Chimpanzee Genome Project

The Chimpanzee Genome Project is an effort to determine the DNA sequence of the Chimpanzee genome. It is expected that by comparing the genomes of humans and other apes, it will be possible to better understand what makes humans distinct from other species from a genetic perspective. Human and chimpanzee chromosomes are very similar. The […]

The Chimpanzee Genome Project is an effort to determine the DNA sequence of the Chimpanzee genome. It is expected that by comparing the genomes of humans and other apes, it will be possible to better understand what makes humans distinct from other species from a genetic perspective.

Human and chimpanzee chromosomes are very similar. The primary difference is that humans have one fewer pair of chromosomes than do other great apes. Humans have 23 pairs of chromosomes and other great apes have 24 pairs of chromosomes. In the human evolutionary lineage, two ancestral ape chromosomes fused at their telomeres, producing human chromosome 2.[3] There are nine other major chromosomal differences between chimpanzees and humans: chromosome segment inversions on human chromosomes 1, 4, 5, 9,12, 15, 16, 17, and 18. After the completion of the Human genome project, a common chimpanzee genome project was initiated. In December 2003, a preliminary analysis of 7600 genes shared between the two genomes confirmed that certain genes such as theforkhead-box P2 transcription factor, which is involved in speech development, are different in the human lineage. Several genes involved in hearing were also found to have changed during human evolution, suggesting selection involving human language-related behavior. Differences between individual humans and common chimpanzees are estimated to be about 10 times the typical difference between pairs of humans.[4]

About 600 genes have been identified that may have been undergoing strong positive selection in the human and chimp lineages; many of these genes are involved in immune system defense against microbial disease (example: granulysin is protective against Mycobacterium tuberculosis [8]) or are targeted receptors of pathogenic microorganisms (example: Glycophorin C and Plasmodium falciparum). By comparing human and chimp genes to the genes of other mammals, it has been found that genes coding fortranscription factors, such as forkhead-box P2 (FOXP2), have often evolved faster in the human relative to chimp; relatively small changes in these genes may account for the morphological differences between humans and chimps. A set of 348 transcription factor genes code for proteins with an average of about 50 percent more amino acid changes in the human lineage than in the chimp lineage.

Six human chromosomal regions were found that may have been under particularly strong and coordinated selection during the past 250,000 years. These regions contain at least one marker allele that seems unique to the human lineage while the entire chromosomal region shows lower than normal genetic variation. This pattern suggests that one or a few strongly selected genes in the chromosome region may have been preventing the random accumulation of neutral changes in other nearby genes. One such region on chromosome 7 contains the FOXP2 gene (mentioned above) and this region also includes the Cystic fibrosis transmembrane conductance regulator (CFTR) gene, which is important for ion transport in tissues such as the salt-secreting epithelium of sweat glands. Human mutations in the CFTR gene might be selected for as a way to survivecholera.[9]

Another such region on chromosome 4 may contain elements regulating the expression of a nearby protocadherin gene that may be important for brain development and function. Although changes in expression of genes that are expressed in the brain tend to be less than for other organs (such as liver) on average, gene expression changes in the brain have been more dramatic in the human lineage than in the chimp lineage.[10] This is consistent with the dramatic divergence of the unique pattern of human brain development seen in the human lineage compared to the ancestral great ape pattern. The protocadherin-beta gene cluster on chromosome 5 also shows evidence of possible positive selection.[11]

Results from the human and chimp genome analyses should help in understanding some human diseases. Humans appear to have lost a functional caspase-12 gene, which in other primates codes for an enzyme that may protect against Alzheimer’s disease.

The results of the chimpanzee genome project suggest that when ancestral chromosomes 2A and 2B fused to produce human chromosome 2, no genes were lost from the fused ends of 2A and 2B. At the site of fusion, there are approximately 150,000 base pairs of sequence not found in chimpanzee chromosomes 2A and 2B. Additional linked copies of the PGML/FOXD/CBWD genes exist elsewhere in the human genome, particularly near the p end of chromosome 9. This suggests that a copy of these genes may have been added to the end of the ancestral 2A or 2B prior to the fusion event. It remains to be determined if these inserted genes confer a selective advantage.

