Developmental biology

Developmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, differentiation and "morphogenesis", which is the process that gives rise to tissues, organs and anatomy.

Related fields of study

Embryology is a subfield, the study of organisms between the one-cell stage (generally, the zygote) and the end of the embryonic stage. Embryology was originally a more descriptive science until the 20th century. Embryology and developmental biology today deal with the various steps necessary for the correct and complete formation of the body of a living organism.

The related field of evolutionary developmental biology was formed largely in the 1990s and is a synthesis of findings from molecular developmental biology and evolutionary biology which considers the diversity of organismal form in an evolutionary context.

Perspectives

The development of a new life is a spectacular process and represents a masterpiece of temporal and spatial control of gene expression. Developmental genetics studies the effect that genes have in a phenotype, given normal or abnormal epigenetic parameters. The findings of developmental biology can help to understand developmental abnormalities such as chromosomal aberrations that cause Down syndrome. An understanding of the specialization of cells during embryogenesis has provided information on how stem cells specialize into specific tissues and organs. This information has led, for example, to the cloning of specific organs for medical purposes.Another biologically important process that occurs during development is apoptosis—programmed cell death or "suicide." Many developmental models are used to elucidate the physiology and molecular basis of this cellular process. Similarly, a deeper understanding of developmental biology can foster greater progress in the treatment of congenital disorders and diseases, e.g. studying human sex determination can lead to treatment for disorders such as congenital adrenal hyperplasia.

Developmental model organisms

Gene expression pattern determined by histochemical GUS assays in Physcomitrella patens. The Polycomb gene FIE is expressed (blue) in unfertilised egg cells of the moss Physcomitrella patens (right) and expression ceases after fertilisation in the developing diploid sporophyte (left). In situ GUS staining of two female sex organs (archegonia) of a transgenic plant expressing a translational fusion of FIE-uidA under control of the native FIE promoter

Often used model organisms in developmental biology include the following:

• Vertebrates
  • Zebrafish Danio rerio
  • Medakafish Oryzias latipes
  • Fugu (pufferfish) Takifugu rubripes
  • Frog Xenopus laevis, Xenopus tropicalis
  • Chicken Gallus gallus
  • Mouse Mus musculus (Mammalian embryogenesis)

• Invertebrates
  • Lancelet Branchiostoma lanceolatum
  • Ascidian Ciona intestinalis
  • Sea urchin Strongylocentrotus purpuratus
  • Roundworm Caenorhabditis elegans
  • Fruit fly Drosophila melanogaster (Drosophila embryogenesis)

• Plants (Plant embryogenesis)
  • Physcomitrella patens
  • Arabidopsis thaliana
  • Maize
  • Snapdragon Antirrhinum majus

• Other
  • Slime mold Dictyostelium discoideum

Studied phenomena

Cell differentiation

Differentiation is the formation of cell types, from what is originally one cell – the zygote or spore. The formation of cell types like nerve cells occurs with a number of intermediary, less differentiated cell types. A cell stays a certain cell type by maintaining a particular pattern of gene expression. This depends on regulatory genes, e.g. for transcription factors and signaling proteins. These can take part in self-perpetuating circuits in the gene regulatory network, circuits that can involve several cells that communicate with each other. External signals can alter gene expression by activating a receptor, which triggers a signaling cascade that affects transcription factors. For example, the withdrawal of growth factors from myoblasts causes them to stop dividing and instead differentiate into muscle cells.

Embryonal development

The initial stages of human embryogenesis.

Embryogenesis is the step in the life cycle after fertilisation – the development of the embryo, starting from the zygote (fertilised egg). Organisms can differ drastically in the how embryo develops, especially when they belong to different phyla. For example, embryonal development in placental mammals starts with cleavage of the zygote into eight uncommited cells, which then form a ball (morula). The outer cells become the trophectoderm or trophoblast, which will form in combination with maternal uterine endometrial tissue the placenta, needed for fetal nurturing via maternal blood, while inner cells become the inner cell mass that will form all fetal organs (the bridge between these two parts eventually forms the umbilical cord). In contrast, the fruit fly zygote first forms a sausage-shaped syncytium, which is still one cell but with many cell nuclei.

