open Access Journals (Sweden)

    Laurie A Steiner

    Full Text Available CTCF and cohesinSA-1 are regulatory proteins involved in a number of critical cellular processes including transcription, maintenance of chromatin domain architecture, and insulator function. To assess changes in the CTCF and cohesinSA-1 interactomes during erythropoiesis, chromatin immunoprecipitation coupled with high throughput sequencing and mRNA transcriptome analyses via RNA-seq were performed in primary human hematopoietic stem and progenitor cells (HSPC and primary human erythroid cells from single donors.Sites of CTCF and cohesinSA-1 co-occupancy were enriched in gene promoters in HSPC and erythroid cells compared to single CTCF or cohesin sites. Cell type-specific CTCF sites in erythroid cells were linked to highly expressed genes, with the opposite pattern observed in HSPCs. Chromatin domains were identified by ChIP-seq with antibodies against trimethylated lysine 27 histone H3, a modification associated with repressive chromatin. Repressive chromatin domains increased in both number and size during hematopoiesis, with many more repressive domains in erythroid cells than HSPCs. CTCF and cohesinSA-1 marked the boundaries of these repressive chromatin domains in a cell-type specific manner.These genome wide data, changes in sites of protein occupancy, chromatin architecture, and related gene expression, support the hypothesis that CTCF and cohesinSA-1 have multiple roles in the regulation of gene expression during erythropoiesis including transcriptional regulation at gene promoters and maintenance of chromatin architecture. These data from primary human erythroid cells provide a resource for studies of normal and perturbed erythropoiesis.

  20. Developmentally-regulated extended domains of DNA hypomethylation encompass highly transcribed genes of the human β-globin locus

    Science.gov (United States)

    Lathrop, Melissa J.; Hsu, Mei; Richardson, Christine A.; Olivier, Emmanuel N.; Bouhassira, Eric E.; Fiering, Steven; Lowrey, Christopher H.

    2013-01-01

    Objective DNA methylation has long been implicated in developmental β-globin gene regulation. However, the mechanism underlying this regulation is unclear, especially since these genes do not contain CpG islands. This has led us to propose and test the hypothesis that, just as for histone modifications, developmentally-specific changes in human β-like globin gene expression are associated with long-range changes in DNA methylation. Methods Bisulfite sequencing was used to determine the methylation state of individual CpG dinucleotides across the β-globin locus in uncultured primary human erythroblasts from fetal liver and bone marrow, and in primitive-like erythroid cells derived from human embryonic stem cells. Results β-globin locus CpGs are generally highly methylated but domains of DNA hypomethylation spanning thousands of base pairs are established around the most highly expressed genes during each developmental stage. These large domains of DNA hypomethylation are found within domains of histone modifications associated with gene expression. We also find hypomethylation of a small proportion of γ-globin promoters in adult erythroid cells, suggesting a mechanism by which adult erythroid cells produce fetal hemoglobin. Conclusion This is one of the first reports to show that changes in DNA methylation patterns across large domains around non-CpG island genes correspond with changes in developmentally-regulated histone modifications and gene expression. This data supports a new model in which extended domains of DNA hypomethylation and active histone marks are coordinately established to achieve developmentally-specific gene expression of non-CpG island genes. PMID:19460471

  1. Mechanistic studies on the intramolecular one-electron transfer between the two flavins in the human endothelial NOS reductase domain.

    Science.gov (United States)

    Nishino, Yoshitaka; Yamamoto, Keita; Kimura, Shigenobu; Kikuchi, Akihiro; Shiro, Yoshitsugu; Iyanagi, Takashi

    2007-09-01

    The object of this study was to clarify the mechanism of electron transfer in the human endothelial nitric oxide synthase (eNOS) reductase domain using recombinant eNOS reductase domains; the FAD/NADPH domain containing FAD- and NADPH-binding sites and the FAD/FMN domain containing FAD/NADPH-, FMN-, and a calmodulin-binding sites. In the presence of molecular oxygen or menadione, the reduced FAD/NADPH domain is oxidized via the neutral (blue) semiquinone (FADH(*)), which has a characteristic absorption peak at 520 nm. The FAD/NADPH and FAD/FMN domains have high activity for ferricyanide, but the FAD/FMN domain has low activity for cytochrome c. In the presence or absence of calcium/calmodulin (Ca(2+)/CaM), reduction of the oxidized flavins (FAD-FMN) and air-stable semiquinone (FAD-FMNH(*)) with NADPH occurred in at least two phases in the absorbance change at 457nm. In the presence of Ca(2+)/CaM, the reduction rate of both phases was significantly increased. In contrast, an absorbance change at 596nm gradually increased in two phases, but the rate of the fast phase was decreased by approximately 50% of that in the presence of Ca(2+)/CaM. The air-stable semiquinone form was rapidly reduced by NADPH, but a significant absorbance change at 520 nm was not observed. These findings indicate that the conversion of FADH(2)-FMNH(*) to FADH(*)-FMNH(2) is unfavorable. Reduction of the FAD moiety is activated by CaM, but the formation rate of the active intermediate, FADH(*)-FMNH(2) is extremely low. These events could cause a lowering of enzyme activity in the catalytic cycle.

  2. The 10 kDa domain of human erythrocyte protein 4.1 binds the Plasmodium falciparum EBA-181 protein

    Directory of Open Access Journals (Sweden)

    Coetzer Theresa L

    2006-11-01

    Full Text Available Abstract Background Erythrocyte invasion by Plasmodium falciparum parasites represents a key mechanism during malaria pathogenesis. Erythrocyte binding antigen-181 (EBA-181 is an important invasion protein, which mediates a unique host cell entry pathway. A novel interaction between EBA-181 and human erythrocyte membrane protein 4.1 (4.1R was recently demonstrated using phage display technology. In the current study, recombinant proteins were utilized to define and characterize the precise molecular interaction between the two proteins. Methods 4.1R structural domains (30, 16, 10 and 22 kDa domain and the 4.1R binding region in EBA-181 were synthesized in specific Escherichia coli strains as recombinant proteins and purified using magnetic bead technology. Recombinant proteins were subsequently used in blot-overlay and histidine pull-down assays to determine the binding domain in 4.1R. Results Blot overlay and histidine pull-down experiments revealed specific interaction between the 10 kDa domain of 4.1R and EBA-181. Binding was concentration dependent as well as saturable and was abolished by heat denaturation of 4.1R. Conclusion The interaction of EBA-181 with the highly conserved 10 kDa domain of 4.1R provides new insight into the molecular mechanisms utilized by P. falciparum during erythrocyte entry. The results highlight the potential multifunctional role of malaria invasion proteins, which may contribute to the success of the pathogenic stage of the parasite's life cycle.

  3. Expert networks in CLIPS

    Science.gov (United States)

    Hruska, S. I.; Dalke, A.; Ferguson, J. J.; Lacher, R. C.

    1991-01-01

    Rule-based expert systems may be structurally and functionally mapped onto a special class of neural networks called expert networks. This mapping lends itself to adaptation of connectionist learning strategies for the expert networks. A parsing algorithm to translate C Language Integrated Production System (CLIPS) rules into a network of interconnected assertion and operation nodes has been developed. The translation of CLIPS rules to an expert network and back again is illustrated. Measures of uncertainty similar to those rules in MYCIN-like systems are introduced into the CLIPS system and techniques for combining and hiring nodes in the network based on rule-firing with these certainty factors in the expert system are presented. Several learning algorithms are under study which automate the process of attaching certainty factors to rules.

  4. Mercury-induced crystallization and SAD phasing of the human Fe65-PTB1 domain

    OpenAIRE

    Radzimanowski, Jens; Ravaud, Stéphanie; Beyreuther, Konrad; Sinning, Irmgard; Wild, Klemens

    2008-01-01

    Crystals of the phosphotyrosine-binding domain 1 (PTB1) of the neuronal adaptor protein Fe65 grown in the presence of a mercury derivative show a dramatic improvement in resolution, permitting SAD phasing.

  5. Tandem SAM Domain Structure of Human Caskin1: A Presynaptic, Self-Assembling Scaffold for CASK

    Energy Technology Data Exchange (ETDEWEB)

    Stafford, Ryan L.; Hinde, Elizabeth; Knight, Mary Jane; Pennella, Mario A.; Ear, Jason; Digman, Michelle A.; Gratton, Enrico; Bowie, James U. (UCI); (UCLA)

    2012-02-07

    The synaptic scaffolding proteins CASK and Caskin1 are part of the fibrous mesh of proteins that organize the active zones of neural synapses. CASK binds to a region of Caskin1 called the CASK interaction domain (CID). Adjacent to the CID, Caskin1 contains two tandem sterile a motif (SAM) domains. Many SAM domains form polymers so they are good candidates for forming the fibrous structures seen in the active zone. We show here that the SAM domains of Caskin1 form a new type of SAM helical polymer. The Caskin1 polymer interface exhibits a remarkable segregation of charged residues, resulting in a high sensitivity to ionic strength in vitro. The Caskin1 polymers can be decorated with CASK proteins, illustrating how these proteins may work together to organize the cytomatrix in active zones.

  6. Expert Systems--The New International Language of Business.

    Science.gov (United States)

    Sondak, Norman E.; And Others

    A discussion of expert systems, computer programs designed to simulate human reasoning and expertise, begins with the assumption that few business educators understand the impact that expert systems will have on international business. The fundamental principles of the design and development of expert systems in business are outlined, with special…

  7. VAM-1: a new member of the MAGUK family binds to human Veli-1 through a conserved domain.

    Science.gov (United States)

    Tseng, T C; Marfatia, S M; Bryant, P J; Pack, S; Zhuang, Z; O'Brien, J E; Lin, L; Hanada, T; Chishti, A H

    2001-04-16

    The MAGUKs (membrane-associated guanylate kinase homologues) constitute a family of peripheral membrane proteins that function in tumor suppression and receptor clustering by forming multiprotein complexes containing distinct sets of transmembrane, cytoskeletal, and cytoplasmic signaling proteins. Here, we report the characterization of the human vam-1 gene that encodes a novel member of the p55 subfamily of MAGUKs. The complete cDNA sequence of VAM-1, tissue distribution of its mRNA, genomic structure, chromosomal localization, and Veli-1 binding properties are presented. The vam-1 gene is composed of 12 exons and spans approx. 115 kb. By fluorescence in situ hybridization the vam-1 gene was localized to 7p15-21, a chromosome region frequently disrupted in some human cancers. VAM-1 mRNA was abundant in human testis, brain, and kidney with lower levels detectable in other tissues. The primary structure of VAM-1, predicted from cDNA sequencing, consists of 540 amino acids including a single PDZ domain near the N-terminus, a central SH3 domain, and a C-terminal GUK (guanylate kinase-like) domain. Sequence alignment, heterologous transfection, GST pull-down experiments, and blot overlay assays revealed a conserved domain in VAM-1 that binds to Veli-1, the human homologue of the LIN-7 adaptor protein in Caenorhabditis. LIN-7 is known to play an essential role in the basolateral localization of the LET-23 tyrosine kinase receptor, by linking the receptor to LIN-2 and LIN-10 proteins. Our results therefore suggest that VAM-1 may function by promoting the assembly of a Veli-1 containing protein complex in neuronal as well as epithelial cells.

  8. In silico molecular docking analysis of the human Argonaute 2 PAZ domain reveals insights into RNA interference

    Science.gov (United States)

    Kandeel, Mahmoud; Kitade, Yukio

    2013-07-01

    RNA interference (RNAi) is a critical cellular pathway activated by double stranded RNA and regulates the gene expression of target mRNA. During RNAi, the 3' end of siRNA binds with the PAZ domain, followed by release and rebinding in a cyclic manner, which deemed essential for proper gene silencing. Recently, we provided the forces underlying the recognition of small interfering RNA by PAZ in a computational study based on the structure of Drosophila Argonaute 2 (Ago2) PAZ domain. We have now reanalyzed these data within the view of the new available structures from human Argonauts. While the parameters of weak binding are correlated with higher (RNAi) in the Drosophila model, a different profile is predicted with the human Ago2 PAZ domain. On the basis of the human Ago2 PAZ models, the indicators of stronger binding as the total binding energy and the free energy were associated with better RNAi efficacy. This discrepancy might be attributable to differences in the binding site topology and the difference in the conformation of the bound nucleotides.

  9. Expert F# 20

    CERN Document Server

    Syme, Don; Cisternino, Antonio

    2009-01-01

    Expert F# 2.0 is about practical programming in a beautiful language that puts the power and elegance of functional programming into the hands of professional developers. In combination with .NET, F# achieves unrivaled levels of programmer productivity and program clarity. Expert F# 2.0 is * The authoritative guide to F# by the inventor of F# * A comprehensive reference of F# concepts, syntax, and features * A treasury of expert F# techniques for practical, real-world programming F# isn't just another functional programming language. It's a general-purpose language ideal for real-world develop

  10. Benchmarking expert system tools

    Science.gov (United States)

    Riley, Gary

    1988-01-01

    As part of its evaluation of new technologies, the Artificial Intelligence Section of the Mission Planning and Analysis Div. at NASA-Johnson has made timing tests of several expert system building tools. Among the production systems tested were Automated Reasoning Tool, several versions of OPS5, and CLIPS (C Language Integrated Production System), an expert system builder developed by the AI section. Also included in the test were a Zetalisp version of the benchmark along with four versions of the benchmark written in Knowledge Engineering Environment, an object oriented, frame based expert system tool. The benchmarks used for testing are studied.

  11. Transmembrane domain V plays a stabilizing role in the function of human bile acid transporter SLC10A2.

    Science.gov (United States)

    Moore, Robyn H; Chothe, Paresh; Swaan, Peter W

    2013-07-30

    The human apical sodium-dependent bile acid transporter (hASBT, SLC10A2), primarily expressed in the ileum, is involved in both the recycling of bile acids and cholesterol homeostasis. In this study, the structure-function relationship of transmembrane domain 5 (TM5) residues involved in transport is elucidated. Cysteine scanning mutagenesis of each consecutive residue on TM5 resulted in 96% of mutants having a significantly decreased transport activity, although each was expressed at the cell surface. Specifically, G197 and I208 were no longer functional, and G201 and G212 functioned at a level of Conservative alanine mutations of the four residues displayed a higher activity in all but G197A, indicating its functional importance. G197 and G201 form a GxxxG motif, which has been found to be important in helix-helix interactions. According to our model, G197 and G201 face transmembrane domain 4 (TM4) residues G179 and P175, respectively. Similarly, G212 faces G237, which forms part of a GxxxG domain in transmembrane domain 6 (TM6). It is possible that these GxxxG domains and their interacting partners are responsible for maintaining the structure of the helices and their interactions with one another. I205 and I208 are both in positions to anchor the GxxxG domains and direct the change in interaction of TM5 from TM4 to TM6. Combined, the results suggest that residues along TM5 are critical for ASBT function but are not directly involved in substrate translocation.

  12. Feasibility of physician-developed expert systems.

    Science.gov (United States)

    Tuhrim, S; Reggia, J A

    1986-01-01

    The authors developed an experimental domain-independent "expert system generator" intended for direct use by physicians. They then undertook a four-year study to determine whether physicians could use such a system effectively. During this period they taught the use of the expert system generator to 70 medical students, who utilized it to build two small medical expert systems. At the conclusion of the course, students were examined on decision-making concepts and completed anonymous questionnaires. Performance scores, a composite of test and project grades, were calculated for each student. There was no significant association between previous computer experience and performance score. Thirty-two of 47 students responding felt the expert system generator was easy to use; 15 felt it was of moderate difficulty. Forty-three of 47 thought it a useful teaching aid. These data support the conclusion that physicians can learn to use domain-independent software to implement medical expert systems directly, without a knowledge engineer as an intermediary.

  13. Purification, crystallization and preliminary crystallographic characterization of the caspase-recruitment domain of human Nod1

    Energy Technology Data Exchange (ETDEWEB)

    Srimathi, Thiagarajan; Robbins, Sheila L.; Dubas, Rachel L. [Basic Science, Fox Chase Cancer Center, Philadelphia, PA 19111 (United States); Seo, Jang-Hoon [Department of Clinical Laboratory Science, Shinheung College, Uijeongbu, Kyungki-Do 480-701 (Korea, Republic of); Park, Young Chul, E-mail: young.park@fccc.edu [Basic Science, Fox Chase Cancer Center, Philadelphia, PA 19111 (United States)

    2007-01-01

    The caspase-recruitment domain of the cytosolic pathogen receptor Nod1 was crystallized. X-ray diffraction data were collected to 1.9 Å resolution. The caspase-recruitment domain (CARD) is known to play an important role in apoptosis and inflammation as an essential protein–protein interaction domain. The CARD of the cytosolic pathogen receptor Nod1 was overexpressed in Escherichia coli and purified by affinity chromatography and gel filtration. The purified CARD was crystallized at 277 K using the microseeding method. X-ray diffraction data were collected to 1.9 Å resolution. The crystals belong to space group P3{sub 1} or P3{sub 2}, with unit-cell parameters a = b = 79.1, c = 80.9 Å. Preliminary analysis indicates that there is one dimeric CARD molecule in the asymmetric unit.

  14. Different roles of electromagnetic field experts when giving policy advice: an expert consultation.

    Science.gov (United States)

    Spruijt, Pita; Knol, Anne B; Petersen, Arthur C; Lebret, Erik

    2015-01-21

    The overall evidence for adverse health effects of electromagnetic fields (EMF) at levels of exposure normally experienced by the public is generally considered weak. However, whether long-term health effects arise remains uncertain and scientific policy advice is therefore given against a background of uncertainty. Several theories exist about different roles that experts may take when they provide advice on complex issues such as EMF. To provide empirical evidence for these theories, we conducted an expert consultation with as main research question: What are the different roles of EMF experts when they provide policy advice? Q methodology was used to empirically test theoretical notions on the existence and determinants of different expert roles and to analyze which roles actually play out in the domain of EMF. Experts were selected based on a structured nominee process. In total 32 international EMF experts participated. Responses were analyzed using Principal Component Analysis and for the open questions we used Atlas.ti. Four expert roles were found. Most striking differences between the four roles are whether experts consider current EMF policies adequate or not, whether additional -precautionary- measures are needed, and how experts view their position vis-à-vis policymakers and/or other stakeholders. This empirical study provides support for the so far mainly theoretical debate about the existence of different roles of experts when they give policy advice. The experts' assessment of the degree of uncertainty of the issue turned out to be highly associated with their role. We argue that part of the controversy that exists in the debate regarding scientific policy advice on EMF is about different values and roles.

  15. The Specification of an Expert System for Building Bylaws Compliance

    Directory of Open Access Journals (Sweden)

    Sania Bhatti

    2012-04-01

    Full Text Available An Expert System is a computer program that simulates the human intelligence and behaviour in specific and limited domains. It is used to solve problems with tricks, shortcuts and heuristics i.e. rules of thumb. Checking a Plan (Map to verify its compliance with building bylaws is a complex task mainly due to various rules and the exceptions to those rules. Humans are prone to make errors in such situations. Due to the problems faced by Building Control Department, HDA ( Hyderabad Development Authority there is a strong need to develop a computerized system. In this research we have developed a prototype named as ESBBC (Expert System for Building Bylaws Compliance for HDA that can help in their building plan checking system. The proposed solution is merging three frameworks, i.e. Java an OOP (Object Oriented Programming language, Prolog- a rule based language and MS Access- for database. The solution is fulfilling the three main requirements of the HDA, i.e. Determination of whether a particular plan is in compliance with predefined building bylaws or not. (2 Offering search facility. (3 Maintaining records of plans which are entered for compliance checking. We have checked plans of 20 properties according to HDA building regulations using ESBBC and presented their results. The results show that ESBBC has capability to identify errors made by humans.

  16. Back-and-Forth Methodology for Objective Voice Quality Assessment: From/to Expert Knowledge to/from Automatic Classification of Dysphonia

    Science.gov (United States)

    Fredouille, Corinne; Pouchoulin, Gilles; Ghio, Alain; Revis, Joana; Bonastre, Jean-François; Giovanni, Antoine

    2009-12-01

    This paper addresses voice disorder assessment. It proposes an original back-and-forth methodology involving an automatic classification system as well as knowledge of the human experts (machine learning experts, phoneticians, and pathologists). The goal of this methodology is to bring a better understanding of acoustic phenomena related to dysphonia. The automatic system was validated on a dysphonic corpus (80 female voices), rated according to the GRBAS perceptual scale by an expert jury. Firstly, focused on the frequency domain, the classification system showed the interest of 0-3000 Hz frequency band for the classification task based on the GRBAS scale. Later, an automatic phonemic analysis underlined the significance of consonants and more surprisingly of unvoiced consonants for the same classification task. Submitted to the human experts, these observations led to a manual analysis of unvoiced plosives, which highlighted a lengthening of VOT according to the dysphonia severity validated by a preliminary statistical analysis.

  17. NMR assignments of SPOC domain of the human transcriptional corepressor SHARP in complex with a C-terminal SMRT peptide.

    Science.gov (United States)

    Mikami, Suzuka; Kanaba, Teppei; Ito, Yutaka; Mishima, Masaki

    2013-10-01

    The transcriptional corepressor SMRT/HDAC1-associated repressor protein (SHARP) recruits histone deacetylases. Human SHARP protein is thought to function in processes involving steroid hormone responses and the Notch signaling pathway. SHARP consists of RNA recognition motifs (RRMs) in the N-terminal region and the spen paralog and ortholog C-terminal (SPOC) domain in the C-terminal region. It is known that the SPOC domain binds the LSD motif in the C-terminal tail of corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NcoR). We are interested in delineating the mechanism by which the SPOC domain recognizes the LSD motif of the C-terminal tail of SMRT/NcoR. To this end, we are investigating the tertiary structure of the SPOC/SMRT peptide using NMR. Herein, we report on the (1)H, (13)C and (15)N resonance assignments of the SPOC domain in complex with a SMRT peptide, which contributes towards a structural understanding of the SPOC/SMRT peptide and its molecular recognition.

  18. Plasmodium falciparum CS protein - prime malaria vaccine candidate: definition of the human CTL domain and analysis of its variation

    Directory of Open Access Journals (Sweden)

    Denise L. Doolan

    1992-01-01

    Full Text Available Studies in mice have shown that immunity to malaria sporozoites is mediated primarily by citotoxic T lymphocytes (CTL specific for epitopes within the circumsporozoite (CS protein. Humans, had never been shown to generate CTL against any malaria or other parasite protein. The design of a sub-unit vaccine for humans ralies on the epitopes recognized by CTL being identified and polymorphisms therein being defined. We have developed a novel technique using an entire series of overlapping synthetic peptides to define the epitopes of the Plasmodium falciparum CS protein recognized by human CTL and have analyzed the sequence variation of the protein with respect to the identified CTL epitopic domain. We have demonstrated that some humans can indeed generate CTL. against the P. falciparum CS protein. Furthermore, the extent of variation observed for the CTL recognition domain is finite and the combination of peptides necessary for inclusion in a polyvalent vaccine may be small. If ways can be found to increase immune responsiveness, then a vaccine designed to stimulate CS protein-specific CTL activity may prevent malaria.

  19. On modernist social sciences’ understanding of poverty and the role of poverty experts in the “conduct of conduct” of human subjects: a critique

    Directory of Open Access Journals (Sweden)

    Diamantino Machado

    2008-03-01

    Full Text Available The purpose of my paper is to show that modernist social sciences have been directly involved in the construction and reproduction of poverty, and in the "conduct of conduct" of the scientifically labeled poor or the produced and reproduced "object" of poverty experts.

  20. The BRCT domain from the large subunit of human Replication Factor C

    NARCIS (Netherlands)

    Kobayashi, Masakazu

    2006-01-01

    The work described in this thesis deals with characterization of DNA binding by the BRCT domain of the large subunit of RFC. Replication Factor C (RFC) is a five protein complex involved in initiating and regulating new DNA synthesis. The first half of the thesis describes region of the RFC and stru

  1. A sub-domain based regularization method with prior information for human thorax imaging using electrical impedance tomography

    Science.gov (United States)

    In Kang, Suk; Khambampati, Anil Kumar; Jeon, Min Ho; Kim, Bong Seok; Kim, Kyung Youn

    2016-02-01

    Electrical impedance tomography (EIT) is a non-invasive imaging technique that can be used as a bed-side monitoring tool for human thorax imaging. EIT has high temporal resolution characteristics but at the same time it suffers from poor spatial resolution due to ill-posedness of the inverse problem. Often regularization methods are used as a penalty term in the cost function to stabilize the sudden changes in resistivity. In human thorax monitoring, with conventional regularization methods employing Tikhonov type regularization, the reconstructed image is smoothed between the heart and the lungs, that is, it makes it difficult to distinguish the exact boundaries of the lungs and the heart. Sometimes, obtaining structural information of the object prior to this can be incorporated into the regularization method to improve the spatial resolution along with helping create clear and distinct boundaries between the objects. However, the boundary of the heart is changed rapidly due to the cardiac cycle hence there is no information concerning the exact boundary of the heart. Therefore, to improve the spatial resolution for human thorax monitoring during the cardiac cycle, in this paper, a sub-domain based regularization method is proposed assuming the lungs and part of background region is known. In the proposed method, the regularization matrix is modified anisotropically to include sub-domains as prior information, and the regularization parameter is assigned with different weights to each sub-domain. Numerical simulations and phantom experiments for 2D human thorax monitoring are performed to evaluate the performance of the proposed regularization method. The results show a better reconstruction performance with the proposed regularization method.

  2. Cysteine endoprotease activity of human ribosomal protein S4 is entirely due to the C-terminal domain, and is consistent with Michaelis-Menten mechanism.

    Science.gov (United States)

    Sudhamalla, Babu; Kumar, Mahesh; Roy, Karnati R; Kumar, R Sunil; Bhuyan, Abani K

    2013-11-01

    It is known that tandem domains of enzymes can carry out catalysis independently or by collaboration. In the case of cysteine proteases, domain sequestration abolishes catalysis because the active site residues are distributed in both domains. The validity of this argument is tested here by using isolated human ribosomal protein S4, which has been recently identified as an unorthodox cysteine protease. Cleavage of the peptide substrate Z-FR↓-AMC catalyzed by recombinant C-terminal domain of human S4 (CHS4) is studied by fluorescence-monitored steady-state and stopped-flow kinetic methods. Proteolysis and autoproteolysis were analyzed by electrophoresis. The CHS4 domain comprised of sequence residues 116-263 has been cloned and ovreexpressed in Escherichia coli. The purified domain is enzymatically active. Barring minor differences, steady-state kinetic parameters for catalysis by CHS4 are very similar to those for full-length human S4. Further, stopped-flow transient kinetics of pre-steady-state substrate binding shows that the catalytic mechanism for both full-length S4 and CHS4 obeys the Michaelis-Menten model adequately. Consideration of the evolutionary domain organization of the S4e family of ribosomal proteins indicates that the central domain (residues 94-170) within CHS4 is indispensable. The C-terminal domain can carry out catalysis independently and as efficiently as the full-length human S4 does. Localization of the enzyme function in the C-terminal domain of human S4 provides the only example of a cysteine endoprotease where substrate-mediated intramolecular domain interaction is irrelevant for catalytic activity. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Regions within the N-terminal domain of human topoisomerase I exert important functions during strand rotation and DNA binding

    DEFF Research Database (Denmark)

    Hougaard, Rikke Frølich; Andersen, Félicie Faucon; Westergaard, Ole

    2004-01-01

    The human topoisomerase I N-terminal domain is the only part of the enzyme still not crystallized and the function of this domain remains enigmatical. In the present study, we have addressed the specific functions of individual N-terminal regions of topoisomerase I by characterizing mutants lacking...... amino acid residues 1–202 or 191–206 or having tryptophane-205 substituted by glycine in a broad variety of in vitro activity assays. As a result of these investigations we find that mutants altered in the region 191–206 distinguished themselves from the wild-type enzyme by a faster strand rotation step...... support a model according to which tryptophane-205 and possibly other residues located between position 191–206 coordinates the restriction of free strand rotation during the topoisomerization step of catalysis. Moreover, tryptophane-205 appears important for the function of the bulk part of the N...

  4. Common exonic missense variants in the C2 domain of the human KIBRA protein modify lipid binding and cognitive performance.

    Science.gov (United States)

    Duning, K; Wennmann, D O; Bokemeyer, A; Reissner, C; Wersching, H; Thomas, C; Buschert, J; Guske, K; Franzke, V; Flöel, A; Lohmann, H; Knecht, S; Brand, S-M; Pöter, M; Rescher, U; Missler, M; Seelheim, P; Pröpper, C; Boeckers, T M; Makuch, L; Huganir, R; Weide, T; Brand, E; Pavenstädt, H; Kremerskothen, J

    2013-06-18

    The human KIBRA gene has been linked to human cognition through a lead intronic single-nucleotide polymorphism (SNP; rs17070145) that is associated with episodic memory performance and the risk to develop Alzheimer's disease. However, it remains unknown how this relates to the function of the KIBRA protein. Here, we identified two common missense SNPs (rs3822660G/T [M734I], rs3822659T/G [S735A]) in exon 15 of the human KIBRA gene to affect cognitive performance, and to be in almost complete linkage disequilibrium with rs17070145. The identified SNPs encode variants of the KIBRA C2 domain with distinct Ca(2+) dependent binding preferences for monophosphorylated phosphatidylinositols likely due to differences in the dynamics and folding of the lipid-binding pocket. Our results further implicate the KIBRA protein in higher brain function and provide direction to the cellular pathways involved.

  5. Common exonic missense variants in the C2 domain of the human KIBRA protein modify lipid binding and cognitive performance

    Science.gov (United States)

    Duning, K; Wennmann, D O; Bokemeyer, A; Reissner, C; Wersching, H; Thomas, C; Buschert, J; Guske, K; Franzke, V; Flöel, A; Lohmann, H; Knecht, S; Brand, S-M; Pöter, M; Rescher, U; Missler, M; Seelheim, P; Pröpper, C; Boeckers, T M; Makuch, L; Huganir, R; Weide, T; Brand, E; Pavenstädt, H; Kremerskothen, J

    2013-01-01

    The human KIBRA gene has been linked to human cognition through a lead intronic single-nucleotide polymorphism (SNP; rs17070145) that is associated with episodic memory performance and the risk to develop Alzheimer's disease. However, it remains unknown how this relates to the function of the KIBRA protein. Here, we identified two common missense SNPs (rs3822660G/T [M734I], rs3822659T/G [S735A]) in exon 15 of the human KIBRA gene to affect cognitive performance, and to be in almost complete linkage disequilibrium with rs17070145. The identified SNPs encode variants of the KIBRA C2 domain with distinct Ca2+ dependent binding preferences for monophosphorylated phosphatidylinositols likely due to differences in the dynamics and folding of the lipid-binding pocket. Our results further implicate the KIBRA protein in higher brain function and provide direction to the cellular pathways involved. PMID:23778582

  6. Horse-Expert: An aided expert system for diagnosing horse diseases.

    Science.gov (United States)

    Qin, H; Xiao, J; Gao, X; Wang, H

    2016-12-01

    In contrast to the rapid development of the horse husbandry in China, the ability of horse veterinarians to diagnose diseases has not been improved and only a few domain experts have considerable expertise. At present, many expert systems have been developed for diseases diagnosis, but few for horse diseases diagnosis have been studied in depth. This paper presents the design and development of a computer-aided expert system for diagnosing horse diseases. We suggest an approach for diagnosis of horse diseases based on the analysis of diagnostic characteristics and the experiential knowledge of domain experts. It is based on using evidence-weighted uncertainty reasoning theory, which is a combination of evidence theory and an uncertainty pass algorithm of confidence factors. It enables drawing of inferences with atypical clinical signs and the uncertainty of the user's subjective understanding. It reduces the influence of subjective factors on diagnostic accuracy. The system utilizes a user friendly interface for users and requests a confidence factor from users when feedback is given to the system. Horse-Expert combines the confidence factors with weight factors assigned to clinical signs by experts during the knowledge acquisition process to make diagnostic conclusions. The system can diagnose 91 common horse diseases, and provides suggestions for appropriate treatment options. In addition, users can check the medical record through statistical charts. The system has been tested in seven demonstration areas of Xinjiang province in northwestern China. By constantly maintaining and updating the knowledge base, the system has potential application in veterinary practice.

  7. Knowledge Representation Using Multilevel Flow Model in Expert System

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Wenlin; Yang, Ming [Harbin Engineering University, Harbin (China)

    2015-05-15

    As for the knowledge representation, of course, there are a great many methods available for knowledge representation. These include frames, causal models, and many others. This paper presents a novel method called Multilevel Flow Model (MFM), which is used for knowledge representation in G2 expert system. Knowledge representation plays a vital role in constructing knowledge bases. Moreover, it also has impact on building of generic fault model as well as knowledge bases. The MFM is particularly useful to describe system knowledge concisely as domain map in expert system when domain experts are not available.

  8. Isolation and characterization of an IgNAR variable domain specific for the human mitochondrial translocase receptor Tom70.

    Science.gov (United States)

    Nuttall, Stewart D; Krishnan, Usha V; Doughty, Larissa; Pearson, Kylie; Ryan, Michael T; Hoogenraad, Nicholas J; Hattarki, Meghan; Carmichael, Jennifer A; Irving, Robert A; Hudson, Peter J

    2003-09-01

    The new antigen receptor (IgNAR) from sharks is a disulphide bonded dimer of two protein chains, each containing one variable and five constant domains, and functions as an antibody. In order to assess the antigen-binding capabilities of isolated IgNAR variable domains (VNAR), we have constructed an in vitro library incorporating synthetic CDR3 regions of 15-18 residues in length. Screening of this library against the 60 kDa cytosolic domain of the 70 kDa outer membrane translocase receptor from human mitochondria (Tom70) resulted in one dominant antigen-specific clone (VNAR 12F-11) after four rounds of in vitro selection. VNAR 12F-11 was expressed into the Escherichia coli periplasm and purified by anti-FLAG affinity chromatography at yields of 3 mg x L(-1). Purified protein eluted from gel filtration columns as a single monomeric protein and CD spectrum analysis indicated correct folding into the expected beta-sheet conformation. Specific binding to Tom70 was demonstrated by ELISA and BIAcore (Kd = 2.2 +/- 0.31 x 10(-9) m-1) indicating that these VNAR domains can be efficiently displayed as bacteriophage libraries, and selected against target antigens with an affinity and stability equivalent to that obtained for other single domain antibodies. As an initial step in producing 'intrabody' variants of 12F-11, the impact of modifying or removing the conserved immunoglobulin intradomain disulphide bond was assessed. High affinity binding was only retained in the wild-type protein, which combined with our inability to affinity mature 12F-11, suggests that this particular VNAR is critically dependent upon precise CDR loop conformations for its binding affinity.

  9. Cysteine-rich protein 61 (CCN1) domain-specific stimulation of matrix metalloproteinase-1 expression through αVβ3 integrin in human skin fibroblasts.

    Science.gov (United States)

    Qin, Zhaoping; Fisher, Gary J; Quan, Taihao

    2013-04-26

    Human skin largely comprises collagenous extracellular matrix. The hallmark of skin aging is fragmentation of collagen fibrils. Matrix metalloproteinases (MMPs) are largely responsible for collagen degradation. MMP-1, principally derived from dermal fibroblasts, is the major protease capable of initiating degradation of native fibrillar collagens. Presently, we report that CCN1, a secreted and extracellular matrix-associated protein, is elevated in aged human skin dermal fibroblasts in vivo and stimulates MMP-1 expression through functional interaction with αVβ3 integrin in human dermal fibroblasts. CCN1 contains four conserved structural domains. Our results indicate that the three N-terminal domains (IGFBP, VWC, and TSP1), but not the C-terminal CT domain, are required for CCN1 to stimulate MMP-1 expression. This stimulation is dependent on interaction between the active structural domains and αVβ3 integrin. The interaction of VWC domain with integrin αVβ3 is necessary and requires functional cooperation with adjacent IGFBP and TSP1 domains to stimulate MMP-1 expression. Finally, induction of MMP-1 expression in dermal fibroblasts by CCN1 N-terminal domains resulted in fragmentation of type I collagen fibrils in a three-dimensional collagen lattice model. These data suggest that domain-specific interactions of CCN1 with αVβ3 integrin contribute to human skin aging by stimulating MMP-1-mediated collagen fibril fragmentation.

