Cell biology is a branch of biology studying the structure and function of the cell, also known as the basic unit of life. Cell biology encompasses both prokaryotic and eukaryotic cells and can be divided into many sub-topics which may include the study of cell metabolism, cell communication, cell cycle, biochemistry, and cell composition. The study of cells is performed using several techniques such as cell culture, various types of microscopy, and cell fractionation. These have allowed for and are currently being used for discoveries and research pertaining to how cells function, ultimately giving insight into understanding larger organisms. Knowing the components of cells and how cells work is fundamental to all biological sciences while also being essential for research in biomedical fields such as cancer, and other diseases. Research in cell biology is interconnected to other fields such as genetics, molecular genetics, biochemistry, molecular biology, medical microbiology, immunology, and cytochemistry. (W)

A typical animal cell.

Cognitive genomics (or neurative genomics) is the sub-field of genomics pertaining to cognitive function in which the genes and non-coding sequences of an organism's genome related to the health and activity of the brain are studied. By applying comparative genomics, the genomes of multiple species are compared in order to identify genetic and phenotypical differences between species. Observed phenotypical characteristics related to the neurological function include behavior, personality, neuroanatomy, and neuropathology. The theory behind cognitive genomics is based on elements of genetics, evolutionary biology, molecular biology, cognitive psychology, behavioral psychology, and neurophysiology.

Intelligence is the most extensively studied behavioral trait. In humans, approximately 70% of all genes are expressed in the brain. Genetic variation accounts for 40% of phenotypical variation. Approaches in cognitive genomics have been used to investigate the genetic causes for many mental and neurodegenerative disorders including Down syndrome, major depressive disorder, autism, and Alzheimer's disease. (W)

Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences (sequences that share a common ancestry) in the aligned genomes and checking to what extent those sequences are conserved. Based on these, genome and molecular evolution are inferred and this may in turn be put in the context of, for example, phenotypic evolution or population genetics. (W)

Whole genome alignment is a typical method in comparative genomics. This alignment of eight Yersinia bacteria genomes reveals 78 locally collinear blocks conserved among all eight taxa. Each chromosome has been laid out horizontally and homologous blocks in each genome are shown as identically colored regions linked across genomes. Regions that are inverted relative to Y. pestis KIM are shifted below a genome's center axis. Whole genome alignment of eight Yersinia genomes using Mauve reveals 78 locally collinear blocks conserved among all eight taxa. Each chromosome has been laid out horizontally and homologous blocks in each genome are shown as identically colored regions linked across genomes. Regions that are inverted relative to Y. pestis KIM are shifted below a genome's center axis. The origin of replication in each genome is approximately at coordinate 1 and the terminus dif sites are approximately midway through each genome, as marked by grey vertical bars. The termini were identified by sequence comparison with Y. pestis KIM, where they were characterized by extensive sequence analysis. Figure generated by Mauve, free/open-source software available from http://darlinglab.org/mauve/mauve.html.

Complex systems biology (CSB) is a branch or subfield of mathematical and theoretical biology concerned with complexity of both structure and function in biological organisms, as well as the emergence and evolution of organisms and species, with emphasis being placed on the complex interactions of, and within, bionetworks, and on the fundamental relations and relational patterns that are essential to life. CSB is thus a field of theoretical sciences aimed at discovering and modeling the relational patterns essential to life that has only a partial overlap with complex systems theory, and also with the systems approach to biology called systems biology; this is because the latter is restricted primarily to simplified models of biological organization and organisms, as well as to only a general consideration of philosophical or semantic questions related to complexity in biology. Moreover, a wide range of abstract theoretical complex systems are studied as a field of applied mathematics, with or without relevance to biology, chemistry or physics. (W)

Network Representation of a Complex Adaptive System.

Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, ecological, behavioral, and social systems. The field is broadly defined and includes foundations in biology, applied mathematics, statistics, biochemistry, chemistry, biophysics, molecular biology, genetics, genomics, computer science, and evolution.

Computational biology is different from biological computing, which is a subfield of computer science and computer engineering using bioengineering and biology to build computers. (W)

A partially sequenced genome.

Computational epigenetics uses bioinformatic methods to complement experimental research in epigenetics. Due to the recent explosion of epigenome datasets, computational methods play an increasing role in all areas of epigenetic research.. (W)

DNA methylation is an epigenetic mechanism that can be studied with bioinformatics.

ChIP-on-chip technique.

Computational genomics (often referred to as Computational Genetics) refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data, including both DNA and RNA sequence as well as other "post-genomic" data (i.e., experimental data obtained with technologies that require the genome sequence, such as genomic DNA microarrays). These, in combination with computational and statistical approaches to understanding the function of the genes and statistical association analysis, this field is also often referred to as Computational and Statistical Genetics/genomics. As such, computational genomics may be regarded as a subset of bioinformatics and computational biology, but with a focus on using whole genomes (rather than individual genes) to understand the principles of how the DNA of a species controls its biology at the molecular level and beyond. With the current abundance of massive biological datasets, computational studies have become one of the most important means to biological discovery. (W)

Connectomics is the production and study of connectomes: comprehensive maps of connections within an organism's nervous system, typically its brain or eye. Because these structures are extremely complex, methods within this field use a high-throughput application of neural imaging and histological techniques in order to increase the speed, efficiency, and resolution of maps of the multitude of neural connections in a nervous system. While the principal focus of such a project is the brain, any neural connections could theoretically be mapped by connectomics, including, for example, neuromuscular junctions. This study is sometimes referred to by its previous name of hodology. (W)

Cytoarchitecture (Greek κύτος= "cell" + ἀρχιτεκτονική= "architecture"), also known as cytoarchitectonics, is the study of the cellular composition of the central nervous system's tissues under the microscope. Cytoarchitectonics is one of the ways to parse the brain, by obtaining sections of the brain using a microtome and staining them with chemical agents which reveal where different neurons are located.

The study of the parcellation of nerve fibers (primarily axons) into layers forms the subject of myeloarchitectonics (<Gk. μυελός=marrow + ἀρχιτεκτονική=architecture), an approach complementary to cytoarchitectonics. (w)

Cytomics is the study of cell biology (cytology) and biochemistry in cellular systems at the single cell level. It combines all the bioinformatic knowledge to attempt to understand the molecular architecture and functionality of the cell system (Cytome). Much of this is achieved by using molecular and microscopic techniques that allow the various components of a cell to be visualised as they interact in vivo. . (W)

Cells shown with immunostaining observed with a confocal microscope..

The Earth Microbiome Project (EMP) is an initiative founded by Rob Knight in 2010 to collect natural samples and to analyze the microbial community around the globe.

Microbes are highly abundant, diverse, and have an important role in the ecological system. For example, the ocean contains an estimated 1.3 × 10²⁸ archaeal cells, 3.1 × 10²⁸ bacterial cells, and 1 × 10³⁰ virus particles. The bacterial diversity, a measure of the number of types of bacteria in a community, is estimated to be about 160 for a mL of ocean water, 6,400–38,000 for a g of soil, and 70 for a mL of sewage works. Yet as of 2010, it was estimated that the total global environmental DNA sequencing effort had produced less than 1 percent of the total DNA found in a liter of seawater or a gram of soil, and the specific interactions between microbes are largely unknown.

