Economic value of biological control in integrated pest management of managed plant systems.

Science.gov (United States)

Naranjo, Steven E; Ellsworth, Peter C; Frisvold, George B

2015-01-07

Biological control is an underlying pillar of integrated pest management, yet little focus has been placed on assigning economic value to this key ecosystem service. Setting biological control on a firm economic foundation would help to broaden its utility and adoption for sustainable crop protection. Here we discuss approaches and methods available for valuation of biological control of arthropod pests by arthropod natural enemies and summarize economic evaluations in classical, augmentative, and conservation biological control. Emphasis is placed on valuation of conservation biological control, which has received little attention. We identify some of the challenges of and opportunities for applying economics to biological control to advance integrated pest management. Interaction among diverse scientists and stakeholders will be required to measure the direct and indirect costs and benefits of biological control that will allow farmers and others to internalize the benefits that incentivize and accelerate adoption for private and public good.

Self-Organized Biological Dynamics and Nonlinear Control

Science.gov (United States)

Walleczek, Jan

2006-04-01

The frontiers and challenges of biodynamics research Jan Walleczek; Part I. Nonlinear Dynamics in Biology and Response to Stimuli: 1. External signals and internal oscillation dynamics - principal aspects and response of stimulated rhythmic processes Friedemann Kaiser; 2. Nonlinear dynamics in biochemical and biophysical systems: from enzyme kinetics to epilepsy Raima Larter, Robert Worth and Brent Speelman; 3. Fractal mechanisms in neural control: human heartbeat and gait dynamics in health and disease Chung-Kang Peng, Jeffrey M. Hausdorff and Ary L. Goldberger; 4. Self-organising dynamics in human coordination and perception Mingzhou Ding, Yanqing Chen, J. A. Scott Kelso and Betty Tuller; 5. Signal processing in biochemical reaction networks Adam P. Arkin; Part II. Nonlinear Sensitivity of Biological Systems to Electromagnetic Stimuli: 6. Electrical signal detection and noise in systems with long-range coherence Paul C. Gailey; 7. Oscillatory signals in migrating neutrophils: effects of time-varying chemical and electrical fields Howard R. Petty; 8. Enzyme kinetics and nonlinear biochemical amplification in response to static and oscillating magnetic fields Jan Walleczek and Clemens F. Eichwald; 9. Magnetic field sensitivity in the hippocampus Stefan Engström, Suzanne Bawin and W. Ross Adey; Part III. Stochastic Noise-Induced Dynamics and Transport in Biological Systems: 10. Stochastic resonance: looking forward Frank Moss; 11. Stochastic resonance and small-amplitude signal transduction in voltage-gated ion channels Sergey M. Bezrukov and Igor Vodyanoy; 12. Ratchets, rectifiers and demons: the constructive role of noise in free energy and signal transduction R. Dean Astumian; 13. Cellular transduction of periodic and stochastic energy signals by electroconformational coupling Tian Y. Tsong; Part IV. Nonlinear Control of Biological and Other Excitable Systems: 14. Controlling chaos in dynamical systems Kenneth Showalter; 15. Electromagnetic fields and biological

Control of biological growth in recirculating cooling systems using treated secondary effluent as makeup water with monochloramine.

Science.gov (United States)

Chien, Shih-Hsiang; Chowdhury, Indranil; Hsieh, Ming-Kai; Li, Heng; Dzombak, David A; Vidic, Radisav D

2012-12-01

Secondary-treated municipal wastewater, an abundant and widely distributed impaired water source, is a promising alternative water source for thermoelectric power plant cooling. However, excessive biological growth is a major challenge associated with wastewater reuse in cooling systems as it can interfere with normal system operation as well as enhance corrosion and scaling problems. Furthermore, possible emission of biological aerosols (e.g., Legionella pneumophila) with the cooling tower drift can lead to public health concerns within the zone of aerosol deposition. In this study, the effectiveness of pre-formed and in-situ-formed monochloramine was evaluated for its ability to control biological growth in recirculating cooling systems using secondary-treated municipal wastewater as the only makeup water source. Bench-scale studies were compared with pilot-scale studies for their ability to predict system behavior under realistic process conditions. Effectiveness of the continuous addition of pre-formed monochloramine and monochloramine formed in-situ through the reaction of free chlorine with ammonia in the incoming water was evaluated in terms of biocide residual and its ability to control both planktonic and sessile microbial populations. Results revealed that monochloramine can effectively control biofouling in cooling systems employing secondary-treated municipal wastewater and has advantages relative to use of free chlorine, but that bench-scale studies seriously underestimate biocide dose and residual requirements for proper control of biological growth in full-scale systems. Pre-formed monochloramine offered longer residence time and more reliable performance than in-situ-formed monochloramine due to highly variable ammonia concentration in the recirculating water caused by ammonia stripping in the cooling tower. Pilot-scale tests revealed that much lower dosing rate was required to maintain similar total chlorine residual when pre-formed monochloramine

7th Annual Systems Biology Symposium: Systems Biology and Engineering

Energy Technology Data Exchange (ETDEWEB)

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 are 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."

Reliability of unstable periodic orbit based control strategies in biological systems

Energy Technology Data Exchange (ETDEWEB)

Mishra, Nagender; Singh, Harinder P. [Department of Physics and Astrophysics, University of Delhi, Delhi 110007 (India); Hasse, Maria [Institut für Höchstleistungsrechnen, Universität Stuttgart, D-70569 Stuttgart (Germany); Biswal, B. [Cluster Innovation Center, University of Delhi, Delhi 110007 (India); Sri Venkateswara College, University of Delhi, Delhi 110021 (India)

2015-04-15

Presence of recurrent and statistically significant unstable periodic orbits (UPOs) in time series obtained from biological systems is now routinely used as evidence for low dimensional chaos. Extracting accurate dynamical information from the detected UPO trajectories is vital for successful control strategies that either aim to stabilize the system near the fixed point or steer the system away from the periodic orbits. A hybrid UPO detection method from return maps that combines topological recurrence criterion, matrix fit algorithm, and stringent criterion for fixed point location gives accurate and statistically significant UPOs even in the presence of significant noise. Geometry of the return map, frequency of UPOs visiting the same trajectory, length of the data set, strength of the noise, and degree of nonstationarity affect the efficacy of the proposed method. Results suggest that establishing determinism from unambiguous UPO detection is often possible in short data sets with significant noise, but derived dynamical properties are rarely accurate and adequate for controlling the dynamics around these UPOs. A repeat chaos control experiment on epileptic hippocampal slices through more stringent control strategy and adaptive UPO tracking is reinterpreted in this context through simulation of similar control experiments on an analogous but stochastic computer model of epileptic brain slices. Reproduction of equivalent results suggests that far more stringent criteria are needed for linking apparent success of control in such experiments with possible determinism in the underlying dynamics.

Reliability of unstable periodic orbit based control strategies in biological systems

International Nuclear Information System (INIS)

Mishra, Nagender; Singh, Harinder P.; Hasse, Maria; Biswal, B.

2015-01-01

Presence of recurrent and statistically significant unstable periodic orbits (UPOs) in time series obtained from biological systems is now routinely used as evidence for low dimensional chaos. Extracting accurate dynamical information from the detected UPO trajectories is vital for successful control strategies that either aim to stabilize the system near the fixed point or steer the system away from the periodic orbits. A hybrid UPO detection method from return maps that combines topological recurrence criterion, matrix fit algorithm, and stringent criterion for fixed point location gives accurate and statistically significant UPOs even in the presence of significant noise. Geometry of the return map, frequency of UPOs visiting the same trajectory, length of the data set, strength of the noise, and degree of nonstationarity affect the efficacy of the proposed method. Results suggest that establishing determinism from unambiguous UPO detection is often possible in short data sets with significant noise, but derived dynamical properties are rarely accurate and adequate for controlling the dynamics around these UPOs. A repeat chaos control experiment on epileptic hippocampal slices through more stringent control strategy and adaptive UPO tracking is reinterpreted in this context through simulation of similar control experiments on an analogous but stochastic computer model of epileptic brain slices. Reproduction of equivalent results suggests that far more stringent criteria are needed for linking apparent success of control in such experiments with possible determinism in the underlying dynamics

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

NARCIS (Netherlands)

He, F.; Murabito, E.; Westerhoff, H.V.

2016-01-01

Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental

Mammalian Synthetic Biology: Engineering Biological Systems.

Science.gov (United States)

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.

Compact Electro-Permeabilization System for Controlled Treatment of Biological Cells and Cell Medium Conductivity Change Measurement

Directory of Open Access Journals (Sweden)

Novickij Vitalij

2014-10-01

Full Text Available Subjection of biological cells to high intensity pulsed electric field results in the permeabilization of the cell membrane. Measurement of the electrical conductivity change allows an analysis of the dynamics of the process, determination of the permeabilization thresholds, and ion efflux influence. In this work a compact electro-permeabilization system for controlled treatment of biological cells is presented. The system is capable of delivering 5 μs - 5 ms repetitive square wave electric field pulses with amplitude up to 1 kV. Evaluation of the cell medium conductivity change is implemented in the setup, allowing indirect measurement of the ion concentration changes occurring due to the cell membrane permeabilization. The simulation model using SPICE and the experimental data of the proposed system are presented in this work. Experimental data with biological cells is also overviewed

Control Structure Design of an Innovative Enhanced Biological Nutrient Recovery Activated Sludge System Coupled with a Photobioreactor

DEFF Research Database (Denmark)

Valverde Perez, Borja; Fuentes-Martínez, José Manuel; Flores Alsina, Xavier

2015-01-01

The TRENS system is a train of biological units designed for resource recovery from wastewater. It is a sequence of a modified enhanced biological phosphorus removal and recovery system (EBP2R) coupled with a photobioreactor (PBR). The bacteria-based system constructs an optimal culture media...... for the downstream algae cultivation. In this work, we present a control strategy to ensure an optimal nutrient balance to feed to the PBR, so the grown algal suspension is suitable for fertigation (irrigation and fertilization of agricultural crops). The system is able to recover up to 75% of the influent load......, while keeping an optimal N-to-P ratio of 16 in the influent to the PBR. The system is tested under different scenarios, where the influent quality is disturbed following a step change. The control system is able to reject most of the disturbances. However, when the P-recovery is limited by the bacteria...

Biologically-Inspired Control Architecture for Musical Performance Robots

Directory of Open Access Journals (Sweden)

Jorge Solis

2014-10-01

Full Text Available At Waseda University, since 1990, the authors have been developing anthropomorphic musical performance robots as a means for understanding human control, introducing novel ways of interaction between musical partners and robots, and proposing applications for humanoid robots. In this paper, the design of a biologically-inspired control architecture for both an anthropomorphic flutist robot and a saxophone playing robot are described. As for the flutist robot, the authors have focused on implementing an auditory feedback system to improve the calibration procedure for the robot in order to play all the notes correctly during a performance. In particular, the proposed auditory feedback system is composed of three main modules: an Expressive Music Generator, a Feed Forward Air Pressure Control System and a Pitch Evaluation System. As for the saxophone-playing robot, a pressure-pitch controller (based on the feedback error learning to improve the sound produced by the robot during a musical performance was proposed and implemented. In both cases studied, a set of experiments are described to verify the improvements achieved while considering biologically-inspired control approaches.

Compatible biological and chemical control systems for Rhizoctonia solani in potato

NARCIS (Netherlands)

Boogert, van den P.H.J.F.; Luttikholt, A.J.G.

2004-01-01

A series of chemical and biological control agents were tested for compatibility with the Rhizoctonia-specific biocontrol fungus Verticillium biguttatum aimed at designing novel control strategies for black scurf (Rhizoctonia solani) and other tuber diseases in potato. The efficacy of chemicals,

Potential for widespread application of biological control of stored-product pests

DEFF Research Database (Denmark)

Hansen, Lise Stengaard

2007-01-01

Biological control of stored product pests has substantial potential in Europe". This is essentially the conclusion of the activities of a European working group funded by the COST system, an intergovernmental networking system. Working group 4 of COST action 842 (2000-2005) focussed on biologica...... for these situations will contribute to ensuring that stored food products are protected from insect and mite pests using techniques that are safe for consumers, workers and the environment.......Biological control of stored product pests has substantial potential in Europe". This is essentially the conclusion of the activities of a European working group funded by the COST system, an intergovernmental networking system. Working group 4 of COST action 842 (2000-2005) focussed on biological...

The role of bacillus-based biological control agents in integrated pest management systems: plant diseases.

Science.gov (United States)

Jacobsen, B J; Zidack, N K; Larson, B J

2004-11-01

ABSTRACT Bacillus-based biological control agents (BCAs) have great potential in integrated pest management (IPM) systems; however, relatively little work has been published on integration with other IPM management tools. Unfortunately, most research has focused on BCAs as alternatives to synthetic chemical fungicides or bactericides and not as part of an integrated management system. IPM has had many definitions and this review will use the national coalition for IPM definition: "A sustainable approach to managing pests by combining biological, cultural, physical and chemical tools in a way that minimizes economic, health and environmental risks." This review will examine the integrated use of Bacillus-based BCAs with disease management tools, including resistant cultivars, fungicides or bactericides, or other BCAs. This integration is important because the consistency and degree of disease control by Bacillus-based BCAs is rarely equal to the control afforded by the best fungicides or bactericides. In theory, integration of several tools brings stability to disease management programs. Integration of BCAs with other disease management tools often provides broader crop adaptation and both more efficacious and consistent levels of disease control. This review will also discuss the use of Bacillus-based BCAs in fungicide resistance management. Work with Bacillus thuringiensis and insect pest management is the exception to the relative paucity of reports but will not be the focus of this review.

Mapping biological systems to network systems

CERN Document Server

Rathore, Heena

2016-01-01

The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

Transcription control engineering and applications in synthetic biology

Directory of Open Access Journals (Sweden)

Michael D. Engstrom

2017-09-01

Full Text Available In synthetic biology, researchers assemble biological components in new ways to produce systems with practical applications. One of these practical applications is control of the flow of genetic information (from nucleic acid to protein, a.k.a. gene regulation. Regulation is critical for optimizing protein (and therefore activity levels and the subsequent levels of metabolites and other cellular properties. The central dogma of molecular biology posits that information flow commences with transcription, and accordingly, regulatory tools targeting transcription have received the most attention in synthetic biology. In this mini-review, we highlight many past successes and summarize the lessons learned in developing tools for controlling transcription. In particular, we focus on engineering studies where promoters and transcription terminators (cis-factors were directly engineered and/or isolated from DNA libraries. We also review several well-characterized transcription regulators (trans-factors, giving examples of how cis- and trans-acting factors have been combined to create digital and analogue switches for regulating transcription in response to various signals. Last, we provide examples of how engineered transcription control systems have been used in metabolic engineering and more complicated genetic circuits. While most of our mini-review focuses on the well-characterized bacterium Escherichia coli, we also provide several examples of the use of transcription control engineering in non-model organisms. Similar approaches have been applied outside the bacterial kingdom indicating that the lessons learned from bacterial studies may be generalized for other organisms.

Transcription control engineering and applications in synthetic biology.

Science.gov (United States)

Engstrom, Michael D; Pfleger, Brian F

2017-09-01

In synthetic biology, researchers assemble biological components in new ways to produce systems with practical applications. One of these practical applications is control of the flow of genetic information (from nucleic acid to protein), a.k.a. gene regulation. Regulation is critical for optimizing protein (and therefore activity) levels and the subsequent levels of metabolites and other cellular properties. The central dogma of molecular biology posits that information flow commences with transcription, and accordingly, regulatory tools targeting transcription have received the most attention in synthetic biology. In this mini-review, we highlight many past successes and summarize the lessons learned in developing tools for controlling transcription. In particular, we focus on engineering studies where promoters and transcription terminators ( cis -factors) were directly engineered and/or isolated from DNA libraries. We also review several well-characterized transcription regulators ( trans- factors), giving examples of how cis- and trans -acting factors have been combined to create digital and analogue switches for regulating transcription in response to various signals. Last, we provide examples of how engineered transcription control systems have been used in metabolic engineering and more complicated genetic circuits. While most of our mini-review focuses on the well-characterized bacterium Escherichia coli , we also provide several examples of the use of transcription control engineering in non-model organisms. Similar approaches have been applied outside the bacterial kingdom indicating that the lessons learned from bacterial studies may be generalized for other organisms.

Augmentative biological control of arthropods in Latin America

NARCIS (Netherlands)

Lenteren, van J.C.; Bueno, V.H.P.

2003-01-01

Augmentative forms of biological control, where natural enemies are periodically introduced, are applied over large areas in various cropping systems in Latin America. About 25% of the world area under augmentative control is situated in this region. Well-known examples are the use of species of the

Computational Systems Chemical Biology

OpenAIRE

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 (Oprea et al., 2007).

Biological control in agro-systems by means of the handling of entomophagous insects

International Nuclear Information System (INIS)

Nicholls, Clara Ines; Altieri, Miguel A

1998-01-01

From several decades ago the importance of natural enemies of the noxious organisms has been recognized. Unfortunately the introduction of the biological control has not had the desired dimension. The indiscriminate use of biocides products has altered the biodiversity of the agro-ecosystem. The parasitoids and predators have suffered the noxious effects of the plaguicides. These natural enemies of the plagues play a momentous paper in the regulation of noxious insects population. The predators of the insecta class register in diverse orders and the abundance of species is impressive. But the knowledge of their importance is only partial. In many countries the kindness of these organisms has not been specified and does not protect them. In the case of parasitoids something similar occurs. It is say that their biotic diversity is incalculable but very few species are exploited. In these two groups rest the classic biological control projects. The successes in projects of biological control are recognized and they are enlarging in several countries but more impulse is required. Due to demands of a sustainable agricultural production it should support the biological control of plagues. In this document general looks on the topic are expounded

Systems Biology of the Fluxome

Directory of Open Access Journals (Sweden)

Miguel A. Aon

2015-07-01

Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

Biological effect of penetration controlled irradiation with ion beams

Energy Technology Data Exchange (ETDEWEB)

Tanaka, Atsushi; Shimizu, Takashi; Kikuchi, Masahiro; Kobayashi, Yasuhiko; Watanabe, Hiroshi [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment; Yamashita, Takao

1997-03-01

To investigate the effect of local irradiation with ion beams on biological systems, technique for penetration controlled irradiation has been established. The range in a target was controlled by changing the distance from beam window in the atmosphere, and could be controlled linearly up to about 31 {mu}m in biological material. In addition, the effects of the penetration controlled irradiations with 1.5 MeV/u C and He ions were examined using tobacco pollen. The increased frequency of leaky pollen produced by ion beams suggests that the efficient pollen envelope damages would be induced at the range-end of ion beams. (author)

From systems biology to systems biomedicine.

Science.gov (United States)

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 and Health Systems Complexity in;

NARCIS (Netherlands)

Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

2016-01-01

Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

Review of Pasteuria penetrans: Biology, Ecology, and Biological Control Potential.

Science.gov (United States)

Chen, Z X; Dickson, D W

1998-09-01

Pasteuria penetrans is a mycelial, endospore-forming, bacterial parasite that has shown great potential as a biological control agent of root-knot nematodes. Considerable progress has been made during the last 10 years in understanding its biology and importance as an agent capable of effectively suppressing root-knot nematodes in field soil. The objective of this review is to summarize the current knowledge of the biology, ecology, and biological control potential of P. penetrans and other Pasteuria members. Pasteuria spp. are distributed worldwide and have been reported from 323 nematode species belonging to 116 genera of free-living, predatory, plant-parasitic, and entomopathogenic nematodes. Artificial cultivation of P. penetrans has met with limited success; large-scale production of endospores depends on in vivo cultivation. Temperature affects endospore attachment, germination, pathogenesis, and completion of the life cycle in the nematode pseudocoelom. The biological control potential of Pasteuria spp. have been demonstrated on 20 crops; host nematodes include Belonolaimus longicaudatus, Heterodera spp., Meloidogyne spp., and Xiphinema diversicaudatum. Pasteuria penetrans plays an important role in some suppressive soils. The efficacy of the bacterium as a biological control agent has been examined. Approximately 100,000 endospores/g of soil provided immediate control of the peanut root-knot nematode, whereas 1,000 and 5,000 endospores/g of soil each amplified in the host nematode and became suppressive after 3 years.

Asymmetric positive feedback loops reliably control biological responses.

Science.gov (United States)

Ratushny, Alexander V; Saleem, Ramsey A; Sitko, Katherine; Ramsey, Stephen A; Aitchison, John D

2012-04-24

Positive feedback is a common mechanism enabling biological systems to respond to stimuli in a switch-like manner. Such systems are often characterized by the requisite formation of a heterodimer where only one of the pair is subject to feedback. This ASymmetric Self-UpREgulation (ASSURE) motif is central to many biological systems, including cholesterol homeostasis (LXRα/RXRα), adipocyte differentiation (PPARγ/RXRα), development and differentiation (RAR/RXR), myogenesis (MyoD/E12) and cellular antiviral defense (IRF3/IRF7). To understand why this motif is so prevalent, we examined its properties in an evolutionarily conserved transcriptional regulatory network in yeast (Oaf1p/Pip2p). We demonstrate that the asymmetry in positive feedback confers a competitive advantage and allows the system to robustly increase its responsiveness while precisely tuning the response to a consistent level in the presence of varying stimuli. This study reveals evolutionary advantages for the ASSURE motif, and mechanisms for control, that are relevant to pharmacologic intervention and synthetic biology applications.

Systems Biology-an interdisciplinary approach.

Science.gov (United States)

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.

Biological control and sustainable food production

NARCIS (Netherlands)

Bale, J.S.; Lenteren, van J.C.; Bigler, F.

2008-01-01

The use of biological control for the management of pest insects pre-dates the modern pesticide era. The first major successes in biological control occurred with exotic pests controlled by natural enemy species collected from the country or area of origin of the pest (classical control).

Systems Biology — the Broader Perspective

Directory of Open Access Journals (Sweden)

Jonathan Bard

2013-06-01

Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

Exotic biological control agents

NARCIS (Netherlands)

Hajek, Ann E.; Hurley, Brett P.; Kenis, Marc; Garnas, Jeffrey R.; Bush, Samantha J.; Wingfield, Michael J.; Lenteren, van Joop C.; Cock, Matthew J.W.

2016-01-01

Biological control is a valuable and effective strategy for controlling arthropod pests and has been used extensively against invasive arthropods. As one approach for control of invasives, exotic natural enemies from the native range of a pest are introduced to areas where control is needed.

Biological Control in Brazil: an overview

OpenAIRE

Parra,José Roberto Postali

2014-01-01

The use of Biological Control methods is on the increase, mainly as a result of the mobilization of human resources in entomology studies since the establishment of graduate programs in this country in the 1960s. This review approaches the retrospective of Biological Control in Brazil in recent decades, with an emphasis on the "culture of applying agrochemicals" adopted by Brazilian growers, which constrains progress in this area. Successful cases of Biological Control have been reported on i...

Biological conversion system

Science.gov (United States)

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.

Development trend of radiation biology research-systems radiation biology

International Nuclear Information System (INIS)

Min Rui

2010-01-01

Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

Biologically inspired control of humanoid robot arms robust and adaptive approaches

CERN Document Server

Spiers, Adam; Herrmann, Guido

2016-01-01

This book investigates a biologically inspired method of robot arm control, developed with the objective of synthesising human-like motion dynamically, using nonlinear, robust and adaptive control techniques in practical robot systems. The control method caters to a rising interest in humanoid robots and the need for appropriate control schemes to match these systems. Unlike the classic kinematic schemes used in industrial manipulators, the dynamic approaches proposed here promote human-like motion with better exploitation of the robot’s physical structure. This also benefits human-robot interaction. The control schemes proposed in this book are inspired by a wealth of human-motion literature that indicates the drivers of motion to be dynamic, model-based and optimal. Such considerations lend themselves nicely to achievement via nonlinear control techniques without the necessity for extensive and complex biological models. The operational-space method of robot control forms the basis of many of the techniqu...

Use of nuclear techniques in biological control

International Nuclear Information System (INIS)

Greany, Patrick D.; Carpenter, James E.

2000-01-01

As pointed out by Benbrook (1996), pest management is at a crossroads, and there is a great need for new, biointensive pest management strategies. Among these approaches, biological control is a keystone. However, because of increasing concerns about the introduction of exotic natural enemies of insect pests and weeds (Howarth 1991, Delfosse 1997), the overall thrust of biological control has moved toward augmentative biological control, involving releases of established natural enemy species (Knipling 1992). This in turn has created a need to develop more cost-effective mass rearing technologies for beneficial insects. Nuclear techniques could play an especially important role in augmentative biological control, not only in facilitating mass rearing, but in several other ways, as indicated below. Recognising the potential value for use of nuclear techniques in biological control, the Insect and Pest Control Section of the Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, sponsored a Consultants' Group Meeting on this subject in April 1997. The Group produced a document entitled Use of Nuclear Techniques in Biological Control: Managing Pests, Facilitating Trade and Protecting the Environment. The consultants included the authors of this paper as well as Ernest Delfosse (at that time, with the USDA-APHIS National Biological Control Institute), Garry Hill (Intl. Institute for Biological Control), Sinthya Penn (Beneficial Insectary), and Felipe Jeronimo (USDA-APHIS PPQ, Guatemala). The remarks presented in this paper reflect the thoughts presented by these consultants and other participants at the IAEA-sponsored meeting. Several potential uses for nuclear techniques were identified by the Consultants' Group, including: 1) improvements in rearing media (either artificial diets or natural hosts/prey), 2) provision of sterilised natural prey to be used as food during shipment, to ameliorate concerns relating to the

Systems biology: the reincarnation of systems theory applied in biology?

Science.gov (United States)

Wolkenhauer, O

2001-09-01

With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.

Neural systems for preparatory control of imitation.

Science.gov (United States)

Cross, Katy A; Iacoboni, Marco

2014-01-01

Humans have an automatic tendency to imitate others. Previous studies on how we control these tendencies have focused on reactive mechanisms, where inhibition of imitation is implemented after seeing an action. This work suggests that reactive control of imitation draws on at least partially specialized mechanisms. Here, we examine preparatory imitation control, where advance information allows control processes to be employed before an action is observed. Drawing on dual route models from the spatial compatibility literature, we compare control processes using biological and non-biological stimuli to determine whether preparatory imitation control recruits specialized neural systems that are similar to those observed in reactive imitation control. Results indicate that preparatory control involves anterior prefrontal, dorsolateral prefrontal, posterior parietal and early visual cortices regardless of whether automatic responses are evoked by biological (imitative) or non-biological stimuli. These results indicate both that preparatory control of imitation uses general mechanisms, and that preparatory control of imitation draws on different neural systems from reactive imitation control. Based on the regions involved, we hypothesize that preparatory control is implemented through top-down attentional biasing of visual processing.

