• Title, Summary, Keyword: Systems biology

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Systems Biology - A Pivotal Research Methodology for Understanding the Mechanisms of Traditional Medicine

  • Lee, Soojin
    • Journal of Pharmacopuncture
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    • v.18 no.3
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    • pp.11-18
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    • 2015
  • Objectives: Systems biology is a novel subject in the field of life science that aims at a systems' level understanding of biological systems. Because of the significant progress in high-throughput technologies and molecular biology, systems biology occupies an important place in research during the post-genome era. Methods: The characteristics of systems biology and its applicability to traditional medicine research have been discussed from three points of view: data and databases, network analysis and inference, and modeling and systems prediction. Results: The existing databases are mostly associated with medicinal herbs and their activities, but new databases reflecting clinical situations and platforms to extract, visualize and analyze data easily need to be constructed. Network pharmacology is a key element of systems biology, so addressing the multi-component, multi-target aspect of pharmacology is important. Studies of network pharmacology highlight the drug target network and network target. Mathematical modeling and simulation are just in their infancy, but mathematical modeling of dynamic biological processes is a central aspect of systems biology. Computational simulations allow structured systems and their functional properties to be understood and the effects of herbal medicines in clinical situations to be predicted. Conclusion: Systems biology based on a holistic approach is a pivotal research methodology for understanding the mechanisms of traditional medicine. If systems biology is to be incorporated into traditional medicine, computational technologies and holistic insights need to be integrated.

Current Status of Systems Biology in Traditional Chinese medicine - in regards to influences to Korean Medicine (최근 중의학에서 시스템생물학의 발전 현황 - 한의학에 미치는 영향 및 시사점을 중심으로 -)

  • Lee, Seungeun;Lee, Sundong
    • Journal of Society of Preventive Korean Medicine
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    • v.21 no.2
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    • pp.1-13
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    • 2017
  • Objectives : This paper serves to explore current trends of systems biology in Traditional Chinese Medicine (TCM) and examine how it may influence the Traditional Korean medicine. Methods : Literature review method was collectively used to classify Introduction to systems biology, diagnosis and syndrome classification of systems biology in TCM perspective, physiotherapy including acupuncture, herbs and formula functions, TCM systems biology, and directions of academic development. Results : The term 'Systems biology' is coined as a combination of systems science and biology. It is a field of study that tries to understand living organism by establishing a theory based on an ideal model that analyzes and predicts the desired output with understanding of interrelationships and dynamics between variables. Systems biology has an integrated and multi-dimensional nature that observes the interaction among the elements constructing the network. The current state of systems biology in TCM is categorized into 4 parts: diagnosis and syndrome, physical therapy, herbs and formulas and academic development of TCM systems biology and its technology. Diagnosis and syndrome field is focusing on developing TCM into personalized medicine by clarifying Kidney yin deficiency patterns and metabolic differences among five patterns of diabetes and analyzing plasma metabolism and biomarkers of coronary heart disease patients. In the field of physical therapy such as acupuncture and moxibustion, researchers discovered the effect of stimulating acupoint ST40 on gene expression and the effects of acupuncture on treating functional dyspepsia and acute ischemic stroke. Herbs and formulas were analyzed with TCM network pharmacology. The therapeutic mechanisms of Si Wu Tang and its series formulas are explained by identifying potential active substances, targets and mechanism of action, including metabolic pathways of amino acid and fatty acid. For the academic development of TCM systems biology and its technology, it is necessary to integrate massive database, integrate pharmacokinetics and pharmacodynamics, as well as systems biology. It is also essential to establish a platform to maximize herbal treatment through accumulation of research data and diseases-specific, or drug-specific network combined with clinical experiences, and identify functions and roles of molecules in herbs and conduct animal-based studies within TCM frame. So far, few literature reviews exist for systems biology in traditional Korean medicine and they merely re-examine known efficacies of simple substances, herbs and formulas. For the future, it is necessary to identify specific mechanisms of working agents and targets to maximize the effects of traditional medicine modalities. Conclusions : Systems biology is widely accepted and studied in TCM and already advanced into a field known as 'TCM systems biology', which calls for the study of incorporating TCM and systems biology. It is time for traditional Korean medicine to acknowledge the importance of systems biology and present scientific basis of traditional medicine and establish the principles of diagnosis, prevention and treatment of diseases. By doing so, traditional Korean medicine would be innovated and further developed into a personalized medicine.