The EMP aims to process as many as 200,000 samples in different biomes, generating a complete database of microbes on earth to characterize environments and ecosystems by microbial composition and interaction. Using these data, new ecological and evolutionary theories can be proposed and tested. (W)

Logo for Earth Microbiome Project.

In biology, epigenetics is the study of heritable phenotype changes that do not involve alterations in the DNA sequence. The Greek prefix epi- (ἐπι- "over, outside of, around") in epigenetics implies features that are "on top of" or "in addition to" the traditional genetic basis for inheritance. Epigenetics most often involves changes that affect gene activity and expression, but the term can also be used to describe any heritable phenotypic change. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors, or be part of normal development. The standard definition of epigenetics requires these alterations to be heritable in the progeny of either cells or organisms.. (W)

Epigenetic mechanisms. Epigenetic mechanisms are affected by several factors and processes including development in utero and in childhood, environmental chemicals, drugs and pharmaceuticals, aging, and diet. DNA methylation is what occurs when methyl groups, an epigenetic factor found in some dietary sources, can tag DNA and activate or repress genes. Histones are proteins around which DNA can wind for compaction and gene regulation. Histone modification occurs when the binding of epigenetic factors to histone “tails” alters the extent to which DNA is wrapped around histones and the availability of genes in the DNA to be activated. All of these factors and processes can have an effect on people’s health and influence their health possibly resulting in cancer, autoimmune disease, mental disorders, or diabetes among other illnesses. National Institutes of Health

Neurodegenerative diseases are a heterogeneous group of complex disorders linked by the degeneration of neurons in either the peripheral nervous system or the central nervous system. Their underlying causes are extremely variable and complicated by various genetic and/or environmental factors. These diseases cause progressive deterioration of the neuron resulting in decreased signal transduction and in some cases even neuronal death. Peripheral nervous system diseases may be further categorized by the type of nerve cell (motor, sensory, or both) affected by the disorder. Effective treatment of these diseases is often prevented by lack of understanding of the underlying molecular and genetic pathology. Epigenetic therapy is being investigated as a method of correcting the expression levels of misregulated genes in neurodegenerative diseases. (W)

Brain-derived neurotrophic factor.

This is a transverse section of the striatum from a structural MR image. The striatum, in red, includes the caudate nucleus (top), the putamen (right), and, when including the term 'corpus' striatum, the globus pallidus (lower left)..

Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. The field is analogous to genomics and proteomics, which are the study of the genome and proteome of a cell. Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence. Epigenomic maintenance is a continuous process and plays an important role in stability of eukaryotic genomes by taking part in crucial biological mechanisms like DNA repair. Plant flavones are said to be inhibiting epigenomic marks that cause cancers. Two of the most characterized epigenetic modifications are DNA methylation and

histone modification. Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.(W)

Epistasis refers to genetic interactions in which the mutation of one gene masks the phenotypic effects of a mutation at another locus. Systematic analysis of these epistatic interactions can provide insight into the structure and function of genetic pathways. Examining the phenotypes resulting from pairs of mutations helps in understanding how the function of these genes intersects. Genetic interactions are generally classified as either Positive/Alleviating or Negative/Aggravating. Fitness epistasis (an interaction between non-allelic genes) is positive (in other words, diminishing, antagonistic or buffering) when a loss of function mutation of two given genes results in exceeding the fitness predicted from individual effects of deleterious mutations, and it is negative (that is, reinforcing, synergistic or aggravating) when it decreases fitness. Ryszard Korona and Lukas Jasnos showed that the epistatic effect is usually positive in Saccharomyces cerevisiae. Usually, even in case of positive interactions double mutant has smaller fitness than single mutants. The positive interactions occur often when both genes lie within the same pathway Conversely, negative interactions are characterized by an even stronger defect than would be expected in the case of two single mutations, and in the most extreme cases (synthetic sick/lethal) the double mutation is lethal. This aggravated phenotype arises when genes in compensatory pathways are both knocked out. (W)

Evolutionary biology is the subfield of biology that studies the evolutionary processes (natural selection, common descent, speciation) that produced the diversity of life on Earth. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics and paleontology.

The investigational range of current research widened to encompass the genetic architecture of adaptation, molecular evolution, and the different forces that contribute to evolution, such as sexual selection, genetic drift, and biogeography. Moreover, the newer field of evolutionary developmental biology ("evo-devo") investigates how embryogenesis, the development of the embryo, is controlled, thus yielding a wider synthesis that integrates developmental biology with the fields of study covered by the earlier evolutionary synthesis. (W)

Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship (shared descent), progenitor-descendant relationship (serial descent), and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.

Evolutionary taxonomy differs from strict pre-Darwinian Linnaean taxonomy (producing orderly lists only), in that it builds evolutionary trees. While in phylogenetic nomenclature each taxon must consist of a single ancestral node and all its descendants, evolutionary taxonomy allows for groups to be excluded from their parent taxa (e.g. dinosaurs are not considered to include birds, but to have given rise to them), thus permitting paraphyletic taxa. (W)

Forensic biology is the application of biology to associate a person(s), whether suspect or victim, to a location, an item (or collection of items), another person (victim or suspect, respectively). It can be utilized to further investigations for both criminal and civil cases. Two of the most important factors to be constantly considered throughout the collection, processing, and analysis of evidence, are the maintenance of chain of custody as well as contamination prevention, especially considering the nature of the majority of biological evidence. Forensic biology is incorporated into and is a significant aspect of numerous forensic disciplines, some of which include forensic anthropology, forensic entomology, forensic odontology, forensic pathology, forensic toxicology. When the phrase "forensic biology" is utilized, it is often regarded as synonymous with DNA analysis of biological evidence. (W)

TaqMan Probes.

Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic projects (such as genome sequencing projects and RNA sequencing). Functional genomics focuses on the dynamic aspects such as gene transcription, translation, regulation of gene expression and protein–protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional “gene-by-gene” approach. (W)

Deep mutational scan of the RNA recognition motif(RRM2) of a yeast PolyA binding protein (Pab1).

Overview of Perturb-seq workflow.

An example of a CRISPR loss-of-function screen.

Samples used and eQTLs discovered in GTEx v6.

Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism's genes using biotechnology. It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms. New DNA is obtained by either isolating and copying the genetic material of interest using recombinant DNA methods or by artificially synthesising the DNA. A construct is usually created and used to insert this DNA into the host organism. The first recombinant DNA molecule was made by Paul Berg in 1972 by combining DNA from the monkey virus SV40 with the lambda virus. As well as inserting genes, the process can be used to remove, or "knock out", genes. The new DNA can be inserted randomly, or targeted to a specific part of the genome.. (W)

Diagram of a piece of DNA being removed by tweezers.