Patterning is important for determining which cells develop into which organs. This is mediated by signaling between adjacent cells by proteins on their surfaces, and by gradients of signaling secreted molecules. An example is retinoic acid, which forms a gradient in the head to tail direction in animals. Retinoic acid enters cells and activates Hox genes in a concentration-dependent manner – Hox genes differ in how much retinoic acid they require for activation and will thus show differential rostral expression boundaries, in a colinear fashion with their genomic order. As Hox genes code for transcription factors, this causes different activated combinations of both Hox and other genes in discrete anteroposterior transverse segments of the neural tube (neuromeres) and related patterns in surrounding tissues, such as branchial arches, lateral mesoderm, neural crest, skin and endoderm, in the head to tail direction. This is important for e.g. the segmentation of the spine in vertebrates.

Embryonal development does not always proceed correctly, and errors can result in birth defects or miscarriage. Often the reason is genetic (mutation or chromosome abnormality), but there can be environmental influence (like teratogens) or stochastic events. Abnormal development caused by mutation is also of evolutionary interest as it provides a mechanism for changes in body plan

Growth

Growth is the enlargement of a tissue or organism. Growth continues after the embryonal stage, and occurs through cell proliferation, enlargement of cells or accumulation of extracellular material. In plants, growth results in an adult organism that is strikingly different from the embryo. The proliferating cells tend to be distinct from differentiated cells (see stem cell and progenitor cell). In some tissues proliferating cells are restricted to specialised areas, such as the growth plates of bones. But some stem cells migrate to where they are needed, such as mesenchymal stem cells which can migrate from the bone marrow to form e.g. muscle, bone or adipose tissue. The size of an organ frequently determines its growth, as in the case of the liver which grows back to its previous size if a part is removed. Growth factors, such as fibroblast growth factors in the animal embryo and growth hormone in juvenile mammals, also control the extent of growth.

Metamorphosis

Most animals have a larval stage, with a body plan different from that of the adult organism. The larva abrubtly develops into an adult in a process called metamorphosis. For example, caterpillars (butterfly larvae) are specialized for feeding whereas adult butterflies (imagos) are specialised for flight and reproduction. When the caterpillar has grown enough, it turns into an immobile pupa. Here, the imago develops from imaginal discs found inside the larva.

Regeneration

Regeneration is the reactivation of development so that a missing body part grows back. This phenomenon has been studied particularly in salamanders, where the adults can reconstruct a whole limb after it has been amputated. Researchers hope to one day be able to induce regeneration in humans (see regenerative medicine). There is little spontaneous regeneration in adult humans, although the liver is a notable exception. Like for salamanders, the regeneration of the liver involves dedifferentiation of some cells to a more embryonal state.

Developmental systems biology

Computer simulation of multicellular development is a research methodology to understand the function of the very complex processes involved in the development of organisms. This includes simulation of cell signaling, multicell interactions and regulatory genomic networks in development of multicellular structures and processes (see French flag model or Biological Physics of the Developing Embryo for literature). Minimal genomes for minimal multicellular organisms may pave the way to understand such complex processes in vivo.

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 such as 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.

Processes

Movement of proteins

Endothelial cells under the microscope. Nuclei are stained blue with DAPI, microtubles are marked green by an antibody and actin filaments are labelled red with phalloidin.

Each type of protein is usually sent to a particular part of the cell. An important part of cell biology is the investigation of molecular mechanisms by which proteins are moved to different places inside cells or secreted from cells.

Most proteins are synthesized by ribosomes in the cytoplasm. This process is known as protein biosynthesis. Biosynthesis (also called biogenesis) is an enzyme-catalyzed process in cells of living organisms by which substrates are converted to more complex products (also simply known as protein translation). Some proteins, such as those to be incorporated in membranes (known as membrane proteins), are transported into the "rough" endoplasmic reticulum (ER) during synthesis. This process can be followed by transportation and processing in the Golgi apparatus. From the Golgi, membrane proteins can move to the plasma membrane, to other sub-cellular compartments, or they can be secreted from the cell. The ER and Golgi can be thought of as the "membrane protein synthesis compartment" and the "membrane protein processing compartment", respectively. There is a semi-constant flux of proteins through these compartments. ER and Golgi-resident proteins associate with other proteins but remain in their respective compartments. Other proteins "flow" through the ER and Golgi to the plasma membrane. Motor proteins transport membrane protein-containing vesicles along cytoskeletal tracks to distant parts of cells such as axon terminals.

