Portal:Biology/Previous articles
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This is a list of featured articles from the Biology portal, sorted in reverse-chronological order.
[edit] 3 December 2007
Invasive species is a phrase with several definitions. The first definition expresses the phrase in terms of non-indigenous species (e.g. plants or animals) that adversely affect the habitats they invade economically, environmentally or ecologically. It has been used in this sense by government organizations as well as conservation groups such as the IUCN. The second definition broadens the boundaries to include both native and non-native species that heavily colonize a particular habitat.
The third definition is an expansion of the first and defines an invasive species as a widespread non-indigenous species. This last definition is arguably too broad as not all non-indigenous species necessarily have an adverse effect on their adopted environment. An example of this broader use would include the claim that the common goldfish (Carassius auratus) is invasive. True, it is common outside of its range globally but it almost never appears in harmful densities.
Due to the ambiguity of its definition, the phrase - invasive species - is often criticized as an imprecise term within the field of ecology. This article concerns the first two definitions; for the third, see introduced species.
[edit] 23 April 2007
Natural selection is the evolutionary process by which favorable traits that are heritable become more common in successive generations of a population of reproducing organisms, and unfavorable traits that are heritable become less common. Natural selection acts on the phenotype, or observable characteristics of an organism, such that individuals with favorable phenotypes are more likely to survive and reproduce than those with less favorable phenotypes. If these phenotypes have a genetic basis, then the genotype associated with the favorable phenotype will increase in frequency in the next generation. Over time, this process can result in adaptations that specialize organisms for particular ecological niches and may eventually result in the emergence of new species.
Natural selection is one of the cornerstones of modern biology. The term was introduced by Charles Darwin in his groundbreaking 1859 book The Origin of Species in which natural selection was described by analogy to artificial selection, a process by which individuals with traits considered desirable by human breeders are systematically favored for reproduction. The concept of natural selection was originally developed in the absence of a theory of inheritance; at the time of Darwin's writing, nothing was known of modern genetics. Although Gregor Mendel, whose work is now considered the foundation of modern genetics, was a contemporary of Darwin's, this work would lie in obscurity until the early 20th century. The union of traditional Darwinian evolution with subsequent discoveries in classical and later molecular genetics is termed the modern evolutionary synthesis. Although other mechanisms of molecular evolution, such as the neutral theory advanced by Motoo Kimura, have been identified as important causes of genetic diversity, natural selection remains the single primary explanation for adaptive evolution.
[edit] 2007-01-27
Krill are shrimp-like marine invertebrate animals. These small crustaceans are important organisms of the zooplankton, particularly as food for baleen whales, mantas, whale sharks, crabeater seals and other seals, and a few seabird species that feed almost exclusively on them. Another name is euphausiids, after their taxonomic order Euphausiacea. The name krill comes from the Norwegian word krill meaning "young fry of fish".
Krill occur in all oceans of the world. They are considered keystone species near the bottom of the food chain because they feed on phytoplankton and to a lesser extent zooplankton, converting these into a form suitable for many larger animals for whom krill makes up the largest part of their diet. In the Southern Ocean, one species, the Antarctic Krill, Euphausia superba, makes up a biomass of hundreds of millions of tonnes, similar to the entire human consumption of animal protein. Over half of this biomass is eaten by whales, seals, penguins, squid and fish each year, and replaced by growth and reproduction. Most of the species display large daily vertical migrations making a significant amount of biomass available as food for predators near the surface at night and in deeper waters during the day.
Commercial fishing of krill is done in the Southern Ocean and in the waters around Japan. The total global production amounts to 150 – 200,000 tonnes annually, most of this from the Scotia Sea. Most krill is used for aquaculture and aquarium feeds, as bait in sport fishing, or in the pharmaceutical industry. In Japan and Russia, krill is also used for human consumption and known as okiami (オキアミ) in Japan.
[edit] 2006-10-16
In bioinformatics, a sequence alignment is a way of arranging the primary sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that residues with identical or similar characters are aligned in successive columns.
If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In protein sequence alignment, the degree of similarity between amino acids occupying a particular position in the sequence can be interpreted as a rough measure of how conserved a particular region or sequence motif is among lineages. The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence, suggest that this region has structural or functional importance. Although DNA and RNA nucleotide bases are more similar to each other than to amino acids, the conservation of base pairing can indicate a similar functional or structural role. Sequence alignment can be used for non-biological sequences, such as identifying similarities in a series of letters and words present in human language.
