Egils Stalidzans

• Dr.sc.ing.
• Senior Researcher at Riga Stradiņš University

Metabolic modeling of Starmerella bombicola as a model yeast of the Wickerhamiella/Starmerella (W/S) clade is advantageous for studying the characteristics of this clade and to apply for the metabolic engineering of this industrial yeast. A genome-scale metabolic network named iEM759 was reconstructed for S. bombicola using the information from dat...

There are several ways in which mathematical modeling is used in fermentation control, but mechanistic mathematical genome-scale models of metabolism within the cell have not been applied or implemented so far. As part of the metabolic engineering task setting, we propose that metabolite fluxes and/or biomass growth rate be used to search for a fer...

Finding the best knockout strategy for coupling biomass growth and production of a target metabolite using a mathematic model of metabolism is a challenge in biotechnology. In this research, a three-step method named OptEnvelope is presented based on finding minimal set of active reactions for a target point in the feasible solution space (envelope...

The sustainable metabolic engineering (SME) concept was defined by Stalidzans and Dace as an approach to the selection of the most sustainable metabolic engineering designs taking the economic, environmental and social components of sustainability into account. At the centre of the sustainability calculations is a genome-scale metabolic model that...

Biomass residue and waste stream bioconversion is a key pillar for successful transition toward sustainable bioeconomy. Spent microbial biomass (SMB) is a unique type of nutrient-rich residue generated from fermentation. This study addresses the waste–SMB–substrate cycle in fermentation. Data from a range of published fermentation processes using w...

Finding the best knockout strategy for coupling biomass growth and production of a target metabolite using a metabolic model is a challenge in biotechnology. In this research, a three-step method named OptEnvelope is developed based on finding minimal active reactions for a target point in the feasible solution space using a mixed-integer linear pr...

Mathematical modelling is an important approach in metabolic engineering projects to support the design and adaptation of organisms for the needs of biotechnology. Assuming sufficient quality of the model, mechanistic mathematical descriptions of the processes enable the prediction of the systemic impact of metabolic pathway engineering on the orga...

Successful transition to a circular bioeconomy relies on the availability and efficient use of organic feedstocks such as agricultural and food waste. Advances in industrial biotechnology provide novel tools to valorize these feedstocks differently. Less attention, however, has been directed towards assessment of the organic side-residues arising f...

Docosahexaenoic acid (DHA) is one of the most important long-chain polyunsaturated fatty acids (LC-PUFAs), with numerous health benefits. Crypthecodinium cohnii, a marine heterotrophic dinoflagellate, is successfully used for the industrial production of DHA because it can accumulate DHA at high concentrations within the cells. Glycerol is an inter...

Increasing genome-wide data in biological sciences and medicine has contributed to the development of a variety of visualization tools. Several automatic, semiautomatic, and manual visualization tools have already been developed. Some even have integrated flux balance analysis (FBA), but in most cases, it depends on separately installed third party...

Industrial biotechnology represents one of the most innovating and labour-productive industries with an estimated stable economic growth, thus giving space for improvement of the existing and setting up new value chains. In addition, biotechnology has clear environmental advantages over the chemical industry. Still, biotechnology’s environmental co...

Background Metformin has been used for the treatment of type 2 diabetes for over 60 years; however, its mechanism of pharmacological action is not fully clear. Different hypotheses exist regarding metformin distribution and redistribution mechanisms between plasma and erythrocytes/red blood cells (RBCs).Objective We aimed to test the hypothesis tha...

Marine heterotrophic dinoflagellate Crypthecodinium cohnii is an aerobic oleaginous microorganism that accumulates intracellular lipid with high content of 4,7,10,13,16,19-docosahexaenoic acid (DHA), a polyunsaturated ω−3 (22:6) fatty acid with multiple health benefits. C. cohnii can grow on glucose and ethanol, but not on sucrose or fructose. For...

Metformin is the primary drug for type 2 diabetes treatment and a promising candidate for other disease treatment. It has significant deviations between individuals in therapy efficiency and pharmacokinetics, leading to the administration of an unnecessary overdose or an insufficient dose. There is a lack of data regarding the concentration-time pr...

