Systems biology

Systems biology is an academic field motivated by the belief that integrating information from diverse experimental sources will give access to new explanatory or predictive models for biological systems. By studying the relationships and interactions between various parts of a biological system (e.g., gene and protein networks involved in cell signaling, metabolic pathways, organelles, cells, physiological systems, organisms, etc.) it is hoped that eventually explanatory or predictive models of whole systems can be developed. Computer simulation and heuristics are often used as research methods.

History

In 1952, the British neurophysiologists and nobel prize winners Alan Lloyd Hodgkin and Andrew Fielding Huxley constructed a mathematical model of the nerve cell. In 1960, Denis Noble developed the first computer model of a beating heart. Around the year 2000, with the establishment of Institute of Systems Biology was established in Seattle, systems biology emerged as a movement in its own right, spurred on by the completion of various genome projects, the large increase in data from the omics (e.g. genomics and proteomics) and the accompanying advances in high-throughput experiments and bioinformatics. Since then, various research institutes dedicated to systems biology have been developed. As of summer 2006, due to a shortage of people in systems biology[1] several doctoral training centres have been established in the UK for systems biology.

Approaches

• There are two major and complementary foci in systems biology:
  Quantitative Systems Biology - otherwise known as "systems biology measurement", it focuses on measuring and monitoring biological systems on the system level.
• Systems Biology Modeling - focuses on mapping, explaining and predicting systemic biological processes and events through the building of computational and visualization models.

Quantitative systems biology

This subfield is concerned with quantifying molecular reponses in a biological system to a given perturbation.
Some typical technology platforms are:

• Gene expression measurement through DNA microarrays and SAGE
• Protein levels through two-dimensional gel electrophoresis and mass spectrometry, including phosphoproteomics and other methods to detect chemically modified proteins.
• metabolomics for small-molecule metabolites
• glycomics for sugars

These are frequently combined with large scale perturbation methods, including gene-based (RNAi, misexpression of wild type and mutant genes) and chemical approaches using small molecule libraries. Robots and automated sensors enable such large-scale experimentation and data acquisition.
These technologies are still emerging and many face problems that the larger the quantity of data produced, the lower the quality. A wide variety of quantitative scientists (computational biologists, statisticians, mathematicians, computer scientists, engineers, and physicists) are working to improve the quality of these approaches and to create, refine, and retest the models to accurately reflect observations.

Systems biology modeling

Using knowledge from molecular biology, a systems biologist can causally model the biological system of interest and propose hypotheses that describe a system's behavior. These hypotheses can then tested, with the possibility of used as a basis for mathematically model the system. The difference between the two stages of modeling is that causal models have at most the potential to explain the effects of a biological perturbation, while mathematical models, in theory, have predictive power.

Applications

Many predictions concerning the impact of genomics on health care have been proposed. For example, the development of novel therapeutics and the introduction of personalised treatments are conjectured and may become reality as a small number of biotechnology companies are using this cell-biology driven approach to the development of therapeutics. However, these predictions rely upon our ability to understand and quantify the roles that specific genes possess in the context of human and pathogen physiologies. The ultimate goal of systems biology is to derive the prerequisite knowledge and tools. Even with today's resources and expertise, this goal is immeasurably distant.

Biomedical nanotechnology

Diagnostics, drugs delivery, and prostheses & implants are three areas where nanotechnology is entering the bio-medical sector. Diagnostic sensors and “lab-on-a-chip” techniques are designed for analysing blood and other samples, and for inclusion in analytical instruments for R&D on new drugs. In terms of products for use inside the human body, nanotechnology-based applications for anticancer drugs, implanted insulin pumps, and gene therapy are being developed, while other researchers are working on prostheses and implants which contain nanostructured materials.

Molecular biology

Molecular biology is the study of biology at a molecular level. The field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interrelationship of DNA, RNA and protein synthesis and learning how these interactions are regulated. Writing in Nature, William Astbury described molecular biology as1: "... not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and ..... is predominantly three-dimensional and structural - which does not mean, however, that it is merely a refinement of morphology - it must at the same time inquire into genesis and function"

