Medical research

Biomedical research (or experimental medicine), in general simply known as medical research, is the basic research, applied research, or translational research conducted to aid and support the body of knowledge in the field of medicine. Medical research can be divided into two general categories: the evaluation of new treatments for both safety and efficacy in what are termed clinical trials, and all other research that contributes to the development of new treatments. The latter is termed preclinical research if its goal is specifically to elaborate knowledge for the development of new therapeutic strategies. A new paradigm to biomedical research is being termed translational research, which focuses on iterative feedback loops between the basic and clinical research domains to accelerate knowledge translation from the bedside to the bench, and back again.

Protein-DNA Interactions

• ChIP-on-chip
• Chip-Sequencing
• DamID

Protein structures

• X-ray crystallography
• Protein NMR

Protein purification

• Protein Isolation
  • chromatography methods
• Protein Extraction and Solubilization
• Protein Concentration Determination Methods, Bradford protein assay
• Concentrating Protein Solutions
• Gel electrophoresis
  • Gel Electrophoresis Under denaturing conditions
  • Gel Electrophoresis Under non-denaturing conditions
  • 2D Gel Electrophoresis
• Electrofocusing

Detecting proteins

• microscopy, Protein immunostaining
• Protein immunoprecipitation
• Immunoelectrophoresis
• Immunoblotting
• BCA Protein Assay
• Western blot
• Spectrophotometry
• Enzyme assay

Genetic methods

• conceptual translation- many proteins are never directly sequenced, but their sequence of amino acids is known by "conceptual translation" of a known mRNA sequence. See Genetic code.
• site-directed mutagenesis allows new variants of proteins to be produced and tested for how structural changes alter protein function.
  • insertion of protein tags such as the His-tag. See also: Green fluorescent protein.
• evolutionary; analysis of sequence changes in different species using software such as BLAST.
• Proteins that are involved in human diseases can be identified by matching alleles to disease and other phenotypes using methods such as calculation of LOD scores.

Protein methods

Protein methods are the techniques used to study proteins.

There are genetic methods for studying proteins, methods for detecting proteins, methods for isolating and purifying proteins and other methods for characterizing the structure and function of proteins, often requiring that the protein first be purified.

Macromolecule blotting and probing

The terms northern, western and eastern blotting are derived from what initially was a molecular biology joke that played on the term Southern blotting, after the technique described by Edwin Southern for the hybridisation of blotted DNA. Patricia Thomas, developer of the RNA blot which then became known as the northern blot actually didn't use the term. Further combinations of these techniques produced such terms as southwesterns (protein-DNA hybridizations), northwesterns (to detect protein-RNA interactions) and farwesterns (protein-protein interactions), all of which are presently found in the literature.

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, the latter is a method referred to as "Quick change". PCR can also be used to determine whether a particular DNA fragment is found in a cDNA library. PCR has many variations, like reverse transcription PCR (RT-PCR) for amplification of RNA, and, more recently, real-time PCR (QPCR) which allow for quantitative measurement of DNA or RNA molecules.

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 can be done by transformation (via uptake of naked DNA), conjugation (via cell-cell contact) or by transduction (via viral vector). Introducing DNA into eukaryotic cells, such as animal cells, by physical or chemical means is called transfection. Several different transfection techniques are available, such as calcium phosphate transfection, electroporation, microinjection and liposome transfection. DNA can also be introduced into eukaryotic cells using viruses or bacteria as carriers, the latter is sometimes called bactofection and in particular uses Agrobacterium tumefaciens. The plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection.

Ecology

Ecology (from Greek: οἶκος, "house" or "living relations"; -λογία, "study of") is the interdisciplinary scientific study of the distributions, abundance and relations of organisms and their interactions with the environment. Ecology is also the study of ecosystems. Ecosystems describe the web or network of relations among organisms at different scales of organization. Since ecology refers to any form of biodiversity, ecologists research everything from tiny bacteria's role in nutrient recycling to the effects of tropical rain forest on the Earth's atmosphere. The discipline of ecology emerged from the natural sciences in the late 19th century. Ecology is not synonymous with environment, environmentalism, or environmental science. Ecology is closely related to the disciplines of physiology, evolution, genetics and behavior.

