scholarly journals Current systems biology approaches in hazard assessment of nanoparticles

2015 ◽  
Author(s):  
Friederike Ehrhart ◽  
Chris Evelo ◽  
Egon Willighagen
Keyword(s):  
Systems Biology ◽  
Hazard Assessment ◽  
Low Dose ◽  
Bulk Material ◽  
Common Knowledge ◽  
Biological Systems ◽  
Consumer Products ◽  
Human Environment ◽  
Current Systems ◽  
Nano Size

The amount of nanoparticles (NPs) in human environment is increasing. The main sources are the increased introduction in consumer products and air pollution (diesel exhaust). It is meanwhile common knowledge that NPs behave differently as bulk material because of their nano-size. This leads in general to a higher reactivity and some other changed properties, e.g. solubility, surface potential, conductivity, and, to different effects on biological systems. The main impacts of NPs on a cellular and organism level are meanwhile well known: release of toxic ions, increased oxidative stress, and inflammation. Beside these, there is increasing evidence that NPs, especially in low dose/long exposure scenarios, affect biological systems in a broader way, interact with drugs, and exacerbate the effects of diseases. To investigate these effects systems biology approaches are the method of choice. This review summarizes the state of the art of nanoparticle effects on cells and organisms and demonstrate the add value of systems biology investigations to NP hazard assessment.

scholarly journals Modeling Biological Systems Using Crowdsourcing

2018 ◽  
Vol 43 (3) ◽  
pp. 219-243 ◽  
Author(s):  
Szymon Wasik
Keyword(s):  
Systems Biology ◽  
Serious Games ◽  
Domain Knowledge ◽  
Biological Systems ◽  
Effective Technique ◽  
Design Models ◽  
Modeling Systems ◽  
Vast Network

Abstract Crowdsourcing is a very effective technique for outsourcing work to a vast network usually comprising anonymous people. In this study, we review the application of crowdsourcing to modeling systems originating from systems biology. We consider a variety of verified approaches, including well-known projects such as EyeWire, FoldIt, and DREAM Challenges, as well as novel projects conducted at the European Center for Bioinformatics and Genomics. The latter projects utilized crowdsourced serious games to design models of dynamic biological systems, and it was demonstrated that these models could be used successfully to involve players without domain knowledge. We conclude the review of these systems by providing 10 guidelines to facilitate the efficient use of crowdsourcing.

scholarly journals Use of biophysical methods to improve yields and quality of agricultural products

2008 ◽  
Vol 53 (3) ◽  
pp. 235-242 ◽  
Author(s):  
Branko Marinkovic ◽  
Miroslav Grujic ◽  
Dusko Marinkovic ◽  
Jovan Crnobarac ◽  
Jelena Marinkovic ◽  
...  
Keyword(s):  
Radiation Effects ◽  
Biological Systems ◽  
Low Frequency ◽  
Crop Species ◽  
Human Environment ◽  
Electromagnetic Stimulation ◽  
Stimulation Method ◽  
Living Organisms ◽  
Novi Sad ◽  
The University

Until as recently as a century ago, the exposure of biological systems to radiation was limited only to the natural sources. Today, however, a broad range of radiation types and doses have found a wide variety of uses and applications, so much so that it would be difficult to make a list of all the areas of human activity in which radiation is used for one purpose or another. The study of radiation effects on individuals and populations as a whole has become important only with the development of methods and sources of man-made radiation. Given that what is present in this case are physical effects on biological systems (living organisms), all these methods can be placed under the heading of biophysical influences. In the last 50 years, the effects of extremely low-frequency electromagnetic fields (ELF-EMF) have been studied with great diligence. These fields are the ones most commonly found in the human environment and they have been used in our studies in this field. The present paper provides a brief review of the literature data and our findings on the effects of ELF-EMF on various crop species using the RIES (Resonant Impulse Electromagnetic Stimulation) method, developed at the Faculty of Agriculture of the University of Novi Sad.