Drug research, therapy development, and other areas of pharmacology and medicine can benefit from simulations and optimization of mathematical models that contain a mathematical description of interactions between systems elements at the cellular, tissue, organ, body, and population level. This approach is the foundation of systems medicine and pre...

Background: Systems Medicine is a novel approach to medicine, i.e. an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral...

One of use cases for metabolic network optimisation of biotechnologically applied microorganisms is the in silico design of new strains with an improved distribution of metabolic fluxes. Global stochastic optimisation methods (genetic algorithms, evolutionary programing, particle swarm and others) can optimise complicated nonlinear kinetic models a...

The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-base...

Systems medicine holds many promises, but has so far provided only a limited number of proofs of principle. To address this road block, possible barriers and challenges of translating systems medicine into clinical practice need to be identified and addressed. The members of the European Cooperation in Science and Technology (COST) Action CA15120 O...

COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive software suite of interoperable COBRA methods. It has found widespread appli...

COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive software suite of interoperable COBRA methods. It has found widespread appli...

The application of biologically and biochemically relevant constraints during the optimization of kinetic models reduces the impact of suggested changes in processes not included in the scope of the model. This increases the probability that the design suggested by model optimization can be carried out by an organism after implementation of design...

Motivation: Due to their universal applicability, global stochastic optimization methods are popular for designing improvements of biochemical networks. The drawbacks of global stochastic optimization methods are: (i) no guarantee of finding global optima, (ii) no clear optimization run termination criteria and (iii) no criteria to detect stagnatio...

The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modifie...

Honey bee wintering in a wintering building (indoors) with controlled microclimate is used in some cold regions to minimize colony losses due to the hard weather conditions. The behavior and possible state of bee colonies in a dark room, isolated from natural environment during winter season, was studied by indirect temperature measurements to anal...

Precision Beekeeping (or Precision Apiculture) aims to help beekeepers monitor bee colonies remotely and identify different colony states including deviant behaviour. One monitoring target is the remote identification of bee colony swarming since this is one of the factors that can significantly reduce profitability. To identify temperature dynamic...

Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological function by employing experimental data, mathematical m...

Selecting an efficient small set of adjustable parameters to improve metabolic features of an organism is important to for reduction of implementation costs and risks of unpredicted side effects. In practice, to avoid the analysis of a huge combinatorial space for the possible sets of adjustable parameters, experience- and intuition-based subsets o...

A low-cost real-time two-dimensional PC-based ball tracking and control laboratory system is developed to teach real-time control system development with a real physical system instead of computer simulation. The system can be used for a single-student or a two-student competition for the best control algorithm. Training can be given on pattern rec...

Precision Beekeeping (PB), a sub-branch of Precision Agriculture, is an apiary management strategy based on the monitoring of individual bee colonies to minimise resource consumption and maximise the productivity of bees. Although there are sufficient technical means and industrial products for the practical execution of PB, the process is slow due...

Mathematical modeling of metabolism is essential for rational metabolic engineering. The present work focuses on several types of modeling approach to quantitative understanding of central metabolic network and energetics in the bioethanol-producing bacterium Zymomonas mobilis. Combined use of Flux Balance, Elementary Flux Mode, and thermodynamic a...

Robotic systems are replacing humans in increasing number of dangerous tasks. Pesticide spraying in greenhouses is one of tasks where a number of robotic systems have been developed and tested. Therefore it is the right time to raise the question about optimisation of the costs efficiency of robot colony. In case of homogenous robotic system only t...

Biochemical networks of different types such as transcription regulatory, gene regulation, metabolic, protein interaction and signal transduction networks have been extensively studied. One of research directions is related with topological properties of biochemical networks and their structure evolution. Earlier research clearly shows that biochem...

In case of model development, it would be an advantage to assess the quality of available models looking for the best one or to find suitable parts of a published model to build a new one. The differences or contradictions in reconstructions can indicate the level of agreement between different authors about the topic of interest. The intersecting...