Applications of dynamical systems in biology and medicine

CERN Document Server

Radunskaya, Ami

2015-01-01

This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control.  Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction.  Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation. .

Fostering synergy between cell biology and systems biology.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Epigenetics and Why Biological Networks are More Controllable than Expected

Science.gov (United States)

Motter, Adilson

2013-03-01

A fundamental property of networks is that perturbations to one node can affect other nodes, potentially causing the entire system to change behavior or fail. In this talk, I will show that it is possible to exploit this same principle to control network behavior. This approach takes advantage of the nonlinear dynamics inherent to real networks, and allows bringing the system to a desired target state even when this state is not directly accessible or the linear counterpart is not controllable. Applications show that this framework permits both reprogramming a network to a desired task as well as rescuing networks from the brink of failure, which I will illustrate through various biological problems. I will also briefly review the progress our group has made over the past 5 years on related control of complex networks in non-biological domains.

Design of fluidized-bed, biological denitrification systems

International Nuclear Information System (INIS)

Patton, B.D.; Hancher, C.W.; Pitt, W.W.; Walker, J.F.

1982-01-01

Many commercial processes yield nitrate-containing wastewaters that are being discharged to the environment because traditional recovery or disposal methods are economically unacceptable. The anticipated discharge limits (i.e., 10 to 20 g (NO 3 - )/m 3 ) being considered by many states will not allow continued release of these wastewaters. The new discharge standards can be met economically by use of the fluidizied-bed, biological denitrification process. Research and development studies were conducted with 0.05-, 0.10-, 0.20-, and 0.50-m-diam fluidized-bed bioreactor systems. Feed nitrate concentrations were in the 0 to 10,000 g (NO 3 - )/m 3 range. Using the data from these studies, rate expressions were developed for the destruction of nitrate as a function of nitrate concentration. Methods were also developed for sizing bioreactors and biomass control systems. The sizing methods for fluidized-bed denitrification systems are described, and support systems such as sampling and analysis, instrumentation and controls, utilities, and bacteria storage are discussed. Operation of the process is also briefly discussed to aid the designer. Using the methods presented in this report, fluidized-bed, biological denitrification systems can be designed to treat nitrate wastewater streams

Conserving and enhancing biological control of nematodes.

Science.gov (United States)

Timper, Patricia

2014-06-01

Conservation biological control is the modification of the environment or existing practices to protect and enhance antagonistic organisms to reduce damage from pests. This approach to biological control has received insufficient attention compared with inundative applications of microbial antagonists to control nematodes. This review provides examples of how production practices can enhance or diminish biological control of plant-parasitic nematodes and other soilborne pests. Antagonists of nematodes can be enhanced by providing supplementary food sources such as occurs when organic amendments are applied to soil. However, some organic amendments (e.g., manures and plants containing allelopathic compounds) can also be detrimental to nematode antagonists. Plant species and genotype can strongly influence the outcome of biological control. For instance, the susceptibility of the plant to the nematode can determine the effectiveness of control; good hosts will require greater levels of suppression than poor hosts. Plant genotype can also influence the degree of rhizosphere colonization and antibiotic production by antagonists, as well the expression of induced resistance by plants. Production practices such as crop rotation, fallow periods, tillage, and pesticide applications can directly disrupt populations of antagonistic organisms. These practices can also indirectly affect antagonists by reducing their primary nematode host. One of the challenges of conservation biological control is that practices intended to protect or enhance suppression of nematodes may not be effective in all field sites because they are dependent on indigenous antagonists. Ultimately, indicators will need to be identified, such as the presence of particular antagonists, which can guide decisions on where it is practical to use conservation biological control. Antagonists can also be applied to field sites in conjunction with conservation practices to improve the consistency, efficacy, and

Fabrication, Characterization, and Biological Activity of Avermectin Nano-delivery Systems with Different Particle Sizes

Science.gov (United States)

Wang, Anqi; Wang, Yan; Sun, Changjiao; Wang, Chunxin; Cui, Bo; Zhao, Xiang; Zeng, Zhanghua; Yao, Junwei; Yang, Dongsheng; Liu, Guoqiang; Cui, Haixin

2018-01-01

Nano-delivery systems for the active ingredients of pesticides can improve the utilization rates of pesticides and prolong their control effects. This is due to the nanocarrier envelope and controlled release function. However, particles containing active ingredients in controlled release pesticide formulations are generally large and have wide size distributions. There have been limited studies about the effect of particle size on the controlled release properties and biological activities of pesticide delivery systems. In the current study, avermectin (Av) nano-delivery systems were constructed with different particle sizes and their performances were evaluated. The Av release rate in the nano-delivery system could be effectively controlled by changing the particle size. The biological activity increased with decreasing particle size. These results suggest that Av nano-delivery systems can significantly improve the controllable release, photostability, and biological activity, which will improve efficiency and reduce pesticide residues.

A biologically inspired meta-control navigation system for the Psikharpax rat robot

International Nuclear Information System (INIS)

Caluwaerts, K; Staffa, M; N’Guyen, S; Grand, C; Dollé, L; Favre-Félix, A; Girard, B; Khamassi, M

2012-01-01

A biologically inspired navigation system for the mobile rat-like robot named Psikharpax is presented, allowing for self-localization and autonomous navigation in an initially unknown environment. The ability of parts of the model (e.g. the strategy selection mechanism) to reproduce rat behavioral data in various maze tasks has been validated before in simulations. But the capacity of the model to work on a real robot platform had not been tested. This paper presents our work on the implementation on the Psikharpax robot of two independent navigation strategies (a place-based planning strategy and a cue-guided taxon strategy) and a strategy selection meta-controller. We show how our robot can memorize which was the optimal strategy in each situation, by means of a reinforcement learning algorithm. Moreover, a context detector enables the controller to quickly adapt to changes in the environment—recognized as new contexts—and to restore previously acquired strategy preferences when a previously experienced context is recognized. This produces adaptivity closer to rat behavioral performance and constitutes a computational proposition of the role of the rat prefrontal cortex in strategy shifting. Moreover, such a brain-inspired meta-controller may provide an advancement for learning architectures in robotics. (paper)

Biological Control of Plant Disease Caused by Bacteria

Directory of Open Access Journals (Sweden)

Triwidodo Arwiyanto

2014-07-01

Full Text Available Bacterial diseases in plants are difficult to control. The emphasis is on preventing the spread of the bacteria rather than curing the diseased plant. Integrated management measures for bacterial plant pathogens should be applied for successfull control. Biological control is one of the control measures viz. through the use of microorganisms to suppress the growth and development of bacterial plant pathogen and ultimately reduce the possibility of disease onset. The study of biological control of bacterial plant pathogen was just began compared with of fungal plant pathogen. The ecological nature of diverse bacterial plant pathogens has led scientists to apply different approach in the investigation of its biological control. The complex process of entrance to its host plant for certain soil-borne bacterial plant pathogens need special techniques and combination of more than one biological control agent. Problem and progress in controlling bacterial plant pathogens biologically will be discussed in more detail in the paper and some commercial products of biological control agents (biopesticides will be introduced.     Penyakit tumbuhan karena bakteri sulit dikendalikan. Penekanan pengendalian adalah pada pencegahan penyebaran bakteri patogen dan bukan pada penyembuhan tanaman yang sudah sakit. Untuk suksesnya pengendalian bakteri patogen tumbuhan diperlukan cara pengelolaan yang terpadu. Pengendalian secara biologi merupakan salah satu cara pengendalian dengan menggunakan mikroorganisme untuk menekan pertumbuhan dan perkembangan bakteri patogen tumbuhan dengan tujuan akhir menurunkan kemungkinan timbulnya penyakit. Sifat ekologi bakteri patogen tumbuhan yang berbeda-beda mengharuskan pendekatan yang berbeda pula dalam pengendaliannya secara biologi. Masalah dan perkembangan dalam pengendalian bakteri patogen tumbuhan secara biologi didiskusikan secara detail dalam makalah ini.

Biologically controlled minerals as potential indicators of life

Science.gov (United States)

Schwartz, D. E.; Mancinelli, R. L.; Kaneshiro, E.

1991-01-01

Minerals can be produced and deposited either by abiotic or biologic means. Regardless of their origin, mineral crystals reflect the environment conditions (e.g., temperature, pressure, chemical composition, and redox potential) present during crystal formation. Biologically-produced mineral crystals are grown or reworked under the control of their host organism and reflect an environment different from the abiotic environment. In addition, minerals of either biologic or abiotic origin have great longevities. For these reasons, biologically produced minerals have been proposed as biomarkers. Biomarkers are key morphological, chemical, and isotopic signatures of living systems that can be used to determine if life processes have occurred. Studies of biologically controlled minerals produced by the protist, Paramecium tetraurelia, were initiated since techniques have already been developed to culture them and isolate their crystalline material, and methods are already in place to analyze this material. Two direct crystalline phases were identified. One phase, whose chemical composition is high in Mg, was identified as struvite. The second phase, whose chemical composition is high in Ca, has not been previously found occurring naturally and may be considered a newly discovered material. Analyses are underway to determine the characteristics of these minerals in order to compare them with characteristics of these minerals in order to compare them with characteristics of minerals formed abiotically, but with the same chemical composition.

Micro-separation toward systems biology.

Science.gov (United States)

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.

BIOLOGICAL CONTROL OF WEEDS BY MEANS OF PLANT PATHOGENS

OpenAIRE

Marija Ravlić; Renata Baličević

2014-01-01

Biological control is the use of live beneficial organisms and products of their metabolism in the pests control. Plant pathogens can be used for weed control in three different ways: as classical, conservation and augmentative (inoculative and inundated) biological control. Inundated biological control involves the use of bioherbicides (mycoherbicides) or artificial breeding of pathogens and application in specific stages of crops and weeds. Biological control of weeds can be used where chem...

Nutritional Systems Biology

DEFF Research Database (Denmark)

Jensen, Kasper

and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

Informing biological design by integration of systems and synthetic biology.

Science.gov (United States)

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.

Biological control of toxic cyanobacteria

CSIR Research Space (South Africa)

Ndlela, L

2016-04-01

Full Text Available harmful algal blooms and their impacts in over 30 countries. Biological control is a method of introducing natural enemies to control an organism and has been more successful using microorganisms....

Approaches to Quality Risk Management When Using Single-Use Systems in the Manufacture of Biologics.

Science.gov (United States)

Ishii-Watabe, Akiko; Hirose, Akihiko; Katori, Noriko; Hashii, Norikata; Arai, Susumu; Awatsu, Hirotoshi; Eiza, Akira; Hara, Yoshiaki; Hattori, Hideshi; Inoue, Tomomi; Isono, Tetsuya; Iwakura, Masahiro; Kajihara, Daisuke; Kasahara, Nobuo; Matsuda, Hiroyuki; Murakami, Sei; Nakagawa, Taishiro; Okumura, Takehiro; Omasa, Takeshi; Takuma, Shinya; Terashima, Iyo; Tsukahara, Masayoshi; Tsutsui, Maiko; Yano, Takahiro; Kawasaki, Nana

2015-10-01

Biologics manufacturing technology has made great progress in the last decade. One of the most promising new technologies is the single-use system, which has improved the efficiency of biologics manufacturing processes. To ensure safety of biologics when employing such single-use systems in the manufacturing process, various issues need to be considered including possible extractables/leachables and particles arising from the components used in single-use systems. Japanese pharmaceutical manufacturers, together with single-use suppliers, members of the academia and regulatory authorities have discussed the risks of using single-use systems and established control strategies for the quality assurance of biologics. In this study, we describe approaches for quality risk management when employing single-use systems in the manufacturing of biologics. We consider the potential impact of impurities related to single-use components on drug safety and the potential impact of the single-use system on other critical quality attributes as well as the stable supply of biologics. We also suggest a risk-mitigating strategy combining multiple control methods which includes the selection of appropriate single-use components, their inspections upon receipt and before releasing for use and qualification of single-use systems. Communication between suppliers of single-use systems and the users, as well as change controls in the facilities both of suppliers and users, are also important in risk-mitigating strategies. Implementing these control strategies can mitigate the risks attributed to the use of single-use systems. This study will be useful in promoting the development of biologics as well as in ensuring their safety, quality and stable supply.

Echinococcus as a model system: biology and epidemiology.

Science.gov (United States)

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.

Insecticides and Biological Control

Science.gov (United States)

Furness, G. O.

1972-01-01

Use of insecticides has been questioned due to their harmful effects on edible items. Biological control of insects along with other effective practices for checking spread of parasites on crops are discussed. (PS)

Excited states in biological systems

International Nuclear Information System (INIS)

Cilento, G.; Zinner, K.; Bechara, E.J.H.; Duran, N.; Baptista, R.C. de; Shimizu, Y.; Augusto, O.; Faljoni-Alario, A.; Vidigal, C.C.C.; Oliveira, O.M.M.F.; Haun, M.

1979-01-01

Some aspects of bioluminescence related to bioenergetics are discussed: 1. chemical generation of excited species, by means of two general processes: electron transference and cyclic - and linear peroxide cleavage; 2. biological systems capable of generating excited states and 3. biological functions of these states, specially the non-emissive ones (tripletes). The production and the role of non-emissive excited states in biological systems are analysed, the main purpose of the study being the search for non-emissive states. Experiences carried out in biological systems are described; results and conclusions are given. (M.A.) [pt

Biological Control Strategies for Mosquito Vectors of Arboviruses.

Science.gov (United States)

Huang, Yan-Jang S; Higgs, Stephen; Vanlandingham, Dana L

2017-02-10

Historically, biological control utilizes predatory species and pathogenic microorganisms to reduce the population of mosquitoes as disease vectors. This is particularly important for the control of mosquito-borne arboviruses, which normally do not have specific antiviral therapies available. Although development of resistance is likely, the advantages of biological control are that the resources used are typically biodegradable and ecologically friendly. Over the past decade, the advancement of molecular biology has enabled optimization by the manipulation of genetic materials associated with biological control agents. Two significant advancements are the discovery of cytoplasmic incompatibility induced by Wolbachia bacteria, which has enhanced replacement programs, and the introduction of dominant lethal genes into local mosquito populations through the release of genetically modified mosquitoes. As various arboviruses continue to be significant public health threats, biological control strategies have evolved to be more diverse and become critical tools to reduce the disease burden of arboviruses.

The semiotics of control and modeling relations in complex systems.

Science.gov (United States)

Joslyn, C

2001-01-01

We provide a conceptual analysis of ideas and principles from the systems theory discourse which underlie Pattee's semantic or semiotic closure, which is itself foundational for a school of theoretical biology derived from systems theory and cybernetics, and is now being related to biological semiotics and explicated in the relational biological school of Rashevsky and Rosen. Atomic control systems and models are described as the canonical forms of semiotic organization, sharing measurement relations, but differing topologically in that control systems are circularly and models linearly related to their environments. Computation in control systems is introduced, motivating hierarchical decomposition, hybrid modeling and control systems, and anticipatory or model-based control. The semiotic relations in complex control systems are described in terms of relational constraints, and rules and laws are distinguished as contingent and necessary functional entailments, respectively. Finally, selection as a meta-level of constraint is introduced as the necessary condition for semantic relations in control systems and models.

Will the Convention on Biological Diversity put an end to biological control?

NARCIS (Netherlands)

Lenteren, van J.C.; Cock, M.J.W.; Brodeur, J.; Barratt, B.I.P.; Bigler, F.; Bolckmans, K.; Haas, F.; Mason, P.G.; Parra, J.R.P.

2011-01-01

Will the Convention on Biological Diversity put an end to biological control? Under the Convention on Biological Diversity countries have sovereign rights over their genetic resources. Agreements governing the access to these resources and the sharing of the benefits arising from their use need to

Biological Control Strategies for Mosquito Vectors of Arboviruses

Directory of Open Access Journals (Sweden)

Yan-Jang S. Huang

2017-02-01

Full Text Available Historically, biological control utilizes predatory species and pathogenic microorganisms to reduce the population of mosquitoes as disease vectors. This is particularly important for the control of mosquito-borne arboviruses, which normally do not have specific antiviral therapies available. Although development of resistance is likely, the advantages of biological control are that the resources used are typically biodegradable and ecologically friendly. Over the past decade, the advancement of molecular biology has enabled optimization by the manipulation of genetic materials associated with biological control agents. Two significant advancements are the discovery of cytoplasmic incompatibility induced by Wolbachia bacteria, which has enhanced replacement programs, and the introduction of dominant lethal genes into local mosquito populations through the release of genetically modified mosquitoes. As various arboviruses continue to be significant public health threats, biological control strategies have evolved to be more diverse and become critical tools to reduce the disease burden of arboviruses.

Radiochemical and biological control of metaiodobenzyl-guanidine (MIBG) labeled with 131I

International Nuclear Information System (INIS)

Barboza, M.R.F.F. de; Muramoto, E.; Colturato, M.T.; Silva Valente Goncalves, R. da; Pereira, N.P.S. de; Almeida, M.A.T.M. de; Silva, C.P.G. da.

1988-07-01

This study shows the standardization of the radiochemical control of MIBG - 131 I in eletrophoretic system and also the biological control in Wistar rat for a period of time, not longer than 60 minutes after tracer administration. (author) [pt

Telemetry System of Biological Parameters

Directory of Open Access Journals (Sweden)

Jan Spisak

2005-01-01

Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

Glycoengineering in CHO cells: Advances in systems biology

DEFF Research Database (Denmark)

Tejwani, Vijay; Andersen, Mikael Rørdam; Nam, Jong Hyun

2018-01-01

are not well understood. A systems biology approach combining different technologies is needed for complete understanding of the molecular processes accounting for this variability and to open up new venues in cell line development. In this review, we describe several advances in genetic manipulation, modeling......For several decades, glycoprotein biologics have been successfully produced from Chinese hamster ovary (CHO) cells. The therapeutic efficacy and potency of glycoprotein biologics are often dictated by their post translational modifications, particularly glycosylation, which unlike protein synthesis....... Recently, CHO cells have also been explored for production of therapeutic glycosaminoglycans (e.g. heparin), which presents similar challenges as producing glycoproteins biologics. Approaches to controlling heterogeneity in CHO cells and directing the biosynthetic process toward desired glycoforms...

Logical analysis of biological systems

DEFF Research Database (Denmark)

Mardare, Radu Iulian

2005-01-01

R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

The effect of initial density and parasitoid intergenerational survival rate on classical biological control

International Nuclear Information System (INIS)

Xiao Yanni; Tang Sanyi

2008-01-01

Models of biological control have a long history of theoretical development that have focused on the interaction of a parasitoid and its host. The host-parasitoid systems have identified several important and general factors affecting the long-term dynamics of interacting populations. However, much less is known about how the initial densities of host-parasitoid populations affect the biological control as well as the stability of host-parasitoid systems. To do this, the classical Nicholson-Bailey model with host self-regulation and parasitoid intergenerational survival rate is used to uncover the effect of initial densities on the successful biological control. The results indicate that the simplest Nicholson-Bailey model has various coexistence with a wide range of parameters, including boundary attractors where the parasitoid population is absent and interior attractors where host-parasitoid coexists. The final stable states of host-parasitoid populations depend on their initial densities as well as their ratios, and those results are confirmed by basins of attraction of initial densities. The results also indicate that the parasitoid intergenerational survival rate increases the stability of the host-parasitoid systems. Therefore, the present research can help us to further understand the dynamical behavior of host-parasitoid interactions, to improve the classical biological control and to make management decisions

Institute for Genomics and Systems Biology

Science.gov (United States)

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

BIOLOGICAL CONTROL OF WEEDS BY MEANS OF PLANT PATHOGENS

Directory of Open Access Journals (Sweden)

Marija Ravlić

2014-06-01

Full Text Available Biological control is the use of live beneficial organisms and products of their metabolism in the pests control. Plant pathogens can be used for weed control in three different ways: as classical, conservation and augmentative (inoculative and inundated biological control. Inundated biological control involves the use of bioherbicides (mycoherbicides or artificial breeding of pathogens and application in specific stages of crops and weeds. Biological control of weeds can be used where chemical herbicides are not allowed, if resistant weed species are present or in the integrated pest management against weeds with reduced herbicides doses and other non-chemical measures, but it has certain limitations and disadvantages.

Using consumption rate to assess potential predators for biological control of white perch

Directory of Open Access Journals (Sweden)

Gosch N.J.C.

2011-08-01

Full Text Available Control of undesirable fishes is important in aquatic systems, and using predation as a tool for biological control is an attractive option to fishery biologists. However, determining the appropriate predators for biological control is critical for success. The objective of this study was to evaluate the utility of consumption rate as an index to determine the most effective predators for biological control of an invasive fish. Consumption rate values were calculated for nine potential predators that prey on white perch Morone americana in Branched Oak and Pawnee reservoirs, Nebraska. The consumption rate index provided a unique and insightful means of determining the potential effectiveness of each predator species in controlling white perch. Cumulative frequency distributions facilitated interpretation by providing a graphical presentation of consumption rates by all individuals within each predator species. Largemouth bass Micropterus salmoides, walleye Sander vitreus and sauger S. canadensis were the most efficient white perch predators in both reservoirs; however, previous attempts to increase biomass of these predators have failed suggesting that successful biological control is unlikely using existing predator species in these Nebraska reservoirs.

Controlled polymer synthesis--from biomimicry towards synthetic biology.

Science.gov (United States)

Pasparakis, George; Krasnogor, Natalio; Cronin, Leroy; Davis, Benjamin G; Alexander, Cameron

2010-01-01

The controlled assembly of synthetic polymer structures is now possible with an unprecedented range of functional groups and molecular architectures. In this critical review we consider how the ability to create artificial materials over lengthscales ranging from a few nm to several microns is generating systems that not only begin to mimic those in nature but also may lead to exciting applications in synthetic biology (139 references).

Biophysics and systems biology.

Science.gov (United States)

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.

Protein-polymer nano-machines. Towards synthetic control of biological processes

Directory of Open Access Journals (Sweden)

Alexander Cameron

2004-09-01

Full Text Available Abstract The exploitation of nature's machinery at length scales below the dimensions of a cell is an exciting challenge for biologists, chemists and physicists, while advances in our understanding of these biological motifs are now providing an opportunity to develop real single molecule devices for technological applications. Single molecule studies are already well advanced and biological molecular motors are being used to guide the design of nano-scale machines. However, controlling the specific functions of these devices in biological systems under changing conditions is difficult. In this review we describe the principles underlying the development of a molecular motor with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for control of the motor function. The molecular motor is a derivative of a TypeI Restriction-Modification (R-M enzyme and the synthetic polymer is drawn from the class of materials that exhibit a temperature-dependent phase transition. The potential exploitation of single molecules as functional devices has been heralded as the dawn of new era in biotechnology and medicine. It is not surprising, therefore, that the efforts of numerous multidisciplinary teams 12. have been focused in attempts to develop these systems. as machines capable of functioning at the low sub-micron and nanometre length-scales 3. However, one of the obstacles for the practical application of single molecule devices is the lack of functional control methods in biological media, under changing conditions. In this review we describe the conceptual basis for a molecular motor (a derivative of a TypeI Restriction-Modification enzyme with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for controlling the motor function 4.

Inverse problems in systems biology

International Nuclear Information System (INIS)

Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

2009-01-01

Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

Control theory meets synthetic biology.

Science.gov (United States)

Del Vecchio, Domitilla; Dy, Aaron J; Qian, Yili

2016-07-01

The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology. © 2016 The Author(s).

Systems biology in critical-care nursing.

Science.gov (United States)

Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

2011-01-01

Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

Biological Control of Bacterial Wilt in South East Asia

Directory of Open Access Journals (Sweden)

Triwidodo Arwiyanto

2014-12-01

Full Text Available Bacterial wilt disease caused by Ralstonia solanacearum destroys many crops of different plant families in South East Asia despite many researches about the disease, and the availability of developed control method in other parts of the world. There is no chemical available for the bacterial wilt pathogen and biological control is then chosen as an alternative to save the crops. Most of the biological control studies were based on antagonism between biological control agent and the pathogen. The biological control agents were intended to reduce the initial inoculum of the pathogen. The effort to minimize the initial inoculum of the pathogen by baiting with the use of hypersensitive host-plant was only reliable when conducted in the greenhouse experiments. Various microorganisms have been searched as possible biological control agents, for instance avirulent form of the pathogen, soil or rhizosphere bacteria (Bacillus spp. and fluorescent pseudomonads, actinomycetes (Streptomyces spp., yeast (Pichia uillermondii, Candida ethanolica, and a consortium of microorganisms known as effective microorganisms (EM. None of these biological control agents has been used in field application and they need further investigation in order to effectively control bacterial wilt. Opportunities and challenges in developing biological control to combat bacterial wilt are discussed in the paper. Penyakit layu bakteri yang disebabkan oleh Ralstonia solanacearum menghancurkan banyak tanaman dalam famili yang berbeda di Asia Tenggara meskipun telah banyak penelitian tentang metode pengendaliannya. Penyakit ini sulit dikendalikan karena banyaknya variabilitas patogen dan belum tersedianya sumber ketahanan yang mapan. Di samping itu, sampai saat ini belum ada bahan kimia yang tersedia untuk patogen layu bakteri ini sehingga pengendalian biologi kemudian dipilih sebagai cara alternatif untuk menyelamatkan tanaman. Sebagian besar penelitian pengendalian biologi didasarkan

Compartmental study of biological systems

International Nuclear Information System (INIS)

Moretti, J.L.

1975-01-01

The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

Philosophy of Systems and Synthetic Biology

DEFF Research Database (Denmark)

Green, Sara

2017-01-01

This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

SEEK: a systems biology data and model management platform.

Science.gov (United States)

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

Systems Biology

Indian Academy of Sciences (India)

IAS Admin

study and understand the function of biological systems, particu- larly, the response of such .... understand the organisation and behaviour of prokaryotic sys- tems. ... relationship of the structure of a target molecule to its ability to bind a certain ...

Integrating systems biology models and biomedical ontologies.

Science.gov (United States)

Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

2011-08-11

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. 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. 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.