7. The lawless pursuit of biological systems

2020 ◽  
pp. 108-122
Author(s):  
Eberhard O. Voit
Keyword(s):  
Systems Biology ◽  
Biological Systems ◽  
Large Classes ◽  
The Future

The laws of physics are a prerequisite for us to make reliable predictions regarding our surroundings. By extension, making reliable predictions in biology requires laws of biology. The problem is that such laws are almost non-existent, because biological systems are hugely complex and diverse. As a consequence, it is difficult to make true statements covering all organisms on Earth—or even large classes of organisms. This difficulty translates directly into the challenge of identifying rules that govern biological systems. What would such biological rules or laws even look like? ‘The lawless pursuit of biological systems’ considers the future of systems biology and discusses how it might evolve as it matures as a field of investigation.

scholarly journals Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Metabolites ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 76 ◽  
Author(s):  
Farhana R. Pinu ◽  
David J. Beale ◽  
Amy M. Paten ◽  
Konstantinos Kouremenos ◽  
Sanjay Swarup ◽  
...  
Keyword(s):  
New Zealand ◽  
Systems Biology ◽  
Life Science ◽  
Biological Systems ◽  
Research Community ◽  
Data Sets ◽  
Omics Data ◽  
Omics Integration ◽  
Traditional Approaches ◽  
Multiple Interactions

The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent ‘Australian and New Zealand Metabolomics Conference’ (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.

scholarly journals How does homeostasis happen? Integrative physiological, systems biological, and evolutionary perspectives

2019 ◽  
Vol 316 (4) ◽  
pp. R301-R317 ◽  
Author(s):  
David S. Goldstein
Keyword(s):  
Blood Pressure ◽  
Systems Biology ◽  
Internal Variables ◽  
Integrative Physiology ◽  
Continuous Formation ◽  
Biological Phenomena ◽  
History Of ◽  
Founding Principle ◽  
Current Systems ◽  
Evolutionary Perspectives

Homeostasis is a founding principle of integrative physiology. In current systems biology, however, homeostasis seems almost invisible. Is homeostasis a key goal driving body processes, or is it an emergent mechanistic fact? In this perspective piece, I propose that the integrative physiological and systems biological viewpoints about homeostasis reflect different epistemologies, different philosophies of knowledge. Integrative physiology is concept driven. It attempts to explain biological phenomena by continuous formation of theories that experimentation or observation can test. In integrative physiology, “function” refers to goals or purposes. Systems biology is data driven. It explains biological phenomena in terms of “omics”–i.e., genomics, gene expression, epigenomics, proteomics, and metabolomics–it depicts the data in computer models of complex cascades or networks, and it makes predictions from the models. In systems biology, “function” refers more to mechanisms than to goals. The integrative physiologist emphasizes homeostasis of internal variables such as Pco2 and blood pressure. The systems biologist views these emphases as teleological and unparsimonious in that the “regulated variable” (e.g., arterial Pco2 and blood pressure) and the “regulator” (e.g., the “carbistat” and “barostat”) are unobservable constructs. The integrative physiologist views systems biological explanations as not really explanations but descriptions that cannot account for phenomena we humans believe exist, although they cannot be observed directly, such as feelings and, ultimately, the conscious mind. This essay reviews the history of the two epistemologies, emphasizing autonomic neuroscience. I predict rapprochement of integrative physiology with systems biology. The resolution will avoid teleological purposiveness, transcend pure mechanism, and incorporate adaptiveness in evolution, i.e., “Darwinian medicine.”

scholarly journals Systems Biology and Design of Biological Systems

2006 ◽  
Vol 46 (5) ◽  
pp. 244-250
Author(s):  
Hiroyuki KURATA
Keyword(s):  
Systems Biology ◽  
Biological Systems

Effects of long-term low dose exposure to mixtures of pesticides, food additives and consumer products chemicals on biochemical parameters

