John J. Tyson (born December 12, 1947, in Abington, Pennsylvania) is an American systems biologist and mathematical biologist who serves as University Distinguished Professor of Biology at Virginia Tech, and is the former president of the Society for Mathematical Biology. [1] He is known for his research on biochemical switches in the cell cycle, dynamics of biological networks and on excitable media.
Tyson earned a bachelor's degree in chemistry from Wheaton College, and received his PhD in chemical physics from the University of Chicago. After postdoctoral research at the Max Planck Institute for Biophysical Chemistry, a temporary position teaching mathematics at the University at Buffalo, and another post doctorate at the University of Innsbruck for Biochemistry and Experimental Cancer Research, he joined the Virginia Tech faculty in 1978 and is currently a University Distinguished Professor in Biological Sciences. He was president of the Society for Mathematical Biology for 1993–1995, and served as co-editor-in-chief of the Journal of Theoretical Biology from 1995 to 2004. [1]
Since receiving his PhD in chemical physics at the University of Chicago in 1973, John Tyson has been studying temporal and spatial organization in chemical, biochemical and biological systems. Recently he has focused on the macro-molecular reaction networks that process information in living cells and initiate appropriate responses in terms of cell growth, division and death. He represents the dynamics of these reaction networks in terms of mathematical equations, using computer simulations to work out the precise behavior to be expected of the network. By comparing simulations with experimental data, the computer models can be tested, refined and developed, eventually, into tools for accurate predictions of the physiological responses of healthy and diseased cells. [2]
In John J. Tyson's laboratory they study biological systems from a rigorous mathematical perspective, and build realistic models that help gain a deeper understanding of the physiology. Most of their work is on the mechanism of cell cycle control as seen in budding yeast, fission yeast, Xenopus embryos and egg extracts, Drosophila embryos and mammalian cells.
Tyson also worked in chemical kinetics studying oscillations, bistability, traveling' waves, and chaotic behavior in chemical reaction systems.
The unifying theme of the research is the problem of spatial and temporal organization in chemical, biochemical and biological systems. What mechanisms keep time in these various domains? How is spatial information communicated and utilized? How do the molecular regulatory mechanisms of living cells process information and initiate appropriate responses in terms of cell growth, division and death? [3]
John Tyson has published several dynamical models of cell decision making systems in cancer including Estrogen Receptor Signaling, Unfolded Protein Response (UPR) and Autophagy. [4] [5] [6]
John has worked closely with high-profile individuals within the field of cell biology. Cell Cycle Control by a Minimal Cdk Network was written by John in tandem with Claude Gerard, Damien Coudreuse, and Béla Novák. The paper has been highly cited and takes a critical look at the possible origin of the eukaryotic cell and how the minimal cdk network can apply to larger complex cells like those found in humans. John has been featured on television for the annual meeting of the society of cell biology in 2013, as well as being featured on the National Institute of General Medical Sciences website.
In a dynamical system, bistability means the system has two stable equilibrium states. Something that is bistable can be resting in either of two states. An example of a mechanical device which is bistable is a light switch. The switch lever is designed to rest in the "on" or "off" position, but not between the two. Bistable behavior can occur in mechanical linkages, electronic circuits, nonlinear optical systems, chemical reactions, and physiological and biological systems.
In biochemistry, a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule donates a phosphate group to the substrate molecule. This transesterification produces a phosphorylated substrate and ADP. Conversely, it is referred to as dephosphorylation when the phosphorylated substrate donates a phosphate group and ADP gains a phosphate group. These two processes, phosphorylation and dephosphorylation, occur four times during glycolysis.
Biophysics is an interdisciplinary science that applies approaches and methods traditionally used in physics to study biological phenomena. Biophysics covers all scales of biological organization, from molecular to organismic and populations. Biophysical research shares significant overlap with biochemistry, molecular biology, physical chemistry, physiology, nanotechnology, bioengineering, computational biology, biomechanics, developmental biology and systems biology.
Systems biology is the computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach to biological research.
Autophagy is the natural, conserved degradation of the cell that removes unnecessary or dysfunctional components through a lysosome-dependent regulated mechanism. It allows the orderly degradation and recycling of cellular components. Although initially characterized as a primordial degradation pathway induced to protect against starvation, it has become increasingly clear that autophagy also plays a major role in the homeostasis of non-starved cells. Defects in autophagy have been linked to various human diseases, including neurodegeneration and cancer, and interest in modulating autophagy as a potential treatment for these diseases has grown rapidly.