An Encounter of Korean Medicine with Systems Biology: Meanings and Prospects (한의학과 시스템생물학의 만남, 의미와 전망)

  • Kim, Chang-Eop;Lee, Choong Yeol
    • Journal of Physiology & Pathology in Korean Medicine
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    • v.30 no.6
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    • pp.370-375
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    • 2016
  • Recent advances in systems biology are shedding a new light on the traditional medicine research. The systems biology highlights the way each component interacts with each other within a system, and the network behavior that emerges from such interactions. This feature of systems biology can accent the systemic aspects of Korean medicine such as the mechanism of action of herbal formulae, pattern differentiation, and the meridian systems, as both the Korean medicine and the systems biology theorize the human physiological functions and phenomena from a holistic point of view. This paper outlines the meaning of the recent Korean medicine research using the systems biology methodology. We discuss the methodologies of the two fields in a comparative manner, and overview the advantages and limitations of the integrated approaches. Finally, we suggest the future prospects for the systems biology inspired approaches to the Korean medicine research. The systems biology may provide a new modernized research methodology for the Korean medicine that can highlight its unique features.

Guide to Learning Systems Biology for Korean Medicine Researchers (한의학 연구자를 위한 시스템 생물학 학습 가이드)

  • Kim, Chang-Eop
    • Journal of Physiology & Pathology in Korean Medicine
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    • v.30 no.6
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    • pp.412-418
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    • 2016
  • The emergence of systems biology in the 21st century is changing the paradigm of biomedical research. Whereas the reductionist approaches focus on components rather than time or contexts, systems biology focus more on interrelationships, dynamics, and contexts. The key ideas of the systems biology shares much with the philosophy of Korean Medicine(KM) and therefore, the paradigm shift is shedding light on understanding the mechanism of action of KM at system level. In this article, I provide a guide to learning systems biology for KM researchers using online learning resources. Thanks to the recent development of MOOC(massive open online courses) and other online learning platforms, learners can access to plenty of high-quality resources from top-tier universities in the world. I expect this guide help researchers to employ systems biology methods into their KM researches, and will lead to the development of future curricula for training "bi-lingual" experts, KM and computational approaches.

Current Challenges of Streptococcus Infection and Effective Molecular, Cellular, and Environmental Control Methods in Aquaculture

  • Mishra, Anshuman;Nam, Gyu-Hwi;Gim, Jeong-An;Lee, Hee-Eun;Jo, Ara;Kim, Heui-Soo
    • Molecules and Cells
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    • v.41 no.6
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    • pp.495-505
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    • 2018
  • Several bacterial etiological agents of streptococcal disease have been associated with fish mortality and serious global economic loss. Bacterial identification based on biochemical, molecular, and phenotypic methods has been routinely used, along with assessment of morphological analyses. Among these, the molecular method of 16S rRNA sequencing is reliable, but presently, advanced genomics are preferred over other traditional identification methodologies. This review highlights the geographical variation in strains, their relatedness, as well as the complexity of diagnosis, pathogenesis, and various control methods of streptococcal infections. Several limitations, from diagnosis to control, have been reported, which make prevention and containment of streptococcal disease difficult. In this review, we discuss the challenges in diagnosis, pathogenesis, and control methods and suggest appropriate molecular (comparative genomics), cellular, and environmental solutions from among the best available possibilities.

RING E3 ligases: key regulatory elements are involved in abiotic stress responses in plants

  • Cho, Seok Keun;Ryu, Moon Young;Kim, Jong Hum;Hong, Jeong Soo;Oh, Tae Rin;Kim, Woo Taek;Yang, Seong Wook
    • BMB Reports
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    • v.50 no.8
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    • pp.393-400
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    • 2017
  • Plants are constantly exposed to a variety of abiotic stresses, such as drought, heat, cold, flood, and salinity. To survive under such unfavorable conditions, plants have evolutionarily developed their own resistant-mechanisms. For several decades, many studies have clarified specific stress response pathways of plants through various molecular and genetic studies. In particular, it was recently discovered that ubiquitin proteasome system (UPS), a regulatory mechanism for protein turn over, is greatly involved in the stress responsive pathways. In the UPS, many E3 ligases play key roles in recognizing and tethering poly-ubiquitins on target proteins for subsequent degradation by the 26S proteasome. Here we discuss the roles of RING ligases that have been defined in related to abiotic stress responses in plants.

Databases and tools for constructing signal transduction networks in cancer

  • Nam, Seungyoon
    • BMB Reports
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    • v.50 no.1
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    • pp.12-19
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    • 2017
  • Traditionally, biologists have devoted their careers to studying individual biological entities of their own interest, partly due to lack of available data regarding that entity. Large, high-throughput data, too complex for conventional processing methods (i.e., "big data"), has accumulated in cancer biology, which is freely available in public data repositories. Such challenges urge biologists to inspect their biological entities of interest using novel approaches, firstly including repository data retrieval. Essentially, these revolutionary changes demand new interpretations of huge datasets at a systems-level, by so called "systems biology". One of the representative applications of systems biology is to generate a biological network from high-throughput big data, providing a global map of molecular events associated with specific phenotype changes. In this review, we introduce the repositories of cancer big data and cutting-edge systems biology tools for network generation, and improved identification of therapeutic targets.