Biological Control Systems Research Articles

AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology.

Motivation: Many problems of interest in dynamic modeling and control of biological systems can be posed as non-linear optimization problems subject to algebraic and dynamic constraints. In the context of modeling, this is the case of, e.g. parameter estimation, optimal experimental design and dynamic flux balance analysis. In the context of control, model-based metabolic engineering or drug dose optimization problems can be formulated as (multi-objective) optimal control problems. Finding a solution to those problems is a very challenging task which requires advanced numerical methods.Results: This work presents the AMIGO2 toolbox: the first multiplatform software tool that automatizes the solution of all those problems, offering a suite of state-of-the-art (multi-objective) global optimizers and advanced simulation approaches.Availability and Implementation: The toolbox and its documentation are available at: sites.google.com/site/amigo2toolbox.Contact: ebalsa@iim.csic.esSupplementary information: Supplementary data are available at Bioinformatics online.

Effect of Habitat Modifications on Predation Potential of <i>Anisops sardea</i> (Hemiptera: Notonectidae) against Larvae of Culex vishnui, Vector of Japanease Encephalitis

To prevent emergence of insecticide resistance in vector population & biological magnification of toxic insecticides through food chain, more attention is now put on application of biological control system to reduce the population of vectors. Present study was carried out to assess the effect of habitat modifications on the predatory ability of Anisops sardea (Hemiptera: Notonectidae) against immature of Culex Vishnui (Diptera: Culicidae) group of mosquitoes in laboratory and semi-field bioassay.To study the effect of habitat modifications, laboratory based predatory experiments were carried with A. sardea as predator and Cx.vishnui group of mosquitoes as prey species. To determine prey preference of predator species, predatory experiment was done in presence of mosquitoes belongs to different genera. For a long-term study on predation rate, for 15 consecutive days, 10 adult individuals of A. sardea were kept in a plastic bucket of 20 L capacity in open natural condition and number of mosquito larvae consumed/per day was calculated.Result of single factor ANOVA analysis revealed that habitat modifications have significant effect on the predatory rate of A sardea as calculated F value (34.10) is significantly higher than table value (F crit =2.156). Pair wise ‘t test’ revealed significant variations in the predation rate when different habitat combinations were analyzed. Results of selectivity index, niche breadth and food breadth were also evaluated. Long term bioassay in semi-field condition revealed that predatory rates were almost similar throughout the study period.Considering the habitat specificity, prey preference and the rate of predation in semi field condition, it can be concluded that A. sardea can be used as potential biological control agent against Culex Vishnui group of mosquitoes.

Preparation and evaluation of alginate/chitosan microspheres containing pheromones for pest control of Megaplatypus mutatus Chapuis (Platypodinae: Platypodidae)

AbstractThis work describes the optimization of an alginate/chitosan microsphere preparation for the encapsulation of a sexual pheromone, 6‐methyl‐5‐hepten‐2‐ol (sulcatol), to realize a slow‐release device for the biological control of the Megaplatypus mutatus pest. To evaluate and select the best encapsulation/release conditions three parameters were studied: alginate concentration, pH of gelling solution and Ca2+/COO− ratio. The preparation was optimized using biopolymers with improved mechanical properties and swelling behavior. The obtained microspheres were characterized using Fourier transform infrared spectroscopy, scanning electron and optical microscopies, swelling degree, mechanical properties and in vitro release of encapsulated pheromone. The microspheres performed best when they were synthesized using an alginate concentration of 4% w/v, at pH = 9 and with a Ca2+/COO− ratio of 3.5. The attractiveness of the alginate/chitosan microspheres towards M. mutatus was demonstrated by behavioral bioassay with the completed pheromonal blend of the species (sulcatol, sulcatone and 3‐pentanol). The formulation can be considered as an efficient slow‐release biological control system, with no negative environmental impact. © 2015 Society of Chemical Industry