Genetic engineering can be accomplished using multiple techniques. There are a number of steps that are followed before a genetically modified organism (GMO) is created. Genetic engineers must first choose what gene they wish to insert, modify, or delete. The gene must then be isolated and incorporated, along with other genetic elements, into a suitable vector. This vector is then used to insert the gene into the host genome, creating a transgenic or edited organism. The ability to genetically engineer organisms is built on years of research and discovery on how genes function and how we can manipulate them. Important advances included the discovery of restriction enzymes and DNA ligases and the development of polymerase chain reaction and sequencing. (W)

Bacterial transformation involves moving a gene from one bacteria to another. It is integrated into the recipients plasmid. and can then be expressed by the new host. Bacterial Transformation In this diagram, a gene from bacterial cell 1 is moved from bacterial cell 1 to bacterial cell 2. This process of bacterial cell 2 taking up new genetic material is called transformation. Step I: The DNA of a bacterial cell is located in the cytoplasm (1), but also in the plasmid, an independent, circular loop of DNA. The gene to be transferred (4) is located on the plasmid of cell 1 (3), but not on the plasmid of bacterial cell 2 (2). In order to remove the gene from the plasmid of bacterial cell 1, a restriction enzyme (5) is used. The restriction enzyme binds to a specific site on the DNA and “cuts” it, releasing the satisfactory gene. Genes are naturally removed and released into the environment usually after a cell dies and disintegrates. Step II: Bacterial cell 2 takes up the gene. This integration of genetic material from the environment is an evolutionary tool and is common in bacterial cells. Step III: The enzyme DNA ligase (6) adds the gene to the plasmid of bacterial cell 2 by forming chemical bonds between the two segments which join them together. Step IV: The plasmid of bacterial cell 2 now contains the gene from bacterial cell 1 (7). The gene has been transferred from one bacterial cell to another, and transformation is complete. (W)

Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.

Though heredity had been observed for millennia, Gregor Mendel, a scientist and Augustinian friar working in the 19th century, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene.

Trait inheritance and molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded beyond inheritance to studying the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism (e.g. dominance), and within the context of a population. Genetics has given rise to a number of subfields, including molecular genetics, epigenetics and population genetics. Organisms studied within the broad field span the domains of life (archaea, bacteria, and eukarya).

Genetic processes work in combination with an organism's environment and experiences to influence development and behavior, often referred to as nature versus nurture. The intracellular or extracellular environment of a living cell or organism may switch gene transcription on or off. A classic example is two seeds of genetically identical corn, one placed in a temperate climate and one in an arid climate (lacking sufficient waterfall or rain). While the average height of the two corn stalks may be genetically determined to be equal, the one in the arid climate only grows to half the height of the one in the temperate climate due to lack of water and nutrients in its environment. (W)

Gene duplication allows diversification by providing redundancy: one gene can mutate and lose its original function without harming the organism.

Genome editing, or genome engineering, or gene editing, is a type of genetic engineering in which DNA is inserted, deleted, modified or replaced in the genome of a living organism. Unlike early genetic engineering techniques that randomly inserts genetic material into a host genome, genome editing targets the insertions to site specific locations. (W)

The different generations of nucleases used for genome editing and the DNA repair pathways used to modify target DNA.

Groups of engineered nucleases. Matching colors signify DNA recognition patterns. Various categories of engineered nucleases currently used for genome editing. ZFN (zinc finger nuclease) and TALEN (Transcription activator-like effector nuclease) are linked to the active catalytic domains of FokI endonuclease. FokI subunits can be engineered to function as heterodimers only to increase specificity. Naturally occurring meganucleases can be engineered into hybrids to cover greater sequence diversity. (W)

General overview of the TALEN process.

Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.

The field also includes studies of intragenomic (within the genome) phenomena such as epistasis (effect of one gene on another), pleiotropy (one gene affecting more than one trait), heterosis (hybrid vigour), and other interactions between loci and alleles within the genome. (W)

General schema showing the relationships of the genome, transcriptome, proteome, and metabolome (lipidome).

An example of a protein structure determined by the Midwest Center for Structural Genomics.

Cognitive genomics (or neurative genomics) is the sub-field of genomics pertaining to cognitive function in which the genes and non-coding sequences of an organism's genome related to the health and activity of the brain are studied. By applying comparative genomics, the genomes of multiple species are compared in order to identify genetic and phenotypical differences between species. Observed phenotypical characteristics related to the neurological function include behavior, personality, neuroanatomy, and neuropathology. The theory behind cognitive genomics is based on elements of genetics, evolutionary biology, molecular biology, cognitive psychology, behavioral psychology, and neurophysiology.

Intelligence is the most extensively studied behavioral trait. In humans, approximately 70% of all genes are expressed in the brain. Genetic variation accounts for 40% of phenotypical variation. Approaches in cognitive genomics have been used to investigate the genetic causes for many mental and neurodegenerative disorders including Down syndrome, major depressive disorder, autism, and Alzheimer's disease. (W)

General schema showing the relationships of the genome, transcriptome, proteome, and metabolome (lipidome).

An example of a protein structure determined by the Midwest Center for Structural Genomics.

Global biodiversity

Global biodiversity is the measure of biodiversity on planet Earth and is defined as the total variability of life forms. More than 99 percent of all species that ever lived on Earth are estimated to be extinct. Estimates on the number of Earth's current species range from 2 million to 1012, of which about 1.74 million have been databased thus far and over 80 percent have not yet been described. More recently, in May 2016, scientists reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described. The total amount of DNA base pairs on Earth, as a possible approximation of global biodiversity, is estimated at 5.0 x 1037, and weighs 50 billion tonnes. In comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC (trillion tons of carbon). (W)

The distribution of numbers of known and undescribed (estimated) species on Earth, grouped by major taxonomic groups; according to Chapman 2009. Absolute number of species on the left (orange = estimated number of yet to be described species, blue = already described). Right: percentage of species already described (green) and estimated to be not yet known (yellow).

The global brain is a neuroscience-inspired and futurological vision of the planetary information and communications technology network that interconnects all humans and their technological artifacts. As this network stores ever more information, takes over ever more functions of coordination and communication from traditional organizations, and becomes increasingly intelligent, it increasingly plays the role of a brain for the planet Earth.. (W)

Opte Project visualization of routing paths through a portion of the Internet. The connections and pathways of the internet could be seen as the pathways of neurons and synapses in a global brain. Partial map of the Internet based on the January 15, 2005 data found on opte.org. Each line is drawn between two nodes, representing two IP addresses. The length of the lines are indicative of the delay between those two nodes. This graph represents less than 30% of the Class C networks reachable by the data collection program in early 2005. Lines are color-coded according to their corresponding RFC 1918 allocation as follows: Dark blue: net, ca, us Green: com, org Red: mil, gov, edu Yellow: jp, cn, tw, au, de Magenta: uk, it, pl, fr Gold: br, kr, nl White: unknown

Glycobiology

Defined in the narrowest sense, glycobiology is the study of the structure, biosynthesis, and biology of saccharides (sugar chains or glycans) that are widely distributed in nature. Sugars or saccharides are essential components of all living things and aspects of the various roles they play in biology are researched in various medical, biochemical and biotechnological fields. (W)