Biological Efficacy of Herbicides for Weed Control in Noncropped Areas

Directory of Open Access Journals (Sweden)

Tsvetanka Dimitrova

2009-01-01

Full Text Available An increasing problem facing agricultural producers is the invasion of weeds, perennial in particular, so that implementation of industrial technologies is impossible without their highly efficient and rational control. For the purpose of studying efficient herbicides for weed control in noncropped areas (stubbles, a biological study of five total systemic herbicides was conducted in areas under natural weed infestation and pressure from othersurrounding weeds at the Institute of Forage Crops in Pleven in 2005-2007. The trials were carried out in field conditions using the block method with plot size of 20 m². Treatment was conducted at the predominant stage of budding of perennial dicotyledonous weeds and earing of monocotyledonous weeds. Herbicidal efficacy was recorded on the EWRS 9-score scale (0-100% killed weeds = score 9-1. It was found that treatment of noncropped areas (stubbles with the total systemic herbicides Touchdown System 4 (360 g/l glyphosate; Cosmic (360 g/l glyphosate; Roundup Plus (441 g/l glyphosate potassium salt; Leon 36 SL (360 g/l glyphosate and Glyphos Super 45 SL (450 g/l glyphosate was highly efficient, so that it was a successful element of a strategy for controlling weeds of different biological groups, and was especially effective against perennial weeds.

Calculating life? Duelling discourses in interdisciplinary systems biology.

Science.gov (United States)

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.

A Novel Robot System Integrating Biological and Mechanical Intelligence Based on Dissociated Neural Network-Controlled Closed-Loop Environment.

Science.gov (United States)

Li, Yongcheng; Sun, Rong; Wang, Yuechao; Li, Hongyi; Zheng, Xiongfei

2016-01-01

We propose the architecture of a novel robot system merging biological and artificial intelligence based on a neural controller connected to an external agent. We initially built a framework that connected the dissociated neural network to a mobile robot system to implement a realistic vehicle. The mobile robot system characterized by a camera and two-wheeled robot was designed to execute the target-searching task. We modified a software architecture and developed a home-made stimulation generator to build a bi-directional connection between the biological and the artificial components via simple binomial coding/decoding schemes. In this paper, we utilized a specific hierarchical dissociated neural network for the first time as the neural controller. Based on our work, neural cultures were successfully employed to control an artificial agent resulting in high performance. Surprisingly, under the tetanus stimulus training, the robot performed better and better with the increasement of training cycle because of the short-term plasticity of neural network (a kind of reinforced learning). Comparing to the work previously reported, we adopted an effective experimental proposal (i.e. increasing the training cycle) to make sure of the occurrence of the short-term plasticity, and preliminarily demonstrated that the improvement of the robot's performance could be caused independently by the plasticity development of dissociated neural network. This new framework may provide some possible solutions for the learning abilities of intelligent robots by the engineering application of the plasticity processing of neural networks, also for the development of theoretical inspiration for the next generation neuro-prostheses on the basis of the bi-directional exchange of information within the hierarchical neural networks.

A Novel Robot System Integrating Biological and Mechanical Intelligence Based on Dissociated Neural Network-Controlled Closed-Loop Environment.

Directory of Open Access Journals (Sweden)

Yongcheng Li

Full Text Available We propose the architecture of a novel robot system merging biological and artificial intelligence based on a neural controller connected to an external agent. We initially built a framework that connected the dissociated neural network to a mobile robot system to implement a realistic vehicle. The mobile robot system characterized by a camera and two-wheeled robot was designed to execute the target-searching task. We modified a software architecture and developed a home-made stimulation generator to build a bi-directional connection between the biological and the artificial components via simple binomial coding/decoding schemes. In this paper, we utilized a specific hierarchical dissociated neural network for the first time as the neural controller. Based on our work, neural cultures were successfully employed to control an artificial agent resulting in high performance. Surprisingly, under the tetanus stimulus training, the robot performed better and better with the increasement of training cycle because of the short-term plasticity of neural network (a kind of reinforced learning. Comparing to the work previously reported, we adopted an effective experimental proposal (i.e. increasing the training cycle to make sure of the occurrence of the short-term plasticity, and preliminarily demonstrated that the improvement of the robot's performance could be caused independently by the plasticity development of dissociated neural network. This new framework may provide some possible solutions for the learning abilities of intelligent robots by the engineering application of the plasticity processing of neural networks, also for the development of theoretical inspiration for the next generation neuro-prostheses on the basis of the bi-directional exchange of information within the hierarchical neural networks.

Heuristic Strategies in Systems Biology

Directory of Open Access Journals (Sweden)

Fridolin Gross

2016-06-01

Full Text Available Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences.

Control of self-organizing nonlinear systems

CERN Document Server

Klapp, Sabine; Hövel, Philipp

2016-01-01

The book summarizes the state-of-the-art of research on control of self-organizing nonlinear systems with contributions from leading international experts in the field. The first focus concerns recent methodological developments including control of networks and of noisy and time-delayed systems. As a second focus, the book features emerging concepts of application including control of quantum systems, soft condensed matter, and biological systems. Special topics reflecting the active research in the field are the analysis and control of chimera states in classical networks and in quantum systems, the mathematical treatment of multiscale systems, the control of colloidal and quantum transport, the control of epidemics and of neural network dynamics.

Biological Control of Bacterial Wilt in South East Asia

OpenAIRE

Arwiyanto, Triwidodo

2014-01-01

Bacterial wilt disease caused by Ralstonia solanacearum destroys many crops of different plant families in South East Asia despite many researches about the disease, and the availability of developed control method in other parts of the world. There is no chemical available for the bacterial wilt pathogen and biological control is then chosen as an alternative to save the crops. Most of the biological control studies were based on antagonism between biological control agent and the pathogen. ...

Magnetic Actuation of Biological Systems

Science.gov (United States)

Lauback, Stephanie D.

Central to the advancement of many biomedical and nanotechnology capabilities is the capacity to precisely control the motion of micro and nanostructures. These applications range from single molecule experiments to cell isolation and separation, to drug delivery and nanomachine manipulation. This dissertation focuses on actuation of biological micro- and nano-entities through the use of weak external magnetic fields, superparamagnetic beads, and ferromagnetic thin films. The magnetic platform presents an excellent method for actuation of biological systems due to its ability to directly control the motion of an array of micro and nanostructures in real-time with calibrated picoNewton forces. The energy landscape of two ferromagnetic thin film patterns (disks and zigzag wires) is experimentally explored and compared to corresponding theoretical models to quantify the applied forces and trajectories of superparamagnetic beads due to the magnetic traps. A magnetic method to directly actuate DNA nanomachines in real-time with nanometer resolution and sub-second response times using micromagnetic control was implemented through the use of stiff DNA micro-levers which bridged the large length scale mismatch between the micro-actuator and the nanomachine. Compared to current alternative methods which are limited in the actuation speeds and the number of reconfiguration states of DNA constructs, this magnetic approach enables fast actuation (˜ milliseconds) and reconfigurable conformations achieved through a continuous range of finely tuned steps. The system was initially tested through actuation of the stiff arm tethered to the surface, and two prototype DNA nanomachines (rotor and hinge) were successfully actuated using the stiff mechanical lever. These results open new possibilities in the development of functional robotic systems at the molecular scale. In exploiting the use of DNA stiff levers, a new technique was also developed to investigate the emergence of the

Creating biological nanomaterials using synthetic biology

International Nuclear Information System (INIS)

Rice, MaryJoe K; Ruder, Warren C

2014-01-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

Creating biological nanomaterials using synthetic biology.

Science.gov (United States)

Rice, MaryJoe K; Ruder, Warren C

2014-02-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

Biological Control of Diseases of Vegetables Grown Hydroponically in Thailand: Challenge and Opportunity.

Science.gov (United States)

Kanjanamaneesathian, Mana

2015-01-01

In Thailand, yield loss due to plant diseases in vegetables grown hydroponically is very high as a result of the growers` lack of knowledge for controlling diseases and their un- willingness to invest in setting-up the proper hydroponic system from the beginning. Severe root rot disease caused by Pythium spp. is frequent and can be anticipated in the hot climate in Thailand. This review focuses on the diseases in temperate lettuces which have been produced hydroponically and have been attacked by plant pathogens, particularly Pythium spp. Biological control of vegetable diseases grown hydroponically has been investigated in Thailand. Research is being carried out to identify effective strains of the antagonists, formulating the applicable products and delivering them appropriately to control the disease. Products of Bacillus subtilis, Chaetomium globosom and Trichoderma harzianum have been recommended for use to control diseases in vegetables grown hydroponically. Control efficacy of these products is varied as the biological products have been used by the growers in the paradigm of using chemical fungicide for disease control in hydroponic production system, overlooking the intrinsic characteristics of the biological control products. The recent patent, which minimizes the effects of sunlight and heat on the nutrient solution without the use of an external energy for cooling the nutrient, should be applied in producing hydroponic vegetables to mitigate poor plant growth and root rot disease outbreak in Thailand.

Applicability of Computational Systems Biology in Toxicology

DEFF Research Database (Denmark)

Kongsbak, Kristine Grønning; Hadrup, Niels; Audouze, Karine Marie Laure

2014-01-01

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......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...

Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

Science.gov (United States)

De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

2010-03-01

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

Editorial overview : Systems biology for biotechnology

NARCIS (Netherlands)

Heinemann, Matthias; Pilpel, Yitzhak

About 15 years ago, systems biology was introduced as a novel approach to biological research. On the one side, its introduction was a result of the recognition that through solely the reductionist approach, we would ulti- mately not be able to understand how biological systems function as a whole.

Quantum Effects in Biological Systems

CERN Document Server

2016-01-01

Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

Static Analysis for Systems Biology

DEFF Research Database (Denmark)

Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

2004-01-01

This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

Biological control component [Management of water hyacinth

International Nuclear Information System (INIS)

Harley, K.L.S.

1981-01-01

Both chemical and biological control have been used with limited success for the management of water hyacinth in Fiji. In some cases heavy application of chemicals have been successful in completely killing limited areas of water hyacinth, but have resulted in the destruction of biological agents introduced to control the water hyacinth and high contamination of natural water supplies. It is proposed that under the direction of Mr S R Singh, the Senior Research Scientist (Entomology) of the Koronivia Research Station, Suva, Fiji, a collaborative programme with Dr Harley of Australia on chemical and biological control of water hyacinth be initiated. This programme would be fundamentally short-term with the prime objective being an investigation of levels of insect population following varying levels of application of chemical sprays. By comparison with control areas, observations would be made of both chemical damage and insect damage within the limited time span of the period

Effectiveness of a biological control agent Palexorista gilvoides in ...

African Journals Online (AJOL)

ACSS

Effectiveness of a biological control agent Palexorista gilvoides in controlling Gonometa podorcarpi in conifer ... gilvoides as a potential biological control agent for G. podocarpi. Field and laboratory studies further established that P. .... version for windows (SPSS, 2002). Results. Gonometa podocarpi was present in.

Omics/systems biology and cancer cachexia.

Science.gov (United States)

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.

Biological stability of drinking water: controlling factors, methods and challenges

Directory of Open Access Journals (Sweden)

Emmanuelle ePrest

2016-02-01

Full Text Available Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g. development of opportunistic pathogens, aesthetic (e.g. deterioration of taste, odour, colour or operational (e.g. fouling or biocorrosion of pipes problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors such as (i type and concentration of available organic and inorganic nutrients, (ii type and concentration of residual disinfectant, (iii presence of predators such as protozoa and invertebrates, (iv environmental conditions such as water temperature, and (v spatial location of microorganisms (bulk water, sediment or biofilm. Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i existing knowledge on biological stability controlling factors and (ii how these factors are affected by drinking water production and distribution conditions. In addition, (iii the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discuss how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order to

Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges

Science.gov (United States)

Prest, Emmanuelle I.; Hammes, Frederik; van Loosdrecht, Mark C. M.; Vrouwenvelder, Johannes S.

2016-01-01

Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order

Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges

KAUST Repository

Prest, Emmanuelle I.

2016-02-01

Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order

Analyzing the Biology on the System Level

OpenAIRE

Tong, Wei

2016-01-01

Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

Biological control agents elevate hantavirus by subsidizing deer mouse populations

Science.gov (United States)

Dean E. Pearson; Ragan M. Callaway

2006-01-01

Biological control of exotic invasive plants using exotic insects is practiced under the assumption that biological control agents are safe if they do not directly attack non-target species. We tested this assumption by evaluating the potential for two host-specific biological control agents (Urophora spp.), widely established in North America for spotted...

Engineering challenges of BioNEMS: the integration of microfluidics, micro- and nanodevices, models and external control for systems biology.

Science.gov (United States)

Wikswo, J P; Prokop, A; Baudenbacher, F; Cliffel, D; Csukas, B; Velkovsky, M

2006-08-01

Systems biology, i.e. quantitative, postgenomic, postproteomic, dynamic, multiscale physiology, addresses in an integrative, quantitative manner the shockwave of genetic and proteomic information using computer models that may eventually have 10(6) dynamic variables with non-linear interactions. Historically, single biological measurements are made over minutes, suggesting the challenge of specifying 10(6) model parameters. Except for fluorescence and micro-electrode recordings, most cellular measurements have inadequate bandwidth to discern the time course of critical intracellular biochemical events. Micro-array expression profiles of thousands of genes cannot determine quantitative dynamic cellular signalling and metabolic variables. Major gaps must be bridged between the computational vision and experimental reality. The analysis of cellular signalling dynamics and control requires, first, micro- and nano-instruments that measure simultaneously multiple extracellular and intracellular variables with sufficient bandwidth; secondly, the ability to open existing internal control and signalling loops; thirdly, external BioMEMS micro-actuators that provide high bandwidth feedback and externally addressable intracellular nano-actuators; and, fourthly, real-time, closed-loop, single-cell control algorithms. The unravelling of the nested and coupled nature of cellular control loops requires simultaneous recording of multiple single-cell signatures. Externally controlled nano-actuators, needed to effect changes in the biochemical, mechanical and electrical environment both outside and inside the cell, will provide a major impetus for nanoscience.

Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

Science.gov (United States)

Degrazio, Dominick

Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

[Establishment of Quality Control System of Nucleic Acid Detection for Ebola Virus in Sierra Leone-China Friendship Biological Safety Laboratory].

Science.gov (United States)

Wang, Qin; Zhang, Yong; Nie, Kai; Wang, Huanyu; Du, Haijun; Song, Jingdong; Xiao, Kang; Lei, Wenwen; Guo, Jianqiang; Wei, Hejiang; Cai, Kun; Wang, Yanhai; Wu, Jiang; Gerald, Bangura; Kamara, Idrissa Laybohr; Liang, Mifang; Wu, Guizhen; Dong, Xiaoping

2016-03-01

The quality control process throughout the Ebola virus nucleic acid detection in Sierra Leone-China Friendship Biological Safety Laboratory (SLE-CHN Biosafety Lab) was described in detail, in order to comprehensively display the scientific, rigorous, accurate and efficient practice in detection of Ebola virus of first batch detection team in SLE-CHN Biosafety Lab. Firstly, the key points of laboratory quality control system was described, including the managements and organizing, quality control documents and information management, instrument, reagents and supplies, assessment, facilities design and space allocation, laboratory maintenance and biosecurity. Secondly, the application of quality control methods in the whole process of the Ebola virus detection, including before the test, during the test and after the test, was analyzed. The excellent and professional laboratory staffs, the implementation of humanized management are the cornerstone of the success; High-level biological safety protection is the premise for effective quality control and completion of Ebola virus detection tasks. And professional logistics is prerequisite for launching the laboratory diagnosis of Ebola virus. The establishment and running of SLE-CHN Biosafety Lab has landmark significance for the friendship between Sierra Leone and China, and the lab becomes the most important base for Ebola virus laboratory testing in Sierra Leone.

Status of biological control in vegetation management in forestry

Science.gov (United States)

George P. Markin; Donald E. Gardner

1993-01-01

Biological control traditionally depends upon importing the natural enemies of introduced weeds. Since vegetation management in forestry has primarily been aimed at protecting economic species of trees from competition from other native plants, biological control has been of little use in forestry. An alternative approach to controlling unwanted native plants,...

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

Science.gov (United States)

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.

The Glucose-Insulin Control System

DEFF Research Database (Denmark)

Hallgreen, Christine Erikstrup; Korsgaard, Thomas Vagn; Hansen, RenéNormann N.

2008-01-01

This chapter reviews the glucose-insulin control system. First, classic control theory is described briefly and compared with biological control. The following analysis of the control system falls into two parts: a glucose-sensing part and a glucose-controlling part. The complex metabolic pathways...... are divided into smaller pieces and analyzed via several small biosimulation models that describe events in beta cells, liver, muscle and adipose tissue etc. In the glucose-sensing part, the beta cell are shown to have some characteristics of a classic PID controller, but with nonlinear properties...... control, the analysis shows that the system has many more facets than just keeping the glucose concentration within narrow limits. After glucose enters the cell and is phosphorylated to glucose-6-phosphate, the handling of glucose-6-phosphate is critical for glucose regulation. Also, this handling...

How do precision medicine and system biology response to human body's complex adaptability?

Science.gov (United States)

Yuan, Bing

2016-12-01

In the field of life sciences, although system biology and "precision medicine" introduce some complex scientifific methods and techniques, it is still based on the "analysis-reconstruction" of reductionist theory as a whole. Adaptability of complex system increase system behaviour uncertainty as well as the difficulties of precise identifification and control. It also put systems biology research into trouble. To grasp the behaviour and characteristics of organism fundamentally, systems biology has to abandon the "analysis-reconstruction" concept. In accordance with the guidelines of complexity science, systems biology should build organism model from holistic level, just like the Chinese medicine did in dealing with human body and disease. When we study the living body from the holistic level, we will fifind the adaptability of complex system is not the obstacle that increases the diffificulty of problem solving. It is the "exceptional", "right-hand man" that helping us to deal with the complexity of life more effectively.

Ten questions about systems biology

DEFF Research Database (Denmark)

Joyner, Michael J; Pedersen, Bente K

2011-01-01

to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many......In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...

Ten questions about systems biology

DEFF Research Database (Denmark)

Joyner, Michael J; Pedersen, Bente K

2011-01-01

In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

Economic Benefits of Advanced Control Strategies in Biological Nutrient Removal Systems

DEFF Research Database (Denmark)

Carstensen, J.; Nielsen, M.K.; Harremoës, Poul

1994-01-01

little regards to the variations in load and biomass activity. However, these dynamics can be evaluated on-line using grey box models to describe the most important features of the hydraulic and biological processes. Simulation studies of plants with an alternating process have shown that control...... strategies incorporating information from the grey box models are capable of reducing the total nitrogen discharge as well as energy costs. These results have a major impact on both existing and future plants. In fact, it is expected that future plants can be reduced with 10-20 per cent in size...

A functional overview of conservation biological control

DEFF Research Database (Denmark)

Begg, Graham S; Cook, Samantha M; Dye, Richard

2017-01-01

Conservation biological control (CBC) is a sustainable approach to pest management that can contribute to a reduction in pesticide use as part of an Integrated Pest Management (IPM) strategy. CBC is based on the premise that countering habitat loss and environmental disturbance associated...... CBC prescriptions have proved elusive. To tackle this, we consolidate existing knowledge of CBC using a simple conceptual model that organises the functional elements of CBC into a common, unifying framework. We identify and integrate the key biological processes affecting natural enemies...... and their biological control function across local and regional scales, and consider the interactions, interdependencies and constraints that determine the outcome of CBC strategies. Conservation measures are often effective in supporting natural enemy populations but their success cannot be guaranteed; the greatest...

Genomes, Phylogeny, and Evolutionary Systems Biology

Energy Technology Data Exchange (ETDEWEB)

Medina, Monica

2005-03-25

With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

Social and economic factors for the adoption of biological control of ...

African Journals Online (AJOL)

The results also showed that the decision on the application of biological control is determined by the educational level, income, mechanization level, extension activities, biological control awareness, social participation, attitude toward biological control and access to information sources which have significant influence.

Control of the cassava mealybug in Africa: lessons from a biological ...

African Journals Online (AJOL)

Control of the cassava mealybug in Africa: lessons from a biological control project. ... Such studies are needed in order to attribute the observed effects to various causes and to advance the science of biological control. ( 4) It is concluded that biological control is the basis ofiPM but cannot usually be manipulated by the ...

Aspergilli: Systems biology and industrial applications

DEFF Research Database (Denmark)

Knuf, Christoph; Nielsen, Jens

2012-01-01

possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

Model checking biological systems described using ambient calculus

DEFF Research Database (Denmark)

Mardare, Radu Iulian; Priami, Corrado; Qualia, Paola

2005-01-01

Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005.......Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005....

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

Science.gov (United States)

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.

Biologically Inspired Modular Neural Control for a Leg-Wheel Hybrid Robot

DEFF Research Database (Denmark)

Manoonpong, Poramate; Wörgötter, Florentin; Laksanacharoen, Pudit

2014-01-01

In this article we present modular neural control for a leg-wheel hybrid robot consisting of three legs with omnidirectional wheels. This neural control has four main modules having their functional origin in biological neural systems. A minimal recurrent control (MRC) module is for sensory signal...... processing and state memorization. Its outputs drive two front wheels while the rear wheel is controlled through a velocity regulating network (VRN) module. In parallel, a neural oscillator network module serves as a central pattern generator (CPG) controls leg movements for sidestepping. Stepping directions...... or they can serve as useful modules for other module-based neural control applications....

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

Science.gov (United States)

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.

Bio-inspired spiking neural network for nonlinear systems control.

Science.gov (United States)

Pérez, Javier; Cabrera, Juan A; Castillo, Juan J; Velasco, Juan M

2018-08-01

Spiking neural networks (SNN) are the third generation of artificial neural networks. SNN are the closest approximation to biological neural networks. SNNs make use of temporal spike trains to command inputs and outputs, allowing a faster and more complex computation. As demonstrated by biological organisms, they are a potentially good approach to designing controllers for highly nonlinear dynamic systems in which the performance of controllers developed by conventional techniques is not satisfactory or difficult to implement. SNN-based controllers exploit their ability for online learning and self-adaptation to evolve when transferred from simulations to the real world. SNN's inherent binary and temporary way of information codification facilitates their hardware implementation compared to analog neurons. Biological neural networks often require a lower number of neurons compared to other controllers based on artificial neural networks. In this work, these neuronal systems are imitated to perform the control of non-linear dynamic systems. For this purpose, a control structure based on spiking neural networks has been designed. Particular attention has been paid to optimizing the structure and size of the neural network. The proposed structure is able to control dynamic systems with a reduced number of neurons and connections. A supervised learning process using evolutionary algorithms has been carried out to perform controller training. The efficiency of the proposed network has been verified in two examples of dynamic systems control. Simulations show that the proposed control based on SNN exhibits superior performance compared to other approaches based on Neural Networks and SNNs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Biological indicators for monitoring water quality of MTF canals system

Science.gov (United States)

Sethi, S. L.

1975-01-01

Biological models, diversity indexes, were developed to predict environmental effects of NASA's Mississippi test facility (MTF) chemical operations on canal systems in the area. To predict the effects on local streams, a physical model of unpolluted streams was established. The model is fed by artesian well water free of background levels of pollutants. The species diversity and biota composition of unpolluted MTF stream was determined; resulting information will be used to form baseline data for future comparisons. Biological modeling was accomplished by adding controlled quantities or kinds of chemical pollutants and evaluating the effects of these chemicals on the biological life of the stream.

Biologically inspired autonomous structural materials with controlled toughening and healing

Science.gov (United States)

Garcia, Michael E.; Sodano, Henry A.

2010-04-01

The field of structural health monitoring (SHM) has made significant contributions in the field of prognosis and damage detection in the past decade. The advantageous use of this technology has not been integrated into operational structures to prevent damage from propagating or to heal injured regions under real time loading conditions. Rather, current systems relay this information to a central processor or human operator, who then determines a course of action such as altering the mission or scheduling repair maintenance. Biological systems exhibit advanced sensory and healing traits that can be applied to the design of material systems. For instance, bone is the major structural component in vertebrates; however, unlike modern structural materials, bone has many properties that make it effective for arresting the propagation of cracks and subsequent healing of the fractured area. The foremost goal for the development of future adaptive structures is to mimic biological systems, similar to bone, such that the material system can detect damage and deploy defensive traits to impede damage from propagating, thus preventing catastrophic failure while in operation. After sensing and stalling the propagation of damage, the structure must then be repaired autonomously using self healing mechanisms motivated by biological systems. Here a novel autonomous system is developed using shape memory polymers (SMPs), that employs an optical fiber network as both a damage detection sensor and a network to deliver stimulus to the damage site initiating adaptation and healing. In the presence of damage the fiber optic fractures allowing a high power laser diode to deposit a controlled level of thermal energy at the fractured sight locally reducing the modulus and blunting the crack tip, which significantly slows the crack growth rate. By applying a pre-induced strain field and utilizing the shape memory recovery effect, thermal energy can be deployed to close the crack and return

Study of the effects of radon in three biological systems

International Nuclear Information System (INIS)

Tavera, L.; Balcazar, M.; Lopez, A.; Brena, M.; Rosa, M.E. De la; Villalobos P, R.

2002-01-01

The radon and its decay products are responsible of the 3/4 parts of the exposure of the persons to the environmental radiation. The discovery at the end of XIX Century of the illnesses, mainly of cancer, which appeared in the presence of radon, lead to an accelerated growing of the radon studies: monitoring, dosimetry, effects on the persons, etc. Several epidemiological studies of radon in miners and population in general have been realized; advancing in the knowledge about the concentration-lung cancer risk relationship, but with discrepancies in the results depending on the concentration levels. Therefor, studies which consuming time, efforts and money go on doing. The research of the radon effects in biological systems different to human, allows to realize studies in less time, in controlled conditions and generally at lower cost, generating information about the alpha radiation effects in the cellular field. Therefor it was decided to study the response of three biological systems exposed to radon: an unicellular bacteria Escherichia Coli which was exposed directly to alpha particles from an electrodeposited source for determining the sensitivity limit of the chose technique. A plant, Tradescantia, for studying the cytogenetic effect of the system exposed to controlled concentrations of radon. An insect, Drosophila Melanogaster, for studying the genetic effects and the accumulated effects in several generations exposed to radon. In this work the experimental settlements are presented for the expositions of the systems and the biological results commenting the importance of these. (Author)

Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

DEFF Research Database (Denmark)

Green, Sara; Serban, Maria; Scholl, Raphael

2018-01-01

of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

[Cybernetics and biology].

Science.gov (United States)

Vasil'ev, G F

2013-01-01

Owing to methodical disadvantages, the theory of control still lacks the potential for the analysis of biological systems. To get the full benefit of the method in addition to the algorithmic model of control (as of today the only used model in the theory of control) a parametric model of control is offered to employ. The reasoning for it is explained. The approach suggested provides the possibility to use all potential of the modern theory of control for the analysis of biological systems. The cybernetic approach is shown taking a system of the rise of glucose concentration in blood as an example.

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

Science.gov (United States)

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.

Science.gov (United States)

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.

Biological control of Fusarium moniliforme in maize.

