Systems biology and the quest for correlates of protection to guide the development of an HIV vaccine.

PubMed

Kuri-Cervantes, Leticia; Fourati, Slim; Canderan, Glenda; Sekaly, Rafick-Pierre

2016-08-01

Over the last three decades, a myriad of data has been generated regarding HIV/SIV evolution, immune evasion, immune response, and pathogenesis. Much of this data can be integrated and potentially used to generate a successful vaccine. Although individual approaches have begun to shed light on mechanisms involved in vaccine-conferred protection from infection, true correlates of protection have not yet been identified. The systems biology approach helps unify datasets generated using different techniques and broaden our understanding of HIV immunopathogenesis. Moreover, systems biology is a tool that can provide correlates of protection, which can be targeted for the production of a successful HIV vaccine. Copyright © 2016. Published by Elsevier Ltd.

Designing a WebQuest

ERIC Educational Resources Information Center

Salsovic, Annette R.

2009-01-01

A WebQuest is an inquiry-based lesson plan that uses the Internet. This article explains what a WebQuest is, shows how to create one, and provides an example. When engaged in a WebQuest, students use technology to experience cooperative learning and discovery learning while honing their research, writing, and presentation skills. It has been found…

Instrument Pointing Control System for the Stellar Interferometry Mission - Planet Quest

NASA Technical Reports Server (NTRS)

Brugarolas, Paul B.; Kang, Bryan

2006-01-01

This paper describes the high precision Instrument Pointing Control System (PCS) for the Stellar Interferometry Mission (SIM) - Planet Quest. The PCS system provides front-end pointing, compensation for spacecraft motion, and feedforward stabilization, which are needed for proper interference. Optical interferometric measurements require very precise pointing (0.03 as, 1-(sigma) radial) for maximizing the interference pattern visibility. This requirement is achieved by fine pointing control of articulating pointing mirrors with feedback from angle tracking cameras. The overall pointing system design concept is presentcd. Functional requirements and an acquisition concept are given. Guide and Science pointing control loops are discussed. Simulation analyses demonstrate the feasibility of the design.

Organizing principles as tools for bridging the gap between system theory and biological experimentation.

PubMed

Mekios, Constantinos

2016-04-01

Twentieth-century theoretical efforts towards the articulation of general system properties came short of having the significant impact on biological practice that their proponents envisioned. Although the latter did arrive at preliminary mathematical formulations of such properties, they had little success in showing how these could be productively incorporated into the research agenda of biologists. Consequently, the gap that kept system-theoretic principles cut-off from biological experimentation persisted. More recently, however, simple theoretical tools have proved readily applicable within the context of systems biology. In particular, examples reviewed in this paper suggest that rigorous mathematical expressions of design principles, imported primarily from engineering, could produce experimentally confirmable predictions of the regulatory properties of small biological networks. But this is not enough for contemporary systems biologists who adopt the holistic aspirations of early systemologists, seeking high-level organizing principles that could provide insights into problems of biological complexity at the whole-system level. While the presented evidence is not conclusive about whether this strategy could lead to the realization of the lofty goal of a comprehensive explanatory integration, it suggests that the ongoing quest for organizing principles is pragmatically advantageous for systems biologists. The formalisms postulated in the course of this process can serve as bridges between system-theoretic concepts and the results of molecular experimentation: they constitute theoretical tools for generalizing molecular data, thus producing increasingly accurate explanations of system-wide phenomena.

CosmoQuest: Galvanizing a Dynamic, Inclusive Professional Learning Network

NASA Astrophysics Data System (ADS)

Cobb, W. H.; Buxner, S.; Bracey, G.; Noel-Storr, J.; Gay, P.; Graff, P. V.

2016-12-01

The CosmoQuest Virtual Research Facility offers experiences to audiences around the nation and globally through pioneering citizen science. An endeavor between universities, research institutes, and NASA centers, CosmoQuest brings together scientists, educators, researchers, programmers—and individuals of all ages—to explore and make sense of our solar system and beyond. Scaffolded by an educational framework that inspires 21stCentury learners, CosmoQuest engages people—you, me!—in analyzing and interpreting real NASA data, inspiring questions and defining problems. Linda Darling-Hammond calls for professional development to be: "focused on the learning and teaching of specific curriculum content [i.e. NGSS disciplinary core ideas]; organized around real problems of practice [i.e. NGSS science and engineering practices] …; [and] connected to teachers' collaborative work in professional learning community...." (2012). In light of that, what can CosmoQuest offer NASA STEM education as a virtual research facility? CosmoQuest engages scientists with learners, and learners with science. As a virual research facility, its focal point must be its online platform. CosmoQuest empowers and expands community through a variety of social channels, including science and education-focused hangouts, podcasts, virtual star parties, and social media. In addition to creating standards-aligned materials, CosmoQuest channels are a hub for excellent resources throughout NASA and the larger astronomical community. In support of CosmoQuest citizen science opportunities, the process and outcomes of CosmoQuest initiatives will be leveraged and shared. Thus, CosmoQuest will be present and alive in the awareness of its growing community. Finally, to make CosmoQuest truly relevant, partnerships between scientists and educators are encouraged and facilitated, and "just-in-time" opportunities to support constituents exploring emerging NASA STEM education and new NASA data will be

REQUEST: A Recursive QUEST Algorithm for Sequential Attitude Determination

NASA Technical Reports Server (NTRS)

Bar-Itzhack, Itzhack Y.

1996-01-01

In order to find the attitude of a spacecraft with respect to a reference coordinate system, vector measurements are taken. The vectors are pairs of measurements of the same generalized vector, taken in the spacecraft body coordinates, as well as in the reference coordinate system. We are interested in finding the best estimate of the transformation between these coordinate system.s The algorithm called QUEST yields that estimate where attitude is expressed by a quarternion. Quest is an efficient algorithm which provides a least squares fit of the quaternion of rotation to the vector measurements. Quest however, is a single time point (single frame) batch algorithm, thus measurements that were taken at previous time points are discarded. The algorithm presented in this work provides a recursive routine which considers all past measurements. The algorithm is based on on the fact that the, so called, K matrix, one of whose eigenvectors is the sought quaternion, is linerly related to the measured pairs, and on the ability to propagate K. The extraction of the appropriate eigenvector is done according to the classical QUEST algorithm. This stage, however, can be eliminated, and the computation simplified, if a standard eigenvalue-eigenvector solver algorithm is used. The development of the recursive algorithm is presented and illustrated via a numerical example.

CosmoQuest: Creative Engagement & Citizen Science Ignite Authentic Science

NASA Astrophysics Data System (ADS)

Cobb, W. H.; Noel-Storr, J.; Tweed, A.; Asplund, S.; Aiello, M. P.; Lebofsky, L. A.; Chilton, H.; Gay, P.

2016-12-01

The CosmoQuest Virtual Research Facility offers in-depth experiences to diverse audiences nationally and internationally through pioneering citizen science. An endeavor between universities, research institutes, and NASA centers, CosmoQuest brings together scientists, educators, researchers, programmers—and individuals of all ages—to explore and make sense of our solar system and beyond. CosmoQuest creates pathways for engaging diverse audiences in authentic science, encouraging scientists to engage with learners, and learners to engage with scientists. Here is a sequence of activities developed by CosmoQuest, leveraging a NASA Discovery and New Frontiers Programs activity developed for the general STEAM community, that activates STEM learning. The Spark: Igniting Curiosity Art and the Cosmic Connection uses the elements of art—shape, line, color, texture, value—to hone observation skills and inspire questions. Learners explore NASA image data from celestial bodies in our solar system—planets, asteroids, moons. They investigate their geology, analyzing features and engaging in scientific discourse rising from evidence while creating a beautiful piece of art. The Fuel: Making Connections Crater Comparisons explore authentic NASA image data sets, engrossing learners at a deeper level. With skills learned in Art and the Cosmic Connection, learners analyze specific image sets with the feedback of mission team members. The Burn: Evolving Community Become a Solar System Mapper. Investigate and analyze NASA mission image data of Mars, Mercury, the Moon and Vesta through CosmoQuest's citizen science projects. Learners make real-world connections while contributing to NASA science. Scaffolded by an educational framework that inspires 21st century learners, CosmoQuest engages people in analyzing and interpreting real NASA data, inspiring questions, defining problems, and realizing their potential to contribute to genuine scientific results. Through social channels

7th Annual Systems Biology Symposium: Systems Biology and Engineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering aremore » now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."« less

A WebQuest for Spatial Skills

ERIC Educational Resources Information Center

Wood, Pamela L.; Quitadamo, Ian J.; DePaepe, James L.; Loverro, Ian

2007-01-01

The WebQuest is a four-step process integrated at appropriate points in the Animal Studies unit. Through the WebQuest, students create a series of habitat maps that build on the knowledge gained from conducting the various activities of the unit. The quest concludes with an evaluation using the WebQuest rubric and an oral presentation of a final…

New quests for better attitudes

NASA Technical Reports Server (NTRS)

Shuster, Malcolm D.

1991-01-01

During the past few years considerable insight was gained into the QUEST algorithm both as a maximum likelihood estimator and as a Kalman filter/smoother for systems devoid of dynamical noise. The new algorithms and software are described and analytical comparisons are made with the more conventional attitude Kalman filter. It is also described how they may be accommodated to noisy dynamical systems.

Corner Office: ProQuest's Marty Kahn

ERIC Educational Resources Information Center

Fialkoff, Francine; Oder, Norman

2009-01-01

In a scant three years at ProQuest, Marty Kahn, CEO, has moved a company coming out of a financial morass back onto solid ground. He came on board after the purchase of ProQuest Information and Learning by the (mostly) privately owned Cambridge Information Group in late 2006 and the merger of ProQuest and CSA to form ProQuest CSA. (It's now just…

CosmoQuest Collaborative: Galvanizing a Dynamic Professional Learning Network

NASA Astrophysics Data System (ADS)

Cobb, Whitney; Bracey, Georgia; Buxner, Sanlyn; Gay, Pamela L.; Noel-Storr, Jacob; CosmoQuest Team

2016-10-01

The CosmoQuest Collaboration offers in-depth experiences to diverse audiences around the nation and the world through pioneering citizen science in a virtual research facility. An endeavor between universities, research institutes, and NASA centers, CosmoQuest brings together scientists, educators, researchers, programmers—and citizens of all ages—to explore and make sense of our solar system and beyond. Leveraging human networks to expand NASA science, scaffolded by an educational framework that inspires lifelong learners, CosmoQuest engages citizens in analyzing and interpreting real NASA data, inspiring questions and defining problems.The QuestionLinda Darling-Hammond calls for professional development to be: "focused on the learning and teaching of specific curriculum content [i.e. NGSS disciplinary core ideas]; organized around real problems of practice [i.e. NGSS science and engineering practices] … [and] connected to teachers' collaborative work in professional learning community...." (2012) In light of that, what is the unique role CosmoQuest's virtual research facility can offer NASA STEM education?A Few AnswersThe CosmoQuest Collaboration actively engages scientists in education, and educators (and learners) in science. CosmoQuest uses social channels to empower and expand NASA's learning community through a variety of media, including science and education-focused hangouts, virtual star parties, and social media. In addition to creating its own supportive, standards-aligned materials, CosmoQuest offers a hub for excellent resources and materials throughout NASA and the larger astronomy community.In support of CosmoQuest citizen science opportunities, CQ initiatives (Learning Space, S-ROSES, IDEASS, Educator Zone) will be leveraged and shared through the CQPLN. CosmoQuest can be present and alive in the awareness its growing learning community.Finally, to make the CosmoQuest PLN truly relevant, it aims to encourage partnerships between scientists

Development of a WebQuest as instructional material in teaching biodiversity for grade 8 learners

NASA Astrophysics Data System (ADS)

Genovia, Jerson A.; Eslit, April Rose C.; Tamse, Agnes Lera G.; Barquilla, Manuel B.

2018-01-01

WebQuest is an inquiry-based learning activity that allows students to learn the lesson using the information provided in the internet resources. The study aimed to develop and implement the WebQuest on Biodiversity. Primarily, this research determines the students' performances in the achievement test after WebQuest was implemented to them. Secondly, it is also to investigate on their attitudes towards Biology before and after the activity as well as the level of development of their 21st Century Skills. This research utilized Quasi-experimental Non-randomized One Group Pretest/Posttest Design. The developed WebQuest that is based from the K-12 curriculum competencies were evaluated by selected experts in the Content (2), Pedagogy (2) and ICT (2) to assess the said activity in terms of content, pedagogy and ICT effects. It was then implemented in an intact group of grade 8 students. Findings revealed that the developed WebQuest was rated "Excellent" for Content, Pedagogy and TCT effects. After utilizing the WebQuest activity on Biodiversity, students acquired more knowledge on the topic shows by the mean difference of 2.42, which is highly significant based on t-test result. The overall students' attitude towards Biology as a subject changed positively after they did the activity due to novelty effects and the WebQuest itself with the mean difference of 0.46. Moreover, results shows that the students can developed 21st century skills considering that the Likert scale survey was given only to the students after the activity. Based on the result, 97% of total responses favored to have developed Critical Thinking skills, 98% on Collaboration skills, 97% on Creativity and Innovative skills, 94% on Communication skills, 97% on Self-Decision skills, and 97% on ICT skills. The concentration of percentage of responses differed in two classes because Class A was composed of highlyselected students who underwent an entrance examination upon admission in school and Class B

Interacting Science through Web Quests

ERIC Educational Resources Information Center

Unal, Ahmet; Karakus, Melek Altiparmak

2016-01-01

The purpose of this paper is to examine the effects of WebQuests on elementary students' science achievement, attitude towards science and attitude towards web supported education in teaching 7th grade subjects (Ecosystems, Solar System). With regard to this research, "Science Achievement Test," "Attitude towards Science Scale"…

The MarsQuest Education Project

NASA Astrophysics Data System (ADS)

Dusenbery, P. B.; Lee, S. W.

1998-09-01

The upcoming decade of Mars exploration will provide numerous opportunities for a variety of educational efforts. One of these, MarsQuest, is a travelling exhibition being developed by the Space Science Institute with partial funding from NSF and NASA. MarsQuest's Education and Outreach Program will take advantage of the many Mars-related educational resources currently available, as well as those in the planning stages. Materials reflecting the exhibit content will be disseminated to teachers at sites where the exhibit is visiting and via presentations at annual and regional meetings of the National Science Teachers Association, and via a web site containing interactive educational resources. The goals of the MarsQuest Education Program are to: 1) Make use of the rich educational resources and coincident occurrence of ongoing Mars missions; 2) Captivate broad public interest in Mars exploration and use it to promote scientific literacy; 3) Provide opportunities for teachers, students, and families to connect in real-time to the Mars missions, the people involved, and the science experiments underway; 4) Enhance the overall education experience of the MarsQuest exhibition. The MarsQuest Education Program is focused on teacher training/enhancement and parental involvement. The main mechanism for teacher enhancement and encouragement of parental participation will be through two education workshops organized by MarsQuest personnel at each host site. The first will target museum staff and "master" K-12 teachers. The second will target local K-12 teachers. The MarsQuest Education Program will also provide museum staff, exhibit liaisons, and astronomy volunteers information on offering one-day workshops designed for family groups. The MarsQuest project will provide a wide ranging dissemination effort, ultimately reaching an estimated two to three million people during its three-year tour.

Is nursing ready for WebQuests?

PubMed

Lahaie, Ulysses David

2008-12-01

Based on an inquiry-oriented framework, WebQuests facilitate the construction of effective learning activities. Developed by Bernie Dodge and Tom March in 1995 at the San Diego State University, WebQuests have gained worldwide popularity among educators in the kindergarten through grade 12 educational sector. However, their application at the college and university levels is not well documented. WebQuests enhance and promote higher order-thinking skills, are consistent with Bloom's Taxonomy, and reflect a learner-centered instructional methodology (constructivism). They are based on solid theoretical foundations and promote critical thinking, inquiry, and problem solving. There is a role for WebQuests in nursing education. A WebQuest example is described in this article.

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

PubMed Central

Chen, Bor-Sen; Wu, Chia-Chou

2013-01-01

Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

PubMed

Chen, Bor-Sen; Wu, Chia-Chou

2013-10-11

Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

Systems interface biology

PubMed Central

Doyle, Francis J; Stelling, Jörg

2006-01-01

The field of systems biology has attracted the attention of biologists, engineers, mathematicians, physicists, chemists and others in an endeavour to create systems-level understanding of complex biological networks. In particular, systems engineering methods are finding unique opportunities in characterizing the rich behaviour exhibited by biological systems. In the same manner, these new classes of biological problems are motivating novel developments in theoretical systems approaches. Hence, the interface between systems and biology is of mutual benefit to both disciplines. PMID:16971329

A Good Teaching Technique: WebQuests

ERIC Educational Resources Information Center

Halat, Erdogan

2008-01-01

In this article, the author first introduces and describes a new teaching tool called WebQuests to practicing teachers. He then provides detailed information about the structure of a good WebQuest. Third, the author shows the strengths and weaknesses of using Web-Quests in teaching and learning. Last, he points out the challenges for practicing…

Working with WebQuests

ERIC Educational Resources Information Center

Raulston, Cassie; Moellinger, Donna

2007-01-01

With the evolution of technology, students can now take online classes that may not be offered in their home schools. While online courses are commonly found in many high schools, WebQuests are used more commonly in elementary schools. Through the exploration of WebQuests, students are able to integrate the Internet into classroom activities. The…

"Life-bearing molecules" versus "life-embodying systems": Two contrasting views on the what-is-life (WIL) problem persisting from the early days of molecular biology to the post-genomic cell- and organism-level biology.

PubMed

Sato, Naoki

2018-05-01

"What is life?" is an ultimate biological quest for the principle that makes organisms alive. This 'WIL problem' is not, however, a simple one that we have a straightforward strategy to attack. From the beginning, molecular biology tried to identify molecules that bear the essence of life: the double helical DNA represented replication, and enzymes were micro-actuators of biological activities. A dominating idea behind these mainstream biological studies relies on the identification of life-bearing molecules, which themselves are models of life. Another, prevalent idea emphasizes that life resides in the whole system of an organism, but not in some particular molecules. The behavior of a complex system may be considered to embody the essence of life. The thermodynamic view of life system in the early 20th century was remodeled as physics of complex systems and systems biology. The two views contrast with each other, but they are no longer heritage of the historical dualism in biology, such as mechanism/materialism versus vitalism, or reductionism versus holism. These two views are both materialistic and mechanistic, and act as driving forces of modern biology. In reality, molecules function in a context of systems, whereas systems presuppose functional molecules. A key notion to reconcile this conflict is that subjects of biological studies are given before we start to study them. Cell- or organism-level biology is destined to the dialectic of molecules and systems, but this antagonism can be resolved by dynamic thinking involving biological evolution. Copyright © 2018 Elsevier B.V. All rights reserved.

The WebQuest: constructing creative learning.

PubMed

Sanford, Julie; Townsend-Rocchiccioli, Judith; Trimm, Donna; Jacobs, Mike

2010-10-01

An exciting expansion of online educational opportunities is occurring in nursing. The use of a WebQuest as an inquiry-based learning activity can offer considerable opportunity for nurses to learn how to analyze and synthesize critical information. A WebQuest, as a constructivist, inquiry-oriented strategy, requires learners to use higher levels of thinking as a means to analyze and apply complex information, providing an exciting online teaching and learning strategy. A WebQuest is an inquiry-oriented lesson format in which most or all of the information learners work with comes from the web. This article provides an overview of the WebQuest as a teaching strategy and provides examples of its use. Copyright 2010, SLACK Incorporated.

WebQuests: Tools for Differentiation

ERIC Educational Resources Information Center

Schweizer, Heidi; Kossow, Ben

2007-01-01

This article features the WebQuest, an inquiry-oriented activity in which some or all of the information that learners interact with comes from resources on the Internet. WebQuests, when properly constructed, are activities, usually authentic in nature, that require the student to use Internet-based resources to deepen their understanding and…

The Well-Constructed WebQuest

ERIC Educational Resources Information Center

Kennedy, Shelly

2004-01-01

In this article, the author offers criteria for evaluating WebQuests that are intended for use by students in the elementary grades. There are two general areas that teachers should consider: (1) Pedagogy--whether a WebQuest is developmentally appropriate and educationally useful for their students; and (2) Scholarship--whether the content is…

Woman's Quest in Contemporary Fiction.

ERIC Educational Resources Information Center

Semeiks, Jonna Gormely

Depending primarily on Joseph Campbell's treatment of the quest or hero myth, this paper provides analyses of recent women's fiction in terms of contemporary women's quests for personal identity and freedom. Following discussions of a proposed definition of myth, its connotations, and its use as a literary device and as a tool for critical…

Validation of the QUEST for German-speaking countries.

PubMed

Hopfner, Franziska; Nebel, Adelheid; Lyons, Kelly E; Tröster, Alexander I; Kuhlenbäumer, Gregor; Deuschl, Günther; Martinez-Martin, Pablo

2016-01-01

To explore the clinimetric attributes of the German version of the quality of life in essential tremor (ET) questionnaire (QUEST) as a tremor-specific measure of quality of life. This was an observational, cross-sectional study. The QUEST German version was obtained by translation-back translation procedure. ET cases were diagnosed according to the tremor investigation group criteria. Assessments included Archimedes spirals rating, EQ-5D, Beck Depression Inventory (BDI-II) and QUEST German version. Missing data were imputed for those cases in which the loss of data for one domain of the QUEST was <30%. Ninety three patients out of 138 (67.4%) with definite or probable ET had complete QUEST data after 43 item imputations and they constituted the sample for this study. The QUEST summary index (QSI) displayed no floor or ceiling effects. QUEST internal consistency (Cronbach's alpha) ranged between 0.50 and 0.89. Item-total domain correlations ranged from 0.26 to 0.82 and the item homogeneity indexes were satisfactory (range: 0.28-0.60). The QSI correlated weakly with the EQ-5D (rS=0.20) and moderately with the BDI-II (rS = 0.31) and the QUEST self-evaluation of tremor severity (rS = 0.44). The QUEST German version has, despite recognized data quality problems, satisfactory acceptability and internal consistency as a whole. The correlation analysis showed that tremor in the head, voice and right hand was moderately associated with quality of life.

DrugQuest - a text mining workflow for drug association discovery.

PubMed

Papanikolaou, Nikolas; Pavlopoulos, Georgios A; Theodosiou, Theodosios; Vizirianakis, Ioannis S; Iliopoulos, Ioannis

2016-06-06

Text mining and data integration methods are gaining ground in the field of health sciences due to the exponential growth of bio-medical literature and information stored in biological databases. While such methods mostly try to extract bioentity associations from PubMed, very few of them are dedicated in mining other types of repositories such as chemical databases. Herein, we apply a text mining approach on the DrugBank database in order to explore drug associations based on the DrugBank "Description", "Indication", "Pharmacodynamics" and "Mechanism of Action" text fields. We apply Name Entity Recognition (NER) techniques on these fields to identify chemicals, proteins, genes, pathways, diseases, and we utilize the TextQuest algorithm to find additional biologically significant words. Using a plethora of similarity and partitional clustering techniques, we group the DrugBank records based on their common terms and investigate possible scenarios why these records are clustered together. Different views such as clustered chemicals based on their textual information, tag clouds consisting of Significant Terms along with the terms that were used for clustering are delivered to the user through a user-friendly web interface. DrugQuest is a text mining tool for knowledge discovery: it is designed to cluster DrugBank records based on text attributes in order to find new associations between drugs. The service is freely available at http://bioinformatics.med.uoc.gr/drugquest .

InfoQUEST: An Online Catalog for Small Libraries.

ERIC Educational Resources Information Center

Campbell, Bonnie

1984-01-01

InfoQUEST is a microcomputer-based online public access catalog, designed for the small library handling file sizes up to 25,000 records. Based on the IBM-PC, or compatible machines, the system will accept downloading, in batch mode, of records from the library's file on the UTLAS Catalog Support System. (Author/EJS)

Computational systems chemical biology.

PubMed

Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander

2011-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

Computational Systems Chemical Biology

PubMed Central

Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

2013-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007). The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology / systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology. PMID:20838980

Canadarm2 Maneuvers Quest Airlock

NASA Technical Reports Server (NTRS)

2001-01-01

At the control of Expedition Two Flight Engineer Susan B. Helms, the newly-installed Canadian-built Canadarm2, Space Station Remote Manipulator System (SSRMS) maneuvers the Quest Airlock into the proper position to be mated onto the starboard side of the Unity Node I during the first of three extravehicular activities (EVA) of the STS-104 mission. The Quest Airlock makes it easier to perform space walks, and allows both Russian and American spacesuits to be worn when the Shuttle is not docked with the International Space Station (ISS). American suits will not fit through Russion airlocks at the Station. The Boeing Company, the space station prime contractor, built the 6.5-ton (5.8 metric ton) airlock and several other key components at the Marshall Space Flight Center (MSFC), in the same building where the Saturn V rocket was built. Installation activities were supported by the development team from the Payload Operations Control Center (POCC) located at the MSFC and the Mission Control Center at NASA's Johnson Space Flight Center in Houston, Texas.

Biological life-support systems

NASA Technical Reports Server (NTRS)

Shepelev, Y. Y.

1975-01-01

The establishment of human living environments by biologic methods, utilizing the appropriate functions of autotrophic and heterotrophic organisms is examined. Natural biologic systems discussed in terms of modeling biologic life support systems (BLSS), the structure of biologic life support systems, and the development of individual functional links in biologic life support systems are among the factors considered. Experimental modeling of BLSS in order to determine functional characteristics, mechanisms by which stability is maintained, and principles underlying control and regulation is also discussed.

Implementing WebQuest Based Instruction on Newton's Second Law

ERIC Educational Resources Information Center

Gokalp, Muhammed Sait; Sharma, Manjula; Johnston, Ian; Sharma, Mia

2013-01-01

The purpose of this study was to investigate how WebQuests can be used in physics classes for teaching specific concepts. The study had three stages. The first stage was to develop a WebQuest on Newton's second law. The second stage involved developing a lesson plan to implement the WebQuest in class. In the final stage, the WebQuest was…

From systems biology to systems biomedicine.

PubMed

Antony, Paul M A; Balling, Rudi; Vlassis, Nikos

2012-08-01

Systems Biology is about combining theory, technology, and targeted experiments in a way that drives not only data accumulation but knowledge as well. The challenge in Systems Biomedicine is to furthermore translate mechanistic insights in biological systems to clinical application, with the central aim of improving patients' quality of life. The challenge is to find theoretically well-chosen models for the contextually correct and intelligible representation of multi-scale biological systems. In this review, we discuss the current state of Systems Biology, highlight the emergence of Systems Biomedicine, and highlight some of the topics and views that we think are important for the efficient application of Systems Theory in Biomedicine. Copyright © 2011 Elsevier Ltd. All rights reserved.

Systems Biology-an interdisciplinary approach.

PubMed

Friboulet, Alain; Thomas, Daniel

2005-06-15

System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

PropertyQuest

Science.gov Websites

range of site-related information easily, especially for historic resources. PropertyQuest draws from databases provided by other DC agencies. Information is presented here for planning purposes only. Please , including: The Office of Planning for historic resources, census information, and boundaries of Chinatown

CosmoQuest MoonMappers: Citizen Lunar Exploration

NASA Astrophysics Data System (ADS)

Gay, P. L.; Antonenko, I.; Robbins, S. J.; Bracey, G.; Lehan, C.; Moore, J.; Huang, D.

2012-09-01

The MoonMappers citizen science project is part of CosmoQuest, a virtual research facility designed for the public. CosmoQuest seeks to take the best aspects of a research center - research, seminars, journal clubs, and community discussions - and provide them to a community of citizen scientists through a virtual facility. MoonMappers was the first citizen science project within CosmoQuest, and is being used to define best practices in getting the public to effectively learn and do science.

WebQuests as Language-Learning Tools

ERIC Educational Resources Information Center

Aydin, Selami

2016-01-01

This study presents a review of the literature that examines WebQuests as tools for second-language acquisition and foreign language-learning processes to guide teachers in their teaching activities and researchers in further research on the issue. The study first introduces the theoretical background behind WebQuest use in the mentioned…

Quest airlock maneuvered into position

NASA Image and Video Library

2001-07-15

STS104-E-5068 (15 July 2001) --- Backdropped against a blue and white Earth, some 237 miles below, the Quest airlock is in the process of being installed onto the starboard side of Unity Node 1 of the International Space Station (ISS). Astronaut Susan J. Helms, Expedition Two flight engineer, used controls onboard the station to maneuver the Airlock into place with the Canadarm2 or Space Station Remote Manipulator System (SSRMS). This image was recorded with a digital still camera.

Quest for Continual Growth Takes Root

ERIC Educational Resources Information Center

Surdey, Mary M.; Hashey, Jane M.

2006-01-01

In this article, the authors describe how the quest for continual growth has taken its root at Vestal Central School district. Located at the heart of upstate New York, educators at Vestal Central School district have created a spirit of "kaizen," a Japanese word meaning the relentless quest for continual improvement and higher-quality…

NASA Quest.

ERIC Educational Resources Information Center

Ashby, Susanne

2000-01-01

Introduces NASA Quest as part of NASA's Learning Technologies Project, which connects students to the people of NASA through the various pages at the website where students can glimpse the various types of work performed at different NASA facilities and talk to NASA workers about the type of work they do. (ASK)

WebQuests: Are They Developmentally Appropriate?

ERIC Educational Resources Information Center

Maddux, Cleborne D.; Cummings, Rhoda

2007-01-01

A topic that currently is receiving a great deal of attention by educators is the nature and use of WebQuests--computer-based activities that guide student learning through use of the World Wide Web (Sharp 2004). Despite their popularity, questions remain about the effectiveness with which WebQuests are being used with students. This article…

An Evaluation of a Nutrition WebQuest: The Malaysian Experience

ERIC Educational Resources Information Center

Wui, Lee Sheh; Saat, Rohaida Mohd.

2008-01-01

The main purpose of the present study was to develop and evaluate a WebQuest instruction on Nutrition using WebQuest template, known as NutriQuest. NutriQuest was developed to improve Form 2 students' understanding of fundamental nutrition concepts and its application in daily life, to improve critical and creative thinking skills and to enhance…

WebQuests: a new instructional strategy for nursing education.

PubMed

Lahaie, Ulysses

2007-01-01

A WebQuest is a model or framework for designing effective Web-based instructional strategies featuring inquiry-oriented activities. It is an innovative approach to learning that is enhanced by the use of evolving instructional technology. WebQuests have invigorated the primary school (grades K through 12) educational sector around the globe, yet there is sparse evidence in the literature of WebQuests at the college and university levels. WebQuests are congruent with pedagogical approaches and cognitive activities commonly used in nursing education. They are simple to construct using a step-by-step approach, and nurse educators will find many related resources on the Internet to help them get started. Included in this article are a discussion of the critical attributes and main features of WebQuests, construction tips, recommended Web sites featuring essential resources, a discussion of WebQuest-related issues identified in the literature, and some suggestions for further research.

Computational Systems Biology

DOE Office of Scientific and Technical Information (OSTI.GOV)

McDermott, Jason E.; Samudrala, Ram; Bumgarner, Roger E.

2009-05-01

Computational systems biology is the term that we use to describe computational methods to identify, infer, model, and store relationships between the molecules, pathways, and cells (“systems”) involved in a living organism. Based on this definition, the field of computational systems biology has been in existence for some time. However, the recent confluence of high throughput methodology for biological data gathering, genome-scale sequencing and computational processing power has driven a reinvention and expansion of this field. The expansions include not only modeling of small metabolic{Ishii, 2004 #1129; Ekins, 2006 #1601; Lafaye, 2005 #1744} and signaling systems{Stevenson-Paulik, 2006 #1742; Lafaye, 2005more » #1744} but also modeling of the relationships between biological components in very large systems, incluyding whole cells and organisms {Ideker, 2001 #1124; Pe'er, 2001 #1172; Pilpel, 2001 #393; Ideker, 2002 #327; Kelley, 2003 #1117; Shannon, 2003 #1116; Ideker, 2004 #1111}{Schadt, 2003 #475; Schadt, 2006 #1661}{McDermott, 2002 #878; McDermott, 2005 #1271}. Generally these models provide a general overview of one or more aspects of these systems and leave the determination of details to experimentalists focused on smaller subsystems. The promise of such approaches is that they will elucidate patterns, relationships and general features that are not evident from examining specific components or subsystems. These predictions are either interesting in and of themselves (for example, the identification of an evolutionary pattern), or are interesting and valuable to researchers working on a particular problem (for example highlight a previously unknown functional pathway). Two events have occurred to bring about the field computational systems biology to the forefront. One is the advent of high throughput methods that have generated large amounts of information about particular systems in the form of genetic studies, gene expression analyses (both

Biological conversion system

DOEpatents

Scott, C.D.

A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

CosmoQuest: Building community around Citizen Science Collaboration

NASA Astrophysics Data System (ADS)

Gay, P.

