Introduction to a biological systems science - Preliminaries
Biological systems analysis for developing dynamic physiological models
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Results for “biological system modeling”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Combined effect of flight factors
The effects of various combinations of space flight stresses are discussed. Included are weightlessness, acceleration, vibration, ionizing radiation, hypoxia, and ambient temperature. The problem of constructing mathematical models to describe the dynamics of biological systems, including those to analyze and predict adaptation and restoration processes following combined stresses, is also considered.
Antipov, V. V.↗
Sampling and noise in vision networks
This research is part of the Human Interface Research Branch-Vision Group's program to develop computable models of biological solutions to general vision system problems. Two problem areas are addressed: effects of discrete sampling by receptors, and effects of visual system noise.
Ahumada, Albert J., Jr.↗
Neural network for processing both spatial and temporal data with time based back-propagation
Neural networks are computing systems modeled after the paradigm of the biological brain. For years, researchers using various forms of neural networks have attempted to model the brain's information processing and decision-making capabilities. Neural network algorithms have impressively demonstrated the capability of modeling spatial information. On the other hand, the application of parallel distributed models to the processing of temporal data has been severely restricted. The invention introduces a novel technique which adds the dimension of time to the well known back-propagation neural network algorithm. In the space-time neural network disclosed herein, the synaptic weights between two artificial neurons (processing elements) are replaced with an adaptable-adjustable filter. Instead of a single synaptic weight, the invention provides a plurality of weights representing not only association, but also temporal dependencies. In this case, the synaptic weights are the coefficients to the adaptable digital filters. Novelty is believed to lie in the disclosure of a processing element and a network of the processing elements which are capable of processing temporal as well as spacial data.
Villarreal, James A.↗
A New NASA Flagship Facility: PRECISE – Proton Radiation Environmentally Controlled Investigations for Space Exploration
This paper proposes a NASA-led investment in a flagship user facility at NASA Ames Research Center for simulating high energy protons and combined exposures to other spaceflight stressors for a wide variety of in vivo, ex vivo, and in vitro biological systems, as well as non-biological models of spacecraft and instruments.
Sylvain V. Costes↗
The application of sensitivity analysis to models of large scale physiological systems
A survey of the literature of sensitivity analysis as it applies to biological systems is reported as well as a brief development of sensitivity theory. A simple population model and a more complex thermoregulatory model illustrate the investigatory techniques and interpretation of parameter sensitivity analysis. The role of sensitivity analysis in validating and verifying models, and in identifying relative parameter influence in estimating errors in model behavior due to uncertainty in input data is presented. This analysis is valuable to the simulationist and the experimentalist in allocating resources for data collection. A method for reducing highly complex, nonlinear models to simple linear algebraic models that could be useful for making rapid, first order calculations of system behavior is presented.
Leonard, J. I.↗
Networks for image acquisition, processing and display
The human visual system comprises layers of networks which sample, process, and code images. Understanding these networks is a valuable means of understanding human vision and of designing autonomous vision systems based on network processing. Ames Research Center has an ongoing program to develop computational models of such networks. The models predict human performance in detection of targets and in discrimination of displayed information. In addition, the models are artificial vision systems sharing properties with biological vision that has been tuned by evolution for high performance. Properties include variable density sampling, noise immunity, multi-resolution coding, and fault-tolerance. The research stresses analysis of noise in visual networks, including sampling, photon, and processing unit noises. Specific accomplishments include: models of sampling array growth with variable density and irregularity comparable to that of the retinal cone mosaic; noise models of networks with signal-dependent and independent noise; models of network connection development for preserving spatial registration and interpolation; multi-resolution encoding models based on hexagonal arrays (HOP transform); and mathematical procedures for simplifying analysis of large networks.
Ahumada, Albert J., Jr.↗
Modeling the effects of light, carbon dioxide, and temperature on the growth of potato
This study examined the effects of light, temperature and carbon dioxide on the growth of potato (Solanum tuberosum L.) in a controlled environment in order to ascertain the best growing conditions for potato in life support systems in space. 'Norland' and 'Russet Burbank' were grown in 6-L pots of peat-vermiculite for 56 d in growth chambers at the University of Wisconsin Biotron. Environmental factor levels included continuous light (24-h photoperiod) at 250, 400, and 550 micromoles m-2 s-1 PPF; constant temperature at 16, 20, and 24 degrees C; and CO2 at approximately 400, 1000, and 1600 microliters L-1. Separate effects analysis and ridge analysis provided a means to examine the effects of individual environmental factors and to determine combinations of factors that are expected to give the best increases in yields over the central design point. The response surface of Norland indicated that tuber yields were highest with moderately low temperature (18.7 degrees C), low CO2 (400 microliters L-1) and high light (550 micromoles m-2 s-1 PPF). These conditions also favored shorter stem growth. Russet Burbank tuber yields were highest at moderately low temperature (17.5 degrees C), high CO2 (1600 microliters L-1) and medium analyses will be used to project the most efficient conditions for growth of potatoes in closed ecological life support systems (CELSS) in space colonies.