Science.gov (United States)

Bacon, C W; Yates, I E; Hinton, D M; Meredith, F

2001-05-01

Fusarium moniliforme Sheldon, a biological species of the mating populations within the (italic)Gibberella fujikuroi species complex, i.e., population A [= G. moniliformis (Sheld.) Wineland], is an example of a facultative fungal endophyte. During the biotrophic endophytic association with maize, as well as during saprophytic growth, F. moniliforme produces the fumonisins. The fungus is transmitted vertically and horizontally to the next generation of plants via clonal infection of seeds and plant debris. Horizontal infection is the manner by which this fungus is spread contagiously and through which infection occurs from the outside that can be reduced by application of certain fungicides. The endophytic phase is vertically transmitted. This type infection is important because it is not controlled by seed applications of fungicides, and it remains the reservoir from which infection and toxin biosynthesis takes place in each generation of plants. Thus, vertical transmission of this fungus is just as important as horizontal transmission. A biological control system using an endophytic bacterium, Bacillus subtilis, has been developed that shows great promise for reducing mycotoxin accumulation during the endophytic (vertical transmission) growth phase. Because this bacterium occupies the identical ecological niche within the plant, it is considered an ecological homologue to F. moniliforme, and the inhibitory mechanism, regardless of the mode of action, operates on the competitive exclusion principle. In addition to this bacterium, an isolate of a species of the fungus Trichoderma shows promise in the postharvest control of the growth and toxin accumulation from F. moniliforme on corn in storage.

Design control considerations for biologic-device combination products.

Science.gov (United States)

Anderson, Dave; Liu, Roger; Anand Subramony, J; Cammack, Jon

2017-03-01

Combination products are therapeutic and diagnostic medical products that combine drugs, devices, and/or biological products with one another. Historically, biologics development involved identifying efficacious doses administered to patients intravenously or perhaps by a syringe. Until fairly recently, there has been limited focus on developing an accompanying medical device, such as a prefilled syringe or auto-injector, to enable easy and more efficient delivery. For the last several years, and looking forward, where there may be little to distinguish biologics medicines with relatively similar efficacy profiles, the biotechnology market is beginning to differentiate products by patient-focused, biologic-device based combination products. As innovative as biologic-device combination products are, they can pose considerable development, regulatory, and commercialization challenges due to unique physicochemical properties and special clinical considerations (e.g., dosing volumes, frequency, co-medications, etc.) of the biologic medicine. A biologic-device combination product is a marriage between two partners with "cultural differences," so to speak. There are clear differences in the development, review, and commercialization processes of the biologic and the device. When these two cultures come together in a combination product, developers and reviewers must find ways to address the design controls and risk management processes of both the biologic and device, and knit them into a single entity with supporting product approval documentation. Moreover, digital medicine and connected health trends are pushing the boundaries of combination product development and regulations even further. Despite an admirable cooperation between industry and FDA in recent years, unique product configurations and design features have resulted in review challenges. These challenges have prompted agency reviewers to modernize consultation processes, while at the same time, promoting

An engineering design approach to systems biology.

Science.gov (United States)

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

Science.gov (United States)

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…

[Network structures in biological systems].

Science.gov (United States)

Oleskin, A V

2013-01-01

Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

Next-generation mammalian genetics toward organism-level systems biology.

Science.gov (United States)

Susaki, Etsuo A; Ukai, Hideki; Ueda, Hiroki R

2017-01-01

Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.

Answering biological questions: Querying a systems biology database for nutrigenomics

NARCIS (Netherlands)

Evelo, C.T.; Bochove, K. van; Saito, J.T.

2011-01-01

The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A

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

Science.gov (United States)

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

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.

Science.gov (United States)

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.

Prospects for biological soil-borne disease control: application of indigenous versus synthetic microbiomes

Science.gov (United States)

Biological disease control of soil-borne plant diseases has traditionally employed the biopesticide approach whereby single strains or strain mixtures are introduced into production systems through inundative/inoculative release. The approach has significant barriers that have long been recognized,...

Biological control of biofilms on membranes by metazoans.

Science.gov (United States)

Klein, Theresa; Zihlmann, David; Derlon, Nicolas; Isaacson, Carl; Szivak, Ilona; Weissbrodt, David G; Pronk, Wouter

2016-01-01

Traditionally, chemical and physical methods have been used to control biofouling on membranes by inactivating and removing the biofouling layer. Alternatively, the permeability can be increased using biological methods while accepting the presence of the biofouling layer. We have investigated two different types of metazoans for this purpose, the oligochaete Aelosoma hemprichi and the nematode Plectus aquatilis. The addition of these grazing metazoans in biofilm-controlled membrane systems resulted in a flux increase of 50% in presence of the oligochaetes (Aelosoma hemprichi), and a flux increase of 119-164% in presence of the nematodes (Plectus aquatilis) in comparison to the control system operated without metazoans. The change in flux resulted from (1) a change in the biofilm structure, from a homogeneous, cake-like biofilm to a more heterogeneous, porous structure and (2) a significant reduction in the thickness of the basal layer. Pyrosequencing data showed that due to the addition of the predators, also the community composition of the biofilm in terms of protists and bacteria was strongly affected. The results have implications for a range of membrane processes, including ultrafiltration for potable water production, membrane bioreactors and reverse osmosis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Integrative radiation systems biology

International Nuclear Information System (INIS)

Unger, Kristian

2014-01-01

Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group “Personalized Radiotherapy in Head and Neck Cancer” of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology

Pakistan's national legislation entitled: 'Export Control on Goods, Technologies, Material and Equipment related to Nuclear and Biological Weapons and their Delivery Systems Act, 2004'

International Nuclear Information System (INIS)

2004-01-01

The Director General has received a letter from the Permanent Mission of Pakistan, dated 4 November 2004, concerning Pakistan's national legislation entitled 'Export Control on Goods, Technologies, Material and Equipment related to Nuclear and Biological Weapons and their Delivery Systems Act, 2004'. As requested by the Permanent Mission of Pakistan, the letter and the Export Control Act of 2004, are reproduced herein for the information of the Member States

Economic Benefit for Cuban Laurel Thrips Biological Control.

Science.gov (United States)

Shogren, C; Paine, T D

2016-02-01

The Cuban laurel thrips, Gynaikothrips ficorum Marchal (Thysanoptera: Phlaeothripidae), is a critical insect pest of Ficus microcarpa in California urban landscapes and production nurseries. Female thrips feed and oviposit on young Ficus leaves, causing the expanding leaves to fold or curl into a discolored leaf gall. There have been attempts to establish specialist predator natural enemies of the thrips, but no success has been reported. We resampled the same areas in 2013-2014 where we had released Montandoniola confusa (= morguesi) Streito and Matocq (Hemiptera: Anthocoridae) in southern California in 1995 but had been unable to recover individuals in 1997-1998. Thrips galls were significantly reduced in all three of the locations in the recent samples compared with the earlier samples. M. confusa was present in all locations and appears to be providing successful biological control. The value of the biological control, the difference between street trees in good foliage condition and trees with poor foliage, was $58,766,166. If thrips damage reduced the foliage to very poor condition, the value of biological control was $73,402,683. Total cost for the project was $61,830. The benefit accrued for every dollar spent on the biological control of the thrips ranged from $950, if the foliage was in poor condition, to $1,187, if the foliage was in very poor condition. The value of urban forest is often underappreciated. Economic analyses that clearly demonstrate the very substantial rates of return on investment in successful biological control in urban forests provide compelling arguments for supporting future efforts. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

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...

Metabolomics: Definitions and Significance in Systems Biology.

Science.gov (United States)

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.

Biological control of Mycosphaerella fragariae in strawberry culture

Directory of Open Access Journals (Sweden)

Anderson Luis Heling

2015-12-01

Full Text Available The Mycosphaerella spot is one of the main foliar diseases of strawberry, degrating great leaf regions and reducing the photosynthetic area. Its control is mainly by the use of chemical fungicides, but, due the increasing demand for food free of pesticide, alternative control methods have been researched, such as biological control. This work aimed to evaluate the effect on strawberry plants, treated with the biological control agents Bacillus cereus, Saccharomyces boulardii and Saccharomyces cerevisiae, in the severity of Mycosphaerella fragariae, productivity and in the activity of β-1.3 glucanases, peroxidases and chitinases enzymes. It was verified that S. cerevisiae and B. cereus treatments were similar to fungicide for disease control. However, even reducing the severity of the disease, there was no increase in productivity, and the different control agents do not cause changes in the evaluated defense mechanisms.

Entomopatogenic fungi as an alternative for biological pest control

Directory of Open Access Journals (Sweden)

Pablo Andrés Motta Delgado

2011-08-01

Full Text Available The entomopatogenic fungi are a diverse group of microorganisms that provide multiple services to agroecological systems. Among those the capacity to regulate the pests to keep them in suitable levels stands out. The present paper shows a description of the entomopatogenic fungi of most extensively used for the biological control of pests, their mechanism of action on their host, and also investigations about the in vitro and in situ behavior of the mostly used fungi for the control of some insects. Also, the formulations that are used for the development of this biotechnology in the field are described. In the development of bioinsecticides the entomopatogenic fungi are a viable option to minimize environmental damage.

A Biomechanical Comparison of Proportional Electromyography Control to Biological Torque Control Using a Powered Hip Exoskeleton

Directory of Open Access Journals (Sweden)

Aaron J. Young

2017-06-01

Full Text Available BackgroundDespite a large increase in robotic exoskeleton research, there are few studies that have examined human performance with different control strategies on the same exoskeleton device. Direct comparison studies are needed to determine how users respond to different types of control. The purpose of this study was to compare user performance using a robotic hip exoskeleton with two different controllers: a controller that targeted a biological hip torque profile and a proportional myoelectric controller.MethodsWe tested both control approaches on 10 able-bodied subjects using a pneumatically powered hip exoskeleton. The state machine controller targeted a biological hip torque profile. The myoelectric controller used electromyography (EMG of lower limb muscles to produce a proportional control signal for the hip exoskeleton. Each subject performed two 30-min exoskeleton walking trials (1.0 m/s using each controller and a 10-min trial with the exoskeleton unpowered. During each trial, we measured subjects’ metabolic cost of walking, lower limb EMG profiles, and joint kinematics and kinetics (torques and powers using a force treadmill and motion capture.ResultsCompared to unassisted walking in the exoskeleton, myoelectric control significantly reduced metabolic cost by 13% (p = 0.005 and biological hip torque control reduced metabolic cost by 7% (p = 0.261. Subjects reduced muscle activity relative to the unpowered condition for a greater number of lower limb muscles using myoelectric control compared to the biological hip torque control. More subjects subjectively preferred the myoelectric controller to the biological hip torque control.ConclusionMyoelectric control had more advantages (metabolic cost and muscle activity reduction compared to a controller that targeted a biological torque profile for walking with a robotic hip exoskeleton. However, these results were obtained with a single exoskeleton device with specific

A Biomechanical Comparison of Proportional Electromyography Control to Biological Torque Control Using a Powered Hip Exoskeleton.

Science.gov (United States)

Young, Aaron J; Gannon, Hannah; Ferris, Daniel P

2017-01-01

Despite a large increase in robotic exoskeleton research, there are few studies that have examined human performance with different control strategies on the same exoskeleton device. Direct comparison studies are needed to determine how users respond to different types of control. The purpose of this study was to compare user performance using a robotic hip exoskeleton with two different controllers: a controller that targeted a biological hip torque profile and a proportional myoelectric controller. We tested both control approaches on 10 able-bodied subjects using a pneumatically powered hip exoskeleton. The state machine controller targeted a biological hip torque profile. The myoelectric controller used electromyography (EMG) of lower limb muscles to produce a proportional control signal for the hip exoskeleton. Each subject performed two 30-min exoskeleton walking trials (1.0 m/s) using each controller and a 10-min trial with the exoskeleton unpowered. During each trial, we measured subjects' metabolic cost of walking, lower limb EMG profiles, and joint kinematics and kinetics (torques and powers) using a force treadmill and motion capture. Compared to unassisted walking in the exoskeleton, myoelectric control significantly reduced metabolic cost by 13% ( p  = 0.005) and biological hip torque control reduced metabolic cost by 7% ( p  = 0.261). Subjects reduced muscle activity relative to the unpowered condition for a greater number of lower limb muscles using myoelectric control compared to the biological hip torque control. More subjects subjectively preferred the myoelectric controller to the biological hip torque control. Myoelectric control had more advantages (metabolic cost and muscle activity reduction) compared to a controller that targeted a biological torque profile for walking with a robotic hip exoskeleton. However, these results were obtained with a single exoskeleton device with specific control configurations while level walking at a

Systems Biology of Industrial Microorganisms

Science.gov (United States)

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.

Efficiency of using green algae as biological controllers against toxic ...

African Journals Online (AJOL)

Efficiency of using green algae as biological controllers against toxic algal taxa in cultured ... of two green algal species as biological control of the growth of toxic blue-green algae. ... African Journal of Aquatic Science 2014, 39(4): 443–450 ...

Advances in analysis and control of timedelayed dynamical systems

CERN Document Server

Sun, Jianqiao

2013-01-01

Analysis and control of timedelayed systems have been applied in a wide range of applications, ranging from mechanical, control, economic, to biological systems. Over the years, there has been a steady stream of interest in timedelayed dynamic systems, this book takes a snap shot of recent research from the world leading experts in analysis and control of dynamic systems with time delay to provide a bird's eye view of its development. The topics covered in this book include solution methods, stability analysis and control of periodic dynamic systems with time delay, bifurcations, stochastic dy

Sensitivity analysis approaches applied to systems biology models.

Science.gov (United States)

Zi, Z

2011-11-01

With the rising application of systems biology, sensitivity analysis methods have been widely applied to study the biological systems, including metabolic networks, signalling pathways and genetic circuits. Sensitivity analysis can provide valuable insights about how robust the biological responses are with respect to the changes of biological parameters and which model inputs are the key factors that affect the model outputs. In addition, sensitivity analysis is valuable for guiding experimental analysis, model reduction and parameter estimation. Local and global sensitivity analysis approaches are the two types of sensitivity analysis that are commonly applied in systems biology. Local sensitivity analysis is a classic method that studies the impact of small perturbations on the model outputs. On the other hand, global sensitivity analysis approaches have been applied to understand how the model outputs are affected by large variations of the model input parameters. In this review, the author introduces the basic concepts of sensitivity analysis approaches applied to systems biology models. Moreover, the author discusses the advantages and disadvantages of different sensitivity analysis methods, how to choose a proper sensitivity analysis approach, the available sensitivity analysis tools for systems biology models and the caveats in the interpretation of sensitivity analysis results.

Water quality and emergy evaluation of two freshwater aquacultural systems for eutrophic water in the Controlling by Biological Chains

Science.gov (United States)

Xi, L. M.; Liu, C. Q.; Liu, D. F.; Huang, W. L.; Sun, Y.

2017-08-01

According to the ecological restoration theory, this experiment establishes aquaculture systems controlled by biological chains in both Xiaoxidian area and Dujiadian area of Baiyangdian Lake separately in order to improve the environment and bring economic benefits. The appearance of Emergy Theory provides a new method for the quantitative analysis of ecological economic system. Based on the analysis of Emergy Theory, this thesis compares the eco-economic systems under different polyculture models between Xiaoxidian area and Dujiadian area. The result demonstrates that Xiaoxidian ecological system is of high Emergy Transformity with higher emergy output and economic income per unit area compared with Dujiadian area. While Dujiadian area has higher Emergy Yield Rate and lower Environment Load Rate. So Dujiadian area is more sustainable due to the overload non-renewable energy of Xiaoxidian area devoted by human. Therefore, it will be better if we adjust and optimize the management of aquaculture system in Xiaoxidian area in order to find a stable equilibrium point between environmental sustainability and economic benefits.

Systems Biology for Organotypic Cell Cultures

Energy Technology Data Exchange (ETDEWEB)

Grego, Sonia [RTI International, Research Triangle Park, NC (United States); Dougherty, Edward R. [Texas A & M Univ., College Station, TX (United States); Alexander, Francis J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Auerbach, Scott S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Berridge, Brian R. [GlaxoSmithKline, Research Triangle Park, NC (United States); Bittner, Michael L. [Translational Genomics Research Inst., Phoenix, AZ (United States); Casey, Warren [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Cooley, Philip C. [RTI International, Research Triangle Park, NC (United States); Dash, Ajit [HemoShear Therapeutics, Charlottesville, VA (United States); Ferguson, Stephen S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Fennell, Timothy R. [RTI International, Research Triangle Park, NC (United States); Hawkins, Brian T. [RTI International, Research Triangle Park, NC (United States); Hickey, Anthony J. [RTI International, Research Triangle Park, NC (United States); Kleensang, Andre [Johns Hopkins Univ., Baltimore, MD (United States). Center for Alternatives to Animal Testing; Liebman, Michael N. [IPQ Analytics, Kennett Square, PA (United States); Martin, Florian [Phillip Morris International, Neuchatel (Switzerland); Maull, Elizabeth A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Paragas, Jason [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qiao, Guilin [Defense Threat Reduction Agency, Ft. Belvoir, VA (United States); Ramaiahgari, Sreenivasa [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Sumner, Susan J. [RTI International, Research Triangle Park, NC (United States); Yoon, Miyoung [The Hamner Inst. for Health Sciences, Research Triangle Park, NC (United States); ScitoVation, Research Triangle Park, NC (United States)

2016-08-04

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. This consensus report summarizes the discussions held.

Impact of Thermodynamic Principles in Systems Biology

NARCIS (Netherlands)

Heijnen, J.J.

2010-01-01

It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects

Systems Biology of Metabolism: Annual Review of Biochemistry

DEFF Research Database (Denmark)

Nielsen, Jens

2017-01-01

Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are descr...

Iterative Systems Biology for Medicine – time for advancing from network signature to mechanistic equations

KAUST Repository

Gomez-Cabrero, David

2017-05-09

The rise and growth of Systems Biology following the sequencing of the human genome has been astounding. Early on, an iterative wet-dry methodology was formulated which turned out as a successful approach in deciphering biological complexity. Such type of analysis effectively identified and associated molecular network signatures operative in biological processes across different systems. Yet, it has proven difficult to distinguish between causes and consequences, thus making it challenging to attack medical questions where we require precise causative drug targets and disease mechanisms beyond a web of associated markers. Here we review principal advances with regard to identification of structure, dynamics, control, and design of biological systems, following the structure in the visionary review from 2002 by Dr. Kitano. Yet, here we find that the underlying challenge of finding the governing mechanistic system equations enabling precision medicine remains open thus rendering clinical translation of systems biology arduous. However, stunning advances in raw computational power, generation of high-precision multi-faceted biological data, combined with powerful algorithms hold promise to set the stage for data-driven identification of equations implicating a fundamental understanding of living systems during health and disease.

A geometric initial guess for localized electronic orbitals in modular biological systems

Energy Technology Data Exchange (ETDEWEB)

Beckman, P. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of Chicago, IL (United States); Fattebert, J. L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lau, E. Y. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Osei-Kuffuor, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2017-09-11

Recent first-principles molecular dynamics algorithms using localized electronic orbitals have achieved O(N) complexity and controlled accuracy in simulating systems with finite band gaps. However, accurately deter- mining the centers of these localized orbitals during simulation setup may require O(N³) operations, which is computationally infeasible for many biological systems. We present an O(N) approach for approximating orbital centers in proteins, DNA, and RNA which uses non-localized solutions for a set of fixed-size subproblems to create a set of geometric maps applicable to larger systems. This scalable approach, used as an initial guess in the O(N) first-principles molecular dynamics code MGmol, facilitates first-principles simulations in biological systems of sizes which were previously impossible.

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

Science.gov (United States)

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.

The Systems Biology Research Tool: evolvable open-source software

Directory of Open Access Journals (Sweden)

Wright Jeremiah

2008-06-01

Full Text Available Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability, to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

Arms Control: US and International efforts to ban biological weapons

Energy Technology Data Exchange (ETDEWEB)

1992-12-01

The Bacteriological (Biological) and Toxin Weapons Convention, the treaty that bans the development, production, and stockpiling and acquisition of biological weapons was opened for signature in 1972 and came into force in 1975 after being ratified by 22 governments, including the depository nations of the USA, the United Kingdom, and the former Soviet Union. In support of the Convention, the USA later established export controls on items used to make biological weapons. Further, in accordance with the 1990 President`s Enhanced Proliferation Control Initiative, actions were taken to redefine and expand US export controls, as well as to encourage multilateral controls through the Australia Group. Thus far, the Convention has not been effective in stopping the development of biological weapons. The principal findings as to the reasons of the failures of the Convention are found to be: the Convention lacks universality, compliance measures are effective, advantage of verification may outweigh disadvantages. Recommendations for mitigating these failures are outlined in this report.

Characterization and control of biological microrobots

NARCIS (Netherlands)

Khalil, I.S.M.; Pichel, Marc Philippe; Zondervan, L.; Abelmann, Leon; Misra, Sarthak; Desai, Jaydev P.; Dudek, Gregory; Khatib, Oussama; Kumar, Vijay

2013-01-01

This work addresses the characterization and control of Magnetotactic Bacterium (MTB) which can be considered as a biological microrobot. Magnetic dipole moment of the MTB and response to a field-with-alternating-direction are characterized. First, the magnetic dipole moment is characterized using

Characterization and Control of Biological Microrobots

NARCIS (Netherlands)

Khalil, I.S.M.; Pichel, Marc Philippe; Pichel, M.P.; Zondervan, L.; Abelmann, Leon; Misra, Sarthak

2012-01-01

This work addresses the characterization and control of Magnetotactic Bacterium (MTB) which can be considered as a biological microrobot. Magnetic dipole moment of the MTB and response to a field-with-alternating-direction are characterized. First, the magnetic dipole moment is characterized using

Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions.

Science.gov (United States)

Liu, Yanfeng; Li, Jianghua; Du, Guocheng; Chen, Jian; Liu, Long

By combining advanced omics technology and computational modeling, systems biologists have identified and inferred thousands of regulatory events and system-wide interactions of the bacterium Bacillus subtilis, which is commonly used both in the laboratory and in industry. This dissection of the multiple layers of regulatory networks and their interactions has provided invaluable information for unraveling regulatory mechanisms and guiding metabolic engineering. In this review, we discuss recent advances in the systems biology and metabolic engineering of B. subtilis and highlight current gaps in our understanding of global metabolism and global pathway engineering in this organism. We also propose future perspectives in the systems biology of B. subtilis and suggest ways that this approach can be used to guide metabolic engineering. Specifically, although hundreds of regulatory events have been identified or inferred via systems biology approaches, systematic investigation of the functionality of these events in vivo has lagged, thereby preventing the elucidation of regulatory mechanisms and further rational pathway engineering. In metabolic engineering, ignoring the engineering of multilayer regulation hinders metabolic flux redistribution. Post-translational engineering, allosteric engineering, and dynamic pathway analyses and control will also contribute to the modulation and control of the metabolism of engineered B. subtilis, ultimately producing the desired cellular traits. We hope this review will aid metabolic engineers in making full use of available systems biology datasets and approaches for the design and perfection of microbial cell factories through global metabolism optimization. Copyright © 2016 Elsevier Inc. All rights reserved.

Distribution and Biological Effects of Nanoparticles in the Reproductive System.

Science.gov (United States)

Liu, Ying; Li, Hongxia; Xiao, Kai

2016-01-01

Nanoparticles have shown great potential in biomedical applications such as imaging probes and drug delivery. However, the increasing use of nanoparticles has raised concerns about their adverse effects on human health and environment. Reproductive tissues and gametes represent highly delicate biological systems with the essential function of transmitting genetic information to the offspring, which is highly sensitive to environmental toxicants. This review aims to summarzie the penetration of physiological barriers (blood-testis barrier and placental barrier), distribution and biological effects of nanoparticles in the reproductive system, which is essential to control the beneficial effects of nanoparticles applications and to avoid their adverse effects on the reproductive system. We referred to a large number of relevant peer-reviewed research articles about the reproductive toxicity of nanoparticles. The comprehensive information was summarized into two parts: physiological barrier penetration and biological effects of nanoparticles in male or female reproductive system; distribution and metabolism of nanoparticles in the reproductive system. The representative examples were also presented in four tables. The in vitro and in vivo studies imply that some nanoparticles are able to cross the blood-testis barrier or placental barrier, and their penetration depends on the physicochemical characteristics of nanoparticles (e.g., composition, shape, particle size and surface coating). The toxicity assays indicate that nanoparticles might induce adverse physiological effects and impede fertility or embryogenesis. The barrier penetration, adverse physiological effects, distribution and metabolism are closely related to physicochemical characteristics of nanoparticles. Further systematic and mechanistic studies using well-characterized nanoparticles, relevant administration routes, and doses relevant to the expected exposure level are required to improve our

Plant Systems Biology at the Single-Cell Level.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Computational Modeling of Biological Systems From Molecules to Pathways

CERN Document Server

2012-01-01

Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

Cardiocladius oliffi (Diptera: Chironomidae as a potential biological control agent against Simulium squamosum (Diptera: Simuliidae

Directory of Open Access Journals (Sweden)

Wilson Michael D

2009-04-01

Full Text Available Abstract Background The control of onchocerciasis in the African region is currently based mainly on the mass drug administration of ivermectin. Whilst this has been found to limit morbidity, it does not stop transmission. In the absence of a macrofilaricide, there is a need for an integrated approach for disease management, which includes vector control. Vector control using chemical insecticides is expensive to apply, and therefore the use of other measures such as biological control agents is needed. Immature stages of Simulium squamosum, reared in the laboratory from egg masses collected from the field at Boti Falls and Huhunya (River Pawnpawn in Ghana, were observed to be attacked and fed upon by larvae of the chironomid Cardiocladius oliffi Freeman, 1956 (Diptera: Chironomidae. Methods Cardiocladius oliffi was successfully reared in the rearing system developed for S. damnosum s.l. and evaluated for its importance as a biological control agent in the laboratory. Results Even at a ratio of one C. oliffi to five S. squamosum, they caused a significant decrease in the number of adult S. squamosum emerging from the systems (treatments. Predation was confirmed by the amplification of Simulium DNA from C. oliffi observed to have fed on S. squamosum pupae. The study also established that the chironomid flies could successfully complete their development on a fish food diet only. Conclusion Cardiocladius oliffi has been demonstrated as potential biological control agent against S. squamosum.

The role of ionizing radiation in biological control of agricultural pests

International Nuclear Information System (INIS)

Mansour, M.