2015-12-01

CosmoQuest was envisioned in 2011 with a singular goal: to create a place where people of all backgrounds can learn and do science in a virtual research community. Like a brick-and-mortar center, CosmoQuest includes facilities for doing science and for educating its members through classes, seminars, and other forms of professional development. CosmoQuest is unique with its combination of public engagement in doing science—known as "citizen science"— and its diversity of learning opportunities that enable STEM education. Our suite of activities is able maximize people's ability to learn and do science, while improving scientific literacy. Since its launch on January 1, 2012, CosmoQuest has grown to become the most trafficked astronomy citizen science site on the English-language internet. It has hosted five citizen science portals supporting NASA SMD science and is the only citizen science site to have produced peer-reviewed surface science results [Robbins, et al. 2014]. CosmoQuest, however, is more than just citizen science. It is a virtual research center for the public, and for the educators who teach in classrooms and science centers. Like with with any research center, CosmoQuest's success hinges on its ability to build a committed research community, and the challenge has been creating this community without the benefit of real-world interactions. In this talk, we overview how CosmoQuest has built a virtual community through screen-to-screen interactions using a suite of technologies that must constantly evolve as the internet evolves.

Virtual Quests As Learning Environments for K-12 Students.

ERIC Educational Resources Information Center

Spudic, Linda

Perhaps some of the most engaging, unique, Web-based activities are virtual quests that take student participants along on real expeditions, following a team in the field as they explore new territory or do research on authentic scientific problems. Virtual quests, such as the MayaQuest expedition produced by Classroom Connect, are excellent…

Engineering scalable biological systems

PubMed Central

2010-01-01

Synthetic biology is focused on engineering biological organisms to study natural systems and to provide new solutions for pressing medical, industrial and environmental problems. At the core of engineered organisms are synthetic biological circuits that execute the tasks of sensing inputs, processing logic and performing output functions. In the last decade, significant progress has been made in developing basic designs for a wide range of biological circuits in bacteria, yeast and mammalian systems. However, significant challenges in the construction, probing, modulation and debugging of synthetic biological systems must be addressed in order to achieve scalable higher-complexity biological circuits. Furthermore, concomitant efforts to evaluate the safety and biocontainment of engineered organisms and address public and regulatory concerns will be necessary to ensure that technological advances are translated into real-world solutions. PMID:21468204

LegiQuest

ERIC Educational Resources Information Center

Buck Institute for Education, 2004

2004-01-01

This unit is designed to teach students about how a bill becomes law and how interest groups participate in and impact this process. LegiQuest teaches students about the roles of Congress, the President, and the courts in the legislative process. It can be used at the beginning of the course to introduce the functions and branches of government.…

6th Institute for Systems Biology International Symposium: Systems Biology and the Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galitski, Timothy P.

2007-04-23

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology is an annual two-day event gathering the most influential researchers transforming biology into an integrative discipline investigating complex systems. In recognition of the fundamental similarity between the scientific problems addressed in environmental science and systems biology studies at the molecular, cellular, and organismal levels, the 2007 Symposium featured global leaders in “Systems Biology and the Environment.” The objective of the 2007 “Systems Biology and the Environment” International Symposium was to stimulate interdisciplinary thinking and research that spans systems biology andmore » environmental science. This Symposium was well aligned with the DOE’s Genomics: GTL program efforts to achieve scientific objectives for each of the three DOE missions: Develop biofuels as a major secure energy source for this century; Develop biological solutions for intractable environmental problems; Understand biosystems’ climate impacts and assess sequestration strategies. Our scientific program highlighted world-class research exemplifying these priorities. The Symposium featured 45 minute lectures from 12 researchers including: Penny/Sallie Chisholm of MIT gave the keynote address “Tiny Cells, Global Impact: What Prochlorococcus Can Teach Us About Systems Biology”, plus Jim Fredrickson of PNNL, Nitin Baliga of ISB, Steve Briggs of UCSD, David Cox of Perlegen Sciences, Antoine Danchin of Institut Pasteur, John Delaney of the U of Washington, John Groopman of Johns Hopkins, Ben Kerr of the U of Washington, Steve Koonin of BP, Elliott Meyerowitz of Caltech, and Ed Rubin of LBNL. The 2007 Symposium promoted DOE’s three mission areas among scientists from multiple disciplines representing academia, non-profit research institutions, and the private sector. As in all previous Symposia

Fostering synergy between cell biology and systems biology.

PubMed

Eddy, James A; Funk, Cory C; Price, Nathan D

2015-08-01

In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Working with WebQuests: Making the Web Accessible to Students with Disabilities.

ERIC Educational Resources Information Center

Kelly, Rebecca

2000-01-01

This article describes how students with disabilities in regular classes are using the WebQuest lesson format to access the Internet. It explains essential WebQuest principles, creating a draft Web page, and WebQuest components. It offers an example of a WebQuest about salvaging the sunken ships, Titanic and Lusitania. A WebQuest planning form is…

Biology. Teacher's Guide. Investigations in Natural Science.

ERIC Educational Resources Information Center

Renner, John W.; And Others

Investigations in Natural Science is a program in secondary school biology, chemistry, and physics based upon the description of science as a quest for knowledge, not the knowledge itself. This teaching guide is designed for use with the 18 biology investigations found in the student manual. These investigations focus on concepts related to:…

Hierarchical structure of biological systems

PubMed Central

Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

2014-01-01

A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems. PMID:24145961

Integrating WebQuests in Preservice Teacher Education

ERIC Educational Resources Information Center

Wang, Feng; Hannafin, Michael J.

2008-01-01

During the past decade, WebQuests have been widely used by teachers to integrate technology into teaching and learning. Recently, teacher educators have applied the WebQuest model with preservice teachers in order to develop technology integration skills akin to those used in everyday schools. Scaffolding, used to support the gradual acquisition…

Hospitals' quest for financial success is elusive, but not impossible.

PubMed

Heckler, T M

1984-09-01

As the hospital industry moves from a heavily regulated, cost-reimbursed payment system to a less-regulated, at-risk payment system, the financial and business acumen of boards and management will become increasingly important in the quest for adequate capital. This article discusses ways of reducing the need for, and increasing the supply of, debt and equity capital.

Plant systems biology: network matters.

PubMed

Lucas, Mikaël; Laplaze, Laurent; Bennett, Malcolm J

2011-04-01

Systems biology is all about networks. A recent trend has been to associate systems biology exclusively with the study of gene regulatory or protein-interaction networks. However, systems biology approaches can be applied at many other scales, from the subatomic to the ecosystem scales. In this review, we describe studies at the sub-cellular, tissue, whole plant and crop scales and highlight how these studies can be related to systems biology. We discuss the properties of system approaches at each scale as well as their current limits, and pinpoint in each case advances unique to the considered scale but representing potential for the other scales. We conclude by examining plant models bridging different scales and considering the future prospects of plant systems biology. © 2011 Blackwell Publishing Ltd.

Informing Biological Design by Integration of Systems and Synthetic Biology

PubMed Central

Smolke, Christina D.; Silver, Pamela A.

2011-01-01

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. PMID:21414477

The Quest CCS Project - MMV Technology Deployment Through Two Years of Operation

NASA Astrophysics Data System (ADS)

O'Brien, S.

2017-12-01

In September 2012, Shell, on behalf of the Athabasca Oil Sands Project venture (Shell Canada Energy, Chevron Canada Limited, Marathon Oil Canada Corporation), announced that it was proceeding to construct the Quest Carbon Capture and Storage (CCS) project near Fort Saskatchewan. Quest is the world's first large-scale commercial application of CCS at an oil sands operation, and it is now capturing more than one million tonnes of CO2 per year from the Scotford Upgrader. It is a fully integrated project, involving CO2 capture at the bitumen upgrader, transportation along a 65 km pipeline, and CO2 storage in a deep saline aquifer (the Basal Cambrian Sands). Construction was completed in August 2015, and the Quest project was certified for commercial operation in September 2015. The Measurement, Monitoring and Verification (MMV) program for Quest is comprehensive, with a variety of technologies being used to monitor the atmosphere, hydrosphere, biosphere and geosphere. These include a Lightsource system for atmospheric monitoring, extensive groundwater sampling, DAS VSPs to assess the development of the CO2 plume, a microseismic array to measure any induced seismic activity, and temperature and pressure gauges for reservoir monitoring. Over two years of operations, this program has been optimized to address key risks while improving operational efficiency. Quest has now successfully captured and stored more than 2 million tonnes of CO2 with no MMV indications of any storage issues.

Development and Evaluation of an Interactive WebQuest Environment: "Web Macerasi"

ERIC Educational Resources Information Center

Gulbahar, Yasemin; Madran, R. Orcun; Kalelioglu, Filiz

2010-01-01

This study was conducted to develop a web-based interactive system, Web Macerasi, for teaching-learning and evaluation purposes, and to find out the possible effects of this system. The study has two stages. In the first stage, a WebQuest site was designed as an interactive system in which various Internet and web technologies were used for…

QUEST/Ada (Query Utility Environment for Software Testing) of Ada: The development of a program analysis environment for Ada

NASA Technical Reports Server (NTRS)

Brown, David B.

1988-01-01

A history of the Query Utility Environment for Software Testing (QUEST)/Ada is presented. A fairly comprehensive literature review which is targeted toward issues of Ada testing is given. The definition of the system structure and the high level interfaces are then presented. The design of the three major components is described. The QUEST/Ada IORL System Specifications to this point in time are included in the Appendix. A paper is also included in the appendix which gives statistical evidence of the validity of the test case generation approach which is being integrated into QUEST/Ada.

Biology. Student Investigations and Readings. Investigations in Natural Science.

ERIC Educational Resources Information Center

Renner, John W.; And Others

Investigations in Natural Science is a program in secondary school biology, chemistry, and physics based upon the description of science as a quest for knowledge, not the knowledge itself. This student manual contains the 18 biology investigations. These investigations focus on concepts related to: organisms; classification; populations;…

Issues to Consider in Designing WebQuests: A Literature Review

ERIC Educational Resources Information Center

Kurt, Serhat

2012-01-01

A WebQuest is an inquiry-based online learning technique. This technique has been widely adopted in K-16 education. Therefore, it is important that conditions of effective WebQuest design are defined. Through this article the author presents techniques for improving WebQuest design based on current research. More specifically, the author analyzes…

Micro-separation toward systems biology.

PubMed

Liu, Bi-Feng; Xu, Bo; Zhang, Guisen; Du, Wei; Luo, Qingming

2006-02-17

Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

Informing biological design by integration of systems and synthetic biology.

PubMed

Smolke, Christina D; Silver, Pamela A

2011-03-18

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

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

PubMed

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

2017-06-26

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

Strategies for Adapting WebQuests for Students with Learning Disabilities

ERIC Educational Resources Information Center

Skylar, Ashley A.; Higgins, Kyle; Boone, Randall

2007-01-01

WebQuests are gaining popularity as teachers explore using the Internet for guided learning activities. A WebQuest involves students working on a task that is broken down into clearly defined steps. Students often work in groups to actively conduct the research. This article suggests a variety of methods for adapting WebQuests for students with…

Teachers' Attitudes Toward WebQuests as a Method of Teaching

ERIC Educational Resources Information Center

Perkins, Robert; McKnight, Margaret L.

2005-01-01

One of the latest uses of technology gaining popular status in education is the WebQuest, a process that involves students using the World Wide Web to solve a problem. The goals of this project are to: (a) determine if teachers are using WebQuests in their classrooms; (b) ascertain whether teachers feel WebQuests are effective for teaching…

SYSTEMS BIOLOGY MODEL DEVELOPMENT AND APPLICATION

EPA Science Inventory

System biology models holistically describe, in a quantitative fashion, the relationships between different levels of a biologic system. Relationships between individual components of a system are delineated. System biology models describe how the components of the system inter...

Method for photo-altering a biological system to improve biological effect

DOEpatents

Hill, Richard A.; Doiron, Daniel R.; Crean, David H.

2000-08-01

Photodynamic therapy is a new adjunctive therapy for filtration surgery that does not use chemotherapy agents or radiation, but uses pharmacologically-active sensitizing compounds to produce a titratable, localized, transient, post operative avascular conjunctiva. A photosensitizing agent in a biological system is selectively activated by delivering the photosensitive agent to the biological system and laser activating only a spatially selected portion of the delivered photosensitive agent. The activated portion of the photosensitive agent reacts with the biological system to obtain a predetermined biological effect. As a result, an improved spatial disposition and effectuation of the biological effect by the photosensitive agent in the biological system is achieved.

Inquiry-Based Learning and Technology: Designing and Exploring WebQuests

ERIC Educational Resources Information Center

Lacina, Jan

2007-01-01

A WebQuest is an inquiry-based technology activity designed by Bernie Dodge and Tom March at San Diego State University in 1995. Dodge and March describe WebQuests as activities in which most, or all, of the information used by learners is drawn from the Web. WebQuests are a powerful instructional activity for teachers and students. Students will…

Behavioral asymmetries in ticks - Lateralized questing of Ixodes ricinus to a mechatronic apparatus delivering host-borne cues.

PubMed

Benelli, Giovanni; Romano, Donato; Rocchigiani, Guido; Caselli, Alice; Mancianti, Francesca; Canale, Angelo; Stefanini, Cesare

2018-02-01

Ticks are considered among the most dangerous arthropod vectors of disease agents to both humans and animals worldwide. Lateralization contributes to biological fitness in many animals, conferring important functional advantages, therefore studying its role in tick perception would critically improve our knowledge about their host-seeking behavior. In this research, we evaluated if Ixodes ricinus (L.) (Ixodiidae) ticks have a preference in using the right or the left foreleg to climb on a host. We developed a mechatronic device moving a tuft of fox skin with fur as host-mimicking combination of cues. This engineered approach allows to display a realistic combination of both visual and olfactory host-borne stimuli, which is prolonged over the time and standardized for each replicate. In the first experiment, the mechatronic apparatus delivered host-borne cues frontally, to evaluate the leg preference during questing as response to a symmetrical stimulus. In the second experiment, host-borne cues were provided laterally, in an equal proportion to the left and to the right of the tick, to investigate if the host direction affected the questing behavior. In both experiments, the large majority of the tested ticks showed individual-level left-biased questing acts, if compared to the ticks showing right-biased ones. Furthermore, population-level left-biased questing responses were observed post-exposure to host-mimicking cues provided frontally or laterally to the tick. Overall, this is the first report on behavioral asymmetries in ticks of medical and veterinary importance. Moreover, the mechatronic apparatus developed in this research can be exploited to evaluate the impact of repellents on tick questing in highly reproducible standardized conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Systems biology and mechanics of growth.

PubMed

Eskandari, Mona; Kuhl, Ellen

2015-01-01

In contrast to inert systems, living biological systems have the advantage to adapt to their environment through growth and evolution. This transfiguration is evident during embryonic development, when the predisposed need to grow allows form to follow function. Alterations in the equilibrium state of biological systems breed disease and mutation in response to environmental triggers. The need to characterize the growth of biological systems to better understand these phenomena has motivated the continuum theory of growth and stimulated the development of computational tools in systems biology. Biological growth in development and disease is increasingly studied using the framework of morphoelasticity. Here, we demonstrate the potential for morphoelastic simulations through examples of volume, area, and length growth, inspired by tumor expansion, chronic bronchitis, brain development, intestine formation, plant shape, and myopia. We review the systems biology of living systems in light of biochemical and optical stimuli and classify different types of growth to facilitate the design of growth models for various biological systems within this generic framework. Exploring the systems biology of growth introduces a new venue to control and manipulate embryonic development, disease progression, and clinical intervention. © 2015 Wiley Periodicals, Inc.

Evaluating smokers' reactions to advertising for new lower nicotine quest cigarettes.

PubMed

Shadel, William G; Lerman, Caryn; Cappella, Joseph; Strasser, Andrew A; Pinto, Angela; Hornik, Robert

2006-03-01

Quest cigarettes are a relatively new (2003) product that has been marketed as a way for smokers to gradually reduce the nicotine they receive from cigarettes in order to, according to marketing materials, become nicotine free. However, despite lower levels of nicotine, Quest cigarettes do not have reduced tar levels and, thus, still pose health hazards. This study evaluated beliefs about Quest cigarettes following exposure to a single print advertisement among 200 regular smokers who had never heard of the brand itself. Descriptively, smokers made several specific false inferences about Quest cigarettes after exposure (i.e., lower in tar, healthier, less likely to cause cancer). Two individual-differences variables, need for cognition and perceived vulnerability, moderated smokers' health beliefs about Quest cigarettes.

Lexington Children`s Museum final report on EnergyQuest

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

EnergyQuest is a museum-wide exhibit that familiarizes children and their families with energy sources, uses, and issues and with the impact of those issues on their lives. It was developed and built by Lexington Children`s Museum with support from the US Department of Energy, Kentucky Utilities, and the Kentucky Coal Marketing and Export Council. EnergyQuest featured six hands-on exhibit stations in each of six museum galleries. Collectively, the exhibits examine the sources, uses and conservation of energy. Each EnergyQuest exhibit reflects the content of its gallery setting. During the first year after opening EnergyQuest, a series of 48 public educationalmore » programs on energy were conducted at the Museum as part of the Museum`s ongoing schedule of demonstrations, performances, workshops and classes. In addition, teacher training was conducted.« less

Developing Higher-Order Thinking Skills through WebQuests

ERIC Educational Resources Information Center

Polly, Drew; Ausband, Leigh

2009-01-01

In this study, 32 teachers participated in a year-long professional development project related to technology integration in which they designed and implemented a WebQuest. This paper describes the extent to which higher-order thinking skills (HOTS) and levels of technology implementation (LoTI) occur in the WebQuests that participants designed.…

Robust Design of Biological Circuits: Evolutionary Systems Biology Approach

PubMed Central

Chen, Bor-Sen; Hsu, Chih-Yuan; Liou, Jing-Jia

2011-01-01

Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter fluctuations and environmental molecular noise from the cellular context in the host cell. Based on evolutionary systems biology algorithm, the design parameters of target gene circuits can evolve to specific values in order to robustly track a desired biologic function in spite of intrinsic and environmental noise. The fitness function is selected to be inversely proportional to the tracking error so that the evolutionary biological circuit can achieve the optimal tracking mimicking the evolutionary process of a gene circuit. Finally, several design examples are given in silico with the Monte Carlo simulation to illustrate the design procedure and to confirm the robust performance of the proposed design method. The result shows that the designed gene circuits can robustly track desired behaviors with minimal errors even with nontrivial intrinsic and external noise. PMID:22187523

Robust design of biological circuits: evolutionary systems biology approach.

PubMed

Chen, Bor-Sen; Hsu, Chih-Yuan; Liou, Jing-Jia

2011-01-01

Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter fluctuations and environmental molecular noise from the cellular context in the host cell. Based on evolutionary systems biology algorithm, the design parameters of target gene circuits can evolve to specific values in order to robustly track a desired biologic function in spite of intrinsic and environmental noise. The fitness function is selected to be inversely proportional to the tracking error so that the evolutionary biological circuit can achieve the optimal tracking mimicking the evolutionary process of a gene circuit. Finally, several design examples are given in silico with the Monte Carlo simulation to illustrate the design procedure and to confirm the robust performance of the proposed design method. The result shows that the designed gene circuits can robustly track desired behaviors with minimal errors even with nontrivial intrinsic and external noise.

Systems Approaches to Cancer Biology.

PubMed

Archer, Tenley C; Fertig, Elana J; Gosline, Sara J C; Hafner, Marc; Hughes, Shannon K; Joughin, Brian A; Meyer, Aaron S; Piccolo, Stephen R; Shajahan-Haq, Ayesha N

2016-12-01

Cancer systems biology aims to understand cancer as an integrated system of genes, proteins, networks, and interactions rather than an entity of isolated molecular and cellular components. The inaugural Systems Approaches to Cancer Biology Conference, cosponsored by the Association of Early Career Cancer Systems Biologists and the National Cancer Institute of the NIH, focused on the interdisciplinary field of cancer systems biology and the challenging cancer questions that are best addressed through the combination of experimental and computational analyses. Attendees found that elucidating the many molecular features of cancer inevitably reveals new forms of complexity and concluded that ensuring the reproducibility and impact of cancer systems biology studies will require widespread method and data sharing and, ultimately, the translation of important findings to the clinic. Cancer Res; 76(23); 6774-7. ©2016 AACR. ©2016 American Association for Cancer Research.

Web2Quests: Updating a Popular Web-Based Inquiry-Oriented Activity

ERIC Educational Resources Information Center

Kurt, Serhat

2009-01-01

WebQuest is a popular inquiry-oriented activity in which learners use Web resources. Since the creation of the innovation, almost 15 years ago, the Web has changed significantly, while the WebQuest technique has changed little. This article examines possible applications of new Web trends on WebQuest instructional strategy. Some possible…

QUEST for Quality for Students: A Student Quality Concept. Volume 3

ERIC Educational Resources Information Center

Galán Palomares, Fernando Miguel; Todorovski, Blazhe; Kažoka, Asnate; Saarela, Henni

2013-01-01

This is the final publication of the QUEST for Quality for Students (QUEST) project, run by the European Students' Union. The QUEST project has managed to analyse students' views on the quality of higher education to identify areas in which students can become increasingly involved in quality assurance and enhancement processes. This publication…

Power Plants, Steam and Gas Turbines WebQuest

ERIC Educational Resources Information Center

Ulloa, Carlos; Rey, Guillermo D.; Sánchez, Ángel; Cancela, Ángeles

2012-01-01

A WebQuest is an Internet-based and inquiry-oriented learning activity. The aim of this work is to outline the creation of a WebQuest entitled "Power Generation Plants: Steam and Gas Turbines." This is one of the topics covered in the course "Thermodynamics and Heat Transfer," which is offered in the second year of Mechanical…

The Quest for Deeper Learning: An Investigation into the Impact of a Knowledge-Pooling WebQuest in Primary Initial Teacher Training

ERIC Educational Resources Information Center

Allan, Jo; Street, Mark

2007-01-01

This paper explores the impact on learning in higher education of the integration of a knowledge-pooling stage into a WebQuest. We explain the concept of WebQuests, consider recent literature regarding the effects and difficulties of this approach to learning, and examine students' perceptions of the impact of this tool on high-order learning. The…

Pieter Cullis' quest for a lipid-based, fusogenic delivery system for nucleic acid therapeutics: success with siRNA so what about mRNA?

PubMed

Tam, Ying K; Madden, Thomas D; Hope, Michael J

2016-11-01

For the best part of 40 years, lipids and membrane fusion have been at the center of Pieter's research. Projects range from the purely academic quest of understanding the roles of lipids in biological membranes, to the translation of this knowledge into the most advanced lipid nanoparticle (LNP) drug delivery systems in clinical trials to-date. Pieter's pioneering work in lipid polymorphism and characterizing the unique properties of unsaturated phospatidyethanolamines (PE), together with the introduction of ionizable, dialkylamino lipids to trigger membrane fusion at acidic pH, provided the foundation on which a new generation of highly potent, well-tolerated LNPs for intravenous delivery of nucleic acid therapeutics has been built. In this contribution to the special edition honoring Pieter's achievements we highlight key research conducted in Pieter's laboratory and at several biotechnology companies, some spun out of his research group, which resulted in the development of a fusogenic delivery system for siRNA therapeutics. Patisiran®, an LNP encapsulating siRNA for hepatic gene silencing, is currently in Phase III clinical trials for treatment of Transthyretin amyloidosis as are several other siRNA products employing this delivery technology. Finally, we describe more recent work in which the platform shows real promise in the rapidly growing new field of mRNA therapeutics.

Biophysics and systems biology.

PubMed

Noble, Denis

2010-03-13

Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

Biophysics and systems biology

PubMed Central

Noble, Denis

2010-01-01

Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights. PMID:20123750

QUEST+: A general multidimensional Bayesian adaptive psychometric method.

PubMed

Watson, Andrew B

2017-03-01

QUEST+ is a Bayesian adaptive psychometric testing method that allows an arbitrary number of stimulus dimensions, psychometric function parameters, and trial outcomes. It is a generalization and extension of the original QUEST procedure and incorporates many subsequent developments in the area of parametric adaptive testing. With a single procedure, it is possible to implement a wide variety of experimental designs, including conventional threshold measurement; measurement of psychometric function parameters, such as slope and lapse; estimation of the contrast sensitivity function; measurement of increment threshold functions; measurement of noise-masking functions; Thurstone scale estimation using pair comparisons; and categorical ratings on linear and circular stimulus dimensions. QUEST+ provides a general method to accelerate data collection in many areas of cognitive and perceptual science.

Institute for Genomics and Systems Biology

Science.gov Websites

Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

Scaffolding Preservice Teachers' WebQuest Design: A Qualitative Study

ERIC Educational Resources Information Center

Wang, Feng; Hannafin, Michael J.

2009-01-01

This study examined how participating preservice teachers reported their perceptions and use of different scaffolds provided to support their WebQuest design. Sixteen preservice teachers participated in a succession of course activities designed to guide WebQuest design and development. Results indicated that while participants followed, adapted,…

FoodQuest for Health.

ERIC Educational Resources Information Center

Joseph, Linda C.

2000-01-01

Explains the WebQuest framework developed to help students investigate the topic of nutrition. Highlights include food labels; the Food Guide Pyramid; three levels of inquiry related to nutrition and ingredients in foods; how food choices affect health; historical background of food and food companies; and online grocery shopping. (LRW)

Integrating systems biology models and biomedical ontologies

PubMed Central

2011-01-01

Background Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. Results We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. Conclusions We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms. PMID:21835028

Calculating life? Duelling discourses in interdisciplinary systems biology.

PubMed

Calvert, Jane; Fujimura, Joan H

2011-06-01

A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

Musings on mechanism: quest for a quark theory of proteins?

PubMed

Phillips, Rob

2017-10-01

The give and take between biology and physics is an important part of the history of modern science, with this partnership perhaps now more intimate than ever. In this essay, I explore the ways in which these different fields can strengthen each other through their distinct outlooks on some of the most important questions being asked about the living world. In particular, I highlight three areas where the perspective from physics might lead to deeper insights into the workings of cells. First, I consider what it means for two ostensibly unrelated problems to be the same, and how such sameness can provide unexpected insights into apparently unrelated phenomena. Second, I consider different conceptions of what constitutes a mechanistic understanding of a given phenomenon with an emphasis on nonmolecular notions of mechanism. The third idea is the importance of "toy problems" as a way of providing foundational insights into the real problems. Though my focus here is primarily on ways in which physics approaches might prove interesting in biology, I close with an example of how biology might substantially alter physics by providing a forum and the tools to uncover a fundamental understanding of nonequilibrium phenomena.-Phillips, R. Musings on mechanism: quest for a quark theory of proteins? © FASEB.

Brief or New: WebQuests: An Instructional Strategy for the Occupational Therapy Classroom.

PubMed

Wooster, Donna; Lemcool, Kathy

2004-01-01

SUMMARY WebQuests are an innovative teaching activity that promotes students to actively engage in their learning and work cooperatively in small groups. WebQuests have been widely used in K-12 environments in a variety of subjects and are gaining respect in universities. This paper will briefly describe the basic concept of a WebQuest and provide two examples of WebQuests developed for use in an occupational therapy curriculum.

WebQuest on Conic Sections as a Learning Tool for Prospective Teachers

ERIC Educational Resources Information Center

Kurtulus, Aytac; Ada, Tuba

2012-01-01

WebQuests incorporate technology with educational concepts through integrating online resources with student-centred and activity-based learning. In this study, we describe and evaluate a WebQuest based on conic sections, which we have used with a group of prospective mathematics teachers. The WebQuest entitled: "Creating a Carpet Design Using…

Discovering the intelligence in molecular biology.

PubMed

Uberbacher, E

1995-12-01

The Third International Conference on Intelligent Systems in Molecular Biology was truly an outstanding event. Computational methods in molecular biology have reached a new level of maturity and utility, resulting in many high-impact applications. The success of this meeting bodes well for the rapid and continuing development of computational methods, intelligent systems and information-based approaches for the biosciences. The basic technology, originally most often applied to 'feasibility' problems, is now dealing effectively with the most difficult real-world problems. Significant progress has been made in understanding protein-structure information, structural classification, and how functional information and the relevant features of active-site geometry can be gleaned from structures by automated computational approaches. The value and limits of homology-based methods, and the ability to classify proteins by structure in the absence of homology, have reached a new level of sophistication. New methods for covariation analysis in the folding of large structures such as RNAs have shown remarkably good results, indicating the long-term potential to understand very complicated molecules and multimolecular complexes using computational means. Novel methods, such as HMMs, context-free grammars and the uses of mutual information theory, have taken center stage as highly valuable tools in our quest to represent and characterize biological information. A focus on creative uses of intelligent systems technologies and the trend toward biological application will undoubtedly continue and grow at the 1996 ISMB meeting in St Louis.

Systems biology of human atherosclerosis.

PubMed

Shalhoub, Joseph; Sikkel, Markus B; Davies, Kerry J; Vorkas, Panagiotis A; Want, Elizabeth J; Davies, Alun H

2014-01-01

Systems biology describes a holistic and integrative approach to understand physiology and pathology. The "omic" disciplines include genomics, transcriptomics, proteomics, and metabolic profiling (metabonomics and metabolomics). By adopting a stance, which is opposing (yet complimentary) to conventional research techniques, systems biology offers an overview by assessing the "net" biological effect imposed by a disease or nondisease state. There are a number of different organizational levels to be understood, from DNA to protein, metabolites, cells, organs and organisms, even beyond this to an organism's context. Systems biology relies on the existence of "nodes" and "edges." Nodes are the constituent part of the system being studied (eg, proteins in the proteome), while the edges are the way these constituents interact. In future, it will be increasingly important to collaborate, collating data from multiple studies to improve data sets, making them freely available and undertaking integrative analyses.

Systems Biology Approach in Hypertension Research.

PubMed

Delles, Christian; Husi, Holger

2017-01-01

Systems biology is an approach to study all genes, gene transcripts, proteins, metabolites, and their interactions in specific cells, tissues, organs, or the whole organism. It is based on data derived from high-throughput analytical technologies and bioinformatics tools to analyze these data, and aims to understand the whole system rather than individual aspects of it. Systems biology can be applied to virtually all conditions and diseases and therefore also to hypertension and its underlying vascular disorders. Unlike other methods in this book there is no clear-cut protocol to explain a systems biology approach. We will instead outline some of the most important and common steps in the generation and analysis of systems biology data.

A Sample WebQuest Applicable in Teaching Topological Concepts

ERIC Educational Resources Information Center

Yildiz, Sevda Goktepe; Korpeoglu, Seda Goktepe

2016-01-01

In recent years, WebQuests have received a great deal of attention and have been used effectively in teaching-learning process in various courses. In this study, a WebQuest that can be applicable in teaching topological concepts for undergraduate level students was prepared. A number of topological concepts, such as countability, infinity, and…

Using WebQuests to Teach Content: Comparing Instructional Strategies

ERIC Educational Resources Information Center

Strickland, Janet

2005-01-01

The purpose of this study was to compare the use of WebQuests with traditional instruction. Specifically, the study examined the end-of-unit exam scores for students who completed a WebQuest on the Texas Revolution and those students completing a poster activity. Both of the instructional activities were implemented as additional enhancement to…

Circadian systems biology in Metazoa.

PubMed

Lin, Li-Ling; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

2015-11-01

Systems biology, which can be defined as integrative biology, comprises multistage processes that can be used to understand components of complex biological systems of living organisms and provides hierarchical information to decoding life. Using systems biology approaches such as genomics, transcriptomics and proteomics, it is now possible to delineate more complicated interactions between circadian control systems and diseases. The circadian rhythm is a multiscale phenomenon existing within the body that influences numerous physiological activities such as changes in gene expression, protein turnover, metabolism and human behavior. In this review, we describe the relationships between the circadian control system and its related genes or proteins, and circadian rhythm disorders in systems biology studies. To maintain and modulate circadian oscillation, cells possess elaborative feedback loops composed of circadian core proteins that regulate the expression of other genes through their transcriptional activities. The disruption of these rhythms has been reported to be associated with diseases such as arrhythmia, obesity, insulin resistance, carcinogenesis and disruptions in natural oscillations in the control of cell growth. This review demonstrates that lifestyle is considered as a fundamental factor that modifies circadian rhythm, and the development of dysfunctions and diseases could be regulated by an underlying expression network with multiple circadian-associated signals. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Modeling formalisms in Systems Biology

PubMed Central

2011-01-01

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future. PMID:22141422

Mammalian Synthetic Biology: Engineering Biological Systems.

PubMed

Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

2017-06-21

The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

WebQuests in Special Primary Education: Learning in a Web-Based Environment

ERIC Educational Resources Information Center

Kleemans, Tijs; Segers, Eliane; Droop, Mienke; Wentink, Hanneke

2011-01-01

The present study investigated the differences in learning gain when performing a WebQuest with a well-defined versus an ill-defined assignment. Twenty boys and twenty girls (mean age 11; 10), attending a special primary education school, performed two WebQuests. In each WebQuest, they performed either a well-defined or an ill-defined assignment.…

A Physicist's Quest in Biology: Max Delbrück and "Complementarity".