  10. Andes virus recognition of human and Syrian hamster beta3 integrins is determined by an L33P substitution in the PSI domain.

    Science.gov (United States)

    Matthys, Valery S; Gorbunova, Elena E; Gavrilovskaya, Irina N; Mackow, Erich R

    2010-01-01

    Andes virus (ANDV) causes a fatal hantavirus pulmonary syndrome (HPS) in humans and Syrian hamsters. Human alpha(v)beta(3) integrins are receptors for several pathogenic hantaviruses, and the function of alpha(v)beta(3) integrins on endothelial cells suggests a role for alpha(v)beta(3) in hantavirus directed vascular permeability. We determined here that ANDV infection of human endothelial cells or Syrian hamster-derived BHK-21 cells was selectively inhibited by the high-affinity alpha(v)beta(3) integrin ligand vitronectin and by antibodies to alpha(v)beta(3) integrins. Further, antibodies to the beta(3) integrin PSI domain, as well as PSI domain polypeptides derived from human and Syrian hamster beta(3) subunits, but not murine or bovine beta(3), inhibited ANDV infection of both BHK-21 and human endothelial cells. These findings suggest that ANDV interacts with beta(3) subunits through PSI domain residues conserved in both Syrian hamster and human beta(3) integrins. Sequencing the Syrian hamster beta(3) integrin PSI domain revealed eight differences between Syrian hamster and human beta(3) integrins. Analysis of residues within the PSI domains of human, Syrian hamster, murine, and bovine beta(3) integrins identified unique proline substitutions at residues 32 and 33 of murine and bovine PSI domains that could determine ANDV recognition. Mutagenizing the human beta(3) PSI domain to contain the L33P substitution present in bovine beta(3) integrin abolished the ability of the PSI domain to inhibit ANDV infectivity. Conversely, mutagenizing either the bovine PSI domain, P33L, or the murine PSI domain, S32P, to the residue present human beta(3) permitted PSI mutants to inhibit ANDV infection. Similarly, CHO cells transfected with the full-length bovine beta(3) integrin containing the P33L mutation permitted infection by ANDV. These findings indicate that human and Syrian hamster alpha(v)beta(3) integrins are key receptors for ANDV and that specific residues within the

  11. Molecular cloning of a novel human I-mfa domain-containing protein that differently regulates human T-cell leukemia virus type I and HIV-1 expression.

    Science.gov (United States)

    Thébault, S; Gachon, F; Lemasson, I; Devaux, C; Mesnard, J M

    2000-02-18

    Regulation of viral genome expression is the result of complex cooperation between viral proteins and host cell factors. We report here the characterization of a novel cellular factor sharing homology with the specific cysteine-rich C-terminal domain of the basic helix-loop-helix repressor protein I-mfa. The synthesis of this new factor, called HIC for Human I-mfa domain-Containing protein, is controlled at the translational level by two different codons, an ATG and an upstream non-ATG translational initiator, allowing the production of two protein isoforms, p32 and p40, respectively. We show that the HIC protein isoforms present different subcellular localizations, p32 being mainly distributed throughout the cytoplasm, whereas p40 is targeted to the nucleolus. Moreover, in trying to understand the function of HIC, we have found that both isoforms stimulate in T-cells the expression of a luciferase reporter gene driven by the human T-cell leukemia virus type I-long terminal repeat in the presence of the viral transactivator Tax. We demonstrate by mutagenesis that the I-mfa-like domain of HIC is involved in this regulation. Finally, we also show that HIC is able to down-regulate the luciferase expression from the human immunodeficiency virus type 1-long terminal repeat induced by the viral transactivator Tat. From these results, we propose that HIC and I-mfa represent two members of a new family of proteins regulating gene expression and characterized by a particular cysteine-rich C-terminal domain.

  12. Molecular level interaction of inositol hexaphosphate with the C2B domain of human synaptotagmin I.

    Science.gov (United States)

    Joung, Meng-Je; Mohan, Sepuru K; Yu, Chin

    2012-05-01

    Synaptotagmin I is a synaptic vesicle membrane protein that serves as a multifunctional regulator during the exocytosis of neurotransmitter release. It contains C2A and C2B domains. The binding of Ca(2+) to the C2A domain activates the exocytosis of secretory vesicles, while the binding of inositol polyphosphates (IP4-IP6) to the C2B domain inhibits this process. To understand the IP6-induced inhibition of exocytosis of secretory vesicles, we determined the three-dimensional structure of the C2B-IP6 complex by nuclear magnetic resonance (NMR). In this study, we have determined the binding constant by isothermal titration calorimetry. The circular dichroism measurements demonstrated that IP6 can stabilize the C2B molecule. We identified the binding site using (1)H-(15)N heteronuclear single-quantum coherence spectroscopy titration data and determined the structure of the C2B-IP6 complex using multidimensional NMR studies. This information will aid in the design of better pharmacological treatments for neurological disorders.

  13. Expert Opinions on Improving Femicide Data Collection across Europe: A Concept Mapping Study.

    Directory of Open Access Journals (Sweden)

    Carmen Vives-Cases

    Full Text Available Femicide, defined as the killings of females by males because they are females, is becoming recognized worldwide as an important ongoing manifestation of gender inequality. Despite its high prevalence or widespread prevalence, only a few countries have specific registries about this issue. This study aims to assemble expert opinion regarding the strategies which might feasibly be employed to promote, develop and implement an integrated and differentiated femicide data collection system in Europe at both the national and international levels. Concept mapping methodology was followed, involving 28 experts from 16 countries in generating strategies, sorting and rating them with respect to relevance and feasibility. The experts involved were all members of the EU-Cost-Action on femicide, which is a scientific network of experts on femicide and violence against women across Europe. As a result, a conceptual map emerged, consisting of 69 strategies organized in 10 clusters, which fit into two domains: "Political action" and "Technical steps". There was consensus among participants regarding the high relevance of strategies to institutionalize national databases and raise public awareness through different stakeholders, while strategies to promote media involvement were identified as the most feasible. Differences in perceived priorities according to the level of human development index of the experts' countries were also observed.

  14. CSIR at TREC 2008 Expert Search Task: Modeling Expert Evidence in Expert Search

    Science.gov (United States)

    2008-11-01

    CSIR at TREC 2008 Expert Search Task: Modeling Expert Evidence in Expert Search Jiepu Jiang1, Wei Lu1, Haozhen Zhao2 1 Center for Studies of...AND SUBTITLE CSIR at TREC 2008 Expert Search Task: Modeling Expert Evidence in Expert Search 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...15. J. Jiang, W. Lu, D. Liu. CSIR at TREC 2007. In Proceedings of the 16th Text REtrieval Conference (TREC 2007), 2007. 16. J. Jiang, W. Lu. IR

  15. Production of Slit2 LRR domains in mammalian cells for structural studies and the structure of human Slit2 domain 3

    NARCIS (Netherlands)

    Morlot, C.; Hemrika, W.; Romijn, R.A.; Gros, P.; Cusack, S.; McCarthy, A.A.

    2007-01-01

    Slit2 and Roundabout 1 (Robo1) provide a key ligand-receptor interaction for the navigation of commissural neurons during the development of the central nervous system. Slit2 is a large multidomain protein containing an unusual domain organization of four tandem leucine-rich repeat (LRR) domains at

  16. The 1.7 A X-ray crystal structure of the porcine factor VIII C2 domain and binding analysis to anti-human C2 domain antibodies and phospholipid surfaces.

    Directory of Open Access Journals (Sweden)

    Caileen M Brison

    Full Text Available The factor VIII C2 domain is essential for binding to activated platelet surfaces as well as the cofactor activity of factor VIII in blood coagulation. Inhibitory antibodies against the C2 domain commonly develop following factor VIII replacement therapy for hemophilia A patients, or they may spontaneously arise in cases of acquired hemophilia. Porcine factor VIII is an effective therapeutic for hemophilia patients with inhibitor due to its low cross-reactivity; however, the molecular basis for this behavior is poorly understood. In this study, the X-ray crystal structure of the porcine factor VIII C2 domain was determined, and superposition of the human and porcine C2 domains demonstrates that most surface-exposed differences cluster on the face harboring the "non-classical" antibody epitopes. Furthermore, antibody-binding results illustrate that the "classical" 3E6 antibody can bind both the human and porcine C2 domains, although the inhibitory titer to human factor VIII is 41 Bethesda Units (BU/mg IgG versus 0.8 BU/mg IgG to porcine factor VIII, while the non-classical G99 antibody does not bind to the porcine C2 domain nor inhibit porcine factor VIII activity. Further structural analysis of differences between the electrostatic surface potentials suggest that the C2 domain binds to the negatively charged phospholipid surfaces of activated platelets primarily through the 3E6 epitope region. In contrast, the G99 face, which contains residue 2227, should be distal to the membrane surface. Phospholipid binding assays indicate that both porcine and human factor VIII C2 domains bind with comparable affinities, and the human K2227A and K2227E mutants bind to phospholipid surfaces with similar affinities as well. Lastly, the G99 IgG bound to PS-immobilized factor VIII C2 domain with an apparent dissociation constant of 15.5 nM, whereas 3E6 antibody binding to PS-bound C2 domain was not observed.

  17. The epidermal growth factor-like domain of the human cartilage large aggregating proteoglycan, aggrecan: increased serum concentration in rheumatoid arthritis

    DEFF Research Database (Denmark)

    Møller, H J; Ingemann-Hansen, T; Poulsen, J H

    1994-01-01

    The large aggregating proteoglycan from human cartilage, aggrecan, has recently been shown to possess an immunologically detectable domain with close homology to epidermal growth factor (EGF), that is variably expressed by alternative mRNA splicing. Using a competitive ELISA we detected this domain...... in sera from both patients with RA and normal controls. The EGF-like domain could only be detected after digestion of sera with chondroitinase ABC, which demonstrates its proteoglycan origin. The concentration of the aggrecan EGF-like domain was considerably elevated in sera from patients with RA...

  18. Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4

    Institute of Scientific and Technical Information of China (English)

    Nianshuang Wang; Xuanling Shi; Liwei Jiang; Senyan Zhang; Dongli Wang; Pei Tong; Dongxing Guo

    2013-01-01

    The spike glycoprotein (S) of recently identified Middle East respiratory syndrome coronavirus (MERS-CoV) targets the cellular receptor,dipeptidyl peptidase 4 (DPP4).Sequence comparison and modeling analysis have revealed a putative receptor-binding domain (RBD) on the viral spike,which mediates this interaction.We report the 3.0 (A)resolution crystal structure of MERS-CoV RBD bound to the extracellular domain of human DPP4.Our results show that MERS-CoV RBD consists of a core and a receptor-binding subdomain.The receptor-binding subdomain interacts with DPP4 p-propeller but not its intrinsic hydrolase domain.MERS-CoV RBD and related SARS-CoV RBD share a high degree of structural similarity in their core subdomains,but are notably divergent in the receptorbinding subdomain.Mutagenesis studies have identified several key residues in the receptor-binding subdomain that are critical for viral binding to DPP4 and entry into the target cell.The atomic details at the interface between MERS-CoV RBD and DPP4 provide structural understanding of the virus and receptor interaction,which can guide development of therapeutics and vaccines against MERS-CoV infection.

  19. [Cloning and expression of a single human immunoglobulin heavy-chain variable domain with vascular endothelial growth factor binding activity].

    Science.gov (United States)

    Liu, Heng; Liu, Siguo; Wu, Yi; Zili, M; Liu, Yu; Zhang, Aimin; Chen, Jianquan; Cheng, Guoxiang

    2010-11-01

    In the application of therapeutic antibodies, large molecular weight of antibodies is always a problem that prevents them from penetrating into tissues or binding to antigenic determinants. To overcome this problem, we investigated the function of the heavy chain variable domain of a monoclonal anti-VEGF human IgM antibody derived from the Five-Feature Translocus Mice. We cloned the cDNA of the heavy chain variable domain, which was then inserted into pET28a vector and expressed in Escherichia coli. After purification and renaturation of the denatured recombinant protein, we obtained a 16 kDa antibody fragment, which is named as rhVVH. By immunoassaying its VEGF-binding capability in vitro, we proved that rhVVH retains this activity as the complete IgM. Importantly, rhVVH is shown to inhibit the HUVEC cell proliferation in a concentration-dependent manner. Our results indicate that the single heavy chain variable domain might inherit part of the biological function of the complete IgM antibody, which provided a valuable potential in further research on antibody miniaturisation.

  20. Expert Oracle application express

    CERN Document Server

    Scott, John Edward

    2011-01-01

    Expert Oracle Application Express brings you groundbreaking insights into developing with Oracle's enterprise-level, rapid-development tool from some of the best practitioners in the field today. Oracle Application Express (APEX) is an entirely web-based development framework that is built into every edition of Oracle Database. The framework rests upon Oracle's powerful PL/SQL language, enabling power users and developers to rapidly develop applications that easily scale to hundreds, even thousands of concurrent users. The 13 authors of Expert Oracle Application Express build their careers aro

  1. The NMR structure of the inhibited catalytic domain of human stromelysin-1.

    Science.gov (United States)

    Gooley, P R; O'Connell, J F; Marcy, A I; Cuca, G C; Salowe, S P; Bush, B L; Hermes, J D; Esser, C K; Hagmann, W K; Springer, J P

    1994-02-01

    The three-dimensional structure of the catalytic domain of stromelysin-1 complexed with an N-carboxyl alkyl inhibitor has been determined by NMR methods. The global fold consists of three helices, a five stranded beta-sheet and a methionine located in a turn near the catalytic histidines, classifying stromelysin-1 as a metzincin. Stromelysin-1 is unique in having two independent zinc binding sites: a catalytic site and a structural site. The inhibitor binds in an extended conformation. The S1' subsite is a deep hydrophobic pocket, whereas S2' appears shallow and S3' open.

  2. Structural Basis for Human PHF2 Jumonji Domain Interaction with Metal Ions

    Energy Technology Data Exchange (ETDEWEB)

    Horton, John R.; Upadhyay, Anup K.; Hashimotoa, Hideharu; Zhanga, Xing; Cheng, Xiaodong (Emory-MED)

    2011-08-29

    PHF2 belongs to a class of {alpha}-ketoglutarate-Fe{sup 2+}-dependent dioxygenases. PHF2 harbors a plant homeodomain (PHD) and a Jumonji domain. PHF2, via its PHD, binds Lys4-trimethylated histone 3 in submicromolar affinity and has been reported to have the demethylase activity of monomethylated lysine 9 of histone 3 in vivo. However, we did not detect demethylase activity for PHF2 Jumonji domain (with and without its linked PHD) in the context of histone peptides. We determined the crystal structures of PHF2 Jumonji domain in the absence and presence of additional exogenous metal ions. When Fe{sup 2+} or Ni{sup 2+} was added at a high concentration (50 mM) and allowed to soak in the preformed crystals, Fe{sup 2+} or Ni{sup 2+} was bound by six ligands in an octahedral coordination. The side chains of H249 and D251 and the two oxygen atoms of N-oxalylglycine (an analog of {alpha}-ketoglutarate) provide four coordinations in the equatorial plane, while the hydroxyl oxygen atom of Y321 and one water molecule provide the two axial coordinations as the fifth and sixth ligands, respectively. The metal binding site in PHF2 closely resembles the Fe{sup 2+} sites in other Jumonji domains examined, with one important difference -- a tyrosine (Y321 of PHF2) replaces histidine as the fifth ligand. However, neither Y321H mutation nor high metal concentration renders PHF2 an active demethylase on histone peptides. Wild type and Y321H mutant bind Ni{sup 2+} with an approximately equal affinity of 50 {mu}M. We propose that there must be other regulatory factors required for the enzymatic activity of PHF2 in vivo or that perhaps PHF2 acts on non-histone substrates. Furthermore, PHF2 shares significant sequence homology throughout the entire region, including the above-mentioned tyrosine at the corresponding iron-binding position, with that of Schizosaccharomyces pombe Epe1, which plays an essential role in heterochromatin function but has no known enzymatic activity.

  3. Localization and distribution of fibrinogen C domain containing 1 (FIBCD1) in human tissues

    DEFF Research Database (Denmark)

    von Huth, Sebastian; Møller, Jesper Bonnet; Schlosser, Anders

    in an immunohistochemistry-based analysis and demonstrate that FIBCD1 protein is highly expressed at the apical surfaces of the epithelium throughout the gastrointestinal tract, in the uterus, testis, bladder, gallbladder and the salivary glands. To a lesser extent, FIBCD1 is expressed in the pancreas, the spleen......Introduction: We have previously identified and characterized fibrinogen C domain-containing 1 (FIBCD1) as a homotetrameric type II transmembrane protein. FIBCD1 is a member of the fibrinogen- related protein (FReP) family, and is thought to play a crucial role in the innate immune system...

  4. Methods to uncover an antibody epitope in the KPI domain of Alzheimer's amyloid precursor protein for immunohistochemistry in human brain.

    Science.gov (United States)

    Campbell, E; Pearson, R C; Parkinson, D

    1999-11-15

    A novel polyclonal antibody (Ab993), specific for a KPI domain epitope of APP, was characterised for use in immunoprecipitation, Western blotting and immunohistochemistry. Conditioned medium from NTera2/D1 cells was used for immunoprecipitation and Western blots. Paraffin-embedded human brain sections were used for immunohistochemistry. The antibody recognised KPI-containing APP on Western blots after standard solubilisation but immunoprecipitation of soluble APP required reduction with 2-mercaptoethanol followed by alkylation of reduced sulphydryl bonds with sodium iodoacetate. Immunohistochemical staining of human brain sections was significantly enhanced by this pre-treatment. Microwaving of sections also increased immunolabelling, by a mechanism that was additive to reduction and alkylation. Incubation in 80% formic acid did not confer any enhancement of immunoreactivity. Ab993, applied with the methods reported here, is expected to be valuable in investigations of the pathogenesis of Alzheimer's disease to determine the source of the beta-amyloid peptide.

  5. Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells

    Science.gov (United States)

    Shinkai, Soya; Nozaki, Tadasu; Maeshima, Kazuhiro

    2016-01-01

    The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement. It is unclear how single nucleosomes within CDs fluctuate and how the CD structure reflects the nucleosome movement. Here, we present a polymer model wherein CDs are characterized by fractal dimensions and the nucleosome fibers fluctuate in a viscoelastic medium with memory. We analytically show that the mean-squared displacement (MSD) of nucleosome fluctuations within CDs is subdiffusive. The diffusion coefficient and the subdiffusive exponent depend on the structural information of CDs. This analytical result enabled us to extract information from the single-nucleosome imaging data for HeLa cells. Our observation that the MSD is lower at the nuclear periphery region than the interior region indicates that CDs in the heterochromatin-rich nuclear periphery region are more compact than those in the euchromatin-rich interior region with respect to the fractal dimensions as well as the size. Finally, we evaluated that the average size of CDs is in the range of 100–500 nm and that the relaxation time of nucleosome movement within CDs is a few seconds. Our results provide physical and dynamic insights into the genome architecture in living cells. PMID:27764097

  6. Hinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C.

    Science.gov (United States)

    Orlikowska, Marta; Jankowska, Elżbieta; Kołodziejczyk, Robert; Jaskólski, Mariusz; Szymańska, Aneta

    2011-02-01

    Cystatins are natural inhibitors of cysteine proteases, enzymes that are widely distributed in animals, plants, and microorganisms. Human cystatin C (hCC) has been also recognized as an aggregating protein directly involved in the formation of pathological amyloid fibrils, and these amyloidogenic properties greatly increase in a naturally occurring L68Q hCC variant. For a long time only dimeric structure of wild-type hCC has been known. The dimer is created through 3D domain swapping process, in which two parts of the cystatin structure become separated from each other and next exchanged between two molecules. Important role in the domain swapping plays the L1 loop, which connects the exchanging segments and, upon dimerization, transforms from a β-turn into a part of a long β-strand. In the very recently published first monomeric structure of human cystatin C (hCC-stab1), dimerization was abrogated due to clasping of the β-strands from the swapping domains by an engineered disulfide bridge. We have designed and constructed another mutated cystatin C with the smallest possible structural intervention, that is a single-point mutation replacing hydrophobic V57 from the L1 loop by polar asparagine, known as a stabilizer of a β-turn motif. V57N hCC mutant occurred to be stable in its monomeric form and crystallized as a monomer, revealing typical cystatin fold with a five-stranded antiparallel β-sheet wrapped around an α-helix. Here we report a 2.04 Å resolution crystal structure of V57N hCC and discuss the architecture of the protein in comparison to chicken cystatin, hCC-stab1 and dimeric hCC.

  7. VP2 capsid domain of the H-1 parvovirus determines susceptibility of human cancer cells to H-1 viral infection.

    Science.gov (United States)

    Cho, I-R; Kaowinn, S; Song, J; Kim, S; Koh, S S; Kang, H-Y; Ha, N-C; Lee, K H; Jun, H-S; Chung, Y-H

    2015-05-01

    Although H-1 parvovirus is used as an antitumor agent, not much is known about the relationship between its specific tropism and oncolytic activity. We hypothesize that VP2, a major capsid protein of H-1 virus, determines H-1-specific tropism. To assess this, we constructed chimeric H-1 viruses expressing Kilham rat virus (KRV) capsid proteins, in their complete or partial forms. Chimeric H-1 viruses (CH1, CH2 and CH3) containing the whole KRV VP2 domain could not induce cytolysis in HeLa, A549 and Panc-1 cells. However, the other chimeric H-1 viruses (CH4 and CH5) expressing a partial KRV VP2 domain induced cytolysis. Additionally, the significant cytopathic effect caused by CH4 and CH5 infection in HeLa cells resulted from preferential viral amplification via DNA replication, RNA transcription and protein synthesis. Modeling of VP2 capsid protein showed that two variable regions (VRs) (VR0 and VR2) of H-1 VP2 protein protrude outward, because of the insertion of extra amino-acid residues, as compared with those of KRV VP2 protein. This might explain the precedence of H-1 VP2 protein over KRV in determining oncolytic activity in human cancer cells. Taking these results together, we propose that the VP2 protein of oncolytic H-1 parvovirus determines its specific tropism in human cancer cells.

  8. Transactivation Domain of Human c-Myc Is Essential to Alleviate Poly(Q)-Mediated Neurotoxicity in Drosophila Disease Models.

    Science.gov (United States)

    Raj, Kritika; Sarkar, Surajit

    2017-03-18

    Polyglutamine (poly(Q)) disorders, such as Huntington's disease (HD) and spinocerebellar ataxias, represent a group of neurological disorders which arise due to an atypically expanded poly(Q) tract in the coding region of the affected gene. Pathogenesis of these disorders inside the cells begins with the assembly of these mutant proteins in the form of insoluble inclusion bodies (IBs), which progressively sequester several vital cellular transcription factors and other essential proteins, and finally leads to neuronal dysfunction and apoptosis. We have shown earlier that targeted upregulation of Drosophila myc (dmyc) dominantly suppresses the poly(Q) toxicity in Drosophila. The present study examines the ability of the human c-myc proto-oncogene and also identifies the specific c-Myc isoform which drives the mitigation of poly(Q)-mediated neurotoxicity, so that it could be further substantiated as a potential drug target. We report for the first time that similar to dmyc, tissue-specific induced expression of human c-myc also suppresses poly(Q)-mediated neurotoxicity by an analogous mechanism. Among the three isoforms of c-Myc, the rescue potential was maximally manifested by the full-length c-Myc2 protein, followed by c-Myc1, but not by c-MycS which lacks the transactivation domain. Our study suggests that strategies focussing on the transactivation domain of c-Myc could be a very useful approach to design novel drug molecules against poly(Q) disorders.

  9. Ask an Expert.

    Science.gov (United States)

    Trautman, Steve; Klein, Kate

    1993-01-01

    Offers guidelines for determining when and how to recruit subject matter experts (SMEs) and for ensuring that they deliver high quality training. Considers common problems of SMEs, such as giving too much information, conflicts with their job commitments, and stage fright. (JOW)

  10. Bloggers as experts

    NARCIS (Netherlands)

    K. Balog; M. de Rijke; W. Weerkamp

    2008-01-01

    We address the task of (blog) feed distillation: to find blogs that are principally devoted to a given topic. The task may be viewed as an association finding task, between topics and bloggers. Under this view, it resembles the expert finding task, for which a range of models have been proposed. We

  11. Human formyl peptide receptor ligand binding domain(s). Studies using an improved mutagenesis/expression vector reveal a novel mechanism for the regulation of receptor occupancy.

    Science.gov (United States)

    Perez, H D; Vilander, L; Andrews, W H; Holmes, R

    1994-09-09

    Recently, we reported the domain requirements for the binding of formyl peptide to its specific receptor. Based on experiments using receptor chimeras, we also postulated an importance for the amino-terminal domain of the receptor in ligand binding (Perez, H. D., Holmes, R., Vilander, L., Adams, R., Manzana, W., Jolley, D., and Andrews, W. H. (1993) J. Biol. Chem. 268, 2292-2295). We have begun to perform a detailed analysis of the regions within the formyl peptide receptor involved in ligand binding. To address the importance of the receptor amino-terminal domain, we substituted (or inserted) hydrophilic sequences within the amino-terminal domain, expressed the receptors, and determined their ability to bind ligand. A stretch of nine amino acids next to the initial methionine was identified as crucial for receptor occupancy. A peptide containing such a sequence specifically completed binding of the ligand to the receptor. Alanine screen mutagenesis of the second extracellular domain also identified amino acids involved in ligand binding as well as a disulfide bond (Cys98 to Cys176) crucial for maintaining the binding pocket. These studies provide evidence for a novel mechanism involved in regulation of receptor occupancy. Binding of the ligand induces conformational changes in the receptor that result in the apposition of the amino-terminal domain over the ligand, providing a lid to the binding pocket.

  12. Generation and characterization of small single domain antibodies inhibiting human tumor necrosis factor receptor 1.

    Science.gov (United States)

    Steeland, Sophie; Puimège, Leen; Vandenbroucke, Roosmarijn E; Van Hauwermeiren, Filip; Haustraete, Jurgen; Devoogdt, Nick; Hulpiau, Paco; Leroux-Roels, Geert; Laukens, Debby; Meuleman, Philip; De Vos, Martine; Libert, Claude

    2015-02-13

    The cytokine TNF is a well known drug target for several inflammatory diseases such as Crohn disease. Despite the great success of TNF blockers, therapy could be improved because of high costs and side effects. Selective inhibition of TNF receptor (TNFR) 1 signaling holds the potential to greatly reduce the pro-inflammatory activity of TNF, thereby preserving the advantageous immunomodulatory signals mediated by TNFR2. We generated a selective human TNFR1 inhibitor based on Nanobody (Nb) technology. Two anti-human TNFR1 Nbs were linked with an anti-albumin Nb to generate Nb Alb-70-96 named "TNF Receptor-One Silencer" (TROS). TROS selectively binds and inhibits TNF/TNFR1 and lymphotoxin-α/TNFR1 signaling with good affinity and IC50 values, both of which are in the nanomolar range. Surface plasmon resonance analysis reveals that TROS competes with TNF for binding to human TNFR1. In HEK293T cells, TROS strongly reduces TNF-induced gene expression, like IL8 and TNF, in a dose-dependent manner; and in ex vivo cultured colon biopsies of CD patients, TROS inhibits inflammation. Finally, in liver chimeric humanized mice, TROS antagonizes inflammation in a model of acute TNF-induced liver inflammation, reflected in reduced human IL8 expression in liver and reduced IL6 levels in serum. These results demonstrate the considerable potential of TROS and justify the evaluation of TROS in relevant disease animal models of both acute and chronic inflammation and eventually in patients.

  13. The roles of cysteines in the heme domain of human soluble guanylate cyclase

    Institute of Scientific and Technical Information of China (English)

    Fang Fang Zhong; Xiao Xiao Liu; Jie Pan; Zhong Xian Huang; Xiang Shi Tan

    2012-01-01

    Soluble guanylate cyclase (sGC) is a critical heme-containing enzyme involved in NO signaling.The dimerization of sGC subunits is necessary for its bioactivity and its mechanism is a striiking and an indistinct issue.The roles of heme domain cysteines of the sGC on the dimerization and heme binding were investigated herein.The site-directed mutations of three conserved cysteines (C78A,C 122A and C 174S) were studied systematically and the three mutants were characterized by gel filtration analysis,UV-vis spectroscopy and heime transfer examination.Cys78 was involved in heme binding but not referred to the dimerization,while Cys174 was demonstrated to be involved in the homodimerization.These results provide new insights into the cysteine-related dimerization regulation of sGC.

  14. Aspects Concerning the Opportunities of Career Development in the Human Resources Domain

    Directory of Open Access Journals (Sweden)

    Horia Demian

    2007-10-01

    Full Text Available The function of human resources is an unusual matter concerning the evolution of other functions of the organization. The enriching and changing process of its status determined, at the same time, a movement of its instruments and activities as far as all the departments and activities are concerned, so that it can ensure a true partnership with the personnel and to be closer to reality. Our step can’t situate itself outside the new context of the evolution of the human resources function.

  15. Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein

    Energy Technology Data Exchange (ETDEWEB)

    Kellner, Julian N.; Meinhart, Anton, E-mail: anton.meinhart@mpimf-heidelberg.mpg.de [Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)

    2015-08-25

    The structure of the SPRY domain of the human RNA helicase DDX1 was determined at 2.0 Å resolution. The SPRY domain provides a putative protein–protein interaction platform within DDX1 that differs from other SPRY domains in its structure and conserved regions. The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein–protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 Å resolution. The structure reveals two layers of concave, antiparallel β-sheets that stack onto each other and a third β-sheet beneath the β-sandwich. A comparison with SPRY-domain structures from other eukaryotic proteins showed that the general β-sandwich fold is conserved; however, differences were detected in the loop regions, which were identified in other SPRY domains to be essential for interaction with cognate partners. In contrast, in hDSPRY these loop regions are not strictly conserved across species. Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein–protein interaction surface. The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein. By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.

  16. The PGRS Domain from PE_PGRS33 of Mycobacterium tuberculosis is Target of Humoral Immune Response in Mice and Humans

    Science.gov (United States)

    Cohen, Ingrid; Parada, Cristina; Acosta-Gío, Enrique; Espitia, Clara

    2014-01-01

    The PE_PGRS33 protein is a member of the PE family, which encompasses the PE and the PE_PGRS subfamilies. Among PE_PGRS’s, this protein is one of the most studied antigens and its immunomodulatory properties are influence by both PE and PGRS domains. However, the contribution of these domains to the host immune recognition of the PE_PGRS33 protein and their potential role in latent tuberculosis infection in humans is still unknown. In this study, the immunogenic properties of the complete PE_PGRS33 protein and each domain separately were evaluated in BALB/c mice and latent tuberculosis infected (LTBI) humans. In mice, PE_PGRS33 and its domains induced similar antibody production and secretion of IFN-γ. PE_PGRS33 and the PE domain stimulated higher CD4+ and CD8+ T-cell proliferation compared to the PGRS domain. This demonstrated that the principal difference in the immune recognition of the domains is the higher activation of T-cell subpopulations involved in the control of tuberculosis. In humans, the secretion of IFN-γ in response to PE_PGRS33 was detected in both LTBI and in non-infected vaccinated individuals. The same was observed for antibody response, which targets epitopes located in the PGRS domain but not in the PE domain. These observations suggest that T and B cell responses to PE_PGRS33 are induced by BCG vaccination and can be maintained for many years in non-infected individuals. This also indicates that the IFN-γ response detected might not be associated with latent tuberculosis infection. These results contribute to the elucidation of the role of the PE_PGRS33 protein and its PE and PGRS domains in the immune response against Mycobacterium tuberculosis. PMID:24904584

  17. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    The domain concept, originally suggested by Schmidt-Rohr in the 1930’s (as credited in Fishman’s writings in the 1970s), was an attempt to sort out different areas of language use in multilingual societies, which are relevant for language choice. In Fishman’s version, domains were considered...... not described in terms of domains, and recent research e.g. about the multilingual communities in the Danish-German border area seems to confirm this....

  18. Human mitochondrial Hsp70 (mortalin): shedding light on ATPase activity, interaction with adenosine nucleotides, solution structure and domain organization.

    Science.gov (United States)

    Dores-Silva, Paulo R; Barbosa, Leandro R S; Ramos, Carlos H I; Borges, Júlio C

    2015-01-01

    The human mitochondrial Hsp70, also called mortalin, is of considerable importance for mitochondria biogenesis and the correct functioning of the cell machinery. In the mitochondrial matrix, mortalin acts in the importing and folding process of nucleus-encoded proteins. The in vivo deregulation of mortalin expression and/or function has been correlated with age-related diseases and certain cancers due to its interaction with the p53 protein. In spite of its critical biological roles, structural and functional studies on mortalin are limited by its insoluble recombinant production. This study provides the first report of the production of folded and soluble recombinant mortalin when co-expressed with the human Hsp70-escort protein 1, but it is still likely prone to self-association. The monomeric fraction of mortalin presented a slightly elongated shape and basal ATPase activity that is higher than that of its cytoplasmic counterpart Hsp70-1A, suggesting that it was obtained in the functional state. Through small angle X-ray scattering, we assessed the low-resolution structural model of monomeric mortalin that is characterized by an elongated shape. This model adequately accommodated high resolution structures of Hsp70 domains indicating its quality. We also observed that mortalin interacts with adenosine nucleotides with high affinity. Thermally induced unfolding experiments indicated that mortalin is formed by at least two domains and that the transition is sensitive to the presence of adenosine nucleotides and that this process is dependent on the presence of Mg2+ ions. Interestingly, the thermal-induced unfolding assays of mortalin suggested the presence of an aggregation/association event, which was not observed for human Hsp70-1A, and this finding may explain its natural tendency for in vivo aggregation. Our study may contribute to the structural understanding of mortalin as well as to contribute for its recombinant production for antitumor compound screenings.

  19. Human mitochondrial Hsp70 (mortalin: shedding light on ATPase activity, interaction with adenosine nucleotides, solution structure and domain organization.