2011-01-01

Although the commercial biological control industry is growing, it still represents only a small portion of the international market of pest control sales (about 3%). This low ratio is due to several factors including high cost of production of biological control agents and technical and regulatory difficulties that complicate the shipping procedures and create trade barriers. This article summarizes the role of ionizing radiation in supporting the use of biological control agents in insect pest control and concentrates on its role in the production, transport, distribution, and release of parasites and predators and the advantages that ionizing radiation can offer, in comparison with traditional techniques. (author)

Systems Biology and Stem Cell Pluripotency

DEFF Research Database (Denmark)

Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

2016-01-01

Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

Invited review: gravitational biology of the neuromotor systems: a perspective to the next era

Science.gov (United States)

Edgerton, V. R.; Roy, R. R.

2000-01-01

Earth's gravity has had a significant impact on the designs of the neuromotor systems that have evolved. Early indications are that gravity also plays a key role in the ontogenesis of some of these design features. The purpose of the present review is not to assess and interpret a body of knowledge in the usual sense of a review but to look ahead, given some of the general concepts that have evolved and observations made to date, which can guide our future approach to gravitational biology. We are now approaching an era in gravitational biology during which well-controlled experiments can be conducted for sustained periods in a microgravity environment. Thus it is now possible to study in greater detail the role of gravity in phylogenesis and ontogenesis. Experiments can range from those conducted on the simplest levels of organization of the components that comprise the neuromotor system to those conducted on the whole organism. Generally, the impact of Earth's gravitational environment on living systems becomes more complex as the level of integration of the biological phenomenon of interest increases. Studies of the effects of gravitational vectors on neuromotor systems have and should continue to provide unique insight into these mechanisms that control and maintain neural control systems designed to function in Earth's gravitational environment. A number of examples are given of how a gravitational biology perspective can lead to a clearer understanding of neuromotor disorders. Furthermore, the technologies developed for spaceflight studies have contributed and should continue to contribute to studies of motor dysfunctions, such as spinal cord injury and stroke. Disorders associated with energy support and delivery systems and how these functions are altered by sedentary life styles at 1 G and by space travel in a microgravity environment are also discussed.

Biology of Leptoypha hospita (Hemiptera: Tingidae), a Potential Biological Control Agent of Chinese Privet

Science.gov (United States)

Yanzhuo Zhang; James L. Hanula; Scott Horn; Kristine Braman; Jianghua Sun

2011-01-01

The biology of Leptoypha hospita Drake et Poor (Hemiptera: Tingidae), a potential biological control agent from China for Chinese privet, Ligustrum sinense Lour., was studied in quarantine in the United States. Both nymphs and adults feed on Chinese privet mesophyll cells that lead to a bleached appearance of leaves and dieback of branch tips. L. hospita has five...

21 CFR 310.4 - Biologics; products subject to license control.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 5 2010-04-01 2010-04-01 false Biologics; products subject to license control... to license control. (a) If a drug has an approved license under section 351 of the Public Health.... (b) To obtain marketing approval for radioactive biological products for human use, as defined in...

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

Science.gov (United States)

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.

Evaluation of biologic occupational risk control practices: quality indicators development and validation.

Science.gov (United States)

Takahashi, Renata Ferreira; Gryschek, Anna Luíza F P L; Izumi Nichiata, Lúcia Yasuko; Lacerda, Rúbia Aparecida; Ciosak, Suely Itsuko; Gir, Elucir; Padoveze, Maria Clara

2010-05-01

There is growing demand for the adoption of qualification systems for health care practices. This study is aimed at describing the development and validation of indicators for evaluation of biologic occupational risk control programs. The study involved 3 stages: (1) setting up a research team, (2) development of indicators, and (3) validation of the indicators by a team of specialists recruited to validate each attribute of the developed indicators. The content validation method was used for the validation, and a psychometric scale was developed for the specialists' assessment. A consensus technique was used, and every attribute that obtained a Content Validity Index of at least 0.75 was approved. Eight indicators were developed for the evaluation of the biologic occupational risk prevention program, with emphasis on accidents caused by sharp instruments and occupational tuberculosis prevention. The indicators included evaluation of the structure, process, and results at the prevention and biologic risk control levels. The majority of indicators achieved a favorable consensus regarding all validated attributes. The developed indicators were considered validated, and the method used for construction and validation proved to be effective. Copyright (c) 2010 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

Optoelectronic system and apparatus for connection to biological systems

Science.gov (United States)

Okandan, Murat; Nielson, Gregory N.

2018-03-06

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.

Dynamic Analysis of a Phytoplankton-Fish Model with Biological and Artificial Control

OpenAIRE

Wang, Yapei; Zhao, Min; Pan, Xinhong; Dai, Chuanjun

2014-01-01

We investigate a nonlinear model of the interaction between phytoplankton and fish, which uses a pair of semicontinuous systems with biological and artificial control. First, the existence of an order-1 periodic solution to the system is analyzed using a Poincaré map and a geometric method. The stability conditions of the order-1 periodic solution are obtained by a theoretical mathematical analysis. Furthermore, based on previous analysis, we investigate the bifurcation in the order-1 periodi...

A review of imaging techniques for systems biology

Directory of Open Access Journals (Sweden)

Po Ming J

2008-08-01

Full Text Available Abstract This paper presents a review of imaging techniques and of their utility in system biology. During the last decade systems biology has matured into a distinct field and imaging has been increasingly used to enable the interplay of experimental and theoretical biology. In this review, we describe and compare the roles of microscopy, ultrasound, CT (Computed Tomography, MRI (Magnetic Resonance Imaging, PET (Positron Emission Tomography, and molecular probes such as quantum dots and nanoshells in systems biology. As a unified application area among these different imaging techniques, examples in cancer targeting are highlighted.

Casual Games and Casual Learning About Human Biological Systems

Science.gov (United States)

Price, C. Aaron; Gean, Katherine; Christensen, Claire G.; Beheshti, Elham; Pernot, Bryn; Segovia, Gloria; Person, Halcyon; Beasley, Steven; Ward, Patricia

2016-02-01

Casual games are everywhere. People play them throughout life to pass the time, to engage in social interactions, and to learn. However, their simplicity and use in distraction-heavy environments can attenuate their potential for learning. This experimental study explored the effects playing an online, casual game has on awareness of human biological systems. Two hundred and forty-two children were given pretests at a Museum and posttests at home after playing either a treatment or control game. Also, 41 children were interviewed to explore deeper meanings behind the test results. Results show modest improvement in scientific attitudes, ability to identify human biological systems and in the children's ability to describe how those systems work together in real-world scenarios. Interviews reveal that children drew upon their prior school learning as they played the game. Also, on the surface they perceived the game as mainly entertainment but were easily able to discern learning outcomes when prompted. Implications for the design of casual games and how they can be used to enhance transfer of knowledge from the classroom to everyday life are discussed.

BIOMASS PRODUCTION AND FORMULATION OF Bacillus subtilis FOR BIOLOGICAL CONTROL

Directory of Open Access Journals (Sweden)

Amran Muis

2016-10-01

Full Text Available Bacillus subtilis is a widespread bacterium found in soil, water, and air. It controls the growth of certain harmful bacteria and fungi, presumably by competing for nutrients, growth sites on plants, and by directly colonizing and attaching to fungal pathogens. When applied to seeds, it colonizes the developing root system of the plants and continues to live on the root system and provides protection throughout the growing season. The study on biomass production and formulation of B. subtilis for biological control was conducted in the laboratory of Department of Plant Pathology, College of Agriculture, University of the Philippines Los Baños (UPLB-CA, College, Laguna from May to July 2005. The objective of the study was to determine the optimum pH and a good carbon source for biomass production of B. subtilis and to develop a seed treatment formulation of B. subtilis as biological control agent. Results showed that the optimum pH for growth of B. subtilis was pH 6 (1.85 x 109 cfu/ml. In laboratory tests for biomass production using cassava flour, corn flour, rice flour, and brown sugar as carbon sources, it grew best in brown sugar plus yeast extract medium (6.8 x 108 cfu ml-1 in sterile distilled water and 7.8 x 108 cfu ml-1 in coconut water. In test for bacterial biomass carriers, talc proved to be the best in terms of number of bacteria recovered from the seeds (3.98 x 105 cfu seed-1.

Understanding Federal regulations as guidelines for classical biological control programs

Science.gov (United States)

Michael E. Montgomery

2011-01-01

This chapter reviews the legislation and rules that provide the foundation for federal regulation of the introduction of natural enemies of insects as biological control agents. It also outlines the steps for complying with regulatory requirements, using biological control of Adelges tsugae Annand, the hemlock woolly adelgid (HWA), as an example. The...

Is the efficacy of biological control against plant diseases likely to be more durable than that of chemical pesticides?

Directory of Open Access Journals (Sweden)

Marc eBardin

2015-07-01

Full Text Available The durability of a control method for plant protection is defined as the persistence of its efficacy in space and time. It depends on (i the selection pressure exerted by it on populations of plant pathogens and (ii on the capacity of these pathogens to adapt to the control method. Erosion of effectiveness of conventional plant protection methods has been widely studied in the past. For example, apparition of resistance to chemical pesticides in plant pathogens or pests has been extensively documented. The durability of biological control has often been assumed to be higher than that of chemical control. Results concerning pest management in agricultural systems have shown that this assumption may not always be justified. Resistance of various pests to one or several toxins of Bacillus thuringensis and apparition of resistance of the codling moth Cydia pomonella to the Cydia pomonella granulovirus have, for example, been described. In contrast with the situation for pests, the durability of biological control of plant diseases has hardly been studied and no scientific reports proving the loss of efficiency of biological control agents against plant pathogens in practice has been published so far. Knowledge concerning the possible erosion of effectiveness of biological control is essential to ensure a durable efficacy of biological control agents on target plant pathogens. This knowledge will result in identifying risk factors that can foster the selection of strains of plant pathogens resistant to biological control agents. It will also result in identifying types of biological control agents with lower risk of efficacy loss i.e. modes of action of biological control agents that does not favor the selection of resistant isolates in natural populations of plant pathogens. An analysis of the scientific literature was then conducted to assess the potential for plant pathogens to become resistant to biological control agents.

Modelling biological control with wild-type and genetically modified baculoviruses in the Helicoverpa armigera-cotton system

NARCIS (Netherlands)

Sun, X.; Werf, van der W.; Bianchi, F.J.J.A.; Hu, Z.; Vlak, J.M.

2006-01-01

A comprehensive model was developed to simulate virus epizootics in a stage structured insect population and analyse scenarios for the biological control of cotton bollworm (CBW), Helicoverpa armigera, in cotton, using wild-type or genetically modified baculoviruses. In simulations on dosage and

Designing and testing a classroom curriculum to teach preschoolers about the biology of physical activity: The respiration system as an underlying biological causal mechanism

Science.gov (United States)

Ewing, Tracy S.

The present study examined young children's understanding of respiration and oxygen as a source of vital energy underlying physical activity. Specifically, the purpose of the study was to explore whether a coherent biological theory, characterized by an understanding that bodily parts (heart and lungs) and processes (oxygen in respiration) as part of a biological system, can be taught as a foundational concept to reason about physical activity. The effects of a biology-based intervention curriculum designed to teach preschool children about bodily functions as a part of the respiratory system, the role of oxygen as a vital substance and how physical activity acts an energy source were examined. Participants were recruited from three private preschool classrooms (two treatment; 1 control) in Southern California and included a total of 48 four-year-old children (30 treatment; 18 control). Findings from this study suggested that young children could be taught relevant biological concepts about the role of oxygen in respiratory processes. Children who received biology-based intervention curriculum made significant gains in their understanding of the biology of respiration, identification of physical and sedentary activities. In addition these children demonstrated that coherence of conceptual knowledge was correlated with improved accuracy at activity identification and reasoning about the inner workings of the body contributing to endurance. Findings from this study provided evidence to support the benefits of providing age appropriate but complex coherent biological instruction to children in early childhood settings.

Using biological control research in the classroom to promote scientific inquiry and literacy

Science.gov (United States)

Many scientists who research biological control also teach at universities or more informally through cooperative outreach. The purpose of this paper is to review biological control activities for the classroom in four refereed journals, The American Biology Teacher, Journal of Biological Education...

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

OpenAIRE

Webb Penelope A; Hodgkinson Matt J

2007-01-01

Abstract 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.

Systems biology of neutrophil differentiation and immune response

DEFF Research Database (Denmark)

Theilgaard-Mönch, Kim; Porse, Bo T; Borregaard, Niels

2005-01-01

Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies. These stu......Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies....... These studies have identified a plethora of novel effector proteins stored in the granules of neutrophils. In addition, these studies provide evidence that neutrophil differentiation and immune response are governed by a highly coordinated transcriptional programme that regulates cellular fate and function...

Biological Potential in Serpentinizing Systems

Science.gov (United States)

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.

Design, modeling and control of a pneumatically actuated manipulator inspired by biological continuum structures

International Nuclear Information System (INIS)

Kang, Rongjie; Zheng Tianjiang; Guglielmino, Emanuele; Caldwell, Darwin G; Branson, David T

2013-01-01

Biological tentacles, such as octopus arms, have entirely flexible structures and virtually infinite degrees of freedom (DOF) that allow for elongation, shortening and bending at any point along the arm length. The amazing dexterity of biological tentacles has driven the growing implementation of continuum manipulators in robotic systems. This paper presents a pneumatic manipulator inspired by biological continuum structures in some of their key features and functions, such as continuum morphology, intrinsic compliance and stereotyped motions with hyper redundant DOF. The kinematics and dynamics of the manipulator are formulated and identified, and a hierarchical controller taking inspiration from the structure of an octopus nervous system is used to relate desired stereotyped motions to individual actuator inputs. Simulations and experiments are carried out to validate the model and prototype where good agreement was found between the two. (paper)

Biological control of ticks

Science.gov (United States)

Samish, M.; Ginsberg, H.; Glazer, I.; Bowman, A.S.; Nuttall, P.

2004-01-01

Ticks have numerous natural enemies, but only a few species have been evaluated as tick biocontrol agents (BCAs). Some laboratory results suggest that several bacteria are pathogenic to ticks, but their mode of action and their potential value as biocontrol agents remain to be determined. The most promising entomopathogenic fungi appear to be Metarhizium anisopliae and Beauveria bassiana, strains of which are already commercially available for the control of some pests. Development of effective formulations is critical for tick management. Entomopathogenic nematodes that are pathogenic to ticks can potentially control ticks, but improved formulations and selection of novel nematode strains are needed. Parasitoid wasps of the genus Ixodiphagus do not typically control ticks under natural conditions, but inundative releases show potential value. Most predators of ticks are generalists, with a limited potential for tick management (one possible exception is oxpeckers in Africa). Biological control is likely to play a substantial role in future IPM programmes for ticks because of the diversity of taxa that show high potential as tick BCAs. Considerable research is required to select appropriate strains, develop them as BCAs, establish their effectiveness, and devise production strategies to bring them to practical use.

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

Science.gov (United States)

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.

Using Biological-Control Research in the Classroom to Promote Scientific Inquiry & Literacy

Science.gov (United States)

Richardson, Matthew L.; Richardson, Scott L.; Hall, David G.

2012-01-01

Scientists researching biological control should engage in education because translating research programs into classroom activities is a pathway to increase scientific literacy among students. Classroom activities focused on biological control target all levels of biological organization and can be cross-disciplinary by drawing from subject areas…

Systems biology approach to bioremediation

Energy Technology Data Exchange (ETDEWEB)

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 potential for making bioremediation breakthroughs and illuminating the ‘black box’.

BetaWB - A language for modular representation of biological systems

DEFF Research Database (Denmark)

Ihekwaba, Adoha; Larcher, Roberto; Mardare, Radu Iulian

2007-01-01

A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007......A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007...

Dynamic optimization of distributed biological systems using robust and efficient numerical techniques.

Science.gov (United States)

Vilas, Carlos; Balsa-Canto, Eva; García, Maria-Sonia G; Banga, Julio R; Alonso, Antonio A

2012-07-02

Systems biology allows the analysis of biological systems behavior under different conditions through in silico experimentation. The possibility of perturbing biological systems in different manners calls for the design of perturbations to achieve particular goals. Examples would include, the design of a chemical stimulation to maximize the amplitude of a given cellular signal or to achieve a desired pattern in pattern formation systems, etc. Such design problems can be mathematically formulated as dynamic optimization problems which are particularly challenging when the system is described by partial differential equations.This work addresses the numerical solution of such dynamic optimization problems for spatially distributed biological systems. The usual nonlinear and large scale nature of the mathematical models related to this class of systems and the presence of constraints on the optimization problems, impose a number of difficulties, such as the presence of suboptimal solutions, which call for robust and efficient numerical techniques. Here, the use of a control vector parameterization approach combined with efficient and robust hybrid global optimization methods and a reduced order model methodology is proposed. The capabilities of this strategy are illustrated considering the solution of a two challenging problems: bacterial chemotaxis and the FitzHugh-Nagumo model. In the process of chemotaxis the objective was to efficiently compute the time-varying optimal concentration of chemotractant in one of the spatial boundaries in order to achieve predefined cell distribution profiles. Results are in agreement with those previously published in the literature. The FitzHugh-Nagumo problem is also efficiently solved and it illustrates very well how dynamic optimization may be used to force a system to evolve from an undesired to a desired pattern with a reduced number of actuators. The presented methodology can be used for the efficient dynamic optimization of

Isolation of microorganisms for biological control the moniliophthora roreri

OpenAIRE

suarez contreras, liliana yanet; Rangel Riaño, Alba Luz

2014-01-01

Moniliophlhora roreri is the causal agent of cocoa Moniliasis, which produces losses of up to 60% of the crop, as it affects only its commercial product, the cob. Biological control appears as an alternative management, using endophytic microorganisms. The reason because of this research came up was that it was aimed to isolate microorganisms with antagonist potential for biological control towards the phytopathogen M. roreri in Norte de Santander. This is done through isolation and identifica...

Yeast systems biology to unravel the network of life

DEFF Research Database (Denmark)

Mustacchi, Roberta; Hohmann, S; Nielsen, Jens

2006-01-01

Systems biology focuses on obtaining a quantitative description of complete biological systems, even complete cellular function. In this way, it will be possible to perform computer-guided design of novel drugs, advanced therapies for treatment of complex diseases, and to perform in silico design....... Furthermore, it serves as an industrial workhorse for production of a wide range of chemicals and pharmaceuticals. Systems biology involves the combination of novel experimental techniques from different disciplines as well as functional genomics, bioinformatics and mathematical modelling, and hence no single...... laboratory has access to all the necessary competences. For this reason the Yeast Systems Biology Network (YSBN) has been established. YSBN will coordinate research efforts, in yeast systems biology and, through the recently obtained EU funding for a Coordination Action, it will be possible to set...

3S - Systematic, systemic, and systems biology and toxicology.

Science.gov (United States)

Smirnova, Lena; Kleinstreuer, Nicole; Corvi, Raffaella; Levchenko, Andre; Fitzpatrick, Suzanne C; Hartung, Thomas

2018-01-01

A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to reca-pitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organ-on-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the chal-lenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

41 CFR 101-42.1102-5 - Drugs, biologicals, and reagents other than controlled substances.

Science.gov (United States)

2010-07-01

... 41 Public Contracts and Property Management 2 2010-07-01 2010-07-01 true Drugs, biologicals, and reagents other than controlled substances. 101-42.1102-5 Section 101-42.1102-5 Public Contracts and Property Management Federal Property Management Regulations System FEDERAL PROPERTY MANAGEMENT REGULATIONS...

Microbiome studies in the biological control of plant pathogens

Science.gov (United States)

Biological control of plant pathogens, although it has been a successful alternative that has allowed to select microorganisms for the generation of bioproducts and to understand multiple biological mechanisms, cannot be considered as a strategy defined only from the selection of a range of cultiva...

Macro to microfluidics system for biological environmental monitoring.

Science.gov (United States)

Delattre, Cyril; Allier, Cédric P; Fouillet, Yves; Jary, Dorothée; Bottausci, Frederic; Bouvier, Denis; Delapierre, Guillaume; Quinaud, Manuelle; Rival, Arnaud; Davoust, Laurent; Peponnet, Christine

2012-01-01

Biological environmental monitoring (BEM) is a growing field of research which challenges both microfluidics and system automation. The aim is to develop a transportable system with analysis throughput which satisfies the requirements: (i) fully autonomous, (ii) complete protocol integration from sample collection to final analysis, (iii) detection of diluted molecules or biological species in a large real life environmental sample volume, (iv) robustness and (v) flexibility and versatility. This paper discusses all these specifications in order to define an original fluidic architecture based on three connected modules, a sampling module, a sample preparation module and a detection module. The sample preparation module highly concentrates on the pathogens present in a few mL samples of complex and unknown solutions and purifies the pathogens' nucleic acids into a few μL of a controlled buffer. To do so, a two-step concentration protocol based on magnetic beads is automated in a reusable macro-to-micro fluidic system. The detection module is a PCR based miniaturized platform using digital microfluidics, where reactions are performed in 64 nL droplets handled by electrowetting on dielectric (EWOD) actuation. The design and manufacture of the two modules are reported as well as their respective performances. To demonstrate the integration of the complete protocol in the same system, first results of pathogen detection are shown. Copyright © 2012 Elsevier B.V. All rights reserved.

Quantum and classical dynamics in biologically inspired systems

International Nuclear Information System (INIS)

Guerreschi, G.

2012-01-01

Quantum biology is an emerging field in which traditional believes and paradigms are under examination. Typically, quantum effects are witnessed inside quantum optics or atomic physics laboratories in systems which are kept under control and isolated from any noise source by means of very advanced technology. Biological systems exhibit opposite characteristics: They are usually constituted of macromolecules continuously exposed to a warm and wet environment, well beyond our control; but at the same time, they operate far away from equilibrium. Recently, the experimental observation of excitonic coherence in photosynthetic complexes has con firmed that, in non-equilibrium scenarios, quantum phenomena can survive even in presence of a noisy environment. The challenge faced by the ongoing research is twofold: On one side, considering biological molecules as effective nanomachines, one has to address questions of principle regarding their design and functioning; on the other side, one has to investigate real systems which are experimentally accessible and identify such features in these concrete scenarios. The present thesis contributes to both of these aspects. In Part I, we demonstrate how entanglement can be persistently generated even under unfavorable environmental conditions. The physical mechanism is modeled after the idea of conformational changes, and it relies on the interplay of classical oscillations of large structures with the quantum dynamics of a few interacting degrees of freedom. In a similar context, we show that the transfer of an excitation through a linear chain of sites can be enhanced when the inter-site distances oscillate periodically. This enhancement is present even in comparison with the static con figuration which is optimal in the classical case and, therefore, it constitutes a clear signature of the underlying quantum dynamics. In Part II of this thesis, we study the radical pair mechanism from the perspective of quantum control and

Strategies for structuring interdisciplinary education in Systems Biology

DEFF Research Database (Denmark)

Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure

2016-01-01

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...

Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle

DEFF Research Database (Denmark)

Mazzoni, Gianluca; Pedersen, Hanne S.; de Oliveira Junior, Gerson A.

2017-01-01

by both conventional and ARTs such as OPU-IVP. The integration of systems biology information across different biological layers generates a complete view of the different molecular networks that control complex traits and can provide a strong contribution to the understanding of traits related to ARTs....

Redefining plant systems biology: from cell to ecosystem

NARCIS (Netherlands)

Keurentjes, J.J.B.; Angenent, G.C.; Dicke, M.; Martins Dos Santos, V.A.P.; Molenaar, J.; Van der Putten, W.H.; de Ruiter, P.C.; Struik, P.C.; Thomma, B.P.H.J.

2011-01-01

Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase

Multi-level and hybrid modelling approaches for systems biology.

Science.gov (United States)

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.

Electromagnetic fields in biological systems

National Research Council Canada - National Science Library

Lin, James C

2012-01-01

"Focusing on exposure, induced fields, and absorbed energy, this volume covers the interaction of electromagnetic fields and waves with biological systems, spanning static fields to terahertz waves...

Tunable promoters in synthetic and systems biology

DEFF Research Database (Denmark)

Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

2012-01-01

in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...... for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression...

Fiber laser-microscope system for femtosecond photodisruption of biological samples.

Science.gov (United States)

Yavaş, Seydi; Erdogan, Mutlu; Gürel, Kutan; Ilday, F Ömer; Eldeniz, Y Burak; Tazebay, Uygar H

2012-03-01

We report on the development of a ultrafast fiber laser-microscope system for femtosecond photodisruption of biological targets. A mode-locked Yb-fiber laser oscillator generates few-nJ pulses at 32.7 MHz repetition rate, amplified up to ∼125 nJ at 1030 nm. Following dechirping in a grating compressor, ∼240 fs-long pulses are delivered to the sample through a diffraction-limited microscope, which allows real-time imaging and control. The laser can generate arbitrary pulse patterns, formed by two acousto-optic modulators (AOM) controlled by a custom-developed field-programmable gate array (FPGA) controller. This capability opens the route to fine optimization of the ablation processes and management of thermal effects. Sample position, exposure time and imaging are all computerized. The capability of the system to perform femtosecond photodisruption is demonstrated through experiments on tissue and individual cells.

Systems biology solutions for biochemical production challenges

DEFF Research Database (Denmark)

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

2017-01-01

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...

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Science.gov (United States)

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.

How causal analysis can reveal autonomy in models of biological systems

Science.gov (United States)

Marshall, William; Kim, Hyunju; Walker, Sara I.; Tononi, Giulio; Albantakis, Larissa

2017-11-01

Standard techniques for studying biological systems largely focus on their dynamical or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system elements or the dynamics of the system as a whole disregards the organizational structure of the system-whether there are subsets of elements with joint causes or effects, and whether the system is strongly integrated or composed of several loosely interacting components. Integrated information theory offers a theoretical framework to (1) investigate the compositional cause-effect structure of a system and to (2) identify causal borders of highly integrated elements comprising local maxima of intrinsic cause-effect power. Here we apply this comprehensive causal analysis to a Boolean network model of the fission yeast (Schizosaccharomyces pombe) cell cycle. We demonstrate that this biological model features a non-trivial causal architecture, whose discovery may provide insights about the real cell cycle that could not be gained from holistic or reductionist approaches. We also show how some specific properties of this underlying causal architecture relate to the biological notion of autonomy. Ultimately, we suggest that analysing the causal organization of a system, including key features like intrinsic control and stable causal borders, should prove relevant for distinguishing life from non-life, and thus could also illuminate the origin of life problem. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Application of hierarchical dissociated neural network in closed-loop hybrid system integrating biological and mechanical intelligence.

Directory of Open Access Journals (Sweden)

Yongcheng Li

Full Text Available Neural networks are considered the origin of intelligence in organisms. In this paper, a new design of an intelligent system merging biological intelligence with artificial intelligence was created. It was based on a neural controller bidirectionally connected to an actual mobile robot to implement a novel vehicle. Two types of experimental preparations were utilized as the neural controller including 'random' and '4Q' (cultured neurons artificially divided into four interconnected parts neural network. Compared to the random cultures, the '4Q' cultures presented absolutely different activities, and the robot controlled by the '4Q' network presented better capabilities in search tasks. Our results showed that neural cultures could be successfully employed to control an artificial agent; the robot performed better and better with the stimulus because of the short-term plasticity. A new framework is provided to investigate the bidirectional biological-artificial interface and develop new strategies for a future intelligent system using these simplified model systems.