Biomedical Effects of Acupuncture

Biomedical effects of acupuncture Introduction: The use of acupuncture as a method of pain relief in western medicine is based on a wide range of clinical trials, and there is no doubt that it has significant effect in the treatment of acute and chronic pain. Method: We were going a summary on past decades performed acupuncture studies on effects. Studies found that in chronic pain the concentration of endorphins in the spinal fluid is markedly reduced. Cholecystokinin octapeptide has been shown to function in the CNS as a neuropeptide with potent antiopioid activity. Electro acupuncture stimulation caused a substantial increase of immunoreactivity in CSF perforates of the rat spinal cord. The diffuse noxious inhibitory controls may be involved in the mechanisms. DNIC are part of the biological pain control system. Our summary examines the analgesic effect of the TRR 469 adenosine receptor agonist. Upon acupuncture points stimulation Zu San Li (St 36) significantly higher concentrations of adenosine were recorded. Results: Acupuncture induces a variety of biological responses, which occur both locally as well as in a remote location. Studies on the stress response show that acupuncture techniques can reduce the neither concentration of nor adrenaline at cerebral perfusion and in the blood circulation, reduce the production of epinephrine in animals exposed to restraint stress, induce long-term behavioural and cardiovascular depression in behaviour and anxiolytic effects common in animals in captivity. Forced restraint has shown to be a simple physiological stressor that causes significant increase of heart activity, blood pressure and levels of nor epinephrine and epinephrine, activation of the simpatico-adrenal system and the hypothalamic-pituitary axis. Discussion: CCK 8 is in fact increasingly released at frequencies from 100 Hz to 15 Hz. Opioid peptides are activated and CCK 8 is not produced at low frequencies 1-2 Hz. The known effect of the endogenous opioids which are produced in electro acupuncture stimulation and hindered by naloxone does not apply unequivocally, since the low frequency EA stimulation have been found to activate opioid peptides derived from propio-enkephalins, while the high frequency of 100 Hz activates the preprodynorphin group, in laboratory animals as well as in humans. The needle stimulation or low frequency electro acupuncture was effective in certain nociceptive some states, whereas the high frequency stimulation proves more effective in comparison with manual acupuncture. The lack of acupuncture effectiveness may be attributed to the high levels of cholecystokinin opioid antagonist in the brain (1). Conclusion: Acupuncture and associated therapies have come to the fore. More further basic and applied researches need for deeper understand its effect. They are always related to the patients lifestyle for elevate QoL.

Robot-Aided Rehabilitation Methodology for Enhancing Movement Smoothness by Using a Human Trajectory Generation Model With Task-Related Constraints

Natural motion produced by the biological motor control system presents movement smoothness, but neurological disorders or injuries severely deteriorates motor functions. This paper proposes a robot-aided training methodology focusing on smooth transient trajectory generation by the arm while performing a complex task (i.e., virtual curling). The aim of the proposed approach is that a trainee should be taught a reference velocity profile with high movement smoothness in the complex task via the interaction with a robotic device while improving coordination ability for natural arm movements. In the virtual curling training, a trainee manipulates the handle of an impedance-controlled robot to move a virtual stone to the center of a circular target on ice while predicting transient behaviors of the released stone. First, a reference hand motion is clarified through a set of preliminary experiments for different task conditions carried out with four well-trained subjects, and the characteristics of skilled hand velocity profiles are coded with a set of quantitative factors as task-related constraints. The skilled hand motions according to task conditions are successfully simulated in the framework of a minimum-jerk model with the task-related constraints. Next, the training program for enhancing movement smoothness is developed using the computational model, which has four training modes of operation: 1) diagnosis, 2) teaching with active-assistance by the robot, 3) training with passive-assistance, and 4) training with no assistance. Finally, training experiments with ten novice healthy volunteers demonstrate that the proposed approach can be utilized in the recovery of motor functions necessary for desired velocity profiles with high motion smoothness.

Arrangement and Applying of Movement Patterns in the Cerebellum Based on Semi-supervised Learning.

Biological control systems have long been studied as a possible inspiration for the construction of robotic controllers. The cerebellum is known to be involved in the production and learning of smooth, coordinated movements. Therefore, highly regular structure of the cerebellum has been in the core of attention in theoretical and computational modeling. However, most of these models reflect some special features of the cerebellum without regarding the whole motor command computational process. In this paper, we try to make a logical relation between the most significant models of the cerebellum and introduce a new learning strategy to arrange the movement patterns: cerebellar modular arrangement and applying of movement patterns based on semi-supervised learning (CMAPS). We assume here the cerebellum like a big archive of patterns that has an efficient organization to classify and recall them. The main idea is to achieve an optimal use of memory locations by more than just a supervised learning and classification algorithm. Surely, more experimental and physiological researches are needed to confirm our hypothesis.

Implementation of integral feedback control in biological systems.

Integral control design ensures that a key variable in a system is tightly maintained within acceptable levels. This approach has been widely used in engineering systems to ensure offset free operation in the presence of perturbations. Several biological systems employ such an integral control design to regulate cellular processes. An integral control design motif requires a negative feedback and an integrating process in the network loop. This review describes several biological systems, ranging from bacteria to higher organisms in which the presence of integral control principle has been hypothesized. The review highlights that in addition to the negative feedback, occurrence of zero-order kinetics in the process is a key element to realize the integral control strategy. Although the integral control motif is common to these systems, the mechanisms involved in achieving it are highly specific and can be incorporated at the level of signaling, metabolism, or at the phenotypic levels.