PubMed

Strauss, Bernard S

2017-06-01

Max Delbrück was trained as a physicist but made his major contribution in biology and ultimately shared a Nobel Prize in Physiology or Medicine. He was the acknowledged leader of the founders of molecular biology, yet he failed to achieve his key scientific goals. His ultimate scientific aim was to find evidence for physical laws unique to biology: so-called "complementarity." He never did. The specific problem he initially wanted to solve was the nature of biological replication but the discovery of the mechanism of replication was made by others, in large part because of his disdain for the details of biochemistry. His later career was spent investigating the effect of light on the fungus Phycomyces , a topic that turned out to be of limited general interest. He was known both for his informality but also for his legendary displays of devastating criticism. His life and that of some of his closest colleagues was acted out against a background of a world in conflict. This essay describes the man and his career and searches for an explanation of his profound influence. Copyright © 2017 by the Genetics Society of America.

Metabolic systems biology: a brief primer.

PubMed

Edwards, Lindsay M

2017-05-01

In the early to mid-20th century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome. The complexity and scale of these data require computational models for their interpretation. The combination of these - systems thinking, high-dimensional data and computation - defines systems biology, typically accompanied by some notion of iterative model refinement. Only sequencing-based technologies, however, offer full coverage. Other 'omics' platforms trade coverage for sensitivity, although the densely connected nature of biological networks suggests that full coverage may not be necessary. Systems biology models are often characterised as either 'bottom-up' (mechanistic) or 'top-down' (statistical). This distinction can mislead, as all models rely on data and all are, to some degree, 'middle-out'. Systems biology has matured as a discipline, and its methods are commonplace in many laboratories. However, many challenges remain, especially those related to large-scale data integration. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

Biological Systems, Energy Sources, and Biology Teaching. Biology and Human Welfare.

ERIC Educational Resources Information Center

Tribe, Michael; Pritchard, Alan J.

This five-chapter document (part of a series on biology and human welfare) focuses on biological systems as energy sources and on the teaching of this subject area. Chapter 1 discusses various topics related to energy and ecology, including biomass, photosynthesis and world energy balances, energy flow through ecosystems, and others. Chapter 2…

Dynamics of biological systems: role of systems biology in medical research.

PubMed

Assmus, Heike E; Herwig, Ralf; Cho, Kwang-Hyun; Wolkenhauer, Olaf

2006-11-01

Cellular systems are networks of interacting components that change with time in response to external and internal events. Studying the dynamic behavior of these networks is the basis for an understanding of cellular functions and disease mechanisms. Quantitative time-series data leading to meaningful models can improve our knowledge of human physiology in health and disease, and aid the search for earlier diagnoses, better therapies and a healthier life. The advent of systems biology is about to take the leap into clinical research and medical applications. This review emphasizes the importance of a dynamic view and understanding of cell function. We discuss the potential for computer-aided mathematical modeling of biological systems in medical research with examples from some of the major therapeutic areas: cancer, cardiovascular, diabetic and neurodegenerative medicine.

A framework for evolutionary systems biology

PubMed Central

Loewe, Laurence

2009-01-01

Background Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects. Results Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions in silico. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism. Conclusion EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications. PMID:19239699

CosmoQuest: Exploring the Needs of Current & Future Citizen Scientists

NASA Astrophysics Data System (ADS)

Bracey, G.; Glushko, A.; Bakerman, M. N.; Gay, P.; Buxner, S.

2016-12-01

The CosmoQuest Virtual Research Facility aims to engage and support professional scientists and the general public-including parents, children, teachers, and students-in learning and doing science. Through the facility's online portal (cosmoquest.org), anyone with internet access can participate in NASA Science Mission Directorate related research by engaging in several online citizen science projects. To support this endeavor, the CosmoQuest team is developing a variety of programs, opportunities, and resources that parallel those available in real-world institutions and that have the potential to reach and impact a large and diverse audience. In order to guide this development and ensure the success of the facility, it is essential to assess the needs of the growing CosmoQuest community. In this presentation, we present the results of a suite of online surveys designed to gauge the interests, motivations, and needs of several groups within the CosmoQuest Community : teachers, parents, adult learners, planetarium professionals, subject matter experts (SMEs), and the general public. Each survey was targeted to a particular group and a particular CosmoQuest program. All surveys asked about attitudes towards technology and social media use. Basic demographics were also collected. We discuss the needs of the various groups and share plans for meeting these needs.

NursingQuest: supporting an analysis of nursing issues.

PubMed

Bassendowski, Sandra L

2007-02-01

With the development and use of new strategies, practices, applications, and resources in technology, the teaching and learning context is shifting. Nurse educators are challenged to create instructional strategies that appeal to the newer generation of students and have the potential to enhance learning. Effective learning programs for these students require new digital communication skills, new pedagogies, and new practices. Nursing students should not be seeking the right answer as much as they should be seeking appropriate information and then developing approaches to issues or resolutions for problems. The focus of the teaching and learning context is shifting from the individual to the group, with the purpose of constructing new knowledge from available information. This article discusses the value of WebQuest activities as inquiry-oriented strategies and the process of adapting the WebQuest format for the development of a strategy called NursingQuest.

Quest to Learn: Developing the School for Digital Kids

ERIC Educational Resources Information Center

Salen, Katie; Torres, Robert; Wolozin, Loretta; Rufo-Tepper, Rebecca; Shapiro, Arana

2011-01-01

Quest to Learn, an innovative school for grades 6 to 12 in New York City, grew out of the idea that gaming and game design offer a promising new paradigm for curriculum and learning. The designers of Quest to Learn developed an approach to learning that draws from what games do best: drop kids into inquiry-based, complex problem spaces that are…

Omics/systems biology and cancer cachexia.

PubMed

Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

2016-06-01

Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

Tramesan, a novel polysaccharide from Trametes versicolor. Structural characterization and biological effects

PubMed Central

Sveronis, Aris; Cescutti, Paola; Rizzo, Roberto

2017-01-01

Mushrooms represent a formidable source of bioactive compounds. Some of these may be considered as biological response modifiers; these include compounds with a specific biological function: antibiotics (e.g. plectasin), immune system stimulator (e,g, lentinan), antitumor agents (e.g. krestin, PSK) and hypolipidemic agents (e.g. lovastatin) inter alia. In this study, we focused on the Chinese medicinal mushroom “yun zhi”, Trametes versicolor, traditionally used for (cit.) “replenish essence and qi (vital energy)”. Previous studies indicated the potential activity of extracts from culture filtrate of asexual mycelia of T. versicolor in controlling the growth and secondary metabolism (e.g. mycotoxins) of plant pathogenic fungi. The quest of active principles produced by T. versicolor, allowed us characterising an exo-polysaccharide released in its culture filtrate and naming it Tramesan. Herein we evaluate the biological activity of Tramesan in different organisms: plants, mammals and plant pathogenic fungi. We suggest that the bioactivity of Tramesan relies mostly on its ability to act as pro antioxidant molecule regardless the biological system on which it was applied. PMID:28829786

Tramesan, a novel polysaccharide from Trametes versicolor. Structural characterization and biological effects.

PubMed

Scarpari, Marzia; Reverberi, Massimo; Parroni, Alessia; Scala, Valeria; Fanelli, Corrado; Pietricola, Chiara; Zjalic, Slaven; Maresca, Vittoria; Tafuri, Agostino; Ricciardi, Maria R; Licchetta, Roberto; Mirabilii, Simone; Sveronis, Aris; Cescutti, Paola; Rizzo, Roberto

2017-01-01

Mushrooms represent a formidable source of bioactive compounds. Some of these may be considered as biological response modifiers; these include compounds with a specific biological function: antibiotics (e.g. plectasin), immune system stimulator (e,g, lentinan), antitumor agents (e.g. krestin, PSK) and hypolipidemic agents (e.g. lovastatin) inter alia. In this study, we focused on the Chinese medicinal mushroom "yun zhi", Trametes versicolor, traditionally used for (cit.) "replenish essence and qi (vital energy)". Previous studies indicated the potential activity of extracts from culture filtrate of asexual mycelia of T. versicolor in controlling the growth and secondary metabolism (e.g. mycotoxins) of plant pathogenic fungi. The quest of active principles produced by T. versicolor, allowed us characterising an exo-polysaccharide released in its culture filtrate and naming it Tramesan. Herein we evaluate the biological activity of Tramesan in different organisms: plants, mammals and plant pathogenic fungi. We suggest that the bioactivity of Tramesan relies mostly on its ability to act as pro antioxidant molecule regardless the biological system on which it was applied.

Systems biology of personalized nutrition

PubMed Central

van Ommen, Ben; van den Broek, Tim; de Hoogh, Iris; van Erk, Marjan; van Someren, Eugene; Rouhani-Rankouhi, Tanja; Anthony, Joshua C; Hogenelst, Koen; Pasman, Wilrike; Boorsma, André; Wopereis, Suzan

2017-01-01

Abstract Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the basis of a person’s health status and goals. The biology underpinning these recommendations is complex, and thus any recommendations must account for multiple biological processes and subprocesses occurring in various tissues and must be formed with an appreciation for how these processes interact with dietary nutrients and environmental factors. Therefore, a systems biology–based approach that considers the most relevant interacting biological mechanisms is necessary to formulate the best recommendations to help people meet their wellness goals. Here, the concept of “systems flexibility” is introduced to personalized nutrition biology. Systems flexibility allows the real-time evaluation of metabolism and other processes that maintain homeostasis following an environmental challenge, thereby enabling the formulation of personalized recommendations. Examples in the area of macro- and micronutrients are reviewed. Genetic variations and performance goals are integrated into this systems approach to provide a strategy for a balanced evaluation and an introduction to personalized nutrition. Finally, modeling approaches that combine personalized diagnosis and nutritional intervention into practice are reviewed. PMID:28969366

Web-Based Inquiry Learning: Facilitating Thoughtful Literacy with WebQuests

ERIC Educational Resources Information Center

Ikpeze, Chinwe H.; Boyd, Fenice B.

2007-01-01

An action research study investigated how the multiple tasks found in WebQuests facilitate fifth-grade students' literacy skills and higher order thinking. Findings indicate that WebQuests are most successful when activities are carefully selected and systematically delivered. Implications for teaching include the necessity for adequate planning,…

Unravelling biology and shifting paradigms in cancer with single-cell sequencing.

PubMed

Baslan, Timour; Hicks, James

2017-08-24

The fundamental operative unit of a cancer is the genetically and epigenetically innovative single cell. Whether proliferating or quiescent, in the primary tumour mass or disseminated elsewhere, single cells govern the parameters that dictate all facets of the biology of cancer. Thus, single-cell analyses provide the ultimate level of resolution in our quest for a fundamental understanding of this disease. Historically, this quest has been hampered by technological shortcomings. In this Opinion article, we argue that the rapidly evolving field of single-cell sequencing has unshackled the cancer research community of these shortcomings. From furthering an elemental understanding of intra-tumoural genetic heterogeneity and cancer genome evolution to illuminating the governing principles of disease relapse and metastasis, we posit that single-cell sequencing promises to unravel the biology of all facets of this disease.

Mass spectrometry in systems biology an introduction.

PubMed

Dunn, Warwick B

2011-01-01

The qualitative detection, quantification, and structural characterization of analytes in biological systems are important requirements for objectives to be fulfilled in systems biology research. One analytical tool applied to a multitude of systems biology studies is mass spectrometry, particularly for the study of proteins and metabolites. Here, the role of mass spectrometry in systems biology will be assessed, the advantages and disadvantages discussed, and the instrument configurations available described. Finally, general applications will be briefly reviewed. Copyright © 2011 Elsevier Inc. All rights reserved.

Use of WebQuests in Mathematics Instruction: Academic Achievement, Teacher and Student Opinions

ERIC Educational Resources Information Center

Yenmez, Arzu Aydogan; Özpinar, Ilknur; Gökçe, Semirhan

2017-01-01

WebQuests are designed to ensure meaningful learning by combining technology with a constructivist approach in the classroom setting. This study aims to examine the effect of WebQuests used in instruction on students' academic achievements and the student and teacher opinions on WebQuests. The participants of this study using the…

Systems cell biology

PubMed Central

Mast, Fred D.; Ratushny, Alexander V.

2014-01-01

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. PMID:25225336

Reilly in Quest airlock hatch

NASA Image and Video Library

2001-07-16

S104-E-5108 (16 July 2001) --- James F. Reilly, STS-104 mission specialist, reads over a checklist in the hatchway of the newly installed Quest Airlock. In the background, cosmonaut Yury V. Usachev of Rosaviakosmos, Expedition Two mission commander, is working in Unity Node 1.

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

PubMed

Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

2016-06-17

Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

Theoretical aspects of Systems Biology.

PubMed

Bizzarri, Mariano; Palombo, Alessandro; Cucina, Alessandra

2013-05-01

The natural world consists of hierarchical levels of complexity that range from subatomic particles and molecules to ecosystems and beyond. This implies that, in order to explain the features and behavior of a whole system, a theory might be required that would operate at the corresponding hierarchical level, i.e. where self-organization processes take place. In the past, biological research has focused on questions that could be answered by a reductionist program of genetics. The organism (and its development) was considered an epiphenomenona of its genes. However, a profound rethinking of the biological paradigm is now underway and it is likely that such a process will lead to a conceptual revolution emerging from the ashes of reductionism. This revolution implies the search for general principles on which a cogent theory of biology might rely. Because much of the logic of living systems is located at higher levels, it is imperative to focus on them. Indeed, both evolution and physiology work on these levels. Thus, by no means Systems Biology could be considered a 'simple' 'gradual' extension of Molecular Biology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Art Treasure Quests in Second Life: A Multi-Literacy Adventure

ERIC Educational Resources Information Center

Stokrocki, Mary

2014-01-01

Treasure quests in virtual worlds can help students develop multi-literacy communication skills and promote community, offering insights about art teaching and learning. As part of the new media literacy, students explore the offerings of Second Life (SL), a virtual world, as a series of quests. Multi-literacy involves communication. Through their…

Exponential bound in the quest for absolute zero

NASA Astrophysics Data System (ADS)

Stefanatos, Dionisis

2017-10-01

In most studies for the quantification of the third law of thermodynamics, the minimum temperature which can be achieved with a long but finite-time process scales as a negative power of the process duration. In this article, we use our recent complete solution for the optimal control problem of the quantum parametric oscillator to show that the minimum temperature which can be obtained in this system scales exponentially with the available time. The present work is expected to motivate further research in the active quest for absolute zero.

Exponential bound in the quest for absolute zero.

PubMed

Stefanatos, Dionisis

2017-10-01

In most studies for the quantification of the third law of thermodynamics, the minimum temperature which can be achieved with a long but finite-time process scales as a negative power of the process duration. In this article, we use our recent complete solution for the optimal control problem of the quantum parametric oscillator to show that the minimum temperature which can be obtained in this system scales exponentially with the available time. The present work is expected to motivate further research in the active quest for absolute zero.

Systems cell biology.

PubMed

Mast, Fred D; Ratushny, Alexander V; Aitchison, John D

2014-09-15

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. © 2014 Mast et al.

Radiation interactions with biological systems.

PubMed

Islam, Muhammad Torequl

2017-05-01

The use of radiation, especially ionizing radiation (IR), is currently attracting great attention in the field of medical sciences. However, it should be mentioned that IR has both beneficial and harmful effects in biological systems. This review aims to focus on IR-mediated physiological events in a mechanistic way. Evidence from the databases, mainly from PUBMED and SCIENCE DIRECT were considered. IR directly and/or with their lyses products (indirect) causes oxidative stresses to biological systems. These activities may be localized and systematic. Otherwise, IR-induced non-/multi-targeted effects are also evident. IR in diagnosis and cancer radiotherapy is well-known. Reactive species produced by IR are not only beneficial, but also can exert harmful effects in a biological system such as aging, genetic instability and mutagenicity, membrane lysis and cell death, alteration of enzymatic activity and metabolic events, mitochondrial dysfunction, and even cancer. Additionally, DNA adducts formation, after IR-induced DNA breakage, is a cause of blockage of DNA repair capability with an increase in cellular radiosensitivity. These may allow cellular ruin even at low IR levels. Dependent on the dose, duration of action and quality, IR plays diverse roles in biological systems.

Bending Knee Elementary: A Case Study of the Quest Network.

ERIC Educational Resources Information Center

Howley-Rowe, Caitlin

As part of its Regional Educational Laboratory contract to develop a framework for continuous school improvement in its four-state region, AEL, Inc., staff designed the Quest project. Formative evaluation had revealed the high level of satisfaction participants had with Quest and the great extent to which the project met its goals at each event. A…

Using WebQuests to Successfully Engage Students in Learning Science

ERIC Educational Resources Information Center

Simpson, Gary

2003-01-01

WebQuests are a powerful teaching and learning device that have developed rapidly in recent years, especially in the Humanities. In Australia, the use of WebQuests in Science has become popular. The multimedia product of students' investigations can be shared with a variety of audiences. In this article, I will explain what I understand to be a…

Determination of ReQuest-based symptom thresholds to define symptom relief in GERD clinical studies.

PubMed

Stanghellini, Vincenzo; Armstrong, David; Mönnikes, Hubert; Berghöfer, Peter; Gatz, Gudrun; Bardhan, Karna Dev

2007-01-01

The growing importance of symptom assessment is evident from the numerous clinical studies on gastroesophageal reflux disease (GERD) assessing treatment-induced symptom relief. However, to date, the a priori selection of criteria defining symptom relief has been arbitrary. The present study was designed to prospectively identify GERD symptom thresholds for the broad spectrum of GERD-related symptoms assessed by the validated reflux questionnaire (ReQuest) and its subscales, ReQuest-GI (gastrointestinal symptoms) and ReQuest-WSO (general well-being, sleep disturbances, other complaints), in individuals without evidence of GERD. In this 4-day evaluation in Germany, 385 individuals without evidence of GERD were included. On the first day, participants completed the ReQuest, the Gastrointestinal Symptom Rating Scale, and the Psychological General Well-Being scale. On the other days, participants filled in the ReQuest only. GERD symptom thresholds were calculated for ReQuest and its subscales, based on the respective 90th percentiles. GERD symptom thresholds were 3.37 for ReQuest, 0.95 for ReQuest-GI, and 2.46 for ReQuest-WSO. Even individuals without evidence of GERD may experience some mild symptoms that are commonly ascribed to GERD. GERD symptom thresholds derived in this study can be used to define the global symptom relief in patients with GERD. Copyright 2007 S. Karger AG, Basel.

Systems Biology, Systems Medicine, Systems Pharmacology: The What and The Why.

PubMed

Stéphanou, Angélique; Fanchon, Eric; Innominato, Pasquale F; Ballesta, Annabelle

2018-05-09

Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences.

Focus issue: series on computational and systems biology.

PubMed

Gough, Nancy R

2011-09-06

The application of computational biology and systems biology is yielding quantitative insight into cellular regulatory phenomena. For the month of September, Science Signaling highlights research featuring computational approaches to understanding cell signaling and investigation of signaling networks, a series of Teaching Resources from a course in systems biology, and various other articles and resources relevant to the application of computational biology and systems biology to the study of signal transduction.

Graphics processing units in bioinformatics, computational biology and systems biology.

PubMed

Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

2017-09-01

Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

The effect and value of a WebQuest activity on weather in a 5th grade classroom

NASA Astrophysics Data System (ADS)

Oliver, Deborah

WebQuests are increasing in popularity across the country, yet it remains unclear whether WebQuests confer a significant benefit in student content learning. In addition, the perceptions of teachers regarding the classroom value and efficacy of WebQuests in teaching higher level thinking skills are still unclear. The goals of the study were (a) to determine the effect of WebQuests on elementary students' content area knowledge gains; (b) to investigate teacher perceptions of students' higher order thinking skills while engaged in a WebQuest activity and the value the of the WebQuest, as perceived by teacher. To accomplish the above research goals, a quasi-experimental design was used in this study. The subjects were four teachers and classes at an elementary school in southern California. Results of the study showed that the WebQuest did increase content knowledge in fifth grade students, but not significantly more than traditional teaching as measured by a researcher-modified WebQuest For Teacher Questionnaire (WQFT) (Zheng, Perez, Williamson & Flygare, 2007) and teacher interviews. Teachers responded positively to the value of the WebQuest in their daily teaching. Teachers also indicated that their students engaged in higher level thinking skills while engaged in the WebQuest activity. Keywords: WebQuest, higher level thinking, learning

Method of measurement in biological systems

DOEpatents

Turteltaub, K.W.; Vogel, J.S.; Felton, J.S.; Gledhill, B.L.; Davis, J.C.

1994-12-27

Disclosed is a method of quantifying molecules in biological substances comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering the chemical specie to the biological host in doses sufficiently low to avoid significant overt damage to the biological system, d. allowing a period of time to elapse sufficient for dissemination and interaction of the chemical specie with the host throughout the biological system of the host, e. isolating a reacted fraction of the biological substance from the host in a manner sufficient to avoid contamination of the substance from extraneous sources, f. converting the fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in the material by means of direct isotopic counting. 5 figures.

Method of measurement in biological systems

DOEpatents

Turteltaub, K.W.; Vogel, J.S.; Felton, J.S.; Gledhill, B.L.: Davis, J.C.; Stanker, L.H.

1993-05-11

A method is disclosed of quantifying molecules in biological substances, comprising: selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere; preparing a long-lived radioisotope labeled reactive chemical specie; administering the chemical specie to the biological host in doses sufficiently low to avoid significant overt damage to the biological system; allowing a period of time to elapse sufficient for dissemination and interaction of the chemical specie with the host throughout the biological system of the host; isolating a reacted fraction of the biological substance from the host in a manner sufficient to avoid contamination of the substance from extraneous sources; converting the fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation; and measuring the radioisotope concentration in the material by means of direct isotopic counting.

Method of measurement in biological systems

DOEpatents

Turteltaub, Kenneth W.; Vogel, John S.; Felton, James S.; Gledhill, Barton L.; Davis, Jay C.; Stanker, Larry H.

1993-05-11

Disclosed is a method of quantifying molecules in biological substances, comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering said chemical specie to said biological host in doses sufficiently low to avoid significant overt damage to the biological system thereof, d. allowing a period of time to elapse sufficient for dissemination and interaction of said chemical specie with said host throughout said biological system of said host, e. isolating a reacted fraction of the biological substance from said host in a manner sufficient to avoid contamination of said substance from extraneous sources, f. converting said fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in said material by means of direct isotopic counting.

Method of measurement in biological systems

DOEpatents

Turteltaub, Kenneth W.; Vogel, John S.; Felton, James S.; Gledhill, Barton L.; Davis, Jay C.

1994-01-01

Disclosed is a method of quantifying molecules in biological substances comprising: a. selecting a biological host in which radioisotopes are present in concentrations equal to or less than those in the ambient biosphere, b. preparing a long-lived radioisotope labeled reactive chemical specie, c. administering said chemical specie to said biological host in doses sufficiently low to avoid significant overt damage to the biological system thereof, d. allowing a period of time to elapse sufficient for dissemination and interaction of said chemical specie with said host throughout said biological system of said host, e. isolating a reacted fraction of the biological substance from said host in a manner sufficient to avoid contamination of said substance from extraneous sources, f. converting said fraction of biological substance by suitable means to a material which efficiently produces charged ions in at least one of several possible ion sources without introduction of significant isotopic fractionation, and, g. measuring the radioisotope concentration in said material by means of direct isotopic counting.

Expedition Two Helms in Quest airlock

NASA Image and Video Library

2001-07-20

STS104-E-5198 (20 July 2001) --- Astronaut Susan J. Helms, Expedition Two flight engineer, works in the Equipment Lock of Airlock Quest during its internal outfitting on STS-104. The image was recorded with a digital still camera.

Expedition Two Helms in Quest airlock

NASA Image and Video Library

2001-07-20

STS104-E-5199 (20 July 2001) --- Astronaut Susan J. Helms, Expedition Two flight engineer, works in the Equipment Lock of Airlock Quest during its internal outfitting on STS-104. The image was recorded with a digital still camera.

Translational Systems Biology and Voice Pathophysiology

PubMed Central

Li, Nicole Y. K.; Abbott, Katherine Verdolini; Rosen, Clark; An, Gary; Hebda, Patricia A.; Vodovotz, Yoram

2011-01-01

Objectives/Hypothesis Personalized medicine has been called upon to tailor healthcare to an individual's needs. Evidence-based medicine (EBM) has advocated using randomized clinical trials with large populations to evaluate treatment effects. However, due to large variations across patients, the results are likely not to apply to an individual patient. We suggest that a complementary, systems biology approach using computational modeling may help tackle biological complexity in order to improve ultimate patient care. The purpose of the article is: 1) to review the pros and cons of EBM, and 2) to discuss the alternative systems biology method and present its utility in clinical voice research. Study Design Tutorial Methods Literature review and discussion. Results We propose that translational systems biology can address many of the limitations of EBM pertinent to voice and other health care domains, and thus complement current health research models. In particular, recent work using mathematical modeling suggests that systems biology has the ability to quantify the highly complex biologic processes underlying voice pathophysiology. Recent data support the premise that this approach can be applied specifically in the case of phonotrauma and surgically induced vocal fold trauma, and may have particular power to address personalized medicine. Conclusions We propose that evidence around vocal health and disease be expanded beyond a population-based method to consider more fully issues of complexity and systems interactions, especially in implementing personalized medicine in voice care and beyond. PMID:20025041

A system for success: BMC Systems Biology, a new open access journal.

PubMed

Hodgkinson, Matt J; Webb, Penelope A

2007-09-04

BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

Hierarchical structure of biological systems: a bioengineering approach.

PubMed

Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

2014-01-01

A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

Conceptual Foundations of Systems Biology Explaining Complex Cardiac Diseases.

PubMed

Louridas, George E; Lourida, Katerina G

2017-02-21

Systems biology is an important concept that connects molecular biology and genomics with computing science, mathematics and engineering. An endeavor is made in this paper to associate basic conceptual ideas of systems biology with clinical medicine. Complex cardiac diseases are clinical phenotypes generated by integration of genetic, molecular and environmental factors. Basic concepts of systems biology like network construction, modular thinking, biological constraints (downward biological direction) and emergence (upward biological direction) could be applied to clinical medicine. Especially, in the field of cardiology, these concepts can be used to explain complex clinical cardiac phenotypes like chronic heart failure and coronary artery disease. Cardiac diseases are biological complex entities which like other biological phenomena can be explained by a systems biology approach. The above powerful biological tools of systems biology can explain robustness growth and stability during disease process from modulation to phenotype. The purpose of the present review paper is to implement systems biology strategy and incorporate some conceptual issues raised by this approach into the clinical field of complex cardiac diseases. Cardiac disease process and progression can be addressed by the holistic realistic approach of systems biology in order to define in better terms earlier diagnosis and more effective therapy.

Applicability of computational systems biology in toxicology.

PubMed

Kongsbak, Kristine; Hadrup, Niels; Audouze, Karine; Vinggaard, Anne Marie

2014-07-01

Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search. However, computational systems biology offers more advantages than providing a high-throughput literature search; it may form the basis for establishment of hypotheses on potential links between environmental chemicals and human diseases, which would be very difficult to establish experimentally. This is possible due to the existence of comprehensive databases containing information on networks of human protein-protein interactions and protein-disease associations. Experimentally determined targets of the specific chemical of interest can be fed into these networks to obtain additional information that can be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method in the hypothesis-generating phase of toxicological research. © 2014 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).

An engineering design approach to systems biology.

PubMed

Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

2017-07-17

Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

The Feasibility of Systems Thinking in Biology Education

ERIC Educational Resources Information Center

Boersma, Kerst; Waarlo, Arend Jan; Klaassen, Kees

2011-01-01

Systems thinking in biology education is an up and coming research topic, as yet with contrasting feasibility claims. In biology education systems thinking can be understood as thinking backward and forward between concrete biological objects and processes and systems models representing systems theoretical characteristics. Some studies claim that…

TURKISH VERSION QUALITY OF LIFE IN ESSENTIAL TREMOR QUESTIONNAIRE (QUEST): VALIDITY AND RELIABILITY STUDY.

PubMed

Güler, Sibel; Turan, F Nesrin

2015-09-30

Our aim was to translate the Quality of Life in Essential Tremor Questionnaire (QUEST) advanced by Troster (2005) and to analyse the validity and reliability of this questionnaire. Two hundred twelve consecutive patients with essential tremor (ET) and forty-three control subjects were included in the study. Permission for the translation and validation of the QUEST scale was obtained. The translation was performed according to the guidelines provided by the publisher. After the translation, the final version of the scale was administered to both groups to determine its reliability and validity. The QUEST Physical, Psychosocial, communication, Hobbies/leisure and Work/finance scores were 0.967, 0.968, 0.933, 0.964 and 0.925, respectively. There were good correlations between each of the QUEST scores that were indicative of good internal consistency. Additionally, we observed that all of the QUEST scores were most strongly related to the right and left arms (p=0.0001). However, we observed that all of the QUEST scores were weakly related to the voice, head and right leg (p=0.0001). These findings support the notion that the Turkish version of the Quality of Life in Essential Tremor (QUEST) questionnaire is a valid and reliable tool for the assessment of the quality of life of patients with ET.

The Effects of Using WebQuests on Reading Comprehension Performance of Saudi EFL Students

ERIC Educational Resources Information Center

Alshumaimeri, Yousif A.; Almasri, Meshail M.

2012-01-01

This paper is a report on the effects of using WebQuest on Saudi male EFL students reading comprehension performance. WebQuests expose students to several online resources and require them to gather information about a specific topic. The experimental group received traditional teaching plus WebQuests as supplementary activities. The control group…

Searching for Dark Photons with the SeaQuest Spectrometer

NASA Astrophysics Data System (ADS)

Uemura, Sho; SeaQuest Collaboration

2017-09-01

The existence of a dark sector, containing families of particles that do not couple directly to the Standard Model, is motivated as a possible model for dark matter. A ``dark photon'' - a massive vector boson that couples weakly to electric charge - is a common component of dark sector models. The SeaQuest spectrometer at Fermilab is designed to detect dimuon pairs produced by the interaction of a 120 GeV proton beam with a rotating set of thin fixed targets. An iron-filled magnet downstream of the target, 5 meters in length, serves as a beam dump. The SeaQuest spectrometer is sensitive to dark photons that are mostly produced in the beam dump and decay to dimuons, and a SeaQuest search for dark sector particles was approved as Fermilab experiment E1067. As part of E1067, a displaced-vertex trigger was built, installed and commissioned this year. This trigger uses two planes of extruded scintillators to identify dimuons originating far downstream of the target, and is sensitive to dark photons that travel deep inside the beam dump before decaying to dimuons. This trigger will be used to take data parasitically with the primary SeaQuest physics program. In this talk I will present the displaced-vertex trigger and its performance, and projected sensitivity from future running.

New Tools and New Biology: Recent Miniaturized Systems for Molecular and Cellular Biology

PubMed Central

Hamon, Morgan; Hong, Jong Wook

2013-01-01

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology. PMID:24305843

Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

PubMed Central

2011-01-01

Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

WebQuests and Collaborative Learning in Teacher Preparation: A Singapore Study

ERIC Educational Resources Information Center

Yang, Chien-Hui; Tzuo, Pei-Wen; Komara, Cecile

2011-01-01

This research project aimed to introduce WebQuests to train special education preservice teachers in Singapore. The following research questions were posed: (1) Does the use of WebQuests in teacher preparation promote special education teacher understanding on Universal Design for Learning in accommodating students with diverse learning needs? (2)…

QuEST: Qualifying Environmentally Sustainable Technologies, Volume 5

NASA Technical Reports Server (NTRS)

Lewis, Pattie

2010-01-01

This edition of the QuEST newsletter contains brief articles that discuss the NASA Technology Evaluation for Environmental Risk Mitigation (TEERM) program, and the importance of collaboration, efforts in materials management and substitution for coatings for launch structures, Low volatile organic compound (VOC) Coatings Field Testing, Non-Chrome Coating Systems, Life Cycle Corrosion Testing, Lead-Free Electronics Testing and Corn Based Depainting and efforts in Pollution Control in the area of Hypergolic Propellant Destruction Evaluation, efforts in development of alternative energy in particular Hydrogen Sensors, Energy and Water Management, and efforts in remediation in the removal of Polychlorinated Biphenyl (PCB) contamination

The Joyless Quest for Tenure

ERIC Educational Resources Information Center

Perlmutter, David D.

2007-01-01

In this article, the author talks about the tenure process of being a professor which can be gloomy for assistant professors as they share a common culture of the joyless quest for promotion and tenure. Life as an assistant professor has its bleak moments; however, the downbeat cosmology is, in the end, dysfunctional and hurts more than it…

Systems Biology Analysis of Heterocellular Signaling.

PubMed

Tape, Christopher J

2016-08-01

Tissues comprise multiple heterotypic cell types (e.g., epithelial, mesenchymal, and immune cells). Communication between heterotypic cell types is essential for biological cohesion and is frequently dysregulated in disease. Despite the importance of heterocellular communication, most systems biology techniques do not report cell-specific signaling data from mixtures of cells. As a result, our existing perspective of cellular behavior under-represents the influence of heterocellular signaling. Recent technical advances now permit the resolution of systems-level cell-specific signaling data. This review discusses how new physical, spatial, and isotopic resolving methods are facilitating unique systems biology studies of heterocellular communication. Copyright © 2016 Elsevier Ltd. All rights reserved.