    Directory of Open Access Journals (Sweden)

    Paulo R Dores-Silva

    Full Text Available The human mitochondrial Hsp70, also called mortalin, is of considerable importance for mitochondria biogenesis and the correct functioning of the cell machinery. In the mitochondrial matrix, mortalin acts in the importing and folding process of nucleus-encoded proteins. The in vivo deregulation of mortalin expression and/or function has been correlated with age-related diseases and certain cancers due to its interaction with the p53 protein. In spite of its critical biological roles, structural and functional studies on mortalin are limited by its insoluble recombinant production. This study provides the first report of the production of folded and soluble recombinant mortalin when co-expressed with the human Hsp70-escort protein 1, but it is still likely prone to self-association. The monomeric fraction of mortalin presented a slightly elongated shape and basal ATPase activity that is higher than that of its cytoplasmic counterpart Hsp70-1A, suggesting that it was obtained in the functional state. Through small angle X-ray scattering, we assessed the low-resolution structural model of monomeric mortalin that is characterized by an elongated shape. This model adequately accommodated high resolution structures of Hsp70 domains indicating its quality. We also observed that mortalin interacts with adenosine nucleotides with high affinity. Thermally induced unfolding experiments indicated that mortalin is formed by at least two domains and that the transition is sensitive to the presence of adenosine nucleotides and that this process is dependent on the presence of Mg2+ ions. Interestingly, the thermal-induced unfolding assays of mortalin suggested the presence of an aggregation/association event, which was not observed for human Hsp70-1A, and this finding may explain its natural tendency for in vivo aggregation. Our study may contribute to the structural understanding of mortalin as well as to contribute for its recombinant production for antitumor

  20. Sustaining expression of B domain-deleted human factor VIII mediated by using lentiviral vectors in NOD/SCID mouse.

    Science.gov (United States)

    Li, Yan-Jie; Chen, Chong; Zeng, Ling-Yu; Cao, Jiang; Xu, Kai-Lin

    2012-06-01

    Recently, gene therapy has been become a promising approach to cure hemophilia A, a most common recessive bleeding disease. The aim of this study was to determine the perspective of lentiviral vector in hemophilia A gene therapy in vitro and in NOD/SCID mice. Lentivirus transfer vector pXZ9/BDDFVIII containing human B-domain-deleted Factor VIII-IRES-eGFP coding sequence and mock control pXZ9 were constructed. Lentivirus was prepared by co-transfecting 3 plasmids into 293FT cells. 293FT, HLF, human bone marrow mesenchymal stem cells and Chang-liver cells were transfected with the prepared virus. Coagulant activity of human FVIII, human FVIII antigen, human FVIII mRNA transcription and genomic integration were assayed by ELISA, one-step method, RT-PCR and PCR after infection. Lentiviral particles were concentrated by ultracentrifugation and NOD/SCID mice were transfected via portal vein injection. Human FVIII antigen in mouse blood plasma was analyzed by ELISA. eGFP expression was observed by fluorescent microscopy and human FVIII transcription in mouse liver was analyzed by RT-PCR at one month after transduction. The results showed that the high titer of recombinant virus was prepared and used to efficiently transduce the target cells in vitro. At 72 h after transfection, high levels of FVIII activity and FVIII antigen were detected. Human FVIII gene transcription could be detected in the liver of NOD/SCID mice received lentiviral particles carrying FVIII gene. Mouse hepatocytes were transfected with recombinant lentivirus efficiently in vivo. Human FVIII level in mouse blood plasma reached to (49 ± 6) mU, (54 ± 8) mU and (23 ± 4) mU at 72 h, one week and one month after transfection respectively. It is concluded that the lentiviral particles carrying BDDhFVIII gene can high efficiently transfect the target cells both in vitro and in vivo, and the transfected target cells can secrete hFVIII efficiently. The sustained expression of human FVIII in NOD/SCID mice is

  1. Cysteine-rich domain of human ADAM 12 (meltrin alpha) supports tumor cell adhesion

    DEFF Research Database (Denmark)

    Iba, K; Albrechtsen, R; Gilpin, B J;

    1999-01-01

    The ADAMs (A disintegrin and metalloprotease) comprise a family of membrane-anchored cell surface proteins with a putative role in cell-cell and/or cell-matrix interactions. By immunostaining, ADAM 12 (meltrin alpha) was up-regulated in several human carcinomas and could be detected along the tum...

  2. Insight into the interactive residues between two domains of human somatic Angiotensin-converting enzyme and Angiotensin II by MM-PBSA calculation and steered molecular dynamics simulation.

    Science.gov (United States)

    Guan, Shan-shan; Han, Wei-wei; Zhang, Hao; Wang, Song; Shan, Ya-ming

    2016-01-01

    Angiotensin-converting enzyme (ACE), a membrane-bound zinc metallopeptidase, catalyzes the formation of Angiotensin-II (AngII) and the deactivation of bradykinin in the renin-angiotensin-aldosterone and kallikrein-kinin systems. As a hydrolysis product of ACE, AngII is regarded as an inhibitor and displays stronger competitive inhibition in the C-domain than the N-domain of ACE. However, the AngII binding differences between the two domains and the mechanisms behind AngII dissociation from the C-domain are rarely explored. In this work, molecular docking, Molecular Mechanics/Poisson-Boltzmann Surface Area calculation, and steered molecular dynamics (SMD) are applied to explore the structures and interactions in the binding or unbinding of AngII with the two domains of human somatic ACE. Calculated free energy values suggest that the C-domain-AngII complex is more stable than the N-domain-AngII complex, consistent with available experimental data. SMD simulation results imply that electrostatic interaction is dominant in the dissociation of AngII from the C-domain. Moreover, Gln106, Asp121, Glu123, and Tyr213 may be the key residues in the unbinding pathway of AngII. The simulation results in our work provide insights into the interactions between the two domains of ACE and its natural peptide inhibitor AngII at a molecular level. Moreover, the results provide theoretical clues for the design of new inhibitors.

  3. Hepatitis E virus ORF1 encoded macro domain protein interacts with light chain subunit of human ferritin and inhibits its secretion.

    Science.gov (United States)

    Ojha, Nishant Kumar; Lole, Kavita S

    2016-06-01

    Hepatitis E Virus (HEV) is the major causative agent of acute hepatitis in developing countries. Its genome has three open reading frames (ORFs)-called as ORF1, ORF2, and ORF3. ORF1 encodes nonstructural polyprotein having multiple domains, namely: Methyltransferase, Y domain, Protease, Macro domain, Helicase, and RNA-dependent RNA polymerase. In the present study, we show that HEV-macro domain specifically interacts with light chain subunit of human ferritin (FTL). In cultured hepatoma cells, HEV-macro domain reduces secretion of ferritin without causing any change in the expression levels of FTL. This inhibitory effect was further enhanced upon Brefeldin-A treatment. The levels of transferrin Receptor 1 or ferroportin, two important proteins in iron metabolism, remained unchanged in HEV-macro domain expressing cells. Similarly, there were no alterations in the levels of cellular labile iron pool and reactive oxygen species, indicating that HEV-macro domain does not influence cellular iron homeostasis/metabolism. As ferritin is an acute-phase protein, secreted in higher level in infected persons and HEV-macro domain has the property of reducing synthesis of inflammatory cytokines, we propose that by directly binding to FTL, macro domain prevents ferritin from entering into circulation and helps in further attenuation of the host immune response.

  4. Bioethics for Technical Experts

    Science.gov (United States)

    Asano, Shigetaka

    Along with rapidly expanding applications of life science and technology, technical experts have been implicated more and more often with ethical, social, and legal problems than before. It should be noted that in this background there are scientific and social uncertainty elements which are inevitable during the progress of life science in addition to the historically-established social unreliability to scientists and engineers. In order to solve these problems, therefore, we should establish the social governance with ‘relief’ and ‘reliance’ which enables for both citizens and engineers to share the awareness of the issues, to design social orders and criterions based on hypothetical sense of values for bioethics, to carry out practical use management of each subject carefully, and to improve the sense of values from hypothetical to universal. Concerning these measures, the technical experts can learn many things from the present performance in the medical field.

  5. Expert Script Generator

    Science.gov (United States)

    Sliwa, Nancy E.; Cooper, Eric G.

    1991-01-01

    Program provides additional level of interface to facilitate use of telerobotic system. ESG (Expert Script Generator) is software package automatically generating high-level task objective commands from complex menu-driven language of the NASA Intelligent Systems Research Laboratory (ISRL). Makes telerobotics laboratory accessible to researchers not familiar with comprehensive language developed by ISRL for interacting with various systems of ISRL test bed. Incorporates expert-system technology to capture typical rules of operation that skilled operator uses. Result: operator interfact optimizing ability of system to perform task remotely in hazardous environment, in timely manner, and without undue stress to operator, while minimizing change for operator erros that damage equipment. Written in CLIPS.

  6. Expert PLSQL Practices

    CERN Document Server

    Beresniewicz, John

    2011-01-01

    Expert PL/SQL Practices is a book of collected wisdom on PL/SQL programming from some of the best and the brightest in the field. Each chapter is a deep-dive into a specific problem, technology, or feature set that you'll face as a PL/SQL programmer. Each author has chosen their topic out of the strong belief that what they share can make a positive difference in the quality and scalability of code that you write. The path to mastery begins with syntax and the mechanics of writing statements to make things happen. If you've reached that point with PL/SQL, then let the authors of Expert PL/SQL

  7. Expression, purification and identification of LBD domain of human PPARδ in E. coli

    Institute of Scientific and Technical Information of China (English)

    Liu Hua; Li Changqing; Ling Baodong; Zhou Qinxin

    2009-01-01

    Peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors known to play a pivotal role in regulations of metabolism. In order to yield soluble ligand binding domain of PPARδ (PPARδLBD) for screening ligands, the cDNA was amplified using total RNA from HepG2 cells by RT-PCR. Then the enzyme-digested product was inserted downstream of the malE gene in the vector pMAL-p2x, which encoded maltose-binding protein (MBP), resulting in the expression of an MBP-PPARδLBD fusion protein. The recombinant plasmid was transformed into E. coli TB1 that was cultured shakily at 30 ℃, 200 r/min and induced by 0.4 mmol/L IPTG for 6 h. The cells were harvested by centrifugation and broken by sonication. The expressed fusion protein was soluble and accounted for 0.31 of the total protein in the supernatant. Western blot analysis showed that the expressed MBP-PPARδLBD could bind to anti-MBP-antibody. The MBP-PPARδLBD fusion protein of 77 kDa and the PPARδLBD protein of 34 kDa were obtained by amylose-resin affinity chromatography without or with digestion of Factor Xa.They were both homogeneity, judged by SDS-PAGE. The recombinant MBP-PPARδLBD and PPARδLBD protein with high purity is obtained, which provides the necessary material for screening and researching PPARδ ligands.

  8. Low statistical power in biomedical science: a review of three human research domains

    Science.gov (United States)

    Dumas-Mallet, Estelle; Button, Katherine S.; Boraud, Thomas; Gonon, Francois

    2017-01-01

    Studies with low statistical power increase the likelihood that a statistically significant finding represents a false positive result. We conducted a review of meta-analyses of studies investigating the association of biological, environmental or cognitive parameters with neurological, psychiatric and somatic diseases, excluding treatment studies, in order to estimate the average statistical power across these domains. Taking the effect size indicated by a meta-analysis as the best estimate of the likely true effect size, and assuming a threshold for declaring statistical significance of 5%, we found that approximately 50% of studies have statistical power in the 0–10% or 11–20% range, well below the minimum of 80% that is often considered conventional. Studies with low statistical power appear to be common in the biomedical sciences, at least in the specific subject areas captured by our search strategy. However, we also observe evidence that this depends in part on research methodology, with candidate gene studies showing very low average power and studies using cognitive/behavioural measures showing high average power. This warrants further investigation. PMID:28386409

  9. Structure and function of the N-terminal domain of the human mitochondrial calcium uniporter.

    Science.gov (United States)

    Lee, Youngjin; Min, Choon Kee; Kim, Tae Gyun; Song, Hong Ki; Lim, Yunki; Kim, Dongwook; Shin, Kahee; Kang, Moonkyung; Kang, Jung Youn; Youn, Hyung-Seop; Lee, Jung-Gyu; An, Jun Yop; Park, Kyoung Ryoung; Lim, Jia Jia; Kim, Ji Hun; Kim, Ji Hye; Park, Zee Yong; Kim, Yeon-Soo; Wang, Jimin; Kim, Do Han; Eom, Soo Hyun

    2015-10-01

    The mitochondrial calcium uniporter (MCU) is responsible for mitochondrial calcium uptake and homeostasis. It is also a target for the regulation of cellular anti-/pro-apoptosis and necrosis by several oncogenes and tumour suppressors. Herein, we report the crystal structure of the MCU N-terminal domain (NTD) at a resolution of 1.50 Å in a novel fold and the S92A MCU mutant at 2.75 Å resolution; the residue S92 is a predicted CaMKII phosphorylation site. The assembly of the mitochondrial calcium uniporter complex (uniplex) and the interaction with the MCU regulators such as the mitochondrial calcium uptake-1 and mitochondrial calcium uptake-2 proteins (MICU1 and MICU2) are not affected by the deletion of MCU NTD. However, the expression of the S92A mutant or a NTD deletion mutant failed to restore mitochondrial Ca(2+) uptake in a stable MCU knockdown HeLa cell line and exerted dominant-negative effects in the wild-type MCU-expressing cell line. These results suggest that the NTD of MCU is essential for the modulation of MCU function, although it does not affect the uniplex formation.

  10. Direct visualization of lipid domains in human skin stratum corneum's lipid membranes

    DEFF Research Database (Denmark)

    Plasencia, I; Norlen, Lars; Bagatolli, Luis

    2007-01-01

    ; and iii), whether pH has a direct effect on the lipid matrix phase behavior. In this work the lateral structure of membranes composed of lipids extracted from human skin stratum corneum was studied in a broad temperature range (10 degrees C-90 degrees C) using different techniques such as differential......The main function of skin is to serve as a physical barrier between the body and the environment. This barrier capacity is in turn a function of the physical state and structural organization of the stratum corneum extracellular lipid matrix. This lipid matrix is essentially composed of very long...... scanning calorimetry, fluorescence spectroscopy, and two-photon excitation and laser scanning confocal fluorescence microscopy. Here we show that hydrated bilayers of human skin stratum corneum lipids express a giant sponge-like morphology with dimensions corresponding to the global three...

  11. Comparing human and automatic thesaurus mapping approaches in the agricultural domain

    CERN Document Server

    Lauser, Boris; Caracciolo, Caterina; Keizer, Johannes; van Hage, Willem Robert; Mayr, Philipp

    2008-01-01

    Knowledge organization systems (KOS), like thesauri and other controlled vocabularies, are used to provide subject access to information systems across the web. Due to the heterogeneity of these systems, mapping between vocabularies becomes crucial for retrieving relevant information. However, mapping thesauri is a laborious task, and thus big efforts are being made to automate the mapping process. This paper examines two mapping approaches involving the agricultural thesaurus AGROVOC, one machine-created and one human created. We are addressing the basic question "What are the pros and cons of human and automatic mapping and how can they complement each other?" By pointing out the difficulties in specific cases or groups of cases and grouping the sample into simple and difficult types of mappings, we show the limitations of current automatic methods and come up with some basic recommendations on what approach to use when.

  12. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Yong-Geun [Gyeongsang National University, Department of Chemistry and Research Institute of Natural Science (Korea, Republic of); Park, Chin-Ju [Gwangju Institute of Science and Technology, Division of Liberal Arts and Sciences and Department of Chemistry (Korea, Republic of); Kim, Hee-Eun; Seo, Yeo-Jin; Lee, Ae-Ree; Choi, Seo-Ree; Lee, Shim Sung; Lee, Joon-Hwa, E-mail: joonhwa@gnu.ac.kr [Gyeongsang National University, Department of Chemistry and Research Institute of Natural Science (Korea, Republic of)

    2015-02-15

    Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 3{sub 10}-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.

  13. NMR investigation of the isolated second voltage-sensing domain of human Nav1.4 channel.

    Science.gov (United States)

    Paramonov, A S; Lyukmanova, E N; Myshkin, M Yu; Shulepko, M A; Kulbatskii, D S; Petrosian, N S; Chugunov, A O; Dolgikh, D A; Kirpichnikov, M P; Arseniev, A S; Shenkarev, Z O

    2017-03-01

    Voltage-gated Na(+) channels are essential for the functioning of cardiovascular, muscular, and nervous systems. The α-subunit of eukaryotic Na(+) channel consists of ~2000 amino acid residues and encloses 24 transmembrane (TM) helices, which form five membrane domains: four voltage-sensing (VSD) and one pore domain. The structural complexity significantly impedes recombinant production and structural studies of full-sized Na(+) channels. Modular organization of voltage-gated channels gives an idea for studying of the isolated second VSD of human skeletal muscle Nav1.4 channel (VSD-II). Several variants of VSD-II (~150a.a., four TM helices) with different N- and C-termini were produced by cell-free expression. Screening of membrane mimetics revealed low stability of VSD-II samples in media containing phospholipids (bicelles, nanodiscs) associated with the aggregation of electrically neutral domain molecules. The almost complete resonance assignment of (13)C,(15)N-labeled VSD-II was obtained in LPPG micelles. The secondary structure of VSD-II showed similarity with the structures of bacterial Na(+) channels. The fragment of S4 TM helix between the first and second conserved Arg residues probably adopts 310-helical conformation. Water accessibility of S3 helix, observed by the Mn(2+) titration, pointed to the formation of water-filled crevices in the micelle embedded VSD-II. (15)N relaxation data revealed characteristic pattern of μs-ms time scale motions in the VSD-II regions sharing expected interhelical contacts. VSD-II demonstrated enhanced mobility at ps-ns time scale as compared to isolated VSDs of K(+) channels. These results validate structural studies of isolated VSDs of Na(+) channels and show possible pitfalls in application of this 'divide and conquer' approach.

  14. The D2 period of collagen II contains a specific binding site for the human discoidin domain receptor, DDR2.

    Science.gov (United States)

    Leitinger, Birgit; Steplewski, Andrzej; Fertala, Andrzej

    2004-12-03

    The human discoidin domain receptors (DDRs), DDR1 and DDR2, are expressed widely and, uniquely among receptor tyrosine kinases, activated by the extracellular matrix protein collagen. This activation is due to a direct interaction of collagen with the DDR discoidin domain. Here, we localised a specific DDR2 binding site on the triple-helical region of collagen II. Collagen II was found to be a much better ligand for DDR2 than for DDR1. As expected, DDR2 binding to collagen II was dependent on triple-helical collagen and was mediated by the DDR2 discoidin domain. Collagen II served as a potent stimulator of DDR2 autophosphorylation, the first step in transmembrane signalling. To map the DDR2 binding site(s) on collagen II, we used recombinant collagen II variants with specific deletions of one of the four repeating D periods. We found that the D2 period of collagen II was essential for DDR2 binding and receptor autophosphorylation, whereas the D3 and D4 periods were dispensable. The DDR2 binding site on collagen II was further defined by recombinant collagen II-like proteins consisting predominantly of tandem repeats of the D2 or D4 period. The D2 construct, but not the D4 construct, mediated DDR2 binding and receptor autophosphorylation, demonstrating that the D2 period of collagen II harbours a specific DDR2 recognition site. The discovery of a site-specific interaction of DDR2 with collagen II gives novel insight into the nature of the interaction of collagen II with matrix receptors.

  15. Organizing to Understand: How to Operate Effectively in the Human Domain

    Science.gov (United States)

    2015-05-21

    study of ethno- cultural dynamics. Instead of culture-specific training, intercultural learning seeks to develop the skills at bridging communication ...national security community and military practitioners. To deal with the increasingly important human aspects, the US military has proposed the...studies of the early years of Operation Iraqi Freedom provide sufficient material with which to analyze how the security community has approached issues

  16. Interactive domains in the molecular chaperone human alphaB crystallin modulate microtubule assembly and disassembly.

    Directory of Open Access Journals (Sweden)

    Joy G Ghosh

    Full Text Available Small heat shock proteins regulate microtubule assembly during cell proliferation and in response to stress through interactions that are poorly understood.Novel functions for five interactive sequences in the small heat shock protein and molecular chaperone, human alphaB crystallin, were investigated in the assembly/disassembly of microtubules and aggregation of tubulin using synthetic peptides and mutants of human alphaB crystallin.The interactive sequence (113FISREFHR(120 exposed on the surface of alphaB crystallin decreased microtubule assembly by approximately 45%. In contrast, the interactive sequences, (131LTITSSLSSDGV(142 and (156ERTIPITRE(164, corresponding to the beta8 strand and the C-terminal extension respectively, which are involved in complex formation, increased microtubule assembly by approximately 34-45%. The alphaB crystallin peptides, (113FISREFHR(120 and (156ERTIPITRE(164, inhibited microtubule disassembly by approximately 26-36%, and the peptides (113FISREFHR(120 and (131LTITSSLSSDGV(142 decreased the thermal aggregation of tubulin by approximately 42-44%. The (131LTITSSLSSDGV(142 and (156ERTIPITRE(164 peptides were more effective than the widely used anti-cancer drug, Paclitaxel, in modulating tubulinmicrotubule dynamics. Mutagenesis of these interactive sequences in wt human alphaB crystallin confirmed the effects of the alphaB crystallin peptides on microtubule assembly/disassembly and tubulin aggregation. The regulation of microtubule assembly by alphaB crystallin varied over a narrow range of concentrations. The assembly of microtubules was maximal at alphaB crystallin to tubulin molar ratios between 1:4 and 2:1, while molar ratios >2:1 inhibited microtubule assembly.Interactive sequences on the surface of human alphaB crystallin collectively modulate microtubule assembly through a dynamic subunit exchange mechanism that depends on the concentration and ratio of alphaB crystallin to tubulin. These are the first

  17. Implementation of expert systems to support the functional evaluation of stand-to-sit activity.

    Science.gov (United States)

    Junkes-Cunha, Maíra; Cardozo, Glauco; Boos, Christine F; de Azevedo, Fernando

    2014-07-21

    Functional evaluation of sit-to-stand and stand-to-sit activities is often used by physiotherapists in patients with neurological and musculoskeletal disorders. The observation of the way these activities are executed is essential in identifying kinesiological problems. There are different methodologies used to describe the stand-to-sit activity and its evaluation is not yet standardized, which makes the practical application of resources on clinical observation difficult. The objective of this study is to automate the decision making process of an evaluation protocol, developed in previous study, and facilitate its utilization by professionals in the area. A decision-making system has been implemented through a computational tool, more specifically an Expert System that due its inherent characteristics emulates the decision-making process of a human expert in the domain area. A Shell called Expert Sinta was used to develop two knowledge bases, i.e. two expert systems, one for the anterior view and another for the lateral view of stand-to-sit activity. Variables, values, associated rules and confidence factors, objectives, and additional information questions were defined by the expert of domain and once implemented each expert system generates a number of questions to its user. These questions serve as a guide to physiotherapists and support the standardization of the activity evaluation. The developed systems were evaluated by physiotherapists through the application of a questionnaire that evaluates the knowledge base and the usability of the system. The physiotherapists' answers were then evaluated through statistical estimation and percentage analysis. When asked about the systems' "utility for clinical practice of the physiotherapist", 67% of evaluators answered positively. An interesting finding was that most physiotherapists (i.e. 92%) considered that the systems are suitable for educational purposes, which was not the main objective of this study. The

  18. Expert system prototype developments for NASA-KSC business and engineering applications

    Science.gov (United States)

    Ragusa, James M.; Gonzalez, Avelino J.

    1988-01-01

    Prototype expert systems developed for a variety of NASA projects in the business/management and engineering domains are discussed. Business-related problems addressed include an assistant for simulating launch vehicle processing, a plan advisor for the acquisition of automated data processing equipment, and an expert system for the identification of customer requirements. Engineering problems treated include an expert system for detecting potential ignition sources in LOX and gaseous-oxygen transportation systems and an expert system for hazardous-gas detection.

  19. Expression, refolding and spectroscopic characterization of fibronectin type III (FnIII)-homology domains derived from human fibronectin leucine rich transmembrane protein (FLRT)-1,-2, and-3

    DEFF Research Database (Denmark)

    Yang, Lila; Falkesgaard, Maria Hansen; Thulstrup, Peter Waaben

    2017-01-01

    The fibronectin leucine rich transmembrane (FLRT) protein family consists in humans of 3 proteins, FLRT1, -2, and -3. The FLRT proteins contain two extracellular domains separated by an unstructured linker. The most membrane distal part is a leucine rich repeat (LRR) domain responsible for both cis......- and trans-interactions, whereas the membrane proximal part is a fibronectin type III (FnIII) domain responsible for a cis-interaction with members of the fibroblast growth factor receptor 1 (FGFR1) family, which results in FGFR tyrosine kinase activation. Whereas the structures of FLRT LRR domains from...... in inclusion bodies in Escherichia coli. His-tags permitted affinity purification of the domains, which subsequently were refolded on a Ni-NTA agarose column by reducing the concentration of urea. The refolding was confirmed by circular dichroism (CD) and 1H-NMR. By thermal unfolding experiments we show...

  20. The Mycoplasma hominis P120 membrane protein contains a 216 amino acid hypervariable domain that is recognized by the human humoral immune response

    DEFF Research Database (Denmark)

    Nyvold, Charlotte Guldborg; Birkelund, Svend; Christiansen, Gunna

    1997-01-01

    domain. Based on restriction endonuclease cleavage patterns of the hypervariable domain the 18 isolates could be divided into four cases. Reactivity with both mAb 26.7D and pAb 121 confirmed these classes. The hypervariable, but not the constant, part of P120 was recognized by the human humoral immune...... and found to have a sequence identity of 91% with the gene of strain 7488. One hypervariable and two semivariable regions were detected. The epitope for mAb 26.7D was mapped to the hypervariable domain by expression of various parts of this domain in Escherichia coli using expression vector systems....... A polyclonal antiserum (pAb 121) generated against the hypervariable region of P120 from PG21 identified the P120 homologue in M. hominis PG21. Fusion proteins of the hypervariable and constant parts of the proteins were constructed and tested for reactivity with 21 human sera. Twelve sera reacted...

  1. Construction of TNF-binding proteins by grafting hypervariable regions of F10 antibody on human fibronectin domain scaffold.

    Science.gov (United States)

    Petrovskaya, L E; Shingarova, L N; Kryukova, E A; Boldyreva, E F; Yakimov, S A; Guryanova, S V; Novoseletsky, V N; Dolgikh, D A; Kirpichnikov, M P

    2012-01-01

    Tumor necrosis factor (TNF) plays a key role in the pathogenesis of various diseases. To study the possibility of constructing TNF-binding proteins by grafting hypervariable regions of immunoglobulins (CDR), we have replaced amino acid sequences of loops from the tenth type III domain of human fibronectin ((10)Fn3) by amino acid sequences of CDR from the light and heavy chains of the anti-TNF antibody F10. The assessment of TNF-binding properties of the resulting proteins by ELISA has revealed the highest activity of Hd3 containing sequences CDR-H1 and CDR-H2 of the antibody F10 and of Hd2 containing sequences CDR-H1 and CDR-H3. The proteins constructed by us on the fibronectin domain scaffold specifically bound TNF during Western blotting and also weakened its cytotoxic effect on L929 line cells. The highest neutralizing activity was demonstrated by the proteins Hd2 and Hd3, which induced, respectively, 10- and 50-fold increase in the EC(50) of TNF.

  2. MMP-12 catalytic domain recognizes and cleaves at multiple sites in human skin collagen type I and type III.

    Science.gov (United States)

    Taddese, Samuel; Jung, Michael C; Ihling, Christian; Heinz, Andrea; Neubert, Reinhard H H; Schmelzer, Christian E H

    2010-04-01

    Collagens of either soft connective or mineralized tissues are subject to continuous remodeling and turnover. Undesired cleavage can be the result of an imbalance between proteases and their inhibitors. Owing to their superhelical structure, collagens are resistant to many proteases and matrix metalloproteinases (MMPs) are required to initiate further degradation by other enzymes. Several MMPs are known to degrade collagens, but the action of MMP-12 has not yet been studied in detail. In this work, the potential of MMP-12 in recognizing sites in human skin collagen types I and III has been investigated. The catalytic domain of MMP-12 binds to the triple helix and cleaves the typical sites -Gly(775)-Leu(776)- in alpha-2 type I collagen and -Gly(775)-Ile(776)- in alpha-1 type I and type III collagens and at multiple other sites in both collagen types. Moreover, it was observed that the region around these typical sites contains comparatively less prolines, of which some have been proven to be only partially hydroxylated. This is of relevance since partial hydroxylation in the vicinity of a potential scissile bond may have a local effect on the conformational thermodynamics with probable consequences on the collagenolysis process. Taken together, the results of the present work confirm that the catalytic domain of MMP-12 alone binds and degrades collagens I and III. Copyright 2009 Elsevier B.V. All rights reserved.

  3. fau and its ubiquitin-like domain (FUBI) transforms human osteogenic sarcoma (HOS) cells to anchorage-independence.

    Science.gov (United States)

    Rossman, Toby G; Visalli, Melissa A; Komissarova, Elena V

    2003-03-27

    Arsenite is the most likely carcinogenic form of arsenic in the environment. Previously, expression cloning for cDNAs whose overexpression confers arsenite-resistance in Chinese hamster V79 cells identified two genes: fau and a novel gene, asr2. The fau gene encodes a ubiquitin-like protein (here called FUBI) fused to the ribosomal S30 protein. Since the expression of the fox sequence (antisense to fau) increased the tumorigenicity of a mouse sarcoma virus, it was proposed that fau might be a tumor suppressor gene. We intended to test its ability to block arsenite-induced transformation of human osteogenic sarcoma (HOS) cells to anchorage-independence. Instead, we found that overexpressing fau itself was able to transform HOS cells. When the two domains were expressed separately, only FUBI was transforming and only the S30 domain conferred arsenite resistance. An incidental finding was the transforming activity of the selectable marker, hyg. FUBI belongs to the ubiquitin-like protein group that is capable of forming conjugates to other proteins, although none have so far been identified. Alternatively, FUBI may act as a substitute or inhibitor of ubiquitin, to which it is most closely related, or to close ubiquitin-like relatives UCRP, FAT10, and/or Nedd8.

  4. Using Expert Systems To Build Cognitive Simulations.

    Science.gov (United States)

    Jonassen, David H.; Wang, Sherwood

    2003-01-01

    Cognitive simulations are runnable computer programs for modeling human cognitive activities. A case study is reported where expert systems were used as a formalism for modeling metacognitive processes in a seminar. Building cognitive simulations engages intensive introspection, ownership and meaning making in learners who build them. (Author/AEF)

  5. Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel

    Energy Technology Data Exchange (ETDEWEB)

    Inada, Hitoshi; Procko, Erik; Sotomayor, Marcos; Gaudet, Rachelle (Harvard-Med); (Harvard)

    2012-10-23

    The TRPV4 calcium-permeable cation channel plays important physiological roles in osmosensation, mechanosensation, cell barrier formation, and bone homeostasis. Recent studies reported that mutations in TRPV4, including some in its ankyrin repeat domain (ARD), are associated with human inherited diseases, including neuropathies and skeletal dysplasias, probably because of the increased constitutive activity of the channel. TRPV4 activity is regulated by the binding of calmodulin and small molecules such as ATP to the ARD at its cytoplasmic N-terminus. We determined structures of ATP-free and -bound forms of human TRPV4-ARD and compared them with available TRPV-ARD structures. The third inter-repeat loop region (Finger 3 loop) is flexible and may act as a switch to regulate channel activity. Comparisons of TRPV-ARD structures also suggest an evolutionary link between ARD structure and ATP binding ability. Thermal stability analyses and molecular dynamics simulations suggest that ATP increases stability in TRPV-ARDs that can bind ATP. Biochemical analyses of a large panel of TRPV4-ARD mutations associated with human inherited diseases showed that some impaired thermal stability while others weakened ATP binding ability, suggesting molecular mechanisms for the diseases.

  6. Entamoeba lysyl-tRNA synthetase contains a cytokine-like domain with chemokine activity towards human endothelial cells.

    Directory of Open Access Journals (Sweden)

    Manuel Castro de Moura

    2011-11-01

    Full Text Available Immunological pressure encountered by protozoan parasites drives the selection of strategies to modulate or avoid the immune responses of their hosts. Here we show that the parasite Entamoeba histolytica has evolved a chemokine that mimics the sequence, structure, and function of the human cytokine HsEMAPII (Homo sapiens endothelial monocyte activating polypeptide II. This Entamoeba EMAPII-like polypeptide (EELP is translated as a domain attached to two different aminoacyl-tRNA synthetases (aaRS that are overexpressed when parasites are exposed to inflammatory signals. EELP is dispensable for the tRNA aminoacylation activity of the enzymes that harbor it, and it is cleaved from them by Entamoeba proteases to generate a standalone cytokine. Isolated EELP acts as a chemoattractant for human cells, but its cell specificity is different from that of HsEMAPII. We show that cell specificity differences between HsEMAPII and EELP can be swapped by site directed mutagenesis of only two residues in the cytokines' signal sequence. Thus, Entamoeba has evolved a functional mimic of an aaRS-associated human cytokine with modified cell specificity.

  7. Entamoeba lysyl-tRNA synthetase contains a cytokine-like domain with chemokine activity towards human endothelial cells.

    Directory of Open Access Journals (Sweden)

    Manuel Castro de Moura

    2011-11-01

    Full Text Available Immunological pressure encountered by protozoan parasites drives the selection of strategies to modulate or avoid the immune responses of their hosts. Here we show that the parasite Entamoeba histolytica has evolved a chemokine that mimics the sequence, structure, and function of the human cytokine HsEMAPII (Homo sapiens endothelial monocyte activating polypeptide II. This Entamoeba EMAPII-like polypeptide (EELP is translated as a domain attached to two different aminoacyl-tRNA synthetases (aaRS that are overexpressed when parasites are exposed to inflammatory signals. EELP is dispensable for the tRNA aminoacylation activity of the enzymes that harbor it, and it is cleaved from them by Entamoeba proteases to generate a standalone cytokine. Isolated EELP acts as a chemoattractant for human cells, but its cell specificity is different from that of HsEMAPII. We show that cell specificity differences between HsEMAPII and EELP can be swapped by site directed mutagenesis of only two residues in the cytokines' signal sequence. Thus, Entamoeba has evolved a functional mimic of an aaRS-associated human cytokine with modified cell specificity.

  8. Experts bodies, experts minds: How physical and mental training shape the brain.

    Science.gov (United States)

    Debarnot, Ursula; Sperduti, Marco; Di Rienzo, Franck; Guillot, Aymeric

    2014-01-01

    Skill learning is the improvement in perceptual, cognitive, or motor performance following practice. Expert performance levels can be achieved with well-organized knowledge, using sophisticated and specific mental representations and cognitive processing, applying automatic sequences quickly and efficiently, being able to deal with large amounts of information, and many other challenging task demands and situations that otherwise paralyze the performance of novices. The neural reorganizations that occur with expertise reflect the optimization of the neurocognitive resources to deal with the complex computational load needed to achieve peak performance. As such, capitalizing on neuronal plasticity, brain modifications take place over time-practice and during the consolidation process. One major challenge is to investigate the neural substrates and cognitive mechanisms engaged in expertise, and to define "expertise" from its neural and cognitive underpinnings. Recent insights showed that many brain structures are recruited during task performance, but only activity in regions related to domain-specific knowledge distinguishes experts from novices. The present review focuses on three expertise domains placed across a motor to mental gradient of skill learning: sequential motor skill, mental simulation of the movement (motor imagery), and meditation as a paradigmatic example of "pure" mental training. We first describe results on each specific domain from the initial skill acquisition to expert performance, including recent results on the corresponding underlying neural mechanisms. We then discuss differences and similarities between these domains with the aim to identify the highlights of the neurocognitive processes underpinning expertise, and conclude with suggestions for future research.

  9. The amino-terminal domain of human signal transducers and activators of transcription 1: Overexpression, purification and characterization

    Indian Academy of Sciences (India)

    Arati Prabhu; Evans Coutinho; Sudha Srivastava

    2005-12-01

    The dual functional signal transducers and activators of transcription (STAT) proteins are latent cytoplasmic transcription factors that play crucial roles in host defense. Animals that lack these proteins are highly susceptible to microbial and viral infections and chemically induced primary tumours. We have over expressed the aminoterminal domain of human STAT1 (hSTAT1) in Escherichia coli and purified it by affinity chromatography and gel filtration chromatography. The entire process has been monitored by gel electrophoresis. The pure protein has been characterized by mass spectrometry and 2-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy. Our results indicate that the N-terminus of hSTAT1 exists as a dimer in solution.