Mathematical and theoretical biology or, biomathematics, is a branch of biology which employs theoretical analysis, mathematical models and abstractions of the living organisms to investigate the principles that govern the structure, development and behavior of the systems, as opposed to experimental biology which deals with the conduction of experiments to prove and validate the scientific theories. The field is sometimes called mathematical biology or biomathematics to stress the mathematical side, or theoretical biology to stress the biological side. Theoretical biology focuses more on the development of theoretical principles for biology while mathematical biology focuses on the use of mathematical tools to study biological systems, even though the two terms are sometimes interchanged.
Modelling biological systems is a significant task of systems biology and mathematical biology. Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems. It involves the use of computer simulations of biological systems, including cellular subsystems, to both analyze and visualize the complex connections of these cellular processes.
The philosophy of biology is a subfield of philosophy of science, which deals with epistemological, metaphysical, and ethical issues in the biological and biomedical sciences. Although philosophers of science and philosophers generally have long been interested in biology, philosophy of biology only emerged as an independent field of philosophy in the 1960s and 1970s. Philosophers of science then began paying increasing attention to biology, from the rise of Neodarwinism in the 1930s and 1940s to the discovery of the structure of DNA in 1953 to more recent advances in genetic engineering. Other key ideas include the reduction of all life processes to biochemical reactions, and the incorporation of psychology into a broader neuroscience.
Marc Wallace Kirschner is an American cell biologist and biochemist and the founding chair of the Department of Systems Biology at Harvard Medical School. He is known for major discoveries in cell and developmental biology related to the dynamics and function of the cytoskeleton, the regulation of the cell cycle, and the process of signaling in embryos, as well as the evolution of the vertebrate body plan. He is a leader in applying mathematical approaches to biology. He is the John Franklin Enders University Professor at Harvard University. In 2021 he was elected to the American Philosophical Society.
The MAPK/ERK pathway is a chain of proteins in the cell that communicates a signal from a receptor on the surface of the cell to the DNA in the nucleus of the cell.
Systems immunology is a research field under systems biology that uses mathematical approaches and computational methods to examine the interactions within cellular and molecular networks of the immune system. The immune system has been thoroughly analyzed as regards to its components and function by using a "reductionist" approach, but its overall function can't be easily predicted by studying the characteristics of its isolated components because they strongly rely on the interactions among these numerous constituents. It focuses on in silico experiments rather than in vivo.
Cyclin-dependent kinase 2, also known as cell division protein kinase 2, or Cdk2, is an enzyme that in humans is encoded by the CDK2 gene. The protein encoded by this gene is a member of the cyclin-dependent kinase family of Ser/Thr protein kinases. This protein kinase is highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2, also known as Cdk1 in humans. It is a catalytic subunit of the cyclin-dependent kinase complex, whose activity is restricted to the G1-S phase of the cell cycle, where cells make proteins necessary for mitosis and replicate their DNA. This protein associates with and is regulated by the regulatory subunits of the complex including cyclin E or A. Cyclin E binds G1 phase Cdk2, which is required for the transition from G1 to S phase while binding with Cyclin A is required to progress through the S phase. Its activity is also regulated by phosphorylation. Multiple alternatively spliced variants and multiple transcription initiation sites of this gene have been reported. The role of this protein in G1-S transition has been recently questioned as cells lacking Cdk2 are reported to have no problem during this transition.
Creating a cellular model has been a particularly challenging task of systems biology and mathematical biology. It involves developing efficient algorithms, data structures, visualization and communication tools to orchestrate the integration of large quantities of biological data with the goal of computer modeling.
A series of biochemical switches control transitions between and within the various phases of the cell cycle. The cell cycle is a series of complex, ordered, sequential events that control how a single cell divides into two cells, and involves several different phases. The phases include the G1 and G2 phases, DNA replication or S phase, and the actual process of cell division, mitosis or M phase. During the M phase, the chromosomes separate and cytokinesis occurs.
The following outline is provided as an overview of and topical guide to biophysics:
James Ellsworth Ferrell is an American systems biologist. He is a Professor of Chemical and Systems Biology and Biochemistry at Stanford University School of Medicine. He was Chair of the Dept. of Chemical and Systems Biology from its inception in 2006 until 2011.
Eberhard O. Voit is a Professor and David D. Flanagan Chair in Biological Systems at the Georgia Institute of Technology and a Georgia Research Alliance Eminent Scholar. He leads the Laboratory for Biological Systems Analysis.
The Novak-Tyson Model is a non-linear dynamics framework developed in the context of cell-cycle control by Bela Novak and John J. Tyson. It is a prevalent theoretical model that describes a hysteretic, bistable bifurcation of which many biological systems have been shown to express.
Robert Clarke is a Northern Irish oncology researcher and academic administrator. He is the Executive Director of The Hormel Institute, a professor of Biochemistry, Molecular Biology and Biophysics at the University of Minnesota, and ab Adjunct Professor of Oncology at Georgetown University.
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