Glycomics is the comprehensive study of glycomes (the entire complement of sugars, whether free or present in more complex molecules of an organism), including genetic, physiologic, pathologic, and other aspects. Glycomics "is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology. The term glycomics is derived from the chemical prefix for sweetness or a sugar, "glyco-", and was formed to follow the omics naming convention established by genomics (which deals with genes) and proteomics (which deals with proteins).. (W)

Health informatics (also called health care informatics, healthcare informatics, medical informatics, nursing informatics, clinical informatics, or biomedical informatics) is information engineering applied to the field of health care, essentially the management and use of patient health care information. It is a multidisciplinary field that uses health information technology (HIT) to improve health care via any combination of higher quality, higher efficiency (spurring lower cost and thus greater availability), and new opportunities. The disciplines involved include information science, computer science, social science, behavioral science, management science, and others. The United States National Library of Medicine (NLM) defines health informatics as "the interdisciplinary study of the design, development, adoption and application of IT-based innovations in health care services delivery, management and planning". (W)

Electronic patient chart from a health information system.

Immunomics is the study of immune system regulation and response to pathogens using genome-wide approaches. With the rise of genomic and proteomic technologies, scientists have been able to visualize biological networks and infer interrelationships between genes and/or proteins; recently, these technologies have been used to help better understand how the immune system functions and how it is regulated. Two thirds of the genome is active in one or more immune cell types and less than 1% of genes are uniquely expressed in a given type of cell. Therefore, it is critical that the expression patterns of these immune cell types be deciphered in the context of a network, and not as an individual, so that their roles be correctly characterized and related to one another. Defects of the immune system such as autoimmune diseases, immunodeficiency, and malignancies can benefit from genomic insights on pathological processes. For example, analyzing the systematic variation of gene expression can relate these patterns with specific diseases and gene networks important for immune functions. (W)

mmunoproteomics is the study of large sets of proteins (proteomics) involved in the immune response.

Examples of common applications of immunoproteomics include:

• The isolation and mass spectrometric identification of MHC (major histocompatibility complex) binding peptides
• Purification and identification of protein antigens binding specific antibodies (or other affinity reagents)
• Comparative immunoproteomics to identify proteins and pathways modulated by a specific infectious organism, disease or toxin.

The identification of proteins in immunoproteomics is carried out by techniques including gel based, microarray based, and DNA based techniques, with mass spectroscopy typically being the ultimate identification method. (W)

Lipidomics is the large-scale study of pathways and networks of cellular lipids in biological systems The word "lipidome" is used to describe the complete lipid profile within a cell, tissue, organism, or ecosystem and is a subset of the "metabolome" which also includes the three other major classes of biological molecules: proteins/amino-acids, sugars and nucleic acids. Lipidomics is a relatively recent research field that has been driven by rapid advances in technologies such as mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy, dual polarisation interferometry and computational methods, coupled with the recognition of the role of lipids in many metabolic diseases such as obesity, atherosclerosis, stroke, hypertension and diabetes. This rapidly expanding field complements the huge progress made in genomics and proteomics, all of which constitute the family of systems biology.. (W)

General schema showing the relationships of the lipidome to the genome, transcriptome, proteome and metabolome. Lipids also regulate protein function and gene transcription as part of a dynamic "interactome" within the cell.

Schema showing detection of a fatty acid by LC-MS/MS using a linear ion-trap instrument and an electrospray (ESI) ion source.

Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics.

Yellow chamomile head showing the Fibonacci numbers in spirals consisting of 21 (blue) and 13 (aqua). Such arrangements have been noticed since the Middle Ages and can be used to make mathematical models of a wide variety of plants.

While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods.

Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before. Recent studies use either "shotgun" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. (W)

Medical image computing (MIC) is an interdisciplinary field at the intersection of computer science, information engineering, electrical engineering, physics, mathematics and medicine. This field develops computational and mathematical methods for solving problems pertaining to medical images and their use for biomedical research and clinical care.

The main goal of MIC is to extract clinically relevant information or knowledge from medical images. While closely related to the field of medical imaging, MIC focuses on the computational analysis of the images, not their acquisition. The methods can be grouped into several broad categories: image segmentation, image registration, image-based physiological modeling, and others. (W)

A T1 weighted MR image of the brain of a patient with a meningioma after injection of a MRI contrast agent (top left), and the same image with the result of an interactive segmentation overlaid in green (3D model of the segmentation on the top right, axial and coronal views at the bottom).

CT image (left), PET image (center) and overlay of both (right) after correct registration.

Medicine is the science and practice of establishing the diagnosis, prognosis, treatment, and prevention of disease. Medicine encompasses a variety of health care practices evolved to maintain and restore health by the prevention and treatment of illness. Contemporary medicine applies biomedical sciences, biomedical research, genetics, and medical technology to diagnose, treat, and prevent injury and disease, typically through pharmaceuticals or surgery, but also through therapies as diverse as psychotherapy, external splints and traction, medical devices, biologics, and ionizing radiation, amongst others.

Medicine has been practiced since prehistoric times, during most of which it was an art (an area of skill and knowledge) frequently having connections to the religious and philosophical beliefs of local culture. For example, a medicine man would apply herbs and say prayers for healing, or an ancient philosopher and physician would apply bloodletting according to the theories of humorism. In recent centuries, since the advent of modern science, most medicine has become a combination of art and science (both basic and applied, under the umbrella of medical science). While stitching technique for sutures is an art learned through practice, the knowledge of what happens at the cellular and molecular level in the tissues being stitched arises through science. (W)

Statue of Asclepius, the Greek god of medicine, holding the symbolic Rod of Asclepius with its coiled serpent.

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Metabolic network reconstruction and simulation allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways (such as glycolysis and the citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology.

In general, the process to build a reconstruction is as follows:

1. Draft a reconstruction
2. Refine the model
3. Convert model into a mathematical/computational representation
4. Evaluate and debug model through experimentation (W)
   
   

Metabolic network showing interactions between enzymes and metabolites in the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are the red dots and interactions between them are the lines.

A visual representation of the process to draft a metabolic network reconstruction.

Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates and products of metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the complete set of metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes. mRNA gene expression data and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell, and thus, metabolomics provides a direct "functional readout of the physiological state" of an organism. One of the challenges of systems biology and functional genomics is to integrate genomics, transcriptomic, proteomic, and metabolomic information to provide a better understanding of cellular biology. (W)

Human metabolome project.

Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics.

While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods.

Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before. Recent studies use either "shotgun" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. (W)

In metagenomics, the genetic materials (DNA, C) are extracted directly from samples taken from the environment (e.g. soil, sea water, human gut, A) after filtering (B), and are sequenced (E) after multiplication by cloning (D) in an approach called shotgun sequencing. These short sequences can then be put together again using assembly methods (F) to deduce the individual genomes or parts of genomes that constitute the original environmental sample. This information can then be used to study the species diversity and functional potential of the microbial community of the environment.