Very short or very similar sequences can be aligned by hand; however, most interesting problems require the alignment of lengthy, highly variable or extremely numerous sequences that cannot be aligned solely by human effort. Instead, human knowledge is primarily applied in constructing algorithms to produce high-quality sequence alignments, and occasionally in adjusting the final results to reflect patterns that are difficult to represent algorithmically (especially in the case of nucleotide sequences). Computational approaches to sequence alignment generally fall into two categories: global alignments and local alignments. Calculating a global alignment is a form of global optimization that "forces" the alignment to span the entire length of all query sequences. By contrast, local alignments identify regions of similarity within long sequences that are often widely divergent overall. Local alignments are often preferable, but can be more difficult to calculate because of the additional challenge of identifying the regions of similarity. A variety of computational algorithms have been applied to the sequence alignment problem, including slow but formally optimizing methods like dynamic programming and efficient heuristic or probabilistic methods designed for large-scale database search.
[edit] 2006-08-16
Black Pepper (Piper nigrum) is a flowering vine in the family Piperaceae, cultivated for its fruit, which is usually dried and used as a spice and seasoning. The same fruit is also used to produce white pepper and green pepper. Black pepper is native to South India and is extensively cultivated there and elsewhere in tropical regions. The fruit, known as a peppercorn when dried, is a small drupe five millimetres in diameter, dark red when fully mature, containing a single seed.
Dried, ground pepper is one of the most common spices in European cuisine and its descendants, having been known and prized since antiquity for both its flavour and its use as a medicine. The spiciness of black pepper is due to the chemical piperine. Ground black peppercorn, usually referred to simply as "pepper", may be found on nearly every dinner table in some parts of the world, often alongside table salt.
[edit] 2006-07-25
AIDS is a collection of symptoms and infections in humans resulting from the specific damage to the immune system caused by infection with the human immunodeficiency virus (HIV), the late stage of which leaves individuals prone to opportunistic infections and tumours. Although treatments for AIDS and HIV exist that slow the virus's progression, there is no known cure. HIV is transmitted through direct contact of a mucous membrane or the bloodstream with a bodily fluid containing HIV, such as blood, semen, vaginal fluid, preseminal fluid and breast milk. This transmission can come in the form of: anal or vaginal sex; blood transfusion; contaminated needles; exchange between mother and infant during pregnancy, childbirth, or breastfeeding; or other exposure to one of the above bodily fluids. Most researchers believe that HIV originated in sub-Saharan Africa during the twentieth century; it is now a pandemic, with more than 40 million people now living with the disease worldwide.
[edit] July 11, 2006
Stem cells in animals are primal undifferentiated cells that retain the ability to divide and differentiate into other cell types. In higher plants this function is the defining property of the meristematic cells. Stem cells have the ability to act as a repair system for the body, because they can divide and differentiate, replenishing other cells as long as the host organism is alive.
Medical researchers believe stem cell research has the potential to change the face of human disease by being used to repair specific tissues or to grow organs. Yet there is general agreement that, "significant technical hurdles remain that will only be overcome through years of intensive research."
The study of stem cells is attributed as beginning in the 1960s after research by Canadian scientists Ernest A. McCulloch and James E. Till.
[edit] April 9, 2006
Tiktaalik is a genus of extinct sarcopterygian (lobe-finned) fishes from the late Devonian period, with many tetrapod-like features. Excellent fossilised forms of the Tiktaalik, which is generally described as the fish that evolved from water dweller to land dweller, were found in 2004 on Ellesmere Island in Nunavut, Canada.
It lived approximately 375 million years ago. Paleontologists suggest that Tiktaalik was an intermediate form between fish such as Panderichthys, which lived about 385 million years ago and early tetrapods such as Acanthostega and Ichthyostega that lived about 20 million years later. Its mixture of fish and tetrapod characteristics led its discoverers to characterize Tiktaalik as a "fishapod". Tiktaalik was discovered very recently and is widely regarded as a significant find of a transitional species between marine fishes and terrestrial tetrapods.
[edit] March 2, 2006
A whale song is a sound made by whales to communicate. The word "song" is used in particular to describe the pattern of regular and predictable sounds made by some species of whales (notably the humpback) in a way that is reminiscent of human singing.
The mechanisms used to produce sound vary from one family of cetaceans to another. Marine mammals, such as whales, dolphins, and porpoises, are much more dependent on sound for communication and sensation than land mammals are, as other senses are of limited effectiveness in water. Sight is limited for marine mammals because of the way water absorbs light. Smell is also limited, as molecules diffuse more slowly in water than air, which makes smelling less effective. In addition, the speed of sound in water is roughly four times that in the atmosphere at sea level. Because sea-mammals are so dependent on hearing to communicate and feed, environmentalists and cetologists are concerned that they are being harmed by the increased ambient noise in the world's oceans caused by ships and marine seismic surveys.