  • PGML. The phosphoglucomutase-like gene of human chromosome 2. This gene is incomplete and may not produce a functional transcript.[12]
  • FOXD. The forkhead box D4-like gene is an example of an intronless gene. The function of this gene is not known, but it may code for a transcription control protein.
  • CBWD. Cobalamin synthetase is a bacterial enzyme that makes vitamin B12. In the distant past, a common ancestor to mice and apes incorporated a copy of a cobalamin synthetase gene (see: Horizontal gene transfer). Humans are unusual in that they have several copies of cobalamin synthetase-like genes, including the one on chromosome 2. It remains to be determined what the function of these human cobalamin synthetase-like genes is. If these genes are involved in vitamin B12 metabolism, this could be relevant to human evolution. A major change in human development is greater post-natal brain growth than is observed in other apes. Vitamin B12is important for brain development, and vitamin B12 deficiency during brain development results in severe neurological defects in human children.
  • CXYorf1-like protein. Several transcripts of unknown function corresponding to this region have been isolated. This region is also present in the closely related chromosome 9p terminal region that contains copies of the PGML/FOXD/CBWD genes.
  • Many ribosomal protein L23a pseudogenes are scattered through the human genome.

cells

A eukaryote (/juːˈkæri.oʊt/ or /juːˈkæriət/ yoo-karr-ee-oht or yoo-karr-ee-ət) is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota. The defining feature that sets eukaryotic cells apart from prokaryotic cells (Bacteria and Archaea) is that they have membrane-bound organelles, especially the nucleus, which contains the […]

A eukaryote (/ju??kæri.o?t/ or /ju??kæri?t/ yoo-karr-ee-oht or yoo-karr-ee-?t) is any organism whose cells contain a nucleus and other organelles enclosed within membranes.

Eukaryotes belong to the taxon Eukarya or Eukaryota. The defining feature that sets eukaryotic cells apart from prokaryotic cells (Bacteria and Archaea) is that they have membrane-bound organelles, especially the nucleus, which contains the genetic material, and is enclosed by the nuclear envelope.[2][3][4] The presence of a nucleus gives eukaryotes their name, which comes from the Greek?? (eu, “well”) and ?????? (karyon, “nut” or “kernel”).[5] Eukaryotic cells also contain other membrane-bound organelles such asmitochondria and the Golgi apparatus. In addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular, ormulticellular. Only eukaryotes have many kinds of tissue made up of different cell types.

Eukaryotes can reproduce both by asexual reproduction through mitosis and sexual reproduction through meiosis. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, DNA replication is followed by two rounds of cell division to produce four daughter cells each with half the number of chromosomes as the original parent cell (haploid cells). These act as sex cells (gametes – each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes) resulting from genetic recombination during meiosis.

The domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains,Bacteria and Archaea, are prokaryotes and have none of the above features. Eukaryotes represent a tiny minority of all living things;[6]even the cells in a human’s body are outnumbered ten to one by bacteria in the gut.[7][8] However, due to their much larger size, eukaryotes’ collective worldwide biomass is estimated at about equal to that of prokaryotes.[6] Eukaryotes first developed approximately 1.6–2.1 billion years ago.

A prokaryote is a single-celled organism that lacks a membrane-bound nucleus (karyon), mitochondria, or any other membrane-bound organelle.[1] The word prokaryote comes from the Greek ??? (pro) “before” and ?????? (karyon) “nut orkernel“.[2][3] Prokaryotes can be divided into two domains, Archaea and Bacteria. Species with nuclei and organelles are placed in the domain Eukaryota.[4]

In the prokaryotes all the intracellular water-soluble components (proteins, DNA and metabolites) are located together in thecytoplasm enclosed by the cell membrane, rather than in separate cellular compartments. Bacteria, however, do possess protein-based bacterial microcompartments, which are thought to act as primitive organelles enclosed in protein shells.[5][6]Some prokaryotes, such as cyanobacteria may form large colonies. Others, such as myxobacteria, have multicellular stages in their life cycles.[7]

