In biology, a gene is a sequence of nucleotides in DNA or RNA that codes for a molecule that has a function. During gene expression, the DNA is first copied into RNA; the RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait; these genes make up different DNA sequences called genotypes. Genotypes along with developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions; some genetic traits are visible, such as eye color or number of limbs, some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life. Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population; these alleles encode different versions of a protein, which cause different phenotypical traits.
Usage of the term "having a gene" refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection / survival of the fittest and genetic drift of the alleles; the concept of a gene continues to be refined. For example, regulatory regions of a gene can be far removed from its coding regions, coding regions can be split into several exons; some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression; the term gene was introduced by Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1909. It is inspired by the ancient Greek: γόνος, that means offspring and procreation; the existence of discrete inheritable units was first suggested by Gregor Mendel. From 1857 to 1864, in Brno, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring.
He described these mathematically as 2n combinations where n is the number of differing characteristics in the original peas. Although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics; this description prefigured Wilhelm Johannsen's distinction between phenotype. Mendel was the first to demonstrate independent assortment, the distinction between dominant and recessive traits, the distinction between a heterozygote and homozygote, the phenomenon of discontinuous inheritance. Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance, which suggested that each parent contributed fluids to the fertilisation process and that the traits of the parents blended and mixed to produce the offspring. Charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan and genesis / genos. Darwin used the term gemmule to describe hypothetical particles. Mendel's work went unnoticed after its first publication in 1866, but was rediscovered in the late 19th century by Hugo de Vries, Carl Correns, Erich von Tschermak, who reached similar conclusions in their own research.
In 1889, Hugo de Vries published his book Intracellular Pangenesis, in which he postulated that different characters have individual hereditary carriers and that inheritance of specific traits in organisms comes in particles. De Vries called these units "pangenes", after Darwin's 1868 pangenesis theory. Sixteen years in 1905, Wilhelm Johannsen introduced the term'gene' and William Bateson that of'genetics' while Eduard Strasburger, amongst others, still used the term'pangene' for the fundamental physical and functional unit of heredity. Advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s; the structure of DNA was studied by Rosalind Franklin and Maurice Wilkins using X-ray crystallography, which led James D. Watson and Francis Crick to publish a model of the double-stranded DNA molecule whose paired nucleotide bases indicated a compelling hypothesis for the mechanism of genetic replication.
In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities, indivisible by recombination and arranged like beads on a string. The experiments of Benzer using mutants defective in the rII region of bacteriophage T4 showed that individual genes have a simple linear structure and are to be equivalent to a linear section of DNA. Collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, transcribed from DNA; this dogma has since been shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics. In 1972, Walter Fiers and his team were the first to determine the sequence of a gene: that of Bacteriophage MS2 coat protein; the subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing and turned it into a routine laboratory tool.
An automated version of the Sanger method was used in early phases of the
In anatomy, a lobe is a clear anatomical division or extension of an organ that can be determined without the use of a microscope at the gross anatomy level. This is in contrast to the much smaller lobule, a clear division only visible under the microscope. Interlobar ducts connect; the four lobes of the human cerebral cortex the frontal lobe the parietal lobe the occipital lobe the temporal lobe The three lobes of the human cerebellum the flocculonodular lobe the anterior lobe the posterior lobe The two lobes of the thymus The two and three lobes of the lungs Left lung: superior and inferior Right lung: superior and inferior The four lobes of the liver Left lobe of liver Right lobe of liver Quadrate lobe of liver Caudate lobe of liver The renal lobes of the kidney the cortical lobules of the kidney the testicular lobules the lobules of the mammary gland the lobules of the lung the lobules of the thymus
Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most used by cells to repair harmful breaks that occur on both strands of DNA, known as double-strand breaks. Homologous recombination produces new combinations of DNA sequences during meiosis, the process by which eukaryotes make gamete cells, like sperm and egg cells in animals; these new combinations of DNA represent genetic variation in offspring, which in turn enables populations to adapt during the course of evolution. Homologous recombination is used in horizontal gene transfer to exchange genetic material between different strains and species of bacteria and viruses. Although homologous recombination varies among different organisms and cell types, most forms involve the same basic steps. After a double-strand break occurs, sections of DNA around the 5' ends of the break are cut away in a process called resection. In the strand invasion step that follows, an overhanging 3' end of the broken DNA molecule "invades" a similar or identical DNA molecule, not broken.