[edit] February 23, 2006
Lesch-Nyhan syndrome (LNS) is a rare, inherited disorder caused by a deficiency of the enzyme hypoxanthine-guanine phosphoribosyltransferase (HPRT). LNS is an X-linked recessive disease: the gene is carried by the mother and passed on to her son. LNS is present at birth in baby boys. Patients have severe mental and physical problems throughout life. The lack of HPRT causes a build-up of uric acid (pictured) in all body fluids, and leads to symptoms such as severe gout, poor muscle control, and moderate mental retardation, which appear in the first year of life. A striking feature of LNS is self-mutilating behaviors, characterized by lip and finger biting, that begin in the second year of life. Abnormally high uric acid levels can cause sodium urate crystals to form in the joints, kidneys, central nervous system and other tissues of the body, leading to gout-like swelling in the joints and severe kidney problems. Neurological symptoms include facial grimacing, involuntary writhing, and repetitive movements of the arms and legs similar to those seen in Huntington's disease. The direct cause of the neurological abnormalities remains unknown. Because a lack of HPRT causes the body to poorly utilize vitamin B12, some boys may develop a rare disorder called megaloblastic anemia.
The symptoms caused by the buildup of uric acid (arthritis and renal symptoms) respond well to treatment with drugs such as allopurinol that reduce the levels of uric acid in the blood. The mental deficits and self-mutilating behavior do not respond to treatment. There is no cure, but many patients live to adulthood. LNS is rare, affecting about one in 380,000 live births. It was first described in 1964 by Dr. Michael Lesch and Dr. William Nyhan.
[edit] February 8, 2006
Adenosine 5'-triphosphate (ATP) is the nucleotide known in biochemistry as the "molecular currency" of intracellular energy transfer; that is, ATP is able to store and transport chemical energy within cells. ATP also plays an important role in the synthesis of nucleic acids. ATP molecules are also used to store energy during the process of photosynthesis, as well as being the store of energy output from cellular respiration. In signal transduction pathways, ATP is used to provide the phosphate for the protein-kinase reactions.
The total quantity of ATP in the human body is about 0.1 mole. The energy used by human cells requires the hydrolysis of 200 to 300 moles of ATP daily. This means that each ATP molecule is recycled 2000 to 3000 times during a single day. ATP cannot be stored, hence its consumption must closely follow its synthesis. On a per-hour basis, 1 kilogram of ATP is created, processed and then recycled in the body.
[edit] January 31, 2006
Mitochondria are organelles found in most eukaryotic cells, including those of plants, animals, fungi, and protists. A few cells, such as the trypanosome protozoan, have a single large mitochondrion, but usually a cell has hundreds or thousands of mitochondria. The exact number of mitochondria depends on the cell's level of metabolic activity: more activity means more mitochondria. Mitochondria can occupy up to 25% of the cell's cytosol.
Mitochondria are sometimes described as "cellular power plants", because their primary function is to convert organic materials into energy in the form of ATP via the process of oxidative phosphorylation.
[edit] January 23, 2006
Caenorhabditis elegans is a free-living nematode (a roundworm), about 1 mm in length, which lives in a temperate soil environment. Research into the molecular and developmental biology of C. elegans began in 1965 by Sydney Brenner (he was awarded the 2002 Nobel Prize in Medicine for his work). C. elegans has a male (very rare, makes up 0.05% of the C. elegans population) and hermaphrodite sex.
C. elegans is used as a model organism. Specimens are cheap and easy to maintain in the laboratory. C. elegans has been especially useful for studying cellular differentiation, and was the first multicellular organism to have its genome completely sequenced. From a research perspective, C. elegans has the advantage of being a multicellular eukaryotic organism which is simple enough to be studied in great detail. The developmental fate of every single somatic cell (959 in the adult hermaphrodite; 1031 in the adult male) has been mapped out. These patterns of cell lineage are largely invariant between individuals. In both sexes, a large number of additional cells (131 in the hermaphrodite, most of which would otherwise become neurons), are eliminated by programmed cell death (apoptosis).
[edit] January 15, 2006
DNA repair is a process constantly operating in cells; it is essential to survival because it protects the genome from damage and harmful mutations. In human cells, both normal metabolic activities and environmental factors (such as UV radiation) can cause DNA damage, resulting in as many as 500,000 individual molecular lesions per cell per day. These lesions cause structural damage to the DNA molecule, and can dramatically alter the cell's way of reading the information encoded in its genes. Consequently, the DNA repair process must be constantly operating, to correct rapidly any damage in the DNA structure.