Like many of the natural sciences, a conceptual understanding of ecology is found in the broader details of study, including:

• life processes explaining adaptations
• distribution and abundance of organisms
• the movement of materials and energy through living communities
• the successional development of ecosystems, and
• the abundance and distribution of biodiversity in context of the environment

Human systems

Humans have a variety of systems due to the complexity of the species' organism. These specific systems are widely studied in Human anatomy. "Human" systems are also present in many animals.

• Circulatory system: pumping and channeling blood to and from the body and lungs with heart, blood and blood vessels.
• Digestive system: digestion and processing food with salivary glands, esophagus, stomach, liver, gallbladder, pancreas, intestines, rectum and anus.
• Endocrine system: communication within the body using hormones made by endocrine glands such as the hypothalamus, pituitary or pituitary gland, pineal body or pineal gland, thyroid, parathyroids and adrenals, i.e., adrenal glands.
• Integumentary system: skin, hair, fat, and nails.
• Lymphatic system: structures involved in the transfer of lymph between tissues and the blood stream, the lymph and the nodes and vessels that transport it including the Immune system: defending against disease-causing agents with leukocytes, tonsils, adenoids, thymus and spleen.
• Muscular system: movement with muscles.
• Nervous system: collecting, transferring and processing information with brain, spinal cord, peripheral nerves and nerves.
• Reproductive system: the sex organs, such as ovaries, fallopian tubes, uterus, vagina, mammary glands, testes, vas deferens, seminal vesicles, prostate and penis.
• Respiratory system: the organs used for breathing, the pharynx, larynx, trachea, bronchi, lungs and diaphragm.
• Skeletal system: structural support and protection with bones, cartilage, ligaments and tendons.
• Urinary system: kidneys, ureters, bladder and urethra involved in fluid balance, electrolyte balance and excretion of urine.
• Endocannabinoid system: neuromodulatory lipids and receptors involved in a variety of physiological processes including appetite, pain-sensation, mood, motor learning, synaptic plasticity, and memory.

Biological system

In biology, a Biological system (or Organ system) is a group of organs that work together to perform a certain task. Common systems, such as those present in mammals and other animals, seen in human anatomy, are those such as the circulatory system, the respiratory system, the nervous system, etc.

A group of systems composes an organism, e.g. the human body.

Physiology

Physiology is the science of the functioning of living systems. It is a subcategory of biology. In physiology, the scientific method is applied to determine how organisms, organ systems, organs, cells and biomolecules carry out the chemical or physical function that they have in a living system. The word physiology is from Greek φύσις, physis, "nature, origin"; and -λογία, -logia, "study of". Physiology is a scientific study of the ways in which the bodies of living things work.

Cell (biology)

The cell is the functional basic unit of life. It was discovered by Robert Hooke and is the functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. Some organisms, such as most bacteria, are unicellular (consist of a single cell). Other organisms, such as humans, are multicellular. (Humans have an estimated 100 trillion or 10¹⁴ cells; a typical cell size is 10 µm; a typical cell mass is 1 nanogram.) The largest known cell is an unfertilised ostrich egg cell.[

Cell biology

Cell biology (formerly cytology, from the Greek kytos, "container") is an academic discipline that studies cells – their physiological properties, their structure, the organelles they contain, interactions with their environment, their life cycle, division and death. This is done both on a microscopic and molecular level. Cell biology research encompasses both the great diversity of single-celled organisms like bacteria and protozoa, as well as the many specialized cells in multicellular organisms like humans.

Knowing the components of cells and how cells work is fundamental to all biological sciences. Appreciating the similarities and differences between cell types is particularly important to the fields of cell and molecular biology as well as to biomedical fields such as cancer research and developmental biology. These fundamental similarities and differences provide a unifying theme, sometimes allowing the principles learned from studying one cell type to be extrapolated and generalized to other cell types. Hence, research in cell biology is closely related to genetics, biochemistry, molecular biology, immunology, and developmental biology.

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 interactions between DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated.

Writing in Nature in 1961, William Astbury described molecular biology as

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==

Biochemistry

Biochemistry is the study of the chemical processes in living organisms. It deals with the structures and functions of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules.

Among the vast number of different biomolecules, many are complex and large molecules (called polymers), which are composed of similar repeating subunits (called monomers). Each class of polymeric biomolecule has a different set of subunit types.^[1] For example, a protein is a polymer whose subunits are selected from a set of 20 or more amino acids. Biochemistry studies the chemical properties of important biological molecules, like proteins, and in particular the chemistry of enzyme-catalyzed reactions.