After strand invasion, the further sequence of events may follow either of two main pathways discussed below. Homologous recombination that occurs during DNA repair tends to result in non-crossover products, in effect restoring the damaged DNA molecule as it existed before the double-strand break. Homologous recombination is conserved across all three domains of life as well as viruses, suggesting that it is a nearly universal biological mechanism; the discovery of genes for homologous recombination in protists—a diverse group of eukaryotic microorganisms—has been interpreted as evidence that meiosis emerged early in the evolution of eukaryotes. Since their dysfunction has been associated with increased susceptibility to several types of cancer, the proteins that facilitate homologous recombination are topics of active research. Homologous recombination is used in gene targeting, a technique for introducing genetic changes into target organisms. For their development of this technique, Mario Capecchi, Martin Evans and Oliver Smithies were awarded the 2007 Nobel Prize for Physiology or Medicine.
Researching the plasmid-induced DSB, using γ-irradiation in the 1970s-1980s, led to experiments using endonucleases to cut chromosomes for genetic engineering of mammalian cells, where nonhomologous recombination is more frequent than in yeast. In the early 1900s, William Bateson and Reginald Punnett found an exception to one of the principles of inheritance described by Gregor Mendel in the 1860s. In contrast to Mendel's notion that traits are independently assorted when passed from parent to child—for example that a cat's hair color and its tail length are inherited independent of each other—Bateson and Punnett showed that certain genes associated with physical traits can be inherited together, or genetically linked. In 1911, after observing that linked traits could on occasion be inherited separately, Thomas Hunt Morgan suggested that "crossovers" can occur between linked genes, where one of the linked genes physically crosses over to a different chromosome. Two decades Barbara McClintock and Harriet Creighton demonstrated that chromosomal crossover occurs during meiosis, the process of cell division by which sperm and egg cells are made.
Within the same year as McClintock's discovery, Curt Stern showed that crossing over—later called "recombination"—could occur in somatic cells like white blood cells and skin cells that divide through mitosis. In 1947, the microbiologist Joshua Lederberg showed that bacteria—which had been assumed to reproduce only asexually through binary fission—are capable of genetic recombination, more similar to sexual reproduction; this work established E. coli as a model organism in genetics, helped Lederberg win the 1958 Nobel Prize in Physiology or Medicine. Building on studies in fungi, in 1964 Robin Holliday proposed a model for recombination in meiosis which introduced key details of how the process can work, including the exchange of material between chromosomes through Holliday junctions. In 1983, Jack Szostak and colleagues presented a model now known as the DSBR pathway, which accounted for observations not explained by the Holliday model. During the next decade, experiments in Drosophila, budding yeast and mammalian cells led to the emergence of other models of homologous recombination, called SDSA pathways, which do not always rely on Holliday junctions.