Some proteins that are made in the cytoplasm contain structural features that target them for transport into mitochondria or the nucleus. Some mitochondrial proteins are made inside mitochondria and are coded for by mitochondrial DNA. In plants, chloroplasts also make some cell proteins.

Extracellular and cell surface proteins destined to be degraded can move back into intracellular compartments upon being incorporated into endocytosed vesicles some of which fuse with lysosomes where the proteins are broken down to their individual amino acids. The degradation of some membrane proteins begins while still at the cell surface when they are cleaved by secretases. Proteins that function in the cytoplasm are often degraded by proteasomes.

Other cellular processes

• Active transport and Passive transport - Movement of molecules into and out of cells.
• Autophagy - The process whereby cells "eat" their own internal components or microbial invaders.
• Adhesion - Holding together cells and tissues.
• Reproduction - Made possible by the combination of sperm made in the testiculi(contained in some male cells nucleus') and the egg made in the ovary(contained in the nucleus of a female cell). When the sperm breaks through the hard outer shell of the egg a new cell embryo is formed, which, in humans, grows to full size in 9 months.
• Cell movement: Chemotaxis, Contraction, cilia and flagella.
• Cell signaling - Regulation of cell behavior by signals from outside.
• DNA repair and Cell death
• Metabolism: Glycolysis, respiration, Photosynthesis
• Transcription and mRNA splicing - gene expression.

Internal cellular structures

Electron micrograph.

• Chloroplast - key organelle for photosynthesis (only found in plant cells)
• Cilia - motile microtubule-containing structures of eukaryotes
• Cytoplasm - contents of the main fluid-filled space inside cells
• Cytoskeleton - protein filaments inside cells
• Endoplasmic reticulum - major site of membrane protein synthesis
• Flagella - motile structures of bacteria, archaea and eukaryotes
• Golgi apparatus - site of protein glycosylation in the endomembrane system
• Lipid bilayer - fundamental organizational structure of cell membranes
• Membrane lipid and protein barrier
• Mitochondrion - major energy-producing organelle by releasing it in the form of ATP
• Nucleus - holds most of the DNA of eukaryotic cells and controls all cellular activities
• Organelle - term used for major subcellular structures
• Ribosome - RNA and protein complex required for protein synthesis in cells
• Vesicle - small membrane-bounded spheres inside cells

Techniques used to study cells

Cells may be observed under the microscope. This includes the Optical Microscope, Transmission Electron Microscope, Scanning Electron Microscope, Fluorescence Microscope, and by Confocal Microscopy.

Several different techniques exist to study cells.

• Cell culture is the basic technique of growing cells in a laboratory independent of an organism.
• Immunostaining, also known as immunohistochemistry, is a specialized histological method used to localize proteins in cells or tissue slices. Unlike regular histology, which uses stains to identify cells, cellular components or protein classes, immunostaining requires the reaction of an antibody directed against the protein of interest within the tissue or cell. Through the use of proper controls and published protocols (need to add reference links here), specificity of the antibody-antigen reaction can be achieved. Once this complex is formed, it is identified via either a "tag" attached directly to the antibody, or added in an additional technical step. Commonly used "tags" include fluorophores or enzymes. In the case of the former, detection of the location of the "immuno-stained" protein occurs via fluorescence microscopy. With an enzymatic tag, such as horse radish peroxidase, a chemical reaction is carried out that results in a dark color in the location of the protein of interest. This darkened pattern is then detected using light microscopy.
• Computational genomics is used to find patterns in genomic information
• DNA microarrays identify changes in transcript levels between different experimental conditions.
• Gene knockdown mutates a selected gene.
• In situ hybridization shows which cells are expressing a particular RNA transcript.
• PCR can be used to determine how many copies of a gene are present in a cell.
• Transfection introduces a new gene into a cell, usually an expression construct

Purification of cells and their parts Purification may be performed using the following methods:

• Cell fractionation
  • Release of cellular organelles by disruption of cells.
  • Separation of different organelles by centrifugation.
• Flow cytometry
• Immunoprecipitation
• Proteins extracted from cell membranes by detergents and salts or other kinds of chemicals.