  10. Transcriptional Activation of a Constitutive Heterochromatic Domain of the Human Genome in Response to Heat ShockD⃞

    Science.gov (United States)

    Rizzi, Nicoletta; Denegri, Marco; Chiodi, Ilaria; Corioni, Margherita; Valgardsdottir, Rut; Cobianchi, Fabio; Riva, Silvano; Biamonti, Giuseppe

    2004-01-01

    Heat shock triggers the assembly of nuclear stress bodies that contain heat shock factor 1 and a subset of RNA processing factors. These structures are formed on the pericentromeric heterochromatic regions of specific human chromosomes, among which chromosome 9. In this article we show that these heterochromatic domains are characterized by an epigenetic status typical of euchromatic regions. Similarly to transcriptionally competent portions of the genome, stress bodies are, in fact, enriched in acetylated histone H4. Acetylation peaks at 6 h of recovery from heat shock. Moreover, heterochromatin markers, such as HP1 and histone H3 methylated on lysine 9, are excluded from these nuclear districts. In addition, heat shock triggers the transient accumulation of RNA molecules, heterogeneous in size, containing the subclass of satellite III sequences found in the pericentromeric heterochromatin of chromosome 9. This is the first report of a transcriptional activation of a constitutive heterochromatic portion of the genome in response to stress stimuli. PMID:14617804

  11. Crystal structure of the FK506 binding domain of human FKBP25 in complex with FK506.

    Science.gov (United States)

    Prakash, Ajit; Rajan, Sreekanth; Yoon, Ho Sup

    2016-04-01

    Human FKBP25 (hFKBP25) is a nuclear immunophilin and interacts with several nuclear proteins, hence involving in many nuclear events. Similar to other FKBPs, FK506 binding domain (FKBD) of hFKBP25 also binds to immunosuppressive drugs such as rapamycin and FK506, albeit with a lower affinity for the latter. The molecular basis underlying this difference in affinity could not be addressed due to the lack of the crystal structure of hFKBD25 in complex with FK506. Here, we report the crystal structure of hFKBD25 in complex with FK506 determined at 1.8 Å resolution and its comparison with the hFKBD25-rapamycin complex, bringing out the microheterogeneity in the mode of interaction of these drugs, which could possibly explain the lower affinity for FK506.

  12. Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III.

    Science.gov (United States)

    Bezerra, Gustavo A; Dobrovetsky, Elena; Viertlmayr, Roland; Dong, Aiping; Binter, Alexandra; Abramic, Marija; Macheroux, Peter; Dhe-Paganon, Sirano; Gruber, Karl

    2012-04-24

    Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft ("entropy reservoir") as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.

  13. Using Expert Systems in the Management of Industrial Equipment Maintenance

    OpenAIRE

    IOAN CUCU; CODRUŢA DURA; IMOLA DRIGĂ

    2009-01-01

    The term “expert system” generally evokes new management techniques in various fields of activity. The definition of the expert systems in terms of their architecture reveals three basic elements: the knowledgebase containing specialized knowledge in a certain area, taken from the human expert in that field; the facts which include information related to the situation of management and data concerning a certain problem to be solved and the inference engine which is intended to exploit the set...

  14. The substrate binding domains of human SIAH E3 ubiquitin ligases are now crystal clear

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qi; Wang, Zhongduo; Hou, Feng; Harding, Rachel; Huang, Xinyi; Dong, Aiping; Walker, John R.; Tong, Yufeng

    2017-01-01

    Seven in absentia homologs (SIAHs) comprise a family of highly conserved E3 ubiquitin ligases that play an important role in regulating signalling pathways in tumorigenesis, including the DNA damage repair and hypoxia response pathways. SIAH1 and SIAH2 have been found to function as a tumour repressor and a proto-oncogene, respectively, despite the high sequence identity of their substrate binding domains (SBDs). Ubiquitin-specific protease USP19 is a deubiquitinase that forms a complex with SIAHs and counteracts the ligase function. Much effort has been made to find selective inhibitors of the SIAHs E3 ligases. Menadione was reported to inhibit SIAH2 specifically. We used X-ray crystallography, peptide array, bioinformatic analysis, and biophysical techniques to characterize the structure and interaction of SIAHs with deubiquitinases and literature reported compounds. We solved the crystal structures of SIAH1 in complex with a USP19 peptide and of the apo form SIAH2. Phylogenetic analysis revealed the SIAH/USP19 complex is conserved in evolution. We demonstrated that menadione destabilizes both SIAH1 and SIAH2 non-specifically through covalent modification. The SBDs of SIAH E3 ligases are structurally similar with a subtle stability difference. USP19 is the only deubiquitinase that directly binds to SIAHs through the substrate binding pocket. Menadione is not a specific inhibitor for SIAH2. The crystallographic models provide structural insights into the substrate binding of the SIAH family E3 ubiquitin ligases that are critically involved in regulating cancer-related pathways. Our results suggest caution should be taken when using menadione as a specific SIAH2 inhibitor.

  15. Research and Design of a Fuzzy Neural Expert System

    Institute of Scientific and Technical Information of China (English)

    王仕军; 王树林

    1995-01-01

    We have developed a fuzzy neural expert system that has the precision and learning ability of a neural network.Knowledge is acquired from domain experts as fuzzy rules and membership functions.Then,they are converted into a neural network which implements fuzzy inference without rule matching.The neural network is applied to problem-solving and learns from the data obtained during operation to enhance the accuracy.The learning ability of the neural network makes it easy to modify the membership functions defined by domain experts.Also,by modifying the weights of neural networks adaptively,the problem of belief propagation in conventional expert systems can be solved easily.Converting the neural network back into fuzzy rules and membership functions helps explain the inner representation and operation of the neural network.

  16. Variant-specific monoclonal and group-specific polyclonal human immunodeficiency virus type 1 neutralizing antibodies raised with synthetic peptides from the gp120 third variable domain.

    OpenAIRE

    Laman, J. D.; Schellekens, M M; Abacioglu, Y H; Lewis, G K; Tersmette, M; Fouchier, R A; Langedijk, J. P.; Claassen, E.; Boersma, W J

    1992-01-01

    The third variable (V3) domain of the human immunodeficiency virus type 1 (HIV-1) external membrane glycoprotein gp120 is of crucial importance in eliciting neutralizing antibodies in infected persons. Polyclonal (PAb) and monoclonal (MAb) antibodies directed against selected epitopes in the V3 domain are valuable tools for analysis of the involvement of such sequences in neutralization and for definition of the relation between amino acid variability and immunological cross-reactions. The ai...

  17. Purification, crystallization and preliminary X-ray diffraction analysis of the kinase domain of human tousled-like kinase 2

    Energy Technology Data Exchange (ETDEWEB)

    Garrote, Ana M.; Redondo, Pilar [Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid (Spain); Montoya, Guillermo, E-mail: gmontoya@cnio.es [Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid (Spain); University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen (Denmark); Muñoz, Inés G., E-mail: gmontoya@cnio.es [Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid (Spain)

    2014-02-19

    The C-terminal kinase domain of TLK2 (a human tousled-like kinase) has been cloned and overexpressed in Escherichia coli followed by purification to homogeneity. Crystallization experiments in the presence of ATP-γ-S yielded crystals suitable for X-ray diffraction analysis belonging to two different space groups: tetragonal I4{sub 1}22 and cubic P2{sub 1}3. Tousled-like kinases (TLKs) are an evolutionarily conserved family of serine/threonine protein kinases involved in chromatin dynamics, including DNA replication and repair, transcription and chromosome segregation. The two members of the family reported in humans, namely TLK1 and TLK2, localize to the cell nucleus and are capable of forming homo- or hetero-oligomers by themselves. To characterize the role of TLK2, its C-terminal kinase domain was cloned and overexpressed in Escherichia coli followed by purification to homogeneity. Crystallization experiments in the presence of ATP-γ-S yielded crystals suitable for X-ray diffraction analysis belonging to two different space groups: tetragonal I4{sub 1}22 and cubic P2{sub 1}3. The latter produced the best diffracting crystal (3.4 Å resolution using synchrotron radiation), with unit-cell parameters a = b = c = 126.05 Å, α = β = γ = 90°. The asymmetric unit contained one protein molecule, with a Matthews coefficient of 4.59 Å{sup 3} Da{sup −1} and a solvent content of 73.23%.

  18. Suramin blocks interaction between human FGF1 and FGFR2 D2 domain and reduces downstream signaling activity

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Zong-Sian, E-mail: gary810426@hotmail.com [Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan (China); Liu, Che Fu, E-mail: s9823002@m98.nthu.edu.tw [Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan (China); Fu, Brian, E-mail: brianfu9@gmail.com [Northwood High School, Irvine, CA (United States); Chou, Ruey-Hwang, E-mail: rhchou@mail.cmu.edu.tw [Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, No.91, Hsueh-Shih Road, Taichung 40402, Taiwan (China); Department of Biotechnology, Asia University, Taiwan (China); Yu, Chin, E-mail: cyu.nthu@gmail.com [Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan (China)

    2016-09-02

    The extracellular portion of the human fibroblast growth factor receptor2 D2 domain (FGFR2 D2) interacts with human fibroblast growth factor 1 (hFGF1) to activate a downstream signaling cascade that ultimately affects mitosis and differentiation. Suramin is an antiparasiticdrug and a potent inhibitor of FGF-induced angiogenesis. Suramin has been shown to bind to hFGF1, and might block the interaction between hFGF1 and FGFR2 D2. Here, we titrated hFGF1 with FGFR2 D2 and suramin to elucidate their interactions using the detection of NMR. The docking results of both hFGF1-FGFR2 D2 domain and hFGF1-suramin complex were superimposed. The results indicate that suramin blocks the interaction between hFGF1 and FGFR2 D2. We used the PyMOL software to show the hydrophobic interaction of hFGF1-suramin. In addition, we used a Water-soluble Tetrazolium salts assay (WST1) to assess hFGF1 bioactivity. The results will be useful for the development of new antimitogenic activity drugs. - Highlights: • The interfacial residues on hFGF1-FGFR2 D2 and hFGF1-Suramin contact surface were mapped by {sup 1}H-{sup 15}N HSQC experiments. • hFGF1-FGFR2 D2 and hFGF1-Suramin complex models were generated from NMR restraints by using HADDOCK program. • We analyzed hFGF1-Suramin complex models and found the interaction between hFGF1-Suramin is hydrophobic. • The bioactivity of the hFGF1-FGFR2 D2 and hFGF1-Suramin complex was studied by using WST1 assay.

  19. Inhibition of HCV replication by humanized-single domain transbodies to NS4B.

    Science.gov (United States)

    Glab-Ampai, Kittirat; Malik, Aijaz Ahmad; Chulanetra, Monrat; Thanongsaksrikul, Jeeraphong; Thueng-In, Kanyarat; Srimanote, Potjanee; Tongtawe, Pongsri; Chaicumpa, Wanpen

    2016-08-05

    NS4B of hepatitis C virus (HCV) initiates membrane web formation, binds RNA and other HCV proteins for viral replication complex (RC) formation, hydrolyses NTP, and inhibits innate anti-viral immunity. Thus, NS4B is an attractive target of a novel anti-HCV agent. In this study, humanized-nanobodies (VHs/VHHs) that bound to recombinant NS4B were produced by means of phage display technology. The nanobodies were linked molecularly to a cell penetrating peptide, penetratin (PEN), for making them cell penetrable (become transbodies). Human hepatic (Huh7) cells transfected with HCV JFH1-RNA that were treated with transbodies from four Escherichia coli clones (PEN-VHH7, PEN-VHH9, PEN-VH33, and PEN-VH43) had significant reduction of HCV RNA amounts in their culture fluids and intracellularly when compared to the transfected cells treated with control transbody and medium alone. The results were supported by the HCV foci assay. The transbody treated-transfected cells also had upregulation of the studied innate cytokine genes, IRF3, IFNβ and IL-28b. The transbodies have high potential for testing further as a novel anti-HCV agent, either alone, adjunct of existing anti-HCV agents/remedies, or in combination with their cognates specific to other HCV enzymes/proteins.

  20. Development of an expert planning system for OSSA

    Science.gov (United States)

    Groundwater, B.; Lembeck, M. F.; Sarsfield, L.; Diaz, Alphonso

    1988-01-01

    This paper presents concepts related to preliminary work for the development of an expert planning system for NASA's Office for Space Science and Applications (OSSA). The expert system will function as a planner's decision aid in preparing mission plans encompassing sets of proposed OSSA space science initiatives. These plans in turn will be checked against budgetary and technical constraints and tested for constraint violations. Appropriate advice will be generated by the system for making modifications to the plans to bring them in line with the constraints. The OSSA Planning Expert System (OPES) has been designed to function as an integral part of the OSSA mission planning process. It will be able to suggest a best plan, be able to accept and check a user-suggested strawman plan, and should provide a quick response to user request and actions. OPES will be written in the C programming language and have a transparent user interface running under Windows 386 on a Compaq 386/20 machine. The system's sorted knowledge and inference procedures will model the expertise of human planners familiar with the OSSA planning domain. Given mission priorities and budget guidelines, the system first sets the launch dates for each mission. It will check to make sure that planetary launch windows and precursor mission relationships are not violated. Additional levels of constraints will then be considered, checking such things as the availability of a suitable launch vehicle, total mission launch mass required vs. the identified launch mass capability, and the total power required by the payload at its destination vs. the actual power available. System output will be in the form of Gantt charts, spreadsheet hardcopy, and other presentation quality materials detailing the resulting OSSA mission plan.

  1. Expert and Knowledge Based Systems.

    Science.gov (United States)

    Demaid, Adrian; Edwards, Lyndon

    1987-01-01

    Discusses the nature and current state of knowledge-based systems and expert systems. Describes an expert system from the viewpoints of a computer programmer and an applications expert. Addresses concerns related to materials selection and forecasts future developments in the teaching of materials engineering. (ML)

  2. Identification of an antigenic domain in the N-terminal region of avian hepatitis E virus (HEV) capsid protein that is not common to swine and human HEVs.

    Science.gov (United States)

    Wang, Lizhen; Sun, Yani; Du, Taofeng; Wang, Chengbao; Xiao, Shuqi; Mu, Yang; Zhang, Gaiping; Liu, Lihong; Widén, Frederik; Hsu, Walter H; Zhao, Qin; Zhou, En-Min

    2014-12-01

    The antigenic domains located in the C-terminal 268 amino acid residues of avian hepatitis E virus (HEV) capsid protein have been characterized. This region shares common epitopes with swine and human HEVs. However, epitopes in the N-terminal 338 amino acid residues have never been reported. In this study, an antigenic domain located between amino acids 23 and 85 was identified by indirect ELISA using the truncated recombinant capsid proteins as coating antigens and anti-avian HEV chicken sera as primary antibodies. In addition, this domain did not react with anti-swine and human HEV sera. These results indicated that the N-terminal 338 amino acid residues of avian HEV capsid protein do not share common epitopes with swine and human HEVs. This finding is important for our understanding of the antigenicity of the avian HEV capsid protein. Furthermore, it has important implications in the selection of viral antigens for serological diagnosis.

  3. Localization and distribution of fibrinogen C domain containing 1 (FIBCD1) in human tissues

    DEFF Research Database (Denmark)

    von Huth, Sebastian; Møller, Jesper Bonnet; Schlosser, Anders

    have previously shown that FIBCD1 is present at mucosal surfaces in the lung and large intestine. Aim: The present study investigates the distribution and localization of FIBCD1 in various healthy human tissues. Results: We used a monoclonal antibody directed towards the FIBCD1 ectodomain...... in an immunohistochemistry-based analysis and demonstrate that FIBCD1 protein is highly expressed at the apical surfaces of the epithelium throughout the gastrointestinal tract, in the uterus, testis, bladder, gallbladder and the salivary glands. To a lesser extent, FIBCD1 is expressed in the pancreas, the spleen...... and the tonsils. Moreover, using quantitative real-time PCR we demonstrate that FIBCD1 mRNA is highly expressed in the gastrointestinal tract, the lung, the adrenal gland and the testis, which is in coherence with our immunohistochemical findings. Conclusion: FIBCD1 is present at the apical epithelial surfaces...

  4. Leishmania donovani Nucleoside Hydrolase (NH36) Domains Induce T-Cell Cytokine Responses in Human Visceral Leishmaniasis

    Science.gov (United States)

    Barbosa Santos, Micheli Luize; Nico, Dirlei; de Oliveira, Fabrícia Alvisi; Barreto, Aline Silva; Palatnik-de-Sousa, Iam; Carrillo, Eugenia; Moreno, Javier; de Luca, Paula Mello; Morrot, Alexandre; Rosa, Daniela Santoro; Palatnik, Marcos; Bani-Corrêa, Cristiane; de Almeida, Roque Pacheco; Palatnik-de-Sousa, Clarisa Beatriz

    2017-01-01

    Development of immunoprotection against visceral leishmaniasis (VL) focused on the identification of antigens capable of inducing a Th1 immune response. Alternatively, antigens targeting the CD8 and T-regulatory responses are also relevant in VL pathogenesis and worthy of being included in a preventive human vaccine. We assessed in active and cured patients and VL asymptomatic subjects the clinical signs and cytokine responses to the Leishmania donovani nucleoside hydrolase NH36 antigen and its N-(F1), central (F2) and C-terminal (F3) domains. As markers of VL resistance, the F2 induced the highest levels of IFN-γ, IL-1β, and TNF-α and, together with F1, the strongest secretion of IL-17, IL-6, and IL-10 in DTH+ and cured subjects. F2 also promoted the highest frequencies of CD3+CD4+IL-2+TNF-α−IFN-γ−, CD3+CD4+IL-2+TNF-α+IFN-γ−, CD3+CD4+IL-2+TNF-α−IFN-γ+, and CD3+CD4+IL-2+TNF-α+IFN-γ+ T cells in cured and asymptomatic subjects. Consistent with this, the IFN-γ increase was correlated with decreased spleen (R = −0.428, P = 0.05) and liver sizes (R = −0.428, P = 0.05) and with increased hematocrit counts (R = 0.532, P = 0.015) in response to F1 domain, and with increased hematocrit (R = 0.512, P 0.02) and hemoglobin counts (R = 0.434, P = 0.05) in response to F2. Additionally, IL-17 increases were associated with decreased spleen and liver sizes in response to F1 (R = −0.595, P = 0.005) and F2 (R = −0.462, P = 0.04). Conversely, F1 and F3 increased the CD3+CD8+IL-2+TNF-α−IFN-γ−, CD3+CD8+IL-2+TNF-α+IFN-γ−, and CD3+CD8+IL-2+TNF-α+IFN-γ+ T cell frequencies of VL patients correlated with increased spleen and liver sizes and decreased hemoglobin and hematocrit values. Therefore, cure and acquired resistance to VL correlate with the CD4+-Th1 and Th-17 T-cell responses to F2 and F1 domains. Clinical VL outcomes, by contrast, correlate with CD8+ T-cell responses against F3 and F1

  5. EyeFrame: Real-time memory aid improves human multitasking via domain-general eye tracking procedures

    Directory of Open Access Journals (Sweden)

    P. eTaylor

    2015-09-01

    Full Text Available OBJECTIVE: We developed an extensively general closed-loop system to improve human interaction in various multitasking scenarios, with semi-autonomous agents, processes, and robots. BACKGROUND: Much technology is converging toward semi-independent processes with intermittent human supervision distributed over multiple computerized agents. Human operators multitask notoriously poorly, in part due to cognitive load and limited working memory. To multitask optimally, users must remember task order, e.g., the most neglected task, since longer times not monitoring an element indicates greater probability of need for user input. The secondary task of monitoring attention history over multiple spatial tasks requires similar cognitive resources as primary tasks themselves. Humans can not reliably make more than ~2 decisions/s. METHODS: Participants managed a range of 4-10 semi-autonomous agents performing rescue tasks. To optimize monitoring and controlling multiple agents, we created an automated short term memory aid, providing visual cues from users' gaze history. Cues indicated when and where to look next, and were derived from an inverse of eye fixation recency. RESULTS: Contingent eye tracking algorithms drastically improved operator performance, increasing multitasking capacity. The gaze aid reduced biases, and reduced cognitive load, measured by smaller pupil dilation. CONCLUSIONS: Our eye aid likely helped by delegating short-term memory to the computer, and by reducing decision making load. Past studies used eye position for gaze-aware control and interactive updating of displays in application-specific scenarios, but ours is the first to successfully implement domain-general algorithms. Procedures should generalize well to: process control, factory operations, robot control, surveillance, aviation, air traffic control, driving, military, mobile search and rescue, and many tasks where probability of utility is predicted by duration since last

  6. Planning bioinformatics workflows using an expert system.

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T

    2017-04-15

    Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. https://github.com/jefftc/changlab. jeffrey.t.chang@uth.tmc.edu.

  7. Development of expert thinking: The role of goal-oriented practice and practicing

    Directory of Open Access Journals (Sweden)

    Krnjaić Zora

    2013-01-01

    Full Text Available Exceptional achievements, expert masteries, masterful performances and creative products can be attained only after a number of years of guided and well-devised practice or goal-oriented practicing. We are dealing with a long-term, systematic and carefully guided training which gradually, step by step, leads towards developing expertise and producing supreme achievements and performances in different areas of human activities. This paper explores the role of goal-oriented practice in the development of expert thinking in science, its characteristics and levels of development. Expert thinking in science is defined as the competence developed through learning and practicing of a certain scientific discipline within systematic education and training as an integral part of artificial development. The goal-oriented practice takes place in phases. Its important feature is a gradual and carefully guided progress and enhancement of abilities that is achieved through meaningful tasks and relevant activities suited to age and the level of expertise in a particular domain, along with constant improvement of activities based on feedback provided by mentors. On the path of development of expertise and expert thinking in science, as one of the forms of manifesting giftedness, an individual needs to be ready to invest efforts, set aside the time and be dedicated to work, as well as to have the possibilities and opportunities to pursue scientific research. [Projekat Ministarstva nauke Republike Srbije, br. 179018: Identifikacija, merenje i razvoj kognitivnih i emocionalnih kompetencija važnih društvu orijentisanom na evropske integracije

  8. Human and mouse ZFY genes produce a conserved testis-specific transcript encoding a zinc finger protein with a short acidic domain and modified transactivation potential.

    Science.gov (United States)

    Decarpentrie, Fanny; Vernet, Nadège; Mahadevaiah, Shantha K; Longepied, Guy; Streichemberger, Eric; Aknin-Seifer, Isabelle; Ojarikre, Obah A; Burgoyne, Paul S; Metzler-Guillemain, Catherine; Mitchell, Michael J

    2012-06-15

    Mammalian ZFY genes are located on the Y chromosome, and code putative transcription factors with 12-13 zinc fingers preceded by a large acidic (activating) domain. In mice, there are two genes, Zfy1 and Zfy2, which are expressed mainly in the testis. Their transcription increases in germ cells as they enter meiosis, both are silenced by meiotic sex chromosome inactivation (MSCI) during pachytene, and Zfy2 is strongly reactivated later in spermatids. Recently, we have shown that mouse Zfy2, but not Zfy1, is involved in triggering the apoptotic elimination of specific types of sex chromosomally aberrant spermatocytes. In humans, there is a single widely transcribed ZFY gene, and there is no evidence for a specific role in the testis. Here, we characterize ZFY transcription during spermatogenesis in mice and humans. In mice, we define a variety of Zfy transcripts, among which is a Zfy2 transcript that predominates in spermatids, and a Zfy1 transcript, lacking an exon encoding approximately half of the acidic domain, which predominates prior to MSCI. In humans, we have identified a major testis-specific ZFY transcript that encodes a protein with the same short acidic domain. This represents the first evidence that ZFY has a conserved function during human spermatogenesis. We further show that, in contrast to the full acidic domain, the short domain does not activate transcription in yeast, and we hypothesize that this explains the functional difference observed between Zfy1 and Zfy2 during mouse meiosis.

  9. Experts on public trial

    DEFF Research Database (Denmark)

    Blok, Anders

    2007-01-01

    Citizen deliberation on technoscientific developments is regularly regarded as a hallmark of Danish democracy, embodied in particular by the Danish Board of Technology. Few empirically guided questions have been raised, however, as to how the Board's democratic projects actually work. Through...... a case study of the May 2003 Danish consensus conference on environmental economics as a policy tool, the article reflects on the politics of expert authority permeating practices of public participation. Adopting concepts from the sociology of scientific knowledge (SSK), the conference is seen...

  10. Expert Oracle Exadata

    CERN Document Server

    Johnson, Randy

    2011-01-01

    Throughout history, advances in technology have come in spurts. A single great idea can often spur rapid change as the idea takes hold and is propagated, often in totally unexpected directions. Exadata embodies such a change in how we think about and manage relational databases. The key change lies in the concept of offloading SQL processing to the storage layer. That concept is a huge win, and its implementation in the form of Exadata is truly a game changer. Expert Oracle Exadata will give you a look under the covers at how the combination of hardware and software that comprise Exadata actua

  11. Expert Systems Development Methodology

    Science.gov (United States)

    1989-07-28

    expert systems has been hardware development. In the middle 1950’s at the very birth of AI, hardware was large very slow and extremely expensive. In...into another report. For example, MOBPLEX provides output into the Lotus spreadsheet as a semi-automated destination. From the spreadsheet the user of...designed on top of the Lotus 1-2- 3 interface. Lotus was used because it was decided there was no need to build a powerful ad hoc report generator

  12. Transmembrane domain II of the human bile acid transporter SLC10A2 coordinates sodium translocation.

    Science.gov (United States)

    Sabit, Hairat; Mallajosyula, Sairam S; MacKerell, Alexander D; Swaan, Peter W

    2013-11-01

    Human apical sodium-dependent bile acid transporter (hASBT, SLC10A2) is responsible for intestinal reabsorption of bile acids and plays a key role in cholesterol homeostasis. We used a targeted and systematic approach to delineate the role of highly conserved transmembrane helix 2 on the expression and function of hASBT. Cysteine mutation significantly depressed transport activity for >60% of mutants without affecting cell surface localization of the transporter. All mutants were inaccessible toward chemical modification by membrane-impermeant MTSET reagent, strongly suggesting that transmembrane 2 (TM2) plays an indirect role in bile acid substrate translocation. Both bile acid uptake and sodium dependence of TM2 mutants revealed a distinct α-helical periodicity. Kinetic studies with conservative and non-conservative mutants of sodium sensitive residues further underscored the importance of Gln(75), Phe(76), Met(79), Gly(83), Leu(86), Phe(90), and Asp(91) in hASBT function. Computational analysis indicated that Asp(91) may coordinate with sodium during the transport cycle. Combined, our data propose that a consortium of sodium-sensitive residues along with previously reported residues (Thr(134), Leu(138), and Thr(149)) from TM3 may form the sodium binding and translocation pathway. Notably, residues Gln(75), Met(79), Thr(82), and Leu(86) from TM2 are highly conserved in TM3 of a putative remote bacterial homologue (ASBTNM), suggesting a universal mechanism for the SLC10A transporter family.

  13. Solution structure and membrane-binding property of the N-terminal tail domain of human annexin I.

    Science.gov (United States)

    Yoon, M K; Park, S H; Won, H S; Na, D S; Lee, B J

    2000-11-10

    The conformational preferences of AnxI(N26), a peptide corresponding to residues 2-26 of human annexin I, were investigated using CD and NMR spectroscopy. CD results showed that AnxI(N26) adopts a mainly alpha-helical conformation in membrane-mimetic environments, TFE/water and SDS micelles, while a predominantly random structure with slight helical propensity in aqueous buffer. The helical region of AnxI(N26) showed a nearly identical conformation between in TFE/water and in SDS micelles, except for the orientation of the Trp-12 side-chain, which was quite different between the two. The N-terminal region of the AnxI(N26) helix showed a typical amphipathic nature, which could be stabilized by the neighboring hydrophobic cluster. The helical stability of the peptide in SDS micelles was increased by addition of calcium ions. These results suggest that the N-terminal tail domain of human annexin I interacts with biological membranes in a partially calcium-dependent manner.

  14. Extending the Serum Half-Life of G-CSF via Fusion with the Domain III of Human Serum Albumin

    Directory of Open Access Journals (Sweden)

    Shuqiang Zhao

    2013-01-01

    Full Text Available Protein fusion technology is one of the most commonly used methods to extend the half-life of therapeutic proteins. In this study, in order to prolong the half-life of Granulocyte colony stimulating factor (G-CSF, the domain III of human serum albumin (3DHSA was genetically fused to the N-terminal of G-CSF. The 3DHSA-G-CSF fusion gene was cloned into pPICZαA along with the open reading frame of the α-factor signal under the control of the AOX1 promoter. The recombinant expression vector was transformed into Pichia pastoris GS115, and the recombinant strains were screened by SDS-PAGE. As expected, the 3DHSA-G-CSF showed high binding affinity with HSA antibody and G-CSF antibody, and the natural N-terminal of 3DHSA was detected by N-terminal sequencing. The bioactivity and pharmacokinetic studies of 3DHSA-G-CSF were respectively determined using neutropenia model mice and human G-CSF ELISA kit. The results demonstrated that 3DHSA-G-CSF has the ability to increase the peripheral white blood cell (WBC counts of neutropenia model mice, and the half-life of 3DHSA-G-CSF is longer than that of native G-CSF. In conclusion, 3DHSA can be used to extend the half-life of G-CSF.

  15. The SET2-RPB1 interaction domain of human RECQ5 is important for transcription-associated genome stability.

    Science.gov (United States)

    Li, Min; Xu, Xiaohua; Liu, Yilun

    2011-05-01

    The conserved RECQ5 DNA helicase is a tumor suppressor in mammalian cells. Defects in RECQ5 lead to the accumulation of spontaneous DNA double-stranded breaks (DSBs) during replication, despite the fact that these cells are proficient in DSB repair by homologous recombination (HR). The reason for this is unknown. Here, we demonstrate that these DSBs are linked to RNA polymerase II (RNAPII)-dependent transcription. In human RECQ5-depleted cells, active RNAPII accumulates on chromatin, and DNA breaks are associated with an RNAPII-dependent transcribed locus. Hence, transcription inhibition eliminates both active RNAPII and spontaneous DSB formation. In addition, the regulatory effect of RECQ5 on transcription and its interaction with RNAPII are enhanced in S-phase cells, supporting a role for RECQ5 in preventing transcription-associated DSBs during replication. Finally, we show that the SET2-RPB1 interaction (SRI) domain of human RECQ5 is important for suppressing spontaneous DSBs and the p53-dependent transcription stress response caused by the stalling of active RNAPII on DNA. Thus, our studies provide novel insights into a mechanism by which RECQ5 regulates the transcription machinery via its dynamic interaction with RNAPII, thereby preventing genome instability.

  16. Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication

    Science.gov (United States)

    Rustiguel, Joane K.; Soares, Ricardo O. S.; Meisburger, Steve P.; Davis, Katherine M.; Malzbender, Kristina L.; Ando, Nozomi; Dias-Baruffi, Marcelo; Nonato, Maria Cristina

    2016-09-01

    Galectins are proteins involved in diverse cellular contexts due to their capacity to decipher and respond to the information encoded by β-galactoside sugars. In particular, human galectin-4, normally expressed in the healthy gastrointestinal tract, displays differential expression in cancerous tissues and is considered a potential drug target for liver and lung cancer. Galectin-4 is a tandem-repeat galectin characterized by two carbohydrate recognition domains connected by a linker-peptide. Despite their relevance to cell function and pathogenesis, structural characterization of full-length tandem-repeat galectins has remained elusive. Here, we investigate galectin-4 using X-ray crystallography, small- and wide-angle X-ray scattering, molecular modelling, molecular dynamics simulations, and differential scanning fluorimetry assays and describe for the first time a structural model for human galectin-4. Our results provide insight into the structural role of the linker-peptide and shed light on the dynamic characteristics of the mechanism of carbohydrate recognition among tandem-repeat galectins.

  17. Artificial Experts: The Computer as Diagnostician Has Definite Limits.

    Science.gov (United States)

    Pournelle, Jerry

    1984-01-01

    Argues that, although expert systems--which are supposed to give users all the advantages of consulting with human experts--can be useful for medical diagnosis, where tests tend to be reliable, they can be hazardous in such areas as psychological testing, where test reliability is difficult to measure. (MBR)

  18. Artificial Experts: The Computer as Diagnostician Has Definite Limits.

    Science.gov (United States)

    Pournelle, Jerry

    1984-01-01

    Argues that, although expert systems--which are supposed to give users all the advantages of consulting with human experts--can be useful for medical diagnosis, where tests tend to be reliable, they can be hazardous in such areas as psychological testing, where test reliability is difficult to measure. (MBR)

  19. Social Work Expert Testimony Regarding Mitigation in Capital Sentencing Proceedings.

    Science.gov (United States)

    Andrews, Arlene Bowers

    1991-01-01

    Notes that, during sentencing phase of capital trial, social worker can have potentially powerful influence on proceedings by presenting comprehensive, reliable social history, and expert opinion based on accepted theory and research regarding human behavior in social environment. Reviews social worker's role as expert witness, ethical issues,…

  20. Human ClC-6 is a late endosomal glycoprotein that associates with detergent-resistant lipid domains.

    Directory of Open Access Journals (Sweden)

    Sofie Ignoul

    and ClC-7 when cotransfected in COS-1 cells. CONCLUSIONS: We conclude that human ClC-6 is an endosomal glycoprotein that partitions in detergent resistant lipid domains. The differential sorting of endogenous (late endosomal versus overexpressed (early and recycling endosomal ClC-6 is reminiscent of that of other late endosomal/lysosomal membrane proteins (e.g. LIMP II, and is consistent with a rate-limiting sorting step for ClC-6 between early endosomes and its final destination in late endosomes.

  1. The B-subdomain of the Xenopus laevis XFIN KRAB-AB domain is responsible for its weaker transcriptional repressor activity compared to human ZNF10/Kox1.

    Directory of Open Access Journals (Sweden)

    Nadine Born

    Full Text Available The Krüppel-associated box (KRAB domain interacts with the nuclear hub protein TRIM28 to initiate or mediate chromatin-dependent processes like transcriptional repression, imprinting or suppression of endogenous retroviruses. The prototype KRAB domain initially identified in ZNF10/KOX1 encompasses two subdomains A and B that are found in hundreds of zinc finger transcription factors studied in human and murine genomes. Here we demonstrate for the first time transcriptional repressor activity of an amphibian KRAB domain. After sequence correction, the updated KRAB-AB domain of zinc finger protein XFIN from the frog Xenopus laevis was found to confer transcriptional repression in reporter assays in Xenopus laevis A6 kidney cells as well as in human HeLa, but not in the minnow Pimephales promelas fish cell line EPC. Binding of the XFIN KRAB-AB domain to human TRIM28 was demonstrated in a classical co-immunoprecipitation approach and visualized in a single-cell compartmentalization assay. XFIN-AB displayed reduced potency in repression as well as lower strength of interaction with TRIM28 compared to ZNF10 KRAB-AB. KRAB-B subdomain swapping between the two KRAB domains indicated that it was mainly the KRAB-B subdomain of XFIN that was responsible for its lower capacity in repression and binding to human TRIM28. In EPC fish cells, ZNF10 and XFIN KRAB repressor activity could be partially restored to low levels by adding exogenous human TRIM28. In contrast to XFIN, we did not find any transcriptional repression activity for the KRAB-like domain of human PRDM9 in HeLa cells. PRDM9 is thought to harbor an evolutionary older domain related to KRAB whose homologs even occur in invertebrates. Our results support the notion that functional bona fide KRAB domains which confer transcriptional repression and interact with TRIM28 most likely co-evolved together with TRIM28 at the beginning of tetrapode evolution.

  2. The Research of System Architecture in Expert System

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper illustrated the software architecture of our concretesafet y expert system. Three advanced technologies are proposed and have been applied to our expert system to greatly improve the intelligent level, which are human- compu ter interaction technology (conceptual model, dialogue management, interface ent ity and interface construct), intelligent agency user interface (IAUI) and compo nent technology. The i mportant character of the system architecture in our expert system is adapting a dvanced intelligent interface and scientific integration of various components d ifferent from common system architecture of expert system. Especially, in the in terface-friendly multimedia system intelligent interface is required.

  3. Activation of nucleotide oligomerization domain 2 (NOD2 by human cytomegalovirus initiates innate immune responses and restricts virus replication.