"I Guess It Was Pretty Fun": Using WebQuests in the Middle School Classroom.

ERIC Educational Resources Information Center

Lipscomb, George

2003-01-01

Notes that the WebQuest helps students harness the vast amount of on-line resources available. Presents a list of 10 suggestions that may help teachers unfamiliar with WebQuests, especially those in the history classroom, to use them more effectively. Concludes that students learned a great deal about the Civil War by doing the WebQuest, and the…

Consistent design schematics for biological systems: standardization of representation in biological engineering

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kitano, Hiroaki

2009-01-01

The discovery by design paradigm driving research in synthetic biology entails the engineering of de novo biological constructs with well-characterized input–output behaviours and interfaces. The construction of biological circuits requires iterative phases of design, simulation and assembly, leading to the fabrication of a biological device. In order to represent engineered models in a consistent visual format and further simulating them in silico, standardization of representation and model formalism is imperative. In this article, we review different efforts for standardization, particularly standards for graphical visualization and simulation/annotation schemata adopted in systems biology. We identify the importance of integrating the different standardization efforts and provide insights into potential avenues for developing a common framework for model visualization, simulation and sharing across various tools. We envision that such a synergistic approach would lead to the development of global, standardized schemata in biology, empowering deeper understanding of molecular mechanisms as well as engineering of novel biological systems. PMID:19493898

Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

NASA Astrophysics Data System (ADS)

Jalili, Mahdi

2018-03-01

I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

Another Face of the Hero: "The Matrix" as Modern Hero-Quest.

ERIC Educational Resources Information Center

Stroud, Scott R.

This paper analyzes the interesting narrative structure of the hero-quest myth contained within the 1999 film, "The Matrix," and explicates the implications of this message upon the audience. Initially, the relevance of myth to movies and the format of Joseph Campbell's hero-quest is illustrated. This format is then applied to "The…

Biologically inspired dynamic material systems.

PubMed

Studart, André R

2015-03-09

Numerous examples of material systems that dynamically interact with and adapt to the surrounding environment are found in nature, from hair-based mechanoreceptors in animals to self-shaping seed dispersal units in plants to remodeling bone in vertebrates. Inspired by such fascinating biological structures, a wide range of synthetic material systems have been created to replicate the design concepts of dynamic natural architectures. Examples of biological structures and their man-made counterparts are herein revisited to illustrate how dynamic and adaptive responses emerge from the intimate microscale combination of building blocks with intrinsic nanoscale properties. By using top-down photolithographic methods and bottom-up assembly approaches, biologically inspired dynamic material systems have been created 1) to sense liquid flow with hair-inspired microelectromechanical systems, 2) to autonomously change shape by utilizing plantlike heterogeneous architectures, 3) to homeostatically influence the surrounding environment through self-regulating adaptive surfaces, and 4) to spatially concentrate chemical species by using synthetic microcompartments. The ever-increasing complexity and remarkable functionalities of such synthetic systems offer an encouraging perspective to the rich set of dynamic and adaptive properties that can potentially be implemented in future man-made material systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Folktale Frenzy: WebQuest Writing.

ERIC Educational Resources Information Center

Gaines, Lisa

This folktale unit supports 6th- through 8th-grade students exploration of the many subgenres of folktales: trickster tales, fairy tales, fables, tall tales, and legends. The unit focuses heavily on the use of technology as a learning tool as students work together to create WebQuests for their peers to explore. During the 10 one-hour sessions,…

New Currents in Education: A Preliminary Review. QuEST Paper 10.

ERIC Educational Resources Information Center

Bhaerman, Robert D.

This booklet describes nine "new currents" in education with the recommendation that local and state federations of the American Federation of Teachers create QuEST committees of teachers to study the implications of all these issues and develop statements and QuEST action programs on them as they relate to local and state situations. The issues…

Learning in a Sheltered Internet Environment: The Use of WebQuests

ERIC Educational Resources Information Center

Segers, Eliane; Verhoeven, Ludo

2009-01-01

The present study investigated the effects on learning in a sheltered Internet environment using so-called WebQuests in elementary school classrooms in the Netherlands. A WebQuest is an assignment presented together with a series of web pages to help guide children's learning. The learning gains and quality of the work of 229 sixth graders…

MarsQuest: Bringing the Excitement of Mars Exploration to the Public

NASA Astrophysics Data System (ADS)

Dusenbery, P. B.; Morrow, C. A.; Harold, J. B.; Klug, S. L.

2002-12-01

We are living in an extraordinary era of Mars exploration. NASA's Odyssey spacecraft has recently discovered vast amounts of hydrogen beneath the surface of Mars, suggesting the presence of sub-surface ice. Two Mars Exploration Rovers are scheduled to land in early 2004. To bring the excitement and discoveries of Mars exploration to the public, the Space Science Institute (SSI) of Boulder, CO, has developed a comprehensive Mars Education Program that includes: 1) large and small traveling exhibits, 2) workshops for museum and classroom educators (in partnership with the Mars Education Program at Arizona State University (ASU)), and 3) an interactive Website called MarsQuest Online (in partnership with TERC and JPL). All three components will be presented and offered as a good model for actively involving scientists and their discoveries to improve science education in museums and the classroom. The centerpiece of SSI's Mars Education Program is the 5,000-square-foot traveling exhibition, MarsQuest: Exploring the Red Planet, which was developed with support from the National Science Foundation (NSF), NASA, and several corporate donors. The MarsQuest exhibit is nearing the end of a highly successful, fully-booked three-year tour. The Institute plans to send an enhanced and updated MarsQuest on a second three-year tour and is also developing Destination: Mars, a mini-version of MarsQuest designed for smaller venues. Workshops for museum educators, docents, and local teachers are conducted at host sites. These workshops were developed collaboratively by Dr. Cheri Morrow, SSI's Education and Public Outreach Manager, and Sheri Klug, Director of the Mars K-12 Education Program at ASU. They are designed to inspire and empower participants to extend the excitement and science content of the exhibitions into classrooms and museum-based education programs in an ongoing fashion. The MarsQuest Online project is developing a Website that will use the MarsQuest exhibit as a

MarsQuest: Bringing the Excitement of Mars Exploration to the Public

NASA Astrophysics Data System (ADS)

Dusenbery, P. B.; Morrow, C. A.; Harold, J. B.; Klug, S. L.

2002-09-01

We are living in an extraordinary era of Mars exploration. NASA's Odyssey spacecraft has recently discovered vast amounts of hydrogen beneath the surface of Mars, suggesting the presence of sub-surface ice. Two Mars Exploration Rovers are scheduled to land in early 2004. To bring the excitement and discoveries of Mars exploration to the public, the Space Science Institute (SSI) of Boulder, CO, has developed a comprehensive Mars Education Program that includes: 1) large and small traveling exhibits, 2) workshops for museum and classroom educators (in partnership with the Mars Education Program at Arizona State University (ASU)), and 3) an interactive Website called MarsQuest Online (in partnership with TERC and JPL). All three components will be presented and offered as a good model for actively involving scientists and their discoveries to improve science education in museums and the classroom. The centerpiece of SSI's Mars Education Program is the 5,000-square-foot traveling exhibition, MarsQuest: Exploring the Red Planet, which was developed with support from the National Science Foundation (NSF), NASA, and several corporate donors. The MarsQuest exhibit is nearing the end of a highly successful, fully-booked three-year tour. The Institute plans to send an enhanced and updated MarsQuest on a second three-year tour and is also developing Destination: Mars, a mini-version of MarsQuest designed for smaller venues. Workshops for museum educators, docents, and local teachers are conducted at host sites. These workshops were developed collaboratively by Dr. Cheri Morrow, SSI's Education and Public Outreach Manager, and Sheri Klug, Director of the Mars K-12 Education Program at ASU. They are designed to inspire and empower participants to extend the excitement and science content of the exhibitions into classrooms and museum-based education programs in an ongoing fashion. The MarsQuest Online project is developing a Website that will use the MarsQuest exhibit as a

Metabolomics: Definitions and Significance in Systems Biology.

PubMed

Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

2017-01-01

Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

Systems biology for organotypic cell cultures.

PubMed

Grego, Sonia; Dougherty, Edward R; Alexander, Francis J; Auerbach, Scott S; Berridge, Brian R; Bittner, Michael L; Casey, Warren; Cooley, Philip C; Dash, Ajit; Ferguson, Stephen S; Fennell, Timothy R; Hawkins, Brian T; Hickey, Anthony J; Kleensang, Andre; Liebman, Michael N J; Martin, Florian; Maull, Elizabeth A; Paragas, Jason; Qiao, Guilin Gary; Ramaiahgari, Sreenivasa; Sumner, Susan J; Yoon, Miyoung

2017-01-01

Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, "organotypic" cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data.

Stochastic simulation in systems biology

PubMed Central

Székely, Tamás; Burrage, Kevin

2014-01-01

Natural systems are, almost by definition, heterogeneous: this can be either a boon or an obstacle to be overcome, depending on the situation. Traditionally, when constructing mathematical models of these systems, heterogeneity has typically been ignored, despite its critical role. However, in recent years, stochastic computational methods have become commonplace in science. They are able to appropriately account for heterogeneity; indeed, they are based around the premise that systems inherently contain at least one source of heterogeneity (namely, intrinsic heterogeneity). In this mini-review, we give a brief introduction to theoretical modelling and simulation in systems biology and discuss the three different sources of heterogeneity in natural systems. Our main topic is an overview of stochastic simulation methods in systems biology. There are many different types of stochastic methods. We focus on one group that has become especially popular in systems biology, biochemistry, chemistry and physics. These discrete-state stochastic methods do not follow individuals over time; rather they track only total populations. They also assume that the volume of interest is spatially homogeneous. We give an overview of these methods, with a discussion of the advantages and disadvantages of each, and suggest when each is more appropriate to use. We also include references to software implementations of them, so that beginners can quickly start using stochastic methods for practical problems of interest. PMID:25505503

Systems biology: the case for a systems science approach to diabetes.

PubMed

Petrasek, Danny

2008-01-01

The unprecedented accumulation of biological data in recent decades has underscored the need to organize and integrate the massive collection of information. In addition, there is rising agreement among biologists that a complete understanding of a single cell will not lead directly to a complete understanding of a system of cells. The success of a systems science approach in engineering and physics may be of great value in the evolution of biological science. This article reviews some examples that suggest the importance of a systems biology approach and, in addition, advance one specific systems science principle, the conservation of uncertainty, which may give insight into the emergent behavior of numerous biological and physiological phenomena.

A Quest for Equity? Measuring the Effect of QuestBridge on Economic Diversity at Selective Institutions

ERIC Educational Resources Information Center

Furquim, Fernando; Glasener, Kristen M.

2017-01-01

In response to growing income stratification in higher education, President Obama convened a White House Summit in 2014 where over 100 selective institutions committed to increasing the number of low-income students on their campus. One way colleges proposed to do so is through partnerships with college access organizations like QuestBridge, a…

Mathematical and Computational Modeling in Complex Biological Systems

PubMed Central

Li, Wenyang; Zhu, Xiaoliang

2017-01-01

The biological process and molecular functions involved in the cancer progression remain difficult to understand for biologists and clinical doctors. Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases. Computational and mathematical models are gradually being used to help us understand the omics data produced by high-throughput experimental techniques. The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy optimization and new drug discovery. Currently, it is urgent to bridge the gap between the developments of high-throughput technologies and systemic modeling of the biological process in cancer research. In this review, we firstly studied several typical mathematical modeling approaches of biological systems in different scales and deeply analyzed their characteristics, advantages, applications, and limitations. Next, three potential research directions in systems modeling were summarized. To conclude, this review provides an update of important solutions using computational modeling approaches in systems biology. PMID:28386558

Mathematical and Computational Modeling in Complex Biological Systems.

PubMed

Ji, Zhiwei; Yan, Ke; Li, Wenyang; Hu, Haigen; Zhu, Xiaoliang

2017-01-01

The biological process and molecular functions involved in the cancer progression remain difficult to understand for biologists and clinical doctors. Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases. Computational and mathematical models are gradually being used to help us understand the omics data produced by high-throughput experimental techniques. The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy optimization and new drug discovery. Currently, it is urgent to bridge the gap between the developments of high-throughput technologies and systemic modeling of the biological process in cancer research. In this review, we firstly studied several typical mathematical modeling approaches of biological systems in different scales and deeply analyzed their characteristics, advantages, applications, and limitations. Next, three potential research directions in systems modeling were summarized. To conclude, this review provides an update of important solutions using computational modeling approaches in systems biology.

Electron cyclotron heating/current-drive system using high power tubes for QUEST spherical tokamak

NASA Astrophysics Data System (ADS)

Onchi, Takumi; Idei, H.; Hasegawa, M.; Nagata, T.; Kuroda, K.; Hanada, K.; Kariya, T.; Kubo, S.; Tsujimura, T. I.; Kobayashi, S.; Quest Team

2017-10-01

Electron cyclotron heating (ECH) is the primary method to ramp up plasma current non-inductively in QUEST spherical tokamak. A 28 GHz gyrotron is employed for short pulses, where the radio frequency (RF) power is about 300 kW. Current ramp-up efficiency of 0.5 A/W has been obtained with focused beam of the second harmonic X-mode. A quasi-optical polarizer unit has been newly installed to avoid arcing events. For steady-state tokamak operation, 8.56 GHz klystron with power of 200 kW is used as the CW-RF source. The high voltage power supply (54 kV/13 A) for the klystron has been built recently, and initial bench test of the CW-ECH system is starting. The array of insulated-gate bipolar transistor works to quickly cut off the input power for protecting the klystron. This work is supported by JSPS KAKENHI (15H04231), NIFS Collaboration Research program (NIFS13KUTR085, NIFS17KUTR128), and through MEXT funding for young scientists associated with active promotion of national university reforms.

Systems Biology of Industrial Microorganisms

NASA Astrophysics Data System (ADS)

Papini, Marta; Salazar, Margarita; Nielsen, Jens

The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

Systems biology of industrial microorganisms.

PubMed

Papini, Marta; Salazar, Margarita; Nielsen, Jens

2010-01-01

The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

Synthetic biology of antimicrobial discovery.

PubMed

Zakeri, Bijan; Lu, Timothy K

2013-07-19

Antibiotic discovery has a storied history. From the discovery of penicillin by Sir Alexander Fleming to the relentless quest for antibiotics by Selman Waksman, the stories have become like folklore used to inspire future generations of scientists. However, recent discovery pipelines have run dry at a time when multidrug-resistant pathogens are on the rise. Nature has proven to be a valuable reservoir of antimicrobial agents, which are primarily produced by modularized biochemical pathways. Such modularization is well suited to remodeling by an interdisciplinary approach that spans science and engineering. Herein, we discuss the biological engineering of small molecules, peptides, and non-traditional antimicrobials and provide an overview of the growing applicability of synthetic biology to antimicrobials discovery.

On the interplay between mathematics and biology. Hallmarks toward a new systems biology

NASA Astrophysics Data System (ADS)

Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M.; Alghamdi, Mohammed Ali

2015-03-01

This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach.

Integrative Systems Biology for Data Driven Knowledge Discovery

PubMed Central

Greene, Casey S.; Troyanskaya, Olga G.

2015-01-01

Integrative systems biology is an approach that brings together diverse high throughput experiments and databases to gain new insights into biological processes or systems at molecular through physiological levels. These approaches rely on diverse high-throughput experimental techniques that generate heterogeneous data by assaying varying aspects of complex biological processes. Computational approaches are necessary to provide an integrative view of these experimental results and enable data-driven knowledge discovery. Hypotheses generated from these approaches can direct definitive molecular experiments in a cost effective manner. Using integrative systems biology approaches, we can leverage existing biological knowledge and large-scale data to improve our understanding of yet unknown components of a system of interest and how its malfunction leads to disease. PMID:21044756

Influence of Game Quests on Pupils' Enjoyment and Goal-Pursuing in Math Learning

ERIC Educational Resources Information Center

Chen, Zhi-Hong; Liao, Calvin C. Y.; Cheng, Hercy N. H.; Yeh, Charles Y. C.; Chan, Tak-Wai

2012-01-01

As a medium for learning, digital games provide promising possibilities to motivate and engage students in subject learning. In this study, a game-based learning system, My-Pet-My-Quest, is developed to support pupils' math learning. This is due to the fact that most students in Taiwan have relatively lower positive attitude towards math learning,…

QUEST for Quality for Students: Institutional Analysis. Volume 2, Part 2

ERIC Educational Resources Information Center

Saarela, Henni; Gavra, Alina

2013-01-01

This publication is the second part of Volume 2 of the project called "QUEST for Quality for Students", or "QUEST" for short, run by the European Students' Union (ESU). It follows-up on the research work that has been completed in the last three years, the results of which are presented in Volume 1 and the first part of Volume…

Experience of Elementary School Students with the Use of WebQuests

ERIC Educational Resources Information Center

Halat, Erdogan

2013-01-01

The aim of this study was to examine the perspectives of primary school students on the use of WebQuests in learning. There were nine graduate students, twenty-six 4th grade and thirty 5th grade pupils involved in this study, which took place over eight weeks in a graduate course. The graduate students designed and developed their WebQuests as a…

Bursch on outside of Quest Airlock during EVA 3, Expedition Four

NASA Image and Video Library

2002-02-20

ISS004-E-8043 (20 February 2002) --- Astronaut Daniel W. Bursch, Expedition Four flight engineer, participates in the five-hour, 47-minute space walk on February 20, 2002. He moves among the oxygen and nitrogen tanks on the exterior of Quest Airlock. The square device (left) on the Space Station Remote Manipulator System (SSRMS) or Canadarm2 is the Materials International Space Station Experiment (MISSE). The image was recorded with a digital still camera.

Systems Biology for Organotypic Cell Cultures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grego, Sonia; Dougherty, Edward R.; Alexander, Francis J.

Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomicmore » data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the

CINRG: Systems Biology of Glucocorticoids in Muscle Disease

DTIC Science & Technology

2012-10-01

Duchenne Muscular dystrophy , Glucocorticoids, Systems biology, Drug mechanism CINRG: Systems Biology of Glucocorticoids in Muscle Disease Zuyi Wang, Ph.D...2011-2012) for Contract W81XWH-09-1-0726 SYSTEMS BIOLOGY OF GLUCOCORTICOIDS IN MUSCLE DISEASE Introduction Duchenne muscular dystrophy ...DMD) is the most common and incurable muscular dystrophy of childhood. Muscle regeneration fails with advancing age, leading to considerable fibrosis

Natural production of biological optical systems

NASA Astrophysics Data System (ADS)

Choi, Seung Ho; Kim, Young L.

2015-03-01

Synthesis and production in nature often provide ideas to design and fabricate advanced biomimetic photonic materials and structures, leading to excellent physical properties and enhanced performance. In addition, the recognition and utilization of natural or biological substances have been typical routes to develop biocompatible and biodegradable materials for medical applications. In this respect, biological lasers utilizing such biomaterials and biostructures have been received considerable attention, given a variety of implications and potentials for bioimaging, biosensing, implantation, and therapy. However, without relying on industrial facilities, eco-friendly massive production of such optical components or systems has not yet been investigated. We show examples of bioproduction of biological lasers using agriculture and fisheries. We anticipate that such approaches will open new possibilities for scalable eco-friendly `green' production of biological photonics components and systems.

Final Report: Quantification of Uncertainty in Extreme Scale Computations (QUEST)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marzouk, Youssef; Conrad, Patrick; Bigoni, Daniele

QUEST (\\url{www.quest-scidac.org}) is a SciDAC Institute that is focused on uncertainty quantification (UQ) in large-scale scientific computations. Our goals are to (1) advance the state of the art in UQ mathematics, algorithms, and software; and (2) provide modeling, algorithmic, and general UQ expertise, together with software tools, to other SciDAC projects, thereby enabling and guiding a broad range of UQ activities in their respective contexts. QUEST is a collaboration among six institutions (Sandia National Laboratories, Los Alamos National Laboratory, the University of Southern California, Massachusetts Institute of Technology, the University of Texas at Austin, and Duke University) with a historymore » of joint UQ research. Our vision encompasses all aspects of UQ in leadership-class computing. This includes the well-founded setup of UQ problems; characterization of the input space given available data/information; local and global sensitivity analysis; adaptive dimensionality and order reduction; forward and inverse propagation of uncertainty; handling of application code failures, missing data, and hardware/software fault tolerance; and model inadequacy, comparison, validation, selection, and averaging. The nature of the UQ problem requires the seamless combination of data, models, and information across this landscape in a manner that provides a self-consistent quantification of requisite uncertainties in predictions from computational models. Accordingly, our UQ methods and tools span an interdisciplinary space across applied math, information theory, and statistics. The MIT QUEST effort centers on statistical inference and methods for surrogate or reduced-order modeling. MIT personnel have been responsible for the development of adaptive sampling methods, methods for approximating computationally intensive models, and software for both forward uncertainty propagation and statistical inverse problems. A key software product of the MIT QUEST effort is

Quantification of Uncertainty in Extreme Scale Computations (QUEST)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghanem, Roger

QUEST was a SciDAC Institute comprising Sandia National Laboratories, Los Alamos National Laboratory, the University of Southern California, the Massachusetts Institute of Technology, the University of Texas at Austin, and Duke University. The mission of QUEST is to: (1) develop a broad class of uncertainty quantification (UQ) methods/tools, and (2) provide UQ expertise and software to other SciDAC projects, thereby enabling/guiding their UQ activities. The USC effort centered on the development of reduced models and efficient algorithms for implementing various components of the UQ pipeline. USC personnel were responsible for the development of adaptive bases, adaptive quadrature, and reduced modelsmore » to be used in estimation and inference.« less

WebQuests for Reflection and Conceptual Change: Variations on a Popular Model for Guided Inquiry.

ERIC Educational Resources Information Center

Young, David L.; Wilson, Brent G.

WebQuests have become a popular form of guided inquiry using Web resources. The goal of WebQuests is to help students think and reason at higher levels,and use information to solve problems. This paper presents modifications to the WebQuest model drawing on primarily on schema theory. It is believed that these changes will further enhance student…

A multi-level analysis of the relationship between environmental factors and questing Ixodes ricinus dynamics in Belgium

PubMed Central

2012-01-01

Background Ticks are the most important pathogen vectors in Europe. They are known to be influenced by environmental factors, but these links are usually studied at specific temporal or spatial scales. Focusing on Ixodes ricinus in Belgium, we attempt to bridge the gap between current “single-sided” studies that focus on temporal or spatial variation only. Here, spatial and temporal patterns of ticks are modelled together. Methods A multi-level analysis of the Ixodes ricinus patterns in Belgium was performed. Joint effects of weather, habitat quality and hunting on field sampled tick abundance were examined at two levels, namely, sampling level, which is associated with temporal dynamics, and site level, which is related to spatial dynamics. Independent variables were collected from standard weather station records, game management data and remote sensing-based land cover data. Results At sampling level, only a marginally significant effect of daily relative humidity and temperature on the abundance of questing nymphs was identified. Average wind speed of seven days prior to the sampling day was found important to both questing nymphs and adults. At site level, a group of landscape-level forest fragmentation indices were highlighted for both questing nymph and adult abundance, including the nearest-neighbour distance, the shape and the aggregation level of forest patches. No cross-level effects or spatial autocorrelation were found. Conclusions Nymphal and adult ticks responded differently to environmental variables at different spatial and temporal scales. Our results can advise spatio-temporal extents of environment data collection for continuing empirical investigations and potential parameters for biological tick models. PMID:22830528

Search for organising principles: understanding in systems biology.

PubMed

Mesarovic, M D; Sreenath, S N; Keene, J D

2004-06-01

Due in large measure to the explosive progress in molecular biology, biology has become arguably the most exciting scientific field. The first half of the 21st century is sometimes referred to as the 'era of biology', analogous to the first half of the 20th century, which was considered to be the 'era of physics'. Yet, biology is facing a crisis--or is it an opportunity--reminiscent of the state of biology in pre-double-helix time. The principal challenge facing systems biology is complexity. According to Hood, 'Systems biology defines and analyses the interrelationships of all of the elements in a functioning system in order to understand how the system works.' With 30000+ genes in the human genome the study of all relationships simultaneously becomes a formidably complex problem. Hanahan and Weinberg raised the question as to whether progress will consist of 'adding further layers of complexity to a scientific literature that is already complex almost beyond measure' or whether the progress will lead to a 'science with a conceptual structure and logical coherence that rivals that of chemistry or physics.' At the core of the challenge is the need for a new approach, a shift from reductionism to a holistic perspective. However, more than just a pronouncement of a new approach is needed. We suggest that what is needed is to provide a conceptual framework for systems biology research. We propose that the concept of a complex system, i.e. a system of systems as defined in mathematical general systems theory (MGST), is central to provide such a framework. We further argue that for a deeper understanding in systems biology investigations should go beyond building numerical mathematical or computer models--important as they are. Biological phenomena cannot be predicted with the level of numerical precision as in classical physics. Explanations in terms of how the categories of systems are organised to function in ever changing conditions are more revealing. Non

Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

PubMed

Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

2017-07-05

Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

Final Technical Report: Quantification of Uncertainty in Extreme Scale Computations (QUEST)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knio, Omar M.

QUEST is a SciDAC Institute comprising Sandia National Laboratories, Los Alamos National Laboratory, University of Southern California, Massachusetts Institute of Technology, University of Texas at Austin, and Duke University. The mission of QUEST is to: (1) develop a broad class of uncertainty quantification (UQ) methods/tools, and (2) provide UQ expertise and software to other SciDAC projects, thereby enabling/guiding their UQ activities. The Duke effort focused on the development of algorithms and utility software for non-intrusive sparse UQ representations, and on participation in the organization of annual workshops and tutorials to disseminate UQ tools to the community, and to gather inputmore » in order to adapt approaches to the needs of SciDAC customers. In particular, fundamental developments were made in (a) multiscale stochastic preconditioners, (b) gradient-based approaches to inverse problems, (c) adaptive pseudo-spectral approximations, (d) stochastic limit cycles, and (e) sensitivity analysis tools for noisy systems. In addition, large-scale demonstrations were performed, namely in the context of ocean general circulation models.« less

The SeaQuest Spectrometer at Fermilab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aidala, C.A.; et al.

The SeaQuest spectrometer at Fermilab was designed to detect oppositely-charged pairs of muons (dimuons) produced by interactions between a 120 GeV proton beam and liquid hydrogen, liquid deuterium and solid nuclear targets. The primary physics program uses the Drell-Yan process to probe antiquark distributions in the target nucleon. The spectrometer consists of a target system, two dipole magnets and four detector stations. The upstream magnet is a closed-aperture solid iron magnet which also serves as the beam dump, while the second magnet is an open aperture magnet. Each of the detector stations consists of scintillator hodoscopes and a high-resolution trackingmore » device. The FPGA-based trigger compares the hodoscope signals to a set of pre-programmed roads to determine if the event contains oppositely-signed, high-mass muon pairs.« less

Plant Systems Biology at the Single-Cell Level.

PubMed

Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

2017-11-01

Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quest for steroidomimetics: Amino acids derived steroidal and nonsteroidal architectures.

PubMed

Shagufta; Ahmad, Irshad; Panda, Gautam

2017-06-16

The chiral pool amino acids have been utilized for the construction of steroidal and non-steroidal architectures in the quest for steroidomimetics. Chirality derived from amino acid-based architectures provides new and easy to incorporate chiral chemical space, which is otherwise very difficult to introduce and comprised of several synthetic steps for asymmetric steroids. The different and exciting ligand-receptor interactions may arise from the use of each amino acid enantiomer that was introduced into the chiral steroidal backbone. The A and D rings of steroidal architectures can be mimicked by the phenyl group of the amino acid tyrosine. The Mitsunobu reaction, nucleophilic substitution and elimination, etc. were utilized for constructing diverse tri- and tetracyclic steroidal skeletons as well as benzofused seco-steroids from amino acids. These benzofused, amino acid-derived steroidal and nonsteroidal molecules had promising biological activity in hormonal related disorders. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

On the interplay between mathematics and biology: hallmarks toward a new systems biology.

PubMed

Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

2015-03-01

This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

Dupuytren's: a systems biology disease

PubMed Central

2011-01-01

Dupuytren's disease (DD) is an ill-defined fibroproliferative disorder of the palm of the hands leading to digital contracture. DD commonly occurs in individuals of northern European extraction. Cellular components and processes associated with DD pathogenesis include altered gene and protein expression of cytokines, growth factors, adhesion molecules, and extracellular matrix components. Histology has shown increased but varying levels of particular types of collagen, myofibroblasts and myoglobin proteins in DD tissue. Free radicals and localised ischaemia have been suggested to trigger the proliferation of DD tissue. Although the existing available biological information on DD may contain potentially valuable (though largely uninterpreted) information, the precise aetiology of DD remains unknown. Systems biology combines mechanistic modelling with quantitative experimentation in studies of networks and better understanding of the interaction of multiple components in disease processes. Adopting systems biology may be the ideal approach for future research in order to improve understanding of complex diseases of multifactorial origin. In this review, we propose that DD is a disease of several networks rather than of a single gene, and show that this accounts for the experimental observations obtained to date from a variety of sources. We outline how DD may be investigated more effectively by employing a systems biology approach that considers the disease network as a whole rather than focusing on any specific single molecule. PMID:21943049

Systems Biology to Support Nanomaterial Grouping.

PubMed

Riebeling, Christian; Jungnickel, Harald; Luch, Andreas; Haase, Andrea

2017-01-01

The assessment of potential health risks of engineered nanomaterials (ENMs) is a challenging task due to the high number and great variety of already existing and newly emerging ENMs. Reliable grouping or categorization of ENMs with respect to hazards could help to facilitate prioritization and decision making for regulatory purposes. The development of grouping criteria, however, requires a broad and comprehensive data basis. A promising platform addressing this challenge is the systems biology approach. The different areas of systems biology, most prominently transcriptomics, proteomics and metabolomics, each of which provide a wealth of data that can be used to reveal novel biomarkers and biological pathways involved in the mode-of-action of ENMs. Combining such data with classical toxicological data would enable a more comprehensive understanding and hence might lead to more powerful and reliable prediction models. Physico-chemical data provide crucial information on the ENMs and need to be integrated, too. Overall statistical analysis should reveal robust grouping and categorization criteria and may ultimately help to identify meaningful biomarkers and biological pathways that sufficiently characterize the corresponding ENM subgroups. This chapter aims to give an overview on the different systems biology technologies and their current applications in the field of nanotoxicology, as well as to identify the existing challenges.

Engaging Scientists with the CosmoQuest Citizen Science Virtual Research Facility

NASA Astrophysics Data System (ADS)

Grier, Jennifer A.; Gay, Pamela L.; Buxner, Sanlyn; Noel-Storr, Jacob; CosmoQuest Team

2016-10-01

NASA Science Mission Directorate missions and research return more data than subject matter experts (SMEs - scientists and engineers) can effectively utilize. Citizen scientist volunteers represent a robust pool of energy and talent that SMEs can draw upon to advance projects that require the processing of large quantities of images, and other data. The CosmoQuest Virtual Research Facility has developed roles and pathways to engage SMEs in ways that advance the education of the general public while producing science results publishable in peer-reviewed journals, including through the CosmoQuest Facility Small Grants Program and CosmoAcademy. Our Facility Small Grants Program is open to SMEs to fund them to work with CosmoQuest and engage the public in analysis. Ideal projects have a specific and well-defined need for additional eyes and minds to conduct basic analysis and data collection (such as crater counting, identifying lineaments, etc.) Projects selected will undergo design and implementation as Citizen Science Portals, and citizen scientists will be recruited and trained to complete the project. Users regularly receive feedback on the quality of their data. Data returned will be analyzed by the SME and the CQ Science Team for joint publication in a peer-reviewed journal. SMEs are also invited to consider presenting virtual learning courses in the subjects of their choice in CosmoAcademy. The audience for CosmoAcademy are lifelong-learners and education professionals. Classes are capped at 10, 15, or 20 students. CosmoAcademy can also produce video material to archive seminars long-term. SMEs function as advisors in many other areas of CosmoQuest, including the Educator's Zone (curricular materials for K-12 teachers), Science Fair Projects, and programs that partner to produce material for podcasts and planetaria. Visit the CosmoQuest website at cosmoquest.org to learn more, and to investigate current opportunities to engage with us. CosmoQuest is funded

WebQuests as Perceived by Teachers: Implications for Online Teaching and Learning

ERIC Educational Resources Information Center

Zheng, R.; Perez, J.; Williamson, J.; Flygare, J.

2008-01-01

The WebQuest as an instructional tool has recently been widely adopted in K-16 education. However, its underlying principles and functionality are not well understood, which has resulted in an inconsistency in practice. This study identifies the underlying constructs of WebQuests as perceived by teachers and variables affecting their perceptions…

Taking the Measure of the Universe : Precision Astrometry with SIM PlanetQuest

NASA Technical Reports Server (NTRS)

Unwin, Stephen C.; Shao, Michael; Tanner, Angelle M.; Allen, Ronald J.; Beichman, Charles A.; Boboltz, David; Catanzarite, Joseph H.; Chaboyer, Brian C.; Ciardi, David R.; Edberg, Stephen J.;

The Lunar Quest Program and the International Lunar Network (ILN)

NASA Technical Reports Server (NTRS)

Cohen, Barbara A.