Botany

Botany, plant science(s), phytology, or plant biology is a branch of biology that involves the scientific study of plant life. Botany covers a wide range of scientific disciplines concerned with the study of plants, algae and fungi, including structure, growth, reproduction, metabolism, development, diseases, chemical properties, and evolutionary relationships among taxonomic groups. Botany began with early human efforts to identify edible, medicinal and poisonous plants, making it one of the oldest sciences. Today botanists study over 550,000 species of living organisms.

Scope and importance of botany

Hibiscus

As with other life forms in biology, plant life can be studied from different perspectives, from the molecular, genetic and biochemical level through organelles, cells, tissues, organs, individuals, plant populations, and communities of plants. At each of these levels a botanist might be concerned with the classification (taxonomy), structure (anatomy and morphology), or function (physiology) of plant life.

Historically all living things were grouped as animals or plants, and botany covered all organisms not considered animals. Some organisms once included in the field of botany are no longer considered to belong to the plant kingdom – these include fungi (studied in mycology), lichens (lichenology), bacteria (bacteriology), viruses (virology) and single-celled algae, which are now grouped as part of the Protista. However, attention is still given to these groups by botanists, and fungi, lichens, bacteria and photosynthetic protists are usually covered in introductory botany courses.

The study of plants is vital because they are a fundamental part of life on Earth, which generates the oxygen, food, fibres, fuel and medicine that allow humans and other life forms to exist. Through photosynthesis, plants absorb carbon dioxide, a greenhouse gas that in large amounts can affect global climate. Additionally, they prevent soil erosion and are influential in the water cycle. A good understanding of plants is crucial to the future of human societies as it allows us to:

• Produce food to feed an expanding population
• Understand fundamental life processes
• Produce medicine and materials to treat diseases and other ailments
• Understand environmental changes more clearly

Paleobotanists study ancient plants in the fossil record. It is believed that early in the Earth's history, the evolution of photosynthetic plants altered the global atmosphere of the earth, changing the ancient atmosphere by oxidation.

Human nutrition

Nearly all the food we eat comes (directly and indirectly) from plants like this American long grain rice

Virtually all foods eaten come from plants, either directly from staple foods and other fruit and vegetables, or indirectly through livestock or other animals, which rely on plants for their nutrition. Plants are the fundamental base of nearly all food chains because they use the energy from the sun and nutrients from the soil and atmosphere, converting them into a form that can be consumed and utilized by animals; this is what ecologists call the first trophic level. Botanists also study how plants produce food we can eat and how to increase yields and therefore their work is important in mankind's ability to feed the world and provide food security for future generations, for example, through plant breeding. Botanists also study weeds, plants which are considered to be a nuisance in a particular location. Weeds are a considerable problem in agriculture, and botany provides some of the basic science used to understand how to minimize 'weed' impact in agriculture and native ecosystems. Ethnobotany is the study of the relationships between plants and people.

Fundamental life processes

Plants are convenient organisms in which fundamental life processes (like cell division and protein synthesis) can be studied, without the ethical dilemmas of studying animals or humans. The genetic laws of inheritanceGregor Mendel, who was studying the way pea shape is inherited. What Mendel learned from studying plants has had far reaching benefits outside of botany. Additionally, Barbara McClintock discovered 'jumping genes' by studying maize. These are a few examples that demonstrate how botanical research has an ongoing relevance to the understanding of fundamental biological processes. were discovered in this way by

Medicine and materials

Many medicinal and recreational drugs, like tetrahydrocannabinol, caffeine, and nicotine come directly from the plant kingdom. Others are simple derivatives of botanical natural products; for example, aspirin is based on the pain killer salicylic acid which originally came from the bark of willow trees. As well, the narcoticanalgesics such as morphine are derived from the opium poppy. There may be many novel cures for diseasesstimulants like coffee, chocolate, tobacco, and tea also come from plants. Most alcoholic beverages come from fermenting plants such as barley (beer), rice (sake) and grapes (wine). provided by plants, waiting to be discovered. Popular

Plants also provide us with many natural materials, such as hemp, cotton, wood, paper, linen, vegetable oils, some types of rope, and rubber. The production of silk would not be possible without the cultivation of the mulberry plant. Sugarcane, rapeseed, soy and other plants with a highly fermentable sugar or oil content have recently been put to use as sources of biofuels, which are important alternatives to fossil fuels (see biodiesel).