NASA Discipline Life Support Systems↗
Design patterns of biological cells
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.
59 BASIC BIOLOGICAL SCIENCES↗
Biological Potential in Serpentinizing Systems
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.
the potential of serpentinizing systems to support↗
Models to study gravitational biology of Mammalian reproduction
Mammalian reproduction evolved within Earth's 1-g gravitational field. As we move closer to the reality of space habitation, there is growing scientific interest in how different gravitational states influence reproduction in mammals. Habitation of space and extended spaceflight missions require prolonged exposure to decreased gravity (hypogravity, i.e., weightlessness). Lift-off and re-entry of the spacecraft are associated with exposure to increased gravity (hypergravity). Existing data suggest that spaceflight is associated with a constellation of changes in reproductive physiology and function. However, limited spaceflight opportunities and confounding effects of various nongravitational factors associated with spaceflight (i.e., radiation, stress) have led to the development of ground-based models for studying the effects of altered gravity on biological systems. Human bed rest and rodent hindlimb unloading paradigms are used to study exposure to hypogravity. Centrifugation is used to study hypergravity. Here, we review the results of spaceflight and ground-based models of altered gravity on reproductive physiology. Studies utilizing ground-based models that simulate hyper- and hypogravity have produced reproductive results similar to those obtained from spaceflight and are contributing new information on biological responses across the gravity continuum, thereby confirming the appropriateness of these models for studying reproductive responses to altered gravity and the underlying mechanisms of these responses. Together, these unique tools are yielding new insights into the gravitational biology of reproduction in mammals.
Review, Tutorial↗
Modeling Space Radiation with Radiomimetic Agent Bleomycin
Space radiation consists of proton and helium from solar particle events (SPE) and high energy heavy ions from galactic cosmic ray (GCR). This mixture of radiation with particles at different energy levels has different effects on biological systems. Currently, majority studies of radiation effects on human were based on single-source radiation due to the limitation of available method to model effects of space radiation on living organisms. While NASA Space Radiation Laboratory is working on advanced switches to make it possible to have a mixed field radiation with particles of different energies, the radiation source will be limited. Development of an easily available experimental model for studying effects of mixed field radiation could greatly speed up our progress in our understanding the molecular mechanisms of damage and responses from exposure to space radiation, and facilitate the discovery of protection and countermeasures against space radiation, which is critical for the mission to Mars. Bleomycin, a radiomimetic agent, has been widely used to study radiation induced DNA damage and cellular responses. Previously, bleomycin was often compared to low low Linear Energy Transfer (LET) gamma radiation without defined characteristics. Our recent work demonstrated that bleomycin could induce complex clustered DNA damage in human fibroblasts that is similar to DNA damage induced by high LET radiation. These type of DNA damage is difficult to repair and can be visualized by gamma-H2Ax staining weeks after the initial insult. The survival ratio between early and late plating of human fibroblasts after bleomycin treatment is between low LET and high LET radiation. Our results suggest that bleomycin induces DNA damage and other cellular stresses resembling those resulted from mixed field radiation with both low and high LET particles. We hypothesize that bleomycin could be used to mimic space radiation in biological systems. Potential advantages and limitations of using bleomycin to treat biological specimen as an easily available model to study effects of space radiation on biological systems and to develop countermeasures for space radiation associated risks will be discussed.
Lu, Tao↗
The Roles of Tidal Marshes in the Estuarine Biochemical Processes: A Numerical Modeling Study
Observations suggest that the existence of tidal marsh can alter the oxygen and nutrient dynamics in adjacent water bodies, but assessing the impacts of large tidal marshes on an estuary is challenging. In this study, we use a modeling approach to investigate the roles of tidal marshes on the estuarine biochemical processes. The marsh model, which simulates the ecological functions of marshes at seasonal and annual time-scales, is embedded inside an unstructured-grid three-dimensional hydrodynamic and eutrophication model (SCHISM-ICM). This modeling system simulates the growth and metabolism of the tidal marshes and links biological processes to nutrient dynamics in the water column and sediment. This model dynamically simulates nutrient recycling and physical transport of the materials between marshes and open water through wetting-drying processes. This coupled model system is validated and successfully applied to the York River Estuary. Model results suggest that tidal marshes influence the local diurnal dissolved oxygen (DO) cycle by exporting dissolved organic carbon and high sediment oxygen demand in the marsh system through the tidal exchange. The high deposition rates of organics and diurnal DO cycle enhance the sediment release of phosphorus. On the other hand, marshes tend to decrease dissolved inorganic nitrogen in the water column by settling particulate nutrients and enhancing the denitrification process. The study demonstrates that tidal marshes exert substantial impacts on the estuarine biochemical processes. The developed tidal marsh model enhances eutrophication modeling and advances the understanding of the feedback effects between marsh biogeochemistry and estuarine eutrophication processes on a systemic scale.