Energy

In physics, energy (from the Greek ἐνέργεια - energeia, "activity, operation", from ἐνεργός - energos, "active, working") is a quantity that can be assigned to every particle, object, and system of objects as a consequence of the state of that particle, object or system of objects. Different forms of energy include kinetic, potential, thermal, gravitational, sound, elastic, light, and electromagnetic energy. The forms of energy are often named after a related force. German physicist Hermann von Helmholtz established that all forms of energy are equivalent - energy in one form can disappear but the same amount of energy will appear in another form. Energy is subject to a conservation law. Energy is a scalar physical quantity. In the International System of Units (SI), energy is measured in joules, but in some fields other units such as kilowatt-hours and kilocalories are also used.

Biological

With regards to any given life system parameter, an organism may be a conformer or a regulator. On one hand, Regulators try to maintain the parameter at a constant level over possibly wide ambient environmental variations. While on the other hand, conformers allow the environment to determine the parameter. For instance, endothermic animals maintain a constant body temperature, while exothermic (both ectotherm and poikilotherm) animals exhibit wide body temperature variation. Examples of endothermic animals include mammals and birds, examples of exothermic animals include reptiles and some sea animals. Humans beings are nature's ultimate example of "regulators" because they control their paramater's in a variety of climates and conditions.

Behavioral adaptations allow exothermic animals to exert some control over a given parameter. For instance, reptiles often rest on sun-heated rocks in the morning to raise their body temperature. Regulators are also responsive to external circumstances, however: if the same sun-baked boulder happens to host a ground squirrel, the animal's metabolism will adjust to the lesser need for internal heat production.

Thermal image of a cold-blooded tarantula (cold-blooded or exothermic) on a warm-blooded human hand (endothermic).

An advantage of homeostatic regulation is that it allows an organism to function effectively in a broad range of environmental conditions. For example, ectotherms tend to become sluggish at low temperatures, whereas a co-located endotherm may be fully active. That thermal stability comes at a price since an automatic regulation system requires additional energy. One reason snakes may eat only once a week is that they use much less energy to maintain homeostasis.

Homeostasis

Homeostasis (from Greek: ὅμοιος, homoios, "similar"; and ἵστημι, histēmi, "standing still"; defined by Claude Bernard and later by Walter Bradford Cannon in 1929 + 1932) is the property of a system, either open or closed, that regulates its internal environment and tends to maintain a stable, constant condition. Typically used to refer to a living organism, the concept came from that of milieu interieur that was created by Claude Bernard and published in 1865. Multiple dynamic equilibria adjustment and regulation mechanisms make homeostasis possible.

Genetics

Genetics (from Ancient Greek γενετικός genetikos, “genitive” and that from γένεσις genesis, “origin”), a discipline of biology, is the science of heredity and variation in living organisms.The fact that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding. However, the modern science of genetics, which seeks to understand the process of inheritance, only began with the work of Gregor Mendel in the mid-nineteenth century.Although he did not know the physical basis for heredity, Mendel observed that organisms inherit traits via discrete units of inheritance, which are now called genes.

Gene

A gene is the basic unit of heredity in a living organism. All living things depend on genes. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring. A modern working definition of a gene is "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions ". Incorrect colloquial usage of the term gene may actually refer to an allele: a gene is the basic instruction, a sequence of nucleic acid (DNA or, in the case of certain viruses RNA), while an allele is one variant of that instruction.

Evolution

Evolution is the change in the inherited traits of a population of organisms through successive generations. After a population splits into smaller groups, these groups evolve independently and may eventually diversify into new species. A nested hierarchy of anatomical and genetic similarities, geographical distribution of similar species and the fossil record indicate that all organisms are descended from a common ancestor through a long series of these divergent events, stretching back in a tree of life that has grown over the 3,500 million years of life on Earth

Cell theory

Cell theory refers to the idea that cells are the basic unit of structure in every living thing. Development of this theory during the mid 1600s was made possible by advances in microscopy. This theory is one of the foundations of biology. The theory says that new cells are formed from other existing cells, and that the cell is a fundamental unit of structure, function and organization in all living organisms.