Time irreversibility of heart rate oscillations in newborns – Does it reflect system nonlinearity?

The aim of our research was to find out if the time irreversibility as a sign of specific class of nonlinear dynamics is present even in the newborn's heart rate oscillations. Multiscale irreversibility indices (Porta's index P%, Guzik index G% and Ehlers index E) of the heart rate signals were computed in 20 healthy neonates. The presence of system nonlinearity was assessed by surrogate data analysis. The results of our analysis revealed asymmetrical nature of heart rate oscillations present in the majority of neonatal heart rate recordings. Moreover, time irreversibility index P% was able to detect shift of sympathovagal balance toward sympathetic dominance in newborns. Our findings support the concept of nonlinearity as a universal feature of the biological control system even in the early stage of the system maturation. This finding supports the application of nonlinear methods to heart rate variability analysis.

Demystifying cognitive science: explaining cognition through network-based modeling.

Network science has made what once seemed miracle into practical science: we can set up conditions for self-building systems, and we can use their patterns of variability to identify and explain processes underlying prospective control in biological systems.

Increased seed consumption by biological control weevil tempers positive CO2 effect on invasive plant (Centaurea diffusa) fitness

Predicted increases in atmospheric CO2 and temperature may benefit some invasive plants, increasing the need for effective invasive plant management. Biological control can be an effective means of managing invasive plants, but the anticipated range in responses of plant–insect interactions to climate change make it difficult to predict how effective biological control will be in the future. Field experiments that manipulate climate within biological control systems could improve predictive power, but are challenging to implement and therefore rare to date. Here, we show that free air CO2 enrichment in the field increased the fitness of Centaurea diffusa Lam., a problematic invader in much of the western United States. However, CO2 enrichment also increased the impact of the biological control agent Larinus minutus (Coleoptera: Curculionidae) on C. diffusa fitness. C. diffusa plants flowered earlier and seed heads developed faster with both elevated CO2 and increased temperature. Natural dispersal of L. minutus into the experimental plots provided a unique opportunity to examine weevil preference for and effects on C. diffusa grown under the different climate change treatments. Elevated CO2 increased both the proportion of seed heads infested by L. minutus and, correspondingly, the amount of seed removed by weevils. Warming had no detectable effect on weevil utilization of plants. Higher weevil densities on elevated CO2 plants reduced, but did not eliminate, the positive effects of CO2 on C. diffusa fitness. Correlations between plant development time and weevil infestation suggest that climate change increased weevil infestation by hastening plant phenology. Phenological mismatches are anticipated with climate change in many plant–insect systems, but in the case of L. minutus and C. diffusa in mixed-grass prairie, a better phenological match may make the biological control agent more effective as CO2 levels rise.

Time delays and the control of biological systems: An overview

This special session provides an introduction for engineers to the applications of delay differential equations to biological control. Topics include the regulation of populations of organisms and neurons, the stabilization of unstable states and the design of drug delivery systems.

Use of Quantitative Real-Time PCR to Unravel Ecological Complexity in a Biological Control System

Biological control of soilborne plant pathogens using beneficial fungi, such as the mycoparasite Trichoderma harzianum, offers the prospect of environmentally benign pest control. However, biocontrol organisms have their own natural enemies; for example the fungivorous nematode Aphelenchoides saprophilus preys on T. harzianum. A trophic cascade occurs when three or more trophic levels are present in a food chain, and consumption of the intermediate species affects biomass or productivity of a lower trophic level; such an interaction in this system might reduce the biocontrol efficacy of T. harzianum. However, the presence of refuges, where intermediate-level species are protected from predation, may reduce the ecological impact of a trophic cascade. Interactions among microscopic organisms in a complex medium such as soil are difficult to observe and quantify. We evaluated the potential of quantitative real-time PCR (qRT-PCR) as a tool to investigate the trophic cascade interaction among T. harzianum, A. saprophilus, and the plant pathogen Sclerotinia sclerotiorum. Results indicate that the mycoparasite colonized and persisted inside structures (sclerotia) of the target plant pathogen, where it was relatively protected from predation compared to the surrounding soil environment. In this way, colonization of sclerotia may provide a refuge that reduces trophic cascade effects in this system. qRT-PCR provided a sensitive method to investigate fungal dynamics over time in this multitrophic system.

What does the term microbiome mean? And where did it come from? A bit of a surprise ..