    Directory of Open Access Journals (Sweden)

    Arun Kapoor

    Full Text Available Nucleotide-binding oligomerization domain 2 (NOD2 is an important innate immune sensor of bacterial pathogens. Its induction results in activation of the classic NF-κB pathway and alternative pathways including type I IFN and autophagy. Although the importance of NOD2 in recognizing RNA viruses has recently been identified, its role in sensing DNA viruses has not been studied. We report that infection with human cytomegalovirus (HCMV results in significant induction of NOD2 expression, beginning as early as 2 hours post infection and increasing steadily 24 hours post infection and afterwards. Infection with human herpesvirus 1 and 2 does not induce NOD2 expression. While the HCMV-encoded glycoprotein B is not required for NOD2 induction, a replication competent virion is necessary. Lentivirus-based NOD2 knockdown in human foreskin fibroblasts (HFFs and U373 glioma cells leads to enhanced HCMV replication along with decreased levels of interferon beta (IFN-β and the pro-inflammatory cytokine, IL8. NOD2 induction in HCMV-infected cells activates downstream NF-κB and interferon pathways supported by reduced nuclear localization of NF-κB and pIRF3 in NOD2 knockdown HFFs. Stable overexpression of NOD2 in HFFs restricts HCMV replication in association with increased levels of IFN-β and IL8. Similarly, transient overexpression of NOD2 in U373 cells or its downstream kinase, RIPK2, results in decreased HCMV replication and enhanced cytokine responses. However, overexpression of a mutant NOD2, 3020insC, associated with severe Crohn's disease, results in enhanced HCMV replication and decreased levels of IFN-β in U373 cells. These results show for the first time that NOD2 plays a significant role in HCMV replication and may provide a model for studies of HCMV recognition by the host cell and HCMV colitis in Crohn's disease.

  4. Enhancing Transparency in Multidisciplinary Expert Communication

    Energy Technology Data Exchange (ETDEWEB)

    Hukki, Kristiina; Pulkkinen, Urho [VTT Industrial Systems (Finland)

    2003-10-01

    enhancing mutual understanding the models help in the integration of the knowledge produced by different disciplines and in the reconciliation of the requirements of different parties. They also improve the interaction between the domain experts and the experts of safety assessment. Better awareness of the knowledge-related dependencies enhance the unity of the experts' safety conceptions and contributes to more unified communicating practices in the organization. On the basis of its holistic and integrating character, the safety assessment seems to provide a common perspective to the modelling of the work processes. Using it as a tool for understanding the significance of the safety-critical aspects of work will probably make it more accessible for the domain experts. The safety assessment aims at results, which are expected to be transdisciplinary by nature. It can be assumed, that the common conceptualization and modelling with the help of it facilitate the development from multidisciplinarity to true transdisciplinarity in the expert work.

  5. Regulatory roles of the N-terminal domain based on crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands.

    Science.gov (United States)

    Knoechel, Thorsten R; Tucker, Alec D; Robinson, Colin M; Phillips, Chris; Taylor, Wendy; Bungay, Peter J; Kasten, Shane A; Roche, Thomas E; Brown, David G

    2006-01-17

    Pyruvate dehydrogenase kinase (PDHK) regulates the activity of the pyruvate dehydrogenase multienzyme complex. PDHK inhibition provides a route for therapeutic intervention in diabetes and cardiovascular disorders. We report crystal structures of human PDHK isozyme 2 complexed with physiological and synthetic ligands. Several of the PDHK2 structures disclosed have C-terminal cross arms that span a large trough region between the N-terminal regulatory (R) domains of the PDHK2 dimers. The structures containing bound ATP and ADP demonstrate variation in the conformation of the active site lid, residues 316-321, which enclose the nucleotide beta and gamma phosphates at the active site in the C-terminal catalytic domain. We have identified three novel ligand binding sites located in the R domain of PDHK2. Dichloroacetate (DCA) binds at the pyruvate binding site in the center of the R domain, which together with ADP, induces significant changes at the active site. Nov3r and AZ12 inhibitors bind at the lipoamide binding site that is located at one end of the R domain. Pfz3 (an allosteric inhibitor) binds in an extended site at the other end of the R domain. We conclude that the N-terminal domain of PDHK has a key regulatory function and propose that the different inhibitor classes act by discrete mechanisms. The structures we describe provide insights that can be used for structure-based design of PDHK inhibitors.

  6. DNA double-strand breaks coupled with PARP1 and HNRNPA2B1 binding sites flank coordinately expressed domains in human chromosomes.

    Directory of Open Access Journals (Sweden)

    Nickolai A Tchurikov

    2013-04-01

    Full Text Available Genome instability plays a key role in multiple biological processes and diseases, including cancer. Genome-wide mapping of DNA double-strand breaks (DSBs is important for understanding both chromosomal architecture and specific chromosomal regions at DSBs. We developed a method for precise genome-wide mapping of blunt-ended DSBs in human chromosomes, and observed non-random fragmentation and DSB hot spots. These hot spots are scattered along chromosomes and delimit protected 50-250 kb DNA domains. We found that about 30% of the domains (denoted forum domains possess coordinately expressed genes and that PARP1 and HNRNPA2B1 specifically bind DNA sequences at the forum domain termini. Thus, our data suggest a novel type of gene regulation: a coordinated transcription or silencing of gene clusters delimited by DSB hot spots as well as PARP1 and HNRNPa2B1 binding sites.

  7. MOORE: A prototype expert system for diagnosing spacecraft problems

    Science.gov (United States)

    Howlin, Katherine; Weissert, Jerry; Krantz, Kerry

    1988-01-01

    MOORE is a rule-based, prototype expert system that assists in diagnosing operational Tracking and Data Relay Satellite (TDRS) problems. It is intended to assist spacecraft engineers at the TDRS ground terminal in trouble shooting problems that are not readily solved with routine procedures, and without expert counsel. An additional goal of the prototype system is to develop in-house expert system and knowledge engineering skills. The prototype system diagnoses antenna pointing and earth pointing problems that may occur within the TDRS Attitude Control System (ACS). Plans include expansion to fault isolation of problems in the most critical subsystems of the TDRS spacecraft. Long term benefits are anticipated with use of an expert system during future TDRS programs with increased mission support time, reduced problem solving time, and retained expert knowledge and experience. Phase 2 of the project is intended to provide NASA the necessary expertise and capability to define requirements, evaluate proposals, and monitor the development progress of a highly competent expert system for NASA's Tracking Data Relay Satellite. Phase 2 also envisions addressing two unexplored applications for expert systems, spacecraft integration and tests (I and T) and support to launch activities. The concept, goals, domain, tools, knowledge acquisition, developmental approach, and design of the expert system. It will explain how NASA obtained the knowledge and capability to develop the system in-house without assistance from outside consultants. Future plans will also be presented.

  8. Mutagenesis in the switch IV of the helical domain of the human Gsalpha reduces its GDP/GTP exchange rate.

    Science.gov (United States)

    Echeverría, V; Hinrichs, M V; Torrejón, M; Ropero, S; Martinez, J; Toro, M J; Olate, J

    2000-01-01

    The Galpha subunits of heterotrimeric G proteins are constituted by a conserved GTPase "Ras-like" domain (RasD) and by a unique alpha-helical domain (HD). Upon GTP binding, four regions, called switch I, II, III, and IV, have been identified as undergoing structural changes. Switch I, II, and III are located in RasD and switch IV in HD. All Galpha known functions, such as GTPase activity and receptor, effector, and Gbetagamma interaction sites have been found to be localized in RasD, but little is known about the role of HD and its switch IV region. Through the construction of chimeras between human and Xenopus Gsalpha we have previously identified a HD region, encompassing helices alphaA, alphaB, and alphaC, that was responsible for the observed functional differences in their capacity to activate adenylyl cyclase (Antonelli et al. [1994]: FEBS Lett 340:249-254). Since switch IV is located within this region and contains most of the nonconservative amino acid differences between both Gsalpha proteins, in the present work we constructed two human Gsalpha mutant proteins in which we have changed four and five switch IV residues for the ones present in the Xenopus protein. Mutants M15 (hGsalphaalphaS133N, M135P, P138K, P143S) and M17 (hGsalphaalphaS133N, M135P, V137Y, P138K, P143S) were expressed in Escherichia coli, purified, and characterized by their ability to bind GTPgammaS, dissociate GDP, hydrolyze GTP, and activate adenylyl cyclase. A decreased rate of GDP release, GTPgammaS binding, and GTP hydrolysis was observed for both mutants, M17 having considerably slower kinetics than M15 for all functions tested. Reconstituted adenylyl cyclase activity with both mutants showed normal activation in the presence of AlF(4)(-), but a decreased activation with GTPgammaS, which is consistent with the lower GDP dissociating rate they displayed. These data provide new evidence on the role that HD is playing in modulating the GDP/GTP exchange of the Gsalpha subunit.

  9. Expert system rheometry

    Directory of Open Access Journals (Sweden)

    Samiul Amin

    2009-09-01

    Full Text Available Inks, drilling fluids, shower gels and drug delivery vehicles are just a few examples of the many industrial and consumer products based on colloidal and nanostructured complex fluids. The successful formulation of these materials is promoted by understanding how rheological behaviour, which typically dictates performance, relates to underlying microstructure. However, this knowledge can be difficult to obtain for those without the necessary expertise. This article shows how recent developments in rheometer technology address this issue. New rheometers, exemplified by the Kinexus from Malvern have expert knowledge embedded within the instrument and are able to guide users through measurement and data analysis to relevant information. Such systems facilitate development of the design rules to optimize formulations and generate novel and high performance materials of the future.

  10. WES: A well test analysis expert system

    Energy Technology Data Exchange (ETDEWEB)

    Mensch, A.

    1988-06-01

    This report describes part of the development of an expert system in the domain of well-test analysis. This work has been done during my final internship, completed at the Lawrence Berkeley Laboratory. The report is divided in three parts: the first one gives a description of the state of the project at the time I first began to work on it, and raises some problems that have to be solved. The second section shows the results that have been reached, and the last one draws conclusions from these results and proposes extensions that would be useful in the future.

  11. Typing of core and backbone domains of mucin-type oligosaccharides from human ovarian-cyst glycoproteins by 500-MHz 1H-NMR spectroscopy

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Mutsaers, J.H.G.M.; Halbeek, H. van; Wu, A.M.; Kabat, E.A.

    1986-01-01

    Human blood-group A active glycoproteins from ovarian-cyst fluid were subjected to Smith degradation and subsequent beta-elimination. The resulting oligosaccharide-alditols represent the core and backbone domains of the O-linked carbohydrate chains. Nine of these, ranging in size from disaccharides

  12. Conclusions, Research Needs, and Recommendations of the Expert Panel: Technical Workshop on Human Milk Surveillance and Research for Environmental Chemicals in the U.S.

    Science.gov (United States)

    Proceedings of "The Technical Workshop on Human Milk Surveillance and Research on Environmental Chemicals in the United States" was organized to develop state-of-the-science protocols describing the various aspects of such a program. The 2-day workshop was held at the Mi...

  13. Expert Systems for the Analytical Laboratory.

    Science.gov (United States)

    de Monchy, Allan R.; And Others

    1988-01-01

    Discusses two computer problem solving programs: rule-based expert systems and decision analysis expert systems. Explores the application of expert systems to automated chemical analyses. Presents six factors to consider before using expert systems. (MVL)

  14. Expert Systems as Tools for Technical Communicators.

    Science.gov (United States)

    Grider, Daryl A.

    1994-01-01

    Discusses expertise, what an expert system is, what an expert system shell is, what expert systems can and cannot do, knowledge engineering and technical communicators, and planning and managing expert system projects. (SR)

  15. Kinase domain insert containing receptor promoter controlled suicide gene system selectively kills human umbilical vein endothelial cells

    Institute of Scientific and Technical Information of China (English)

    Wen-Yu Yang; Zong-Hai Huang; Li-Jun Lin; Zhou Li; Jing-Long Yu; Hui-Juan Song; Yong Qian; Xiao-Yan Che

    2006-01-01

    AIM: To study the selective killing of human umbilical vein endothelial cells (HUVECs) by a double suicide gene under the regulation of a kinase domain insert containing receptor (KDR) promoter and mediated by an adenoviral gene vector.METHODS: Human KDR promoter was cloned by polymerase chain reaction (PCR), and two recombinant adenoviral plasmids pAdKDR-CdglyTK, pAdCMV-CDglyTK were constructed according to a two-step transformation protocol. These two newly constructed plasmids were then transfected into 293 packaging cells to grow adenovirus, which were further multiplied and purified.HUVECs and LoVo cells were infected with either of the two resultant recombinant adenoviruses (AdKDR-CDglyTK and AdCMV-CDglyTK) respectively, and the infection rates were estimated by detection of green fluorescent protein (GFP) expression. Infected cells were cultured in culture media containing different concentrations of 5-fluorocytosine (5-FC) and ganciclovir (GCV), and the killing effects were measured.RESULTS: The two recombinant adenoviral plasmids pAdKDR-CdglyTK, pAdCMV-CDglyTK were successfully constructed and transfected into 293 cells. The resultant recombinant adenoviruses infected cells caused similar infection rates; and the infected cells exhibited different sensitivity to the prodrugs: HUVECs infected with AdCMV-CDglyTK and LoVo cells infected with AdCMVCDglyTK were highly sensitive to the prodrugs, and HUVECs infected with AdKDR-CDglyTK were similarly sensitive but significantly more sensitive than the LoVo cells infected with AdKDR-CdglyTK (P<0.001).CONCLJSION: Selective killing of HUVECs may be achieved by gene transfer of double suicide gene under the regulation of the KDR promoter. This finding may provide an optional way to target gene therapy of malignant tumors by abrogation of tumor blood vessels.

  16. Deficiency of caspase recruitment domain family, member 11 (CARD11), causes profound combined immunodeficiency in human subjects.

    Science.gov (United States)

    Stepensky, Polina; Keller, Baerbel; Buchta, Mary; Kienzler, Anne-Kathrin; Elpeleg, Orly; Somech, Raz; Cohen, Sivan; Shachar, Idit; Miosge, Lisa A; Schlesier, Michael; Fuchs, Ilka; Enders, Anselm; Eibel, Hermann; Grimbacher, Bodo; Warnatz, Klaus

    2013-02-01

    Profound combined immunodeficiency can present with normal numbers of T and B cells, and therefore the functional defect of the cellular and humoral immune response is often not recognized until the first severe clinical manifestation. Here we report a patient of consanguineous descent presenting at 13 months of age with hypogammaglobulinemia, Pneumocystis jirovecii pneumonia, and a suggestive family history. We sought to identify the genetic alteration in a patient with combined immunodeficiency and characterize human caspase recruitment domain family, member 11 (CARD11), deficiency. Molecular, immunologic, and functional assays were performed. The immunologic characterization revealed only subtle changes in the T-cell and natural killer cell compartment, whereas B-cell differentiation, although normal in number, was distinctively blocked at the transitional stage. Genetic evaluation revealed a homozygous deletion of exon 21 in CARD11 as the underlying defect. This deletion abrogated protein expression and activation of the canonical nuclear factor κB (NF-κB) pathway in lymphocytes after antigen receptor or phorbol 12-myristate 13-acetate stimulation, whereas CD40 signaling in B cells was preserved. The abrogated activation of the canonical NF-κB pathway was associated with severely impaired upregulation of inducible T-cell costimulator, OX40, cytokine production, proliferation of T cells, and B cell-activating factor receptor expression on B cells. Thus in patients with CARD11 deficiency, the combination of impaired activation and especially upregulation of inducible T-cell costimulator on T cells, together with severely disturbed peripheral B-cell differentiation, apparently leads to a defective T-cell/B-cell cooperation and probably germinal center formation and clinically results in severe immunodeficiency. This report discloses the crucial and nonredundant role of canonical NF-κB activation and specifically CARD11 in the antigen-specific immune response

  17. Downregulation of discoidin domain receptor 2 in A375 human melanoma cells reduces its experimental liver metastasis ability.

    Science.gov (United States)

    Badiola, Iker; Villacé, Patricia; Basaldua, Iratxe; Olaso, Elvira

    2011-10-01

    Discoidin domain receptors (DDR1 and DDR2) are tyrosine kinase receptors for fibrillar collagen implicated in postnatal development, tissue repair, and primary and metastatic cancer progression. While DDR1 has been described in tumor cells, DDR2 has been localized in the tumor stroma, but its presence in the tumor cells remains unknown. The aim of this study was to elucidate the role of DDR2 signaling in tumor cells during hepatic metastasis progression. DDR2 expression and phosphorylation in cultured human A375 melanoma cells was documented by Western blot analysis. A375 cells were stably transfected with a small interfering RNA (siRNA) against DDR2 and two clones were selected: A375R2-70 and A375R2-40, with 70 and 40% of the DDR2 protein expression respectively, compared to mock-transfected cells (A375R2-100). Development of experimental liver metastasis by intrasplenic inoculation of A375R2-70 and A37R2-40 clones was reduced by 60 and 75%, respectively, measured as tumor volume, compared to livers injected with A375R2-100 cells. Accordingly, A375R2-70 and A37R2-40 clones showed reduced in vitro gelatinase activity and JNK phosphorylation, compared to mock transfected cells, with maximal inhibition in A375R2-40. Additionally, A375 melanoma, SK-HEP hepatoma and HT-29 colon carcinoma human cell lines transiently transfected with siRNA against DDR2 also showed reduced proliferation and migration rates compared to mock-transfected ones. In conclusion, DDR2 promotes A375 melanoma metastasis to the liver and the underlying mechanism implicates regulation of metalloproteinase release, cell growth and chemotactic invasion of the host tissue.

  18. Non-Linear and Flexible Regions of the Human Notch1 Extracellular Domain Revealed by High-Resolution Structural Studies.

    Science.gov (United States)

    Weisshuhn, Philip C; Sheppard, Devon; Taylor, Paul; Whiteman, Pat; Lea, Susan M; Handford, Penny A; Redfield, Christina

    2016-04-05

    The Notch receptor is a key component of a core metazoan signaling pathway activated by Delta/Serrate/Lag-2 ligands expressed on an adjacent cell. This results in a short-range signal with profound effects on cell-fate determination, cell proliferation, and cell death. Key to understanding receptor function is structural knowledge of the large extracellular portion of Notch which contains multiple repeats of epidermal growth factor (EGF)-like domains. Here we investigate the EGF4-13 region of human Notch1 (hN1) using a multidisciplinary approach. Ca(2+)-binding measurements, X-ray crystallography, {(1)H}-(15)N heteronuclear nuclear Overhauser effects, and residual dipolar couplings support a non-linear organization for the EGF4-13 region with a rigid, bent conformation for EGF4-7 and a single flexible linkage between EGF9 and EGF10. These data allow us to construct an informed model for EGF10-13 which, in conjunction with comparative binding studies, demonstrates that EGF10 has an important role in determining Notch receptor sensitivity to Dll-4.

  19. Energetic domains and conformational analysis of human serum albumin upon co-incubation with sodium benzoate and glucose.

    Science.gov (United States)

    Taghavi, F; Moosavi-Movahedi, A A; Bohlooli, M; Habibi-Rezaei, M; Hadi Alijanvand, H; Amanlou, M; Sheibani, N; Saboury, A A; Ahmad, F

    2014-01-01

    Sodium benzoate (SB), a powerful inhibitor of microbial growth, is one of the most commonly used food preservative. Here, we determined the effects of SB on human serum albumin (HSA) structure in the presence or absence of glucose after 35 days of incubation under physiological conditions. The biochemical, biophysical, and molecular approaches including free amine content assay (TNBSA assay), fluorescence, and circular dichroism spectroscopy (CD), differential scanning calorimetry (DSC), and molecular docking and LIGPLOT studies were utilized for structural studies. The TNBSA results indicated that SB has the ability to bind Lys residues in HSA through covalent bonds. The docking and LIGPLOT studies also determined another specific site via hydrophobic interactions. The CD results showed more structural helicity for HSA incubated with SB, while HSA incubated with glucose had the least, and HSA incubated with glucose + SB had medium helicity. Fluorescence spectrophotometry results demonstrated partial unfolding of HSA incubated with SB in the presence or absence of glucose, while maximum partial unfolding was observed in HSA incubated with glucose. These results were confirmed by DSC and its deconvoluted thermograms. The DSC results also showed significant changes in HSA energetic structural domains due to HSA incubation with SB in the presence or absence of glucose. Together, our studies showed the formation of three different intermediates and indicate that biomolecular investigation are effective in providing new insight into safety determinations especially in health-related conditions including diabetes.

  20. Combined analysis of whole human blood parameters by Raman spectroscopy and spectral-domain low-coherence interferometry

    Science.gov (United States)

    Gnyba, M.; Wróbel, M. S.; Karpienko, K.; Milewska, D.; Jedrzejewska-Szczerska, M.

    2015-07-01

    In this article the simultaneous investigation of blood parameters by complementary optical methods, Raman spectroscopy and spectral-domain low-coherence interferometry, is presented. Thus, the mutual relationship between chemical and physical properties may be investigated, because low-coherence interferometry measures optical properties of the investigated object, while Raman spectroscopy gives information about its molecular composition. A series of in-vitro measurements were carried out to assess sufficient accuracy for monitoring of blood parameters. A vast number of blood samples with various hematological parameters, collected from different donors, were measured in order to achieve a statistical significance of results and validation of the methods. Preliminary results indicate the benefits in combination of presented complementary methods and form the basis for development of a multimodal system for rapid and accurate optical determination of selected parameters in whole human blood. Future development of optical systems and multivariate calibration models are planned to extend the number of detected blood parameters and provide a robust quantitative multi-component analysis.

  1. Expression and characterization of Kunitz domain 3 and C-terminal of human tissue factor pathway inhibitor-2

    Institute of Scientific and Technical Information of China (English)

    Lina Zhu; Jiping Wang; Jingui Mu; Huijun Wang; Chenqi Zhang; Jue Wang; Xingang Liu; Xiaomin Yan; Linsen Dai; Duan Ma

    2009-01-01

    Human tissue factor pathway inhibitor-2 (hTFPI-2) is a serine protease inhibitor and its inhibitory activity is enhanced by heparin. The Kunitz domain 3 and C-terminal of hTFPI-2 (bTFPI-2/KD3C), which has the activity toward heparin calcium, have been successfully expressed in Pichia pastoris and purified by SP-Sepharose and heparin-Sepharose chromatography. The Fourier transformed infrared spectroscopy (FTIR),Raman spectroscopy, and circular dichroism (CD)experiment results implied that hTFPI-2/KD3C con-tained small contents of or-helix and β-strand, but large amounts of random coil and two kinds of disulfide bonds, gauche-gauche-gauche (ggg) and trans-gauche-trans (tgt). The interaction of hTFPI-2/KD3C with heparin calcium was investigated by CD. It was found that heparin calcium induced β-strands in hTFPI-2/KD3C to different extents depending on the ratio of hTFPI-2/KD3C and heparin calcium.

  2. HIV Tat Domain Improves Cross-correction of Human Galactocerebrosidase in a Gene- and Flanking Sequence-dependent Manner

    Directory of Open Access Journals (Sweden)

    Xing-Li Meng

    2013-01-01

    Full Text Available Krabbe disease is a devastating neurodegenerative lysosomal storage disorder caused by a deficiency of β-galactocerebrosidase (GALC. Gene therapy is a promising therapeutic approach for Krabbe disease. As the human brain is large and it is difficult to achieve global gene transduction, the efficacy of cross-correction is a critical determinant of the outcome of gene therapy for this disease. We investigated whether HIV Tat protein transduction domain (PTD can improve the cross-correction of GALC. Tat-PTD significantly increased (~6-fold cross-correction of GALC through enhanced secretion and uptake in a cell-culture model system. The effects of Tat-PTD were gene and flanking amino acids dependent. Tat-fusion increased the secretion of α-galactosidase A (α-gal A, but this did not improve its cross-correction. Tat-fusion did not change either secretion or uptake of β-glucocerebrosidase (GC. Tat-PTD increased GALC protein synthesis, abolished reactivity of GC to the 8E4 antibody, and likely reduced mannose phosphorylation in all these lysosomal enzymes. This study demonstrated that Tat-PTD can be useful for increasing cross-correction efficiency of lysosomal enzymes. However, Tat-PTD is not a mere adhesive motif but possesses a variety of biological functions. Therefore, the potential beneficial effect of Tat-PTD should be assessed individually on each lysosomal enzyme.

  3. Contribution of cysteine residues in the extracellular domain of the F protein of human respiratory syncytial virus to its function

    Directory of Open Access Journals (Sweden)

    Melero José A

    2006-05-01

    Full Text Available Abstract The mature F protein of all known isolates of human respiratory syncytial virus (HRSV contains fifteen absolutely conserved cysteine (C residues that are highly conserved among the F proteins of other pneumoviruses as well as the paramyxoviruses. To explore the contribution of the cysteines in the extracellular domain to the fusion activity of HRSV F protein, each cysteine was changed to serine. Mutation of cysteines 37, 313, 322, 333, 343, 358, 367, 393, 416, and 439 abolished or greatly reduced cell surface expression suggesting these residues are critical for proper protein folding and transport to the cell surface. As expected, the fusion activity of these mutations was greatly reduced or abolished. Mutation of cysteine residues 212, 382, and 422 had little to no effect upon cell surface expression or fusion activity at 32°C, 37°C, or 39.5°C. Mutation of C37 and C69 in the F2 subunit either abolished or reduced cell surface expression by 75% respectively. None of the mutations displayed a temperature sensitive phenotype.

  4. Interaction of Bordetella pertussis filamentous hemagglutinin with human TLR2: identification of the TLR2-binding domain.

    Science.gov (United States)

    Asgarian-Omran, Hossein; Amirzargar, Ali Akbar; Zeerleder, Sacha; Mahdavi, Marzieh; van Mierlo, Gerard; Solati, Shabnam; Jeddi-Tehrani, Mahmood; Rabbani, Hodjatallah; Aarden, Leucien; Shokri, Fazel

    2015-02-01

    Filamentous hemagglutinin (FHA) is a major adhesion and virulence factor of Bordetella pertussis and also a main component of acellular pertussis vaccines. Interaction of FHA with different receptors on human epithelial and immune cells facilitates entrance and colonization of bacteria as well as immunomodulation of the host immune response. Three overlapping segments of the FHA gene were cloned in a prokaryotic expression vector and the recombinant proteins were purified. These recombinant fragments along with the native FHA protein were employed to assess their potential Toll-like receptor (TLR) stimulatory effects and to localize the TLR binding region. TLR stimulation was monitored by applying HEK293-Blue cell lines cotransfected with TLR2, 4, or 5 and a NF-κB reporter gene. Culture supernatants were checked for secretion of the reporter gene product and IL-8 as indicators of TLR stimulation. Native FHA was found to strongly stimulate TLR2, but not TLR4 or TLR5 transfected cells. Among recombinant FHA fragments only the fragment spanning amino acid residues 1544-1917 was able to exhibit the TLR2 stimulating property of FHA. Interaction of FHA with TLR2 suggests its involvement in induction of the innate immune system against Bordetella pertussis. The TLR2-binding domain of FHA may contribute to immunoprotection against pertussis infection.

  5. Discovery of small-molecule inhibitors selectively targeting the DNA-binding domain of the human androgen receptor.

    Science.gov (United States)

    Li, Huifang; Ban, Fuqiang; Dalal, Kush; Leblanc, Eric; Frewin, Kate; Ma, Dennis; Adomat, Hans; Rennie, Paul S; Cherkasov, Artem

    2014-08-14

    The human androgen receptor (AR) is considered as a master regulator in the development and progression of prostate cancer (PCa). As resistance to clinically used anti-AR drugs remains a major challenge for the treatment of advanced PCa, there is a pressing need for new anti-AR therapeutic avenues. In this study, we identified a binding site on the DNA binding domain (DBD) of the receptor and utilized virtual screening to discover a set of micromolar hits for the target. Through further exploration of the most potent hit (1), a structural analogue (6) was identified demonstrating 10-fold improved anti-AR potency. Further optimization resulted in a more potent synthetic analogue (25) with anti-AR potency comparable to a newly FDA-approved drug Enzalutamide. Site-directed mutagenesis demonstrated that the developed inhibitors do interact with the intended target site. Importantly, the AR DBD inhibitors could effectively inhibit the growth of Enzalutamide-resistant cells as well as block the transcriptional activity of constitutively active AR splice variants, such as V7.

  6. Comparing the performance of expert user heuristics and an integer linear program in aircraft carrier deck operations.

    Science.gov (United States)

    Ryan, Jason C; Banerjee, Ashis Gopal; Cummings, Mary L; Roy, Nicholas

    2014-06-01

    Planning operations across a number of domains can be considered as resource allocation problems with timing constraints. An unexplored instance of such a problem domain is the aircraft carrier flight deck, where, in current operations, replanning is done without the aid of any computerized decision support. Rather, veteran operators employ a set of experience-based heuristics to quickly generate new operating schedules. These expert user heuristics are neither codified nor evaluated by the United States Navy; they have grown solely from the convergent experiences of supervisory staff. As unmanned aerial vehicles (UAVs) are introduced in the aircraft carrier domain, these heuristics may require alterations due to differing capabilities. The inclusion of UAVs also allows for new opportunities for on-line planning and control, providing an alternative to the current heuristic-based replanning methodology. To investigate these issues formally, we have developed a decision support system for flight deck operations that utilizes a conventional integer linear program-based planning algorithm. In this system, a human operator sets both the goals and constraints for the algorithm, which then returns a proposed schedule for operator approval. As a part of validating this system, the performance of this collaborative human-automation planner was compared with that of the expert user heuristics over a set of test scenarios. The resulting analysis shows that human heuristics often outperform the plans produced by an optimization algorithm, but are also often more conservative.

  7. The human YB-1 cold shock domain : structural, dynamical and binding properties of the central nucleic acid binding domain of the human Y-box protein YB-1, a transcription and translation regulating protein

    NARCIS (Netherlands)

    Kloks, Cathelijne Petra Anne Marie

    2003-01-01

    Y-box proteins are a highly conserved group of proteins present in bacteria, plants and animals. They are essential in regulating transcription and translation and the coupling between theses two processes. Their central domain, the so-called cold shock domain (CSD), is responsible for the nucleic a

  8. The human YB-1 cold shock domain : structural, dynamical and binding properties of the central nucleic acid binding domain of the human Y-box protein YB-1, a transcription and translation regulating protein

    NARCIS (Netherlands)

    Kloks, Cathelijne Petra Anne Marie

    2003-01-01

    Y-box proteins are a highly conserved group of proteins present in bacteria, plants and animals. They are essential in regulating transcription and translation and the coupling between theses two processes. Their central domain, the so-called cold shock domain (CSD), is responsible for the nucleic

  9. Human IgG1 monoclonal antibody against human collagen 17 noncollagenous 16A domain induces blisters via complement activation in experimental bullous pemphigoid model.

    Science.gov (United States)

    Li, Qiang; Ujiie, Hideyuki; Shibaki, Akihiko; Wang, Gang; Moriuchi, Reine; Qiao, Hong-jiang; Morioka, Hiroshi; Shinkuma, Satoru; Natsuga, Ken; Long, Heather A; Nishie, Wataru; Shimizu, Hiroshi

    2010-12-15

    Bullous pemphigoid (BP) is an autoimmune blistering disease caused by IgG autoantibodies targeting the noncollagenous 16A (NC16A) domain of human collagen 17 (hCOL17), which triggers blister formation via complement activation. Previous in vitro analysis demonstrated that IgG1 autoantibodies showed much stronger pathogenic activity than IgG4 autoantibodies; however, the exact pathogenic role of IgG1 autoantibodies has not been fully demonstrated in vivo. We constructed a recombinant IgG1 mAb against hCOL17 NC16A from BP patients. In COL17-humanized mice, this mAb effectively reproduced a BP phenotype that included subepidermal blisters, deposition of IgG1, C1q and C3, neutrophil infiltration, and mast cell degranulation. Subsequently, alanine substitutions at various C1q binding sites were separately introduced to the Fc region of the IgG1 mAb. Among these mutated mAbs, the one that was mutated at the P331 residue completely failed to activate the complement in vitro and drastically lost pathogenic activity in COL17-humanized mice. These findings indicate that P331 is a key residue required for complement activation and that IgG1-dependent complement activation is essential for blister formation in BP. This study is, to our knowledge, the first direct evidence that IgG1 Abs to hCOL17 NC16A can induce blister formation in vivo, and it raises the possibility that IgG1 mAbs with Fc modification may be used to block pathogenic epitopes in autoimmune diseases.

  10. Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase

    Energy Technology Data Exchange (ETDEWEB)

    He, Yuan [Northwest University, Xi’an 710069 (China); The University of York, York YO10 5DD (United Kingdom); Roth, Christian; Turkenburg, Johan P.; Davies, Gideon J., E-mail: gideon.davies@york.ac.uk [The University of York, York YO10 5DD (United Kingdom); Northwest University, Xi’an 710069 (China)

    2014-01-01

    The crystal structure of a bacterial acetyltransferase with 27% sequence identity to the C-terminal domain of human O-GlcNAcase has been solved at 1.5 Å resolution. This S. sviceus protein is compared with known GCN5-related acetyltransferases, adding to the diversity observed in this superfamily. The mammalian O-GlcNAc hydrolysing enzyme O-GlcNAcase (OGA) is a multi-domain protein with glycoside hydrolase activity in the N-terminus and with a C-terminal domain that has low sequence similarity to known acetyltransferases, prompting speculation, albeit controversial, that the C-terminal domain may function as a histone acetyltransferase (HAT). There are currently scarce data available regarding the structure and function of this C-terminal region. Here, a bacterial homologue of the human OGA C-terminal domain, an acetyltransferase protein (accession No. ZP-05014886) from Streptomyces sviceus (SsAT), was cloned and its crystal structure was solved to high resolution. The structure reveals a conserved protein core that has considerable structural homology to the acetyl-CoA (AcCoA) binding site of GCN5-related acetyltransferases (GNATs). Calorimetric data further confirm that SsAT is indeed able to bind AcCoA in solution with micromolar affinity. Detailed structural analysis provided insight into the binding of AcCoA. An acceptor-binding cavity was identified, indicating that the physiological substrate of SsAT may be a small molecule. Consistent with recently published work, the SsAT structure further questions a HAT function for the human OGA domain.

  11. Modulation of Sonic hedgehog signaling and WW domain containing oxidoreductase WOX1 expression enhances radiosensitivity of human glioblastoma cells.

    Science.gov (United States)

    Chiang, Ming-Fu; Chen, Hsin-Hong; Chi, Chih-Wen; Sze, Chun-I; Hsu, Ming-Ling; Shieh, Hui-Ru; Lin, Chin-Ping; Tsai, Jo-Ting; Chen, Yu-Jen

    2015-03-01

    WW domain containing oxidoreductase, designated WWOX, FOR or WOX1, is a known pro-apoptotic factor when ectopically expressed in various types of cancer cells, including glioblastoma multiforme (GBM). The activation of sonic hedgehog (Shh) signaling, especially paracrine Shh secretion in response to radiation, is associated with impairing the effective irradiation of cancer cells. Here, we examined the role of Shh signaling and WOX1 overexpression in the radiosensitivity of human GBM cells. Our results showed that ionizing irradiation (IR) increased the cytoplasmic Shh and nuclear Gli-1 content in GBM U373MG and U87MG cells. GBM cells with exogenous Shh treatment exhibited similar results. Pretreatment with Shh peptides protected U373MG and U87MG cells against IR in a dose-dependent manner. Cyclopamine, a Hedgehog/Smoothened (SMO) inhibitor, reversed the protective effect of Shh in U87MG cells. Cyclopamine increased Shh plus IR-induced H2AX, a marker of DNA double-strand breaks, in these cells. To verify the role of Shh signaling in the radiosensitivity of GBM cells, we tested the effect of the Gli family zinc finger 1 (Gli-1) inhibitor zerumbone and found that it could sensitize GBM cells to IR. We next examined the role of WOX1 in radiosensitivity. Overexpression of WOX1 enhanced the radiosensitivity of U87MG (possessing wild type p53 or WTp53) but not U373MG (harboring mutant p53 or MTp53) cells. Pretreatment with Shh peptides protected both WOX1-overexpressed U373MG and U87MG cells against IR and increased the cytoplasmic Shh and nuclear Gli-1 content. Zerumbone enhanced the radiosensitivity of WOX1-overexpressed U373MG and U87MG cells. In conclusion, overexpression of WOX1 preferentially sensitized human GBM cells possessing wild type p53 to radiation therapy. Blocking of Shh signaling may enhance radiosensitivity independently of the expression of p53 and WOX1. The crosstalk between Shh signaling and WOX1 expression in human glioblastoma warrants further

  12. Specificity and versatility of substrate binding sites in four catalytic domains of human N-terminal acetyltransferases.