As cells age, however, the rate of DNA repair decreases until it can no longer keep up with ongoing DNA damage. The cell then suffers one of three possible fates: an irreversible state of dormancy (senescence), cell suicide (apoptosis or programmed cell death), or cancer. Most cells in the body become senescent. Then, after irreparable DNA damage, apoptosis occurs. In this case, apoptosis functions as a "last resort" mechanism to prevent a cell from becoming tumorigenic and endangering the organism. When cells become senescent, alterations in biosynthesis and turnover cause them to function less efficiently, which inevitably causes disease. The DNA repair ability of a cell is vital to the integrity of its genome and thus to its normal functioning and that of the organism. Many genes that were initially shown to influence lifespan have turned out to be involved in DNA damage repair and protection.
[edit] January 5, 2006
Cladistics is the branch of biology that determines the evolutionary relationships between living things based on derived similarity. It is the most prominent of several phylogenetic systematics, which study the evolutionary relationships of living things (see biology). Cladistics is a method of rigorous analysis, using "shared derived properties" (synapomorphies: see below). Cladistic analysis forms the basis for most modern systems of biological classification, which seek to group organisms by evolutionary relationships. In contrast, phenetics groups organisms based on their overall similarity, while approaches that are more traditional tend to rely on key characters. Willi Hennig (1913–1976) is widely regarded as the founder of cladistics.
[edit] December 28, 2005
Helicobacter pylori is a bacterium that infects the mucus lining of the human stomach. Many peptic ulcers and some types of gastritis are caused by H. pylori infection, although most humans who are infected will never develop symptoms. This bacterium lives in the human stomach exclusively and is the only known organism that can thrive in that highly acidic environment. It is helix-shaped (hence the name helicobacter) and can literally screw itself into the stomach lining to colonize. H. pylori is the only bacteria that lives in the human stomach; in fact, it cannot survive for long periods of time outside of a stomach. Compare this to the thousands of various bacteria species that live in the intestines.
The infection rate with H. pylori has been decreasing in developing countries, presumably because of improved hygiene and increased antibiotics use. Accordingly, the incidence of gastric cancer in the U.S. has fallen by 80% from 1900 to 2000. However, gastroesophageal reflux disease and cancer of the esophagus have increased dramatically during the same period. In 1996, Martin J. Blaser put forward the theory that H. pylori might also have a beneficial effect: by regulating the acidity of the stomach contents, it lowers the impact of regurgitation of stomach acids into the esophagus. While some favorable evidence has been accumulated, the theory is not yet universally accepted.
[edit] December 26, 2005
The Antarctic krill (Euphausia superba) is a species of krill found in the Antarctic waters of the Southern Ocean. They are shrimp-like invertebrates that live in large schools called swarms that sometimes reach densities of 10,000–30,000 individual animals per cubic meter. They feed directly on minute phytoplankton, thereby using the primary production energy that the phytoplankton originally derived from the Sun to their pelagic (open ocean) life cycle. They grow to a length of 6 cm, weigh up to 2 g, and can live for up to six years. They are the key species in the Antarctic ecosystem and are likely, in terms of biomass, the most successful species on the planet.
[edit] May 16, 2005
The platypus (Ornithorhynchus anatinus) is a small, semi-aquatic mammal endemic to the eastern part of Australia, and one of the four extant monotremes, the only mammals that lay eggs instead of giving birth to live young (the other three are echidnas). It is the sole representative of its family (Ornithorhynchidae) and genus (Ornithorhynchus), though a number of fossilised relatives have been found, some of them also in the Ornithorhynchus genus.
[edit] 2005-02-10
Synapses are specialized junctions through which cells of the nervous system signal to one another and to non-neuronal cells such as muscles or glands. Synapses form the circuits in which the neurons of the central nervous system interconnect. They are thus crucial to the biological computations that underlie perception and thought. They also provide the means through which the nervous system connects to and controls the other systems of the body.
At a prototypical synapse, such as a dendritic spine, a mushroom-shaped bud projects from each of two cells and the caps of these buds press flat against one another. At this interface, the membranes of the two cells flank each other across a slender gap, the narrowness of which enables signaling molecules known as neurotransmitters to pass rapidly from one cell to the other by diffusion. This gap is sometimes called the synaptic cleft.
[edit] 2005-02-05
The Marginated Tortoise is the largest European tortoise, reaching a weight of up to 5 kg (11 pounds) and a length of 35 cm (14 inches). Its shell is oblong and has a notable thickness around the middle of the body. The posterior end of the shell has a saw-like formation, flanged outward like a bell. The carapace of adult specimens is almost completely black, with yellow highlights. The ventral shell is lighter coloured and has pairs of triangular markings with the points facing the rear of the animal. The front sides of the limbs are covered with large scales. In old female specimens, the rear flaps of the underside of the plastron are somewhat moveable. The tail is notable for a lengthwise marking and for an undivided carapace over the tail. Males have a longer tail, which is thicker at the base than the females. Their underside is more strongly indented. Males are also often larger than the females. The females lay their hard-shelled spherical eggs in the soil in May and June.