Flow diagram of a typical metagenome project

Schematic representation of the main steps necessary for the analysis of whole metagenome shotgun sequencing-derived data. The software related to each step is shown in italics.

Metaproteomics (also Community Proteomics, Environmental Proteomics, or Community Proteogenomics) is the study of all protein samples recovered directly from environmental sources. Metaproteomics is used to classify experiments that deal with all the genes and proteins identified from complex communities, where individuals cannot be binned into species or organisms types. The metaproteomics approach is comparable to gene-centric environmental genomics, or metagenomic. (W)

Microbial ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.

Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (calculated as 5.0×10³⁰ cells; eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged. (W)

The great plate count anomaly. Counts of cells obtained via cultivation are orders of magnitude lower than those directly observed under the microscope. This is because microbiologists are able to cultivate only a minority of naturally occurring microbes using current laboratory techniques, depending on the environment.

Microbiology (from Greek μῑκρος, mīkros, "small"; βίος, bios, "life"; and -λογία, -logia) is the study of microorganisms, those being unicellular (single cell), multicellular (cell colony), or acellular (lacking cells). Microbiology encompasses numerous sub-disciplines including virology, bacteriology, protistology, mycology, immunology and parasitology.

Eukaryotic microorganisms possess membrane-bound organelles and include fungi and protists, whereas prokaryotic organisms—all of which are microorganisms—are conventionally classified as lacking membrane-bound organelles and include Bacteria and Archaea. Microbiologists traditionally relied on culture, staining, and microscopy. However, less than 1% of the microorganisms present in common environments can be cultured in isolation using current means. Microbiologists often rely on molecular biology tools such as DNA sequence based identification, for example 16s rRNA gene sequence used for bacteria identification.

Viruses have been variably classified as organisms, as they have been considered either as very simple microorganisms or very complex molecules. Prions, never considered as microorganisms, have been investigated by virologists, however, as the clinical effects traced to them were originally presumed due to chronic viral infections, and virologists took search—discovering "infectious proteins".

The existence of microorganisms was predicted many centuries before they were first observed, for example by the Jains in India and by Marcus Terentius Varro in ancient Rome. The first recorded microscope observation was of the fruiting bodies of moulds, by Robert Hooke in 1666, but the Jesuit priest Athanasius Kircher was likely the first to see microbes, which he mentioned observing in milk and putrid material in 1658. Antonie van Leeuwenhoek is considered a father of microbiology as he observed and experimented with microscopic organisms in 1676, using simple microscopes of his own design. Scientific microbiology developed in the 19th century through the work of Louis Pasteur and in medical microbiology Robert Koch. (W)

An agar plate streaked with microorganisms.

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 (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks), to both analyze and visualize the complex connections of these cellular processes. (W)

Part of the cell cycle.

Summerhayes and Elton's 1923 food web of Bear Island (Arrows represent an organism being consumed by another organism).

Molecular biology is the branch of biology that concerns the molecular basis of biological activity in and between cells, including molecular synthesis, modification, mechanisms and interactions. The central dogma of molecular biology describes the process in which DNA is transcribed into RNA then translated into protein.

William Astbury described molecular biology in 1961 in Nature, 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.”

Some clinical research and medical therapies arising from molecular biology are covered under gene therapy whereas the use of molecular biology or molecular cell biology in medicine is now referred to as molecular medicine. Molecular biology also plays important role in understanding formations, actions, and regulations of various parts of cells which can be used to efficiently target new drugs, diagnose disease, and understand the physiology of the cell. (W)

Molecular epidemiology is a branch of epidemiology and medical science that focuses on the contribution of potential genetic and environmental risk factors, identified at the molecular level, to the etiology, distribution and prevention of disease within families and across populations. This field has emerged from the integration of molecular biology into traditional epidemiological research. Molecular epidemiology improves our understanding of the pathogenesis of disease by identifying specific pathways, molecules and genes that influence the risk of developing disease. More broadly, it seeks to establish understanding of how the interactions between genetic traits and environmental exposures result in disease.. (W)

Molecular genetics is a sub-field of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the structure and/or function of genes in an organism’s genome using genetic screens. The field of study is based on the merging of several sub-fields in biology: classical Mendelian inheritance, cellular biology, molecular biology, biochemistry, and biotechnology. Researchers search for mutations in a gene or induce mutations in a gene to link a gene sequence to a specific phenotype. Molecular genetics is a powerful methodology for linking mutations to genetic conditions that may aid the search for treatments/cures for various genetics diseases. (W)

Network medicine is the application of network science towards identifying, preventing, and treating diseases. This field focuses on using network topology and network dynamics towards identifying diseases and developing medical drugs. Biological networks, such as protein-protein interactions and metabolic pathways, are utilized by network medicine. Disease networks, which map relationships between diseases and biological factors, also play an important role in the field. Epidemiology is extensively studied using network science as well; social networks and transportation networks are used to model the spreading of disease across populations. Network medicine is a medically focused area of systems biology. A gentle introduction to the field can be found here: https://web.uniroma1.it/stitch/node/5613.. (W)

Neuroanatomy is the study of the structure and organization of the nervous system. In contrast to animals with radial symmetry, whose nervous system consists of a distributed network of cells, animals with bilateral symmetry have segregated, defined nervous systems. Their neuroanatomy is therefore better understood. In vertebrates, the nervous system is segregated into the internal structure of the brain and spinal cord (together called the central nervous system, or CNS) and the routes of the nerves that connect to the rest of the body (known as the peripheral nervous system, or PNS). The delineation of distinct structures and regions of the nervous system has been critical in investigating how it works. For example, much of what neuroscientists have learned comes from observing how damage or "lesions" to specific brain areas affects behavior or other neural functions. (W)

Neuroanatomy is the study of the anatomy and organisation of the nervous system. Pictured here is a cross-section showing the gross anatomy of the human brain.

Nervous system of a generic bilaterian animal, in the form of a nerve cord with segmental enlargements, and a "brain" at the front.

Neurogenetics studies the role of genetics in the development and function of the nervous system. It considers neural characteristics as phenotypes (i.e. manifestations, measurable or not, of the genetic make-up of an individual), and is mainly based on the observation that the nervous systems of individuals, even of those belonging to the same species, may not be identical. As the name implies, it draws aspects from both the studies of neuroscience and genetics, focusing in particular how the genetic code an organism carries affects its expressed traits. Mutations in this genetic sequence can have a wide range of effects on the quality of life of the individual. Neurological diseases, behavior and personality are all studied in the context of neurogenetics. The field of neurogenetics emerged in the mid to late 1900s with advances closely following advancements made in available technology. Currently, neurogenetics is the center of much research utilizing cutting edge techniques. (W)

Neurology (from Greek: νεῦρον (neûron), "string, nerve" and the suffix -logia, "study of") is a branch of medicine dealing with disorders of the nervous system. Neurology deals with the diagnosis and treatment of all categories of conditions and disease involving the central and peripheral nervous systems (and their subdivisions, the autonomic and somatic nervous systems), including their coverings, blood vessels, and all effector tissue, such as muscle. Neurological practice relies heavily on the field of neuroscience, the scientific study of the nervous system.