    Directory of Open Access Journals (Sweden)

    Cédric Grauffel

    Full Text Available Nt-acetylation is among the most common protein modifications in eukaryotes. Although thought for a long time to protect proteins from degradation, the role of Nt-acetylation is still debated. It is catalyzed by enzymes called N-terminal acetyltransferases (NATs. In eukaryotes, several NATs, composed of at least one catalytic domain, target different substrates based on their N-terminal sequences. In order to better understand the substrate specificity of human NATs, we investigated in silico the enzyme-substrate interactions in four catalytic subunits of human NATs (Naa10p, Naa20p, Naa30p and Naa50p. To date hNaa50p is the only human subunit for which X-ray structures are available. We used the structure of the ternary hNaa50p/AcCoA/MLG complex and a structural model of hNaa10p as a starting point for multiple molecular dynamics simulations of hNaa50p/AcCoA/substrate (substrate=MLG, EEE, MKG, hNaa10p/AcCoA/substrate (substrate=MLG, EEE. Nine alanine point-mutants of the hNaa50p/AcCoA/MLG complex were also simulated. Homology models of hNaa20p and hNaa30p were built and compared to hNaa50p and hNaa10p. The simulations of hNaa50p/AcCoA/MLG reproduce the interactions revealed by the X-ray data. We observed strong hydrogen bonds between MLG and tyrosines 31, 138 and 139. Yet the tyrosines interacting with the substrate's backbone suggest that their role in specificity is limited. This is confirmed by the simulations of hNaa50p/AcCoA/EEE and hNaa10p/AcCoA/MLG, where these hydrogen bonds are still observed. Moreover these tyrosines are all conserved in hNaa20p and hNaa30p. Other amino acids tune the specificity of the S1' sites that is different for hNaa10p (acidic, hNaa20p (hydrophobic/basic, hNaa30p (basic and hNaa50p (hydrophobic. We also observe dynamic correlation between the ligand binding site and helix [Formula: see text] that tightens under substrate binding. Finally, by comparing the four structures we propose maps of the peptide

  13. Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues.

    Science.gov (United States)

    Liao, Zhijun; Wang, Xinrui; Zeng, Yeting; Zou, Quan

    2016-12-21

    The Dishevelled/EGL-10/Pleckstrin (DEP) domain-containing (DEPDC) proteins have seven members. However, whether this superfamily can be distinguished from other proteins based only on the amino acid sequences, remains unknown. Here, we describe a computational method to segregate DEPDCs and non-DEPDCs. First, we examined the Pfam numbers of the known DEPDCs and used the longest sequences for each Pfam to construct a phylogenetic tree. Subsequently, we extracted 188-dimensional (188D) and 20D features of DEPDCs and non-DEPDCs and classified them with random forest classifier. We also mined the motifs of human DEPDCs to find the related domains. Finally, we designed experimental verification methods of human DEPDC expression at the mRNA level in hepatocellular carcinoma (HCC) and adjacent normal tissues. The phylogenetic analysis showed that the DEPDCs superfamily can be divided into three clusters. Moreover, the 188D and 20D features can both be used to effectively distinguish the two protein types. Motif analysis revealed that the DEP and RhoGAP domain was common in human DEPDCs, human HCC and the adjacent tissues that widely expressed DEPDCs. However, their regulation was not identical. In conclusion, we successfully constructed a binary classifier for DEPDCs and experimentally verified their expression in human HCC tissues.

  14. Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues

    Science.gov (United States)

    Liao, Zhijun; Wang, Xinrui; Zeng, Yeting; Zou, Quan

    2016-12-01

    The Dishevelled/EGL-10/Pleckstrin (DEP) domain-containing (DEPDC) proteins have seven members. However, whether this superfamily can be distinguished from other proteins based only on the amino acid sequences, remains unknown. Here, we describe a computational method to segregate DEPDCs and non-DEPDCs. First, we examined the Pfam numbers of the known DEPDCs and used the longest sequences for each Pfam to construct a phylogenetic tree. Subsequently, we extracted 188-dimensional (188D) and 20D features of DEPDCs and non-DEPDCs and classified them with random forest classifier. We also mined the motifs of human DEPDCs to find the related domains. Finally, we designed experimental verification methods of human DEPDC expression at the mRNA level in hepatocellular carcinoma (HCC) and adjacent normal tissues. The phylogenetic analysis showed that the DEPDCs superfamily can be divided into three clusters. Moreover, the 188D and 20D features can both be used to effectively distinguish the two protein types. Motif analysis revealed that the DEP and RhoGAP domain was common in human DEPDCs, human HCC and the adjacent tissues that widely expressed DEPDCs. However, their regulation was not identical. In conclusion, we successfully constructed a binary classifier for DEPDCs and experimentally verified their expression in human HCC tissues.

  15. Chapel Hill bisphenol A expert panel consensus statement: Integration of mechanisms, effects in animals and potential to impact human health at current levels of exposure

    Science.gov (United States)

    vom Saal, Frederick S.; Akingbemi, Benson T.; Belcher, Scott M.; Birnbaum, Linda S.; Crain, D. Andrew; Eriksen, Marcus; Farabollini, Francesca; Guillette, Louis J.; Hauser, Russ; Heindel, Jerrold J.; Ho, Shuk-Mei; Hunt, Patricia A.; Iguchi, Taisen; Jobling, Susan; Kanno, Jun; Keri, Ruth A.; Knudsen, Karen E.; Laufer, Hans; LeBlanc, Gerald A.; Marcus, Michele; McLachlan, John A.; Myers, John Peterson; Nadal, Angel; Newbold, Retha R.; Olea, Nicolas; Prins, Gail S.; Richter, Catherine A.; Rubin, Beverly S.; Sonnenschein, Carlos; Soto, Ana M.; Talsness, Chris E.; Vandenbergh, John G.; Vanderberg, Laura N.; Walser-Kuntz, Debby R.; Watson, Cheryl S.; Welshons, Wade V.; Wetherill, Yelena; Zoeller, R. Thomas

    2007-01-01

    This document is a summary statement of the outcome from the meeting: “Bisphenol A: An Examination of the Relevance of Ecological, In vitro and Laboratory Animal Studies for Assessing Risks to Human Health” sponsored by both the NIEHS and NIDCR at NIH/DHHS, as well as the US-EPA and Commonweal on the estrogenic environmental chemical bisphenol A (BPA, 2,2-bis(4-hydroxyphenyl)propane; CAS# 80-05-7). The meeting was held in Chapel Hill, NC, 28–30 November 2006 due to concerns about the potential for a relationship between BPA and negative trends in human health that have occurred in recent decades. Examples include increases in abnormal penile/urethra development in males, early sexual maturation in females, an increase in neurobehavioral problems such as attention deficit hyperactivity disorder (ADHD) and autism, an increase in childhood and adult obesity and type 2 diabetes, a regional decrease in sperm count, and an increase in hormonally mediated cancers, such as prostate and breast cancers. Concern has been elevated by published studies reporting a relationship between treatment with “low doses” of BPA and many of theses negative health outcomes in experimental studies in laboratory animals as well as in vitro studies identifying plausible molecular mechanisms that could mediate such effects. Importantly, much evidence suggests that these adverse effects are occurring in animals within the range of exposure to BPA of the typical human living in a developed country, where virtually everyone has measurable blood, tissue and urine levels of BPA that exceed the levels produced by doses used in the “low dose” animal experiments.

  16. Novel human G protein-coupled receptors with long N-terminals containing GPS domains and Ser/Thr-rich regions.

    Science.gov (United States)

    Fredriksson, Robert; Lagerström, Malin C; Höglund, Pär J; Schiöth, Helgi B

    2002-11-20

    We report eight novel members of the superfamily of human G protein-coupled receptors (GPCRs) found by searches in the human genome databases, termed GPR97, GPR110, GPR111, GPR112, GPR113, GPR114, GPR115 and GPR116. Phylogenetic analysis shows that these are additional members of a family of GPCRs with long N-termini, previously termed EGF-7TM, LNB-7TM, B2 or LN-7TM. Five of the receptors form their own phylogenetic cluster, while three others form a cluster with the previously reported HE6 and GPR56 (TM7XN1). All the receptors have a GPS domain in their N-terminus and long Ser/Thr-rich regions forming mucin-like stalks. GPR113 has a hormone binding domain and one EGF domain. GPR112 has over 20 Ser/Thr repeats and a pentraxin domain. GPR116 has two immunoglobulin-like repeats and a SEA box. We found several human EST sequences for most of the receptors showing differential expression patterns, which may indicate that some of these receptors participate in reproductive functions while others are more likely to have a role in the immune system.

  17. Single-domain antibody-based ligands for immunoaffinity separation of recombinant human lactoferrin from the goat lactoferrin of transgenic goat milk.

    Science.gov (United States)

    Tillib, S V; Privezentseva, M E; Ivanova, T I; Vasilev, L F; Efimov, G A; Gursky, Y G; Georgiev, G P; Goldman, I L; Sadchikova, E R

    2014-02-15

    Single-domain antibody generation technology was applied to make new Sepharose-bound ligands for affinity separation of closely related proteins, such as human and goat lactoferrin. We generated recombinant antibodies that can selectively bind/recognize only lactoferrins having amino acid sequences identical to that of human natural lactoferrin (anti-hLF Ab). Selected and purified histidine-tagged single-domain antibodies were used as ligands, and different lactoferrins were used as analytes in the kinetics analysis of lactoferrin binding to captured anti-hLF Abs using the Bio-Rad ProteOn XPR36 protein interaction array system. The data obtained were consistent with a 1:1 binding model with very high affinity, practically equal in the case of hLF and rec-hLF (calculated KD varied from 0.43nM to 3.7nM). Interaction of captured fsdAbs with goat LF was significantly weaker and not detectable under the same analysis conditions. We demonstrated the high efficiency of the recombinant human lactoferrin purification from goat lactoferrin and other proteins using the obtained single domain antibody-based affinity ligands. We believe this approach can be used for the generation of single-domain antibody-based affinity media for the efficient separation/purification of a wide spectrum of other highly homologous proteins.

  18. Structure of Human J-type Co-chaperone HscB Reveals a Tetracysteine Metal-binding Domain*S⃞

    Science.gov (United States)

    Bitto, Eduard; Bingman, Craig A.; Bittova, Lenka; Kondrashov, Dmitry A.; Bannen, Ryan M.; Fox, Brian G.; Markley, John L.; Phillips, George N.

    2008-01-01

    Iron-sulfur proteins play indispensable roles in a broad range of biochemical processes. The biogenesis of iron-sulfur proteins is a complex process that has become a subject of extensive research. The final step of iron-sulfur protein assembly involves transfer of an iron-sulfur cluster from a cluster-donor to a cluster-acceptor protein. This process is facilitated by a specialized chaperone system, which consists of a molecular chaperone from the Hsc70 family and a co-chaperone of the J-domain family. The 3.0Å crystal structure of a human mitochondrial J-type co-chaperone HscB revealed an L-shaped protein that resembles Escherichia coli HscB. The important difference between the two homologs is the presence of an auxiliary metal-binding domain at the N terminus of human HscB that coordinates a metal via the tetracysteine consensus motif CWXCX9–13FCXXCXXXQ. The domain is found in HscB homologs from animals and plants as well as in magnetotactic bacteria. The metal-binding site of the domain is structurally similar to that of rubredoxin and several zinc finger proteins containing rubredoxin-like knuckles. The normal mode analysis of HscB revealed that this L-shaped protein preferentially undergoes a scissors-like motion that correlates well with the conformational changes of human HscB observed in the crystals. PMID:18713742

  19. EXPERT SYSTEMS - DEVELOPMENT OF AGRICULTURAL INSURANCE TOOL

    Directory of Open Access Journals (Sweden)

    NAN Anca-Petruţa

    2013-07-01

    Full Text Available Because of the fact that specialty agricultural assistance is not always available when the farmers need it, we identified expert systems as a strong instrument with an extended potential in agriculture. This started to grow in scale recently, including all socially-economic activity fields, having the role of collecting data regarding different aspects from human experts with the purpose of assisting the user in the necessary steps for solving problems, at the performance level of the expert, making his acquired knowledge and experience available. We opted for a general presentation of the expert systems as well as their necessity, because, the solution to develop the agricultural system can come from artificial intelligence by implementing the expert systems in the field of agricultural insurance, promoting existing insurance products, farmers finding options in depending on their necessities and possibilities. The objective of this article consists of collecting data about different aspects about specific areas of interest of agricultural insurance, preparing the database, a conceptual presentation of a pilot version which will become constantly richer depending on the answers received from agricultural producers, with the clearest exposure of knowledgebase possible. We can justify picking this theme with the fact that even while agricultural insurance plays a very important role in agricultural development, the registered result got from them are modest, reason why solutions need to be found in the scope of developing the agricultural sector. The importance of this consists in the proposal of an immediate viable solution to correspond with the current necessities of agricultural producers and in the proposal of an innovative solution, namely the implementation of expert system in agricultural insurance as a way of promoting insurance products. Our research, even though it treats the subject at an conceptual level, it wants to undertake an

  20. Expert system aids reliability

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, A.T. [Tennessee Gas Pipeline, Houston, TX (United States)

    1997-09-01

    Quality and Reliability are key requirements in the energy transmission industry. Tennessee Gas Co. a division of El Paso Energy, has applied Gensym`s G2, object-oriented Expert System programming language as a standard tool for maintaining and improving quality and reliability in pipeline operation. Tennessee created a small team of gas controllers and engineers to develop a Proactive Controller`s Assistant (ProCA) that provides recommendations for operating the pipeline more efficiently, reliably and safely. The controller`s pipeline operating knowledge is recreated in G2 in the form of Rules and Procedures in ProCA. Two G2 programmers supporting the Gas Control Room add information to the ProCA knowledge base daily. The result is a dynamic, constantly improving system that not only supports the pipeline controllers in their operations, but also the measurement and communications departments` requests for special studies. The Proactive Controller`s Assistant development focus is in the following areas: Alarm Management; Pipeline Efficiency; Reliability; Fuel Efficiency; and Controller Development.

  1. Expert elicitation on the uncertainties associated with chronic wasting disease.

    Science.gov (United States)

    Tyshenko, Michael G; Oraby, Tamer; Darshan, Shalu; Westphal, Margit; Croteau, Maxine C; Aspinall, Willy; Elsaadany, Susie; Krewski, Daniel; Cashman, Neil

    2016-01-01

    A high degree of uncertainty exists for chronic wasting disease (CWD) transmission factors in farmed and wild cervids. Evaluating the factors is important as it helps to inform future risk management strategies. Expert opinion is often used to assist decision making in a number of health, science, and technology domains where data may be sparse or missing. Using the "Classical Model" of elicitation, a group of experts was asked to estimate the most likely values for several risk factors affecting CWD transmission. The formalized expert elicitation helped structure the issues and hence provide a rational basis for estimating some transmission risk factors for which evidence is lacking. Considered judgments regarding environmental transmission, latency of CWD transmission, management, and species barrier were provided by the experts. Uncertainties for many items were determined to be large, highlighting areas requiring more research. The elicited values may be used as surrogate values until research evidence becomes available.

  2. Generic domain models in software engineering

    Science.gov (United States)

    Maiden, Neil

    1992-01-01

    This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

  3. The structure of the two amino-terminal domains of human intercellular adhesion molecule-1 suggests how it functions as a rhinovirus receptor.

    Science.gov (United States)

    Bella, J; Kolatkar, P R; Marlor, C W; Greve, J M; Rossmann, M G

    1999-08-01

    The normal function of human intercellular adhesion molecule-1 (ICAM-1) is to provide adhesion between endothelial cells and leukocytes after injury or stress. ICAM-1 binds to leukocyte function-associated antigen (LFA-1) or macrophage-1 antigen (Mac-1). However, ICAM-1 is also utilized as a receptor by the major group of human rhinoviruses and is a catalyst for the subsequent viral uncoating during cell entry. The three-dimensional atomic structure of the two amino-terminal domains (D1 and D2) of ICAM-1 has been determined to 2.2 A resolution and fitted into a cryo-electron microscopy reconstruction of a rhinovirus-ICAM-1 complex. Rhinovirus attachment is confined to the BC, CD, DE and FG loops of the amino-terminal immunoglobulin-like domain (D1) at the end distal to the cellular membrane. The loops are considerably different in structure to those of human ICAM-2 or murine ICAM-1 which do not bind rhinoviruses. There are extensive charge interactions between ICAM-1 and human rhinoviruses, which are mostly conserved in both major and minor receptor groups of rhinoviruses. The interaction of ICAMs with LFA-1 is known to be mediated by a divalent cation bound to the I-(insertion) domain on the alpha chain of LFA-1 and the carboxy group of a conserved glutamic acid residue on ICAMs. Domain D1 has been docked with the known structure of the I-domain. The resultant model is consistent with mutational data and provides a structural framework for the adhesion between these molecules.

  4. The structure of the two amino-terminal domains of human ICAM-1 suggests how it functions as a rhinovirus receptor and as an LFA-1 integrin ligand.

    Science.gov (United States)

    Bella, J; Kolatkar, P R; Marlor, C W; Greve, J M; Rossmann, M G

    1998-04-14

    The normal function of human intercellular adhesion molecule-1 (ICAM-1) is to provide adhesion between endothelial cells and leukocytes after injury or stress. ICAM-1 binds to leukocyte function-associated antigen (LFA-1) or macrophage-1 antigen (Mac-1). However, ICAM-1 is also used as a receptor by the major group of human rhinoviruses and is a catalyst for the subsequent viral uncoating during cell entry. The three-dimensional atomic structure of the two amino-terminal domains (D1 and D2) of ICAM-1 has been determined to 2.2-A resolution and fitted into a cryoelectron microscopy reconstruction of a rhinovirus-ICAM-1 complex. Rhinovirus attachment is confined to the BC, CD, DE, and FG loops of the amino-terminal Ig-like domain (D1) at the end distal to the cellular membrane. The loops are considerably different in structure to those of human ICAM-2 or murine ICAM-1, which do not bind rhinoviruses. There are extensive charge interactions between ICAM-1 and human rhinoviruses, which are mostly conserved in both major and minor receptor groups of rhinoviruses. The interaction of ICAMs with LFA-1 is known to be mediated by a divalent cation bound to the insertion (I)-domain on the alpha chain of LFA-1 and the carboxyl group of a conserved glutamic acid residue on ICAMs. Domain D1 has been docked with the known structure of the I-domain. The resultant model is consistent with mutational data and provides a structural framework for the adhesion between these molecules.

  5. Conformational heterogeneity of the Roc domains in C. tepidum Roc-COR and implications for human LRRK2 Parkinson mutations

    NARCIS (Netherlands)

    Rudi, Katharina; Ho, Franz Y; Gilsbach, Bernd Karl; Pots, Henderikus; Wittinghofer, Alfred; Kortholt, Arjan; Klare, Johann P

    2015-01-01

    Ras of complex proteins (Roc) is a Ras-like GTP binding domain that always occurs in tandem with the C-terminal of Roc (COR) domain, and is found in bacteria, plants and animals. Recently, it has been shown that Roco proteins belong to the family of G-proteins activated by nucleotide-dependent dimer

  6. Using molecular repertoires to identify high-affinity peptide ligands of the WW domain of human and mouse YAP.

    Science.gov (United States)

    Linn, H; Ermekova, K S; Rentschler, S; Sparks, A B; Kay, B K; Sudol, M

    1997-06-01

    The WW domain is a globular protein domain that is involved in mediating protein-protein interaction and that ultimately participates in various intracellular signaling events. The domain binds to polyproline ligands containing the xPPxY consensus (where x signifies any amino acid, P is proline and Y is tyrosine). One of the first WW domain-ligand links that was characterized in vitro was the WW domain of Yes-Associated Protein (YAP) and its WBP-1 ligand. To further characterize this molecular interaction, we used two independent approaches, both of which focused on the mutational analysis of the WBP-1 ligand. We screened repertoires of synthetic decamer peptides containing the xPPxY core of WBP-1 in which all ten positions were sequentially replaced with the remaining amino acids. In addition, we screened decamer repertoires with all permutations of the amino acids which individually increased the binding to the WW domain of YAP, as compared to the wild type. In a parallel approach, we used a phage-displayed combinatorial peptide library biased for the presence of two consecutive prolines to study ligand preferences for the WW domain of YAP. Interestingly, these two lines of investigation converged and yielded the core sequence PPPPYP, which is preferred by the YAP-WW domain. This sequence was found within the p53 (tumor suppressor) binding protein-2, a probable cognate or alternative ligand interacting with YAP.

  7. Development of the Expert System Domain Advisor and Analysis Tool

    Science.gov (United States)

    1991-09-01

    analysis. Typical of the current methods in use at this time is the " tarot metric". This method defines a decision rule whose output is whether to go...B - TAROT METRIC B. ::TTRODUCTION The system chart of ESEM, Figure 1, shows the following three risk-based decision points: i. At prolect initiation...34 decisions. B-I 201 PRELIMINARY T" B-I. Evaluais Factan for ES Deyelopsineg FACTORS POSSIBLE VALUE RATINGS TAROT metric (overall suitability) Poor, Fair

  8. FERMI: A Flexible Expert Reasoner with Multi-Domain Inferencing.

    Science.gov (United States)

    2014-09-26

    textbook , or a teacher). In this specific context, this informant applies both general and specific knowledge. The learner or the knowledge engineer...most important principles in physics, chemistry , and biology. " Invariance under spatial changes. Invariance under particular geometrical spatial...the entropy of any system in equilibrium can be decomposed into the sum of the entropies of all the constituent parts of this system. * Chemistry

  9. Experts bodies, experts minds: How physical and mental training shape the brain

    Directory of Open Access Journals (Sweden)

    Ursula eDebarnot

    2014-05-01

    Full Text Available Skill learning is the improvement in perceptual, cognitive, or motor performance following practice. Expert performance levels can be achieved with well-organized knowledge, using sophisticated and specific mental representations and cognitive processing, applying automatic sequences quickly and efficiently, being able to deal with large amounts of information, and many other challenging task demands and situations that otherwise paralyze the performance of novices. The neural reorganizations that occur with expertise reflect the optimization of the neurocognitive resources to deal with the complex computational load needed to achieve peak performance. As such, capitalizing on neuronal plasticity, brain modifications take place over time-practice and during the consolidation process. One major challenge is to investigate the neural substrates and cognitive mechanisms engaged in expertise, and to define expertise from its neural and cognitive underpinnings. Recent insights showed that many brain structures are recruited during task performance, but only activity in regions related to domain-specific knowledge distinguishes experts from novices. The present review focuses on three expertise domains placed across a motor to mental gradient of skill learning: sequential motor skill, mental simulation of the movement (motor imagery, and meditation as a paradigmatic example of pure mental training. We first describe results on each specific domain from the initial skill acquisition to the achieving of expert performance, including recent results on the corresponding underlying neural mechanisms. We then discuss differences and similarities between these domains with the aim to identify the highlights of the neurocognitive processes underpinning expertise, and conclude with suggestions for future research.

  10. Expert and novice facilitated modelling

    DEFF Research Database (Denmark)

    Tavella, Elena; Papadopoulos, Thanos

    2015-01-01

    This paper provides an empirical study based on action research in which expert and novice facilitators in facilitated modelling workshops are compared. There is limited empirical research analysing the differences between expert and novice facilitators. Aiming to address this gap we study...

  11. The construction and expression of chimeric urokinase-type plasminogen activator genes containing kringle domains of human plasminogen.

    Science.gov (United States)

    Boutaud, A; Castellino, F J

    1993-06-01

    A series of chimeric urokinase-type plasminogen activator (uPA) genes, which contain combinations of kringle domains of human plasminogen (HPg) in place of the uPA kringle (KuPA), has been constructed and expressed. Some of the resulting recombinant (r) variant uPA chimeras contain modules that potentially mediate the macroscopic binding of HPg to its activation effectors, fibrin(ogen) and 6-aminohexanoic acid (EACA). Such binding sites are not possessed by KuPA, but are present in certain of the HPg kringles, viz., kringle 1 (K1HPg), kringle 4 (K4HPg), and kringle 5 (K5HPg). The recombinant (r) chimeras constructed included molecules with replacements of KuPA with K1HPg (r-[KuPA-->K1HPg]uPA), and with KuPA replaced by double kringle combinations of K1HPgK4HPg (r-[KuPA-->K1HPgK4HPg]uPA), K2HPgK3HPg (r-[KuPA-->K2HPgK3HPg]uPA), and K4HPgK5HPg (r-[KuPA-->K4HPgK5HPg]uPA). All of these variant genes, along with their wild-type (wt) r-uPA counterparts, were expressed in human kidney 293 cells. In cases wherein EACA-binding kringles from HPg have been placed in uPA, this property has been retained in the chimeric molecule and employed as an essential part of the purification procedures for the variants. The steady state amidolytic activity of two-chain (tc) wtr-uPA toward the chromogenic substrate, H-D-pyroglutamyl-Gly-L-Arg-p-nitroanilide (S2444), is characterized by a kcat/KM (pH 7.4, 37 degrees C) of 120 s-1 mM-1. This value ranges from 92 s-1 mM-1 (tcr-[KuPA-->K1HPg]uPA) to 166 s-1 mM-1 (tcr-[KuPA-->K1HPgK4HPg]uPA) for each of the variants, demonstrating that the catalytic efficiency of the active site is altered only in a small way by changes in the noncatalytic domain of uPA. Small differences are also observed in the abilities of these tcr variants to interact with the fast-acting plasma inhibitor of uPA, viz., plasminogen activator inhibitor-1 (PAI-1). The second-order rate constant for the interaction of PAI-1 with tcr-uPA, 0.46 x 10(7) M-1s-1 (pH 7.4, 10 degrees

  12. Engineering monitoring expert system's developer

    Science.gov (United States)

    Lo, Ching F.

    1991-01-01

    This research project is designed to apply artificial intelligence technology including expert systems, dynamic interface of neural networks, and hypertext to construct an expert system developer. The developer environment is specifically suited to building expert systems which monitor the performance of ground support equipment for propulsion systems and testing facilities. The expert system developer, through the use of a graphics interface and a rule network, will be transparent to the user during rule constructing and data scanning of the knowledge base. The project will result in a software system that allows its user to build specific monitoring type expert systems which monitor various equipments used for propulsion systems or ground testing facilities and accrues system performance information in a dynamic knowledge base.

  13. NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1.

    Science.gov (United States)

    Lyukmanova, Ekaterina N; Shenkarev, Zakhar O; Shulepko, Mikhail A; Mineev, Konstantin S; D'Hoedt, Dieter; Kasheverov, Igor E; Filkin, Sergey Yu; Krivolapova, Alexandra P; Janickova, Helena; Dolezal, Vladimir; Dolgikh, Dmitry A; Arseniev, Alexander S; Bertrand, Daniel; Tsetlin, Victor I; Kirpichnikov, Mikhail P

    2011-03-25

    Discovery of proteins expressed in the central nervous system sharing the three-finger structure with snake α-neurotoxins provoked much interest to their role in brain functions. Prototoxin LYNX1, having homology both to Ly6 proteins and three-finger neurotoxins, is the first identified member of this family membrane-tethered by a GPI anchor, which considerably complicates in vitro studies. We report for the first time the NMR spatial structure for the water-soluble domain of human LYNX1 lacking a GPI anchor (ws-LYNX1) and its concentration-dependent activity on nicotinic acetylcholine receptors (nAChRs). At 5-30 μM, ws-LYNX1 competed with (125)I-α-bungarotoxin for binding to the acetylcholine-binding proteins (AChBPs) and to Torpedo nAChR. Exposure of Xenopus oocytes expressing α7 nAChRs to 1 μM ws-LYNX1 enhanced the response to acetylcholine, but no effect was detected on α4β2 and α3β2 nAChRs. Increasing ws-LYNX1 concentration to 10 μM caused a modest inhibition of these three nAChR subtypes. A common feature for ws-LYNX1 and LYNX1 is a decrease of nAChR sensitivity to high concentrations of acetylcholine. NMR and functional analysis both demonstrate that ws-LYNX1 is an appropriate model to shed light on the mechanism of LYNX1 action. Computer modeling, based on ws-LYNX1 NMR structure and AChBP x-ray structure, revealed a possible mode of ws-LYNX1 binding.

  14. NMR Structure and Action on Nicotinic Acetylcholine Receptors of Water-soluble Domain of Human LYNX1*

    Science.gov (United States)

    Lyukmanova, Ekaterina N.; Shenkarev, Zakhar O.; Shulepko, Mikhail A.; Mineev, Konstantin S.; D'Hoedt, Dieter; Kasheverov, Igor E.; Filkin, Sergey Yu.; Krivolapova, Alexandra P.; Janickova, Helena; Dolezal, Vladimir; Dolgikh, Dmitry A.; Arseniev, Alexander S.; Bertrand, Daniel; Tsetlin, Victor I.; Kirpichnikov, Mikhail P.

    2011-01-01

    Discovery of proteins expressed in the central nervous system sharing the three-finger structure with snake α-neurotoxins provoked much interest to their role in brain functions. Prototoxin LYNX1, having homology both to Ly6 proteins and three-finger neurotoxins, is the first identified member of this family membrane-tethered by a GPI anchor, which considerably complicates in vitro studies. We report for the first time the NMR spatial structure for the water-soluble domain of human LYNX1 lacking a GPI anchor (ws-LYNX1) and its concentration-dependent activity on nicotinic acetylcholine receptors (nAChRs). At 5–30 μm, ws-LYNX1 competed with 125I-α-bungarotoxin for binding to the acetylcholine-binding proteins (AChBPs) and to Torpedo nAChR. Exposure of Xenopus oocytes expressing α7 nAChRs to 1 μm ws-LYNX1 enhanced the response to acetylcholine, but no effect was detected on α4β2 and α3β2 nAChRs. Increasing ws-LYNX1 concentration to 10 μm caused a modest inhibition of these three nAChR subtypes. A common feature for ws-LYNX1 and LYNX1 is a decrease of nAChR sensitivity to high concentrations of acetylcholine. NMR and functional analysis both demonstrate that ws-LYNX1 is an appropriate model to shed light on the mechanism of LYNX1 action. Computer modeling, based on ws-LYNX1 NMR structure and AChBP x-ray structure, revealed a possible mode of ws-LYNX1 binding. PMID:21252236

  15. Display of aggregation-prone ligand binding domain of human PPAR gamma on surface of bacteriophage lambda

    Institute of Scientific and Technical Information of China (English)

    Bo KONG; Wei-jun MA

    2006-01-01

    Aim: To display the aggregation-prone ligand binding domain (LBD) of the human peroxisome proliferator-activated receptor gamma (PPARγ) on the surface of bacteriophages to establish an easy screening assay for the identification of PPARγ ligands. Methods: Plasmids were constructed for the expression of the PPARγ LBD as a fusion to the N-terminus of the g3p protein of filamentous phage or the C-terminus of the capsid protein D (pD) of phage lambda. The fusion proteins were expressed in E coli and solubility characteristics were compared. Polyclonal antibodies against the LBD as well as the pD protein were prepared for Western blot analysis and phage capture assay. Results: The pD-LBD fusion protein was partially soluble, whereas the LBD-g3p fusion protein was detected only in the insoluble fraction. The pD-LBD fusion protein was efficiently incorporated in phage particles. Furthermore, the LBD was shown to be displayed on the surface of bacteriophage lambda. On average, the pD-LBD fusion protein accounted for 28% of the total pD protein in the lambda head capsid. Conclusion: The hydrophobic PPARγLBD was expressed as a soluble form of fusionprotein in E coli and displayed on the surface of bacteriophage lambda when it was fused to the lambda pD protein. The lambda pD fusion system could be used for improving the solubility of proteins that tend to form inclusion bodies when expressed in E coli. The lambda phage particles displaying the LBD of PPARγ may be of great value for the identification of novel PPARγ ligands.

  16. Expression profile and differential regulation of the Human I-mfa domain-Containing protein (HIC) gene in immune cells.

    Science.gov (United States)

    Gu, Lili; Dean, Jonathan; Oliveira, André L A; Sheehy, Noreen; Hall, William W; Gautier, Virginie W

    2009-04-27

    The Human I-mfa domain-Containing protein, HIC, is a 246 amino acid protein that functions as a transcriptional regulator. Although the precise function of HIC remains to be clarified, the association of the HIC gene locus with myeloid neoplasms, its interactions with lymphotropic viruses such as EBV, HIV-1 and HTLV-1 and its expression in immune tissues suggest that HIC might have a modulatory role in immune cells. To further characterise the HIC functional relationship with the immune system, we sought to analyse the HIC gene expression profile in immune cells and to determine if immunomodulatory cytokines, such as interleukin (IL)-2, could regulate the expression of HIC mRNA. Relative quantitative real-time RT-PCR revealed that HIC mRNA is highly expressed in PBMCs and in various hematopoietic cell lines. The immunomodulatory cytokine IL-2 up-regulated HIC gene expression in PBMCs, CEM, MT-2 and U937 but markedly reduced HIC gene expression in Raji. Addition of cycloheximide indicated that the IL-2 effects were independent of de novo protein synthesis and that the HIC gene is a direct target of IL-2. Two cell lines (Jurkat and BJAB) displayed a distinct loss in HIC gene expression. However, when these cell lines were subjected to a combination of DNA methyltransferase and histone-deacetylase inhibitors, (5-aza-2-deoxycytidine and trichostatin A, respectively), HIC expression was de-repressed, indicating possible epigenetic control of HIC expression. Overall, our study describes that the immune expression of HIC is cell-specific, dynamic, and identifies the HIC gene as an IL-2 responsive gene. Furthermore, our de-repression studies support the hypothesis that HIC might represent a candidate tumor suppressor gene. Overall, this report provides new insights for a putative role of HIC in the modulation of immune and inflammatory responses and/or hematological malignancies.

  17. Quantum Mechanics and Molecular Mechanics Study of the Catalytic Mechanism of Human AMSH-LP Domain Deubiquitinating Enzymes.

    Science.gov (United States)

    Zhu, Wenyou; Liu, Yongjun; Ling, Baoping

    2015-08-25

    Deubiquitinating enzymes (DUBs) catalyze the cleavage of the isopeptide bond in polyubiquitin chains to control and regulate the deubiquitination process in all known eukaryotic cells. The human AMSH-LP DUB domain specifically cleaves the isopeptide bonds in the Lys63-linked polyubiquitin chains. In this article, the catalytic mechanism of AMSH-LP has been studied using a combined quantum mechanics and molecular mechanics method. Two possible hydrolysis processes (Path 1 and Path 2) have been considered. Our calculation results reveal that the activation of Zn(2+)-coordinated water molecule is the essential step for the hydrolysis of isopeptide bond. In Path 1, the generated hydroxyl first attacks the carbonyl group of Gly76, and then the amino group of Lys63 is protonated, which is calculated to be the rate limiting step with an energy barrier of 13.1 kcal/mol. The energy barrier of the rate limiting step and the structures of intermediate and product are in agreement with the experimental results. In Path 2, the protonation of amino group of Lys63 is prior to the nucleophilic attack of activated hydroxyl. The two proton transfer processes in Path 2 correspond to comparable overall barriers (33.4 and 36.1 kcal/mol), which are very high for an enzymatic reaction. Thus, Path 2 can be ruled out. During the reaction, Glu292 acts as a proton transfer mediator, and Ser357 mainly plays a role in stabilizing the negative charge of Gly76. Besides acting as a Lewis acid, Zn(2+) also influences the reaction by coordinating to the reaction substrates (W1 and Gly76).