Environmental changes

Plants can also help us understand changes in on our environment in many ways.

• Understanding habitat destruction and species extinction is dependent on an accurate and complete catalog of plant systematics and taxonomy.
• Plant responses to ultraviolet radiation can help us monitor problems like ozone depletion.
• Analyzing pollen deposited by plants thousands or millions of years ago can help scientists to reconstruct past climates and predict future ones, an essential part of climate change research.
• Recording and analyzing the timing of plant life cycles are important parts of phenology used in climate-change research.
• Lichens, which are sensitive to atmospheric conditions, have been extensively used as pollution indicators.

In many different ways, plants can act a little like the 'miners' canary', an early warning system alerting us to important changes in our environment. In addition to these practical and scientific reasons, plants are extremely valuable as recreation for millions of people who enjoy gardening, horticultural and culinary uses of plants every day.

Etymology

From Greek βοτάνη = "pasture, grass, fodder", perhaps via the idea of a livestock keeper needing to know which plants are safe for livestock to eat.

History

The traditional tools of a botanist

Early botany

Ancient India

Early examples of plant taxonomy occur in the Rigveda, that divides plants into Vṛska (tree), Osadhi (herbs useful to humans) and Virudha (creepers), which are then further subdivided. The Atharvaveda divides plants into eight classes, Visakha (spreading branches), Manjari (leaves with long clusters), Sthambini (bushy plants), Prastanavati (which expands); Ekasṛnga (those with monopodial growth), Pratanavati (creeping plants), Amsumati (with many stalks), and Kandini (plants with knotty joints). The Taittiriya Samhitavṛksa, vana and druma (trees), visakha (shrubs with spreading branches), sasa (herbs), amsumali (a spreading or deliquescent plant), vratati (climber), stambini (bushy plant), pratanavati (creeper), and alasala (those spreading on the ground). classifies the plant kingdom into

Manusmriti – Law book of Hindus – proposed a classification of plants in eight major categories. Charaka Samhitā and Sushruta Samhita and the Vaisesikas also present an elaborate taxonomy.

Parashara, the author of Vṛksayurveda (the science of life of trees), classifies plants into Dvimatrka (Dicotyledons) and Ekamatrka (Monocotyledons). These are further classified into Samiganiya (Fabaceae), Puplikagalniya (Rutaceae), Svastikaganiya (Cruciferae), Tripuspaganiya (Cucurbitaceae), MallikaganiyaApocynaceae), and Kurcapuspaganiya (Asteraceae)^. (

Important medieval Indian works of plant physiology include the Prthviniraparyam of Udayana, Nyayavindutika of Dharmottara, Saddarsana-samuccaya of Gunaratna, and Upaskara of Sankaramisra.

Ancient Iranic people

The knowledge of medical plants and botany was considered as secret and holy by the ancient Iranic people. There is evidence of such practices in the documents that have survived from the ancient Zoroastrian writings. The practice and use of botany for medical purposes as well as various Iranic cousins and traditions is still common to this day amongst the Iranic people of the Central Asia, Near East and Europe.

Ancient China

In ancient China, the recorded listing of different plants and herb concoctions for pharmaceutical purposes spans back to at least the Warring States (481 BC-221 BC). Many Chinese writers over the centuries contributed to the written knowledge of herbal pharmaceutics. There was the Han Dynasty (202 BC-220 AD) written work of the Huangdi Neijing and the famous pharmacologist Zhang Zhongjing of the 2nd century. There was also the 11th century scientists and statesmen Su Song and Shen Kuo, who compiled treatises on herbal medicine and included the use of mineralogy.