Relationship to other "molecular-scale" biological sciences

Schematic relationship between biochemistry, genetics and molecular biology Researchers in molecular biology use specific techniques native to molecular biology (see Techniques section later in article), but increasingly combine these with techniques and ideas from genetics, biochemistry and biophysics. There is not a hard-line between these disciplines as there once was. The following figure is a schematic that depicts one possible view of the relationship between the fields: Biochemistry is the study of the chemical substances and vital processes occurring in living organisms. Genetics is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g. one gene). The study of "mutants" – organisms which lack one or more functional components with respect to the so-called "wild type" or normal phenotype. Genetic interactions such as epistasis can often confound simple interpretations of such "knock-out" studies. Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for RNA. Much of the work in molecular biology is quantitative, and recently much work has been done at the interface of molecular biology and computer science in bioinformatics and computational biology. As of the early 2000s, the study of gene structure and function, molecular genetics, has been amongst the most prominent sub-field of molecular biology. Increasingly many other fields of biology focus on molecules, either directly studying their interactions in their own right such as in cell biology and developmental biology, or indirectly, where the techniques of molecular biology are used to infer historical attributes of populations or species, as in fields in evolutionary biology such as population genetics and phylogenetics. There is also a long tradition of studying biomolecules "from the ground up" in biophysics.

Techniques of molecular biology

Since the late 1950s and early 1960s, molecular biologists have learned to characterize, isolate, and manipulate the molecular components of cells and organisms. These components include DNA, the repository of genetic information; RNA, a close relative of DNA whose functions range from serving as a temporary working copy of DNA to actual structural and enzymatic functions as well as a functional and structural part of the translational apparatus; and proteins, the major structural and enzymatic type of molecule in cells.

Expression cloning

One of the most basic techniques of molecular biology to study protein function is expression cloning. In this technique, DNA coding for a protein of interest is cloned (using PCR and/or restriction enzymes) into a plasmid (known as an expression vector). This plasmid may have special promoter elements to drive production of the protein of interest, and may also have antibiotic resistance markers to help follow the plasmid. This plasmid can be inserted into either bacterial or animal cells. Introducing DNA into bacterial cells is called transformation, and can be completed with several methods, including electroporation, microinjection, passive uptake and conjugation. Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Several different transfection techniques are available, including calcium phosphate transfection, liposome transfection, and proprietary transfection reagents such as Fugene. DNA can also be introduced into cells using viruses or pathenogenic bacteria as carriers. In such cases, the technique is called viral/bacterial transduction, and the cells are said to be transduced. In either case, DNA coding for a protein of interest is now inside a cell, and the protein can now be expressed. A variety of systems, such as inducible promoters and specific cell-signaling factors, are available to help express the protein of interest at high levels. Large quantities of a protein can then be extracted from the bacterial or eukaryotic cell. The protein can be tested for enzymatic activity under a variety of situations, the protein may be crystallized so its tertiary structure can be studied, or, in the pharmaceutical industry, the activity of new drugs against the protein can be studied.

Polymerase chain reaction (PCR)

Main article: Polymerase chain reaction

The polymerase chain reaction is an extremely versatile technique for copying DNA. In brief, PCR allows a single DNA sequence to be copied (millions of times), or altered in predetermined ways. For example, PCR can be used to introduce restriction enzyme sites, or to mutate (change) particular bases of DNA. PCR can also be used to determine whether a particular DNA fragment is found in a cDNA library.

Gel electrophoresis

Main article: Gel electrophoresis

Gel electrophoresis is one of the principal tools of molecular biology. The basic principle is that DNA, RNA, and proteins can all be separated using an electric field. In agarose gel electrophoresis, DNA and RNA can be separated based on size by running the DNA through an agarose gel. Proteins can be separated based on size using an SDS-PAGE gel. Proteins can also be separated based on their electric charge, using what is known as an isoelectric gel.

Southern blotting

Main article: Southern blot

The Southern blot is a technique employed to ascertain information about the molecular weight and relative amount of a DNA sequence of interest. The assay was first developed by Edwin Southern and is a combination of gel electrophoresis of DNA (often first fragmented by restriction enzyme digestion), transfer of the same to a charged membrane, and hybridization of a labeled DNA probe. Following hybridization, the membrane is washed to remove unbound probe, and an image obtained via autoradiography or using equipment such as a phosphoimager. The image will indicate the location(s) to which the probe hybridized, with the intensity of the signal observed serving as a measure of relative abundance.

Northern blotting

Main article: Northern blot

The Northern blot is used to study the expression patterns a specific type of RNA molecule as relative comparison among of a set of different samples of RNA. It is essentially a combination of denaturing RNA gel electrophoresis, and a blot. In this process RNA is separated based on size and is then transferred to a membrane that is then probed with a labeled complement of a sequence of interest. The results may be visualized through a variety of ways depending on the label used, however, most result in the revelation of bands representing the sized of the RNA detected in sample. The intensity of these bands is related to the amount of the target RNA in the samples analyzed. The procedure is commonly used to study when and how much gene expressing is occurring by measuring how much of that RNA is present in different samples. It is one of the most basic tools for determing at what time certain genes are expressed in living tissues.