  18. Discoidin Domain Receptor 2 Mediates Collagen-Induced Activation of Membrane-Type 1 Matrix Metalloproteinase in Human Fibroblasts.

    Science.gov (United States)

    Majkowska, Iwona; Shitomi, Yasuyuki; Ito, Noriko; Gray, Nathanael S; Itoh, Yoshifumi

    2017-03-07

    Membrane-Type 1 Matrix Metalloproteinase (MT1-MMP) is a membrane-bound MMP that is highly expressed in cells with invading capacity including fibroblasts and invasive cancer cell. A potential physiological stimulus for MT1-MMP expression is fibrillar collagen, and it has been shown that it upregulates both MT1-MMP gene and functions in various cell types. However, the mechanisms of collagen-mediated MT1-MMP activation is not clearly understood. In this study we identified discoidin domain receptor 2 (DDR2) as a crucial receptor that mediates this process in human fibroblasts. Knocking down DDR2, but not β1 integrin subunit, a common subunit for all collagen-binding integrins, inhibited collagen-induced activation of proMMP-2 and upregulation of MT1-MMP at the gene and protein level. Interestingly DDR2 knockdown or pharmacological inhibition of DDR2 also inhibited MT1-MMP-dependent cellular degradation of collagen film, suggesting that cell surface collagen degradation by MT1-MMP involves DDR2-mediated collagen signalling. This DDR2-mediated mechanism is only present in non-transformed mesenchymal cells, as collagen-induced MT1-MMP activation in HT1080 fibrosarcoma cells and MT1-MMP function in MDA-MB231 breast cancer cells were not affected by DDR kinase inhibition. DDR2 activation was found to be noticeably more effective when cells were stimulated by collagen without non-helical telopeptides region compared to intact collagen fibrils. Those data suggest that DDR2 is a microenvironmental sensor that regulates fibroblasts migration in collagen-rich environment.

  19. Comparative assessment of the recognition of domain-specific CD163 monoclonal antibodies in human monocytes explains wide discrepancy in reported levels of cellular surface CD163 expression

    DEFF Research Database (Denmark)

    Maniecki, Maciej Bogdan; Etzerodt, Anders; Moestrup, Søren Kragh;

    2011-01-01

    continue to exhibit great discrepancy in the measured percentage of CD163-expressing blood monocytes in healthy individuals. In this study we sought to clarify this inconsistency in reported levels of CD163 surface expression by a detailed analysis of a panel of CD163 antibodies used in previous studies...... 1 (MAC2-158), domain 4 (R-20), domain 7 (GHI/61), and domain 9 (RM3/1). The CD163 monoclonal antibodies were characterized in binding and endocytosis experiments in human macrophages and CD163-transfected Flp-In CHO cells. Calcium-dependent ligand binding was assessed using surface plasmon resonance......-terminal part of CD163, remote from the membrane surface. Moreover, the proportion of CD163 positive monocytes observed was highly dependent on free calcium. GHI/61 did not exhibit CD163 binding in the presence of calcium as measured by surface plasmon resonance, which was in agreement with the concordant loss...

  20. ANKRD54 preferentially selects Bruton’s Tyrosine Kinase (BTK) from a Human Src-Homology 3 (SH3) domain library

    Science.gov (United States)

    Mohammad, Dara K.; Ylösmäki, Erkko; Choi, Hyunseok; Shrestha, Subhash; Wang, Qing; Nore, Beston F.; Saksela, Kalle; Smith, C. I. Edvard

    2017-01-01

    Bruton’s Tyrosine Kinase (BTK) is a cytoplasmic protein tyrosine kinase with a fundamental role in B-lymphocyte development and activation. The nucleocytoplasmic shuttling of BTK is specifically modulated by the Ankyrin Repeat Domain 54 (ANKRD54) protein and the interaction is known to be exclusively SH3-dependent. To identify the spectrum of the ANKRD54 SH3-interactome, we applied phage-display screening of a library containing all the 296 human SH3 domains. The BTK-SH3 domain was the prime interactor. Quantitative western blotting analysis demonstrated the accuracy of the screening procedure. Revealing the spectrum and specificity of ANKRD54-interactome is a critical step toward functional analysis in cells and tissues. PMID:28369144

  1. Interactions of human P-glycoprotein transport substrates and inhibitors at the drug binding domain: Functional and molecular docking analyses.

    Science.gov (United States)

    Kadioglu, Onat; Saeed, Mohamed E M; Valoti, Massimo; Frosini, Maria; Sgaragli, Giampietro; Efferth, Thomas

    2016-03-15

    Rhodamine 123 (R123) transport substrate sensitizes P-glycoprotein (P-gp) to inhibition by compound 2c (cis-cis) N,N-bis(cyclohexanolamine)aryl ester isomer in a concentration-dependent manner in human MDR1-gene transfected mouse T-lymphoma L5178 cells as shown previously. By contrast, epirubicin (EPI) concentration changes left unaltered 2c IC50 values of EPI efflux. To clarify this discrepancy, defined molecular docking (DMD) analyses of 12 N,N-bis(cyclohexanolamine)aryl esters, the highly flexible aryl ester analog 4, and several P-gp substrate/non-substrate inhibitors were performed on human P-gp drug- or nucleotide-binding domains (DBD or NBD). DMD measurements yielded lowest binding energy (LBE, kcal/mol) values (mean ± SD) ranging from -11.8 ± 0.54 (valspodar) to -3.98 ± 0.01 (4). Lys234, Ser952 and Tyr953 residues formed H-bonds with most of the compounds. Only 2c docked also at ATP binding site (LBE value of -6.9 ± 0.30 kcal/mol). Inhibition of P-gp-mediated R123 efflux by 12 N,N-bis(cyclohexanolamine)aryl esters and 4 significantly correlated with LBE values. DMD analysis of EPI, (3)H-1EPI, (3)H-2EPI, (14)C-1EPI, (14)C-2EPI, R123 and 2c before and after previous docking of each of them indicated that pre-docking of either 2c or EPI significantly reduced LBE of both EPI and R123, and that of both (3)H-2EPI and (14)C-2EPI, respectively. Since the clusters of DBD amino acid residues interacting with EPI were different, if EPI docked alone or after pre-docking of EPI or 2c, the existence of alternative secondary binding site for EPI on P-gp is credible. In conclusion, 2c may allocate the drug-binding pocket and reduce strong binding of EPI and R123 in agreement with P-gp inhibition experiments, where 2c reduced efflux of EPI and R123.

  2. A Human Antibody That Binds to the Sixth Ig-Like Domain of VCAM-1 Blocks Lung Cancer Cell Migration In Vitro

    Directory of Open Access Journals (Sweden)

    Mi Ra Kim

    2017-03-01

    Full Text Available Vascular cell adhesion molecule-1 (VCAM-1 is closely associated with tumor progression and metastasis. However, the relevance and role of VCAM-1 in lung cancer have not been clearly elucidated. In this study, we found that VCAM-1 was highly overexpressed in lung cancer tissue compared with that of normal lung tissue, and high VCAM-1 expression correlated with poor survival in lung cancer patients. VCAM-1 knockdown reduced migration of A549 human lung cancer cells into Matrigel, and competitive blocking experiments targeting the Ig-like domain 6 of VCAM-1 (VCAM-1-D6 demonstrated that the VCAM-1-D6 domain was critical for VCAM-1 mediated A549 cell migration into Matrigel. Next, we developed a human monoclonal antibody specific to human and mouse VCAM-1-D6 (VCAM-1-D6 huMab, which was isolated from a human synthetic antibody library using phage display technology. Finally, we showed that VCAM-1-D6 huMab had a nanomolar affinity for VCAM-1-D6 and that it potently suppressed the migration of A549 and NCI-H1299 lung cancer cell lines into Matrigel. Taken together, these results suggest that VCAM-1-D6 is a key domain for regulating VCAM-1-mediated lung cancer invasion and that our newly developed VCAM-1-D6 huMab will be a useful tool for inhibiting VCAM-1-expressing lung cancer cell invasion.

  3. Copper metabolism domain-containing 1 represses the mediators involved in the terminal effector pathways of human labour and delivery.

    Science.gov (United States)

    Lappas, Martha

    2016-04-01

    Does Copper Metabolism MURR1 Domain 1 (COMMD1) play a role in regulating the mediators involved in the terminal processes of human labour and delivery? COMMD1 plays a critical role in the termination of nuclear factor-κB (NF-κB) activity and the control of pro-inflammatory and pro-labour mediators. Inflammation and infection are the biggest aetiological factors associated with preterm birth. NF-κB drives the transcription of pro-inflammatory mediators involved in the terminal effector pathways of human labour and delivery. In non-gestational tissues, COMMD1 is a negative regulator of NF-κB-induced inflammation. The mRNA and/or protein level of COMMD1 was assessed in myometrium (n = 8 per group) and fetal membranes (n = 8 per group) obtained from term non-labouring and labouring women at term, and fetal membranes (n = 8 per group) at preterm with and without histological chorioamnionitis. Primary human myometrial cells were used to determine the effect of pro-inflammatory mediators on COMMD1 level, and the effect of COMMD1 small interfering RNA (siRNA) on pro-labour mediators. Statistical significance was ascribed to a P labour in myometrium; in fetal membranes with histologically confirmed chorioamnionitis and in myometrial cells treated with pro-inflammatory cytokines interleukin (IL)-1β and tumour necrosis factor (TNF)-α, the bacterial product fibroblast-stimulating lipopeptide and the viral double stranded RNA analogue polyinosinic polycytidilic acid. Loss-of-function studies revealed an increase in inflammation- and infection-induced TNF-α, IL-1α, IL-1β, IL-6, IL-8 and/or monocyte chemoattractant protein-1 mRNA abundance and/or release; and cyclo-oxygenase-2 mRNA level, release of prostaglandin (PG) F2α and mRNA level of the PGF2α receptor FP. In addition, siRNA knockdown of COMMD1 was associated with significantly increased NF-κB activation as evidenced by increased IL-1β-induced IκB-α protein degradation and NF-κB DNA binding activity. The

  4. The human I-mfa domain-containing protein, HIC, interacts with cyclin T1 and modulates P-TEFb-dependent transcription.

    Science.gov (United States)

    Young, Tara M; Wang, Qi; Pe'ery, Tsafi; Mathews, Michael B

    2003-09-01

    Positive transcription elongation factor b (P-TEFb) hyperphosphorylates the carboxy-terminal domain of RNA polymerase II, permitting productive transcriptional elongation. The cyclin T1 subunit of P-TEFb engages cellular transcription factors as well as the human immunodeficiency virus type 1 (HIV-1) transactivator Tat. To identify potential P-TEFb regulators, we conducted a yeast two-hybrid screen with cyclin T1 as bait. Among the proteins isolated was the human I-mfa domain-containing protein (HIC). HIC has been reported to modulate expression from both cellular and viral promoters via its C-terminal cysteine-rich domain, which is similar to the inhibitor of MyoD family a (I-mfa) protein. We show that HIC binds cyclin T1 in yeast and mammalian cells and that it interacts with intact P-TEFb in mammalian cell extracts. The interaction involves the I-mfa domain of HIC and the regulatory histidine-rich region of cyclin T1. HIC also binds Tat via its I-mfa domain, although the sequence requirements are different. HIC colocalizes with cyclin T1 in nuclear speckle regions and with Tat in the nucleolus. Expression of the HIC cDNA modulates Tat transactivation of the HIV-1 long terminal repeat (LTR) in a cell type-specific fashion. It is mildly inhibitory in CEM cells but stimulates gene expression in HeLa, COS, and NIH 3T3 cells. The isolated I-mfa domain acts as a dominant negative inhibitor. Activation of the HIV-1 LTR by HIC in NIH 3T3 cells occurs at the RNA level and is mediated by direct interactions with P-TEFb.

  5. Using Built-In Domain-Specific Modeling Support to Guide Model-Based Test Generation

    CERN Document Server

    Kanstrén, Teemu; 10.4204/EPTCS.80.5

    2012-01-01

    We present a model-based testing approach to support automated test generation with domain-specific concepts. This includes a language expert who is an expert at building test models and domain experts who are experts in the domain of the system under test. First, we provide a framework to support the language expert in building test models using a full (Java) programming language with the help of simple but powerful modeling elements of the framework. Second, based on the model built with this framework, the toolset automatically forms a domain-specific modeling language that can be used to further constrain and guide test generation from these models by a domain expert. This makes it possible to generate a large set of test cases covering the full model, chosen (constrained) parts of the model, or manually define specific test cases on top of the model while using concepts familiar to the domain experts.

  6. Using Built-In Domain-Specific Modeling Support to Guide Model-Based Test Generation

    Directory of Open Access Journals (Sweden)

    Teemu Kanstrén

    2012-02-01

    Full Text Available We present a model-based testing approach to support automated test generation with domain-specific concepts. This includes a language expert who is an expert at building test models and domain experts who are experts in the domain of the system under test. First, we provide a framework to support the language expert in building test models using a full (Java programming language with the help of simple but powerful modeling elements of the framework. Second, based on the model built with this framework, the toolset automatically forms a domain-specific modeling language that can be used to further constrain and guide test generation from these models by a domain expert. This makes it possible to generate a large set of test cases covering the full model, chosen (constrained parts of the model, or manually define specific test cases on top of the model while using concepts familiar to the domain experts.

  7. Applications of fuzzy sets to rule-based expert system development

    Science.gov (United States)

    Lea, Robert N.

    1989-01-01

    Problems of implementing rule-based expert systems using fuzzy sets are considered. A fuzzy logic software development shell is used that allows inclusion of both crisp and fuzzy rules in decision making and process control problems. Results are given that compare this type of expert system to a human expert in some specific applications. Advantages and disadvantages of such systems are discussed.

  8. Reflection group on 'Expert Culture'

    Energy Technology Data Exchange (ETDEWEB)

    Eggermont, G

    2000-07-01

    As part of SCK-CEN's social sciences and humanities programme, a reflection group on 'Expert Culture' was established. The objectives of the reflection group are: (1) to clarify the role of SCK-CEN experts; (2) to clarify the new role of expertise in the evolving context of risk society; (3) to confront external views and internal SCK-CEN experiences on expert culture; (4) to improve trust building of experts and credibility of SCK-CEN as a nuclear actor in society; (5) to develop a draft for a deontological code; (6) to integrate the approach in training on assertivity and communication; (7) to create an output for a topical day on the subject of expert culture. The programme, achievements and perspectives of the refection group are summarised.

  9. Toward a theory of distributed word expert natural language parsing

    Science.gov (United States)

    Rieger, C.; Small, S.

    1981-01-01

    An approach to natural language meaning-based parsing in which the unit of linguistic knowledge is the word rather than the rewrite rule is described. In the word expert parser, knowledge about language is distributed across a population of procedural experts, each representing a word of the language, and each an expert at diagnosing that word's intended usage in context. The parser is structured around a coroutine control environment in which the generator-like word experts ask questions and exchange information in coming to collective agreement on sentence meaning. The word expert theory is advanced as a better cognitive model of human language expertise than the traditional rule-based approach. The technical discussion is organized around examples taken from the prototype LISP system which implements parts of the theory.

  10. Towards the Semantic Web Expert System

    OpenAIRE

    Verhodubs, O; Grundspeņķis, J

    2011-01-01

    The paper presents a conception of the Semantic Web Expert System which is the logical continuation of the expert system development. The Semantic Web Expert System emerges as the result of evolution of expert system concept and it means expert system moving toward the Web and using new Semantic Web technologies. The proposed conception of the Semantic Web Expert System promises to have new useful features that distinguish it from other types of expert systems

  11. STUDY OF A FAULT DIAGNOSIS EXPERT SYSTEM FOR SYNTHETIC MINING SYSTEM HYDRAULIC SUPPORT

    Institute of Scientific and Technical Information of China (English)

    Han Yilun

    2000-01-01

    Fault diagnosis expert system for hydraulic support is studied.The system is achieved by Turbo-prolong Language, it summaries the experience of the domain expert and sets up a fault tree, knowledge base is developed by a productive rule.According to the feature of diagnosis, the system selects forward non-determination inferring and limited depth-first search strategy.It can accomplish expert diagnosis of more than 50 kinds faults in hydraulic support.

  12. Bacterial over-expression and purification of the 3'phosphoadenosine 5'phosphosulfate (PAPS) reductase domain of human FAD synthase: functional characterization and homology modeling.

    Science.gov (United States)

    Miccolis, Angelica; Galluccio, Michele; Giancaspero, Teresa Anna; Indiveri, Cesare; Barile, Maria

    2012-12-11

    FAD synthase (FADS, EC 2.7.7.2) is a key enzyme in the metabolic pathway that converts riboflavin into the redox cofactor, FAD. Human FADS is organized in two domains: -the 3'phosphoadenosine 5'phosphosulfate (PAPS) reductase domain, similar to yeast Fad1p, at the C-terminus, and -the resembling molybdopterin-binding domain at the N-terminus. To understand whether the PAPS reductase domain of hFADS is sufficient to catalyze FAD synthesis, per se, and to investigate the role of the molybdopterin-binding domain, a soluble "truncated" form of hFADS lacking the N-terminal domain (Δ(1-328)-hFADS) has been over-produced and purified to homogeneity as a recombinant His-tagged protein. The recombinant Δ(1-328)-hFADS binds one mole of FAD product very tightly as the wild-type enzyme. Under turnover conditions, it catalyzes FAD assembly from ATP and FMN and, at a much lower rate, FAD pyrophosphorolytic hydrolysis. The Δ(1-328)-hFADS enzyme shows a slight, but not significant, change of K(m) values (0.24 and 6.23 µM for FMN and ATP, respectively) and of k(cat) (4.2 × 10-2 s-1) compared to wild-type protein in the forward direction. These results demonstrate that the molybdopterin-binding domain is not strictly required for catalysis. Its regulatory role is discussed in light of changes in divalent cations sensitivity of the Δ(1-328)-hFADS versus wild-type protein.

  13. Not All Flavor Expertise Is Equal: The Language of Wine and Coffee Experts.

    Science.gov (United States)

    Croijmans, Ilja; Majid, Asifa

    2016-01-01

    People in Western cultures are poor at naming smells and flavors. However, for wine and coffee experts, describing smells and flavors is part of their daily routine. So are experts better than lay people at conveying smells and flavors in language? If smells and flavors are more easily linguistically expressed by experts, or more "codable", then experts should be better than novices at describing smells and flavors. If experts are indeed better, we can also ask how general this advantage is: do experts show higher codability only for smells and flavors they are expert in (i.e., wine experts for wine and coffee experts for coffee) or is their linguistic dexterity more general? To address these questions, wine experts, coffee experts, and novices were asked to describe the smell and flavor of wines, coffees, everyday odors, and basic tastes. The resulting descriptions were compared on a number of measures. We found expertise endows a modest advantage in smell and flavor naming. Wine experts showed more consistency in how they described wine smells and flavors than coffee experts, and novices; but coffee experts were not more consistent for coffee descriptions. Neither expert group was any more accurate at identifying everyday smells or tastes. Interestingly, both wine and coffee experts tended to use more source-based terms (e.g., vanilla) in descriptions of their own area of expertise whereas novices tended to use more evaluative terms (e.g., nice). However, the overall linguistic strategies for both groups were en par. To conclude, experts only have a limited, domain-specific advantage when communicating about smells and flavors. The ability to communicate about smells and flavors is a matter not only of perceptual training, but specific linguistic training too.

  14. Not All Flavor Expertise Is Equal: The Language of Wine and Coffee Experts.

    Directory of Open Access Journals (Sweden)

    Ilja Croijmans

    Full Text Available People in Western cultures are poor at naming smells and flavors. However, for wine and coffee experts, describing smells and flavors is part of their daily routine. So are experts better than lay people at conveying smells and flavors in language? If smells and flavors are more easily linguistically expressed by experts, or more "codable", then experts should be better than novices at describing smells and flavors. If experts are indeed better, we can also ask how general this advantage is: do experts show higher codability only for smells and flavors they are expert in (i.e., wine experts for wine and coffee experts for coffee or is their linguistic dexterity more general? To address these questions, wine experts, coffee experts, and novices were asked to describe the smell and flavor of wines, coffees, everyday odors, and basic tastes. The resulting descriptions were compared on a number of measures. We found expertise endows a modest advantage in smell and flavor naming. Wine experts showed more consistency in how they described wine smells and flavors than coffee experts, and novices; but coffee experts were not more consistent for coffee descriptions. Neither expert group was any more accurate at identifying everyday smells or tastes. Interestingly, both wine and coffee experts tended to use more source-based terms (e.g., vanilla in descriptions of their own area of expertise whereas novices tended to use more evaluative terms (e.g., nice. However, the overall linguistic strategies for both groups were en par. To conclude, experts only have a limited, domain-specific advantage when communicating about smells and flavors. The ability to communicate about smells and flavors is a matter not only of perceptual training, but specific linguistic training too.

  15. Identification of a novel splice variant of human PD-L1 Mrna encoding an isoform-lacking Igv-like domain

    Institute of Scientific and Technical Information of China (English)

    Xian-hui HE; Li-hui XU; Yi LIU

    2005-01-01

    Aim: To investigate the expression and regulation of PD-1 ligand 1 (PD-L1) in peripheral blood mononuclear cells (PBMC). Methods: The cDNA encoding human PD-L1 precursor was cloned from the total RNA extracted from the resting and phorbol dibutyrate plus ionomycin- or phytohemagglutinin-activated PBMC, by reverse transcription polymerase chain reaction (RT-PCR), and independent clones were sequenced and analyzed. The expression and subcellular localization were examined in transiently transfected cells. The PD-L1 gene expression in different PBMC was also analyzed by RT-PCR. Results: A novel human PD-L1 splice variant was identified from the activated PBMC. It was generated by splicing out exon 2 encoding an immunoglobulin variable domain (Igv)-like domain but retaining all other exons without a frame-shift. Consequently, the putative translated protein contained all other domains including the transmembrane region except for the Igv-like domain. Furthermore, the conventional isoform was expressed on the plasma surface whereas the novel isoform showed a pattern of intmcellular membrane distribution in transiently transfected K562 cells. In addition, the expression pattern of the PD-L1 splice variant was variable in different individuals and in different cellular status. Conclusion: PD-L1 expression may be regulated at the posttranscriptional level through alternative splicing, and modulation of the PD-L1 isoform expression may influence the outcome of specific immune responses in the peripheral tissues.

  16. Domain analysis

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

    The domain-analytic approach to knowledge organization (KO) (and to the broader field of library and information science, LIS) is outlined. The article reviews the discussions and proposals on the definition of domains, and provides an example of a domain-analytic study in the field of art studie....... Varieties of domain analysis as well as criticism and controversies are presented and discussed....

  17. Skill in Expert Dogs

    Science.gov (United States)

    Helton, William S.

    2007-01-01

    The motor control of novice participants is often cognitively demanding and susceptible to interference by other tasks. As people develop expertise, their motor control becomes less susceptible to interference from other tasks. Researchers propose a transition in human motor skill from active control to automaticity. This progression may also be…

  18. Ask the Experts

    Science.gov (United States)

    Science Teacher, 2005

    2005-01-01

    Two science questions are answered: (1) How can someone have one brown eye and one blue eye?, and (2) Why are magnets attracted to some metals, but not all metals? It is very rare that a human will have two irises of different colors. This condition, heterochromia, can be a normal variant or the result of an ocular disease. Heterochromia can…

  19. Comparing Novices & Experts in Their Exploration of Data in Line Graphs

    Science.gov (United States)

    Tsuji, Bruce H.; Lindgaard, Gitte

    2014-01-01

    This research compared undergraduate Novices and PhD Experts in psychology and business in their exploration of psychology and business domain graphs. An overall expertise effect in graph explanation was found. Results indicated that Novices paused longer than Experts before beginning their explanations. Qualitative analyses showed that Experts…

  20. Solution structure of the human BTK SH3 domain complexed with a proline-rich peptide from p120cbl

    Energy Technology Data Exchange (ETDEWEB)

    Tzeng, S.-R.; Lou, Y.-C.; Pai, M.-T.; Jain, Moti L.; Cheng, J.-W. [National Tsing Hua University, Division of Structural Biology and Biomedical Science, Department of Life Science (China)

    2000-04-15

    X-linked agammaglobulinemia (XLA), an inherited disease, is caused by mutations in the Bruton's tyrosine kinase (BTK). The absence of functional BTK leads to failure of B cell differentiation which incapacitates antibody production in XLA patients leading to, sometimes lethal, bacterial infections. Point mutation in the BTK gene that leads to deletion of C-terminal 14 aa residues of BTK SH3 domain was found in one patient family. To understand the role of BTK in B cell development, we have determined the solution structure of BTK SH3 domain complexed with a proline-rich peptide from the protein product of c-cbl protooncogene (p120{sup cbl}). Like other SH3 domains, BTK SH3 domain consists of five {beta}-strands packed in two {beta}-sheets forming a {beta}-barrel-like structure. The rmsd calculated from the averaged coordinates for the BTK SH3 domain residues 218-271 and the p120{sup cbl} peptide residues 6-12 of the complex was 0.87 A ({+-}0.16 A) for the backbone heavy atoms (N, C, and C{sub {alpha}}) and 1.64 A ({+-}0.16 A) for all heavy atoms. Based on chemical shift changes and inter-molecular NOEs, we have found that the residues located in the RT loop, n-Src loop and helix-like loop between {beta}4 and {beta}5 of BTK SH3 domain are involved in ligand binding. We have also determined that the proline-rich peptide from p120{sup cbl} binds to BTK SH3 domain in a class I orientation. These results correlate well with our earlier observation that the truncated BTK SH3 domain (deletion of {beta}4, {beta}5 and the helix-like loop) exhibits weaker affinity for the p120{sup cbl} peptide. It is likely that the truncated SH3 domain fails to present to the ligand the crucial residues in the correct context and hence the weaker binding. These results delineate the importance of the C-terminus in the binding of SH3 domains and also indicate that improper folding and the altered binding behavior of mutant BTK SH3 domain likely lead to XLA.

  1. Development and practice of a Telehealthcare Expert System (TES).

    Science.gov (United States)

    Lin, Hanjun; Hsu, Yeh-Liang; Hsu, Ming-Shinn; Cheng, Chih-Ming

    2013-07-01

    Expert systems have been widely used in medical and healthcare practice for various purposes. In addition to vital sign data, important concerns in telehealthcare include the compliance with the measurement prescription, the accuracy of vital sign measurements, and the functioning of vital sign meters and home gateways. However, few expert system applications are found in the telehealthcare domain to address these issues. This article presents an expert system application for one of the largest commercialized telehealthcare practices in Taiwan by Min-Sheng General Hospital. The main function of the Telehealthcare Expert System (TES) developed in this research is to detect and classify events based on the measurement data transmitted to the database at the call center, including abnormality of vital signs, violation of vital sign measurement prescriptions, and malfunction of hardware devices (home gateway and vital sign meter). When the expert system detects an abnormal event, it assigns an "urgent degree" and alerts the nursing team in the call center to take action, such as phoning the patient for counseling or to urge the patient to return to the hospital for further tests. During 2 years of clinical practice, from 2009 to 2011, 19,182 patients were served by the expert system. The expert system detected 41,755 events, of which 22.9% indicated abnormality of vital signs, 75.2% indicated violation of measurement prescription, and 1.9% indicated malfunction of devices. On average, the expert system reduced by 76.5% the time that the nursing team in the call center spent in handling the events. The expert system helped to reduce cost and improve quality of the telehealthcare service.

  2. Bioenergetics and gene silencing approaches for unraveling nucleotide recognition by the human EIF2C2/Ago2 PAZ domain.

    Directory of Open Access Journals (Sweden)

    Mahmoud Kandeel

    Full Text Available Gene silencing and RNA interference are major cellular processes that control gene expression via the cleavage of target mRNA. Eukaryotic translation initiation factor 2C2 (EIF2C2, Argonaute protein 2, Ago2 is considered to be the major player of RNAi as it is the core component of RISC complexes. While a considerable amount of research has focused on RNA interference and its associated mechanisms, the nature and mechanisms of nucleotide recognition by the PAZ domain of EIF2C2/Ago2 have not yet been characterized. Here, we demonstrate that the EIF2C2/Ago2 PAZ domain has an inherent lack of binding to adenine nucleotides, a feature that highlights the poor binding of 3'-adenylated RNAs with the PAZ domain as well as the selective high trimming of the 3'-ends of miRNA containing adenine nucleotides. We further show that the PAZ domain selectively binds all ribonucleotides (except adenosine, whereas it poorly recognizes deoxyribonucleotides. In this context, the modification of dTMP to its ribonucleotide analogue gave a drastic improvement of binding enthalpy and, hence, binding affinity. Additionally, higher in vivo gene silencing efficacy was correlated with the stronger PAZ domain binders. These findings provide new insights into the nature of the interactions of the EIF2C2/Ago2 PAZ domain.

  3. Bioenergetics and gene silencing approaches for unraveling nucleotide recognition by the human EIF2C2/Ago2 PAZ domain.

    Science.gov (United States)

    Kandeel, Mahmoud; Al-Taher, Abdullah; Nakashima, Remi; Sakaguchi, Tomoya; Kandeel, Ali; Nagaya, Yuki; Kitamura, Yoshiaki; Kitade, Yukio

    2014-01-01

    Gene silencing and RNA interference are major cellular processes that control gene expression via the cleavage of target mRNA. Eukaryotic translation initiation factor 2C2 (EIF2C2, Argonaute protein 2, Ago2) is considered to be the major player of RNAi as it is the core component of RISC complexes. While a considerable amount of research has focused on RNA interference and its associated mechanisms, the nature and mechanisms of nucleotide recognition by the PAZ domain of EIF2C2/Ago2 have not yet been characterized. Here, we demonstrate that the EIF2C2/Ago2 PAZ domain has an inherent lack of binding to adenine nucleotides, a feature that highlights the poor binding of 3'-adenylated RNAs with the PAZ domain as well as the selective high trimming of the 3'-ends of miRNA containing adenine nucleotides. We further show that the PAZ domain selectively binds all ribonucleotides (except adenosine), whereas it poorly recognizes deoxyribonucleotides. In this context, the modification of dTMP to its ribonucleotide analogue gave a drastic improvement of binding enthalpy and, hence, binding affinity. Additionally, higher in vivo gene silencing efficacy was correlated with the stronger PAZ domain binders. These findings provide new insights into the nature of the interactions of the EIF2C2/Ago2 PAZ domain.

  4. The impact of the C-terminal domain on the interaction of human DNA topoisomerase II α and β with DNA.

    Directory of Open Access Journals (Sweden)

    Kathryn L Gilroy

    Full Text Available BACKGROUND: Type II DNA topoisomerases are essential, ubiquitous enzymes that act to relieve topological problems arising in DNA from normal cellular activity. Their mechanism of action involves the ATP-dependent transport of one DNA duplex through a transient break in a second DNA duplex; metal ions are essential for strand passage. Humans have two isoforms, topoisomerase IIα and topoisomerase IIβ, that have distinct roles in the cell. The C-terminal domain has been linked to isoform specific differences in activity and DNA interaction. METHODOLOGY/PRINCIPAL FINDINGS: We have investigated the role of the C-terminal domain in the binding of human topoisomerase IIα and topoisomerase IIβ to DNA in fluorescence anisotropy assays using full length and C-terminally truncated enzymes. We find that the C-terminal domain of topoisomerase IIβ but not topoisomerase IIα affects the binding of the enzyme to the DNA. The presence of metal ions has no effect on DNA binding. Additionally, we have examined strand passage of the full length and truncated enzymes in the presence of a number of supporting metal ions and find that there is no difference in relative decatenation between isoforms. We find that calcium and manganese, in addition to magnesium, can support strand passage by the human topoisomerase II enzymes. CONCLUSIONS/SIGNIFICANCE: The C-terminal domain of topoisomerase IIβ, but not that of topoisomerase IIα, alters the enzyme's K(D for DNA binding. This is consistent with previous data and may be related to the differential modes of action of the two isoforms in vivo. We also show strand passage with different supporting metal ions for human topoisomerase IIα or topoisomerase IIβ, either full length or C-terminally truncated. They all show the same preferences, whereby Mg > Ca > Mn.

  5. Mapping of the mouse homolog of the human runt domain gene, AML2, to the distal region of mouse chromosome 4

    Energy Technology Data Exchange (ETDEWEB)

    Avraham, K.B.; Copeland, N.G.; Jenkins, N.A. [National Cancer Institute-Frederick Cancer Research and Development Center, MD (United States)] [and others

    1995-01-20

    AML2 is a runt domain belonging to a group of transcription factors that appear to play a role in Drosophila embryogenesis and mammalian oncogenic transformation. AML2 maps to human chromosome 1p36, a region involved in the t(1;3)(p36;q21) translocation found in association with myelodysplastic syndrome (MDS), myeloproliferative disease (MPD), and acute nonlymphocytic leukemia. 9 refs., 1 fig.

  6. OFMspert - Inference of operator intentions in supervisory control using a blackboard architecture. [operator function model expert system

    Science.gov (United States)

    Jones, Patricia S.; Mitchell, Christine M.; Rubin, Kenneth S.

    1988-01-01

    The authors proposes an architecture for an expert system that can function as an operator's associate in the supervisory control of a complex dynamic system. Called OFMspert (operator function model (OFM) expert system), the architecture uses the operator function modeling methodology as the basis for the design. The authors put emphasis on the understanding capabilities, i.e., the intent referencing property, of an operator's associate. The authors define the generic structure of OFMspert, particularly those features that support intent inferencing. They also describe the implementation and validation of OFMspert in GT-MSOCC (Georgia Tech-Multisatellite Operations Control Center), a laboratory domain designed to support research in human-computer interaction and decision aiding in complex, dynamic systems.

  7. Expert Robots For Automated Packaging And Processing

    Science.gov (United States)

    Slutzky, G. D.; Hall, E. L.; Shell, R. L.

    1989-02-01

    A variety of problems in automated packaging and processing seem ready for expert robotic solutions. Such problems as automated palletizing, bin-picking, automated stoilw and retrieval, automated kitting of parts for assembly, and automated warehousing are currently being considered. The use of expert robots which consist of specialized computer programs, manipulators and integrated sensors has been demonstrated with robot Chedkers, peg games, etc. Actual solutions for automated palletizing, pit-carb basket loading, etc. have also been developed for industrial applications at our Center. The generic concepts arising from this research will be described, unsolved problems discussed, and some important tools demonstrated. The significance of this work lies in its broad application to a host of generic industrial problems which can improve quality, reduce waste, are eliminate human injuries.

  8. [Expert medical witness testimony of maxillofacial injuries].

    Science.gov (United States)

    Orihovac, Zeljko; Macan, Darko

    2008-07-01

    The basic principles of expert medical witness testimony of the maxillofacial region are described. The specific anatomic characteristics of the region are emphasized, especially in view of the fact that face is the most exposed part of the human body. Post-traumatic deformities of the maxillofacial region involve soft tissues of the face and mouth as well as bony structures of the viscerocranium and teeth. Endured physical pain, lessening of life activities, disfigurement and requirement of assistance by third person are separately described as an important part of expert medical witness testimony of the maxillofacial region. The number of lawsuits raised against physicians has significantly increased in the past several years, more often in cases where the patients are dissatisfied with the results of cosmetic surgery, especially when these procedures are performed on the face.