Greco-Roman world

Among the earliest of botanical works in Europe, written around 300 B.C., are two large treatises by Theophrastus: On the History of Plants (Historia Plantarum) and On the Causes of Plants. Together these books constitute the most important contribution to botanical science during antiquity and on into the Middle Ages. Aristotle also wrote about plants. One theory about plants that Greco-Romans came up with about plants was that they ate soil for nutrients.

The Roman medical writer Pedanius Dioscorides (ca.40-90) provides important evidence on Greek and Roman knowledge of medicinal plants. Dioscorides is famous for writing a five volume book in his native Greek Περί ύλης ιατρικής (De Materia Medica - in the Latin translation) that is one of the most influential herbal books in history. In fact, it remained in use until about CE 1600. Approximately 1300-1400 different plant species were known under Roman reign^.

Medieval botany

The earliest known work from the Muslim world dedicated to the study of agriculture was Ibn Wahshiyya's Nabatean Agriculture, which also dealt with the related field of botany and was also an early cookbook.

The Kurdish biologist Abū Ḥanīfa Dīnawarī (828-896) is considered the founder of Arabic botany for his Book of Plants, in which he described at least 637 plants and discussed plant development from germination to death, describing the phases of plant growth and the production of flowers and fruit.

Theophrastus’s Historia Plantarum served as a reference point in botany for many centuries, and was further developed around 1200 A.D. by Giovanni Bodeo da Stapelio, who added a commentarius and drawings: see Historia Plantarum —Selected pages of a 17th century edition of the 1200 A.D. version (in Italian).

Ibn Bassal is known for his famous work named The Classification of Soils. Al-Asma'i was the earliest known Arab biologist, botanist and zoologist. al-Masihi was the first to recognize the science of Botany.^{[citation needed]}

In the early 13th century, the Andalusian-Arabian biologist Abu al-Abbas al-Nabati developed an early scientific method for botany, introducing empirical and experimental techniques in the testing, description and identification of numerous materia medica, and separating unverified reports from those supported by actual tests and observations.His student Ibn al-Baitar (d. 1248) wrote a pharmaceutical encyclopedia describing 1,400 plants, foods, and drugs, 300 of which were his own original discoveries. A Latin translation of his work was useful to European biologists and pharmacists in the 18th and 19th centuries.

Early modern botany

Crantz's Classis cruciformium..., 1769

German physician Leonhart Fuchs (1501–1566) was one of the three founding fathers of botany, along with Otto Brunfels (1489- 1534) and Hieronymus Bock (1498–1554) (also called Hieronymus Tragus).^[10]

Valerius Cordus (1515–1554) authored one of the greatest pharmacopoeias and one of the most celebrated herbals in history, Dispensatorium (1546).^[11] As early as the 16th century, the Italian Ulisse Aldrovandi was scientifically researching plants. In 1665, using an early microscope, Robert Hooke discovered cells in cork, and a short time later in living plant tissue. The Germans Jacob Theodor Klein and Leonhart Fuchs, the Swiss Conrad von Gesner, and the British author Nicholas Culpeper published herbals that gave information on the medicinal uses of plants.

During the 18th century systems of classification became deliberately artificial and served only for the purpose of identification. These classifications are comparable to diagnostic keys, where taxa are artificially grouped in pairs by few, easily recognisable characters. The sequence of the taxa in keys is often totally unrelated to their natural or phyletic groupings. In the 18th century an increasing number of new plants had arrived in Europe, from newly discovered countries and the European colonies worldwide, and a larger amount of plants became available for study.