Zymomonas mobilis, an ethanol-producing bacterium, possesses the Entner-Doudoroff (E-D) pathway, pyruvate decarboxylase and two alcohol dehydrogenase isoenzymes for the fermentative production of ethanol and carbon dioxide from glucose. Using available kinetic parameters, we have developed a kinetic model that incorporates the enzymatic reactions o...

The size and the number of available genome scale metabolic models and reconstructions of different organisms is growing rapidly. Various computational methods and tools are developed in the last decades for metabolic network construction, analysis and optimization in the interdisciplinary scientific branches of systems biology and synthetic biolog...

The principles of Precision Agriculture (PA) can be applied also to the beekeeping branch. Precision Beekeeping (PB) (Precision Apiculture) can be implemented as a three phase cycle including 1) data collection, 2) data analysis and 3) application. The first two phases are based information technologies in case of remote recognition. The third phas...

Precision Agriculture (PA) methods are adapted to various agricultural branches. One of the PA tasks is to continuously collect real time data about agricultural objects to monitor the object behavior and state of development to recognize any anomalous event or important state. In many cases the objects could have many different important parameter...

The size and number of available genome scale metabolic models and reconstructions is growing rapidly. Various computational methods and tools are developed in the last decades for metabolic network construction, analysis and optimization. A software tool SpaceAnalyzer (SAnalyzer) is developed in Matlab environment for automatic generation of bioch...

The active, yet energetically inefficient electron transport chain of the ethanologenic bacterium Zymomonas mobilis could be used in metabolic engineering for redox-balancing purposes during synthesis of certain products. Although several reconstructions of Z. mobilis metabolism have been published, important aspects of redox balance and aerobic ca...

Determination of the annual development periods of honey bee colonies can help in synchronising the beekeeper’s activities with the developmental stage of individual bee colonies in apiaries. It is proposed to determine the development periods by measuring and analysing the ambient temperature and the temperature above the upper hive body. The temp...

A disadvantage of global stochastic optimization methods is the stochastic convergence of the best value of the objective function to the global optimum. In spite those methods are widely used optimizing kinetic models of biochemical pathways. Moreover, the growing number of adjustable parameters in the model leads to combinatorial explosion of com...

Precision Agriculture approach has proved to be successful in various agricultural subbranches like precision livestock farming, precision farming, precision horticulture and precision viticulture. Apiculture or beekeeping is one of the agriculture’s sub directions, where Precision Agriculture (PA) methods can be successfully applied. Adaptation of...

Economic benefit of an industrial company depends on forethought deployment of an industrial production system. Production processes are being optimized using variety of models in order to maximize revenue of the company. Application of robotic systems on the production sites increases effectiveness of the industrial company providing variety of au...

Honey bee wintering process is one of the biological processes, which nowadays can be monitored and controlled using the information technologies, control methods and tools. Control and monitoring of such process is really complicated and not a trivial task, because behavior of the biological system, biological objects and their reaction to human i...

A visual analysis of reconstructions and large stoichiometric models with elastic change of the visualization scope and representation methods becomes increasingly important due to the rapidly growing size and number of available reconstructions. The Paint4Net is a novel COBRA Toolbox extension for automatic generation of a hypergraph layout of def...

Economic benefit of an industrial company depends on forethought deployment of an industrial production system. Robotic systems are used to increase effectiveness of the production system providing variety of automation approaches. The selection of robotic system for particular mission is considered based on options available on the market. The ana...

Biological systems are extremely complex, nonlinear and self-organized, self-regulated systems that can adjust to the environmental changes due to underlying genetic mechanisms. The key task of systems biology is to understand cellular processes, functions and/or properties of biological system better. It can be done by means of the structure, beha...

Dynamic models of biochemical networks usually are described as a system of nonlinear differential equations. In case of optimization of models for purpose of parameter estimation or design of new properties mainly numerical methods are used. That causes problems of optimization predictability as most of numerical optimization methods have stochast...

by internal control architecture. The number of robot classes used for particular task, as well as the specification of functions for each class of robots is usually predefined and are not considered in scope of optimization. However in most cases such assumption is not verified by any calculations and alternative configurations of multi-robot syst...

The stochastic nature of convergence of steady state stochastic global optimization methods in design optimization tasks with steady state precondition is a hardly predictable step in development of industrially efficient strains of microorganisms. The properties of convergence dynamics of evolutionary programming (EP) and particle swarm (PS) depen...