Much of the work identifying proteins involved in the process and determining their mechanisms has been performed by a number of individuals including James Haber, Patrick Sung, Stephen Kowalczykowski, others. Homologous recombination is essential to cell division in eukaryotes like plants, animals and protists. In cells that divide through mitosis, homologous recombination repairs double-strand breaks in DNA caused by ionizing radiation or DNA-damaging chemicals. Left unrepaired, these double-strand breaks can cause large-scale rearrangement of chromosomes in somatic cells, which can in turn lead to cancer. In addition to repairing DNA, homologous recombination helps produce genetic diversity when cells divide in meiosis to become specialized gamete cells—sperm or egg cells in animals, pollen o
Plants are multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. Plants were treated as one of two kingdoms including all living things that were not animals, all algae and fungi were treated as plants. However, all current definitions of Plantae exclude the fungi and some algae, as well as the prokaryotes. By one definition, plants form the clade Viridiplantae, a group that includes the flowering plants and other gymnosperms and their allies, liverworts and the green algae, but excludes the red and brown algae. Green plants obtain most of their energy from sunlight via photosynthesis by primary chloroplasts that are derived from endosymbiosis with cyanobacteria, their chloroplasts contain b, which gives them their green color. Some plants are parasitic or mycotrophic and have lost the ability to produce normal amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although asexual reproduction is common.
There are about 320 thousand species of plants, of which the great majority, some 260–290 thousand, are seed plants. Green plants provide a substantial proportion of the world's molecular oxygen and are the basis of most of Earth's ecosystems on land. Plants that produce grain and vegetables form humankind's basic foods, have been domesticated for millennia. Plants have many cultural and other uses, as ornaments, building materials, writing material and, in great variety, they have been the source of medicines and psychoactive drugs; the scientific study of plants is known as a branch of biology. All living things were traditionally placed into one of two groups and animals; this classification may date from Aristotle, who made the distincton between plants, which do not move, animals, which are mobile to catch their food. Much when Linnaeus created the basis of the modern system of scientific classification, these two groups became the kingdoms Vegetabilia and Animalia. Since it has become clear that the plant kingdom as defined included several unrelated groups, the fungi and several groups of algae were removed to new kingdoms.
However, these organisms are still considered plants in popular contexts. The term "plant" implies the possession of the following traits multicellularity, possession of cell walls containing cellulose and the ability to carry out photosynthesis with primary chloroplasts; when the name Plantae or plant is applied to a specific group of organisms or taxon, it refers to one of four concepts. From least to most inclusive, these four groupings are: Another way of looking at the relationships between the different groups that have been called "plants" is through a cladogram, which shows their evolutionary relationships; these are not yet settled, but one accepted relationship between the three groups described above is shown below. Those which have been called "plants" are in bold; the way in which the groups of green algae are combined and named varies between authors. Algae comprise several different groups of organisms which produce food by photosynthesis and thus have traditionally been included in the plant kingdom.
The seaweeds range from large multicellular algae to single-celled organisms and are classified into three groups, the green algae, red algae and brown algae. There is good evidence that the brown algae evolved independently from the others, from non-photosynthetic ancestors that formed endosymbiotic relationships with red algae rather than from cyanobacteria, they are no longer classified as plants as defined here; the Viridiplantae, the green plants – green algae and land plants – form a clade, a group consisting of all the descendants of a common ancestor. With a few exceptions, the green plants have the following features in common, they undergo closed mitosis without centrioles, have mitochondria with flat cristae. The chloroplasts of green plants are surrounded by two membranes, suggesting they originated directly from endosymbiotic cyanobacteria. Two additional groups, the Rhodophyta and Glaucophyta have primary chloroplasts that appear to be derived directly from endosymbiotic cyanobacteria, although they differ from Viridiplantae in the pigments which are used in photosynthesis and so are different in colour.