In 1754 Carl von Linné (Carl Linnaeus) divided the plant Kingdom into 25 classes. One, the Cryptogamia, included all the plants with concealed reproductive parts (algae, fungi, mosses and liverworts and ferns).more natural affinities between plants, than the sexual system of Linnaeus indicated. Adanson (1763), de JussieuCandolle (1819) all proposed various alternative natural systems that were widely followed. The ideas of natural selection as a mechanism for evolution required adaptations to the Candollean system, which started the studies on evolutionary relationships and phylogenetic classifications of plants. (1789), and

Modern botany

A considerable amount of new knowledge today is being generated from studying model plants like Arabidopsis thaliana. This weedy species in the mustard family was one of the first plants to have its genomerice (Oryza sativa) genome, its relatively small genome, and a large international research community have made rice an important cereal/grass/monocot model.^[13] Another grass species, Brachypodium distachyon is also emerging as an experimental model for understanding the genetic, cellular and molecular biology of temperate grasses. Other commercially important staple foods like wheat, maize, barley, rye, pearl millet and soybean are also having their genomes sequenced. Some of these are challenging to sequence because they have more than two haploid (n) sets of chromosomes, a condition known as polyploidy, common in the plant kingdom. Chlamydomonas reinhardtii (a single-celled, green alga) is another plant model organism that has been extensively studied and provided important insights into cell biology. sequenced. The sequencing of the

In 1998 the Angiosperm Phylogeny Group published a phylogeny of flowering plants based on an analysis of DNA sequences from most families of flowering plants. As a result of this work, major questions such as which families represent the earliest branches in the genealogy of angiosperms are now understood. Investigating how plant species are related to each other allows botanists to better understand the process of evolution in plants.

Subdisciplines of botany

Agronomy — Application of plant science to crop production Bryology — Mosses, liverworts, and hornworts Economic botany — Study of plants of economic use or value Ethnobotany — Relationship between humans and plants Forestry — Forest management and related studies Horticulture — Cultivated plants Lichenology — The study of lichens Paleobotany — Fossil plants Palynology — Pollen and spores

Phycology — Algae Phytochemistry — Plant secondary chemistry and chemical processes Phytopathology — Plant diseases Plant anatomy — Cell and tissue structure Plant ecology — Role of plants in the environment Plant genetics — Genetic inheritance in plants Plant morphology — Structure and life cycles Plant physiology — Life functions of plants Plant systematics — Classification and naming of plants

Notable botanists

Further information: List of botanists

• Ibn al-Baitar (d. 1248), Andalusian-Arab scientist, botanist, pharmacist, physician, and author of one of the largest botanical encyclopedias.
• L.J.F. Brimble (1904–1965), English botanist and editor of Nature magazine
• Abu al-Abbas al-Nabati (c. 1200), Andalusian-Arab botanist and agricultural scientist, and a pioneer in experimental botany.
• Aimé Bonpland (1773–1858), French explorer and botanist, who accompanied Alexander von Humboldt during five years of travel in Latin America.
• Luther Burbank (1849–1926), American botanist, horticulturist, and a pioneer in agricultural science.
• Augustin Pyramus de Candolle (1778–1841), He originated the idea of "Nature's war", which influenced Charles Darwin.
• Abū Ḥanīfa Dīnawarī (828-896), Persian botanist, historian, geographer, astronomer, mathematician, and founder of Arabic botany.
• David Douglas (1799–1834), Scottish botanical explorer of North America and China, who imported many ornamental plants into Europe.
• Joseph Dalton Hooker (1817–1911), English botanist and explorer. Second winner of Darwin Medal.
• Pedanius Dioscorides (ca. 40-90 AD), physician, pharmacologist, toxicologist and botanist, author of Περὶ ὕλης ἰατρικής (Latin: De Materia Medica, English: "Regarding Medical Matters")
• Thomas Henry Huxley (1825–1895), English biologist, known as "Darwin's Bulldog" for his advocacy of Charles Darwin's theory of evolution. Third winner of Darwin Medal.
• Carl Linnaeus (1707–1778), Swedish botanist, physician and zoologist who laid the foundations for the modern scheme of Binomial nomenclature. He is known as the father of modern taxonomy, and is also considered one of the fathers of modern ecology.
• Gregor Johann Mendel (1822–1884), Augustinian priest and scientist, and is often called the father of genetics for his study of the inheritance of traits in pea plants.
• Charles Sprague Sargent (1841–1927), American botanist, the first director of the Arnold ArboretumHarvard University. at
• Carlos Muñoz Pizarro (1913–1976), Chilean botanist, known for his studies of the Chilean flora, and its conservation.
• Richard Spruce (1817–1893), English botanist and explorer who carried out a detailed study of the Amazon flora.
• Agustín Stahl (1842–1917), conducted investigations and experiments in the fields of ethnology, and zoology in the Caribbean region.
• George Ledyard Stebbins, Jr. (1906–2000), widely regarded as one of the leading evolutionary biologists of the 20th century, developed a comprehensive synthesis of plant evolution incorporating genetics.
• Theophrastus (c. 371 – c. 287 BC), father of botany, established botanical science through his lecture notes, Enquiry into Plants.
• Leonardo da Vinci (1452–1519), Italian polymath; a scientist, mathematician, engineer, inventor, anatomist, painter, sculptor, architect, botanist, musician and writer.