A neurologist is a physician specializing in neurology and trained to investigate, or diagnose and treat neurological disorders. Neurologists may also be involved in clinical research, clinical trials, and basic or translational research. While neurology is a nonsurgical specialty, its corresponding surgical specialty is neurosurgery.

Significant overlap occurs between the fields of neurology and psychiatry, with the boundary between the two disciplines and the conditions they treat being somewhat nebulous.(W)

A network of dendrites from neurons in the hippocampus. After the original figure legend: Coronal section containing the chronically imaged pyramidal neuron “dow” (visualized by green GFP) does not stain for GABA (visualized by antibody staining in red). Confocal image stack, overlay of GFP and GABA channels. Scale bar: 100 μm.

Photograph of a stained neuron in a chicken embryo.

Neuroscience (or neurobiology) is the scientific study of the nervous system. It combines physiology, anatomy, molecular biology, developmental biology, cytology, mathematical modeling, and psychology to understand the fundamental and emergent properties of neurons and neural circuits. The understanding of the biological basis of learning, memory, behavior, perception, and consciousness has been described by Eric Kandel as the "ultimate challenge" of the biological sciences.

The scope of neuroscience has broadened over time to include different approaches used to study the nervous system at different scales and the techniques used by neuroscientists have expanded enormously, from molecular and cellular studies of individual neurons to imaging of sensory, motor and cognitive tasks in the brain. (W)

Human nervous system.

Photograph of a stained neuron in a chicken embryo.

Proposed organization of motor-semantic neural circuits for action language comprehension. Adapted from Shebani et al. (2013)

Noogenesis is the emergence and evolution of intelligence. (W)

Noogenesis: the evolution of the reaction rate. In unicellular organism – the rate of movement of ions through the membrane 10 in -10 degrees m/s, water through the membrane 10 in −6 degree m/s, intracellular liquid (cytoplasm) 2∙10 in −5 degree m/s; Inside multicellular organism – the speed of blood through the vessels ~0.05 m/s, the momentum along the nerve fibers ~100 m/s; In population (humanity) – communications: sound (voice and audio) ~300 km/h, quantum-electron ~3∙10 in 8 degree m/s (the speed of radio-electromagnetic waves, electric current, light, optical, tele-communications).

Iteration of the number of components in Intellectual systems. A - number of neurons in the brain during individual development (ontogenesis), B - number of people (evolution of populations of humanity), C - number of neurons in the nervous systems of organisms during evolution (phylogenesis).

Emergence and evolution of info-interactions within populations of Humanity. A – world human population → 7 billion; B – number of literate persons; C – number of reading books (with beginning of printing); D – number of receivers (radio, TV); E – number of phones, computers, Internet users.

Nutriepigenomics is the study of food nutrients and their effects on human health through epigenetic modifications. There is now considerable evidence that nutritional imbalances during gestation and lactation are linked to non-communicable diseases, such as obesity, cardiovascular disease, diabetes, hypertension, and cancer. If metabolic disturbances occur during critical time windows of development, the resulting epigenetic alterations can lead to permanent changes in tissue and organ structure or function and predispose individuals to disease.. (W)

The nutriepigenetic pathway of maternal choline-deficient diets helps to elucidate the development of fetal alcohol syndrome.

Nutritional genomics, also known as nutrigenomics, is a science studying the relationship between human genome, nutrition and health. People in the field work toward developing an understanding of how the whole body responds to a food via systems biology, as well as single gene/single food compound relationships. Nutritional genomics or Nutrigenomics is the relation between food and inherited genes, it was first expressed in 2001. (W)

In the fields of molecular biology and genetics, a pan-genome (pangenome or supragenome) is the entire set of genes for all strains within a clade. The pangenome includes: the core genome containing genes present in all strains within the clade, the accessory genome containing 'dispensable' genes present in a subset of the strains, and strain-specific genes. The study of the pangenome is called pangenomics. (W)

The S. pneumoniae pan-genome. (a) Number of new genes as a function of the number of sequenced genomes. The predicted number of new genes drops sharply to zero when the number of genomes exceeds 50. (b) Number of core genes as a function of the number of sequenced genomes. The number of core genes converges to 1,647 for number of genomes n→∞. From Donati et al.

Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance, as well as virulence factors (VFs), which enable a microorganism to infect a host and possibly cause disease. This includes studying genomes of pathogens which cannot be cultured outside of a host. In the past, researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms. With newer technology, pathogen genomes can be identified and sequenced in a much shorter time and at a lower cost, thus improving the ability to diagnose, treat, and even predict and prevent pathogenic infections and disease. It has also allowed researchers to better understand genome evolution events - gene loss, gain, duplication, rearrangement - and how those events impact pathogen resistance and ability to cause disease. This influx of information has created a need for making the vast amounts of data accessible to researchers in the form of databases, and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence. (W)

Summary of dynamic genomics events. This is a figure which illustrates the genomic events which account for genome varability in pathogens. In particular, this diagram is illustrating a plasmid.

Pan-genome overview. Illustrating the process of classifying a pan-genome. Sequence data is collected from multiple strains of a microbe species; these strains may be pathogenic or not. Once the data is collected, a pan-genome can be assembled. There are three principle classifications of genes in a pan-genome : core genes, strain-specific genes and disposable genes.

Summary of host-microbe project goals in the Pathogenomics European Research Agenda. his is a summary of the host-pathogen analysis approaches which were outlined in the article: "Pathogenomics: An Updated European Research Agenda". The reference for that article is here: Demuth, A., Aharonowitz, Y., Bachmann, T.T., Blum-Oehler, G., Buchrieser, C., Covacci, A., Dbrindt, G., Emody, L., et al. (2008). "Pathogenomics: An updated European Research Agenda". Infection Genetic and Evolution 8: 386-393. doi:10.1016/j.meegid.2008.01.005.

Pharmacogenomics is the study of the role of the genome in drug response. Its name (pharmaco- + genomics) reflects its combining of pharmacology and genomics. Pharmacogenomics analyzes how the genetic makeup of an individual affects his/her response to drugs. It deals with the influence of acquired and inherited genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms with pharmacokinetics (drug absorption, distribution, metabolism, and elimination) and pharmacodynamics (effects mediated through a drug's biological targets). The term pharmacogenomics is often used interchangeably with pharmacogenetics. Although both terms relate to drug response based on genetic influences, pharmacogenetics focuses on single drug-gene interactions, while pharmacogenomics encompasses a more genome-wide association approach, incorporating genomics and epigenetics while dealing with the effects of multiple genes on drug response.. (W)

An overall process of how pharmacogenomics functions in a clinical practice. From the raw genotype results, this is then translated to the physical trait, the phenotype. Based on these observations, optimal dosing is evaluated.

A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the evolutionary relationships among various biological species or other entities—their phylogeny —based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry.