These groups differ from green plants in that the storage polysaccharide is floridean starch and is stored in the cytoplasm rather than in the plastids. They appear to have had a common origin with Viridiplantae and the three groups form the clade Archaeplastida, whose name implies that their chloroplasts were derived from a single ancient endosymbiotic event; this is the broadest modern definition of the term'plant'. In contrast, most other algae not only have different pigments but have chloroplasts with three or four surrounding membranes, they are not close relatives of the Archaeplastida having acquired chloroplasts separately from ingested or symbiotic green and red algae. They are thus not included in the broadest modern definition of the plant kingdom, although they were in the past; the green plants or Viridiplantae were traditionally divided into the green algae (including
Heterospory is the production of spores of two different sizes and sexes by the sporophytes of land plants. The smaller of these, the microspore, is male and the larger megaspore is female. Heterospory evolved during the Devonian period from isospory independently in several plant groups: the clubmosses, the arborescent horsetails, progymnosperms; this occurred as part of the process of evolution of the timing of sex differentiation. Heterospory developed due to natural selection pressures that encouraged an increase in propagule size; this may first have led to an increase in spore size and resulted in the species producing larger megaspores as well as smaller microspores. Heterospory evolved from homospory many times, but the species in which it first appeared are now extinct. Heterosporic plants that produce seeds are their most widespread descendants. Seed plants constitute the largest subsection of heterosporic plants. Microspores are haploid spores that in endosporic species contain the male gametophyte, carried to the megaspores by wind, water currents or animal vectors.
Microspores are nearly all nonflagellated, are therefore not capable of active movement. The morphology of the microspore consists of an outer double walled structures surrounding the dense cytoplasm and central nucleus. Megaspores contain the female gametophytes in heterosporic plant species, they develop archegonia that produce egg cells that are fertilized by sperm of the male gametophyte originating from the microspore. This results in the formation of a fertilized diploid zygote, that develops into the sporophyte embryo. While heterosporous plants produce fewer megaspores, they are larger than their male counterparts. In exosporic species, the smaller spores germinate into free-living male gametophytes and the larger spores germinate into free-living female gametophytes. In endosporic species, the gametophytes of both sexes are highly reduced and contained within the spore wall; the microspores of both exosporic and endosporic species are free-sporing, distributed by wind, water or animal vectors, but in endosporic species the megaspores and the megagametophyte contained within are retained and nurtured by the sporophyte phase.
Endosporic species are thus dioecious, a condition that promotes outcrossing. Some exosporic species produce micro- and megaspores in the same sporangium, a condition known as homoangy, while in others the micro- and megaspores are produced in separate sporangia; these may both be borne on the same monoecious sporophyte or on different sporophytes in dioicous species. Heterospory was a key event in the evolution of surviving plants; the retention of megaspores and the dispersal of microspores allow for both dispersal and establishment reproductive strategies. This adaptive ability of heterospory increases reproductive success as any type of environment favors having these two strategies. Heterospory stops self-fertilization from occurring in a gametophyte, but does not stop two gametophytes that originated from the same sporophyte from mating; this specific type of self-fertilization is termed as sporophytic selfing, it occurs most among angiosperms. While heterospory stops extreme inbreeding from occurring, it does not prevent inbreeding altogether as sporophytic selfing can still occur.
A complete model for the origin of heterospory, known as the Haig-Westoby model, establishes a connection between minimum spore size and successful reproduction of bisexual gametophytes. For the female function, as minimum spore size increases so does the chance for successful reproduction. For the male function, reproductive success does not change as the minimum spore size increases
Selaginella is the sole genus of vascular plants in the family Selaginellaceae, the spikemosses or lesser clubmosses. This family is distinguished from Lycopodiaceae by having scale-leaves bearing a ligule and by having spores of two types, they are sometimes included in an informal paraphyletic group called the "fern allies". S. moellendorffii is an important model organism. Its genome has been sequenced by the United States Department of Energy's Joint Genome Institute; the name Selaginella was erected by Palisot de Beauvois for the species Selaginella selaginoides, which turns out to be a clade, sister to all other Selaginellas, so any definitive subdivision of the species leaves two taxa in Selaginella, with the hundreds of other species in new or resurrected genera. Selaginella occurs in the tropical regions of the world, with a handful of species to be found in the arctic-alpine zones of both hemispheres. Selaginella species are creeping or ascendant plants with simple, scale-like leaves on branching stems from which roots arise.