2009-01-01

The Lunar and Planetary Science group at Marshall provides core capabilities to support the Agency's lunar exploration goals. ILN Anchor Nodes are currently in development by MSFC and APL under the Lunar Quest Program at MSFC. The Science objectives of the network are to understand the interior structure and composition of the moon. Pre-phase A engineering assessments are complete, showing a design that can achieve the science requirements, either on their own (if 4 launched) or in concert with international partners. Risk reduction activities are ongoing. The Lunar Quest Program is a Science-based program with the following goals: a) Fly small/medium science missions to accomplish key science goals; b) Build a strong lunar science community; c) Provide opportunities to demonstrate new technologies; and d) Where possible, help ESMD and SOMG goals and enhance presence of science in the implementation of the VSE. The Lunar Quest Program will be guided by recommendations from community reports.

Industrial systems biology and its impact on synthetic biology of yeast cell factories.

PubMed

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-06-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Enhancing Nontraditional Informal Programs Using Exhibitions: a case study of MarsQuest

NASA Astrophysics Data System (ADS)

Dusenbery, P. B.

2001-12-01

The Space Science Institute (SSI) of Boulder, Colorado has recently developed a large traveling exhibition called MarsQuest. The 5,000 square foot exhibition will enable millions of Americans to share in the excitement of the scientific exploration of Mars and learn more about their own planet in the process. A large exhibition, like MarsQuest, can provide a memorable experience for visitors, but it does not have to end there. A variety of nontraditional informal activities can tie into such informal science education projects to enhance and extend their impact. I will first discuss the MarsQuest exhibition that features compelling hands-on displays, updateable computer stations, and models that offer memorable experiences for visitors of all ages. The MarsQuest Education Program includes a professional development workshop for teachers, a museum staff orientation, web resources, and a public talk by a Mars scientist. By surrounding visitors with vivid Mars images, the planetarium show, narrated by Patrick Stewart, expands on the exhibition's main themes and allows visitors to delve deeper into the mysteries of Mars. The MarsQuest exhibition is proving to be extraordinarily successful. The exhibit's three-year tour is already fully booked (a second 3-year tour is planned), and the exhibit has been met with tremendous amounts of publicity and press coverage at its venues to date. The MarsQuest experience will be used to explore how a large exhibition can enhance nontraditional informal programs such as public talks by scientists, mall science events, camp-ins, public demonstrations, interactive web events, and the creation of mini versions that can travel to smaller venues in underserved regions of the country. I will then discuss how these activities can best piggyback on the media attention and public awareness that is generated by a large exhibition.

Learning to Design WebQuests: An Exploration in Preservice Social Studies Education

ERIC Educational Resources Information Center

Bates, Alisa

2008-01-01

Effective uses of technology in social studies methods courses is an under-researched field. This study focused on the development of WebQuests to engage teacher candidate's exploration of the Internet as an authentic medium for inquiry in social studies education. Analysis of appropriateness of tasks in the WebQuests, depth of ideas and audience…

Optoelectronic system and apparatus for connection to biological systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okandan, Murat; Nielson, Gregory N.

The present invention relates to a biological probe structure, as well as apparatuses, systems, and methods employing this structure. In particular embodiments, the structure includes a hermetically sealed unit configured to receive and transmit one or more optical signals. Furthermore, the structure can be implanted subcutaneously and interrogated externally. In this manner, a minimally invasive method can be employed to detect, treat, and/or assess the biological target. Additional methods and systems are also provided.

Advances in systems biology: computational algorithms and applications.

PubMed

Huang, Yufei; Zhao, Zhongming; Xu, Hua; Shyr, Yu; Zhang, Bing

2012-01-01

The 2012 International Conference on Intelligent Biology and Medicine (ICIBM 2012) was held on April 22-24, 2012 in Nashville, Tennessee, USA. The conference featured six technical sessions, one tutorial session, one workshop, and 3 keynote presentations that covered state-of-the-art research activities in genomics, systems biology, and intelligent computing. In addition to a major emphasis on the next generation sequencing (NGS)-driven informatics, ICIBM 2012 aligned significant interests in systems biology and its applications in medicine. We highlight in this editorial the selected papers from the meeting that address the developments of novel algorithms and applications in systems biology.

Toward community standards in the quest for orthologs

PubMed Central

Dessimoz, Christophe; Gabaldón, Toni; Roos, David S.; Sonnhammer, Erik L. L.; Herrero, Javier; Altenhoff, Adrian; Apweiler, Rolf; Ashburner, Michael; Blake, Judith; Boeckmann, Brigitte; Bridge, Alan; Bruford, Elspeth; Cherry, Mike; Conte, Matthieu; Dannie, Durand; Datta, Ruchira; Dessimoz, Christophe; Domelevo Entfellner, Jean-Baka; Ebersberger, Ingo; Gabaldón, Toni; Galperin, Michael; Herrero, Javier; Joseph, Jacob; Koestler, Tina; Kriventseva, Evgenia; Lecompte, Odile; Leunissen, Jack; Lewis, Suzanna; Linard, Benjamin; Livstone, Michael S.; Lu, Hui-Chun; Martin, Maria; Mazumder, Raja; Messina, David; Miele, Vincent; Muffato, Matthieu; Perrière, Guy; Punta, Marco; Roos, David; Rouard, Mathieu; Schmitt, Thomas; Schreiber, Fabian; Silva, Alan; Sjölander, Kimmen; Škunca, Nives; Sonnhammer, Erik; Stanley, Eleanor; Szklarczyk, Radek; Thomas, Paul; Uchiyama, Ikuo; Van Bel, Michiel; Vandepoele, Klaas; Vilella, Albert J.; Yates, Andrew; Zdobnov, Evgeny

2012-01-01

The identification of orthologs—genes pairs descended from a common ancestor through speciation, rather than duplication—has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is hampered by the lack of consensus on source proteomes, file formats and benchmarks. The second ‘Quest for Orthologs’ meeting brought together stakeholders from various communities to address these challenges. We report on achievements and outcomes of this meeting, focusing on topics of particular relevance to the research community at large. The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications. Contact: dessimoz@ebi.ac.uk PMID:22332236

Using Activity Theory to Understand Intergenerational Play: The Case of Family Quest

ERIC Educational Resources Information Center

Siyahhan, Sinem; Barab, Sasha A.; Downton, Michael P.

2010-01-01

We implemented a five-week family program called "Family Quest" where parents and children ages 9 to 13 played Quest Atlantis, a multiuser 3D educational computer game, at a local after-school club for 90-minute sessions. We used activity theory as a conceptual and an analytical framework to study the nature of intergenerational play, the…

Hybrid semi-parametric mathematical systems: bridging the gap between systems biology and process engineering.

PubMed

Teixeira, Ana P; Carinhas, Nuno; Dias, João M L; Cruz, Pedro; Alves, Paula M; Carrondo, Manuel J T; Oliveira, Rui

2007-12-01

Systems biology is an integrative science that aims at the global characterization of biological systems. Huge amounts of data regarding gene expression, proteins activity and metabolite concentrations are collected by designing systematic genetic or environmental perturbations. Then the challenge is to integrate such data in a global model in order to provide a global picture of the cell. The analysis of these data is largely dominated by nonparametric modelling tools. In contrast, classical bioprocess engineering has been primarily founded on first principles models, but it has systematically overlooked the details of the embedded biological system. The full complexity of biological systems is currently assumed by systems biology and this knowledge can now be taken by engineers to decide how to optimally design and operate their processes. This paper discusses possible methodologies for the integration of systems biology and bioprocess engineering with emphasis on applications involving animal cell cultures. At the mathematical systems level, the discussion is focused on hybrid semi-parametric systems as a way to bridge systems biology and bioprocess engineering.

A Physicist’s Quest in Biology: Max Delbrück and “Complementarity”

PubMed Central

Strauss, Bernard S.

2017-01-01

Max Delbrück was trained as a physicist but made his major contribution in biology and ultimately shared a Nobel Prize in Physiology or Medicine. He was the acknowledged leader of the founders of molecular biology, yet he failed to achieve his key scientific goals. His ultimate scientific aim was to find evidence for physical laws unique to biology: so-called “complementarity.” He never did. The specific problem he initially wanted to solve was the nature of biological replication but the discovery of the mechanism of replication was made by others, in large part because of his disdain for the details of biochemistry. His later career was spent investigating the effect of light on the fungus Phycomyces, a topic that turned out to be of limited general interest. He was known both for his informality but also for his legendary displays of devastating criticism. His life and that of some of his closest colleagues was acted out against a background of a world in conflict. This essay describes the man and his career and searches for an explanation of his profound influence. PMID:28592501

Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

PubMed

Astakhov, Vadim

2009-01-01

Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

Synthetic biology of antimicrobial discovery

PubMed Central

Zakeri, Bijan; Lu, Timothy K.

2012-01-01

Antibiotic discovery has a storied history. From the discovery of penicillin by Sir Alexander Fleming to the relentless quest for antibiotics by Selman Waksman, the stories have become like folklore, used to inspire future generations of scientists. However, recent discovery pipelines have run dry at a time when multidrug resistant pathogens are on the rise. Nature has proven to be a valuable reservoir of antimicrobial agents, which are primarily produced by modularized biochemical pathways. Such modularization is well suited to remodeling by an interdisciplinary approach that spans science and engineering. Herein, we discuss the biological engineering of small molecules, peptides, and non-traditional antimicrobials and provide an overview of the growing applicability of synthetic biology to antimicrobials discovery. PMID:23654251

Biological system interactions.

PubMed Central

Adomian, G; Adomian, G E; Bellman, R E

1984-01-01

Mathematical modeling of cellular population growth, interconnected subsystems of the body, blood flow, and numerous other complex biological systems problems involves nonlinearities and generally randomness as well. Such problems have been dealt with by mathematical methods often changing the actual model to make it tractable. The method presented in this paper (and referenced works) allows much more physically realistic solutions. PMID:6585837

Biological Potential in Serpentinizing Systems

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.

2016-01-01

Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

Teaching the Use of WebQuests to Master Students in Pablo de Olavide University

ERIC Educational Resources Information Center

Gutiérrez Pérez, Regina

2016-01-01

This paper deals with the new pedagogical approaches that the European Space of Higher Education (ESHE) demands in the university system. More specifically, it describes the experience of teaching the use of WebQuest to future educators in the module of foreign languages belonging to the "Máster de enseñanza de profesorado de educación…

On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

PubMed

Gomez-Ramirez, Jaime; Sanz, Ricardo

2013-09-01

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

MS Kavandi installs cables in Quest airlock

NASA Image and Video Library

2001-07-16

S104-E-5104 (16 July 2001) --- Janet L. Kavandi, STS-104 mission specialist, connects cables and hoses from the newly installed Quest Airlock to Unity Node 1. Other STS-104 and Expedition Two crewmembers are visible in the background working in the Airlock.

Networks’ Characteristics Matter for Systems Biology

PubMed Central

Rider, Andrew K.; Milenković, Tijana; Siwo, Geoffrey H.; Pinapati, Richard S.; Emrich, Scott J.; Ferdig, Michael T.; Chawla, Nitesh V.

2015-01-01

A fundamental goal of systems biology is to create models that describe relationships between biological components. Networks are an increasingly popular approach to this problem. However, a scientist interested in modeling biological (e.g., gene expression) data as a network is quickly confounded by the fundamental problem: how to construct the network? It is fairly easy to construct a network, but is it the network for the problem being considered? This is an important problem with three fundamental issues: How to weight edges in the network in order to capture actual biological interactions? What is the effect of the type of biological experiment used to collect the data from which the network is constructed? How to prune the weighted edges (or what cut-off to apply)? Differences in the construction of networks could lead to different biological interpretations. Indeed, we find that there are statistically significant dissimilarities in the functional content and topology between gene co-expression networks constructed using different edge weighting methods, data types, and edge cut-offs. We show that different types of known interactions, such as those found through Affinity Capture-Luminescence or Synthetic Lethality experiments, appear in significantly varying amounts in networks constructed in different ways. Hence, we demonstrate that different biological questions may be answered by the different networks. Consequently, we posit that the approach taken to build a network can be matched to biological questions to get targeted answers. More study is required to understand the implications of different network inference approaches and to draw reliable conclusions from networks used in the field of systems biology. PMID:26500772

Towards Engineering Biological Systems in a Broader Context.

PubMed

Venturelli, Ophelia S; Egbert, Robert G; Arkin, Adam P

2016-02-27

Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Philosophical Perspective on Evolutionary Systems Biology

PubMed Central

Soyer, Orkun S.; Siegal, Mark L.

2015-01-01

Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB’s progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology. PMID:26085823

Towards Biological Inspiration in the Development of Complex Systems

NASA Technical Reports Server (NTRS)

Hinchey, Michael G.; Sterritt, Roy

2006-01-01

Greater understanding of biology in modem times has enabled significant breakthroughs in improving healthcare, quality of life, and eliminating many diseases and congenital illnesses. Simultaneously there is a move towards emulating nature and copying many of the wonders uncovered in biology, resulting in "biologically inspired" systems. Significant results have been reported in a wide range of areas, with systems inspired by nature enabling exploration, communication, and advances that were never dreamed possible just a few years ago. We warn, that as in many other fields of endeavor, we should be inspired by nature and biology, not engage in mimicry. We describe some results of biological inspiration that augur promise in terms of improving the safety and security of systems, and in developing self-managing systems, that we hope will ultimately lead to self-governing systems.

Oxidative stress measured in vivo without an exogenous contrast agent using QUEST MRI

NASA Astrophysics Data System (ADS)

Berkowitz, Bruce A.

2018-06-01

Decades of experimental studies have implicated excessive generation of reactive oxygen species (ROS) in the decline of tissue function during normal aging, and as a pathogenic factor in a vast array of fatal or debilitating morbidities. This massive body of work has important clinical implications since many antioxidants are FDA approved, readily cross blood-tissue barriers, and are effective at improving disease outcomes. Yet, the potential benefits of antioxidants have remained largely unrealized in patients because conventional methods cannot determine the dose, timing, and drug combinations to be used in clinical trials to localize and decrease oxidative stress. To address this major problem and improve translational success, new methods are urgently needed that non-invasively measure the same ROS biomarker both in animal models and patients with high spatial resolution. Here, we summarize a transformative solution based on a novel method: QUEnch-assiSTed MRI (QUEST MRI). The QUEST MRI index is a significant antioxidant-induced improvement in pathophysiology, or a reduction in 1/T1 (i.e., R1). The latter form of QUEST MRI provides a unique measure of uncontrolled production of endogenous, paramagnetic reactive oxygen species (ROS). QUEST MRI results to-date have been validated by gold standard oxidative stress assays. QUEST MRI has high translational potential because it does not use an exogenous contrast agent and requires only standard MRI equipment. Summarizing, QUEST MRI is a powerful non-invasive approach with unprecedented potential for (i) bridging antioxidant treatment in animal models and patients, (ii) identifying tissue subregions exhibiting oxidative stress, and (iii) coupling oxidative stress localization with behavioral dysfunction, disease pathology, and genetic vulnerabilities to serve as a marker of susceptibility.

A dedicated database system for handling multi-level data in systems biology.

PubMed

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

Peroxisystem: harnessing systems cell biology to study peroxisomes.

PubMed

Schuldiner, Maya; Zalckvar, Einat

2015-04-01

In recent years, high-throughput experimentation with quantitative analysis and modelling of cells, recently dubbed systems cell biology, has been harnessed to study the organisation and dynamics of simple biological systems. Here, we suggest that the peroxisome, a fascinating dynamic organelle, can be used as a good candidate for studying a complete biological system. We discuss several aspects of peroxisomes that can be studied using high-throughput systematic approaches and be integrated into a predictive model. Such approaches can be used in the future to study and understand how a more complex biological system, like a cell and maybe even ultimately a whole organism, works. © 2015 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

Systems Biology-Based Investigation of Host-Plasmodium Interactions.

PubMed

Smith, Maren L; Styczynski, Mark P

2018-05-18

Malaria is a serious, complex disease caused by parasites of the genus Plasmodium. Plasmodium parasites affect multiple tissues as they evade immune responses, replicate, sexually reproduce, and transmit between vertebrate and invertebrate hosts. The explosion of omics technologies has enabled large-scale collection of Plasmodium infection data, revealing systems-scale patterns, mechanisms of pathogenesis, and the ways that host and pathogen affect each other. Here, we provide an overview of recent efforts using systems biology approaches to study host-Plasmodium interactions and the biological themes that have emerged from these efforts. We discuss some of the challenges in using systems biology for this goal, key research efforts needed to address those issues, and promising future malaria applications of systems biology. Copyright © 2018 Elsevier Ltd. All rights reserved.

Wilderness Vision Quest: A Journey of Transformation.

ERIC Educational Resources Information Center

Brown, Michael H.

The Wilderness Vision Quest is an outdoor retreat which helps participants touch, explore, and develop important latent human resources such as imagination, intuition, creativity, inspiration, and insight. Through the careful and focused use of techniques such as deep relaxation, reflective writing, visualization, guided imagery, symbolic drawing,…

Network dynamics and systems biology

NASA Astrophysics Data System (ADS)

Norrell, Johannes A.

The physics of complex systems has grown considerably as a field in recent decades, largely due to improved computational technology and increased availability of systems level data. One area in which physics is of growing relevance is molecular biology. A new field, systems biology, investigates features of biological systems as a whole, a strategy of particular importance for understanding emergent properties that result from a complex network of interactions. Due to the complicated nature of the systems under study, the physics of complex systems has a significant role to play in elucidating the collective behavior. In this dissertation, we explore three problems in the physics of complex systems, motivated in part by systems biology. The first of these concerns the applicability of Boolean models as an approximation of continuous systems. Studies of gene regulatory networks have employed both continuous and Boolean models to analyze the system dynamics, and the two have been found produce similar results in the cases analyzed. We ask whether or not Boolean models can generically reproduce the qualitative attractor dynamics of networks of continuously valued elements. Using a combination of analytical techniques and numerical simulations, we find that continuous networks exhibit two effects---an asymmetry between on and off states, and a decaying memory of events in each element's inputs---that are absent from synchronously updated Boolean models. We show that in simple loops these effects produce exactly the attractors that one would predict with an analysis of the stability of Boolean attractors, but in slightly more complicated topologies, they can destabilize solutions that are stable in the Boolean approximation, and can stabilize new attractors. Second, we investigate ensembles of large, random networks. Of particular interest is the transition between ordered and disordered dynamics, which is well characterized in Boolean systems. Networks at the

"Black Boy": A Story of Soul-Making and a Quest for the Real.

ERIC Educational Resources Information Center

Howland, Jacob

1986-01-01

The general character and significance of a quest for the real gives "Black Boy" its special form. The autobiography displays the development of Wright's soul and the nature of his own specifically artistic quest. The opening scene metaphorically prefigures the shape and movement of Wright's formative experiences as a whole. (LHW)

What We Know about the Impacts of WebQuests: A Review of Research

ERIC Educational Resources Information Center

Abbitt, Jason; Ophus, John

2008-01-01

This article examines the body of research investigating the impacts of the WebQuest instructional strategy on teaching and learning. The WebQuest instructional strategy is often praised as an inquiry-oriented activity, which effectively integrates technology into teaching and learning. The results of research suggest that while this strategy may…

Development and usage of eXtension's HorseQuest: an online resource.

PubMed

Greene, E A; Griffin, A S; Whittle, J; Williams, C A; Howard, A B; Anderson, K P

2010-08-01

eXtension (pronounced e-extension) is an online resource transforming how faculty can collaborate and deliver equine education. As the first Community of Practice launched from eXtension, HorseQuest (HQ) offers free, interactive, peer-reviewed, online resources on a variety of equine-related topics at http://www.extension.org. This group has adapted traditional educational content to the online environment to maximize search engine optimization, to be more discoverable and relevant in the online world. This means that HQ resources are consistently being found on the first page of search results. Also, by researching key words searched by Internet users, HQ has guided new content direction and determined potential webcast topics based on relevance and frequency of those searches. In addition to establishing good search engine optimization, HQ has been utilizing the viral networking aspect of YouTube by uploading clips of existing equine educational videos to YouTube. HorseQuest content appears in mainstream media, is passed on by the user, and helps HQ effectively reach their community of interest (horse enthusiasts). HorseQuest partners with My Horse University to produce webcasts that combine concise knowledge exchange via a scripted presentation with viewer chat and incoming questions. HorseQuest has produced and published content including 12 learning modules, 8 webchats, 21 webcasts, and 572 videos segments. After the official public launch, there was a steady increase in average number of visits/mo and average page views/mo over the 26-mo period. These regressions show a statistically significant increase in visits (P < 0.001) of approximately 450 visits per month and a significant increase in page views (P = 0.004) of about 373 page views per month. HorseQuest is a resource for several state 4-H advancement and competition programs and will continue to be incorporated into traditional extension programs, while reaching and affecting global audiences.

Apparatus and Methods for Manipulation and Optimization of Biological Systems

NASA Technical Reports Server (NTRS)

Sun, Ren (Inventor); Ho, Chih-Ming (Inventor); Wong, Pak Kin (Inventor); Yu, Fuqu (Inventor)

2014-01-01

The invention provides systems and methods for manipulating biological systems, for example to elicit a more desired biological response from a biological sample, such as a tissue, organ, and/or a cell. In one aspect, the invention operates by efficiently searching through a large parametric space of stimuli and system parameters to manipulate, control, and optimize the response of biological samples sustained in the system. In one aspect, the systems and methods of the invention use at least one optimization algorithm to modify the actuator's control inputs for stimulation, responsive to the sensor's output of response signals. The invention can be used, e.g., to optimize any biological system, e.g., bioreactors for proteins, and the like, small molecules, polysaccharides, lipids, and the like. Another use of the apparatus and methods includes is for the discovery of key parameters in complex biological systems.

The common ground of genomics and systems biology

PubMed Central

2014-01-01

The rise of systems biology is intertwined with that of genomics, yet their primordial relationship to one another is ill-defined. We discuss how the growth of genomics provided a critical boost to the popularity of systems biology. We describe the parts of genomics that share common areas of interest with systems biology today in the areas of gene expression, network inference, chromatin state analysis, pathway analysis, personalized medicine, and upcoming areas of synergy as genomics continues to expand its scope across all biomedical fields. PMID:25033072

The emerging genomics and systems biology research lead to systems genomics studies.

PubMed

Yang, Mary Qu; Yoshigoe, Kenji; Yang, William; Tong, Weida; Qin, Xiang; Dunker, A; Chen, Zhongxue; Arbania, Hamid R; Liu, Jun S; Niemierko, Andrzej; Yang, Jack Y

2014-01-01

Synergistically integrating multi-layer genomic data at systems level not only can lead to deeper insights into the molecular mechanisms related to disease initiation and progression, but also can guide pathway-based biomarker and drug target identification. With the advent of high-throughput next-generation sequencing technologies, sequencing both DNA and RNA has generated multi-layer genomic data that can provide DNA polymorphism, non-coding RNA, messenger RNA, gene expression, isoform and alternative splicing information. Systems biology on the other hand studies complex biological systems, particularly systematic study of complex molecular interactions within specific cells or organisms. Genomics and molecular systems biology can be merged into the study of genomic profiles and implicated biological functions at cellular or organism level. The prospectively emerging field can be referred to as systems genomics or genomic systems biology. The Mid-South Bioinformatics Centre (MBC) and Joint Bioinformatics Ph.D. Program of University of Arkansas at Little Rock and University of Arkansas for Medical Sciences are particularly interested in promoting education and research advancement in this prospectively emerging field. Based on past investigations and research outcomes, MBC is further utilizing differential gene and isoform/exon expression from RNA-seq and co-regulation from the ChiP-seq specific for different phenotypes in combination with protein-protein interactions, and protein-DNA interactions to construct high-level gene networks for an integrative genome-phoneme investigation at systems biology level.

Nepal: Quest for Survival.

DTIC Science & Technology

1983-05-02

thesis prqso;i d to hbe faculty.of the U.S. Army Co𔃾d erjkpr .",ta ff- -C9iegs in -~ f~4fM11ment -of the c’i eq~ttkmVAts, for the N, degree er of Mi...REOTAT May 2, 1983 HQ TRADOC, ATTN: ATCS- D IS. NUMBER OF PAGES Ft. Monroe, VA 23651 117 MCLMORIW AGENCY NAME & ADDRESSIt .nffrent from Comfroiiind...concludes with an examination of the three components of Nepal’s current strategy in her quest for survival. Accession r,.- NTIS Gi ., DTIC T&B[ Unariou

Q.U.E.S.T. An Interactive Earth Science Study Tool: Connecting Real Students to Digital Libraries

NASA Astrophysics Data System (ADS)

Moore, A.; Danowski, D.; Brindisi, C.; Sandvol, C.; Seber, D.

2001-05-01

Quick Use Earth Study Tool (QUEST) is an experimental educational interface to the Cornell University's Geoscience Information System (http://atlas.geo.cornell.edu). The information system currently includes more than 100 geographic, geologic, and geophysical data sets along with World Wide Web based interactive mapping tools for data display and analysis. The system is GIS based and accessible via any web browser that support Java applets. QUEST is the companion module that has been developed to assist educators who wish to use these data to their fullest potential, providing tutorials, sample exercises, and suggested projects. Clearly, students learn best when they engage in the practice of science. One means to accomplish this is to have students access primary scientific data. Our experience suggests that a structured exploration of original data sets enhances student learning. For this reason we have selected a subset of Cornell's available geoscience data, and have designed a series of activities that allow students to explore dynamic Earth processes. Currently, these data include the ISC seismicity catalog, volcanism data from the Smithsonian Institution, and digital topography from the USGS and NOAA. The QUEST interface allows students to query the data sets based on a variety of criteria (e.g., earthquakes can be sorted by date, magnitude, depth, and location), or perform computations on data (e.g., sea level can be interactively mapped at any elevation on the DEM). Because the system is GIS-based, multiple data sets can be displayed simultaneously in order for users to examine the spatial relationships between geological features. Users can zoom in to regions of interest, and a map history window keeps track of student work so that comparisons are easily made. QUEST is accompanied by a Teacher's Manual to assist teachers in extracting the most information from the available data and tools. Through these efforts we hope to provide teachers and students

Systems biology approach to bioremediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

2012-06-01

Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potentialmore » for making bioremediation breakthroughs and illuminating the ‘black box’.« less

Multi-level and hybrid modelling approaches for systems biology.

PubMed

Bardini, R; Politano, G; Benso, A; Di Carlo, S

2017-01-01

During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

Jupiter Quest: A Path to Scientific Discovery.

ERIC Educational Resources Information Center

Bollman, Kelly A.; Rodgers, Mark H.; Mauller, Robert L.

2001-01-01

To experience the world of professional science, students must have access to the scientific community and be allowed to become real scientists. A partnership involving the National Aeronautics and Space Administration, the Jet Propulsion Laboratory, and the Lewis Center for Educational Research has produced Jupiter Quest, an engaging curriculum…

Synthetic Biology and the Search for Extraterrestrial Life

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2015-01-01

"Are we alone?" is one of the primary questions of astrobiology, and whose answer defines our significance in the universe. Unfortunately, this quest is hindered by the fact that we have only one confirmed example of life, that of earth. While this is enormously helpful in helping to define the minimum envelope for life, it strains credulity to imagine that life, if it arose multiple times, has not taken other routes. To help fill this gap, our lab has begun using synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - as an enabling technology. One theme, the "Hell Cell" project, focuses on creating artificial extremophiles in order to push the limits for Earth life, and to understand how difficult it is for life to evolve into extreme niches. In another project, we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids.

CosmoQuest: Better Citizen Science Through Education

NASA Technical Reports Server (NTRS)

Gay, P. L.; Lehan, C.; Bracey, G.; Yamani, A.; Francis, M.; Durrell, P.; Spivey, C.; Noel-Storr, J.; Buxner, S.; Cobb, W.;

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

PubMed

Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

2017-03-28

Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Modeling and simulation of biological systems using SPICE language

PubMed Central

Lallement, Christophe; Haiech, Jacques

2017-01-01

The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems), an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE). BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language), a very common description language used in systems biology. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems) have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology). PMID:28787027

System biology of gene regulation.

PubMed

Baitaluk, Michael

2009-01-01

) questions of biological relevance. Thus systems biology could be treated as such a socioscientific phenomenon and a new approach to both experiments and theory that is defined by the strategy of pursuing integration of complex data about the interactions in biological systems from diverse experimental sources using interdisciplinary tools and personnel.

Systems biology of cellular membranes: a convergence with biophysics.

PubMed

Chabanon, Morgan; Stachowiak, Jeanne C; Rangamani, Padmini

2017-09-01

Systems biology and systems medicine have played an important role in the last two decades in shaping our understanding of biological processes. While systems biology is synonymous with network maps and '-omics' approaches, it is not often associated with mechanical processes. Here, we make the case for considering the mechanical and geometrical aspects of biological membranes as a key step in pushing the frontiers of systems biology of cellular membranes forward. We begin by introducing the basic components of cellular membranes, and highlight their dynamical aspects. We then survey the functions of the plasma membrane and the endomembrane system in signaling, and discuss the role and origin of membrane curvature in these diverse cellular processes. We further give an overview of the experimental and modeling approaches to study membrane phenomena. We close with a perspective on the converging futures of systems biology and membrane biophysics, invoking the need to include physical variables such as location and geometry in the study of cellular membranes. WIREs Syst Biol Med 2017, 9:e1386. doi: 10.1002/wsbm.1386 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

The aims of systems biology: between molecules and organisms.

PubMed

Noble, D

2011-05-01

The systems approach to biology has a long history. Its recent rapid resurgence at the turn of the century reflects the problems encountered in interpreting the sequencing of the genome and the failure of that immense achievement to provide rapid and direct solutions to major multi-factorial diseases. This paper argues that systems biology is necessarily multilevel and that there is no privileged level of causality in biological systems. It is an approach rather than a separate discipline. Functionality arises from biological networks that interact with the genome, the environment and the phenotype. This view of biology is very different from the gene-centred views of neo-Darwinism and molecular biology. In neuroscience, the systems approach leads naturally to 2 important conclusions: first, that the idea of 'programs' in the brain is confusing, and second, that the self is better interpreted as a process than as an object. © Georg Thieme Verlag KG Stuttgart · New York.

DaisyQuest. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2006

2006-01-01

"DaisyQuest" is a software bundle that offers computer-assisted instruction in phonological awareness, targeting children aged three to seven years. The instructional activities, framed in a fairy tale involving a search for a friendly dragon named Daisy, teach children how to recognize words that rhyme; words that have the same…

Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach

PubMed Central

Chen, Bor-Sen; Wu, Wei-Sheng

2007-01-01

Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective. PMID:19468310

Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015.

PubMed

Zhao, Zhongming; Liu, Yunlong; Huang, Yufei; Huang, Kun; Ruan, Jianhua

2016-08-26

The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13-15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial sessions, one poster session, and four keynote presentations that covered the frontier research in broad areas related to bioinformatics, systems biology, big data science, biomedical informatics, pharmacogenomics, and intelligent computing. Here, we present a summary of the 10 research articles that were selected from ICIBM 2015 and included in the supplement to BMC Systems Biology.

Systems biology of the structural proteome.

PubMed

Brunk, Elizabeth; Mih, Nathan; Monk, Jonathan; Zhang, Zhen; O'Brien, Edward J; Bliven, Spencer E; Chen, Ke; Chang, Roger L; Bourne, Philip E; Palsson, Bernhard O

2016-03-11

The success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis. Such reconstructions are biochemically, genetically, and genomically structured knowledge bases that can be converted into a mathematical format to enable a myriad of computational biological studies. In recent years, genome-scale reconstructions have been extended to include protein structural information, which has opened up new vistas in systems biology research and empowered applications in structural systems biology and systems pharmacology. Here, we present the generation, application, and dissemination of genome-scale models with protein structures (GEM-PRO) for Escherichia coli and Thermotoga maritima. We show the utility of integrating molecular scale analyses with systems biology approaches by discussing several comparative analyses on the temperature dependence of growth, the distribution of protein fold families, substrate specificity, and characteristic features of whole cell proteomes. Finally, to aid in the grand challenge of big data to knowledge, we provide several explicit tutorials of how protein-related information can be linked to genome-scale models in a public GitHub repository ( https://github.com/SBRG/GEMPro/tree/master/GEMPro_recon/). Translating genome-scale, protein-related information to structured data in the format of a GEM provides a direct mapping of gene to gene-product to protein structure to biochemical reaction to network states to phenotypic function. Integration of molecular-level details of individual proteins, such as their physical, chemical, and structural properties, further expands the description of biochemical network-level properties, and can ultimately influence how to model and predict whole cell phenotypes as well as perform comparative systems biology approaches to study differences between organisms. GEM

Systems Biology: Impressions from a Newcomer Graduate Student in 2016

ERIC Educational Resources Information Center

Simpson, Melanie Rae

2016-01-01

As a newcomer, the philosophical basis of systems biology seems intuitive and appealing, the underlying philosophy being that the whole of a living system cannot be completely understood by the study of its individual parts. Yet answers to the questions "What is systems biology?" and "What constitutes a systems biology approach in…

A Review of the Theory and Research Underlying the StrengthsQuest Program for Students. The Quest for Strengths

ERIC Educational Resources Information Center

Hodges, Timothy D.; Harter, James K.