Western blotting and immunochemistry

Main article: Western blot

Antibodies to most proteins can be created by injecting small amounts of the protein into an animal such as a mouse, rabbit, sheep, or donkey. These antibodies can be used for a variety of analytical and preprative techniques. In Western blotting, proteins are first separated by size, in a thin gel sandwiched between two glass plates in a technique known as SDS-PAGE (for Sodium Dodecyl Sulphate Poly-Acrylamide Gel Electrophoresis). The proteins in the gel are then transferred to a PVDF, nitrocellulose, nylon or other support membrane. This membrane can then be probed with solutions of antibodies. Antibodies that specifically bind to the protein of interest can then be visualized by a variety of techniques, including chemiluminescence or radioactivity. Antibodies can also be used to purify proteins. Antibodies to a protein are generated and are often then coupled to "beads". After the antibody has bound to the protein of interest, this antibody-protein complex can be separated from all other proteins by centrifugation. During centrifugation, the beads, to which the antibody is coupled, will pellet (bringing the protein of interest down with it) whereas all other proteins will remain in the solution. Alternatively, antibodies coupled to a solid support matrix like Sephadex or Sepharose beads, for example, can be used to remove a protein of interest from a complex solution. After washing unbound and non-specifically bound materials away from the "beads", the protein of interest is then eluted from the matrix, usually by adding a solution with a high salt concentration, or by varying the pH of the solution in which the matrix is contained. The beads can either be suspended in solution (batch processing) or packed into a tube (column processing).

Notable molecular biologists

Francis Crick

James D. Watson

Maurice Wilkins

Erwin Chargaff

Rosalind Franklin

Max Perutz

Susumu Tonegawa

Christiane Nüsslein-Volhard

Frederick Sanger

Francois Jacob

Biophysics

Biophysics (also biological physics) is an interdisciplinary science that applies the theories and methods of physical sciences, especially those of physics, to questions of biology. Biophysics research today comprises a number of specific biological studies, which do not share a unique identifying factor, or subject themselves to clear and concise definitions. This is the result of biophysics' relatively recent appearance as a scientific discipline. The studies included under the umbrella of biophysics range from sequence comparison to neural networks. In the recent past, biophysics included creating mechanical limbs and nanomachines to regulate biological functions. Nowadays, these are more commonly referred to as belonging to the fields of bioengineering and nanotechnology respectively. We may expect these definitions to further refine themselves.

Overview

Traditional studies in biology are conducted using statistical ensemble experiments, typically using pico- to micro-molar concentrations of macromolecules. Because the molecules that comprise living cells are so small, techniques such as PCR amplification, gel blotting, fluorescence labeling and in vivo staining are used so that experimental results are observable with an unaided eye or, at most, optical magnification. Using these techniques, biologists attempt to elucidate the complex systems of interactions that give rise to the processes that make life possible. Biophysics typically addresses biological questions similar to those in biology, but the questions are asked at a molecular (i.e. low Reynolds number) level. By drawing knowledge and experimental techniques from a wide variety of disciplines (as described below), biophysicists are able to indirectly observe or model the structures and interactions of individual molecules or complexes of molecules. In addition to things like solving a protein structure or measuring the kinetics of single molecule interactions, biophysics is also understood to encompass research areas that apply models and experimental techniques derived from physics (e.g. electromagnetism and quantum mechanics) to larger systems such as tissues or organs (hence the inclusion of basic neuroscience as well as more applied techniques such as fMRI). Biophysics often does not have university-level departments of its own, but have presence as groups across departments within the fields of biology, biochemistry, chemistry, computer science, mathematics, medicine, pharmacology, physiology, physics, and neuroscience. What follows is a list of examples of how each department applies its efforts toward the study of biophysics. This list is hardly all inclusive. Nor does each subject of study belong exclusively to any particular department. Each academic institution makes its own rules and there is much mixing between departments. Biology and molecular biology - Almost all forms of biophysics efforts are included in some biology department somewhere. To include some: gene regulation, single protein dynamics, bioenergetics, patch clamping, biomechanics. Structural biology - angstrom-resolution structures of proteins, nucleic acids, lipids, carbohydrates, and complexes thereof. Biochemistry and chemistry - biomolecular structure, siRNA, nucleic acid structure, structure-activity relationships. Computer science - molecular simulations, sequence alignment, neural networks, databases. Mathematics - graph/network theory, population modeling, dynamical systems, phylogenetical analysis. Medicine and neuroscience - tackling neural networks experimentally (brain slicing) as well as theoretically (computer models), membrane permitivity, gene therapy, understanding tumors. Pharmacology and physiology - channel biology, biomolecular interactions, cellular membranes, polyketides. Physics - biomolecular free energy, biomolecular structures and dynamics, protein folding, stochastic processes, surface dynamics. Many biophysical techniques are unique to this field. Many of the research traditions in biophysics were initiated by scientists who were straight physicists, chemists, and biologists by training.