Increasing size of biochemical models of cellular processes influence the time consumption for optimization of control systems in biotechnological plants to increase the productivity. Nonlinear systems of differential equations can be optimized by time consuming stochastic numerical methods that work for most different nonlinear models but can not...

Nowadays control and monitoring of bioprocesses is an important problem and challenge for researchers and information technology specialists. Specific task range of bioprocess control is defined, which needs realization of intensive calculations and participation of operator in decision making. In a situation, when bioprocess or production process...

Due to the growing number and size of biochemical network computer models an efficient co-operation among experts industrialists, biologists and modellers in industrial biotechnology is becoming a topical issue. In order to speed up the introduction of systems biology achievements into production an organism independent universal collaboration prot...

Stochastic nature of convergence of steady state stochastic global optimization methods causes several seemingly attractive approaches to reduce the length of the optimization procedure. The properties of convergence dynamics of evolutionary programming (EP) and particle swarm (PS) are studied optimizing yeast glycolysis by COPASI software adjustin...

During the winter time honey bees can be placed in a special wintering building to save physiological resources of bees and honey compared with outdoor wintered bees. This building should have stable and convenient microclimate conditions for bees. The most important parameter of microclimate to be controlled is temperature. For our bee wintering b...

In the cell, tissue, organ and organism under different conditions operate metabolic, gene regulation and signaling networks that determine biochemical reactions, biochemical or biophysical process. Biochemical networks can present the relationships between genes and genes products, between proteins and etc.. Exploring of these networks helps bette...

In the cell, tissue, organ and organism under different conditions operate metabolic, protein interaction, gene or genetic regulatory and signaling networks that describe biochemical reactions, biochemical or biophysical process. The biochemical networks can present the relationship between genes and gene products, proteins, metabolites and etc. Th...

Simulations are widely used in the robotics field as useful tools that provide reasonable methods for verifying various aspects of developed device, such as the control system behaviour testing. However simulated results almost always differ from real world experiments because of combination of various aspects such as sensor perception noises, inac...

Swarming of honey bee colonies is one of the factors that reduces profitability of beekeeping. Therefore recognition of preswarming condition of a bee colony is of industrial importance. The developed beehive observation system consists of 1) control subsystem, 2) measuring (temperature and relative humidity) subsystem and 3) video recording subsys...

The modelling of control loops within functioning biological organisms is a prerequisite for a successful treatment or ther-apy development and implementation in biological systems. Similarities in emergence and sequential lifecycle steps of human made artificial control systems (ACS) and natural biological control systems (BCS) in multigeneration...

There is software for simulation of biological objects (Powersim, Stella et cetera), which are making and presenting different calculations accordingly to the given data about the structure of the object and relationships between elements. Several principles of model creation are described in the literature for technical and biological systems. Sti...

All the year 2000 continuous measurement of temperature in honeybee hives was done in Latvia, Riga region. Measurements were recorded after each 15 minutes. Sensors are located above the bee nest, under the pillow. There are six periods existing with different speed of change of average day and night temperature in hive, which possibly correspond t...

A linear model of bee colony development made in Excel 97 has 13 variables and 13 depending (calculated) input parameters. Birth and death rules are separated and show the colony development round the year. The rule of egg laying is trapezium. Example is based on triangle egg laying rule as a special case of trapezium. The curve of changes for amou...

Methodology for static and dynamic parameter acquisition from experimental dynamic data is developed in case of homeostatic biological process with unknown functional relationships between input and output parameters. Methodology includes assessment of static characteristic curve (including correlation analysis), transition function, reaction delay...

Natural biological and human made artificial control systems are compared from the point of view of their development in scale of life cycle. Understanding of biological processes is based on the targets of biological object as a dynamic system. Behaviour of biological system is analysed as activity of biological control system trying to reach its...

A training set 'TraSe' has been developed for university students specialising in information and communication technologies for industrial applications to simulate physically two types of industrial computer control tasks: 1) early deviation recognition and 2) real-time control. The training set addresses some methodological issues that can be sol...