BIOLOGICAL SCIENCES What does the term microbiome mean? And where did it come from? A bit of a surprise .. JONATHAN EISEN READ REVIEWS ✎ WRITE A REVIEW CORRESPONDENCE: jaeisen@ucdavis.edu DATE RECEIVED: “Microbiome” is such a hot term these days. And one key question many ask is “what does it mean?” A related question is – “where did the term come from?” I tried to tackle this many years ago on my blog with a post: The human microbiome – term being used in many ways – but at least it is getting some \npress. Basically my main point was that it seemed that the term “ microbiome” then should be used to refer to the collection of genomes of microbes in a system and that “microbiota” should be used to refer to the collection of organisms. Some key quotes from that post: June 10, 2015 DOI: 10.15200/winn.142971.16196 ARCHIVED: April 22, 2015 CITATION: Jonathan Eisen, What does the term microbiome mean? And where did it come from? A bit of a surprise .., The Winnower 2:e142971.16196 , 2015 , DOI: 10.15200/winn.142971.16196 © Eisen This article is distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and redistribution in any medium, provided that the original author and source are credited. Well, the human microbiome is all over the news recently thanks to a new paper on the diversity and biogeography of microbes in human saliva. My only complaint is that I and Stoneking and many others have unfortunately made a mess of the terminology. The “microbiome” was originally used to refer to the collection of the genomes of the microbes in a particular ecosystem. And the terms “microbiota” was used to refer to the actual organisms. Since Stoneking et al did not survey the genomes, they surveyed rRNA (which really at best tells you about what types of organisms are present) then they should have used microbiota riight? (And if they had I would not have been searching for the genomics component of their work). Not so fast, even the person who coined the term microbiome (Josh Lederberg) who originally seemed to use it to refer to all the genomes of the microbes also used the term ambiguously (e.g., in one paper he sad “the microbiome flora” meaning I guess the microbiota. I note, everyone seems to cite A paper by Lederberg called “Infectious History” in Science (Science 14 April 2000:) as the place he used microbiome but I cannot find the term there. I did however find the term in a paper in 2001 by Lora Hooper and Jeff Gordon (Commensal Host-Bacterial Relationships in the Gut Science 11 May 2001: Vol. 292. no. 5519, pp. 1115 – 1118). The Nobel laureate Joshua Lederberg has suggested using the term “microbiome” to describe the collective genome of our indigenous microbes (microflora), the idea being that a comprehensive genetic view of Homo sapiens as a life-form should include the genes in our microbiome (4). And reference 4 is “Personal communication” Anyway, others have taken the term microbiome and run with it because it does conjure up to many “microbial biome” which could be used to refer to all the microbes in a system. I prefer the original definitions with microbiota being the organisms and microbiome being the collective genomes of all the organisms. EISEN The Winnower APRIL 22 2015

75 years of the chestnut blight fungus Cryphonectria parasitica (Murr.) Barr in Europe

The chestnut blight fungus Cryphonectria parasitica is a native pathogen in East Asia and has been introduced into North America and Europe. Historical records and population genetic studies revealed at least three major introduction events from Asia into Europe.
 Nowadays, chestnut blight is present in almost the entire distribution range of European chestnut, i.e. from the Iberian Peninsula to the Caucasus. The C. parasitica population in most countries has been studied in respect to the diversity of vegetative compatibility (vc) types and the occurrence of hypovirulence. The vc type diversity of the different populations varied considerably. Typically, a high diversity of vc types has been found in areas with a long history of chestnut blight and where sexual recombination between divergent genotypes commonly has occurred. On the other hand, newly established populations often showed a low diversity with only one, or a few vc types present.
 Hypovirulence, i.e. the occurrence of C. parasitica isolates infected by Cryphonectria hypovirus 1 has been found widespread in Europe. Natural dissemination and active biological control applications have lead to a high prevalence of the hypovirus and to the recovery of many chestnut stands. Virulent cankers became hypovirus-infected within a short time and ceased expansion. There is concern that the diversity of vegetative compatibility types could increase in Europe through sexual reproduction between C. parasitica genotypes originating from different introductions. A higher level of vegetative incompatibility would not only hamper hypovirus spread within a population but could also select for lower virulence in CHV-1 and subsequently lead to an erosion of biological control. Recent studies, however, indicate that the vc type barriers are not so restrictive than previously assumed and that so far no evidence for an erosion of biological control system in high diversity populations can be observed.