In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. Unrooted trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to be known or inferred. (W)

A phylogenetic tree based on rRNA genes, showing the three life domains: bacteria, archaea, and eukaryota. The black branch at the bottom of the phylogenetic tree connects the three branches of living organisms to the last universal common ancestor. In the absence of an outgroup, the root is speculative.

In biology, phylogenetics (Greek: φυλή, φῦλον – phylé, phylon = tribe, clan, race + γενετικός – genetikós = origin, source, birth) is a part of systematics that addresses the inference of the evolutionary history and relationships among or within groups of organisms (e.g. species, or more inclusive taxa). These relationships are hypothesized by phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology, often under a specified model of evolution of these traits. The result of such an analysis is a phylogeny (also known as a phylogenetic tree) — a diagrammatic hypothesis of relationships that reflects the evolutionary history of a group of organisms. The tips of a phylogenetic tree can be living taxa or fossils, and represent the 'end', or the present, in an evolutionary lineage. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor, or ancestral lineage, of the tree. An unrooted tree diagram (a network) makes no assumption about the ancestral line, and does not show the origin or "root" of the taxa in question or the direction of inferred evolutionary transformations. In addition to their proper use for inferring phylogenetic patterns among taxa, phylogenetic analyses are often employed to represent relationships among gene copies or individual organisms. Such uses have become central to understanding biodiversity, evolution, ecology, and genomes.

Taxonomy is the identification, naming and classification of organisms. Classifications are now usually based on phylogenetic data, and many systematists contend that only monophyletic taxa should be recognized as named groups. The degree to which classification depends on inferred evolutionary history differs depending on the school of taxonomy: phenetics ignores phylogenetic speculation altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters (synapomorphies); evolutionary taxonomy tries to take into account both the branching pattern and "degree of difference" to find a compromise between them. (W)

Physiology (φύσις (physis), meaning 'nature, origin', and -λογία (-logia), meaning 'study of') is the scientific study of functions and mechanisms in a living system. As a sub-discipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out the chemical and physical functions in a living system. According to the classes of organisms, the field can be divided into medical physiology, animal physiology, plant physiology, cell physiology, and comparative physiology.

Central to physiological functioning are biophysical and biochemical processes, homeostatic control mechanisms, and communication between cells. Physiological state is the condition of normal function, while pathological state refers to abnormal conditions, including human diseases.

The Nobel Prize in Physiology or Medicine is awarded by the Royal Swedish Academy of Sciences for exceptional scientific achievements in physiology related to the field of medicine. (W)

Oil painting depicting Claude Bernard, the father of modern physiology, with his pupils.

Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.

Population genetics was a vital ingredient in the emergence of the modern evolutionary synthesis. Its primary founders were Sewall Wright, J. B. S. Haldane and Ronald Fisher, who also laid the foundations for the related discipline of quantitative genetics. Traditionally a highly mathematical discipline, modern population genetics encompasses theoretical, lab, and field work. Population genetic models are used both for statistical inference from DNA sequence data and for proof/disproof of concept.

What sets population genetics apart today from newer, more phenotypic approaches to modelling evolution, such as evolutionary game theory and adaptive dynamics, is its emphasis on genetic phenomena as dominance, epistasis, the degree to which genetic recombination breaks up linkage disequilibrium, and the random phenomena of mutation and genetic drift. This makes it appropriate for comparison to population genomics data. (W)

Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions. The proteome is the entire set of proteins that is produced or modified by an organism or system. Proteomics has enabled the identification of ever increasing numbers of protein. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes. Proteomics is an interdisciplinary domain that has benefitted greatly from the genetic information of various genome projects, including the Human Genome Project. It covers the exploration of proteomes from the overall level of protein composition, structure, and activity. It is an important component of functional genomics.

Proteomics generally refers to the large-scale experimental analysis of proteins and proteomes, but often is used specifically to refer to protein purification and mass spectrometry. . (W)

Robotic preparation of MALDI mass spectrometry samples on a sample carrier. Public domain image from cancer.gov http://visualsonline.cancer.gov/details.cfm?imageid=3483. TECAN Genesis 2000 robot preparing Ciphergen SELDI-TOF protein chips for proteomic pattern analysis. Highly accurate cancer prognosis can be accomplished by identifying protein patterns of specific cancers using this device.

Quantum biology is the study of applications of quantum mechanics and theoretical chemistry to biological objects and problems. Many biological processes involve the conversion of energy into forms that are usable for chemical transformations, and are quantum mechanical in nature. Such processes involve chemical reactions, light absorption, formation of excited electronic states, transfer of excitation energy, and the transfer of electrons and protons (hydrogen ions) in chemical processes, such as photosynthesis, olfaction and cellular respiration.

Diagram of FMO complex. Light excites electrons in an antenna. The excitation then transfers through various proteins in the FMO complex to the reaction center to further photosynthesis.

Quantum biology may use computations to model biological interactions in light of quantum mechanical effects. Quantum biology is concerned with the influence of non-trivial quantum phenomena, which can be explained by reducing the biological process to fundamental physics, although these effects are difficult to study and can be speculative. The field of study does not imply any new physical principles are needed, since the quantum mechanical study of reaction rates and energy transfer is well established. To date, there are no observations of quantum biology that imply quantum effects are observable in macroscopic organisms (aside from thought experiments such as Schrödinger's cat), or that are crucial for the existence of life. (W)

Self-organization, also called (in the social sciences) spontaneous order, is a process where some form of overall order arises from local interactions between parts of an initially disordered system. The process can be spontaneous when sufficient energy is available, not needing control by any external agent. It is often triggered by seemingly random fluctuations, amplified by positive feedback. The resulting organization is wholly decentralized, distributed over all the components of the system. As such, the organization is typically robust and able to survive or self-repair substantial perturbation. Chaos theory discusses self-organization in terms of islands of predictability in a sea of chaotic unpredictability.

Self-organization occurs in many physical, chemical, biological, robotic, and cognitive systems. Examples of self-organization include crystallization, thermal convection of fluids, chemical oscillation, animal swarming, neural circuits. (W)

This is a visual, organizational map of complex systems broken into seven sub-groups.

Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules (especially proteins, made up of amino acids, RNA or DNA, made up of nucleotides, membranes, made up of lipids) how they acquire the structures they have, and how alterations in their structures affect their function. This subject is of great interest to biologists because macromolecules carry out most of the functions of cells, and it is only by coiling into specific three-dimensional shapes that they are able to perform these functions. This architecture, the "tertiary structure" of molecules, depends in a complicated way on each molecule's basic composition, or "primary structure."

Biomolecules are too small to see in detail even with the most advanced light microscopes. The methods that structural biologists use to determine their structures generally involve measurements on vast numbers of identical molecules at the same time. These methods include:

• Mass spectrometry
• Macromolecular crystallography
• Neutron diffraction
• Proteolysis
• Nuclear magnetic resonance spectroscopy of proteins (NMR)
• Electron paramagnetic resonance (EPR)
• Cryogenic Electron Microscopy (cryoEM)
• Electron crystallography and Microcrystal electron diffraction
• Multiangle light scattering
• Small angle scattering
• Ultrafast laser spectroscopy
• Dual-polarization interferometry and circular dichroism

Most often researchers use them to study the "native states" of macromolecules. But variations on these methods are also used to watch nascent or denatured molecules assume or reassume their native states. See protein folding.