Application of Hierarchical Dissociated Neural Network in Closed-Loop Hybrid System Integrating Biological and Mechanical Intelligence

Science.gov (United States)

Zhang, Bin; Wang, Yuechao; Li, Hongyi

2015-01-01

Neural networks are considered the origin of intelligence in organisms. In this paper, a new design of an intelligent system merging biological intelligence with artificial intelligence was created. It was based on a neural controller bidirectionally connected to an actual mobile robot to implement a novel vehicle. Two types of experimental preparations were utilized as the neural controller including ‘random’ and ‘4Q’ (cultured neurons artificially divided into four interconnected parts) neural network. Compared to the random cultures, the ‘4Q’ cultures presented absolutely different activities, and the robot controlled by the ‘4Q’ network presented better capabilities in search tasks. Our results showed that neural cultures could be successfully employed to control an artificial agent; the robot performed better and better with the stimulus because of the short-term plasticity. A new framework is provided to investigate the bidirectional biological-artificial interface and develop new strategies for a future intelligent system using these simplified model systems. PMID:25992579

Application of hierarchical dissociated neural network in closed-loop hybrid system integrating biological and mechanical intelligence.

Science.gov (United States)

Li, Yongcheng; Sun, Rong; Zhang, Bin; Wang, Yuechao; Li, Hongyi

2015-01-01

Neural networks are considered the origin of intelligence in organisms. In this paper, a new design of an intelligent system merging biological intelligence with artificial intelligence was created. It was based on a neural controller bidirectionally connected to an actual mobile robot to implement a novel vehicle. Two types of experimental preparations were utilized as the neural controller including 'random' and '4Q' (cultured neurons artificially divided into four interconnected parts) neural network. Compared to the random cultures, the '4Q' cultures presented absolutely different activities, and the robot controlled by the '4Q' network presented better capabilities in search tasks. Our results showed that neural cultures could be successfully employed to control an artificial agent; the robot performed better and better with the stimulus because of the short-term plasticity. A new framework is provided to investigate the bidirectional biological-artificial interface and develop new strategies for a future intelligent system using these simplified model systems.

Evaluation of Orius species for biological control of Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae)

NARCIS (Netherlands)

Tommasini, M.G.

2003-01-01

Key words: Thysanoptera, Frankliniella occidentalis, Heteroptera, Orius leavigatu, Orius majusculu, Orius niger, Orius insidiosus, Biology, Diapause, Biological control.The overall aim of this research was to develop a biological control programme for F. occidentalis through the selection of

Hybridization of an invasive shrub affects tolerance and resistance to defoliation by a biological control agent

Science.gov (United States)

Williams, Wyatt I.; Friedman, Jonathan M.; Gaskin, John F.; Norton, Andrew P.

2014-01-01

Evolution has contributed to the successful invasion of exotic plant species in their introduced ranges, but how evolution affects particular control strategies is still under evaluation. For instance, classical biological control, a common strategy involving the utilization of highly specific natural enemies to control exotic pests, may be negatively affected by host hybridization because of shifts in plant traits, such as root allocation or chemical constituents. We investigated introgression between two parent species of the invasive shrub tamarisk (Tamarix spp.) in the western United States, and how differences in plant traits affect interactions with a biological control agent. Introgression varied strongly with latitude of origin and was highly correlated with plant performance. Increased levels of T. ramosissima introgression resulted in both higher investment in roots and tolerance to defoliation and less resistance to insect attack. Because tamarisk hybridization occurs predictably on the western U.S. landscape, managers may be able to exploit this information to maximize control efforts. Genetic differentiation in plant traits in this system underpins the importance of plant hybridization and may explain why some biological control releases are more successful than others.

The aims of systems biology: between molecules and organisms.

Science.gov (United States)

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.

Hybrid dynamical systems observation and control

CERN Document Server

Defoort, Michael

2015-01-01

This book is a collection of contributions defining the state of current knowledge and new trends in hybrid systems – systems involving both continuous dynamics and discrete events – as described by the work of several well-known groups of researchers. Hybrid Dynamical Systems presents theoretical advances in such areas as diagnosability, observability and stabilization for various classes of system. Continuous and discrete state estimation and self-triggering control of nonlinear systems are advanced. The text employs various methods, among them, high-order sliding modes, Takagi–Sugeno representation and sampled-data switching to achieve its ends. The many applications of hybrid systems from power converters to computer science are not forgotten; studies of flexible-joint robotic arms and – as representative biological systems – the behaviour of the human heart and vasculature, demonstrate the wide-ranging practical significance of control in hybrid systems. The cross-disciplinary origins of study ...

Opportunities for biological weed control in Europe

NARCIS (Netherlands)

Scheepens, P.C.; Müller-Schärer, H.; Kempenaar, C.

2001-01-01

The development and application of biological weed control offer greatopportunities not only for farmers, nature conservationists and othervegetation managers but also for institutions and companies that wish tosell plant protection services and products, and for the general publicthat demands safe

A systems biology approach to study systemic inflammation.

Science.gov (United States)

Chen, Bor-Sen; Wu, Chia-Chou

2014-01-01

Systemic inflammation needs a precise control on the sequence and magnitude of occurring events. The high throughput data on the host-pathogen interactions gives us an opportunity to have a glimpse on the systemic inflammation. In this article, a dynamic Candida albicans-zebrafish interactive infectious network is built as an example to demonstrate how systems biology approach can be used to study systematic inflammation. In particular, based on microarray data of C. albicans and zebrafish during infection, the hyphal growth, zebrafish, and host-pathogen intercellular PPI networks were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host. The signaling pathways for morphogenesis and hyphal growth of C. albicans were 2 significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins to gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. This integrated network consisting of intercellular invasion and cellular defense processes during infection can improve medical therapies and facilitate development of new antifungal drugs.

MIDAS: A Modular DNA Assembly System for Synthetic Biology.

Science.gov (United States)

van Dolleweerd, Craig J; Kessans, Sarah A; Van de Bittner, Kyle C; Bustamante, Leyla Y; Bundela, Rudranuj; Scott, Barry; Nicholson, Matthew J; Parker, Emily J

2018-04-20

A modular and hierarchical DNA assembly platform for synthetic biology based on Golden Gate (Type IIS restriction enzyme) cloning is described. This enabling technology, termed MIDAS (for Modular Idempotent DNA Assembly System), can be used to precisely assemble multiple DNA fragments in a single reaction using a standardized assembly design. It can be used to build genes from libraries of sequence-verified, reusable parts and to assemble multiple genes in a single vector, with full user control over gene order and orientation, as well as control of the direction of growth (polarity) of the multigene assembly, a feature that allows genes to be nested between other genes or genetic elements. We describe the detailed design and use of MIDAS, exemplified by the reconstruction, in the filamentous fungus Penicillium paxilli, of the metabolic pathway for production of paspaline and paxilline, key intermediates in the biosynthesis of a range of indole diterpenes-a class of secondary metabolites produced by several species of filamentous fungi. MIDAS was used to efficiently assemble a 25.2 kb plasmid from 21 different modules (seven genes, each composed of three basic parts). By using a parts library-based system for construction of complex assemblies, and a unique set of vectors, MIDAS can provide a flexible route to assembling tailored combinations of genes and other genetic elements, thereby supporting synthetic biology applications in a wide range of expression hosts.

Systems Biology: Impressions from a Newcomer Graduate Student in 2016

Science.gov (United States)

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…

Microbial stress tolerance for biofuels. Systems biology

Energy Technology Data Exchange (ETDEWEB)

Liu, Zonglin Lewis (ed.) [National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL (United States)

2012-07-01

The development of sustainable and renewable biofuels is attracting growing interest. It is vital to develop robust microbial strains for biocatalysts that are able to function under multiple stress conditions. This Microbiology Monograph provides an overview of methods for studying microbial stress tolerance for biofuels applications using a systems biology approach. Topics covered range from mechanisms to methodology for yeast and bacteria, including the genomics of yeast tolerance and detoxification; genetics and regulation of glycogen and trehalose metabolism; programmed cell death; high gravity fermentations; ethanol tolerance; improving biomass sugar utilization by engineered Saccharomyces; the genomics on tolerance of Zymomonas mobilis; microbial solvent tolerance; control of stress tolerance in bacterial host organisms; metabolomics for ethanologenic yeast; automated proteomics work cell systems for strain improvement; and unification of gene expression data for comparable analyses under stress conditions. (orig.)

Mathematical methods in systems biology.

Science.gov (United States)

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.

Nanoscale technology in biological systems

CERN Document Server

Greco, Ralph S; Smith, R Lane

2004-01-01

Reviewing recent accomplishments in the field of nanobiology Nanoscale Technology in Biological Systems introduces the application of nanoscale matrices to human biology. It focuses on the applications of nanotechnology fabrication to biomedical devices and discusses new physical methods for cell isolation and manipulation and intracellular communication at the molecular level. It also explores the application of nanobiology to cardiovascular diseases, oncology, transplantation, and a range of related disciplines. This book build a strong background in nanotechnology and nanobiology ideal for

Control mechanisms for stochastic biochemical systems via computation of reachable sets.

Science.gov (United States)

Lakatos, Eszter; Stumpf, Michael P H

2017-08-01

Controlling the behaviour of cells by rationally guiding molecular processes is an overarching aim of much of synthetic biology. Molecular processes, however, are notoriously noisy and frequently nonlinear. We present an approach to studying the impact of control measures on motifs of molecular interactions that addresses the problems faced in many biological systems: stochasticity, parameter uncertainty and nonlinearity. We show that our reachability analysis formalism can describe the potential behaviour of biological (naturally evolved as well as engineered) systems, and provides a set of bounds on their dynamics at the level of population statistics: for example, we can obtain the possible ranges of means and variances of mRNA and protein expression levels, even in the presence of uncertainty about model parameters.

Development of Design Tools for the Optimization of Biologically Based Control Systems

Data.gov (United States)

National Aeronautics and Space Administration — I plan to develop software that aids in the design of biomimetic control systems by optimizing the properties of the system in order to produce the desired output....

Modeling of biological intelligence for SCM system optimization.

Science.gov (United States)

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

Directory of Open Access Journals (Sweden)

Shengyong Chen

2012-01-01

Full Text Available 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

Science.gov (United States)

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

Selection of Trichogramma for inundative biological control

NARCIS (Netherlands)

Pak, G.A.

1988-01-01

This thesis presents a study of the potential for biological control of lepidopterous pests on cabbage crops in the Netherlands, by means of inundative releases of the egg parasite Trichogramma (Hymenoptera, Trichogrammatidae). The objective of this study is to investigate the

Incorporating biological control into IPM decision making

Science.gov (United States)

Of the many ways biological control can be incorporated into Integrated Pest Management (IPM) programs, natural enemy thresholds are arguably most easily adopted by stakeholders. Integration of natural enemy thresholds into IPM programs requires ecological and cost/benefit crop production data, thr...

Systems biology at work

NARCIS (Netherlands)

Martins Dos Santos, V.A.P.; Damborsky, J.

2010-01-01

In his editorial overview for the 2008 Special Issue on this topic, the late Jaroslav Stark pointedly noted that systems biology is no longer a niche pursuit, but a recognized discipline in its own right “noisily” coming of age [1]. Whilst general underlying principles and basic techniques are now

New experimental approaches to the biology of flight control systems.

Science.gov (United States)

Taylor, Graham K; Bacic, Marko; Bomphrey, Richard J; Carruthers, Anna C; Gillies, James; Walker, Simon M; Thomas, Adrian L R

2008-01-01

Here we consider how new experimental approaches in biomechanics can be used to attain a systems-level understanding of the dynamics of animal flight control. Our aim in this paper is not to provide detailed results and analysis, but rather to tackle several conceptual and methodological issues that have stood in the way of experimentalists in achieving this goal, and to offer tools for overcoming these. We begin by discussing the interplay between analytical and empirical methods, emphasizing that the structure of the models we use to analyse flight control dictates the empirical measurements we must make in order to parameterize them. We then provide a conceptual overview of tethered-flight paradigms, comparing classical ;open-loop' and ;closed-loop' setups, and describe a flight simulator that we have recently developed for making flight dynamics measurements on tethered insects. Next, we provide a conceptual overview of free-flight paradigms, focusing on the need to use system identification techniques in order to analyse the data they provide, and describe two new techniques that we have developed for making flight dynamics measurements on freely flying birds. First, we describe a technique for obtaining inertial measurements of the orientation, angular velocity and acceleration of a steppe eagle Aquila nipalensis in wide-ranging free flight, together with synchronized measurements of wing and tail kinematics using onboard instrumentation and video cameras. Second, we describe a photogrammetric method to measure the 3D wing kinematics of the eagle during take-off and landing. In each case, we provide demonstration data to illustrate the kinds of information available from each method. We conclude by discussing the prospects for systems-level analyses of flight control using these techniques and others like them.

Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology.

Science.gov (United States)

MacLeod, Miles; Nersessian, Nancy J

2015-02-01

In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding." Copyright © 2014 Elsevier Ltd. All rights reserved.

Population-level compensation impedes biological control of an invasive forb and indirect release of a native grass

Science.gov (United States)

Yvette K. Ortega; Dean E. Pearson; Lauren P. Waller; Nancy J. Sturdevant; John L. Maron

2012-01-01

The intentional introduction of specialist insect herbivores for biological control of exotic weeds provides ideal but understudied systems for evaluating important ecological concepts related to top-down control, plant compensatory responses, indirect effects, and the influence of environmental context on these processes. Centaurea stoebe (spotted knapweed) is a...

Biologically inspired rate control of chaos.

Science.gov (United States)

Olde Scheper, Tjeerd V

2017-10-01

The overall intention of chaotic control is to eliminate chaos and to force the system to become stable in the classical sense. In this paper, I demonstrate a more subtle method that does not eliminate all traces of chaotic behaviour; yet it consistently, and reliably, can provide control as intended. The Rate Control of Chaos (RCC) method is derived from metabolic control processes and has several remarkable properties. RCC can control complex systems continuously, and unsupervised, it can also maintain control across bifurcations, and in the presence of significant systemic noise. Specifically, I show that RCC can control a typical set of chaotic models, including the 3 and 4 dimensional chaotic Lorenz systems, in all modes. Furthermore, it is capable of controlling spatiotemporal chaos without supervision and maintains control of the system across bifurcations. This property of RCC allows a dynamic system to operate in parameter spaces that are difficult to control otherwise. This may be particularly interesting for the control of forced systems or dynamic systems that are chaotically perturbed. These control properties of RCC are applicable to a range of dynamic systems, thereby appearing to have far-reaching effects beyond just controlling chaos. RCC may also point to the existence of a biochemical control function of an enzyme, to stabilise the dynamics of the reaction cascade.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Plant Systems Biology (editorial)

Science.gov (United States)

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 ‘‘...

Biological control of Meloidogyne incognita by Trichoderma ...

African Journals Online (AJOL)

Biological control against the root-knot nematode, Meloidogyne incognita was proven to occur in tomato, Solanum lycopersicom, soil-drenched with different isolates of Trichoderma harzianum and a commercial suspension of Serratia marcescens (Nemaless). The potential of such biocontrol agents to trigger plant defense ...

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

Science.gov (United States)

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.

Systems biology solutions for biochemical production challenges.

Science.gov (United States)

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.

GPSR: A Resource for Genomics Proteomics and Systems Biology

Indian Academy of Sciences (India)

GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

75 FR 64984 - Availability of an Environmental Assessment for a Biological Control Agent for Hawkweeds

Science.gov (United States)

2010-10-21

... hawkweed gall wasp, Aulacidea subterminalis, into the continental United States as a biological control... United States for the biological control of hawkweeds (Hieracium pilosella, H. aurantiacum, H... control, and the use of biological control organisms. The use of herbicides, while effective, is limited...

Advancing metabolic engineering through systems biology of industrial microorganisms

DEFF Research Database (Denmark)

Dai, Zongjie; Nielsen, Jens

2015-01-01

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......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...... 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....

Dietary antioxidant synergy in chemical and biological systems.

Science.gov (United States)

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.

BIOLOGICAL CONTROL - AS A MEANS TO CONTROL INSECT PESTS IN AZERBAIJAN

Directory of Open Access Journals (Sweden)

Z. M. Mamedov

2013-01-01

Full Text Available Two hundreds and twenty species parasites and predators of pests of various agricultures are revealed in Azerbaijan. The complex of entomophages of certain pests of agricultures is studied: 48 species of parasites and predators of Chloridea obsoleta 21 species of entomophages of Pectinophora malvella Hb., over 160 species of entomophages of pests of ozehards and vegetables, 34 species of entomophages of pests of forests. The hundreds species of entomophages and some entomophogenous microbes and antagonists are revealed. Biology and ecology of over 60 species of entomophages and useful microorganisims which are prospective as biological control agents are studied.

Systems of organic farming in spring vetch I: Biological response of sucking insect pests

Directory of Open Access Journals (Sweden)

Ivelina Nikolova

2015-04-01

Full Text Available Four systems of organic farming and a conventional farming system were studied over the period 2012-2014. The organic system trial variants included: I – an organic farming system without any biological products used (growth under natural soil fertility – Control; II – an organic farming system involving the use of a biological foliar fertilizer and a biological plant growth regulator (Polyversum+Biofa; III – an organic farming system in which a biological insecticide (NeemAzal T/S was used; IV – an organic farming system including a combination of three organic products: the foliar fertilizer, the plant growth regulator and the bioinsecticide (Polyversum+Biofa+NeemAzal T/S. Variant V represented a conventional farming system in which synthetic products were used in combination (foliar fertilizer, plant growth regulator and insecticide: Masterblend+Flordimex 420+Nurelle D. Treatment of vetch plants with the biological insecticide NeemAzal in combination with Biofa and Polyversum resulted in the lowest density of sucking pests, compared to all other organic farming methods tested (i.e. without NeemAzal, with NeemAzal alone, and its combination with Biofa and Polyversum. The greatest reduction in pest numbers during the vegetation period in that variant was observed in species of the order Thysanoptera (36.0-41.4%, followed by Hemiptera, and the families Aphididae (31.6-40.3% and Cicadellidae (27.3-28.6%. This combination showed an efficient synergistic interaction and an increase in biological efficacy as compared to individual application of NeemAzal. The highest toxic impact was found against Thrips tabaci, followed by Acyrthosiphon pisum. An analysis of variance regarding the efficacy against the species A. pisum, E. pteridis and T. tabaci showed that type of treatment had the most dominant influence and statistically significant impact.

Do biological-based strategies hold promise to biofouling control in MBRs?

KAUST Repository

Malaeb, Lilian

2013-10-01

Biofouling in membrane bioreactors (MBRs) remains a primary challenge for their wider application, despite the growing acceptance of MBRs worldwide. Research studies on membrane fouling are extensive in the literature, with more than 200 publications on MBR fouling in the last 3 years; yet, improvements in practice on biofouling control and management have been remarkably slow. Commonly applied cleaning methods are only partially effective and membrane replacement often becomes frequent. The reason for the slow advancement in successful control of biofouling is largely attributed to the complex interactions of involved biological compounds and the lack of representative-for-practice experimental approaches to evaluate potential effective control strategies. Biofouling is driven by microorganisms and their associated extra-cellular polymeric substances (EPS) and microbial products. Microorganisms and their products convene together to form matrices that are commonly treated as a black box in conventional control approaches. Biological-based antifouling strategies seem to be a promising constituent of an effective integrated control approach since they target the essence of biofouling problems. However, biological-based strategies are in their developmental phase and several questions should be addressed to set a roadmap for translating existing and new information into sustainable and effective control techniques. This paper investigates membrane biofouling in MBRs from the microbiological perspective to evaluate the potential of biological-based strategies in offering viable control alternatives. Limitations of available control methods highlight the importance of an integrated anti-fouling approach including biological strategies. Successful development of these strategies requires detailed characterization of microorganisms and EPS through the proper selection of analytical tools and assembly of results. Existing microbiological/EPS studies reveal a number of

It's the System, Stupid: How Systems Biology Is Transforming.

Science.gov (United States)

2010-01-01

So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient.

Seasonal allergic rhinitis and systems biology-oriented biomarker discovery

NARCIS (Netherlands)

Baars, E.W.; Nierop, A.F.M.; Savelkoul, H.F.J.

2015-01-01

There is an increasing interest in science and medicine in the systems approach. Instead of the reductionist approach that focuses on the physical and chemical properties of the individual components, systems biology aims to describe, understand, and explain from the complex biological systems

Interactive analysis of systems biology molecular expression data

Directory of Open Access Journals (Sweden)

Prabhakar Sunil

2008-02-01

Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

Tracing organizing principles: Learning from the history of systems biology

DEFF Research Database (Denmark)

Green, Sara; Wolkenhauer, Olaf

2014-01-01

on this historical background in order to increase the understanding of the motivation behind the search for general principles and to clarify different epistemic aims within systems biology. We pinpoint key aspects of earlier approaches that also underlie the current practice. These are i) the focus on relational......With the emergence of systems biology, the identification of organizing principles is being highlighted as a key research aim. Researchers attempt to “reverse engineer” the functional organization of biological systems using methodologies from mathematics, engineering and computer science while...... taking advantage of data produced by new experimental techniques. While systems biology is a relatively new approach, the quest for general principles of biological organization dates back to systems theoretic approaches in early and mid-twentieth century. The aim of this paper is to draw...

Biological control of livestock pests: Pathogens

Science.gov (United States)

Interest in biological methods for livestock and poultry pest management is largely motivated by the development of resistance to most of the available synthetic pesticides by the major pests. There also has been a marked increase in organic systems, and those that promote animal welfare by reducing...

An online model composition tool for system biology models.

Science.gov (United States)

Coskun, Sarp A; Cicek, A Ercument; Lai, Nicola; Dash, Ranjan K; Ozsoyoglu, Z Meral; Ozsoyoglu, Gultekin

2013-09-05

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. 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. 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.

Conservation Biological Control of Pests in the Molecular Era: New Opportunities to Address Old Constraints

Science.gov (United States)

Gurr, Geoff M.; You, Minsheng

2016-01-01

Biological control has long been considered a potential alternative to pesticidal strategies for pest management but its impact and level of use globally remain modest and inconsistent. A rapidly expanding range of molecular – particularly DNA-related – techniques is currently revolutionizing many life sciences. This review identifies a series of constraints on the development and uptake of conservation biological control and considers the contemporary and likely future influence of molecular methods on these constraints. Molecular approaches are now often used to complement morphological taxonomic methods for the identification and study of biological control agents including microbes. A succession of molecular techniques has been applied to ‘who eats whom’ questions in food-web ecology. Polymerase chain reaction (PCR) approaches have largely superseded immunological approaches such as enzyme-linked immunosorbent assay (ELISA) and now – in turn – are being overtaken by next generation sequencing (NGS)-based approaches that offer unparalleled power at a rapidly diminishing cost. There is scope also to use molecular techniques to manipulate biological control agents, which will be accelerated with the advent of gene editing tools, the CRISPR/Cas9 system in particular. Gene editing tools also offer unparalleled power to both elucidate and manipulate plant defense mechanisms including those that involve natural enemy attraction to attacked plants. Rapid advances in technology will allow the development of still more novel pest management options for which uptake is likely to be limited chiefly by regulatory hurdles. PMID:26793225

Biological control of saltcedar (Tamarix spp.) by saltcedar leaf beetles (Diorhabda spp.): effects on small mammals

Science.gov (United States)

The spread of introduced saltcedar (Tamarix spp.) throughout many riparian systems across the western United States motivated the introduction of biological control agents that are specific to saltcedar, saltcedar leaf beetles (Diorhabda carinulata, D. elongata; Chrysomelidae). I monitored small mam...

Advancing metabolic engineering through systems biology of industrial microorganisms.

Science.gov (United States)

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.

Self-Organized Fission Control for Flocking System

Directory of Open Access Journals (Sweden)

Mingyong Liu

2015-01-01

Full Text Available This paper studies the self-organized fission control problem for flocking system. Motivated by the fission behavior of biological flocks, information coupling degree (ICD is firstly designed to represent the interaction intensity between individuals. Then, from the information transfer perspective, a “maximum-ICD” based pairwise interaction rule is proposed to realize the directional information propagation within the flock. Together with the “separation/alignment/cohesion” rules, a self-organized fission control algorithm is established that achieves the spontaneous splitting of flocking system under conflict external stimuli. Finally, numerical simulations are provided to demonstrate the effectiveness of the proposed algorithm.

Genome Scale Modeling in Systems Biology: Algorithms and Resources

Science.gov (United States)

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

Tensegrity I. Cell structure and hierarchical systems biology

Science.gov (United States)

Ingber, Donald E.

2003-01-01

In 1993, a Commentary in this journal described how a simple mechanical model of cell structure based on tensegrity architecture can help to explain how cell shape, movement and cytoskeletal mechanics are controlled, as well as how cells sense and respond to mechanical forces (J. Cell Sci. 104, 613-627). The cellular tensegrity model can now be revisited and placed in context of new advances in our understanding of cell structure, biological networks and mechanoregulation that have been made over the past decade. Recent work provides strong evidence to support the use of tensegrity by cells, and mathematical formulations of the model predict many aspects of cell behavior. In addition, development of the tensegrity theory and its translation into mathematical terms are beginning to allow us to define the relationship between mechanics and biochemistry at the molecular level and to attack the larger problem of biological complexity. Part I of this two-part article covers the evidence for cellular tensegrity at the molecular level and describes how this building system may provide a structural basis for the hierarchical organization of living systems--from molecule to organism. Part II, which focuses on how these structural networks influence information processing networks, appears in the next issue.

Artificial intelligence/expert (AI/EX) systems for steelworks pollution control

Energy Technology Data Exchange (ETDEWEB)

Schofield, N.; Le Louer, P.; Mirabile, D.; Hubner, R. [Corus UK Ltd., Rotherham (United Kingdom)

2002-07-01

The objectives of this project have been to develop and apply artificial intelligence and expert system (AI/EX) methods to improve the control and operational performance of steelworks' pollution control equipment and to assess the viability and benefits of using such systems in dynamic process plant applications. Four distinct sub-projects were carried out: an expert system incorporating knowledge-based rules and neural network simulations has been developed by Corus which provides plant personnel with a real-time condition monitoring tool for the plant. Abnormalities with plant operation are now instantly recognised and alarmed, allowing prioritised maintenance to increase plant availability. The LECES project focused on studies concerning three different sites in order to evaluate predictive emission monitoring systems using neural networks to replace conventional instrumental and controls in steelworks' combustion systems. VAI developed a software template for pollution control expert systems to demonstrate the transferability of AI/EX technology. This has been done through the development of a validated process database containing data from the Corus sub-project and the subsequent integration of this data with dynamic emission models to produce rules for input to an evaluation database. CSM developed a fuzzy logic controlled process management system applied to the biological treatment of coke-oven waste water. A pilot plant has been installed and results on simulations performed using the fuzzy logic system linked to a neural network simulator show that it is possible to obtain great advantages in the biological pilot plant performance.

Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

Energy Technology Data Exchange (ETDEWEB)

Gregurick, S.; Fredrickson, J. K.; Stevens, R.

2009-03-01

Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

The Automatic Radiation Control System Of The Inr Linear Accelerator (troitsk).

CERN Document Server

Grachev, M I; Kuptsov, S I; Peleshko, V N; Shishkin, K I; Shmelev, M O; Skorkin, V M

2004-01-01

The radiation monitor system (RMS) at accelerator INR is a part of radiation safety system of experimental complex INR. RMS is intended for continuous monitoring of radiation field behind biological protection of linear accelerator INR with the personnel dose control and alarm purposes. Three-level system RMS consists of the operator computer, microprocessor data acquisition modules and networks of UDBN-02R neutron detectors and BDRC-01P photon detectors, located inside and behind biological protection of the accelerator (fig. 1).

Quality control of X-ray irradiator by biological markers

International Nuclear Information System (INIS)

Miura, Miwa; Lukmanul Hakkim, F.; Yoshida, Masahiro; Matsuda, Naoki; Morita, Naoko

2011-01-01

The exposure of animals or cultured cells to radiation is the essential and common step in experimental researches to elucidate biological effects of radiation. When an X-ray generator is used as a radiation source, physical parameters including dose, dose rate, and the energy spectrum of X-ray play crucial roles in biological outcome. Therefore, those parameters are the important points to be checked in quality control and to be carefully considered in advance to the irradiation to obtain the accurate and reproductive results. Here we measured radiation dose emitted from the X-ray irradiator for research purposes by using clonogenic survival of cultured mammalian cells as a biological marker in parallel with physical dosimetry. The results drawn from both methods exhibited good consistency in the dose distribution on the irradiation stage. Furthermore, the close relationship was observed between cell survival and the photon energy spectrum by using different filter components. These results suggest that biological dosimetry is applicable to quality control of X-ray irradiator in adjunct to physical dosimetry and that it possibly helps better understanding of the optimal irradiating condition by X-ray users in life-science field. (author)

Notions of similarity for systems biology models.

Science.gov (United States)

Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knüpfer, Christian; Liebermeister, Wolfram; Waltemath, Dagmar

2018-01-01

Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here we survey existing methods for the comparison of models, introduce quantitative measures for model similarity, and discuss potential applications of combined similarity measures. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on a combination of different model aspects. The six aspects that we define as potentially relevant for similarity are underlying encoding, references to biological entities, quantitative behaviour, qualitative behaviour, mathematical equations and parameters and network structure. We argue that future similarity measures will benefit from combining these model aspects in flexible, problem-specific ways to mimic users' intuition about model similarity, and to support complex model searches in databases. © The Author 2016. Published by Oxford University Press.

Thresholds for HLB vector control in infected commercial citrus and compatibility with biological control

OpenAIRE

Monzo, C.; Hendricks, K.; Roberts, P.; Stansly, P. A.

2014-01-01

Control of the HLB vector, Diaphorina citri Kuwayama, is considered a basic component for management this disease, even in a high HLB incidence scenario. Such control is mostly chemically oriented. However, over use of insecticides would increase costs and be incompatible with biological control. Establishment of economic thresholds for psyllid control under different price scenarios could optimize returns on investment.

Exploring Synthetic and Systems Biology at the University of Edinburgh.

Science.gov (United States)

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.

Managing conflict over biological control: the case of strawberry guava in Hawaii

Science.gov (United States)

Tracy Johnson

2016-01-01

Biological control researchers commonly avoid targets with potential for high conflict, but for certain highly damaging invaders with no viable management alternatives, it may be necessary to consider biological control even when it is likely to generate conflict. Discussed here is a case study, strawberry guava (Psidium cattleianum Sabine...

Rearing and Release of Megamelus scutellaris Berg (Hemiptera: Delphacidae) for Biological Control of Water hyacinth in 2015

Science.gov (United States)

2017-06-01

Hemiptera: Delphacidae) for Biological Control of Waterhyacinth in 2015 by Jan Freedman and Nathan Harms PURPOSE: Waterhyacinth biological control ... control agents. Three insects were released in the United States for biological control of waterhyacinth during the 1970s; two weevils, Neochetina...content) and competitive interactions with other biological control agents (e.g., Neochetina spp.), though their consideration in other biological

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

Science.gov (United States)

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).

Noninvasive biological sensor system for detection of drunk driving.

Science.gov (United States)

Murata, Kohji; Fujita, Etsunori; Kojima, Shigeyuki; Maeda, Shinitirou; Ogura, Yumi; Kamei, Tsutomu; Tsuji, Toshio; Kaneko, Shigehiko; Yoshizumi, Masao; Suzuki, Nobutaka

2011-01-01

Systems capable of monitoring the biological condition of a driver and issuing warnings during instances of drowsiness have recently been studied. Moreover, many researchers have reported that biological signals, such as brain waves, pulsation waves, and heart rate, are different between people who have and have not consumed alcohol. Currently, we are developing a noninvasive system to detect individuals driving under the influence of alcohol by measuring biological signals. We used the frequency time series analysis to attempt to distinguish between normal and intoxicated states of a person as the basis of the sensing system.

Biological control by ( Coccinella algerica , Kovar 1977) against the ...

African Journals Online (AJOL)

Inputs from chemicals, particularly pesticides, to control crop pests have adverse effects on soil and the environment, among others. To reduce pest attacks, biological control with indigenous predators is the alternative and the cleanest, most environmentally friendly and ecologically balanced way. In order to achieve this ...

Biological optimization systems for enhancing photosynthetic efficiency and methods of use

Science.gov (United States)

Hunt, Ryan W.; Chinnasamy, Senthil; Das, Keshav C.; de Mattos, Erico Rolim

2012-11-06

Biological optimization systems for enhancing photosynthetic efficiency and methods of use. Specifically, methods for enhancing photosynthetic efficiency including applying pulsed light to a photosynthetic organism, using a chlorophyll fluorescence feedback control system to determine one or more photosynthetic efficiency parameters, and adjusting one or more of the photosynthetic efficiency parameters to drive the photosynthesis by the delivery of an amount of light to optimize light absorption of the photosynthetic organism while providing enough dark time between light pulses to prevent oversaturation of the chlorophyll reaction centers are disclosed.

Precision control of recombinant gene transcription for CHO cell synthetic biology.

Science.gov (United States)

Brown, Adam J; James, David C

2016-01-01

The next generation of mammalian cell factories for biopharmaceutical production will be genetically engineered to possess both generic and product-specific manufacturing capabilities that may not exist naturally. Introduction of entirely new combinations of synthetic functions (e.g. novel metabolic or stress-response pathways), and retro-engineering of existing functional cell modules will drive disruptive change in cellular manufacturing performance. However, before we can apply the core concepts underpinning synthetic biology (design, build, test) to CHO cell engineering we must first develop practical and robust enabling technologies. Fundamentally, we will require the ability to precisely control the relative stoichiometry of numerous functional components we simultaneously introduce into the host cell factory. In this review we discuss how this can be achieved by design of engineered promoters that enable concerted control of recombinant gene transcription. We describe the specific mechanisms of transcriptional regulation that affect promoter function during bioproduction processes, and detail the highly-specific promoter design criteria that are required in the context of CHO cell engineering. The relative applicability of diverse promoter development strategies are discussed, including re-engineering of natural sequences, design of synthetic transcription factor-based systems, and construction of synthetic promoters. This review highlights the potential of promoter engineering to achieve precision transcriptional control for CHO cell synthetic biology. Copyright © 2015. Published by Elsevier Inc.

Ecosystem Services in Biologically Diversified versus Conventional Farming Systems: Benefits, Externalities, and Trade-Offs

Directory of Open Access Journals (Sweden)

Claire Kremen

2012-12-01

Full Text Available We hypothesize that biological diversification across ecological, spatial, and temporal scales maintains and regenerates the ecosystem services that provide critical inputs - such as maintenance of soil quality, nitrogen fixation, pollination, and pest control - to agriculture. Agrobiodiversity is sustained by diversified farming practices and it also supplies multiple ecosystem services to agriculture, thus reducing environmental externalities and the need for off-farm inputs. We reviewed the literature that compares biologically diversified farming systems with conventional farming systems, and we examined 12 ecosystem services: biodiversity; soil quality; nutrient management; water-holding capacity; control of weeds, diseases, and pests; pollination services; carbon sequestration; energy efficiency and reduction of warming potential; resistance and resilience to climate change; and crop productivity. We found that compared with conventional farming systems, diversified farming systems support substantially greater biodiversity, soil quality, carbon sequestration, and water-holding capacity in surface soils, energy-use efficiency, and resistance and resilience to climate change. Relative to conventional monocultures, diversified farming systems also enhance control of weeds, diseases, and arthropod pests and they increase pollination services; however, available evidence suggests that these practices may often be insufficient to control pests and diseases or provide sufficient pollination. Significantly less public funding has been applied to agroecological research and the improvement of diversified farming systems than to conventional systems. Despite this lack of support, diversified farming systems have only somewhat reduced mean crop productivity relative to conventional farming systems, but they produce far fewer environmental and social harms. We recommend that more research and crop breeding be conducted to improve diversified farming

Laser control of natural disperse systems

Science.gov (United States)

Vlasova, Olga L.; Bezrukova, Alexandra G.

2003-10-01

Different water disperse systems were studied by integral (spectroturbidemetry) and differential light scattering method with a laser as a source of light. The investigation done concerns the state of kaolin dispersions at storage and under dilution as an example of mineral dispersion systems such as natural water. The role of some light scattering parameters for an optical analysis of water dispersions, like the dispersion of erythrocytes and bacterial cells -Escherichia coli is discussed. The results obtained can help to elaborate the methods for on-line optical control fo natural disperse systems (water, air) with mineral and biological particles.

Set membership experimental design for biological systems

Directory of Open Access Journals (Sweden)

Marvel Skylar W

2012-03-01

Full Text Available Abstract 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

The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells.

Science.gov (United States)

Poussin, Carine; Mathis, Carole; Alexopoulos, Leonidas G; Messinis, Dimitris E; Dulize, Rémi H J; Belcastro, Vincenzo; Melas, Ioannis N; Sakellaropoulos, Theodore; Rhrissorrakrai, Kahn; Bilal, Erhan; Meyer, Pablo; Talikka, Marja; Boué, Stéphanie; Norel, Raquel; Rice, John J; Stolovitzky, Gustavo; Ivanov, Nikolai V; Peitsch, Manuel C; Hoeng, Julia

2014-01-01

The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to 'translate' the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies.

The species translation challenge—A systems biology perspective on human and rat bronchial epithelial cells

Science.gov (United States)

Poussin, Carine; Mathis, Carole; Alexopoulos, Leonidas G; Messinis, Dimitris E; Dulize, Rémi H J; Belcastro, Vincenzo; Melas, Ioannis N; Sakellaropoulos, Theodore; Rhrissorrakrai, Kahn; Bilal, Erhan; Meyer, Pablo; Talikka, Marja; Boué, Stéphanie; Norel, Raquel; Rice, John J; Stolovitzky, Gustavo; Ivanov, Nikolai V; Peitsch, Manuel C; Hoeng, Julia

2014-01-01

The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to ‘translate’ the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies. PMID:25977767

Ultrasonic treatment for microbiological control of water systems

International Nuclear Information System (INIS)

Broekman, S.; Pohlmann, O.; Beardwooden, E. S.; Cordemans de Meulenaer, E.

2010-01-01

A combination treatment of shear, micro-bubbles, and high-frequency low-power ultrasound introduced via side-stream treatment of industrial water systems has shown excellent results in controlling bacteria and algae; Through the physical, high-stress environment created by ultrasonic waves, sessile and planktonic biological populations, some of which may undergo programmed cell death (PCD), can be controlled. Additionally, the instability and reduction of biofilm have been observed in systems treated by ultrasound and may be attributed to starvation-stress and lack of available cross-linking cations in the biofilm. (authors)

Ultrasonic treatment for microbiological control of water systems

Energy Technology Data Exchange (ETDEWEB)

Broekman, S.; Pohlmann, O.; Beardwooden, E. S.; Cordemans de Meulenaer, E. [Ashland Hercules Water Technologies, Krefeld (Germany)

2010-08-15

A combination treatment of shear, micro-bubbles, and high-frequency low-power ultrasound introduced via side-stream treatment of industrial water systems has shown excellent results in controlling bacteria and algae; Through the physical, high-stress environment created by ultrasonic waves, sessile and planktonic biological populations, some of which may undergo programmed cell death (PCD), can be controlled. Additionally, the instability and reduction of biofilm have been observed in systems treated by ultrasound and may be attributed to starvation-stress and lack of available cross-linking cations in the biofilm. (authors)

Biocellion: accelerating computer simulation of multicellular biological system models.

Science.gov (United States)

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.

SEEK: a systems biology data and model management platform.

NARCIS (Netherlands)

Wolstencroft, K.J.; Owen, S.; Krebs, O.; Nguyen, Q.; Stanford, N.J.; Golebiewski, M.; Weidemann, A.; Bittkowski, M.; An, L.; Shockley, D.; Snoep, J.L.; Mueller, W.; Goble, C.

2015-01-01

Background: 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

Biological control of tortricids and aphids in strawberries

DEFF Research Database (Denmark)

Sigsgaard, Lene; Enkegaard, Annie; Eilenberg, Jørgen

Cropping practice and biological control can contribute to reduced pesticide use in strawberries. Organic strawberries are less attacked by strawberry tortricid and buckwheat flower strips can augment its natural enemies. Against shallot aphid the two-spot ladybird is promising....

Tunable promoters in systems biology

DEFF Research Database (Denmark)

Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

2005-01-01

The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...

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

Science.gov (United States)

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.

Biological control and invading freshwater snails. A case study.

Science.gov (United States)

Pointier, J P; Augustin, D

1999-12-01

Introductions of four species of freshwater snails occurred between 1972 and 1996 onto Guadeloupe Island. Two of them, Melanoides tuberculata and Marisa cornuarietis, were subsequently used as biological control agents against Biomphalaria glabrata, the snail intermediate host of intestinal schistosomiasis. In 1996, a general survey was carried out in 134 sites which had already been investigated in 1972. The total number of mollusc species had increased from 19 to 21. Site numbers housing B. glabrata and two other species had strongly declined. This decline may be mainly attributed to a competitive displacement by M. tuberculata and M. cornuarietis as illustrated by several biological control programmes. There were no changes in the remainder of the malacological fauna.

Complex biological and bio-inspired systems

Energy Technology Data Exchange (ETDEWEB)

Ecke, Robert E [Los Alamos National Laboratory

2009-01-01

The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

Heavy-ion microbeam system at JAEA-Takasaki for microbeam biology

International Nuclear Information System (INIS)

Funayama, Tomoo; Wada, Seiichi; Yokota, Yuichiro

2008-01-01

Research concerning cellular responses to low dose irradiation, radiation-induced bystander effects, and the biological track structure of charged particles has recently received particular attention in the field of radiation biology. Target irradiation employing a microbeam represents a useful means of advancing this research by obviating some of the disadvantages associated with the conventional irradiation strategies. The heavy-ion microbeam system at Japan Atomic Energy Agency (JAEA)-Takasaki, which was planned in 1987 and started in the early 1990's, can provide target irradiation of heavy charged particles to biological material at atmospheric pressure using a minimum beam size 5 μm in diameter. A variety of biological material has been irradiated using this microbeam system including cultured mammalian and higher plant cells, isolated fibers of mouse skeletal muscle, silkworm (Bombyx mori) embryos and larvae, Arabidopsis thaliana roots, and the nematode Caenorhabditis elegans. The system can be applied to the investigation of mechanisms within biological organisms not only in the context of radiation biology, but also in the fields of general biology such as physiology, developmental biology and neurobiology, and should help to establish and contribute to the field of 'microbeam biology'. (author)

Electronic Integrated Disease Surveillance System and Pathogen Asset Control System

Directory of Open Access Journals (Sweden)

Tom G. Wahl

2012-06-01

Full Text Available Electronic Integrated Disease Surveillance System (EIDSS has been used to strengthen and support monitoring and prevention of dangerous diseases within One Health concept by integrating veterinary and human surveillance, passive and active approaches, case-based records including disease-specific clinical data based on standardised case definitions and aggregated data, laboratory data including sample tracking linked to each case and event with test results and epidemiological investigations. Information was collected and shared in secure way by different means: through the distributed nodes which are continuously synchronised amongst each other, through the web service, through the handheld devices. Electronic Integrated Disease Surveillance System provided near real time information flow that has been then disseminated to the appropriate organisations in a timely manner. It has been used for comprehensive analysis and visualisation capabilities including real time mapping of case events as these unfold enhancing decision making. Electronic Integrated Disease Surveillance System facilitated countries to comply with the IHR 2005 requirements through a data transfer module reporting diseases electronically to the World Health Organisation (WHO data center as well as establish authorised data exchange with other electronic system using Open Architecture approach. Pathogen Asset Control System (PACS has been used for accounting, management and control of biological agent stocks. Information on samples and strains of any kind throughout their entire lifecycle has been tracked in a comprehensive and flexible solution PACS. Both systems have been used in a combination and individually. Electronic Integrated Disease Surveillance System and PACS are currently deployed in the Republics of Kazakhstan, Georgia and Azerbaijan as a part of the Cooperative Biological Engagement Program (CBEP sponsored by the US Defense Threat Reduction Agency (DTRA.

Electronic integrated disease surveillance system and pathogen asset control system.

Science.gov (United States)

Wahl, Tom G; Burdakov, Aleksey V; Oukharov, Andrey O; Zhilokov, Azamat K

2012-06-20

Electronic Integrated Disease Surveillance System (EIDSS) has been used to strengthen and support monitoring and prevention of dangerous diseases within One Health concept by integrating veterinary and human surveillance, passive and active approaches, case-based records including disease-specific clinical data based on standardised case definitions and aggregated data, laboratory data including sample tracking linked to each case and event with test results and epidemiological investigations. Information was collected and shared in secure way by different means: through the distributed nodes which are continuously synchronised amongst each other, through the web service, through the handheld devices. Electronic Integrated Disease Surveillance System provided near real time information flow that has been then disseminated to the appropriate organisations in a timely manner. It has been used for comprehensive analysis and visualisation capabilities including real time mapping of case events as these unfold enhancing decision making. Electronic Integrated Disease Surveillance System facilitated countries to comply with the IHR 2005 requirements through a data transfer module reporting diseases electronically to the World Health Organisation (WHO) data center as well as establish authorised data exchange with other electronic system using Open Architecture approach. Pathogen Asset Control System (PACS) has been used for accounting, management and control of biological agent stocks. Information on samples and strains of any kind throughout their entire lifecycle has been tracked in a comprehensive and flexible solution PACS.Both systems have been used in a combination and individually. Electronic Integrated Disease Surveillance System and PACS are currently deployed in the Republics of Kazakhstan, Georgia and Azerbaijan as a part of the Cooperative Biological Engagement Program (CBEP) sponsored by the US Defense Threat Reduction Agency (DTRA).

Collaborative Systems Biology Projects for the Military Medical Community.

Science.gov (United States)

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

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

Directory of Open Access Journals (Sweden)

Sorokin Anatoly

2015-06-01

Full Text Available 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.

Using insects to drive mobile robots - hybrid robots bridge the gap between biological and artificial systems.

Science.gov (United States)

Ando, Noriyasu; Kanzaki, Ryohei

2017-09-01

The use of mobile robots is an effective method of validating sensory-motor models of animals in a real environment. The well-identified insect sensory-motor systems have been the major targets for modeling. Furthermore, mobile robots implemented with such insect models attract engineers who aim to avail advantages from organisms. However, directly comparing the robots with real insects is still difficult, even if we successfully model the biological systems, because of the physical differences between them. We developed a hybrid robot to bridge the gap. This hybrid robot is an insect-controlled robot, in which a tethered male silkmoth (Bombyx mori) drives the robot in order to localize an odor source. This robot has the following three advantages: 1) from a biomimetic perspective, the robot enables us to evaluate the potential performance of future insect-mimetic robots; 2) from a biological perspective, the robot enables us to manipulate the closed-loop of an onboard insect for further understanding of its sensory-motor system; and 3) the robot enables comparison with insect models as a reference biological system. In this paper, we review the recent works regarding insect-controlled robots and discuss the significance for both engineering and biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ionic interactions in biological and physical systems: a variational treatment.

Science.gov (United States)

Eisenberg, Bob

2013-01-01

Chemistry is about chemical reactions. Chemistry is about electrons changing their configurations as atoms and molecules react. Chemistry has for more than a century studied reactions as if they occurred in ideal conditions of infinitely dilute solutions. But most reactions occur in salt solutions that are not ideal. In those solutions everything (charged) interacts with everything else (charged) through the electric field, which is short and long range extending to the boundaries of the system. Mathematics has recently been developed to deal with interacting systems of this sort. The variational theory of complex fluids has spawned the theory of liquid crystals (or vice versa). In my view, ionic solutions should be viewed as complex fluids, particularly in the biological and engineering context. In both biology and electrochemistry ionic solutions are mixtures highly concentrated (to approximately 10 M) where they are most important, near electrodes, nucleic ids, proteins, active sites of enzymes, and ionic channels. Ca2+ is always involved in biological solutions because the concentration (really free energy per mole) of Ca2+ in a particular location is the signal that controls many biological functions. Such interacting systems are not simple fluids, and it is no wonder that analysis of interactions, such as the Hofmeister series, rooted in that tradition has not succeeded as one would hope. Here, we present a variational treatment of ard spheres in a frictional dielectric with the hope that such a treatment of an lectrolyte as a complex fluid will be productive. The theory automatically extends to spatially nonuniform boundary conditions and the nonequilibrium systems and flows they produce. The theory is unavoidably self-consistent since differential equations are derived (not assumed) from models of (Helmholtz free) nergy and dissipation of the electrolyte. The origin of the Hofmeister series is (in my view) an inverse problem that becomes well posed when

Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Nielsen, Jens; Jewett, Michael Christopher

2008-01-01

in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development...... programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given....

The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria

Directory of Open Access Journals (Sweden)

Meghan Zuck

2017-11-01

Full Text Available Despite global eradication efforts over the past century, malaria remains a devastating public health burden, causing almost half a million deaths annually (WHO, 2016. A detailed understanding of the mechanisms that control malaria infection has been hindered by technical challenges of studying a complex parasite life cycle in multiple hosts. While many interventions targeting the parasite have been implemented, the complex biology of Plasmodium poses a major challenge, and must be addressed to enable eradication. New approaches for elucidating key host-parasite interactions, and predicting how the parasite will respond in a variety of biological settings, could dramatically enhance the efficacy and longevity of intervention strategies. The field of systems biology has developed methodologies and principles that are well poised to meet these challenges. In this review, we focus our attention on the Liver Stage of the Plasmodium lifecycle and issue a “call to arms” for using systems biology approaches to forge a new era in malaria research. These approaches will reveal insights into the complex interplay between host and pathogen, and could ultimately lead to novel intervention strategies that contribute to malaria eradication.

EURASIP journal on bioinformatics & systems biology

National Research Council Canada - National Science Library

2006-01-01

"The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

Agent-Based Modeling in Molecular Systems Biology.

Science.gov (United States)

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-06-08

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.

Marine biological data and information management system

Digital Repository Service at National Institute of Oceanography (India)

Sarupria, J.S.

Indian National Oceanographic Data Centre (INODC) is engaged in developing a marine biological data and information management system (BIODIMS). This system will contain the information on zooplankton in the water column, zoobenthic biomass...

Predictive modelling of complex agronomic and biological systems.

Science.gov (United States)

Keurentjes, Joost J B; Molenaar, Jaap; Zwaan, Bas J

2013-09-01

Biological systems are tremendously complex in their functioning and regulation. Studying the multifaceted behaviour and describing the performance of such complexity has challenged the scientific community for years. The reduction of real-world intricacy into simple descriptive models has therefore convinced many researchers of the usefulness of introducing mathematics into biological sciences. Predictive modelling takes such an approach another step further in that it takes advantage of existing knowledge to project the performance of a system in alternating scenarios. The ever growing amounts of available data generated by assessing biological systems at increasingly higher detail provide unique opportunities for future modelling and experiment design. Here we aim to provide an overview of the progress made in modelling over time and the currently prevalent approaches for iterative modelling cycles in modern biology. We will further argue for the importance of versatility in modelling approaches, including parameter estimation, model reduction and network reconstruction. Finally, we will discuss the difficulties in overcoming the mathematical interpretation of in vivo complexity and address some of the future challenges lying ahead. © 2013 John Wiley & Sons Ltd.

Carbon nanomaterials in biological systems

Energy Technology Data Exchange (ETDEWEB)

Pu Chun Ke [Laboratory of Single-Molecule Biophysics and Polymer Physics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634 (United States); Qiao Rui [Department of Mechanical Engineering, Clemson University, Clemson, SC 29634 (United States)

2007-09-19

This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

Carbon nanomaterials in biological systems

International Nuclear Information System (INIS)

Pu Chun Ke; Qiao Rui

2007-01-01

This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

Local and global control of ecological and biological networks

OpenAIRE

Alessandro Ferrarini

2014-01-01

Recently, I introduced a methodological framework so that ecological and biological networks can be controlled both from inside and outside by coupling network dynamics and evolutionary modelling. The endogenous control requires the network to be optimized at the beginning of its dynamics (by acting upon nodes, edges or both) so that it will then go inertially to the desired state. Instead, the exogenous control requires that exogenous controllers act upon the network at each time step. By th...

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

Science.gov (United States)

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.