  9. Conserved Domain Database (CDD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins.

  10. Using Expert System Job Aids: A Primer.

    Science.gov (United States)

    Carr, Clay

    1989-01-01

    Explains how current commercial expert system technology can be used to create useful job aids. Expert systems are defined, situations in which an expert system job aid will be most effective are described, expert system shells are discussed, and three commercial expert system products are described. (LRW)

  11. Using Expert System Job Aids: A Primer.

    Science.gov (United States)

    Carr, Clay

    1989-01-01

    Explains how current commercial expert system technology can be used to create useful job aids. Expert systems are defined, situations in which an expert system job aid will be most effective are described, expert system shells are discussed, and three commercial expert system products are described. (LRW)

  12. A Study of Expert System for Career Selection: Literature Review

    Directory of Open Access Journals (Sweden)

    Waghmode M. L

    2015-09-01

    Full Text Available Expert system uses human knowledge stored inside a computer to solve problems those require human expertise for solving. Knowledge expert system helps to support for making better decision. There is need of career guidance for students at college level. Expert system plays an important role to facilitate decision making, diagnosis of diseases etc. Expert system for career selection can be developed using Fuzzy logic, neural network for guiding students for selecting proper career stream. From the literature review it has found that in Maharashtra comparatively very less research took place on expert system for career selection. Hence there is wide scope in expert system development for career guidance which will assist secondary and higher secondary students in Maharashtra for selecting proper career. Through this paper researcher thrown light on literature review of career selection expert systems. Here for career selection researcher reviewed 43 literatures including 2-conference proceeding, 8-Books, 22- Journals, 1-Report, 5-Thesis, 3-Websites, 2-Encyclopaedia articles and 2-generic articles. Articles referred are from last two decades and majority of them are latest.

  13. Expert music performance: cognitive, neural, and developmental bases.

    Science.gov (United States)

    Brown, Rachel M; Zatorre, Robert J; Penhune, Virginia B

    2015-01-01

    In this chapter, we explore what happens in the brain of an expert musician during performance. Understanding expert music performance is interesting to cognitive neuroscientists not only because it tests the limits of human memory and movement, but also because studying expert musicianship can help us understand skilled human behavior in general. In this chapter, we outline important facets of our current understanding of the cognitive and neural basis for music performance, and developmental factors that may underlie musical ability. We address three main questions. (1) What is expert performance? (2) How do musicians achieve expert-level performance? (3) How does expert performance come about? We address the first question by describing musicians' ability to remember, plan, execute, and monitor their performances in order to perform music accurately and expressively. We address the second question by reviewing evidence for possible cognitive and neural mechanisms that may underlie or contribute to expert music performance, including the integration of sound and movement, feedforward and feedback motor control processes, expectancy, and imagery. We further discuss how neural circuits in auditory, motor, parietal, subcortical, and frontal cortex all contribute to different facets of musical expertise. Finally, we address the third question by reviewing evidence for the heritability of musical expertise and for how expertise develops through training and practice. We end by discussing outlooks for future work.

  14. Epidermal Growth Factor Cytoplasmic Domain Affects ErbB Protein Degradation by the Lysosomal and Ubiquitin-Proteasome Pathway in Human Cancer Cells

    Directory of Open Access Journals (Sweden)

    Aleksandra Glogowska

    2012-05-01

    Full Text Available The cytoplasmic domains of EGF-like ligands, including EGF cytoplasmic domain (EGFcyt, have important biological functions. Using specific constructs and peptides of human EGF cytoplasmic domain, we demonstrate that EGFcyt facilitates lysosomal and proteasomal protein degradation, and this coincided with growth inhibition of human thyroid and glioma carcinoma cells. EGFcyt and exon 22–23-encoded peptide (EGF22.23 enhanced procathepsin B (procathB expression and procathB-mediated lysosomal degradation of EGFR/ErbB1 as determined by inhibitors for procathB and the lysosomal ATPase inhibitor BafA1. Presence of mbEGFctF, EGFcyt, EGF22.23, and exon 23-encoded peptides suppressed the expression of the deubiqitinating enzyme ubiquitin C-terminal hydrolase-L1 (UCH-L1. This coincided with hyperubiquitination of total cellular proteins and ErbB1/2 and reduced proteasome activity. Upon small interfering RNA-mediated silencing of endogenously expressed UCH-L1, a similar hyperubiquitinylation phenotype, reduced ErbB1/2 content, and attenuated growth was observed. The exon 23-encoded peptide region of EGFcyt was important for these biologic actions. Structural homology modeling of human EGFcyt showed that this molecular region formed an exposed surface loop. Peptides derived from this EGFcyt loop structure may aid in the design of novel peptide therapeutics aimed at inhibiting growth of cancer cells.

  15. Balance, Sensorimotor, and Cognitive Performance in Long-Year Expert Senior Ballroom Dancers

    Directory of Open Access Journals (Sweden)

    Jan-Christoph Kattenstroth

    2011-01-01

    Full Text Available Physical fitness is considered a major factor contributing to the maintenance of independent living and everyday competence. In line with this notion, it has been shown that several years of amateur dancing experience can exert beneficial effects not only on balance and posture but also on tactile, motor, and cognitive functions in older people. This raises the question of whether an even more extensive schedule of dancing, including competitive tournaments, would further enhance these positive effects. We therefore assessed posture, balance, and reaction times, as well as motor, tactile, and cognitive performance in older expert ballroom dancers with several years of competitive experience. We found substantially better performance in the expert group than in the controls in terms of expertise-related domains like posture, balance, and reaction times. However, there was no generalization of positive effects to those domains that were found to be improved in amateur dancers, such as tactile and cognitive performance, suggesting that there might be an optimal range of intervention intensity to maintain health and independence throughout the human lifespan.

  16. Design of an expert system for phonetic speech recognition

    Energy Technology Data Exchange (ETDEWEB)

    Carbonell, N.; Haton, J.P.; Pierrel, J.M.; Lonchamp, F.

    1983-07-01

    Expert systems have been extensively used as a means for integrating the expertise of a human being into an artificial intelligence system. The authors are presently designing an expert system which will integrate the strategy and the knowledge of a phonetician reading a speech spectrogram. Their goal is twofold, firstly to obtain a better insight into the acoustic-decoding of speech, and, secondly, to improve the efficiency of present automatic phonetic recognition systems. This paper presents a preliminary description of the project, especially the overall strategy of the expert and the role of duration parameters in the segmentation and identification processes.

  17. Gene transfer and expression in human neutrophils. The phox homology domain of p47phox translocates to the plasma membrane but not to the membrane of mature phagosomes

    Directory of Open Access Journals (Sweden)

    Brzezinska Agnieszka A

    2006-12-01

    Full Text Available Abstract Background Neutrophils are non-dividing cells with poor survival after isolation. Consequently, exogenous gene expression in neutrophils is challenging. We report here the transfection of genes and expression of active proteins in human primary peripheral neutrophils using nucleofection. Results Exogenous gene expression in human neutrophils was achieved 2 h post-transfection. We show that neutrophils transfected by nucleofection are functional cells, able to respond to soluble and particulate stimuli. They conserved the ability to undergo physiological processes including phagocytosis. Using this technique, we were able to show that the phox homology (PX domain of p47phox localizes to the plasma membrane in human neutrophils. We also show that RhoB, but not the PX domain of p47phox, is translocated to the membrane of mature phagosomes. Conclusion We demonstrated that cDNA transfer and expression of exogenous protein in human neutrophils is compatible with cell viability and is no longer a limitation for the study of protein function in human neutrophils.

  18. Expert opinion vs. empirical evidence

    Science.gov (United States)

    Herman, Rod A; Raybould, Alan

    2014-01-01

    Expert opinion is often sought by government regulatory agencies when there is insufficient empirical evidence to judge the safety implications of a course of action. However, it can be reckless to continue following expert opinion when a preponderance of evidence is amassed that conflicts with this opinion. Factual evidence should always trump opinion in prioritizing the information that is used to guide regulatory policy. Evidence-based medicine has seen a dramatic upturn in recent years spurred by examples where evidence indicated that certain treatments recommended by expert opinions increased death rates. We suggest that scientific evidence should also take priority over expert opinion in the regulation of genetically modified crops (GM). Examples of regulatory data requirements that are not justified based on the mass of evidence are described, and it is suggested that expertise in risk assessment should guide evidence-based regulation of GM crops. PMID:24637724

  19. Cornell Mixing Zone Expert System

    Science.gov (United States)

    This page provides an overview Cornell Mixing Zone Expert System water quality modeling and decision support system designed for environmental impact assessment of mixing zones resulting from wastewater discharge from point sources

  20. Experts views' on Digital Competence

    OpenAIRE

    Janssen, José; Stoyanov, Slavi

    2013-01-01

    Janssen, J., & Stoyanov, S. (2012, 20 November). Online Consultation for a Digital Competence Framework: Experts' views on Digital Competence. Workshop presentation at the Institute for Prospective Technological Studies, Seville, Spain.

  1. Expert systems in clinical microbiology.

    Science.gov (United States)

    Winstanley, Trevor; Courvalin, Patrice

    2011-07-01

    This review aims to discuss expert systems in general and how they may be used in medicine as a whole and clinical microbiology in particular (with the aid of interpretive reading). It considers rule-based systems, pattern-based systems, and data mining and introduces neural nets. A variety of noncommercial systems is described, and the central role played by the EUCAST is stressed. The need for expert rules in the environment of reset EUCAST breakpoints is also questioned. Commercial automated systems with on-board expert systems are considered, with emphasis being placed on the "big three": Vitek 2, BD Phoenix, and MicroScan. By necessity and in places, the review becomes a general review of automated system performances for the detection of specific resistance mechanisms rather than focusing solely on expert systems. Published performance evaluations of each system are drawn together and commented on critically.

  2. Crystal Structure of the Human Pol α B Subunit in Complex with the C-terminal Domain of the Catalytic Subunit.

    Science.gov (United States)

    Suwa, Yoshiaki; Gu, Jianyou; Baranovskiy, Andrey G; Babayeva, Nigar D; Pavlov, Youri I; Tahirov, Tahir H

    2015-06-05

    In eukaryotic DNA replication, short RNA-DNA hybrid primers synthesized by primase-DNA polymerase α (Prim-Pol α) are needed to start DNA replication by the replicative DNA polymerases, Pol δ and Pol ϵ. The C terminus of the Pol α catalytic subunit (p180C) in complex with the B subunit (p70) regulates the RNA priming and DNA polymerizing activities of Prim-Pol α. It tethers Pol α and primase, facilitating RNA primer handover from primase to Pol α. To understand these regulatory mechanisms and to reveal the details of human Pol α organization, we determined the crystal structure of p70 in complex with p180C. The structured portion of p70 includes a phosphodiesterase (PDE) domain and an oligonucleotide/oligosaccharide binding (OB) domain. The N-terminal domain and the linker connecting it to the PDE domain are disordered in the reported crystal structure. The p180C adopts an elongated asymmetric saddle shape, with a three-helix bundle in the middle and zinc-binding modules (Zn1 and Zn2) on each side. The extensive p180C-p70 interactions involve 20 hydrogen bonds and a number of hydrophobic interactions resulting in an extended buried surface of 4080 Å(2). Importantly, in the structure of the p180C-p70 complex with full-length p70, the residues from the N-terminal to the OB domain contribute to interactions with p180C. The comparative structural analysis revealed both the conserved features and the differences between the human and yeast Pol α complexes.

  3. Characterization of the in vitro expressed autoimmune rippling muscle disease immunogenic domain of human titin encoded by TTN exons 248-249

    Energy Technology Data Exchange (ETDEWEB)

    Zelinka, L. [Biomedical Sciences Program, Kent State University, Kent, OH (United States); McCann, S.; Budde, J.; Sethi, S.; Guidos, M.; Giles, R. [Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, One University Plaza, Youngstown, OH 44555 (United States); Walker, G.R., E-mail: grwalker@ysu.edu [Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, One University Plaza, Youngstown, OH 44555 (United States); Biomedical Sciences Program, Kent State University, Kent, OH (United States)

    2011-08-05

    Highlights: {yields} Affinity purification of the autoimmune rippling muscle disease immunogenic domain of titin. {yields} Partial sequence analysis confirms that the peptides is in the I band region of titin. {yields} This region of the human titin shows high degree of homology to mouse titin N2-A. -- Abstract: Autoimmune rippling muscle disease (ARMD) is an autoimmune neuromuscular disease associated with myasthenia gravis (MG). Past studies in our laboratory recognized a very high molecular weight skeletal muscle protein antigen identified by ARMD patient antisera as the titin isoform. These past studies used antisera from ARMD and MG patients as probes to screen a human skeletal muscle cDNA library and several pBluescript clones revealed supporting expression of immunoreactive peptides. This study characterizes the products of subcloning the titin immunoreactive domain into pGEX-3X and the subsequent fusion protein. Sequence analysis of the fusion gene indicates the cloned titin domain (GenBank ID: (EU428784)) is in frame and is derived from a sequence of N2-A spanning the exons 248-250 an area that encodes the fibronectin III domain. PCR and EcoR1 restriction mapping studies have demonstrated that the inserted cDNA is of a size that is predicted by bioinformatics analysis of the subclone. Expression of the fusion protein result in the isolation of a polypeptide of 52 kDa consistent with the predicted inferred amino acid sequence. Immunoblot experiments of the fusion protein, using rippling muscle/myasthenia gravis antisera, demonstrate that only the titin domain is immunoreactive.

  4. An expert system based intelligent control scheme for space bioreactors

    Science.gov (United States)

    San, Ka-Yiu

    1988-01-01

    An expert system based intelligent control scheme is being developed for the effective control and full automation of bioreactor systems in space. The scheme developed will have the capability to capture information from various resources including heuristic information from process researchers and operators. The knowledge base of the expert system should contain enough expertise to perform on-line system identification and thus be able to adapt the controllers accordingly with minimal human supervision.

  5. The C1 and C2 domains target human type 6 adenylyl cyclase to lipid rafts and caveolae.

    Science.gov (United States)

    Thangavel, Muthusamy; Liu, Xiaoqiu; Sun, Shu Qiang; Kaminsky, Joseph; Ostrom, Rennolds S

    2009-02-01

    Previous data has shown that adenylyl cyclase type 6 (AC6) is expressed principally in lipid rafts or caveolae of cardiac myocytes and other cell types while certain other isoforms of AC are excluded from these microdomains. The mechanism by which AC6 is localized to lipid rafts or caveolae is unknown. In this study, we show AC6 is localized in lipid rafts of COS-7 cells (expressing caveolin-1) and in HEK-293 cells or cardiac fibroblasts isolated from caveolin-1 knock-out mice (both of which lack prototypical caveolins). To determine the region of AC6 that confers raft localization, we independently expressed each of the major intracellular domains, the N-terminus, C1 and C2 domains, and examined their localization with various approaches. The N-terminus did not associate with lipid rafts or caveolae of either COS-7 or HEK-293 cells nor did it immunoprecipitate with caveolin-1 when expressed in COS-7 cells. By contrast, the C1 and C2 domains each associated with lipid rafts to varying degrees and were present in caveolin-1 immunoprecipitates. There were no differences in the pattern of localization of either the C1 or C2 domains between COS-7 and HEK-293 cells. Further dissection of the C1 domain into four individual proteins indicated that the N-terminal half of this domain is responsible for its raft localization. To probe for a role of a putative palmitoylation motif in the C-terminal portion of the C2 domain, we expressed various truncated forms of AC6 lacking most or all of the C-terminal 41 amino acids. These truncated AC6 proteins were not altered in terms of their localization in lipid rafts or their catalytic activity, implying that this C-terminal region is not required for lipid raft targeting of AC6. We conclude that while the C1 domain may be most important, both the C1 and C2 domains of AC6 play a role in targeting AC6 to lipid rafts.

  6. Mutational analysis of residues in the regulatory CBS domains of Moorella thermoacetica pyrophosphatase corresponding to disease-related residues of human proteins.

    Science.gov (United States)

    Jämsen, Joonas; Tuominen, Heidi; Baykov, Alexander A; Lahti, Reijo

    2011-02-01

    mtCBS-PPase [CBS (cystathionine β-synthase) domain-containing pyrophosphatase from Moorella thermoacetica] contains a pair of CBS domains that strongly bind adenine nucleotides, thereby regulating enzyme activity. Eight residues associated with the CBS domains of mtCBS-PPase were screened to explore possible associations with regulation of enzyme activity. The majority of the substitutions (V99A, R168A, Y169A, Y169F, Y188A and H189A) enhanced the catalytic activity of mtCBS-PPase, two substitutions (R170A and R187G) decreased activity, and one substitution (K100G) had no effect. AMP-binding affinity was markedly decreased in the V99A, R168A and Y169A mutant proteins, and elevated in the R187G and H189A mutant proteins. Remarkably, the R168A and Y169A substitutions changed the effect of AMP from inhibition to activation. The stoichiometry of AMP binding increased from one to two AMP molecules per CBS domain pair in the Y169F, R170A, R187G and Y188A variants. The ADP-binding affinity decreased in three and increased in four mutant proteins. These findings identify residues determining the strength and selectivity of nucleotide binding, as well as the direction (inhibition or activation) of the subsequent effect. The data suggest that mutations in human CBS domain-containing proteins can be translated into a bacterial context. Furthermore, our data support the hypothesis that the CBS domains act as an 'internal inhibitor' of mtCBS-PPase.

  7. High-resolution crystal structure of the PDZ1 domain of human protein tyrosine phosphatase PTP-Bas.

    Science.gov (United States)

    Lee, Sang-Ok; Lee, Mi-Kyung; Ku, Bonsu; Bae, Kwang-Hee; Lee, Sang Chul; Lim, Heon M; Kim, Seung Jun; Chi, Seung-Wook

    2016-09-23

    Protein tyrosine phosphatase-Basophil (PTP-Bas) is a membrane-associated protein tyrosine phosphatase with five PDZ domains and is involved in apoptosis, tumorigenesis, and insulin signaling. The interaction between PTP-Bas and tandem-PH-domain-containing protein 1/2 (TAPP1/2) plays an essential role in the regulation of insulin signaling. Despite its high sequence homology with the other PDZ domains, only the PDZ1 domain of PTP-Bas showed distinct binding specificity for TAPP1/2. Although the interaction between PTP-Bas PDZ1 and TAPP1/2 is a therapeutic target for diabetes, the structural basis for the interaction has not been elucidated. In the present study, we determined the crystal structure of the PTP-Bas PDZ1 domain at 1.6 Å resolution. In addition, we calculated the structural models of complexes of PTP-Bas PDZ1 and the C-terminal peptides of TAPP1/2 (referred to as TAPP1p/2p). Structural comparison with the PTP-Bas PDZ2/RA-GEF2 peptide complex revealed a structural basis for distinct binding specificity of PTP-Bas PDZ1 for TAPP1p/2p peptides. Our high-resolution crystal structure of PTP-Bas PDZ1 will serve as a useful template for rational structure-based design of novel anti-diabetes therapeutics.

  8. Experts in science and society

    CERN Document Server

    Gigerenzer, Gerd

    2004-01-01

    In today's complex world, we have come to rely increasingly on those who have expertise in specific areas and can bring their knowledge to bear on crucial social, political and scientific questions. Taking the viewpoint that experts are consulted when there is something important at stake for an individual, a group, or society at large, Experts in Science and Society explores expertise as a relational concept. How do experts balance their commitment to science with that to society? How does a society actually determine that a person has expertise? What personal traits are valued in an expert? From where does the expert derive authority? What makes new forms of expertise emerge? These and related questions are addressed from a wide range of areas in order to be inclusive, as well as to demonstrate similarities across areas. Likewise, in order to be culturally comparative, this volume includes examples and discussions of experts in different countries and even in different time periods. The topics include the r...

  9. Human-Mouse Chimeras with Normal Expression and Function Reveal That Major Domain Swapping Is Tolerated by P-Glycoprotein (ABCB1).

    Science.gov (United States)

    Pluchino, Kristen M; Hall, Matthew D; Moen, Janna K; Chufan, Eduardo E; Fetsch, Patricia A; Shukla, Suneet; Gill, Deborah R; Hyde, Stephen C; Xia, Di; Ambudkar, Suresh V; Gottesman, Michael M

    2016-02-23

    The efflux transporter P-glycoprotein (P-gp) plays a vital role in the transport of molecules across cell membranes and has been shown to interact with a panoply of functionally and structurally unrelated compounds. How human P-gp interacts with this large number of drugs has not been well understood, although structural flexibility has been implicated. To gain insight into this transporter's broad substrate specificity and to assess its ability to accommodate a variety of molecular and structural changes, we generated human-mouse P-gp chimeras by the exchange of homologous transmembrane and nucleotide-binding domains. High-level expression of these chimeras by BacMam- and baculovirus-mediated transduction in mammalian (HeLa) and insect cells, respectively, was achieved. There were no detectable differences between wild-type and chimeric P-gp in terms of cell surface expression, ability to efflux the P-gp substrates rhodamine 123, calcein-AM, and JC-1, or to be inhibited by the substrate cyclosporine A and the inhibitors tariquidar and elacridar. Additionally, expression of chimeric P-gp was able to confer a paclitaxel-resistant phenotype to HeLa cells characteristic of P-gp-mediated drug resistance. P-gp ATPase assays and photo-cross-linking with [(125)I]iodoarylazidoprazosin confirmed that transport and biochemical properties of P-gp chimeras were similar to those of wild-type P-gp, although differences in drug binding were detected when human and mouse transmembrane domains were combined. Overall, chimeras with one or two mouse P-gp domains were deemed functionally equivalent to human wild-type P-gp, demonstrating the ability of human P-gp to tolerate major structural changes.

  10. Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain.

    Science.gov (United States)

    Croll, Tristan I; Smith, Brian J; Margetts, Mai B; Whittaker, Jonathan; Weiss, Michael A; Ward, Colin W; Lawrence, Michael C

    2016-03-01

    Insulin receptor (IR) signaling is critical to controlling nutrient uptake and metabolism. However, only a low-resolution (3.8 Å) structure currently exists for the IR ectodomain, with some segments ill-defined or unmodeled due to disorder. Here, we revise this structure using new diffraction data to 3.3 Å resolution that allow improved modeling of the N-linked glycans, the first and third fibronectin type III domains, and the insert domain. A novel haptic interactive molecular dynamics strategy was used to aid fitting to low-resolution electron density maps. The resulting model provides a foundation for investigation of structural transitions in IR upon ligand binding.

  11. Semi-quantitative assessment of disease risks at the human, livestock, wildlife interface for the Republic of Korea using a nationwide survey of experts: A model for other countries

    Science.gov (United States)

    Hwang, Jusun; Lee, Kyunglee; Walsh, Daniel P.; Kim, SangWha; Sleeman, Jonathan M.; Lee, Hang

    2017-01-01

    Wildlife-associated diseases and pathogens have increased in importance; however, management of a large number of diseases and diversity of hosts is prohibitively expensive. Thus, the determination of priority wildlife pathogens and risk factors for disease emergence is warranted. We used an online questionnaire survey to assess release and exposure risks, and consequences of wildlife-associated diseases and pathogens in the Republic of Korea (ROK). We also surveyed opinions on pathways for disease exposure, and risk factors for disease emergence and spread. For the assessment of risk, we employed a two-tiered, statistical K-means clustering algorithm to group diseases into three levels (high, medium and low) of perceived risk based on release and exposure risks, societal consequences and the level of uncertainty of the experts’ opinions. To examine the experts’ perceived risk of routes of introduction of pathogens and disease amplification and spread, we used a Bayesian, multivariate normal order-statistics model. Six diseases or pathogens, including four livestock and two wildlife diseases, were identified as having high risk with low uncertainty. Similarly, 13 diseases were characterized as having high risk with medium uncertainty with three of these attributed to livestock, six associated with human disease, and the remainder having the potential to affect human, livestock and wildlife (i.e., One Health). Lastly, four diseases were described as high risk with high certainty, and were associated solely with fish diseases. Experts identified migration of wildlife, international human movement and illegal importation of wildlife as the three routes posing the greatest risk of pathogen introduction into ROK. Proximity of humans, livestock and wildlife was the most significant risk factor for promoting the spread of wildlife-associated diseases and pathogens, followed by high density of livestock populations, habitat loss and environmental degradation, and

  12. The Human Mixed Lineage Leukemia 5 (MLL5), a Sequentially and Structurally Divergent SET Domain-Containing Protein with No Intrinsic Catalytic Activity

    Science.gov (United States)

    Teyssier, Catherine; Déméné, Hélène; Carvalho, João E.; Bird, Louise E.; Lebedev, Andrey; Fattori, Juliana; Schubert, Michael; Dumas, Christian; Bourguet, William; le Maire, Albane

    2016-01-01

    Mixed Lineage Leukemia 5 (MLL5) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. Chromatin binding is ensured by its plant homeodomain (PHD) through a direct interaction with the N-terminus of histone H3 (H3). In addition, MLL5 contains a Su(var)3-9, Enhancer of zeste, Trithorax (SET) domain, a protein module that usually displays histone lysine methyltransferase activity. We report here the crystal structure of the unliganded SET domain of human MLL5 at 2.1 Å resolution. Although it shows most of the canonical features of other SET domains, both the lack of key residues and the presence in the SET-I subdomain of an unusually large loop preclude the interaction of MLL5 SET with its cofactor and substrate. Accordingly, we show that MLL5 is devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptides. Hence, the three dimensional structure of MLL5 SET domain unveils the structural basis for its lack of methyltransferase activity and suggests a new regulatory mechanism. PMID:27812132

  13. Crystal structure of the human LRH-1 DBD-DNA complex reveals Ftz-F1 domain positioning is required for receptor activity.

    Science.gov (United States)

    Solomon, Isaac H; Hager, Janet M; Safi, Rachid; McDonnell, Donald P; Redinbo, Matthew R; Ortlund, Eric A

    2005-12-16

    The DNA-binding and ligand-binding functions of nuclear receptors are localized to independent domains separated by a flexible hinge. The DNA-binding domain (DBD) of the human liver receptor homologue-1 (hLRH-1), which controls genes central to development and metabolic homeostasis, interacts with monomeric DNA response elements and contains an Ftz-F1 motif that is unique to the NR5A nuclear receptor subfamily. Here, we present the 2.2A resolution crystal structure of the hLRH-1 DBD in complex with duplex DNA, and elucidate the sequence-specific DNA contacts essential for the ability of LRH-1 to bind to DNA as a monomer. We show that the unique Ftz-F1 domain folds into a novel helix that packs against the DBD but does not contact DNA. Mutations expected to disrupt the positioning of the Ftz-F1 helix do not eliminate DNA binding but reduce the transcriptional activity of full-length LRH-1 significantly. Moreover, we find that altering the Ftz-F1 helix positioning eliminates the enhancement of LRH-1-mediated transcription by the coactivator GRIP1, an action that is associated primarily with the distantly located ligand-binding domain (LBD). Taken together, these results indicate that subtle structural changes in a nuclear receptor DBD can exert long-range functional effects on the LBD of a receptor, and significantly impact transcriptional regulation.

  14. Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove

    Energy Technology Data Exchange (ETDEWEB)

    Ivanova, Marina E.; Fletcher, Georgina C.; O’Reilly, Nicola; Purkiss, Andrew G.; Thompson, Barry J. [Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY (United Kingdom); McDonald, Neil Q., E-mail: neil.mcdonald@cancer.org.uk [Cancer Research UK, 44 Lincoln’s Inn Fields, London WC2A 3LY (United Kingdom); Birkbeck College, University of London, Malet Street, London WC1E 7HX (United Kingdom)

    2015-03-01

    This study characterizes the interaction between the carboxy-terminal (ERLI) motif of the essential polarity protein Crb and the Pals1/Stardust PDZ-domain protein. Structures of human Pals1 PDZ with and without a Crb peptide are described, explaining the highly conserved nature of the ERLI motif and revealing a sterically blocked peptide-binding groove in the absence of ligand. Many components of epithelial polarity protein complexes possess PDZ domains that are required for protein interaction and recruitment to the apical plasma membrane. Apical localization of the Crumbs (Crb) transmembrane protein requires a PDZ-mediated interaction with Pals1 (protein-associated with Lin7, Stardust, MPP5), a member of the p55 family of membrane-associated guanylate kinases (MAGUKs). This study describes the molecular interaction between the Crb carboxy-terminal motif (ERLI), which is required for Drosophila cell polarity, and the Pals1 PDZ domain using crystallography and fluorescence polarization. Only the last four Crb residues contribute to Pals1 PDZ-domain binding affinity, with specificity contributed by conserved charged interactions. Comparison of the Crb-bound Pals1 PDZ structure with an apo Pals1 structure reveals a key Phe side chain that gates access to the PDZ peptide-binding groove. Removal of this side chain enhances the binding affinity by more than fivefold, suggesting that access of Crb to Pals1 may be regulated by intradomain contacts or by protein–protein interaction.

  15. Human I-mfa domain proteins specifically interact with KSHV LANA and affect its regulation of Wnt signaling-dependent transcription.

    Science.gov (United States)

    Kusano, Shuichi; Eizuru, Yoshito

    2010-06-04

    Kaposi's sarcoma-associated herpes virus (KSHV)-encoded latency-associated nuclear antigen (LANA) protein has been reported to interact with glycogen synthase kinase 3beta (GSK-3beta) and to negatively regulate its activity, leading to stimulation of GSK-3beta-dependent beta-catenin degradation. We show here that the I-mfa domain proteins, HIC (human I-mfa domain-containing protein) and I-mfa (inhibitor of MyoD family a), interacted in vivo with LANA through their C-terminal I-mfa domains. This interaction affected the intracellular localization of HIC, inhibited the LANA-dependent transactivation of a beta-catenin-regulated reporter construct, and decreased the level of the LANA.GSK-3beta complex. These data reveal for the first time that I-mfa domain proteins interact with LANA and negatively regulate LANA-mediated activation of Wnt signaling-dependent transcription by inhibiting the formation of the LANA.GSK-3beta complex.

  16. The solution structure of the N-terminal domain of human tubulin binding cofactor C reveals a platform for tubulin interaction.

    Directory of Open Access Journals (Sweden)

    Ma Flor Garcia-Mayoral

    Full Text Available Human Tubulin Binding Cofactor C (TBCC is a post-chaperonin involved in the folding and assembly of α- and β-tubulin monomers leading to the release of productive tubulin heterodimers ready to polymerize into microtubules. In this process it collaborates with other cofactors (TBC's A, B, D, and E and forms a supercomplex with TBCD, β-tubulin, TBCE and α-tubulin. Here, we demonstrate that TBCC depletion results in multipolar spindles and mitotic failure. Accordingly, TBCC is found at the centrosome and is implicated in bipolar spindle formation. We also determine by NMR the structure of the N-terminal domain of TBCC. The TBCC N-terminal domain adopts a spectrin-like fold topology composed of a left-handed 3-stranded α-helix bundle. Remarkably, the 30-residue N-terminal segment of the TBCC N-terminal domain is flexible and disordered in solution. This unstructured region is involved in the interaction with tubulin. Our data lead us to propose a testable model for TBCC N-terminal domain/tubulin recognition in which the highly charged N-terminus as well as residues from the three helices and the loops interact with the acidic hypervariable regions of tubulin monomers.

  17. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

    Directory of Open Access Journals (Sweden)

    Khoury Muin J

    2007-11-01

    Full Text Available Abstract Background Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base. As a practical application of our infrastructure, we presented two applications – Literature Finder and Investigator Browser – as well as a tool set for automating the data curating process for the human genome published literature database. The design of this infrastructure makes the system potentially extensible to other data sources. Results Information retrieval and usability tests demonstrated that the system had high rates of recall and precision, 90% and 93% respectively. The system was easy to learn, easy to use, reasonably speedy and effective. Conclusion The open source system infrastructure presented in this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data. Using the controlled vocabulary UMLS enhanced data integration and interoperability and the extensibility of the system. In addition, by using MVC-based design and Java as a platform-independent programming language, this system provides a potential infrastructure for any domain-specific knowledge base in the biomedical field.

  18. Novel human mutation and CRISPR/Cas genome-edited mice reveal the importance of C-terminal domain of MSX1 in tooth and palate development.

    Science.gov (United States)

    Mitsui, Silvia Naomi; Yasue, Akihiro; Masuda, Kiyoshi; Naruto, Takuya; Minegishi, Yoshiyuki; Oyadomari, Seiichi; Noji, Sumihare; Imoto, Issei; Tanaka, Eiji

    2016-12-05

    Several mutations, located mainly in the MSX1 homeodomain, have been identified in non-syndromic tooth agenesis predominantly affecting premolars and third molars. We identified a novel frameshift mutation of the highly conserved C-terminal domain of MSX1, known as Msx homology domain 6 (MH6), in a Japanese family with non-syndromic tooth agenesis. To investigate the importance of MH6 in tooth development, Msx1 was targeted in mice with CRISPR/Cas system. Although heterozygous MH6 disruption did not alter craniofacial development, homozygous mice exhibited agenesis of lower incisors with or without cleft palate at E16.5. In addition, agenesis of the upper third molars and the lower second and third molars were observed in 4-week-old mutant mice. Although the upper second molars were present, they were abnormally small. These results suggest that the C-terminal domain of MSX1 is important for tooth and palate development, and demonstrate that that CRISPR/Cas system can be used as a tool to assess causality of human disorders in vivo and to study the importance of conserved domains in genes.

  19. The Solution Structure of the N-Terminal Domain of Human Tubulin Binding Cofactor C Reveals a Platform for Tubulin Interaction

    Science.gov (United States)

    Garcia-Mayoral, Mª Flor; Castaño, Raquel; Fanarraga, Monica L.; Zabala, Juan Carlos; Rico, Manuel; Bruix, Marta

    2011-01-01

    Human Tubulin Binding Cofactor C (TBCC) is a post-chaperonin involved in the folding and assembly of α- and β-tubulin monomers leading to the release of productive tubulin heterodimers ready to polymerize into microtubules. In this process it collaborates with other cofactors (TBC's A, B, D, and E) and forms a supercomplex with TBCD, β-tubulin, TBCE and α-tubulin. Here, we demonstrate that TBCC depletion results in multipolar spindles and mitotic failure. Accordingly, TBCC is found at the centrosome and is implicated in bipolar spindle formation. We also determine by NMR the structure of the N-terminal domain of TBCC. The TBCC N-terminal domain adopts a spectrin-like fold topology composed of a left-handed 3-stranded α-helix bundle. Remarkably, the 30-residue N-terminal segment of the TBCC N-terminal domain is flexible and disordered in solution. This unstructured region is involved in the interaction with tubulin. Our data lead us to propose a testable model for TBCC N-terminal domain/tubulin recognition in which the highly charged N-terminus as well as residues from the three helices and the loops interact with the acidic hypervariable regions of tubulin monomers. PMID:22028797

  20. Human I-mfa domain proteins specifically interact with KSHV LANA and affect its regulation of Wnt signaling-dependent transcription

    Energy Technology Data Exchange (ETDEWEB)

    Kusano, Shuichi, E-mail: skusano@m2.kufm.kagoshima-u.ac.jp [Division of Persistent and Oncogenic Viruses, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan); Eizuru, Yoshito [Division of Persistent and Oncogenic Viruses, Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8544 (Japan)

    2010-06-04

    Kaposi's sarcoma-associated herpes virus (KSHV)-encoded latency-associated nuclear antigen (LANA) protein has been reported to interact with glycogen synthase kinase 3{beta} (GSK-3{beta}) and to negatively regulate its activity, leading to stimulation of GSK-3{beta}-dependent {beta}-catenin degradation. We show here that the I-mfa domain proteins, HIC (human I-mfa domain-containing protein) and I-mfa (inhibitor of MyoD family a), interacted in vivo with LANA through their C-terminal I-mfa domains. This interaction affected the intracellular localization of HIC, inhibited the LANA-dependent transactivation of a {beta}-catenin-regulated reporter construct, and decreased the level of the LANA.GSK-3{beta} complex. These data reveal for the first time that I-mfa domain proteins interact with LANA and negatively regulate LANA-mediated activation of Wnt signaling-dependent transcription by inhibiting the formation of the LANA.GSK-3{beta} complex.