Pilot Test of a UV-enhanced Biological Odor Control System

Pilot Test of a UV-enhanced Biological Odor Control System

Research on Production Control Mode of Manufacturing System Based on Neuroendocrine Hormonal Regulation

With the developing control and configuration pattern of modern manufacturing system, the complexity of manufacturing system is enlarged and the operating environment is filled with uncertainty. Under the influence of many uncertain factors, reducing delivery time, due-date performance and low inventory become the important goals of production enterprise. This paper presents a bio-inspired manufacturing system control model, combining the knowledge of manufacturing system, biological control and control system. The relationship between response time and production rate of manufacturing system with different capacity is analyzed, production capacity controller is designed using PI and PD, and the control strategy differences of production rate deviation and overshoot is also discussed. Finally, an optimized design for the parameters of a two-layer work-in-process (WIP) inventory controller is analyzed, with the reference to the neuroendocrine regulatory mechanism. The simulation analysis shows that in bio-inspired manufacturing system made of organic manufacturing cells, the shorter the response time of production capacity is, the faster its production rate responses. With the combination of two-layer WIP inventory controller and traditional PID production capacity controller, the production system is more responsive and the production offset and overshoot are small when the unexpected external demand changes of manufacturing system occur.

Вивчення рівня функціонального стану організму спортсменок за допомогою нових методичних підходів

Purpose:determining the functional state of the volleyball players of 18–22 years in the preparatory period of the annual cycle of training with a computer program "Sport-Express". Material and methods: the survey was conducted by 11 teams of female players "Orbita University" aged 18–22 years (Zaporozhe, Ukraine Premier League championship in volleyball). Results: shows the dynamics of changes in preparation for the season. Found that under the influence of training sessions at surveyed volleyball observed not only optimize their functional systems, but also significantly improves the level of functional state of the organism as a whole. Conclusions:we prove that the evaluation of the functional state of sportsmen should play an important role in the overall system of medical and biological control due to significant additional information about the state of their body and the possibility of timely correction of physical activity and prevention activities.

State feedback stabilization for probabilistic Boolean networks

A probabilistic Boolean network (PBN) is a discrete-time system composed of a family of Boolean networks (BNs) between which the PBN switches in a stochastic fashion. Studying control-related problems in PBNs may provide new insights into the intrinsic control in biological systems and enable us to develop strategies for manipulating complex biological systems using exogenous inputs. This paper investigates the problem of state feedback stabilization for PBNs. Based on the algebraic representation of logic functions, a necessary and sufficient condition is derived for the existence of a globally stabilizing state feedback controller, and a control design method is proposed when the presented condition holds. It is shown that the controller designed via the proposed procedure can simultaneously stabilize a collection of PBNs that are composed of the same constituent BNs.

Quantifying control effort of biological and technical movements: An information-entropy-based approach

In biomechanics and biorobotics, muscles are often associated with reduced movement control effort and simplified control compared to technical actuators. This is based on evidence that the nonlinear muscle properties positively influence movement control. It is, however, open how to quantify the simplicity aspect of control effort and compare it between systems. Physical measures, such as energy consumption, stability, or jerk, have already been applied to compare biological and technical systems. Here a physical measure of control effort based on information entropy is presented. The idea is that control is simpler if a specific movement is generated with less processed sensor information, depending on the control scheme and the physical properties of the systems being compared. By calculating the Shannon information entropy of all sensor signals required for control, an information cost function can be formulated allowing the comparison of models of biological and technical control systems. Exemplarily applied to (bio-)mechanical models of hopping, the method reveals that the required information for generating hopping with a muscle driven by a simple reflex control scheme is only I=32 bits versus I=660 bits with a DC motor and a proportional differential controller. This approach to quantifying control effort captures the simplicity of a control scheme and can be used to compare completely different actuators and control approaches.

Designing Synthetic Regulatory RNAs: New Tools for Temporal and Spatial Control in Biological Systems

Advances in synthetic biology are transforming our ability to design and build synthetic biological systems. While progress has been made in the design of complex genetic circuits, capabilities for constructing large genetic systems currently surpass our ability to design such systems. This growing ‘design gap’ has highlighted the need to develop methods that support the generation of new functional biological components and scalable design strategies for complex genetic circuits that will lay the foundation for integrated biological devices and systems.As examples of functional RNA molecules playing key roles in the behavior of natural biological systems have grown over the past decade, there has been growing interest in the design and implementation of synthetic counterparts. Researchers are taking advantage of the relative ease with which RNA molecules can be modeled and designed to engineer functional RNA molecules that act as diverse components including sensors, regulators, controllers (ligand-responsive RNA regulators), and scaffolds. These synthetic regulatory RNAs are providing new tools for temporal and spatial control in biological systems. I will describe recent advances in the design of RNA controllers and in addressing challenges in their implementation as user-programmed cellular control systems. In particular, I will discuss how the application of synthetic RNA controllers in biological pathways is leading to the elucidation of integrated systems design strategies and new capabilities for programming genetic systems.