2005-01-01

StrengthsQuest is a student program that focuses on strengths rather than weaknesses. It is intended to lead students to discover their natural talents and gain unique and valuable insights into how to develop such talents into strengths--strengths that equip them to succeed and to make important decisions that enable them to balance the demands…

The Effect and Value of a WebQuest Activity on Weather in a 5th Grade Classroom

ERIC Educational Resources Information Center

Oliver, Deborah

2010-01-01

WebQuests are increasing in popularity across the country, yet it remains unclear whether WebQuests confer a significant benefit in student content learning. In addition, the perceptions of teachers regarding the classroom value and efficacy of WebQuests in teaching higher level thinking skills are still unclear. The goals of the study were (a) to…

Mathematical methods in systems biology.

PubMed

Kashdan, Eugene; Duncan, Dominique; Parnell, Andrew; Schattler, Heinz

2016-12-01

The editors of this Special Issue of Mathematical Biosciences and Engineering were the organizers for the Third International Workshop "Mathematical Methods in System Biology" that took place on June 15-18, 2015 at the University College Dublin in Ireland. As stated in the workshop goals, we managed to attract a good mix of mathematicians and statisticians working on biological and medical applications with biologists and clinicians interested in presenting their challenging problems and looking to find mathematical and statistical tools for their solutions.

The Spring of Systems Biology-Driven Breeding.

PubMed

Lavarenne, Jérémy; Guyomarc'h, Soazig; Sallaud, Christophe; Gantet, Pascal; Lucas, Mikaël

2018-05-12

Genetics and molecular biology have contributed to the development of rationalized plant breeding programs. Recent developments in both high-throughput experimental analyses of biological systems and in silico data processing offer the possibility to address the whole gene regulatory network (GRN) controlling a given trait. GRN models can be applied to identify topological features helping to shortlist potential candidate genes for breeding purposes. Time-series data sets can be used to support dynamic modelling of the network. This will enable a deeper comprehension of network behaviour and the identification of the few elements to be genetically rewired to push the system towards a modified phenotype of interest. This paves the way to design more efficient, systems biology-based breeding strategies. Copyright © 2018 Elsevier Ltd. All rights reserved.

Modeling of biological intelligence for SCM system optimization.

PubMed

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

PubMed Central

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

Lunar Quest in Second Life, Lunar Exploration Island, Phase II

NASA Astrophysics Data System (ADS)

Ireton, F. M.; Day, B. H.; Mitchell, B.; Hsu, B. C.

2010-12-01

Linden Lab’s Second Life is a virtual 3D metaverse created by users. At any one time there may be 40,000-50,000 users on line. Users develop a persona and are seen on screen as a human figure or avatar. Avatars move through Second Life by walking, flying, or teleporting. Users form communities or groups of mutual interest such as music, computer graphics, and education. These groups communicate via e-mail, voice, and text within Second Life. Information on downloading the Second Life browser and joining can be found on the Second Life website: www.secondlife.com. This poster details Phase II in the development of Lunar Exploration Island (LEI) located in Second Life. Phase I LEI highlighted NASA’s LRO/LCROSS mission. Avatars enter LEI via teleportation arriving at a hall of flight housing interactive exhibits on the LRO/ LCROSS missions including full size models of the two spacecraft and launch vehicle. Storyboards with information about the missions interpret the exhibits while links to external websites provide further information on the mission, both spacecraft’s instrument suites, and related EPO. Other lunar related activities such as My Moon and NLSI EPO programs. A special exhibit was designed for International Observe the Moon Night activities with links to websites for further information. The sim includes several sites for meetings, a conference stage to host talks, and a screen for viewing NASATV coverage of mission and other televised events. In Phase II exhibits are updated to reflect on-going lunar exploration highlights, discoveries, and future missions. A new section of LEI has been developed to showcase NASA’s Lunar Quest program. A new exhibit hall with Lunar Quest information has been designed and is being populated with Lunar Quest information, spacecraft models (LADEE is in place) and kiosks. A two stage interactive demonstration illustrates lunar phases with static and 3-D stations. As NASA’s Lunar Quest program matures further

Squire's Quest! Dietary outcome evaluation of a multimedia game.

PubMed

Baranowski, Tom; Baranowski, Janice; Cullen, Karen W; Marsh, Tara; Islam, Noemi; Zakeri, Issa; Honess-Morreale, Lauren; deMoor, Carl

2003-01-01

Fruit, juice, and vegetable (FJV) consumption among children is low. Innovative programs are needed to enable children to increase FJV intake. Psychoeducational multimedia permits the delivery of interventions as designed and capitalizes on known behavior change principles. Elementary school was the unit of recruitment, assignment, and analysis. Twenty-six elementary schools were pair matched on size and percentage of free or reduced-price lunch, and randomly assigned to treatment or control groups. Data were collected just before and just after the program. All fourth-grade students in participating elementary schools were invited to participate. Data were collected on 1578 students. MAIN OUTCOME Servings of fruit, 100% juice, and vegetables consumed. Squire's Quest! is a ten-session, psychoeducational, multimedia game delivered over 5 weeks, with each session lasting about 25 minutes. Based on social cognitive theory, educational activities attempted to increase preferences for FJV through multiple exposures and associating fun with their consumption, increase asking behaviors for FJV at home and while eating out, and increase skills in FJV preparation through making virtual recipes. Four days of dietary intake were assessed before and after the intervention. Assessment was made by the Food Intake Recording Software System (FIRSSt), which conducts a multiple pass, 24-hour dietary intake interview directly with the children. Children participating in Squire's Quest! increased their FJV consumption by 1.0 servings more than the children not receiving the program. Psychoeducational multimedia games have the potential to substantially change dietary behavior. More research is warranted.

Engineering plant metabolism into microbes: from systems biology to synthetic biology.

PubMed

Xu, Peng; Bhan, Namita; Koffas, Mattheos A G

2013-04-01

Plant metabolism represents an enormous repository of compounds that are of pharmaceutical and biotechnological importance. Engineering plant metabolism into microbes will provide sustainable solutions to produce pharmaceutical and fuel molecules that could one day replace substantial portions of the current fossil-fuel based economy. Metabolic engineering entails targeted manipulation of biosynthetic pathways to maximize yields of desired products. Recent advances in Systems Biology and the emergence of Synthetic Biology have accelerated our ability to design, construct and optimize cell factories for metabolic engineering applications. Progress in predicting and modeling genome-scale metabolic networks, versatile gene assembly platforms and delicate synthetic pathway optimization strategies has provided us exciting opportunities to exploit the full potential of cell metabolism. In this review, we will discuss how systems and synthetic biology tools can be integrated to create tailor-made cell factories for efficient production of natural products and fuel molecules in microorganisms. Copyright © 2012 Elsevier Ltd. All rights reserved.

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects.

PubMed

Liu, Yanfeng; Shin, Hyun-dong; Li, Jianghua; Liu, Long

2015-02-01

Metabolic engineering facilitates the rational development of recombinant bacterial strains for metabolite overproduction. Building on enormous advances in system biology and synthetic biology, novel strategies have been established for multivariate optimization of metabolic networks in ensemble, spatial, and dynamic manners such as modular pathway engineering, compartmentalization metabolic engineering, and metabolic engineering guided by genome-scale metabolic models, in vitro reconstitution, and systems and synthetic biology. Herein, we summarize recent advances in novel metabolic engineering strategies. Combined with advancing kinetic models and synthetic biology tools, more efficient new strategies for improving cellular properties can be established and applied for industrially important biochemical production.

Nanoelectromechanical systems: Nanodevice motion at microwave frequencies

NASA Astrophysics Data System (ADS)

Henry Huang, Xue Ming; Zorman, Christian A.; Mehregany, Mehran; Roukes, Michael L.

2003-01-01

It has been almost forgotten that the first computers envisaged by Charles Babbage in the early 1800s were mechanical and not electronic, but the development of high-frequency nanoelectromechanical systems is now promising a range of new applications, including sensitive mechanical charge detectors and mechanical devices for high-frequency signal processing, biological imaging and quantum measurement. Here we describe the construction of nanodevices that will operate with fundamental frequencies in the previously inaccessible microwave range (greater than 1 gigahertz). This achievement represents a significant advance in the quest for extremely high-frequency nanoelectromechanical systems.

Directed evolution and synthetic biology applications to microbial systems.

PubMed

Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

2016-06-01

Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Advances in Structural Biology and the Application to Biological Filament Systems.

PubMed

Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

2018-04-01

Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

76 FR 2144 - Quest Diagnostics, Inc. Information Technology Help Desk Services Including On-Site Leased...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-12

.... Information Technology Help Desk Services Including On-Site Leased Workers From Modis, West Norriton, PA..., applicable to workers of Quest Diagnostics, Inc., Information Technology Help Desk Services, West Norriton... Quest Diagnostics, Inc., Information Technology Help Desk [[Page 2145

Systems biology for molecular life sciences and its impact in biomedicine.

PubMed

Medina, Miguel Ángel

2013-03-01

Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

A SYSTEMS BIOLOGY APPROACH TO DEVELOPMENTAL TOXICOLOGY

EPA Science Inventory

Abstract
Recent advances in developmental biology have yielded detailed models of gene regulatory networks (GRNs) involved in cell specification and other processes in embryonic differentiation. Such networks form the bedrock on which a systems biology approach to developme...

Plant Systems Biology (editorial)

USDA-ARS?s Scientific Manuscript database

In June 2003, Plant Physiology published an Arabidopsis special issue devoted to plant systems biology. The intention of Natasha Raikhel and Gloria Coruzzi, the two editors of this first-of-its-kind issue, was ‘‘to help nucleate this new effort within the plant community’’ as they considered that ‘‘...

Multilayer network modeling of integrated biological systems. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

NASA Astrophysics Data System (ADS)

De Domenico, Manlio

2018-03-01

Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are highlighting how simple networks - obtained by aggregating or neglecting temporal or categorical description of biological data - are not able to account for the richness of information characterizing biological systems. More complex models, namely multilayer networks, are needed to account for interdependencies, often varying across time, of biological interacting units within a cell, a tissue or parts of an organism.

Sixth International Conference on Systems Biology (ICSB 2005)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Professor Andrew Murray

2005-10-22

This grant supported the Sixth International Conference on Systems Biology (ICSB 2005), held in Boston, Massachusetts from October 19th to 22nd, 2005. The ICSB is the only major, annual, international conference focused exclusively on the important emerging field of systems biology. It draws together scientists with expertise in theoretical, computational and experimental approaches to understanding biological systems at many levels. Previous ICSB meetings have been held in Tokyo (2000), at Caltech (2001), at the Karolinska Institute (2002), at Washington University in St. Louis (2003), and in Heidelberg (2004). These conferences have been increasingly successful at bringing together the growing communitymore » of established and junior researchers with interests in this area. Boston is home to several groups that have shown leadership in the field and was therefore an ideal place to hold this conference . The executive committee for the conference comprised Jim Collins (Biomedical Engineering, Boston University), Marc Kirschner (chair of the new Department of Systems Biology at Harvard Medical School), Eric Lander (director of the Broad Institute of MIT and Harvard), Andrew Murray (director of Harvard’s Bauer Center for Genomics Research) and Peter Sorger (director of MIT’s Computational and Systems Biology Initiative). There are almost as many definitions of systems biology as there are systems biologists. We take a broad view of the field, and we succeeded in one of our major aims in organizing a conference that bridges two types of divide. The first is that between traditional academic disciplines: each of our sessions includes speakers from biology and from one or more physical or quantitative sciences. The second type includes those that separate experimental biologists from their colleagues who work on theory or computation. Here again, each session included representatives from at least two of these three categories; indeed, many of the speakers

Systems biology solutions for biochemical production challenges.

PubMed

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

2017-06-01

There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Temporal pattern of questing tick Ixodes ricinus density at differing elevations in the coastal region of western Norway

PubMed Central

2014-01-01

Background Climate change can affect the activity and distribution of species, including pathogens and parasites. The densities and distribution range of the sheep tick (Ixodes ricinus) and it’s transmitted pathogens appears to be increasing. Thus, a better understanding of questing tick densities in relation to climate and weather conditions is urgently needed. The aim of this study was to test predictions regarding the temporal pattern of questing tick densities at two different elevations in Norway. We predict that questing tick densities will decrease with increasing elevations and increase with increasing temperatures, but predict that humidity levels will rarely affect ticks in this northern, coastal climate with high humidity. Methods We described the temporal pattern of questing tick densities at ~100 and ~400 m a.s.l. along twelve transects in the coastal region of Norway. We used the cloth lure method at 14-day intervals during the snow-free season to count ticks in two consecutive years in 20 m2 plots. We linked the temporal pattern of questing tick densities to local measurements of the prevailing weather. Results The questing tick densities were much higher and the season was longer at ~100 compared to at ~400 m a.s.l. There was a prominent spring peak in both years and a smaller autumn peak in one year at ~100 m a.s.l.; but no marked peak at ~400 m a.s.l. Tick densities correlated positively with temperature, from low densities <5°C, then increasing and levelling off >15-17°C. We found no evidence for reduced questing densities during the driest conditions measured. Conclusions Tick questing densities differed even locally linked to elevation (on the same hillside, a few kilometers apart). The tick densities were strongly hampered by low temperatures that limited the duration of the questing seasons, whereas the humidity appeared not to be a limiting factor under the humid conditions at our study site. We expect rising global temperatures to

Dietary antioxidant synergy in chemical and biological systems.

PubMed

Wang, Sunan; Zhu, Fan

2017-07-24

Antioxidant (AOX) synergies have been much reported in chemical ("test-tube" based assays focusing on pure chemicals), biological (tissue culture, animal and clinical models), and food systems during the past decade. Tentative synergies differ from each other due to the composition of AOX and the quantification methods. Regeneration mechanism responsible for synergy in chemical systems has been discussed. Solvent effects could contribute to the artifacts of synergy observed in the chemical models. Synergy in chemical models may hardly be relevant to biological systems that have been much less studied. Apparent discrepancies exist in understanding the molecular mechanisms in both chemical and biological systems. This review discusses diverse variables associated with AOX synergy and molecular scenarios for explanation. Future research to better utilize the synergy is suggested.

Controlled biological and biomimetic systems for landmine detection.

PubMed

Habib, Maki K

2007-08-30

Humanitarian demining requires to accurately detect, locate and deactivate every single landmine and other buried mine-like objects as safely and as quickly as possible, and in the most non-invasive manner. The quality of landmine detection affects directly the efficiency and safety of this process. Most of the available methods to detect explosives and landmines are limited by their sensitivity and/or operational complexities. All landmines leak with time small amounts of their explosives that can be found on surrounding ground and plant life. Hence, explosive signatures represent the robust primary indicator of landmines. Accordingly, developing innovative technologies and efficient techniques to identify in real-time explosives residue in mined areas represents an attractive and promising approach. Biological and biologically inspired detection technology has the potential to compete with or be used in conjunction with other artificial technology to complement performance strengths. Biological systems are sensitive to many different scents concurrently, a property that has proven difficult to replicate artificially. Understanding biological systems presents unique opportunities for developing new capabilities through direct use of trained bio-systems, integration of living and non-living components, or inspiring new design by mimicking biological capabilities. It is expected that controlled bio-systems, biotechnology and microbial techniques will contribute to the advancement of mine detection and other application domains. This paper provides directions, evaluation and analysis on the progress of controlled biological and biomimetic systems for landmine detection. It introduces and discusses different approaches developed, underlining their relative advantages and limitations, and highlighting trends, safety and ecology concern, and possible future directions.

Set membership experimental design for biological systems.

PubMed

Marvel, Skylar W; Williams, Cranos M

2012-03-21

Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. The practicability of our approach is illustrated with a case study. This study shows that our approach is able to 1) identify

Set membership experimental design for biological systems

PubMed Central

2012-01-01

Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This study shows that our

Performance improvement: the organization's quest.

PubMed

McKinley, C O; Parmer, D E; Saint-Amand, R A; Harbin, C B; Roulston, J C; Ellis, R A; Buchanan, J R; Leonard, R B

1999-01-01

In today's health care marketplace, quality has become an expectation. Stakeholders are demanding quality clinical outcomes, and accrediting bodies are requiring clinical performance data. The Roosevelt Institute's quest was to define and quantify quality outcomes, develop an organizational culture of performance improvement, and ensure customer satisfaction. Several of the organization's leaders volunteered to work as a team to develop a specific performance improvement approach tailored to the organization. To date, over 200 employees have received an orientation to the model and its philosophy and nine problem action and process improvement teams have been formed.

Measuring the Density of Liquid Targets in the SeaQuest Experiment

NASA Astrophysics Data System (ADS)

Xi, Zhaojia; SeaQuest/E906 Collaboration

2015-10-01

The SeaQuest (E906) experiment, using the 120 GeV proton beam from the Main Injector at the Fermi National Accelerator Lab (FNAL), is studying the quark and antiquark structure of the nucleon using the Drell-Yan process. Based on the cross section ratios, σ (p + d) / σ (p + p) , SeaQuest will extract the Bjorken-x dependnce of the d / u ratio. The measurement will cover the large region (x > 0 . 25) with improved accuracy compared to the previous E866/Nusea experiment. Liquid D2 (LD2) and Liquid H2 (LH2) are the targets used in the SeaQuest experiment. The densities of LD2 and LH2 targets are two important quantities for the determination of the d / u ratio. We measure the pressure and temperature inside the flasks, from which the densities are calculated. The method, measurements and results of this study will be presented. This work is supported by U.S. DOE MENP Grant DE-FG02-03ER41243.

Synthetic biology: advancing the design of diverse genetic systems

PubMed Central

Wang, Yen-Hsiang; Wei, Kathy Y.; Smolke, Christina D.

2013-01-01

A main objective of synthetic biology is to make the process of designing genetically-encoded biological systems more systematic, predictable, robust, scalable, and efficient. The examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from a simple genetic switch to search-and-destroy systems. While significant advances in synthesis capabilities support the potential for the implementation of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Synthetic biology offers much promise in developing systems to address challenges faced in manufacturing, the environment and sustainability, and health and medicine, but the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems. PMID:23413816

Howard Brenner's Legacy for Biological Transport Processes

NASA Astrophysics Data System (ADS)

Nitsche, Johannes

2014-11-01

This talk discusses the manner in which Howard Brenner's theoretical contributions have had, and long will have, strong and direct impact on the understanding of transport processes occurring in biological systems. His early work on low Reynolds number resistance/mobility coefficients of arbitrarily shaped particles, and particles near walls and in pores, is an essential component of models of hindered diffusion through many types of membranes and tissues, and convective transport in microfluidic diagnostic systems. His seminal contributions to macrotransport (coarse-graining, homogenization) theory presaged the growing discipline of multiscale modeling. For biological systems they represent the key to infusing diffusion models of a wide variety of tissues with a sound basis in their microscopic structure and properties, often over a hierarchy of scales. Both scientific currents are illustrated within the concrete context of diffusion models of drug/chemical diffusion through the skin. This area of theory, which is key to transdermal drug development and risk assessment of chemical exposure, has benefitted very directly from Brenner's contributions. In this as in other areas, Brenner's physicochemical insight, mathematical virtuosity, drive for fully justified analysis free of ad hoc assumptions, quest for generality, and impeccable exposition, have consistently elevated the level of theoretical understanding and presentation. We close with anecdotes showing how his personal qualities and warmth helped to impart high standards of rigor to generations of grateful research students. Authors are Johannes M. Nitsche, Ludwig C. Nitsche and Gerald B. Kasting.

SEEK: a systems biology data and model management platform.

PubMed

Wolstencroft, Katherine; Owen, Stuart; Krebs, Olga; Nguyen, Quyen; Stanford, Natalie J; Golebiewski, Martin; Weidemann, Andreas; Bittkowski, Meik; An, Lihua; Shockley, David; Snoep, Jacky L; Mueller, Wolfgang; Goble, Carole

2015-07-11

Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and

Advancing metabolic engineering through systems biology of industrial microorganisms.

PubMed

Dai, Zongjie; Nielsen, Jens

2015-12-01

Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genome Scale Modeling in Systems Biology: Algorithms and Resources

PubMed Central

Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

2014-01-01

In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

QUEST/Ada: Query utility environment for software testing of Ada

NASA Technical Reports Server (NTRS)

Brown, David B.

1989-01-01

Results of research and development efforts are presented for Task 1, Phase 2 of a general project entitled, The Development of a Program Analysis Environment for Ada. A prototype of the QUEST/Ada system was developed to collect data to determine the effectiveness of the rule-based testing paradigm. The prototype consists of five parts: the test data generator, the parser/scanner, the test coverage analyzer, a symbolic evaluator, and a data management facility, known as the Librarian. These components are discussed at length. Also presented is an experimental design for the evaluations, an overview of the project, and a schedule for its completion.

Biocellion: accelerating computer simulation of multicellular biological system models

PubMed Central

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-01-01

Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. Results: We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. Contact: seunghwa.kang@pnnl.gov PMID:25064572

Apparatus and methods for manipulation and optimization of biological systems

NASA Technical Reports Server (NTRS)

Sun, Ren (Inventor); Ho, Chih-Ming (Inventor); Wong, Pak Kin (Inventor); Yu, Fuqu (Inventor)

2012-01-01

The invention provides systems and methods for manipulating, e.g., optimizing and controlling, biological systems, e.g., for eliciting a more desired biological response of biological sample, such as a tissue, organ, and/or a cell. In one aspect, systems and methods of the invention operate by efficiently searching through a large parametric space of stimuli and system parameters to manipulate, control, and optimize the response of biological samples sustained in the system, e.g., a bioreactor. In alternative aspects, systems include a device for sustaining cells or tissue samples, one or more actuators for stimulating the samples via biochemical, electromagnetic, thermal, mechanical, and/or optical stimulation, one or more sensors for measuring a biological response signal of the samples resulting from the stimulation of the sample. In one aspect, the systems and methods of the invention use at least one optimization algorithm to modify the actuator's control inputs for stimulation, responsive to the sensor's output of response signals. The compositions and methods of the invention can be used, e.g., to for systems optimization of any biological manufacturing or experimental system, e.g., bioreactors for proteins, e.g., therapeutic proteins, polypeptides or peptides for vaccines, and the like, small molecules (e.g., antibiotics), polysaccharides, lipids, and the like. Another use of the apparatus and methods includes combination drug therapy, e.g. optimal drug cocktail, directed cell proliferations and differentiations, e.g. in tissue engineering, e.g. neural progenitor cells differentiation, and discovery of key parameters in complex biological systems.

CosmoQuest Transient Tracker: Opensource Photometry & Astrometry software

NASA Astrophysics Data System (ADS)

Myers, Joseph L.; Lehan, Cory; Gay, Pamela; Richardson, Matthew; CosmoQuest Team

2018-01-01

CosmoQuest is moving from online citizen science, to observational astronomy with the creation of Transient Trackers. This open source software is designed to identify asteroids and other transient/variable objects in image sets. Transient Tracker’s features in final form will include: astrometric and photometric solutions, identification of moving/transient objects, identification of variable objects, and lightcurve analysis. In this poster we present our initial, v0.1 release and seek community input.This software builds on the existing NIH funded ImageJ libraries. Creation of this suite of opensource image manipulation routines is lead by Wayne Rasband and is released primarily under the MIT license. In this release, we are building on these libraries to add source identification for point / point-like sources, and to do astrometry. Our materials released under the Apache 2.0 license on github (http://github.com/CosmoQuestTeam) and documentation can be found at http://cosmoquest.org/TransientTracker.

Multiscale systems biology of trauma-induced coagulopathy.

PubMed

Tsiklidis, Evan; Sims, Carrie; Sinno, Talid; Diamond, Scott L

2018-07-01

Trauma with hypovolemic shock is an extreme pathological state that challenges the body to maintain blood pressure and oxygenation in the face of hemorrhagic blood loss. In conjunction with surgical actions and transfusion therapy, survival requires the patient's blood to maintain hemostasis to stop bleeding. The physics of the problem are multiscale: (a) the systemic circulation sets the global blood pressure in response to blood loss and resuscitation therapy, (b) local tissue perfusion is altered by localized vasoregulatory mechanisms and bleeding, and (c) altered blood and vessel biology resulting from the trauma as well as local hemodynamics control the assembly of clotting components at the site of injury. Building upon ongoing modeling efforts to simulate arterial or venous thrombosis in a diseased vasculature, computer simulation of trauma-induced coagulopathy is an emerging approach to understand patient risk and predict response. Despite uncertainties in quantifying the patient's dynamic injury burden, multiscale systems biology may help link blood biochemistry at the molecular level to multiorgan responses in the bleeding patient. As an important goal of systems modeling, establishing early metrics of a patient's high-dimensional trajectory may help guide transfusion therapy or warn of subsequent later stage bleeding or thrombotic risks. This article is categorized under: Analytical and Computational Methods > Computational Methods Biological Mechanisms > Regulatory Biology Models of Systems Properties and Processes > Mechanistic Models. © 2018 Wiley Periodicals, Inc.

Agent-based models in translational systems biology

PubMed Central

An, Gary; Mi, Qi; Dutta-Moscato, Joyeeta; Vodovotz, Yoram

2013-01-01

Effective translational methodologies for knowledge representation are needed in order to make strides against the constellation of diseases that affect the world today. These diseases are defined by their mechanistic complexity, redundancy, and nonlinearity. Translational systems biology aims to harness the power of computational simulation to streamline drug/device design, simulate clinical trials, and eventually to predict the effects of drugs on individuals. The ability of agent-based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggests that this modeling framework is well suited for translational systems biology. This review describes agent-based modeling and gives examples of its translational applications in the context of acute inflammation and wound healing. PMID:20835989

An online model composition tool for system biology models

PubMed Central

2013-01-01

Background There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. Results We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Conclusions Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well. PMID:24006914

The Quest for Fairness in Language Testing

ERIC Educational Resources Information Center

Karami, Hossein

2013-01-01

The search for fairness in language testing is distinct from other areas of educational measurement as the object of measurement, that is, language, is part of the identity of the test takers. So, a host of issues enter the scene when one starts to reflect on how to assess people's language abilities. As the quest for fairness in language testing…

Exploring Synthetic and Systems Biology at the University of Edinburgh.

PubMed

Fletcher, Liz; Rosser, Susan; Elfick, Alistair

2016-06-15

The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Stem Cells: A Renaissance in Human Biology Research.

PubMed

Wu, Jun; Izpisua Belmonte, Juan Carlos

2016-06-16

The understanding of human biology and how it relates to that of other species represents an ancient quest. Limited access to human material, particularly during early development, has restricted researchers to only scratching the surface of this inherently challenging subject. Recent technological innovations, such as single cell "omics" and human stem cell derivation, have now greatly accelerated our ability to gain insights into uniquely human biology. The opportunities afforded to delve molecularly into scarce material and to model human embryogenesis and pathophysiological processes are leading to new insights of human development and are changing our understanding of disease and choice of therapy options. Copyright © 2016 Elsevier Inc. All rights reserved.

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

PubMed

Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

2015-08-21

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

Quest for Cavities: A Hole-istic Simulation Game.

ERIC Educational Resources Information Center

Stabb, Mark

1990-01-01

Describes adaptation of children's Musical Chairs game, illustrating different animals'"quest for cavities." Game uses role play to simulate wildlife "cavity excavators" and secondary-user animals that compete for nesting holes. Classifies 44 animals according to nesting practice and gives hole sizes for 25. Promotes ecology, conservation studies.…

Universal biology and the statistical mechanics of early life.

PubMed

Goldenfeld, Nigel; Biancalani, Tommaso; Jafarpour, Farshid

2017-12-28

All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators. Dynamical system models of the evolution of the genetic code must explain its universality and its highly refined error-minimization properties. These have both been accounted for in a scenario where life arose from a collective, networked phase where there was no notion of species and perhaps even individuality itself. We show how this phase ultimately terminated during an event sometimes known as the Darwinian transition, leading to the present epoch of tree-like vertical descent of organismal lineages. These examples illustrate concrete examples of universal biology: the quest for a fundamental understanding of the basic properties of living systems, independent of precise instantiation in chemistry or other media.This article is part of the themed issue 'Reconceptualizing the origins of life'. © 2017 The Author(s).

Universal biology and the statistical mechanics of early life

NASA Astrophysics Data System (ADS)

Goldenfeld, Nigel; Biancalani, Tommaso; Jafarpour, Farshid

2017-11-01

All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators. Dynamical system models of the evolution of the genetic code must explain its universality and its highly refined error-minimization properties. These have both been accounted for in a scenario where life arose from a collective, networked phase where there was no notion of species and perhaps even individuality itself. We show how this phase ultimately terminated during an event sometimes known as the Darwinian transition, leading to the present epoch of tree-like vertical descent of organismal lineages. These examples illustrate concrete examples of universal biology: the quest for a fundamental understanding of the basic properties of living systems, independent of precise instantiation in chemistry or other media. This article is part of the themed issue 'Reconceptualizing the origins of life'.

CosmoQuest: Making the public your students and collaborators

NASA Astrophysics Data System (ADS)

Gay, Pamela; Buxner, Sanlyn; Grier, Jennifer; Richardson, Matthew; CosmoQuest Team

2018-01-01

CosmoQuest is a second generation citizen science project that makes it possible for NASA Subject Matter Experts to engage the public as both learners and collaborators in research. Engaging the public in publishable science is termed “Citizen Science.” This is a powerful technique for accomplishing research projects and tasks that require many minds and eyes to complete. While some projects may use undergraduates for help, others simply have too many images or too much data for a small population to sort through. CosmoQuest is a platform that enables scientists to take advantage of already existing science tools to engage the public in their research and to acquire the data analysis they need. Citizen scientists, like students, need their experience properly scaffolded to their understanding, and they require mentoring and training to succeed.This presentation focuses on methods for focusing research projects for successful citizen science engagement, and determining what scaffolding must be built to support citizen education and engagement.This presentation will help you understand how to transform your research project into a successful citizen science engagement. We will also present a flowchart to help you define: what is required, how to focus on what science does and doesn’t work, and what support your project requires. The content presented will allow you to successfully implement a project within the CosmoQuest facility, and determine what educational support you should provide or request aid to provide.

Modeling autism: a systems biology approach

PubMed Central

2012-01-01

Autism is the fastest growing developmental disorder in the world today. The prevalence of autism in the US has risen from 1 in 2500 in 1970 to 1 in 88 children today. People with autism present with repetitive movements and with social and communication impairments. These impairments can range from mild to profound. The estimated total lifetime societal cost of caring for one individual with autism is $3.2 million US dollars. With the rapid growth in this disorder and the great expense of caring for those with autism, it is imperative for both individuals and society that techniques be developed to model and understand autism. There is increasing evidence that those individuals diagnosed with autism present with highly diverse set of abnormalities affecting multiple systems of the body. To this date, little to no work has been done using a whole body systems biology approach to model the characteristics of this disorder. Identification and modelling of these systems might lead to new and improved treatment protocols, better diagnosis and treatment of the affected systems, which might lead to improved quality of life by themselves, and, in addition, might also help the core symptoms of autism due to the potential interconnections between the brain and nervous system with all these other systems being modeled. This paper first reviews research which shows that autism impacts many systems in the body, including the metabolic, mitochondrial, immunological, gastrointestinal and the neurological. These systems interact in complex and highly interdependent ways. Many of these disturbances have effects in most of the systems of the body. In particular, clinical evidence exists for increased oxidative stress, inflammation, and immune and mitochondrial dysfunction which can affect almost every cell in the body. Three promising research areas are discussed, hierarchical, subgroup analysis and modeling over time. This paper reviews some of the systems disturbed in autism and

Adaptive array technique for differential-phase reflectometry in QUEST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Idei, H., E-mail: idei@triam.kyushu-u.ac.jp; Hanada, K.; Zushi, H.

2014-11-15

A Phased Array Antenna (PAA) was considered as launching and receiving antennae in reflectometry to attain good directivity in its applied microwave range. A well-focused beam was obtained in a launching antenna application, and differential-phase evolution was properly measured by using a metal reflector plate in the proof-of-principle experiment at low power test facilities. Differential-phase evolution was also evaluated by using the PAA in the Q-shu University Experiment with Steady State Spherical Tokamak (QUEST). A beam-forming technique was applied in receiving phased-array antenna measurements. In the QUEST device that should be considered as a large oversized cavity, standing wave effectmore » was significantly observed with perturbed phase evolution. A new approach using derivative of measured field on propagating wavenumber was proposed to eliminate the standing wave effect.« less

QUEST1 Variability Survey. III. Light Curve Catalog Update

NASA Astrophysics Data System (ADS)

Rengstorf, A. W.; Thompson, D. L.; Mufson, S. L.; Andrews, P.; Honeycutt, R. K.; Vivas, A. K.; Abad, C.; Adams, B.; Bailyn, C.; Baltay, C.; Bongiovanni, A.; Briceño, C.; Bruzual, G.; Coppi, P.; Della Prugna, F.; Emmet, W.; Ferrín, I.; Fuenmayor, F.; Gebhard, M.; Hernández, J.; Magris, G.; Musser, J.; Naranjo, O.; Oemler, A.; Rosenzweig, P.; Sabbey, C. N.; Sánchez, Ge.; Sánchez, Gu.; Schaefer, B.; Schenner, H.; Sinnott, J.; Snyder, J. A.; Sofia, S.; Stock, J.; van Altena, W.