Biophysics

Biophysics is an interdisciplinary science that uses the methods of physical science to study biological systems. Studies included under the branches of biophysics span all levels of biological organization, from the molecular scale to whole organisms and ecosystems. Biophysical research shares significant overlap with biochemistry, nanotechnology, bioengineering, agrophysics and systems biology.

Molecular biophysics typically addresses biological questions that are similar to those in biochemistry and molecular biology, but the questions are approached quantitatively. Scientists in this field conduct research concerned with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis, as well as how these interactions are regulated. A great variety of techniques are used to answer these questions.

Fluorescent imaging techniques, as well as electron microscopy, x-ray crystallography, NMR spectroscopy and atomic force microscopy (AFM) are often used to visualize structures of biological significance. Conformational change in structure can be measured using techniques such as dual polarisation interferometry and circular dichroism. Direct manipulation of molecules using optical tweezers or AFM can also be used to monitor biological events where forces and distances are at the nanoscale. Molecular biophysicists often consider complex biological events as systems of interacting units which can be understood through statistical mechanics, thermodynamics and chemical kinetics. By drawing knowledge and experimental techniques from a wide variety of disciplines, biophysicists are often able to directly observe, model or even manipulate the structures and interactions of individual molecules or complexes of molecules.

In addition to traditional (i.e. molecular and cellular) biophysical topics like structural biology or enzyme kinetics, modern biophysics encompasses an extraordinarily broad range of research. It is becoming increasingly common for biophysicists to apply the models and experimental techniques derived from physics, as well as mathematics and statistics, to larger systems such as tissues, organs, populations and ecosystems.

Focus as a subfield

Biophysics often does not have university-level departments of its own, but has presence as groups across departments within the fields of molecular biology, biochemistry, chemistry, computer science, mathematics, medicine, pharmacology, physiology, physics, and neuroscience. What follows is a list of examples of how each department applies its efforts toward the study of biophysics. This list is hardly all inclusive. Nor does each subject of study belong exclusively to any particular department. Each academic institution makes its own rules and there is much overlap between departments.

• Biology and molecular biology - Almost all forms of biophysics efforts are included in some biology department somewhere. To include some: gene regulation, single protein dynamics, bioenergetics, patch clamping, biomechanics.
• Structural biology - Ångstrom-resolution structures of proteins, nucleic acids, lipids, carbohydrates, and complexes thereof.
• Biochemistry and chemistry - biomolecular structure, siRNA, nucleic acid structure, structure-activity relationships.
• Computer science - Neural networks, biomolecular and drug databases.
• Computational chemistry - molecular dynamics simulation, molecular docking, quantum chemistry
• Bioinformatics - sequence alignment, structural alignment, protein structure prediction
• Mathematics - graph/network theory, population modeling, dynamical systems, phylogenetics.
• Medicine and neuroscience - tackling neural networks experimentally (brain slicing) as well as theoretically (computer models), membrane permitivity, gene therapy, understanding tumors.
• Pharmacology and physiology - channel biology, biomolecular interactions, cellular membranes, polyketides.
• Physics - biomolecular free energy, stochastic processes, covering dynamics.
• Quantum biophysics involves quantum information processing of coherent states, entanglement between coherent protons and transcriptase components, and replication of decohered isomers to yield time-dependent base substitutions. These studies imply applications in quantum computing.
• Agronomy Agriculture

Many biophysical techniques are unique to this field. Research efforts in biophysics are often initiated by scientists who were traditional physicists, chemists, and biologists by training.