54 ENVIRONMENTAL SCIENCES↗
Tensegrity I. Cell structure and hierarchical systems biology
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.
NASA Program Fundamental Space Biology↗
Toward implementing autonomous adaptive data acquisition for scanning hyperspectral imaging of biological systems
Autonomous experimentation is an emerging area of research, primarily related to autonomous vehicles, scientific combinatorial discovery approaches in materials science and drug discovery, and iterative research loops of planning, experimentation, and analysis. However, autonomous approaches developed in these contexts are difficult to apply to high-dimensional mapping technologies, such as scanning hyperspectral imaging of biological systems, due to sample complexity and heterogeneity. We briefly cover the history of adaptive sampling algorithms and surrogate modeling in order to define autonomous adaptive data acquisition as an objective-based, flexible building block for future biological imaging experimentation driven by intelligent infrastructure. We subsequently summarize the recent implementations of autonomous adaptive data acquisition (AADA) for scanning hyperspectral imaging, assess how these address the difficulties of autonomous approaches in hyperspectral imaging, and highlight the AADA design variation from a goal-oriented perspective. Finally, we present a modular AADA architecture that embeds AADA-driven flexible building blocks to address the challenge of time resolution for high-dimensional scanning hyperspectral imaging of nonequilibrium dynamical systems. In our example research-driven experimental design case, we propose an AADA infrastructure for time-resolved, noninvasive, and label-free scanning hyperspectral imaging of living biological systems. This AADA infrastructure can accurately target the correct state of the system for experimental workflows that utilize subsequent expensive, high-information-content analytical techniques.
59 BASIC BIOLOGICAL SCIENCES↗
Utilizing CellBox to Describe Varied Dynamical Systems
CellBox is a hybrid modeling framework that integrates machine-learning approaches with explicit mathematical modeling to determine the behavior of dynamical systems, intended for determining the complex interactions of molecule and phenotype within a cellular environment using perturbation/response-based data. The original work utilized analysis of a melanoma cell line, SK-Mel-133, which we sought to expand to and evaluate effectiveness in describing other nonlinear systems both within and outside of biology. We evaluated with two models. One model is based upon the free-fall of an object under a velocity-dependent drag force; this produced inherent perturbation/response data. The other model is based upon a form of mass-action molecular kinetics; for this, we ran the simulation to steady state in each species for each perturbation and select the steady state as input for CellBox. We determined that CellBox, outside of its original use case, can still strongly predict even non-biological dynamical systems in the small-perturbation regime, with r = 0.99977 to 0.85123, p < 0.05 for freefall. However, CellBox cannot accurately predict behavior within large-perturbation regimes, p >> 0.05 for freefall. In addition, we performed a naïve comparison of CellBox network structure to known network structure in the mass-action model to assess accuracy.
97 MATHEMATICS AND COMPUTING↗
Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly
Protein self-assembly is a common and essential biological phenomenon, and bacterial microcompartments present a promising model system to study this process. Bacterial microcompartments are large, protein-based organelles which natively carry out processes important for carbon fixation in cyanobacteria and the survival of enteric bacteria. These structures are increasingly popular with biological engineers due to their potential utility as nanobioreactors or drug delivery vehicles. However, the limited understanding of the assembly mechanism of these bacterial microcompartments hinders efforts to repurpose them for non-native functions. Here, we comprehensively investigate proteins involved in the assembly of the 1,2-propanediol utilization bacterial microcompartment from Salmonella enterica serovar Typhimurium LT2, one of the most widely studied microcompartment systems. We first demonstrate that two shell proteins, PduA and PduJ, have a high propensity for self-assembly upon overexpression, and we provide a novel method for self-assembly quantification. Using genomic knock-outs and knock-ins, we systematically show that these two proteins play an essential and redundant role in bacterial microcompartment assembly that cannot be compensated by other shell proteins. At least one of the two proteins PduA and PduJ must be present for the bacterial microcompartment shell to assemble. We also demonstrate that assembly-deficient variants of these proteins are unable to rescue microcompartment formation, highlighting the importance of this assembly property. Our work provides insight into the assembly mechanism of these bacterial organelles and will aid downstream engineering efforts.
1,2-propanediol utilization MCP↗
Artificial Immune System Approaches for Aerospace Applications
Artificial Immune Systems (AIS) combine a priori knowledge with the adapting capabilities of biological immune system to provide a powerful alternative to currently available techniques for pattern recognition, modeling, design, and control. Immunology is the science of built-in defense mechanisms that are present in all living beings to protect against external attacks. A biological immune system can be thought of as a robust, adaptive system that is capable of dealing with an enormous variety of disturbances and uncertainties. Biological immune systems use a finite number of discrete "building blocks" to achieve this adaptiveness. These building blocks can be thought of as pieces of a puzzle which must be put together in a specific way-to neutralize, remove, or destroy each unique disturbance the system encounters. In this paper, we outline AIS models that are immediately applicable to aerospace problems and identify application areas that need further investigation.
KrishnaKumar, Kalmanje↗