The stems are aerial, horizontally creeping on the substratum, sub erect. The vascular steles are polystelic protosteles. Stem section shows the presence of more than two protosteles; each stele is made up of exarch xylem in centre. The steles are connected with the cortex by means of many tube-like structures called trabeculae, which are modified endodermal cells with casparian strips on their lateral walls; the stems contain no pith. Unusually for the lycopods, which have microphylls with a single unbranched vein, the microphylls of Selaginella species contain a branched vascular trace. In Selaginella, each microphyll and sporophyll has a small scale-like outgrowth called a ligule at the base of the upper surface; the plants are heterosporous with spores of two different size classes, known as megaspores and microspores. Under dry conditions, some species of Selaginella can survive dehydration. In this state, they may roll up into brown balls and be uprooted, but can rehydrate under moist conditions, become green again and resume growth.
This phenomenon is known as poikilohydry, poikilohydric plants such as Selaginella bryopteris are sometimes referred to as resurrection plants. Some scientists still place the Selaginellales in the class Lycopodiopsida; some modern authors recognize three generic divisions of Selaginella: Selaginella, Bryodesma Sojak 1992, Lycopodioides Boehm 1760. Lycopodioides would include the North American species S. apoda and S. eclipes, while Bryodesma would include S. rupestris. Stachygynandrum is sometimes used to include the bulk of species; the first major attempt to define and subdivide the group was by Palisot de Beauvois in 1803-1805. He established the genus Selaginella as a monotypic genus, placed the bulk of species in Stachygynandrum. Gymnogynum was another monotypic genus, but that name is superseded by his own earlier name of Didiclis; this turns out, today, to be a group of around 45-50 species known as the Articulatae, since his genus Didiclis/Gymnogynum was based on Selaginella plumosa. He described the genus Diplostachyum to include a group of species similar to Selaginella apoda.
Spring inflated the genus Selaginella to hold all selaginelloid species four decades later. Phylogenetic studies by Korall & Kenrick determined that the Euselaginella group, comprising the type species, Selaginella selaginoides and a related Hawaiian species, Selaginella deflexa, is a basal and anciently diverging sister to all other Selaginella species. Beyond this, their study split the remainder of species into two broad groups, one including the Bryodesma species, the Articulatae, section Ericetorum Jermy and others, the other centered on the broad Stachygynandrum group. In the Manual of Pteridology, the following classification was used by Walton & Alston: genus: Selaginella subgenus: Euselaginella group: selaginoides group: pygmaea group: uliginosa group: rupestris subgenus: Stachygynandrum series: Decumbentes series: Ascendentes series: Sarmentosae series: Caulescentes series: Circinatae series: Articulatae subgenus: Homostachys subgenus: HeterostachysHowever, this is now known to be paraphyletic in most of its groupings.
Two recent classifications, employing modern methods of phylogenetic analysis, are as follows: genus: Selaginella subgenus: Selaginella clade: "Rhizophoric clade" clade A subgenus Rupestrae subgenus Lepidophyllae subgenus Gymnogynum subgenus Exaltatae subgenus Ericetorum clade B subgenus Stachygynandrum genus: Selaginella subgenus: Selaginella Type: Selaginella selaginoides P. Beauv. Ex Mart. & Schrank subgenus: Boreoselaginella Type: Selaginella sanguinolenta Spring subgenus: Ericetorum Type: Selaginella uliginosa Spring section: Lyallia Type: Selaginella uliginosa Spring section: Myosurus Type: Selaginella myosurus Alston section: Megalosporarum Type: Selaginella exaltata Spring section: Articulatae Type: Selaginella kraussiana A. Braun section: Homoeophyllae Type: Selaginella rupestris Spring section: Lepidophyllae Type: Selaginella lepidophylla Spring subgenus: Pulviniella Type: Selaginella pulvinata Maxim subgenus: Heterostachys Type: Selaginella heterostachys Baker section: Oligomacrosporangiatae Type: Selaginella uncinata Spring section: Auriculatae Type: Selaginella douglasii