2009-03-01

This paper reports an update to the QUEST1 (QUasar Equatorial Survey Team, Phase 1) Variability Survey (QVS) light curve catalog, which links QVS instrumental magnitude light curves to Sloan Digital Sky Survey (SDSS) objects and photometry. In the time since the original QVS catalog release, the overlap between publicly available SDSS data and QVS data has increased by 8% in sky coverage and 16,728 in number of matched objects. The astrometric matching and the treatment of SDSS masks have been refined for the updated catalog. We report on these improvements and present multiple bandpass light curves, global variability information, and matched SDSS photometry for 214,941 QUEST1 objects. Based on observations obtained at the Llano del Hato National Astronomical Observatory, operated by the Centro de Investigaciones de Astronomía for the Ministerio de Ciencia y Tecnologia of Venezuela.

The Best of Two Worlds: Combining ITV and Web Quests To Strengthen Distance Learning.

ERIC Educational Resources Information Center

Mosby, Charmaine

This presentation describes an English graduate seminar in Local Color and Regionalism in American Literature at Western Kentucky University that was set up as an experimental hybrid course, i.e., roughly 60% face-to-face and 40% Web course (Web quest format). The focus is on the four tasks that comprised the Web quest segment of the course: (1) a…

A Systems Biology Approach to Iron Metabolism

PubMed Central

Chifman, J.; Laubenbacher, R.; Torti, S.V.

2015-01-01

Iron is critical to the survival of almost all living organisms. However, inappropriately low or high levels of iron are detrimental and contribute to a wide range of diseases. Recent advances in the study of iron metabolism have revealed multiple intricate pathways that are essential to the maintenance of iron homeostasis. Further, iron regulation involves processes at several scales, ranging from the subcellular to the organismal. This complexity makes a systems biology approach crucial, with its enabling technology of computational models based on a mathematical description of regulatory systems. Systems biology may represent a new strategy for understanding imbalances in iron metabolism and their underlying causes. PMID:25480643

Biocellion: accelerating computer simulation of multicellular biological system models.

PubMed

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-11-01

Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Designing WebQuests to Support Creative Problem Solving

ERIC Educational Resources Information Center

Rubin, Jim

2013-01-01

WebQuests have been a popular alternative for collaborative group work that utilizes internet resources, but studies have questioned how effective they are in challenging students to use higher order thinking processes that involve creative problem solving. This article explains how different levels of inquiry relate to categories of learning…

Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers

PubMed Central

Esterhuyse, Maria M.; Weiner, January; Caron, Etienne; Loxton, Andre G.; Iannaccone, Marco; Wagman, Chandre; Saikali, Philippe; Stanley, Kim; Wolski, Witold E.; Mollenkopf, Hans-Joachim; Schick, Matthias; Aebersold, Ruedi; Linhart, Heinz; Walzl, Gerhard

2015-01-01

ABSTRACT An estimated one-third of the world’s population is currently latently infected with Mycobacterium tuberculosis. Latent M. tuberculosis infection (LTBI) progresses into active tuberculosis (TB) disease in ~5 to 10% of infected individuals. Diagnostic and prognostic biomarkers to monitor disease progression are urgently needed to ensure better care for TB patients and to decrease the spread of TB. Biomarker development is primarily based on transcriptomics. Our understanding of biology combined with evolving technical advances in high-throughput techniques led us to investigate the possibility of additional platforms (epigenetics and proteomics) in the quest to (i) understand the biology of the TB host response and (ii) search for multiplatform biosignatures in TB. We engaged in a pilot study to interrogate the DNA methylome, transcriptome, and proteome in selected monocytes and granulocytes from TB patients and healthy LTBI participants. Our study provides first insights into the levels and sources of diversity in the epigenome and proteome among TB patients and LTBI controls, despite limitations due to small sample size. Functionally the differences between the infection phenotypes (LTBI versus active TB) observed in the different platforms were congruent, thereby suggesting regulation of function not only at the transcriptional level but also by DNA methylation and microRNA. Thus, our data argue for the development of a large-scale study of the DNA methylome, with particular attention to study design in accounting for variation based on gender, age, and cell type. PMID:26374119

Light microscopy applications in systems biology: opportunities and challenges

PubMed Central

2013-01-01

Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various biological scales in living cells. The combination of molecular biology and imaging provides a bottom-up tool for direct insight into how molecular processes work on a cellular scale. However, imaging can also be used as a top-down approach to study the behavior of a system without detailed prior knowledge about its underlying molecular mechanisms. In this review, we highlight the recent developments on microscopy-based systems analyses and discuss the complementary opportunities and different challenges with high-content screening and high-throughput imaging. Furthermore, we provide a comprehensive overview of the available platforms that can be used for image analysis, which enable community-driven efforts in the development of image-based systems biology. PMID:23578051

Advanced systems biology methods in drug discovery and translational biomedicine.

PubMed

Zou, Jun; Zheng, Ming-Wu; Li, Gen; Su, Zhi-Guang

2013-01-01

Systems biology is in an exponential development stage in recent years and has been widely utilized in biomedicine to better understand the molecular basis of human disease and the mechanism of drug action. Here, we discuss the fundamental concept of systems biology and its two computational methods that have been commonly used, that is, network analysis and dynamical modeling. The applications of systems biology in elucidating human disease are highlighted, consisting of human disease networks, treatment response prediction, investigation of disease mechanisms, and disease-associated gene prediction. In addition, important advances in drug discovery, to which systems biology makes significant contributions, are discussed, including drug-target networks, prediction of drug-target interactions, investigation of drug adverse effects, drug repositioning, and drug combination prediction. The systems biology methods and applications covered in this review provide a framework for addressing disease mechanism and approaching drug discovery, which will facilitate the translation of research findings into clinical benefits such as novel biomarkers and promising therapies.

Cancer systems biology: signal processing for cancer research

PubMed Central

Yli-Harja, Olli; Ylipää, Antti; Nykter, Matti; Zhang, Wei

2011-01-01

In this editorial we introduce the research paradigms of signal processing in the era of systems biology. Signal processing is a field of science traditionally focused on modeling electronic and communications systems, but recently it has turned to biological applications with astounding results. The essence of signal processing is to describe the natural world by mathematical models and then, based on these models, develop efficient computational tools for solving engineering problems. Here, we underline, with examples, the endless possibilities which arise when the battle-hardened tools of engineering are applied to solve the problems that have tormented cancer researchers. Based on this approach, a new field has emerged, called cancer systems biology. Despite its short history, cancer systems biology has already produced several success stories tackling previously impracticable problems. Perhaps most importantly, it has been accepted as an integral part of the major endeavors of cancer research, such as analyzing the genomic and epigenomic data produced by The Cancer Genome Atlas (TCGA) project. Finally, we show that signal processing and cancer research, two fields that are seemingly distant from each other, have merged into a field that is indeed more than the sum of its parts. PMID:21439242

Workshop Report: Systems Biology for Organotypic Cell Cultures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grego, Sonia; Dougherty, Edward R.; Alexander, Francis Joseph

Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomicmore » data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data.« less

Workshop Report: Systems Biology for Organotypic Cell Cultures

DOE PAGES

Grego, Sonia; Dougherty, Edward R.; Alexander, Francis Joseph; ...

2016-11-14

Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomicmore » data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data.« less

How do biological systems discriminate among physically similar ions?

PubMed

Diamond, J M

1975-10-01

This paper reviews the history of understanding how biological systems can discriminate so strikingly among physically similar ions, especially alkali cations. Appreciation of qualitative regularities ("permitted sequences") and quantitative regularities ("selectivity isotherms") in ion selectivity grew first from studies of ion exchangers and glass electrodes, then of biological systems such as enzymes and cell membranes, and most recently of lipid bilayers doped with model pores and carriers. Discrimination of ions depends on both electrostatic and steric forces. "Black-box" studies on intact biological membranes have in some cases yielded molecular clues to the structure of the actual biological pores and carriers. Major current problems involve the extraction of these molecules; how to do it, what to do when it is achieved, and how (and if) it is relevant to the central problems of membrane function. Further advances are expected soon from studies of rate barriers within membranes, of voltage-dependent ("excitable") conducting channels, and of increasingly complex model systems and biological membranes.

The Quest for Molecular Regulation Underlying Unisexual Flower Development

PubMed Central

Sobral, Rómulo; Silva, Helena G.; Morais-Cecílio, Leonor; Costa, Maria M. R.

2016-01-01

The understanding of the molecular mechanisms responsible for the making of a unisexual flower has been a long-standing quest in plant biology. Plants with male and female flowers can be divided mainly into two categories: dioecious and monoecious, and both sexual systems co-exist in nature in ca of 10% of the angiosperms. The establishment of male and female traits has been extensively described in a hermaphroditic flower and requires the interplay of networks, directly and indirectly related to the floral organ identity genes including hormonal regulators, transcription factors, microRNAs, and chromatin-modifying proteins. Recent transcriptomic studies have been uncovering the molecular processes underlying the establishment of unisexual flowers and there are many parallelisms between monoecious, dioecious, and hermaphroditic individuals. Here, we review the paper entitled “Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber” published in 2014 in the Frontiers of Plant Science (volume 5 |Article 599) and discussed it in the context of recent studies with other dioecious and monoecious plants that utilized high-throughput platforms to obtain transcriptomic profiles of male and female unisexual flowers. In some unisexual flowers, the developmental programs that control organ initiation fail and male or female organs do not form, whereas in other species, organ initiation and development occur but they abort or arrest during different species-specific stages of differentiation. Therefore, a direct comparison of the pathways responsible for the establishment of unisexual flowers in different species are likely to reveal conserved modules of gene regulatory hubs involved in stamen or carpel development, as well as differences that reflect the different stages of development in which male and/or female organ arrest or loss-of-function occurs. PMID:26925078

The role of mechanics in biological and bio-inspired systems.

PubMed

Egan, Paul; Sinko, Robert; LeDuc, Philip R; Keten, Sinan

2015-07-06

Natural systems frequently exploit intricate multiscale and multiphasic structures to achieve functionalities beyond those of man-made systems. Although understanding the chemical make-up of these systems is essential, the passive and active mechanics within biological systems are crucial when considering the many natural systems that achieve advanced properties, such as high strength-to-weight ratios and stimuli-responsive adaptability. Discovering how and why biological systems attain these desirable mechanical functionalities often reveals principles that inform new synthetic designs based on biological systems. Such approaches have traditionally found success in medical applications, and are now informing breakthroughs in diverse frontiers of science and engineering.

Psychophysica: Mathematica notebooks for psychophysical experiments (cinematica--psychometrica--quest)

NASA Technical Reports Server (NTRS)

Watson, A. B.; Solomon, J. A.

1997-01-01

Psychophysica is a set of software tools for psychophysical research. Functions are provided for calibrated visual displays, for fitting and plotting of psychometric functions, and for the QUEST adaptive staircase procedure. The functions are written in the Mathematica programming language.

Holarchical Systems and Emotional Holons : Biologically-Inspired System Designs for Control of Autonomous Aerial Vehicles

NASA Technical Reports Server (NTRS)

Ippolito, Corey; Plice, Laura; Pisanich, Greg

2003-01-01

The BEES (Bio-inspired Engineering for Exploration Systems) for Mars project at NASA Ames Research Center has the goal of developing bio-inspired flight control strategies to enable aerial explorers for Mars scientific investigations. This paper presents a summary of our ongoing research into biologically inspired system designs for control of unmanned autonomous aerial vehicle communities for Mars exploration. First, we present cooperative design considerations for robotic explorers based on the holarchical nature of biological systems and communities. Second, an outline of an architecture for cognitive decision making and control of individual robotic explorers is presented, modeled after the emotional nervous system of cognitive biological systems. Keywords: Holarchy, Biologically Inspired, Emotional UAV Flight Control

Collaborative Systems Biology Projects for the Military Medical Community.

PubMed

Zalatoris, Jeffrey J; Scheerer, Julia B; Lebeda, Frank J

2017-09-01

This pilot study was conducted to examine, for the first time, the ongoing systems biology research and development projects within the laboratories and centers of the U.S. Army Medical Research and Materiel Command (USAMRMC). The analysis has provided an understanding of the breadth of systems biology activities, resources, and collaborations across all USAMRMC subordinate laboratories. The Systems Biology Collaboration Center at USAMRMC issued a survey regarding systems biology research projects to the eight U.S.-based USAMRMC laboratories and centers in August 2016. This survey included a data call worksheet to gather self-identified project and programmatic information. The general topics focused on the investigators and their projects, on the project's research areas, on omics and other large data types being collected and stored, on the analytical or computational tools being used, and on identifying intramural (i.e., USAMRMC) and extramural collaborations. Among seven of the eight laboratories, 62 unique systems biology studies were funded and active during the final quarter of fiscal year 2016. Of 29 preselected medical Research Task Areas, 20 were associated with these studies, some of which were applicable to two or more Research Task Areas. Overall, studies were categorized among six general types of objectives: biological mechanisms of disease, risk of/susceptibility to injury or disease, innate mechanisms of healing, diagnostic and prognostic biomarkers, and host/patient responses to vaccines, and therapeutic strategies including host responses to therapies. We identified eight types of omics studies and four types of study subjects. Studies were categorized on a scale of increasing complexity from single study subject/single omics technology studies (23/62) to studies integrating results across two study subject types and two or more omics technologies (13/62). Investigators at seven USAMRMC laboratories had collaborations with systems biology experts

System approaches of Weiss and Bertalanffy and their relevance for systems biology today.

PubMed

Drack, Manfred; Wolkenhauer, Olaf

2011-06-01

System approaches in biology have a long history. We focus here on the thinking of Paul A. Weiss and Ludwig von Bertalanffy, who contributed a great deal towards making the system concept operable in biology in the early 20th century. To them, considering whole living systems, which includes their organisation or order, is equally important as the dynamics within systems and the interplay between different levels from molecules over cells to organisms. They also called for taking the intrinsic activity of living systems and the conservation of system states into account. We compare these notions with today's systems biology, which is often a bottom-up approach from molecular dynamics to cellular behaviour. We conclude that bringing together the early heuristics with recent formalisms and novel experimental set-ups can lead to fruitful results and understanding. Copyright © 2011 Elsevier Ltd. All rights reserved.

Agent-Based Modeling in Molecular Systems Biology.

PubMed

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-07-01

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

Quantitative computational models of molecular self-assembly in systems biology

PubMed Central

Thomas, Marcus; Schwartz, Russell

2017-01-01

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally. PMID:28535149

Quantitative computational models of molecular self-assembly in systems biology.

PubMed

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

Modeling acclimatization by hybrid systems: condition changes alter biological system behavior models.

PubMed

Assar, Rodrigo; Montecino, Martín A; Maass, Alejandro; Sherman, David J

2014-07-01

In order to describe the dynamic behavior of a complex biological system, it is useful to combine models integrating processes at different levels and with temporal dependencies. Such combinations are necessary for modeling acclimatization, a phenomenon where changes in environmental conditions can induce drastic changes in the behavior of a biological system. In this article we formalize the use of hybrid systems as a tool to model this kind of biological behavior. A modeling scheme called strong switches is proposed. It allows one to take into account both minor adjustments to the coefficients of a continuous model, and, more interestingly, large-scale changes to the structure of the model. We illustrate the proposed methodology with two applications: acclimatization in wine fermentation kinetics, and acclimatization of osteo-adipo differentiation system linking stimulus signals to bone mass. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

CosmoQuest: Building a Community of Skilled Citizen Science Contributors

NASA Astrophysics Data System (ADS)

Gay, P.; Lehan, C.; Bracey, G.; Durrell, P.; Komatsu, T.; Yamani, A.; Francis, M. R.

2016-12-01

The CosmoQuest Virtual Research Facility invites the public to participate in NASA Science Mission Directorate related research that leads to publishable results and data catalogues. CosmoQuest projects range in difficulty from simple crater and transient marking tasks to more complicated mapping tasks. To successfully engage contributors in creating usable results, training and validation are required. This is accomplished through activities that are designed to mirror the experiences students would have in a university, and include mentoring by team scientists, feedback on contributor efforts, seminars to learn about new science, and even formal classes to provide needed background. Recruitment is accomplished using new and social media, and planetarium and Science on the Sphere™ trailers and shows, and community is built through online and real-world collaboration spaces and events. In this presentation, we detail CosmoQuest's four-pronged approach of media recruitment, science education, citizen science, and community collaboration. We also discuss how it is leveraged to create a skilled collaboration of citizen scientists. Training and data validation activities will be be emphasized, with examples of both what can go right and lessons learned from when things go wrong. We conclude with strategies on how to utilize best practices in user interface design to create virtual experiences that allow major citizen science efforts to be scalable to large audiences.

QUEST: An Assessment Tool for Web-Based Learning.

ERIC Educational Resources Information Center

Choren, Ricardo; Blois, Marcelo; Fuks, Hugo

In 1997, the Software Engineering Laboratory at Pontifical Catholic University of Rio de Janeiro (Brazil) implemented the first version of AulaNet (TM) a World Wide Web-based educational environment. Some of the teaching staff will use this environment in 1998 to offer regular term disciplines through the Web. This paper introduces Quest, a tool…

Dynamic sensitivity analysis of biological systems

PubMed Central

Wu, Wu Hsiung; Wang, Feng Sheng; Chang, Maw Shang

2008-01-01

Background A mathematical model to understand, predict, control, or even design a real biological system is a central theme in systems biology. A dynamic biological system is always modeled as a nonlinear ordinary differential equation (ODE) system. How to simulate the dynamic behavior and dynamic parameter sensitivities of systems described by ODEs efficiently and accurately is a critical job. In many practical applications, e.g., the fed-batch fermentation systems, the system admissible input (corresponding to independent variables of the system) can be time-dependent. The main difficulty for investigating the dynamic log gains of these systems is the infinite dimension due to the time-dependent input. The classical dynamic sensitivity analysis does not take into account this case for the dynamic log gains. Results We present an algorithm with an adaptive step size control that can be used for computing the solution and dynamic sensitivities of an autonomous ODE system simultaneously. Although our algorithm is one of the decouple direct methods in computing dynamic sensitivities of an ODE system, the step size determined by model equations can be used on the computations of the time profile and dynamic sensitivities with moderate accuracy even when sensitivity equations are more stiff than model equations. To show this algorithm can perform the dynamic sensitivity analysis on very stiff ODE systems with moderate accuracy, it is implemented and applied to two sets of chemical reactions: pyrolysis of ethane and oxidation of formaldehyde. The accuracy of this algorithm is demonstrated by comparing the dynamic parameter sensitivities obtained from this new algorithm and from the direct method with Rosenbrock stiff integrator based on the indirect method. The same dynamic sensitivity analysis was performed on an ethanol fed-batch fermentation system with a time-varying feed rate to evaluate the applicability of the algorithm to realistic models with time

Vibrational resonances in biological systems at microwave frequencies.

PubMed

Adair, Robert K

2002-03-01

Many biological systems can be expected to exhibit resonance behavior involving the mechanical vibration of system elements. The natural frequencies of such resonances will, generally, be in the microwave frequency range. Some of these systems will be coupled to the electromagnetic field by the charge distributions they carry, thus admitting the possibility that microwave exposures may generate physiological effects in man and other species. However, such microwave excitable resonances are expected to be strongly damped by interaction with their aqueous biological environment. Although those dissipation mechanisms have been studied, the limitations on energy transfers that follow from the limited coupling of these resonances to the electromagnetic field have not generally been considered. We show that this coupling must generally be very small and thus the absorbed energy is so strongly limited that such resonances cannot affect biology significantly even if the systems are much less strongly damped than expected from basic dissipation models.

Bio Computing and Information Systems: A Quest

DTIC Science & Technology

2003-06-01

on Security and Privacy, 1996 4) Dawkins , R. The Selfish Gene . Oxford University Press, 1989 5) Dumpert, K. The Social Biology of Ants...mechanisms of genetic control, which switch genes on and off. The archetypal example of genetic regulation in bacteria is the lac operon of E. coli...first studied in the 1950s by Jacques Monod and François Jacob. The lac operon is a set of genes and regulatory sequences involved in the metabolism of

Virtual Tissues and Developmental Systems Biology (book chapter)

EPA Science Inventory

Virtual tissue (VT) models provide an in silico environment to simulate cross-scale properties in specific tissues or organs based on knowledge of the underlying biological networks. These integrative models capture the fundamental interactions in a biological system and enable ...

Graphic Representation of Carbon Dioxide Equilibria in Biological Systems.

ERIC Educational Resources Information Center

Kindig, Neal B.; Filley, Giles F.

1983-01-01

The log C-pH diagram is a useful means of displaying quantitatively the many variables (including temperature) that determine acid-base equilibria in biological systems. Presents the diagram as extended to open/closed biological systems and derives a new water-ion balance method for determining equilibrium pH. (JN)

Systems biology of eukaryotic superorganisms and the holobiont concept.

PubMed

Kutschera, Ulrich

2018-06-14

The founders of modern biology (Jean Lamarck, Charles Darwin, August Weismann etc.) were organismic life scientists who attempted to understand the morphology and evolution of living beings as a whole (i.e., the phenotype). However, with the emergence of the study of animal and plant physiology in the nineteenth century, this "holistic view" of the living world changed and was ultimately replaced by a reductionistic perspective. Here, I summarize the history of systems biology, i.e., the modern approach to understand living beings as integrative organisms, from genotype to phenotype. It is documented that the physiologists Claude Bernard and Julius Sachs, who studied humans and plants, respectively, were early pioneers of this discipline, which was formally founded 50 years ago. In 1968, two influential monographs, authored by Ludwig von Bertalanffy and Mihajlo D. Mesarović, were published, wherein a "systems theory of biology" was outlined. Definitions of systems biology are presented with reference to metabolic or cell signaling networks, analyzed via genomics, proteomics, and other methods, combined with computer simulations/mathematical modeling. Then, key insights of this discipline with respect to epiphytic microbes (Methylobacterium sp.) and simple bacteria (Mycoplasma sp.) are described. The principles of homeostasis, molecular systems energetics, gnotobiology, and holobionts (i.e., complexities of host-microbiota interactions) are outlined, and the significance of systems biology for evolutionary theories is addressed. Based on the microbe-Homo sapiens-symbiosis, it is concluded that human biology and health should be interpreted in light of a view of the biomedical sciences that is based on the holobiont concept.

[Biological therapies in systemic lupus erythematosus].

PubMed

Cairoli, Ernesto; Espinosa, Gerard; Cervera, Ricard

2010-07-01

The immunosuppressive agents used in patients with systemic lupus erythematosus (SLE) have significantly improved prognosis. However, it is necessary to develop more specific immunosuppressive treatments with less toxicity. Better understanding of the mechanisms involved in the loss of tolerance in autoimmune diseases has contributed to the development of potential new treatments called biologic therapies. The targets of these biological therapies are directed toward the B cell depletion, interference in the co-stimulation signals and the blockade of cytokines. Therapies using anti-CD20 monoclonal antibodies have shown satisfactory results especially in patients with SLE refractory to conventional treatment. The biological therapies provide encouraging results that represent a possible option in the treatment of refractory patients as well as a potential therapy in the future management of SLE.

Cross-cultural adaptation and validation of the Quebec User Evaluation of Satisfaction with Assistive Technology (QUEST 2.0): the development of the Taiwanese version.

PubMed

Mao, Hui-Fen; Chen, Wan-Yin; Yao, Grace; Huang, Sheau-Ling; Lin, Chia-Chi; Huang, Wen-Ni Wennie

2010-05-01

To develop and validate a cross-cultural version of the Quebec User Evaluation of Satisfaction with Assistive Technology (QUEST 2.0) for users of assistive technology devices in Taiwan. A cross-sectional survey. The standard cultural adaptation procedure was used for questionnaire translation and cultural item design. A field test was then conducted for item selection and psychometric properties testing. One hundred and five volunteer assistive device users in community. A questionnaire comprising 12 items of the QUEST 2.0 and 16 culture-specific items. One culture-specific item, 'Cost', was selected based on eight criteria and added to the QUEST 2.0 (12 items) to formulate the Taiwanese version of QUEST 2.0 (T-QUEST). The T-QUEST consisted of 13 items which were classified into two domains: device (8 items) and service (5 items). The internal consistencies of the device, service and total T-QUEST scores were 0.87, 0.84 and 0.90, respectively. The device, services and total T-QUEST scores achieved good test-retest stability (intraclass correlation coefficient (ICC) 0.90, 0.97, 0.95). Exploratory factor analysis revealed that T-QUEST had a two-factor structure for device and service in the construct of user satisfaction (53.42% of the variance explained). Users of assistive device in different culture may have different concerns regarding satisfaction. T-QUEST is the first published version of QUEST with culture-specific items added to the original translated items of QUEST 2.0. T-QUEST was a valid and reliable tool for measuring user satisfaction among Mandarin-speaking individuals using various kinds of assistive devices.

The Black Student's Quest for Identity and Self Determination

ERIC Educational Resources Information Center

Colquit, Jesse L.

1976-01-01

The rising expectations and aspirations of black students in their quest for identity and self determination have given rise to their rejection of the dominant culture's definition of the black man. Top priorities as perceived by blacks in legitimizing their manhood are presented. (Author)

Specifications of Standards in Systems and Synthetic Biology.

PubMed

Schreiber, Falk; Bader, Gary D; Golebiewski, Martin; Hucka, Michael; Kormeier, Benjamin; Le Novère, Nicolas; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar; Weise, Stephan

2015-09-04

Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation). Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/. So far the different standards were published and made accessible through the standards’ web- pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated

Mathematical manipulative models: in defense of "beanbag biology".

PubMed

Jungck, John R; Gaff, Holly; Weisstein, Anton E

2010-01-01

Mathematical manipulative models have had a long history of influence in biological research and in secondary school education, but they are frequently neglected in undergraduate biology education. By linking mathematical manipulative models in a four-step process-1) use of physical manipulatives, 2) interactive exploration of computer simulations, 3) derivation of mathematical relationships from core principles, and 4) analysis of real data sets-we demonstrate a process that we have shared in biological faculty development workshops led by staff from the BioQUEST Curriculum Consortium over the past 24 yr. We built this approach based upon a broad survey of literature in mathematical educational research that has convincingly demonstrated the utility of multiple models that involve physical, kinesthetic learning to actual data and interactive simulations. Two projects that use this approach are introduced: The Biological Excel Simulations and Tools in Exploratory, Experiential Mathematics (ESTEEM) Project (http://bioquest.org/esteem) and Numerical Undergraduate Mathematical Biology Education (NUMB3R5 COUNT; http://bioquest.org/numberscount). Examples here emphasize genetics, ecology, population biology, photosynthesis, cancer, and epidemiology. Mathematical manipulative models help learners break through prior fears to develop an appreciation for how mathematical reasoning informs problem solving, inference, and precise communication in biology and enhance the diversity of quantitative biology education.

Using WebQuests in the Social Sciences Classroom

ERIC Educational Resources Information Center

Kachina, Olga A.

2012-01-01

This article investigates if WebQuests have been an effective instructional tool for teaching Social Sciences subjects. In order to obtain an answer to this question, a review of scholarly literature from 1995 to the present has been undertaken and action research in 8th grade U.S. history course was conducted. The literature investigation has…

Palmer Quest: A Feasible Nuclear Fission "Vision Mission" to the Mars Polar Caps

NASA Technical Reports Server (NTRS)

Carsey, F. D.; Beegle, L. W.; Nakagawa, R.; Elliott, J. O.; Matthews, J. B.; Coleman, M. L.; Hecht, M. H.; Ivaniov, A. B.; Head, J. W.; Milkovich, S.

2005-01-01

We are engaged in a NASA Vision Mission study, called Palmer Quest after the American Antarctic explorer Nathaniel Palmer, to assess the presence of life and evaluate the habitability of the basal domain of the Mars polar caps. We address this goal through four objectives: 1. Determine the presence of amino acids, nutrients, and geochemical heterogeneity in the ice sheet. 2. Quantify and characterize the provenance of the amino acids in Mars ice. 3. Assess the stratification of outcropped units for indications of habitable zones. 4. Determine the accumulation of ice, mineralogic material, and amino acids in Mars ice caps over the present epoch. Because of the defined scientific goal for the vision mission, the Palmer Quest focus is astrobiological; however, the results of the study make us optimistic that aggressive multi-platform in-situ missions that address a wide range of objectives, such as climate change, can be supported by variations of the approach used on this mission. Mission Overview: The Palmer Quest baseline

77 FR 151 - Requested Administrative Waiver of the Coastwise Trade Laws: Vessel SEA QUEST; Invitation for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-03

... Administrative Waiver of the Coastwise Trade Laws: Vessel SEA QUEST; Invitation for Public Comments AGENCY... entered into this docket is available on the World Wide Web at http://www.regulations.gov . FOR FURTHER... QUEST is: Intended Commercial Use of Vessel: ``Short term charters, sport fishing and pleasure cruising...

Engineering biological systems using automated biofoundries

PubMed Central

Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin

2017-01-01

Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges. PMID:28602523

Formal reasoning about systems biology using theorem proving

PubMed Central

Hasan, Osman; Siddique, Umair; Tahar, Sofiène

2017-01-01

System biology provides the basis to understand the behavioral properties of complex biological organisms at different levels of abstraction. Traditionally, analysing systems biology based models of various diseases have been carried out by paper-and-pencil based proofs and simulations. However, these methods cannot provide an accurate analysis, which is a serious drawback for the safety-critical domain of human medicine. In order to overcome these limitations, we propose a framework to formally analyze biological networks and pathways. In particular, we formalize the notion of reaction kinetics in higher-order logic and formally verify some of the commonly used reaction based models of biological networks using the HOL Light theorem prover. Furthermore, we have ported our earlier formalization of Zsyntax, i.e., a deductive language for reasoning about biological networks and pathways, from HOL4 to the HOL Light theorem prover to make it compatible with the above-mentioned formalization of reaction kinetics. To illustrate the usefulness of the proposed framework, we present the formal analysis of three case studies, i.e., the pathway leading to TP53 Phosphorylation, the pathway leading to the death of cancer stem cells and the tumor growth based on cancer stem cells, which is used for the prognosis and future drug designs to treat cancer patients. PMID:28671950

Mapping "StrengthsQuest" Themes to Holland's Vocational Personality Types

ERIC Educational Resources Information Center

Carson, Andrew D.; Evans, Karen; Gitin, Elena; Eads, Jonathan

2011-01-01

A sample of 1,747 students attending undergraduate classes in legal education at an online university completed the "StrengthsQuest" assessment as part of a larger investigation; of this number, 117 students also completed the "Kuder Career Search". Exploratory factor analysis (principal components followed varimax rotation) of…

Tinder Elementary: A Case Study of the Quest Network.

ERIC Educational Resources Information Center

Howley-Rowe, Caitlin

In 1996, Quest staff began working with teams from school communities in three West Virginia county school districts to invigorate efforts for continuous school improvement. This first learning community consisted of students, teachers, administrators, parents, and community members, who ultimately wrote individual school visions and improvement…

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

PubMed

Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Maps, books and other metaphors for systems biology.

PubMed

Ouzounis, Christos; Mazière, Pierre

2006-07-01

We briefly review the use of metaphors in science and progressively focus on fields from biology and molecular biology to genomics and bioinformatics. We discuss how metaphors are both a tool for scientific exploration and a medium for public communication of complex subjects, by various short examples. Finally, we propose a metaphor for systems biology that provides an illuminating perspective for the ambitious goals of this field and delimits its current agenda.

Unified Quest 2010, Part 1. Warfighter Forum

DTIC Science & Technology

2010-01-01

The Warfighter Forum is one of several analytic events in the Chief of Staff of the Army’s Unified Quest 2010 Campaign of Learning . During the event...and Missile Defense Command/Army Strategic Forces Command (USASMDC/ARSTRAT) conducted a Warfighter Forum devoted to gaining direct insights into...Warfighter Forum event was conducted Dec. 8-9, 2009 in Colorado Springs, Colo., to lever- age the availability of combat units at nearby Fort Carson

A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics.

PubMed

Somvanshi, Pramod Rajaram; Venkatesh, K V

2014-03-01

Human physiology is an ensemble of various biological processes spanning from intracellular molecular interactions to the whole body phenotypic response. Systems biology endures to decipher these multi-scale biological networks and bridge the link between genotype to phenotype. The structure and dynamic properties of these networks are responsible for controlling and deciding the phenotypic state of a cell. Several cells and various tissues coordinate together to generate an organ level response which further regulates the ultimate physiological state. The overall network embeds a hierarchical regulatory structure, which when unusually perturbed can lead to undesirable physiological state termed as disease. Here, we treat a disease diagnosis problem analogous to a fault diagnosis problem in engineering systems. Accordingly we review the application of engineering methodologies to address human diseases from systems biological perspective. The review highlights potential networks and modeling approaches used for analyzing human diseases. The application of such analysis is illustrated in the case of cancer and diabetes. We put forth a concept of cell-to-human framework comprising of five modules (data mining, networking, modeling, experimental and validation) for addressing human physiology and diseases based on a paradigm of system level analysis. The review overtly emphasizes on the importance of multi-scale biological networks and subsequent modeling and analysis for drug target identification and designing efficient therapies.

Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems.

PubMed

Roux-Rouquié, Magali; Caritey, Nicolas; Gaubert, Laurent; Rosenthal-Sabroux, Camille

2004-07-01

One of the main issues in Systems Biology is to deal with semantic data integration. Previously, we examined the requirements for a reference conceptual model to guide semantic integration based on the systemic principles. In the present paper, we examine the usefulness of the Unified Modelling Language (UML) to describe and specify biological systems and processes. This makes unambiguous representations of biological systems, which would be suitable for translation into mathematical and computational formalisms, enabling analysis, simulation and prediction of these systems behaviours.

Thermostability of biological systems: fundamentals, challenges, and quantification.

PubMed

He, Xiaoming

2011-01-01

This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems.

Thermostability of Biological Systems: Fundamentals, Challenges, and Quantification

PubMed Central

He, Xiaoming

2011-01-01

This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems. PMID:21769301

Echinococcus as a model system: biology and epidemiology.

PubMed

Thompson, R C A; Jenkins, D J

2014-10-15

The introduction of Echinococcus to Australia over 200 years ago and its establishment in sheep rearing areas of the country inflicted a serious medical and economic burden on the country. This resulted in an investment in both basic and applied research aimed at learning more about the biology and life cycle of Echinococcus. This research served to illustrate the uniqueness of the parasite in terms of developmental biology and ecology, and the value of Echinococcus as a model system in a broad range of research, from fundamental biology to theoretical control systems. These studies formed the foundation for an international, diverse and ongoing research effort on the hydatid organisms encompassing stem cell biology, gene regulation, strain variation, wildlife diseases and models of transmission dynamics. We describe the development, nature and diversity of this research, and how it was initiated in Australia but subsequently has stimulated much international and collaborative research on Echinococcus. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Extravehicular Mobility Unit (EMU) Preparations in Joint Airlock Quest

NASA Image and Video Library

2009-03-23

ISS018-E-042704 (23 March 2009) --- Astronaut Richard Arnold, STS-119 mission specialist, attired in his Extravehicular Mobility Unit (EMU) spacesuit, gives a ?thumbs-up? signal as he prepares for the mission's third scheduled session of extravehicular activity (EVA) in the Quest Airlock of the International Space Station.

CosmoQuest Year 2: Citizen Science Progress, Motivations, and Education

NASA Astrophysics Data System (ADS)

Gugliucci, Nicole E.; Gay, P. L.; Antonenko, I.; Bracey, G.; Costello, K.; Lehan, C.; Moore, J.; Reilly, E.; Robbins, S. J.; Schmidt, B. E.; CosmoQuest Collaboration

2014-01-01

The CosmoQuest citizen science virtual research facility has wrapped up its second year of operations. With projects mapping the surfaces of the Moon, Mercury, and asteroid Vesta, citizen scientists have marked over 2 million craters as well as other surface features. Analysis of the mapping results show that citizen scientists map high resolution features as well as expert crater markers within a small margin of error. We’ve undertaken a study of citizen science motivations with our users, and find that an interest in astronomy and a desire to contribute new knowledge as primary motivating factors. Ten percent of users surveyed list learning or teaching science as the primary motivating factor. A full analysis of this survey will be presented. Along those lines, the CosmoQuest education team has developed a second middle school educational unit to align with its citizen science projects. In-Vesta-Gate explores asteroid science and is in the trial stage, while we report on several teacher professional development opportunities with Terraluna, a Moon-focused educational unit developed last year. We’ve also taken the CosmoQuest citizen science on the road and outside the website, having a booth and activities at several public events. We present visitor survey results from a recent exhibition at Dragon*Con, a sci-fi/fantasy convention with over 50,000 attendees. We discuss future plans for the project, including the release of several mobile apps to be previewed here.

Sender–receiver systems and applying information theory for quantitative synthetic biology

PubMed Central

Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

2015-01-01

Sender–receiver (S–R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S–R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning. PMID:25282688

Applying systems biology methods to the study of human physiology in extreme environments

PubMed Central

2013-01-01

Systems biology is defined in this review as ‘an iterative process of computational model building and experimental model revision with the aim of understanding or simulating complex biological systems’. We propose that, in practice, systems biology rests on three pillars: computation, the omics disciplines and repeated experimental perturbation of the system of interest. The number of ethical and physiologically relevant perturbations that can be used in experiments on healthy humans is extremely limited and principally comprises exercise, nutrition, infusions (e.g. Intralipid), some drugs and altered environment. Thus, we argue that systems biology and environmental physiology are natural symbionts for those interested in a system-level understanding of human biology. However, despite excellent progress in high-altitude genetics and several proteomics studies, systems biology research into human adaptation to extreme environments is in its infancy. A brief description and overview of systems biology in its current guise is given, followed by a mini review of computational methods used for modelling biological systems. Special attention is given to high-altitude research, metabolic network reconstruction and constraint-based modelling. PMID:23849719

CosmoQuest: Training Educators and Engaging Classrooms in Citizen Science through a Virtual Research Facility

NASA Astrophysics Data System (ADS)

Buxner, Sanlyn; Bracey, Georgia; Summer, Theresa; Cobb, Whitney; Gay, Pamela L.; Finkelstein, Keely D.; Gurton, Suzanne; Felix-Strishock, Lisa; Kruse, Brian; Lebofsky, Larry A.; Jones, Andrea J.; Tweed, Ann; Graff, Paige; Runco, Susan; Noel-Storr, Jacob; CosmoQuest Team

2016-10-01

CosmoQuest is a Citizen Science Virtual Research Facility that engages scientists, educators, students, and the public in analyzing NASA images. Often, these types of citizen science activities target enthusiastic members of the public, and additionally engage students in K-12 and college classrooms. To support educational engagement, we are developing a pipeline in which formal and informal educators and facilitators use the virtual research facility to engage students in real image analysis that is framed to provide meaningful science learning. This work also contributes to the larger project to produce publishable results. Community scientists are being solicited to propose CosmoQuest Science Projects take advantage of the virtual research facility capabilities. Each CosmoQuest Science Project will result in formal education materials, aligned with Next Generation Science Standards including the 3-dimensions of science learning; core ideas, crosscutting concepts, and science and engineering practices. Participating scientists will contribute to companion educational materials with support from the CosmoQuest staff of data specialists and education specialists. Educators will be trained through in person and virtual workshops, and classrooms will have the opportunity to not only work with NASA data, but interface with NASA scientists. Through this project, we are bringing together subject matter experts, classrooms, and informal science organizations to share the excitement of NASA SMD science with future citizen scientists. CosmoQuest is funded through individual donations, through NASA Cooperative Agreement NNX16AC68A, and through additional grants and contracts that are listed on our website, cosmoquest.org.

ENFIN a network to enhance integrative systems biology.

PubMed

Kahlem, Pascal; Birney, Ewan

2007-12-01

Integration of biological data of various types and development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing both an adapted infrastructure to connect databases and platforms to enable the generation of new bioinformatics tools as well as the experimental validation of computational predictions. We will give an overview of the projects tackled within ENFIN and discuss the challenges associated with integration for systems biology.

Systems biology of cancer biomarker detection.

PubMed

Mitra, Sanga; Das, Smarajit; Chakrabarti, Jayprokas

2013-01-01

Cancer systems-biology is an ever-growing area of research due to explosion of data; how to mine these data and extract useful information is the problem. To have an insight on carcinogenesis one need to systematically mine several resources, such as databases, microarray and next-generation sequences. This review encompasses management and analysis of cancer data, databases construction and data deposition, whole transcriptome and genome comparison, analysing results from high throughput experiments to uncover cellular pathways and molecular interactions, and the design of effective algorithms to identify potential biomarkers. Recent technical advances such as ChIP-on-chip, ChIP-seq and RNA-seq can be applied to get epigenetic information transformed into a high-throughput endeavour to which systems biology and bioinformatics are making significant inroads. The data from ENCODE and GENCODE projects available through UCSC genome browser can be considered as benchmark for comparison and meta-analysis. A pipeline for integrating next generation sequencing data, microarray data, and putting them together with the existing database is discussed. The understanding of cancer genomics is changing the way we approach cancer diagnosis and treatment. To give a better understanding of utilizing available resources' we have chosen oral cancer to show how and what kind of analysis can be done. This review is a computational genomic primer that provides a bird's eye view of computational and bioinformatics' tools currently available to perform integrated genomic and system biology analyses of several carcinoma.

Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases.

PubMed

Oh, Soo Jin; Choi, Young Ki; Shin, Ok Sarah

2018-03-01

Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs. © Copyright: Yonsei University College of Medicine 2018.

Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases

PubMed Central

2018-01-01

Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs. PMID:29436184

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective

PubMed Central

Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure; Alberghina, Lilia; Almaas, Eivind; Besozzi, Daniela; Blomberg, Anders; Bretschneider, Till; Cascante, Marta; Collin, Olivier; de Atauri, Pedro; Depner, Cornelia; Dickinson, Robert; Dobrzynski, Maciej; Fleck, Christian; Garcia-Ojalvo, Jordi; Gonze, Didier; Hahn, Jens; Hess, Heide Marie; Hollmann, Susanne; Krantz, Marcus; Kummer, Ursula; Lundh, Torbjörn; Martial, Gifta; dos Santos, Vítor Martins; Mauer-Oberthür, Angela; Regierer, Babette; Skene, Barbara; Stalidzans, Egils; Stelling, Jörg; Teusink, Bas; Workman, Christopher T; Hohmann, Stefan

2016-01-01

Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii) a description of possible career paths for students who undergo such an education, (iv) conditions that should improve the recruitment of students to such programmes and (v) mechanisms for collaboration and excellence spreading among education professionals. With the growing interest of industry in applying Systems Biology approaches in their fields, a concerted action between academia and industry is needed to build this expertise. Here we present a reflection of the European situation and expertise, where most of the challenges we discuss are universal, anticipating that our suggestions will be useful internationally. We believe that one of the overriding goals of any Systems Biology education should be a student’s ability to phrase and communicate research questions in

QUEST: Quality of Expert Systems (QUEST: Kwaliteit van Expertsystemen)

DTIC Science & Technology

1990-11-01

methods have been applied building intelligent systems. However, in the research literature there is much speculation about this subject. TNO report Page 37...Netherlands TNO Physics and Electronics organization for Laboratory applied scientifi. research A A2 5 6 0P.O0 Box 96864 AD-A2 5 620 2509 JG The...rights and obligations of contracting parties are subject to either the ’Standard Conditions for Research date: Instructions given to TNO’or the relevant

Exploring TechQuests Through Open Source and Tools That Inspire Digital Natives

NASA Astrophysics Data System (ADS)

Hayden, K.; Ouyang, Y.; Kilb, D.; Taylor, N.; Krey, B.

2008-12-01

"There is little doubt that K-12 students need to understand and appreciate the Earth on which they live. They can achieve this understanding only if their teachers are well prepared". Dan Barstow, Director of Center for Earth and Space Science Education at TERC. The approach of San Diego County's Cyberinfrastructure Training, Education, Advancement, and Mentoring (SD Cyber-TEAM) project is to build understandings of Earth systems for middle school teachers and students through a collaborative that has engaged the scientific community in the use of cyber-based tools and environments for learning. The SD Cyber-TEAM has used Moodle, an open source management system with social networking tools, that engage digital native students and their teachers in collaboration and sharing of ideas and research related to Earth science. Teachers participate in on-line professional dialog through chat, wikis, blogs, forums, journals and other tools and choose the tools that will best fit their classroom. The use of Moodle during the Summer Cyber Academy developed a cyber-collaboratory environment where teaching strategies were discussed, supported and actualized by participants. These experiences supported digital immigrants (teachers) in adapting teaching strategies using technologies that are most attractive and familiar to students (digital natives). A new study by the National School Boards Association and Grunwald Associates LLC indicated that "the online behaviors of U.S. teens and 'tweens shows that 96 percent of students with online access use social networking technologies, such as chatting, text messaging, blogging, and visiting online communities such as Facebook, MySpace, and Webkinz". While SD Cyber-TEAM teachers are implementing TechQuests in classrooms they use these social networking elements to capture student interest and address the needs of digital natives. Through the Moodle environment, teachers have explored a variety of learning objects called TechQuests

Biology-inspired AMO physics

NASA Astrophysics Data System (ADS)

Mathur, Deepak

2015-01-01

This Topical Review presents an overview of increasingly robust interconnects that are being established between atomic, molecular and optical (AMO) physics and the life sciences. AMO physics, outgrowing its historical role as a facilitator—a provider of optical methodologies, for instance—now seeks to partner biology in its quest to link systems-level descriptions of biological entities to insights based on molecular processes. Of course, perspectives differ when AMO physicists and biologists consider various processes. For instance, while AMO physicists link molecular properties and dynamics to potential energy surfaces, these have to give way to energy landscapes in considerations of protein dynamics. But there are similarities also: tunnelling and non-adiabatic transitions occur both in protein dynamics and in molecular dynamics. We bring to the fore some such differences and similarities; we consider imaging techniques based on AMO concepts, like 4D fluorescence microscopy which allows access to the dynamics of cellular processes, multiphoton microscopy which offers a built-in confocality, and microscopy with femtosecond laser beams to saturate the suppression of fluorescence in spatially controlled fashion so as to circumvent the diffraction limit. Beyond imaging, AMO physics contributes with optical traps that probe the mechanical and dynamical properties of single ‘live’ cells, highlighting differences between healthy and diseased cells. Trap methodologies have also begun to probe the dynamics governing of neural stem cells adhering to each other to form neurospheres and, with squeezed light to probe sub-diffusive motion of yeast cells. Strong field science contributes not only by providing a source of energetic electrons and γ-rays via laser-plasma accelerations schemes, but also via filamentation and supercontinuum generation, enabling mainstream collision physics into play in diverse processes like DNA damage induced by low-energy collisions to

Anion binding in biological systems

NASA Astrophysics Data System (ADS)

Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

2009-11-01

We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

Probing Gravitational Sensitivity in Biological Systems Using Magnetic Body Forces

NASA Technical Reports Server (NTRS)

Guevorkian, Karine; Wurzel, Sam; Mihalusova, Mariana; Valles, Jim

2003-01-01

At Brown University, we are developing the use of magnetic body forces as a means to simulate variable gravity body forces on biological systems. This tool promises new means to probe gravi-sensing and the gravi-response of biological systems. It also has the potential as a technique for screening future systems for space flight experiments.

The QuEST for multi-sensor big data ISR situation understanding

NASA Astrophysics Data System (ADS)

Rogers, Steven; Culbertson, Jared; Oxley, Mark; Clouse, H. Scott; Abayowa, Bernard; Patrick, James; Blasch, Erik; Trumpfheller, John

2016-05-01

The challenges for providing war fighters with the best possible actionable information from diverse sensing modalities using advances in big-data and machine learning are addressed in this paper. We start by presenting intelligence, surveillance, and reconnaissance (ISR) related big-data challenges associated with the Third Offset Strategy. Current approaches to big-data are shown to be limited with respect to reasoning/understanding. We present a discussion of what meaning making and understanding require. We posit that for human-machine collaborative solutions to address the requirements for the strategy a new approach, Qualia Exploitation of Sensor Technology (QuEST), will be required. The requirements for developing a QuEST theory of knowledge are discussed and finally, an engineering approach for achieving situation understanding is presented.

Drell-Yan Angular Distributions at the E906 SeaQuest Experiment

NASA Astrophysics Data System (ADS)

Kleinjan, David

2016-09-01

Measurement of Drell-Yan angular distributions in the Collins-Soper frame provide a unique study of QCD. Previous experimental results showed a violation of the Lam-Tung relation (1 - λ ≠ 2 ν). This violation could be described by a range of non-perturbative effects, including the naive T-odd Boer-Mulders TMD, which describes spin-momentum correlations in the nucleon. Presently, E906/SeaQuest experiment at Fermilab can measure Drell-Yan dimuon pairs produced from a 120 GeV unpolarized proton beam directed on various nuclear targets. The Drell-Yan angular distributions will be measured at higher-x than previous experiments, further disentangling the role the Boer-Mulders TMD and other non-perturbative effects play in the structure of the nucleon. SeaQuest.

Demonstration Bulletin: Aqueous Biological Treatment System (Fixed-Film Biodegradation), Biotrol, Inc

EPA Science Inventory

This patented biological treatment system, called the BioTrol Aqueous Treatment System (BATS)., uses an amended microbial population to achieve biological degradation. The system is considered amended when a specific microorganism is added to the indigenous microbial population ...

Skills for Drug-Free Living Curriculum Guide. Future Quest.

ERIC Educational Resources Information Center

de la Garza, Bridget M.; And Others

The Future Quest curriculum is a functional curriculum to teach drug abuse prevention skills to youth with mild disabilities. The curriculum is a one-semester instructional program of lesson plans that incorporate research-based effective teaching practices and are specifically designed to meet the needs of students with learning and behavior…

Making Learning Fun: Quest Atlantis, A Game Without Guns

ERIC Educational Resources Information Center

Barab, Sasha; Thomas, Michael; Dodge, Tyler; Carteaux, Robert; Tuzun, Hakan

2005-01-01

This article describes the Quest Atlantis (QA) project, a learning and teaching project that employs a multiuser, virtual environment to immerse children, ages 9-12, in educational tasks. QA combines strategies used in commercial gaming environments with lessons from educational research on learning and motivation. It allows users at participating…

Review of stochastic hybrid systems with applications in biological systems modeling and analysis.

PubMed

Li, Xiangfang; Omotere, Oluwaseyi; Qian, Lijun; Dougherty, Edward R

2017-12-01

Stochastic hybrid systems (SHS) have attracted a lot of research interests in recent years. In this paper, we review some of the recent applications of SHS to biological systems modeling and analysis. Due to the nature of molecular interactions, many biological processes can be conveniently described as a mixture of continuous and discrete phenomena employing SHS models. With the advancement of SHS theory, it is expected that insights can be obtained about biological processes such as drug effects on gene regulation. Furthermore, combining with advanced experimental methods, in silico simulations using SHS modeling techniques can be carried out for massive and rapid verification or falsification of biological hypotheses. The hope is to substitute costly and time-consuming in vitro or in vivo experiments or provide guidance for those experiments and generate better hypotheses.

The Co-Evolution of Life & Environment, and the Astrobiological Quest

NASA Astrophysics Data System (ADS)

Cabrol, N. A.

2016-12-01

Physicochemical and environmental conditions determine the range of possible biogeochemistries on planets and moons. Yet, the Earth shows that as soon as life took hold, it modified its environment, from the mineralogy of sediments to the global composition of the atmosphere. In their evolution, life and environment are intertwined and cannot be separated. This coevolution is one of the most fundamental concepts in astrobiology, one that is central to our understanding of what, where, and how to search for life beyond Earth. In that quest, Mars will be the first destination for planetary missions seeking biosignatures. Both Earth and Mars had shared traits during the Archean/Noachian period. However, for Mars, the impact of a different environmental evolution on the development of life and the preservation of biosignatures remains unclear. In addition to an irreversible global climate change, Mars always had greater environmental variability than Earth due to its astronomical characteristics. Biological evolution, if any, would have had to proceed in this distinct context. If parallels can be drawn, the major metabolisms supporting Earth's biogeochemical cycles had evolved early. Understanding the succession of physical and environmental processes and their combination in the first 700 million years of Mars history is, therefore, essential to envision possible metabolisms, adaptation strategies life would have required to survive changes, and the biosignatures that could still be preserved today. Ultimately, the astrobiological significance of exploring Mars is also about teaching us invaluable lessons about the uniqueness of each planetary experiment, regardless of similarities. Beyond the Solar System, this notion can be expanded to the search for earth-like exoplanets, and for what it means to search for life as we know it, simple or complex.

On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.

PubMed

Rao, Rohit T; Scherholz, Megerle L; Hartmanshenn, Clara; Bae, Seul-A; Androulakis, Ioannis P

2017-12-05

The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.

Computational approaches to metabolic engineering utilizing systems biology and synthetic biology.

PubMed

Fong, Stephen S

2014-08-01

Metabolic engineering modifies cellular function to address various biochemical applications. Underlying metabolic engineering efforts are a host of tools and knowledge that are integrated to enable successful outcomes. Concurrent development of computational and experimental tools has enabled different approaches to metabolic engineering. One approach is to leverage knowledge and computational tools to prospectively predict designs to achieve the desired outcome. An alternative approach is to utilize combinatorial experimental tools to empirically explore the range of cellular function and to screen for desired traits. This mini-review focuses on computational systems biology and synthetic biology tools that can be used in combination for prospective in silico strain design.

[Translation and validation of the Quebec User Evaluation of Satisfaction with Assistive Technology (QUEST 2.0) into Portuguese].

PubMed

de Carvalho, Karla Emanuelle Cotias; Gois Júnior, Miburge Bolívar; Sá, Katia Nunes

2014-01-01

To translate and validate the Quebec User Evaluation of Satisfaction with Assistive Technology (QUEST 2.0) into Brazilian Portuguese. Certified translators translated and back-translated Quest. Content validity (CVI) was determined by 5 experts and, after the final version of B-Quest, a pre-test was applied to users of manual wheelchairs, walkers and crutches. The psychometric properties were tested to assure the validity of items and the reliability and stability of the scale. Data were obtained from 121 users of the above-mentioned devices. Our study showed a CVI of 91.66% and a satisfactory factor analysis referent to the two-dimensional structure of the instrument that ensured the representativeness of the items. The Cron-bach's alpha of the items device, service and total score of B-Quest were 0.862, 0.717 and 0.826, respectively. Test-retest stability conducted after a time interval of 2 months was analyzed using Spearman's correlation test, which showed high correlation (ρ >0.6) for most items. The study suggests that the B-Quest is a reliable, representative, and valid instrument to measure the satisfaction of users of assistive technology in Brazil. Copyright © 2014 Elsevier Editora Ltda. All rights reserved.

Engineering biological systems using automated biofoundries.

PubMed

Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin

2017-07-01

Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Radiological/biological/aerosol removal system

DOEpatents

Haslam, Jeffery J

2015-03-17

An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

PubMed

Aretz, Ina; Meierhofer, David

2016-04-27

Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

PubMed Central

Aretz, Ina; Meierhofer, David

2016-01-01

Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology. PMID:27128910

The quest for significance model of radicalization: implications for the management of terrorist detainees.

PubMed

Dugas, Michelle; Kruglanski, Arie W

2014-01-01

Radicalization and its culmination in terrorism represent a grave threat to the security and stability of the world. A related challenge is effective management of extremists who are detained in prison facilities. The major aim of this article is to review the significance quest model of radicalization and its implications for management of terrorist detainees. First, we review the significance quest model, which elaborates on the roles of motivation, ideology, and social processes in radicalization. Secondly, we explore the implications of the model in relation to the risks of prison radicalization. Finally, we analyze the model's implications for deradicalization strategies and review preliminary evidence for the effectiveness of a rehabilitation program targeting components of the significance quest. Based on this evidence, we argue that the psychology of radicalization provides compelling reason for the inclusion of deradicalization efforts as an essential component of the management of terrorist detainees. Copyright © 2014 John Wiley & Sons, Ltd.

Development and application of the RE-AIM QuEST mixed methods framework for program evaluation.

PubMed

Forman, Jane; Heisler, Michele; Damschroder, Laura J; Kaselitz, Elizabeth; Kerr, Eve A

2017-06-01

To increase the likelihood of successful implementation of interventions and promote dissemination across real-world settings, it is essential to evaluate outcomes related to dimensions other than Effectiveness alone. Glasgow and colleagues' RE-AIM framework specifies four additional types of outcomes that are important to decision-makers: Reach, Adoption, Implementation (including cost), and Maintenance. To further strengthen RE-AIM, we propose integrating qualitative assessments in an expanded framework: RE-AIM Qualitative Evaluation for Systematic Translation (RE-AIM QuEST), a mixed methods framework. RE-AIM QuEST guides formative evaluation to identify real-time implementation barriers and explain how implementation context may influence translation to additional settings. RE-AIM QuEST was used to evaluate a pharmacist-led hypertension management intervention at 3 VA facilities in 2008-2009. We systematically reviewed each of the five RE-AIM dimensions and created open-ended companion questions to quantitative measures and identified qualitative and quantitative data sources, measures, and analyses. To illustrate use of the RE-AIM QuEST framework, we provide examples of real-time, coordinated use of quantitative process measures and qualitative methods to identify site-specific issues, and retrospective use of these data sources and analyses to understand variation across sites and explain outcomes. For example, in the Reach dimension, we conducted real-time measurement of enrollment across sites and used qualitative data to better understand and address barriers at a low-enrollment site. The RE-AIM QuEST framework may be a useful tool for improving interventions in real-time, for understanding retrospectively why an intervention did or did not work, and for enhancing its sustainability and translation to other settings.

Network science of biological systems at different scales: A review

NASA Astrophysics Data System (ADS)

Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

2018-03-01

Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

Expedition Two Crew photo in Quest airlock

NASA Image and Video Library

2001-07-20

STS104-E-5188 (20 July 2001) --- The Expedition Two crew poses for an in-flight portrait in the newly- delivered Quest Airlock on the International Space Station (ISS). Flanked by two extravehicular mobility unit (EMU) space suits, are, from left, Susan J. Helms, Yury V. Usachev and James S. Voss. Usachev is commander and Voss and Helms are both flight engineers. This image was recorded by one of the visiting STS-104 crew members using a digital still camera.

WebQuest Learning as Perceived by Higher-Education Learners

ERIC Educational Resources Information Center

Zheng, Robert; Stucky, Bradd; McAlack, Matt; Menchaca, Mike; Stoddart, Sue

2005-01-01

The WebQuest as an inquiry-oriented approach in web learning has gained considerable attention from educators and has been integrated widely into curricula in K-12 and higher education. It is considered to be an effective way to organize chaotic internet resources and help learners gain new knowledge through a guided learning environment.…

Use of WebQuest Design for Inservice Teacher Professional Development

ERIC Educational Resources Information Center

Iskeceli-Tunc, Sinem; Oner, Diler

2016-01-01

This study investigated whether a teacher professional development module built around designing WebQuests could improve teachers' technological and pedagogical skills. The technological skills examined included Web searching and Web evaluating skills. The pedagogical skills targeted were developing a working definition for higher-order thinking…

Systems biology and livestock production.

PubMed

Headon, D

2013-12-01

The mapping of complete sets of genes, transcripts and proteins from many organisms has prompted the development of new '-omic' technologies for collecting and analysing very large amounts of data. Now that the tools to generate and interrogate such complete data sets are widely used, much of the focus of biological research has begun to turn towards understanding systems as a whole, rather than studying their components in isolation. This very broadly defined systems approach is being deployed across a range of problems and scales of organisation, including many aspects of the animal sciences. Here I review selected examples of this systems approach as applied to poultry and livestock production, product quality and welfare.

Back to the biology in systems biology: what can we learn from biomolecular networks?

PubMed

Huang, Sui

2004-02-01

Genome-scale molecular networks, including protein interaction and gene regulatory networks, have taken centre stage in the investigation of the burgeoning disciplines of systems biology and biocomplexity. What do networks tell us? Some see in networks simply the comprehensive, detailed description of all cellular pathways, others seek in networks simple, higher-order qualities that emerge from the collective action of the individual pathways. This paper discusses networks from an encompassing category of thinking that will hopefully help readers to bridge the gap between these polarised viewpoints. Systems biology so far has emphasised the characterisation of large pathway maps. Now one has to ask: where is the actual biology in 'systems biology'? As structures midway between genome and phenome, and by serving as an 'extended genotype' or an 'elementary phenotype', molecular networks open a new window to the study of evolution and gene function in complex living systems. For the study of evolution, features in network topology offer a novel starting point for addressing the old debate on the relative contributions of natural selection versus intrinsic constraints to a particular trait. To study the function of genes, it is necessary not only to see them in the context of gene networks, but also to reach beyond describing network topology and to embrace the global dynamics of networks that will reveal higher-order, collective behaviour of the interacting genes. This will pave the way to understanding how the complexity of genome-wide molecular networks collapses to produce a robust whole-cell behaviour that manifests as tightly-regulated switching between distinct cell fates - the basis for multicellular life.

Macro- and microscale fluid flow systems for endothelial cell biology.

PubMed

Young, Edmond W K; Simmons, Craig A

2010-01-21

Recent advances in microfluidics have brought forth new tools for studying flow-induced effects on mammalian cells, with important applications in cardiovascular, bone and cancer biology. The plethora of microscale systems developed to date demonstrate the flexibility of microfluidic designs, and showcase advantages of the microscale that are simply not available at the macroscale. However, the majority of these systems will likely not achieve widespread use in the biological laboratory due to their complexity and lack of user-friendliness. To gain widespread acceptance in the biological research community, microfluidics engineers must understand the needs of cell biologists, while biologists must be made aware of available technology. This review provides a critical evaluation of cell culture flow (CCF) systems used to study the effects of mechanical forces on endothelial cells (ECs) in vitro. To help understand the need for various designs of CCF systems, we first briefly summarize main properties of ECs and their native environments. Basic principles of various macro- and microscale systems are described and evaluated. New opportunities are uncovered for developing technologies that have potential to both improve efficiency of experimentation as well as answer important biological questions that otherwise cannot be tackled with existing systems. Finally, we discuss some of the unresolved issues related to microfluidic cell culture, suggest possible avenues of investigation that could resolve these issues, and provide an outlook for the future of microfluidics in biological research.

Physical methods for investigating structural colours in biological systems

PubMed Central

Vukusic, P.; Stavenga, D.G.

2009-01-01

Many biological systems are known to use structural colour effects to generate aspects of their appearance and visibility. The study of these phenomena has informed an eclectic group of fields ranging, for example, from evolutionary processes in behavioural biology to micro-optical devices in technologically engineered systems. However, biological photonic systems are invariably structurally and often compositionally more elaborate than most synthetically fabricated photonic systems. For this reason, an appropriate gamut of physical methods and investigative techniques must be applied correctly so that the systems' photonic behaviour may be appropriately understood. Here, we survey a broad range of the most commonly implemented, successfully used and recently innovated physical methods. We discuss the costs and benefits of various spectrometric methods and instruments, namely scatterometers, microspectrophotometers, fibre-optic-connected photodiode array spectrometers and integrating spheres. We then discuss the role of the materials' refractive index and several of the more commonly used theoretical approaches. Finally, we describe the recent developments in the research field of photonic crystals and the implications for the further study of structural coloration in animals. PMID:19158009

EPR spectroscopy of complex biological iron-sulfur systems.

PubMed

Hagen, Wilfred R

2018-02-21

From the very first discovery of biological iron-sulfur clusters with EPR, the spectroscopy has been used to study not only purified proteins but also complex systems such as respiratory complexes, membrane particles and, later, whole cells. In recent times, the emphasis of iron-sulfur biochemistry has moved from characterization of individual proteins to the systems biology of iron-sulfur biosynthesis, regulation, degradation, and implications for human health. Although this move would suggest a blossoming of System-EPR as a specific, non-invasive monitor of Fe/S (dys)homeostasis in whole cells, a review of the literature reveals limited success possibly due to technical difficulties in adherence to EPR spectroscopic and biochemical standards. In an attempt to boost application of System-EPR the required boundary conditions and their practical applications are explicitly and comprehensively formulated.

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

PubMed Central

Villaverde, Alejandro F.; Banga, Julio R.

2014-01-01

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology? PMID:24307566

Reverse engineering and identification in systems biology: strategies, perspectives and challenges.

PubMed

Villaverde, Alejandro F; Banga, Julio R

2014-02-06

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology?

QuEST: Qualifying Environmentally Sustainable Technologies. Volume 6

NASA Technical Reports Server (NTRS)

Lewis, Pattie

2011-01-01

QuEST is a publication of the NASA Technology Evaluation for Environmental Risk Mitigation Principal Center (TEERM). This issue contains brief articles on: Risk Identification and Mitigation, Material Management and Substitution Efforts--Hexavalent Chrome-free Coatings and Low volatile organic compounds (VOCs) Coatings, Lead-Free Electronics, Corn-Based Depainting Media; Alternative Energy Efforts Hydrogen Sensors and Solar Air Conditioning. Other TEERM Efforts include: Energy and Water Management and Remediation Technology Collaboration.

The Quest for Less: Activities and Resources for Teaching K-8

EPA Pesticide Factsheets

The Quest for Less provides hands-on lessons and activities, enrichment ideas, journal writing assignments, and other educational tools related to preventing and reusing waste. This document includes factsheets, activities, and teaching notes for 6-8

The Quest for Strategic Malaysian Quality National Primary School Leaders

ERIC Educational Resources Information Center

Ali, Hairuddin Mohd