Topics in biophysics and related fields

Animal locomotion

Cellular biophysics

Channels, receptors and transporters

Electrophysiology

Cell membranes

Bioenergetics

Molecular motors Muscle and contractility

Nucleic acids

Photobiophysics and biophotonics

Proteins

Signaling

Supramolecular assemblies

Spectroscopy, imaging, etc.

Systems neuroscience

Neural encoding

Bionics

Polysulphur membranes

Biosensor and Bioelectronics

Famous biophysicists

Luigi Galvani, discoverer of bioelectricity

Hermann von Helmholtz, first to measure the velocity of nerve impulses; studied hearing and vision

Alan Hodgkin & Andrew Huxley, mathematical theory of how ion fluxes produce nerve impulses

Georg von Békésy, research on the human ear

Bernard Katz, discovered how synapses work

Hermann J. Muller, discovered that X-rays cause mutations

Linus Pauling & Robert Corey, co-discoverers of the alpha helix and beta sheet structures in proteins

Fritz-Albert Popp, pioneer of biophotons work

J. D. Bernal, X-ray crystallography of plant viruses and proteins

Rosalind Franklin, Maurice Wilkins, James D. Watson and Francis Crick, pioneers of DNA crystallography and co-discoverers of the genetic code

Max Perutz & John Kendrew, pioneers of protein crystallography

Allan Cormack & Godfrey Hounsfield, development of computer assisted tomography

Paul Lauterbur & Peter Mansfield, development of magnetic resonance imaging.

Other notable biophysicists

Adolf Eugen Fick, responsible for Fick's law of diffusion and a method to determine cardiac output.

Howard Berg, characterized properties of bacterial chemotaxis

Steven Block, observed the motions of enzymes such as kinesin and RNA polymerase with optical tweezers Carlos Bustamante, known for single-molecule biophysics of molecular motors and biological polymer physics Steven Chu, Nobel Laureate who helped develop optical trapping techniques used by many biophysicists Friedrich Dessauer, research on radiation, especially X-rays

Julio Fernandez Benoit Roux Mikhail Volkenshtein, Revaz Dogonadze & Zurab Urushadze, authors of the 1st Quantum-Mechanical (Physical) Model of Enzyme Catalysis, supported a theory that enzyme catalysis use quantum-mechanical effects such as tunneling.

John P. Wikswo, research on biomagnetism

Douglas Warrick, specializing in bird flight (hummingbirds and pigeons)

Balaji V N, specialized in computational biology.

Fractional Dynamics

The fractional dynamics framework has been to descripte of anomalous transport in complex systems which, for slow diffusion, is close to equilibrium and satisfies linear response. On the basis of the generalised Chapman-Kolmogorov equation, fractional equations of the Klein-Kramers type in phase space and of the Fokker-Planck-Smoluchowski and diffusion types in position space have been derived in which the local time derivative is replaced by a non-local integrodifferential operator. We also proved that the fractional dynamics evolves from a multiple trapping process, during which the free motion events are governed by the standard Langevin equation. We derived similar fractional equations for Lévy flight type processes. Exact solutions can be obtained in the form of Fox "H-functions", and through separation of variables. An important feature is the Mittag-Leffler relaxation pattern that replaces the conventional exponential relaxation of modes and moments, turning from stretched exponential to inverse power-law. The case of spatiotemporally coupled Lévy walks is more subtle. Our recent findings indicate that systems governed by Lévy walk statistics equilibrate in the velocity coordinate, but may not possess a stationary state in the position coordinate. (This feature is connected to the understanding of generalised equilibrium principles for stochastic systems which do not relax to Gibbs-Boltzmann equilibrium.) These properties now have to be further investigated in an exact formulation obtained recently, in which we showed that the spatiotemporal coupling of Lévy walks translates into a fractional material derivative. Conversely, we could show that Lévy flights in a superharmonic external potential exhibit a bifurcation to a multimodal state at some critical time, and that the variance for this process is finite. An important issue for both Lévy flights and Lévy walks is the correct formulation of boundary value problems. We have established a correct way to formulate such first passage problems for Lévy flights, finding that the method of images (known from normal and subdiffusion) becomes inconsistent for processes with long jump lengths, and that the first passage time density differs from the probability density of first arrival.