2017 ◽  
Vol 280 ◽  
pp. S217 ◽  
Author(s):  
Anca Oana Docea ◽  
Daniela Calina ◽  
Eliza Gofita ◽  
Andreea Letitia Arsene ◽  
Dimitrios Kouretas ◽  
...  
Keyword(s):  
Biochemical Parameters ◽  
Low Dose ◽  
Food Additives ◽  
Consumer Products

scholarly journals Assessment of cardiovascular and renal functions during treatment with Desmodium adscendens therapy

2020 ◽  
Vol 5 (2) ◽  
pp. 114-120
Author(s):  
Adinoyi Seriki Samuel
Keyword(s):  
Dose Group ◽  
Low Dose ◽  
Common Knowledge ◽  
Chloride Concentration ◽  
Normal Function ◽  
The Body ◽  
High Dose ◽  
Renal Functions ◽  
Cardiovascular Performance ◽  
Group 2

Desmodium adscendens is a rain forest medicinal herb used in managing quite a number of medical conditions. Its efficacy in the treatment of several diseases has made it a first line herb for doctors, especially in managing all forms of spasm. It is however common knowledge that some of these medicinal herbs impact severely on the normal functioning of some vital organs of the body during their administration. The present study was carried out to assess the renal and cardiovascular performance in subjects undergoing treatment with Desmodium adscendens with a view to advising against its indiscriminate use. The parameters used for the assessment of renal functions were serum creatinine and urea concentrations and their clearance. Also, changes in electrolyte concentration of Sodium, Potassium and Chloride concentration were used to assess cardiovascular performance. The histology of the kidney and heart tissues was also done to determine if the extract has impact on the cyto-architecture of the organs. Twenty-four (24) wistar rats were used for the experiment. The rats were grouped randomly into four groups (n = 6). Group 1 served as control, and the rats in the group were given normal rat feeds and water. Group 2 served as low dose group, and rats in this group were administered with low dose of extract 300 mg/kg. Group 3 served as medium group, and rats in this group were treated with medium dose of extract, 450 mg/kg. Group 4 served as high dose group, and rats in this group were treated with high dose of extract 600 mg/kg. The extract was administered for 28 days. Result showed that the extract did not impact negatively on the normal function of the renal and cardiovascular system of the treated groups, rather it enhanced their performances. It can therefore be concluded that the extract is beneficial to renal and cardiovascular functions if used within the treatment dosage.

scholarly journals MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 288
Author(s):  
Julia Koblitz ◽  
Dietmar Schomburg ◽  
Meina Neumann-Schaal
Keyword(s):  
Experimental Data ◽  
Systems Biology ◽  
Metabolic Pathways ◽  
Common Knowledge ◽  
Numerical Data ◽  
Omics Data ◽  
Web Based ◽  
Ongoing Research ◽  
Complex Interactions ◽  
Biology Research

Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.

Experimental Study on Critical Design of Electro-Hydrostatic Actuators Small in Size and Light in Weight

2020 ◽  
Vol 32 (5) ◽  
pp. 911-922
Author(s):  
Mitsuo Komagata ◽  
Tianyi Ko ◽  
Ko Yamamoto ◽  
Yoshihiko Nakamura ◽  
◽  
...  
Keyword(s):  
Experimental Study ◽  
Theoretical Investigation ◽  
High Reliability ◽  
Viscous Friction ◽  
Human Environment ◽  
Critical Design ◽  
Involute Gear ◽  
Actuation Systems ◽  
Current Systems

Actuation systems for robots and other machines used in critical applications is an area that requires further research. In such applications, a machine works in a human environment and physically interacts with humans. Reliability and backdrivability are still insufficient in current systems. An electro-hydrostatic actuator has the potential advantage of high reliability by nature and high backdrivability in mechanical simplexity when it is designed to be small and light. This study provides a theoretical investigation of the methods for evaluating internal leaks and other mechanical losses, such as Coulomb and viscous friction, and experimentally evaluates two types (trochoid and involute gear) of prototyped hydraulic pumps.

Sign in / Sign up

Export Citation Format

Share Document