Update on the use of systemic biologic agents in the treatment of noninfectious uveitis

Directory of Open Access Journals (Sweden)

Pasadhika S

2014-02-01

Full Text Available Sirichai Pasadhika,1 James T Rosenbaum2 1Department of Ophthalmology, Southern Arizona Veterans Administration Health Care System, Tucson, AZ, USA; 2Legacy Devers Eye Institute, Portland, OR, USA Abstract: Uveitis is one of the leading causes of blindness worldwide. Noninfectious uveitis may be associated with other systemic conditions, such as human leukocyte antigen B27-related spondyloarthropathies, inflammatory bowel disease, juvenile idiopathic arthritis, Behçet's disease, and sarcoidosis. Conventional therapy with corticosteroids and immunosuppressive agents (such as methotrexate, azathioprine, mycophenolate mofetil, and cyclosporine may not be sufficient to control ocular inflammation or prevent non-ophthalmic complications in refractory patients. Off-label use of biologic response modifiers has been studied as primary and secondary therapeutic agents. They are very useful when conventional immunosuppressive therapy has failed or has been poorly tolerated, or to treat concomitant ophthalmic and systemic inflammation that might benefit from these medications. Biologic therapy, primarily infliximab, and adalimumab, have been shown to be rapidly effective for the treatment of various subtypes of refractory uveitis and retinal vasculitis, especially Behçet's disease-related eye conditions and the uveitis associated with juvenile idiopathic arthritis. Other agents such as golimumab, abatacept, canakinumab, gevokizumab, tocilizumab, and alemtuzumab may have great future promise for the treatment of uveitis. It has been shown that with proper monitoring, biologic therapy can significantly improve quality of life in patients with uveitis, particularly those with concurrent systemic symptoms. However, given high cost as well as the limited long-term safety data, we do not routinely recommend biologics as first-line therapy for noninfectious uveitis in most patients. These agents should be used with caution by experienced clinicians. The present

The status of biological control and recommendations for improving uptake for the future

NARCIS (Netherlands)

Barratt, B.I.P.; Moran, V.C.; Bigler, F.; Lenteren, van J.C.

2018-01-01

Classical and augmentative biological control of insect pests and weeds has enjoyed a long history of successes. However, biocontrol practices have not been as universally accepted or optimally utilised as they could be. An International Organisation for Biological Control (IOBC) initiative brought

Multilayer microfluidic systems with indium-tin-oxide microelectrodes for studying biological cells

International Nuclear Information System (INIS)

Wu, Hsiang-Chiu; Chen, Hsin; Lyau, Jia-Bo; Lin, Min-Hsuan; Chuang, Yung-Jen

2017-01-01

Contemporary semiconductor and micromachining technologies have been exploited to develop lab-on-a-chip microsystems, which enable parallel and efficient experiments in molecular and cellular biology. In these microlab systems, microfluidics play an important role for automatic transportation or immobilization of cells and bio-molecules, as well as for separation or mixing of different chemical reagents. However, seldom microlab systems allow both morphology and electrophysiology of biological cells to be studied in situ . This kind of study is important, for example, for understanding how neuronal networks grow in response to environmental stimuli. To fulfill this application need, this paper investigates the possibility of fabricating multi-layer photoresists as microfluidic systems directly above a glass substrate with indium-tin-oxide (ITO) electrodes. The microfluidic channels are designed to guide and trap biological cells on top of ITO electrodes, through which the electrical activities of cells can be recorded or elicited. As both the microfluidic system and ITO electrodes are transparent, the cellular morphology is observable easily during electrophysiological studies. Two fabrication processes are proposed and compared. One defines the structure and curing depth of each photoresist layer simply by controlling the exposure time in lithography, while the other further utilizes a sacrificial layer to defines the structure of the bottom layer. The fabricated microfluidic system is proved bio-compatible and able to trap blood cells or neurons. Therefore, the proposed microsystem will be useful for studying cultured cells efficiently in applications such as drug-screening. (paper)

Pythium species and isolate diversity influence inhibition by the biological control agent Streptomyces lydicus

Science.gov (United States)

Disease control of soilborne pathogens by biological control agents has often been inconsistent under field conditions. One factor that may contribute to this inconsistency is the variability in response among pathogen populations and/or communities to the selected biological control agent. One hund...

Biopesticides: An option for the biological pest control

Directory of Open Access Journals (Sweden)

Eusebio Nava Pérez

2012-09-01

Full Text Available The indiscriminate use of synthetic pesticides and the problems that its cause to human health, agriculture and the environment is comment, this paper also present general aspects about of biopesticides, and their uses in the biological pest control. By the nature these can be safely used in a sustainable agriculture. An example is the use of botanical pesticides whose active ingredient are the terpenes, alkaloids and phenolics, these have insecticide effects for many agriculture pests; also its are less expensive, are biodegradable and safe for humans and the environment, however havelittle residuality. Microbial pesticides are being introduced successfully to pests control in important crops such as; coffee, sugar cane, beans and corn. These products contain bacteria, fungi, viruses or nematodes. However, few entomopathogenic agents have been developed as effective biocontrol agents, one of them is the bacterium Bacillus thuringiensis (Berlinier for control of armyworm Spodoptera frugiperda (J.E Smith covering about 74% of the market,fungus 10% , viruses 5% and 11% others. Other upstanding case is the use of the fungus Beauveria bassiana (Balsamoagainst bean weevil Acanthoscelides obtectus (Say. Biopesticides have shown that when are used properly in the biological pest control its favor the practice of a sustainable agriculture, with less dependence of chemical insecticides.

Vibrational resonances in biological systems at microwave frequencies.

Science.gov (United States)

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.

C.E.B.A.S., a closed equilibrated biological aquatic system as a possible precursor for a long-term life support system?

Science.gov (United States)

Blüm, V.

C.E.B.A.S.-AQUARACK is a long-term multi-generation experimental device for aquatic organisms which is disposed for utlizitation in a space station. It results from the basic idea of a space aquarium for maintaining aquatic animals for longer periods integrated in a AQUARACK which consists of a modular animal holding tank, a semi-biological/physical water recycling system and an electronical control unit. The basic idea to replace a part of the water recycling system by a continuous culture of unicellular algae primarily leads to a second system for experiments with algae, a botanical AQUARACK consisting of an algal reactor, a water recycling and the electronical control unit. The combination of the zoological part, and the botanical part with a common control system in the AQUARACK, however, results in a ``Closed Equilibrated Biological Aquatic System'' (C.E.B.A.S.) representing an closed artificial ecosystem. Although this is disposed primarily as an experimental device for basic zoological, botanical and interdisciplinary research it opens the theoretical possibility to adapt it for combined production of animal and plant biomass on ground or in space. The paper explains the basic conception of the hardware construction of the zoological part of the system, the corresponding scientific frame program including the choice of the experimental animals and gives some selected examples of the hardware-related resrearch. It furtheron discusses the practical and economical relevance of the system in the development of a controlled aquatical life support system in general.

Natural biological control of pest mites in Brazilian sun coffee agroecosystems.

Science.gov (United States)

Teodoro, Adenir V; Sarmento, Renato A; Rêgo, Adriano S; da Graça S Maciel, Anilde

2010-06-01

Coffee is one of the leading commodities in tropical America. Although plantations are usually established under a canopy of trees in most producing countries in the region, Brazilian coffee is mostly produced under full sun conditions. Such simple, single-crop agroecosystems with intensive agrochemical inputs often suffer with pests like mites. Predatory mites of the family Phytoseiidae are the main natural enemies associated with pest mites in the field. However, these beneficial arthropods struggle to survive in intensive agroecosystems such as coffee monocultures due to unfavorable microclimatic conditions, widespread pesticide use, and lack of alternative food (pollen, nectar). Conservation biological control uses a range of management strategies to sustain and enhance populations of indigenous natural enemies such as predatory mites. We discuss here conservation biological control as a strategy to improve biological control of pest mites by native predatory mites in Brazilian coffee monocultures as well as some related patents.

Inverse Problems in Systems Biology: A Critical Review.

Science.gov (United States)

Guzzi, Rodolfo; Colombo, Teresa; Paci, Paola

2018-01-01

Systems Biology may be assimilated to a symbiotic cyclic interplaying between the forward and inverse problems. Computational models need to be continuously refined through experiments and in turn they help us to make limited experimental resources more efficient. Every time one does an experiment we know that there will be some noise that can disrupt our measurements. Despite the noise certainly is a problem, the inverse problems already involve the inference of missing information, even if the data is entirely reliable. So the addition of a certain limited noise does not fundamentally change the situation but can be used to solve the so-called ill-posed problem, as defined by Hadamard. It can be seen as an extra source of information. Recent studies have shown that complex systems, among others the systems biology, are poorly constrained and ill-conditioned because it is difficult to use experimental data to fully estimate their parameters. For these reasons was born the concept of sloppy models, a sequence of models of increasing complexity that become sloppy in the limit of microscopic accuracy. Furthermore the concept of sloppy models contains also the concept of un-identifiability, because the models are characterized by many parameters that are poorly constrained by experimental data. Then a strategy needs to be designed to infer, analyze, and understand biological systems. The aim of this work is to provide a critical review to the inverse problems in systems biology defining a strategy to determine the minimal set of information needed to overcome the problems arising from dynamic biological models that generally may have many unknown, non-measurable parameters.

Pythium invasion of plant-based life support systems: biological control and sources

Science.gov (United States)

Jenkins, D. G.; Cook, K. L.; Garland, J. L.; Board, K. F.; Sager, J. C. (Principal Investigator)

2000-01-01

Invasion of plant-based life support systems by plant pathogens could cause plant disease and disruption of life support capability. Root rot caused by the fungus, Pythium, was observed during tests of prototype plant growth systems containing wheat at the Kennedy Space Center (KSC). We conducted experiments to determine if the presence of complex microbial communities in the plant root zone (rhizosphere) resisted invasion by the Pythium species isolated from the wheat root. Rhizosphere inocula of different complexity (as assayed by community-level physiological profile: CLPP) were developed using a dilution/extinction approach, followed by growth in hydroponic rhizosphere. Pythium growth on wheat roots and concomitant decreases in plant growth were inversely related to the complexity of the inocula during 20-day experiments in static hydroponic systems. Pythium was found on the seeds of several different wheat cultivars used in controlled environmental studies, but it is unclear if the seed-borne fungal strain(s) were identical to the pathogenic strain recovered from the KSC studies. Attempts to control pathogens and their effects in hydroponic life support systems should include early inoculation with complex microbial communities, which is consistent with ecological theory.

The effects of insect biological control on a Tamarix invaded ecosystem: ecosystem water and carbon fluxes and plant-level responses

Science.gov (United States)

Background / Questions / Methods: Tamarix spp. (saltcedar) has invaded many river systems in the western United States with detrimental impacts to flora and fauna. Traditional methods of invasive plant control have been ineffective or costly. Therefore, insect biological control of Tamarix with Di...

Dielectric relaxation in biological systems physical principles, methods, and applications

CERN Document Server

Feldman, Yuri

2015-01-01

This title covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems.

Systems-biology dissection of eukaryotic cell growth

Directory of Open Access Journals (Sweden)

Andrews Justen

2010-05-01

Full Text Available Abstract A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth. See research article http://jbiol.com/content/6/2/4 and http://www.biomedcentral.com/1741-7007/8/68

It’s the System, Stupid: How Systems Biology Is Transforming

Science.gov (United States)

2010-01-01

So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient. PMID:22478806

1H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

International Nuclear Information System (INIS)

Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D.

2011-01-01

The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in 1 H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

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

OpenAIRE

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

2014-01-01

Background 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...

Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering

NARCIS (Netherlands)

Menolascina, F.; Bellomo, D.; Maiwald, T.; Bevilacqua, V.; Ciminelli, C.; Paradiso, A.; Tommasi, S.

2009-01-01

Background: Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the

Onchocerciasis control: biological research is still needed

Directory of Open Access Journals (Sweden)

Boussinesq M.

2008-09-01

Full Text Available Achievements obtained by the onchocerciasis control programmes should not lead to a relaxation in the biological research on Onchocerca volvulus. Issues such as the Loa loa-related postivermectin serious adverse events, the uncertainties as to whether onchocerciasis can be eliminated by ivermectin treatments, and the possible emergence of ivermectin-resistant O. volvulus populations should be addressed proactively. Doxycycline, moxidectin and emodepside appear to be promising as alternative drugs against onchocerciasis but support to researches in immunology and genomics should also be increased to develop new control tools, including both vaccines and macrofilaricidal drugs.

Biology and life history of Argopistes tsekooni (Coleoptera: Chrysomelidae) in China, a promising biological control agent of Chinese privet.

Science.gov (United States)

Y-Z Zhang; J. Sun; J.L. Hanula

2009-01-01

The biology and life history of Argopistes tsekooni Chen (Coleoptera: Chrysomelidae), a potential biological control agent of Chinese privet, Ligustrum sinense Lour., was studied under laboratory and outdoor conditions in Huangshan City of Anhui Province, China, in 2006. A. tsekooni larvae are leafminers that...

Enhancing biological control of basal stem rot disease (Ganoderma boninense) in oil palm plantations.

Science.gov (United States)

Susanto, A; Sudharto, P S; Purba, R Y

2005-01-01

Basal Stem Rot (BSR) disease caused by Ganoderma boninense is the most destructive disease in oil palm, especially in Indonesia and Malaysia. The available control measures for BSR disease such as cultural practices and mechanical and chemical treatment have not proved satisfactory due to the fact that Ganoderma has various resting stages such as melanised mycelium, basidiospores and pseudosclerotia. Alternative control measures to overcome the Ganoderma problem are focused on the use of biological control agents and planting resistant material. Present studies conducted at Indonesian Oil Palm Research Institute (IOPRI) are focused on enhancing the use of biological control agents for Ganoderma. These activities include screening biological agents from the oil palm rhizosphere in order to evaluate their effectiveness as biological agents in glasshouse and field trials, testing their antagonistic activities in large scale experiments and eradicating potential disease inoculum with biological agents. Several promising biological agents have been isolated, mainly Trichoderma harzianum, T. viride, Gliocladium viride, Pseudomonas fluorescens, and Bacillus sp. A glasshouse and field trial for Ganoderma control indicated that treatment with T. harzianum and G. viride was superior to Bacillus sp. A large scale trial showed that the disease incidence was lower in a field treated with biological agents than in untreated fields. In a short term programme, research activities at IOPRI are currently focusing on selecting fungi that can completely degrade plant material in order to eradicate inoculum. Digging holes around the palm bole and adding empty fruit bunches have been investigated as ways to stimulate biological agents.

Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering.

Science.gov (United States)

Menolascina, Filippo; Bellomo, Domenico; Maiwald, Thomas; Bevilacqua, Vitoantonio; Ciminelli, Caterina; Paradiso, Angelo; Tommasi, Stefania

2009-10-15

Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics of complex pathologies like cancer: acquiring information for a system understanding of complex reaction networks is time consuming and expensive. Stimulus response experiments (SRE) have been used to gain a deeper insight into the details of biochemical mechanisms underlying cell life and functioning. Optimisation of the input time-profile, however, still remains a major area of research due to the complexity of the problem and its relevance for the task of information retrieval in systems biology-related experiments. We have addressed the problem of quantifying the information associated to an experiment using the Fisher Information Matrix and we have proposed an optimal experimental design strategy based on evolutionary algorithm to cope with the problem of information gathering in Systems Biology. On the basis of the theoretical results obtained in the field of control systems theory, we have studied the dynamical properties of the signals to be used in cell stimulation. The results of this study have been used to develop a microfluidic device for the automation of the process of cell stimulation for system identification. We have applied the proposed approach to the Epidermal Growth Factor Receptor pathway and we observed that it minimises the amount of parametric uncertainty associated to the identified model. A statistical framework based on Monte-Carlo estimations of the uncertainty ellipsoid confirmed the superiority of optimally designed experiments over canonical inputs. The proposed approach can be easily extended to multiobjective formulations that can also take advantage of identifiability analysis. Moreover, the availability of fully automated

75 FR 28232 - Availability of an Environmental Assessment for a Biological Control Agent for Hemlock Woolly...

Science.gov (United States)

2010-05-20

...] Availability of an Environmental Assessment for a Biological Control Agent for Hemlock Woolly Adelgid AGENCY..., into the continental United States for use as a biological control agent to reduce the severity of... biological control agent to reduce the severity of hemlock woolly adelgid (HWA) infestations. HWA, an...

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

Science.gov (United States)

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.

Systems Biology of Saccharomyces cerevisiae Physiology and its DNA Damage Response

DEFF Research Database (Denmark)

Fazio, Alessandro

The yeast Saccharomyces cerevisiae is a model organism in biology, being widely used in fundamental research, the first eukaryotic organism to be fully sequenced and the platform for the development of many genomics techniques. Therefore, it is not surprising that S. cerevisiae has also been widely...... used in the field of systems biology during the last decade. This thesis investigates S. cerevisiae growth physiology and DNA damage response by using a systems biology approach. Elucidation of the relationship between growth rate and gene expression is important to understand the mechanisms regulating...... set of growth dependent genes by using a multi-factorial experimental design. Moreover, new insights into the metabolic response and transcriptional regulation of these genes have been provided by using systems biology tools (Chapter 3). One of the prerequisite of systems biology should...

77 FR 46373 - Availability of an Environmental Assessment for a Biological Control Agent for Hemlock Woolly...

Science.gov (United States)

2012-08-03

...] Availability of an Environmental Assessment for a Biological Control Agent for Hemlock Woolly Adelgid AGENCY... States for use as a biological control agent to reduce the severity of hemlock woolly adelgid... beetle from the western United States, into the eastern United States for use as a biological control...

PathSys: integrating molecular interaction graphs for systems biology

Directory of Open Access Journals (Sweden)

Raval Alpan

2006-02-01

Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

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

Science.gov (United States)

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.

A Biological Micro Actuator: Graded and Closed-Loop Control of Insect Leg Motion by Electrical Stimulation of Muscles

Science.gov (United States)

Cao, Feng; Zhang, Chao; Vo Doan, Tat Thang; Li, Yao; Sangi, Daniyal Haider; Koh, Jie Sheng; Huynh, Ngoc Anh; Aziz, Mohamed Fareez Bin; Choo, Hao Yu; Ikeda, Kazuo; Abbeel, Pieter; Maharbiz, Michel M.; Sato, Hirotaka

2014-01-01

In this study, a biological microactuator was demonstrated by closed-loop motion control of the front leg of an insect (Mecynorrhina torquata, beetle) via electrical stimulation of the leg muscles. The three antagonistic pairs of muscle groups in the front leg enabled the actuator to have three degrees of freedom: protraction/retraction, levation/depression, and extension/flexion. We observed that the threshold amplitude (voltage) required to elicit leg motions was approximately 1.0 V; thus, we fixed the stimulation amplitude at 1.5 V to ensure a muscle response. The leg motions were finely graded by alternation of the stimulation frequencies: higher stimulation frequencies elicited larger leg angular displacement. A closed-loop control system was then developed, where the stimulation frequency was the manipulated variable for leg-muscle stimulation (output from the final control element to the leg muscle) and the angular displacement of the leg motion was the system response. This closed-loop control system, with an optimized proportional gain and update time, regulated the leg to set at predetermined angular positions. The average electrical stimulation power consumption per muscle group was 148 µW. These findings related to and demonstrations of the leg motion control offer promise for the future development of a reliable, low-power, biological legged machine (i.e., an insect–machine hybrid legged robot). PMID:25140875

A biological micro actuator: graded and closed-loop control of insect leg motion by electrical stimulation of muscles.

Directory of Open Access Journals (Sweden)

Feng Cao

Full Text Available In this study, a biological microactuator was demonstrated by closed-loop motion control of the front leg of an insect (Mecynorrhina torquata, beetle via electrical stimulation of the leg muscles. The three antagonistic pairs of muscle groups in the front leg enabled the actuator to have three degrees of freedom: protraction/retraction, levation/depression, and extension/flexion. We observed that the threshold amplitude (voltage required to elicit leg motions was approximately 1.0 V; thus, we fixed the stimulation amplitude at 1.5 V to ensure a muscle response. The leg motions were finely graded by alternation of the stimulation frequencies: higher stimulation frequencies elicited larger leg angular displacement. A closed-loop control system was then developed, where the stimulation frequency was the manipulated variable for leg-muscle stimulation (output from the final control element to the leg muscle and the angular displacement of the leg motion was the system response. This closed-loop control system, with an optimized proportional gain and update time, regulated the leg to set at predetermined angular positions. The average electrical stimulation power consumption per muscle group was 148 µW. These findings related to and demonstrations of the leg motion control offer promise for the future development of a reliable, low-power, biological legged machine (i.e., an insect-machine hybrid legged robot.

75 FR 69396 - Availability of an Environmental Assessment for a Biological Control Agent for Arundo donax

Science.gov (United States)

2010-11-12

... Biological Control Agent for Arundo donax AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION... alternatives to, the release of Arundo scale into the continental United States for use as a biological control... a biological control agent to reduce the severity of Arundo donax infestations. A. donax is a highly...

Biological Control of Solenopsis Fire Ants by Pseudacteon Parasitoids: Theory and Practice

Directory of Open Access Journals (Sweden)

Lloyd W. Morrison

2012-01-01

Full Text Available Pseudacteon parasitoids are potential biocontrol agents of invasive Solenopsis fire ants. Pseudacteon species that parasitize the invasive S. invicta Buren and S. richteri Forel have been introduced to, and naturally dispersed across, the southeastern USA, although there is no evidence yet that Solenopsis host ant populations have decreased. The ability of introduced Pseudacteon species to regulate Solenopsis populations will depend upon the relative importance of top-down effects in the recipient communities. In this paper, I examine the characteristics of the Pseudacteon/Solenopsis parasitoid/host system and evaluate the extent to which research findings are consistent with top-down control. Laboratory and field experiments evaluating Solenopsis population regulation have been equivocal, and overall the available evidence provides little support for strong top-down effects in this system. Competitive exclusion may occur among introduced Pseudacteon species, and future efforts at biological control are likely to be more efficacious if they focus on other types of natural enemies.

Carbon-13 NMR spectroscopy of biological systems

CERN Document Server

Beckmann, Nicolau

1995-01-01

This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

Models for integrated pest control and their biological implications.

Science.gov (United States)

Tang, Sanyi; Cheke, Robert A

2008-09-01

Successful integrated pest management (IPM) control programmes depend on many factors which include host-parasitoid ratios, starting densities, timings of parasitoid releases, dosages and timings of insecticide applications and levels of host-feeding and parasitism. Mathematical models can help us to clarify and predict the effects of such factors on the stability of host-parasitoid systems, which we illustrate here by extending the classical continuous and discrete host-parasitoid models to include an IPM control programme. The results indicate that one of three control methods can maintain the host level below the economic threshold (ET) in relation to different ET levels, initial densities of host and parasitoid populations and host-parasitoid ratios. The effects of host intrinsic growth rate and parasitoid searching efficiency on host mean outbreak period can be calculated numerically from the models presented. The instantaneous pest killing rate of an insecticide application is also estimated from the models. The results imply that the modelling methods described can help in the design of appropriate control strategies and assist management decision-making. The results also indicate that a high initial density of parasitoids (such as in inundative releases) and high parasitoid inter-generational survival rates will lead to more frequent host outbreaks and, therefore, greater economic damage. The biological implications of this counter intuitive result are discussed.

Operation manual of microbeam system in Takasaki for biological application (MiST-BA)

International Nuclear Information System (INIS)

Sakashita, Tetsuya; Yokota, Yuichiro; Wada, Seiichi; Funayama, Tomoo; Kobayashi, Yasuhiko

2004-03-01

Microbeam System is a powerful tool for micro-radiosurgery studies and direct investigation of cell-to-cell communications such as 'bystander effects'. Microbeam system in Takasaki for biological application (MiST-BA) has been developed for several years and applied to some cases. There were fate mapping of the cellular blastoderm stage egg of the silkworm and bystander effects such as inhibition of cell proliferation, induction of micronuclei, and so on. The aim of this report (operation manual) is to provide a simple and easy usage of MiST-BA for current and new users. MiST-BA consists of three parts; (1) Offline microscope control system for cell-finding. (2) Online microscope control system for cell-targeting and irradiating, and (3) Beam shutter control system for cell irradiation with a precise number of heavy ions. The report presents the outline of MiST-BA, the operation protocol of each part, examples of a microbeam irradiation experiment using CHO-K1 cells, silkworm eggs, and Tobacco protoplast cells, and Trouble shooting. (author)

Biological control of fusarium wilt of tomato by antagonist fungi and ...

African Journals Online (AJOL)

Yomi

2012-01-16

Jan 16, 2012 ... Key words: Biological control, fusarium wilt, tomato, antagonist fungi, cyanobacteria. INTRODUCTION ... severely affected by wilt disease caused by F. oxysporum f. sp. ..... Changing options for the control of deciduous fruit.

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

Science.gov (United States)

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.

Construction of new synthetic biology tools for the control of gene expression in the cyanobacterium Synechococcus sp. strain PCC 7002.

Science.gov (United States)

Zess, Erin K; Begemann, Matthew B; Pfleger, Brian F

2016-02-01

Predictive control of gene expression is an essential tool for developing synthetic biological systems. The current toolbox for controlling gene expression in cyanobacteria is a barrier to more in-depth genetic analysis and manipulation. Towards relieving this bottleneck, this work describes the use of synthetic biology to construct an anhydrotetracycline-based induction system and adapt a trans-acting small RNA (sRNA) system for use in the cyanobacterium Synechococcus sp. strain PCC 7002. An anhydrotetracycline-inducible promoter was developed to maximize intrinsic strength and dynamic range. The resulting construct, PEZtet , exhibited tight repression and a maximum 32-fold induction upon addition of anhydrotetracycline. Additionally, a sRNA system based on the Escherichia coli IS10 RNA-IN/OUT regulator was adapted for use in Synechococcus sp. strain PCC 7002. This system exhibited 70% attenuation of target gene expression, providing a demonstration of the use of sRNAs for differential gene expression in cyanobacteria. These systems were combined to produce an inducible sRNA system, which demonstrated 59% attenuation of target gene expression. Lastly, the role of Hfq, a critical component of sRNA systems in E. coli, was investigated. Genetic studies showed that the Hfq homolog in Synechococcus sp. strain PCC 7002 did not impact repression by the engineered sRNA system. In summary, this work describes new synthetic biology tools that can be applied to physiological studies, metabolic engineering, or sRNA platforms in Synechococcus sp. strain PCC 7002. © 2015 Wiley Periodicals, Inc.

Realization of Flight Control System in Virtual Reality Environment with Biological Signals

OpenAIRE

ALTIN, Cemil; ER, Orhan

2018-01-01

In this study, anunmanned aerial vehicle was flown on a virtual reality gaming platform with thehelp of commands processed by signal processing methods of biological signals. In thedeveloped application, Matlab signal processing environment and Unity 3Denvironment which is a virtual reality software platform are integrated witheach other and made to work. The biological signals obtained from the EEG ve EMGsensors are processed in Matlab environment and then converted to commands andtransferre...

Anion binding in biological systems

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