A third approach that structural biologists take to understanding structure is bioinformatics to look for patterns among the diverse sequences that give rise to particular shapes. Researchers often can deduce aspects of the structure of integral membrane proteins based on the membrane topology predicted by hydrophobicity analysis. See protein structure prediction.

In the past few years it has become possible for highly accurate physical molecular models to complement the in silico study of biological structures. Examples of these models can be found in the Protein Data Bank.

Computational techniques like Molecular Dynamics simulations can be used in conjunction with empirical structure determination strategies to extend and study protein structure, conformation and function. (W)

Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of experimental and modeling approaches. The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large number of sequenced genomes and previously solved protein structures allows scientists to model protein structure on the structures of previously solved homologs. . (W)

An example of a protein structure from Protein Data Bank.

Synthetic biology (SynBio) is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature.

It is a branch of science that encompasses a broad range of methodologies from various disciplines, such as biotechnology, genetic engineering, molecular biology, molecular engineering, systems biology, membrane science, biophysics, chemical and biological engineering, electrical and computer engineering, control engineering and evolutionary biology. . (W)

The Top7 protein was one of the first proteins designed for a fold that had never been seen before in nature.

Gene functions in the minimal genome of the synthetic organism, Syn 3.

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 (holism instead of the more traditional reductionism) to biological research. When it is crossing the field of systems theory and the applied mathematics methods, it develops into the sub-branch of complex systems biology.

Particularly from year 2000 onwards, the concept has been used widely in biology in a variety of contexts. The Human Genome Project is an example of applied systems thinking in biology which has led to new, collaborative ways of working on problems in the biological field of genetics. One of the aims of systems biology is to model and discover emergent properties, properties of cells, tissues and organisms functioning as a system whose theoretical description is only possible using techniques of systems biology. These typically involve metabolic networks or cell signaling networks. (W)

An illustration of the systems approach to biology.

Overview of signal transduction pathways

Systems biomedicine, also called systems biomedical science, is the application of systems biology to the understanding and modulation of developmental and pathological processes in humans, and in animal and cellular models. Whereas systems biology aims at modeling exhaustive networks of interactions (with the long-term goal of, for example, creating a comprehensive computational model of the cell), mainly at intra-cellular level, systems biomedicine emphasizes the multilevel, hierarchical nature of the models (molecule, organelle, cell, tissue, organ, individual/genotype, environmental factor, population, ecosystem) by discovering and selecting the key factors at each level and integrating them into models that reveal the global, emergent behavior of the biological process under consideration.

Such an approach will be favorable when the execution of all the experiments necessary to establish exhaustive models is limited by time and expense (e.g., in animal models) or basic ethics (e.g., human experimentation). (W)

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. (W)

A scheme that describes how mathematical models are used in immunology.

oxicogenomics is a subdiscipline of pharmacology that deals with the collection, interpretation, and storage of information about gene and protein activity within a particular cell or tissue of an organism in response to exposure to toxic substances. Toxicogenomics combines toxicology with genomics or other high-throughput molecular profiling technologies such as transcriptomics, proteomics and metabolomics. Toxicogenomics endeavors to elucidate the molecular mechanisms evolved in the expression of toxicity, and to derive molecular expression patterns (i.e., molecular biomarkers) that predict toxicity or the genetic susceptibility to it.. (W)

The basic scheme of modern classification. Many other levels can be used; domain, the highest level within life, is both new and disputed.

In biology, taxonomy (from Ancient Greek τάξις (taxis), meaning 'arrangement', and -νομία (-nomia), meaning 'method') is the science of naming, defining (circumscribing) and classifying groups of biological organisms on the basis of shared characteristics. Organisms are grouped together into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a super-group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms.

With the advent of such fields of study as phylogenetics, cladistics, and systematics, the Linnaean system has progressed to a system of modern biological classification based on the evolutionary relationships between organisms, both living and extinct. (W)

Theoretical chemistry is the branch of chemistry which develops theoretical generalizations that are part of the theoretical arsenal of modern chemistry: for example, the concepts of chemical bonding, chemical reaction, valence, the surface of potential energy, molecular orbitals, orbital interactions, molecule activation, etc. (W)

Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology lies in understanding how the same genome can give rise to different cell types and how gene expression is regulated.. (W)

Transcriptomics method use over time. Published papers referring to RNA-Seq (black), RNA microarray (red), expressed sequence tag (blue) and serial/cap analysis of gene expression (yellow) since 1990.

Summary of SAGE (Serial analysis of gene expression). Within the organisms, genes are transcribed and spliced (in eukaryotes) to produce mature mRNA transcripts (red). The mRNA is extracted from the organism, and reverse transcriptase is used to copy the mRNA into stable double-stranded–cDNA (ds-cDNA; blue). In SAGE, the ds-cDNA is digested by restriction enzymes (at location ‘X’ and ‘X’+11) to produce 11-nucleotide "tag" fragments. These tags are concatenated and sequenced using long-read Sanger sequencing (different shades of blue indicate tags from different genes). The sequences are deconvoluted to find the frequency of each tag. The tag frequency can be used to report on transcription of the gene that the tag came from.

Summary of DNA Microarrays. Within the organisms, genes are transcribed and spliced (in eukaryotes) to produce mature mRNA transcripts (red). The mRNA is extracted from the organism and reverse transcriptase is used to copy the mRNA into stable ds-cDNA (blue). In microarrays, the ds-cDNA is fragmented and fluorescently labelled (orange). The labelled fragments bind to an ordered array of complementary oligonucleotides, and measurement of fluorescent intensity across the array indicates the abundance of a predetermined set of sequences. These sequences are typically specifically chosen to report on genes of interest within the organism's genome.

Summary of RNA-Seq. Within the organisms, genes are transcribed and spliced (in eukaryotes) to produce mature mRNA transcripts (red). The mRNA is extracted from the organism, fragmented and copied into stable ds-cDNA (blue). The ds-cDNA is sequenced using high-throughput, short-read sequencing methods. These sequences can then be aligned to a reference genome sequence to reconstruct which genome regions were being transcribed. This data can be used to annotate where expressed genes are, their relative expression levels, and any alternative splice variants.

Virology is the study of viruses – submicroscopic, parasitic particles of genetic material contained in a protein coat – and virus-like agents. It focuses on the following aspects of viruses: their structure, classification and evolution, their ways to infect and exploit host cells for reproduction, their interaction with host organism physiology and immunity, the diseases they cause, the techniques to isolate and culture them, and their use in research and therapy. Virology is a subfield of microbiology. (W)

Illustration of a SARS-CoV-2 virion.

Scanning electron micrograph of HIV-1 viruses, coloured green, budding from a lymphocyte.