Molecular studies have provided insight into the evolution and interrelationships of the three domains of biological species.[8]Eukaryotes are organisms, including humans, whose cells have a well defined membrane-bound nucleus (containing chromosomal DNA) and organelles. The division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization. Distinctive types of prokaryotes include extremophiles and methanogens; these are common in some extreme environments.[1]

The genotype–phenotype distinction

The genotype–phenotype distinction is drawn in genetics. “Genotype” is an organism’s full hereditary information. “Phenotype” is an organism’s actual observed properties, such as morphology, development, or behavior. This distinction is fundamental in the study of inheritance of traits and their evolution. It is the organism’s physical properties which directly determine its chances of survival and […]

The genotype–phenotype distinction is drawn in genetics. “Genotype” is an organism’s full hereditary information. “Phenotype” is an organism’s actual observed properties, such as morphology, development, or behavior. This distinction is fundamental in the study of inheritance of traits and their evolution.

It is the organism’s physical properties which directly determine its chances of survival and reproductive output, while the inheritance of physical properties occurs only as a secondary consequence of the inheritance of genes. Therefore, to properly understand the theory of evolution via natural selection, one must understand the genotype–phenotype distinction. The genes contribute to a trait, and the phenotype is the observable expression of the genes (and therefore the genotype that affects the trait). Say a white mouse had the recessive genes that caused the genes that cause the color of the mouse to be inactive (so “cc”). Its genotype would be responsible for its phenotype (the white color).

Norepinephrine

Norepinephrine (NE), also called noradrenaline (NA) or noradrenalin, is an organic chemical in the catecholamine family that functions in the human brain and body as a hormone and neurotransmitter. The name “noradrenaline,” derived from Latin roots meaning “at/alongside the kidneys,” is more commonly used in the United Kingdom; in the United States, “norepinephrine,” derived from […]

Norepinephrine (NE), also called noradrenaline (NA) or noradrenalin, is an organic chemical in the catecholamine family that functions in the human brain and body as a hormone and neurotransmitter. The name “noradrenaline,” derived from Latin roots meaning “at/alongside the kidneys,” is more commonly used in the United Kingdom; in the United States, “norepinephrine,” derived from Greek roots having that same meaning, is usually preferred.[1] “Norepinephrine” is also the International Nonproprietary Namegiven to the compound.[2] Regardless of which name is used for the substance itself, parts of the body that produce or are affected by it are referred to as noradrenergic.

Norepinephrine is synthesized and released by the central nervous system, and also by a division of the autonomic nervous systemcalled the sympathetic nervous system. In the brain, norepinephrine is produced in closely packed brain cell neurons or nuclei that are small yet exert powerful effects on other brain areas. The most important of these nuclei is the locus coeruleus, located in thepons. In the sympathetic nervous system, norepinephrine is used as a neurotransmitter by sympathetic ganglia located near thespinal cord or in the abdomen, and it is also released directly into the bloodstream by the adrenal glands as sympathetic effector organs. Regardless of how and where it is released, norepinephrine acts on target cells by binding to and activating noradrenergic receptors located on the cell surface.

The general function of norepinephrine is to mobilize the brain and body for action. Norepinephrine release is lowest during sleep, rises during wakefulness, and reaches much higher levels during situations of stress or danger, in the so-called fight-or-flight response. In the brain, norepinephrine increases arousal and alertness, promotes vigilance, enhances formation and retrieval of memory, and focuses attention; it also increases restlessness and anxiety. In the rest of the body, norepinephrine increases heart rate and blood pressure, triggers the release of glucose from energy stores, increases blood flow to skeletal muscle, reduces blood flow to the gastrointestinal system, and promotes voiding of the bladder and large intestine.

A variety of medically important drugs work by altering the actions of norepinephrine systems. Norepinephrine itself is widely used as an injectable drug for the treatment of critically low blood pressure. Beta blockers, which counter some of the effects of norepinephrine, are frequently used to treat glaucoma, migraine, and a range of cardiovascular problems. Alpha blockers, which counter a different set of norepinephrine effects, are used to treat several cardiovascular and psychiatric conditions. Alpha-2 agonistsoften have a sedating effect, and are commonly used as anesthesia-enhancers in surgery, as well as in treatment of drug or alcohol dependence. Many important psychiatric drugs exert strong effects on norepinephrine systems in the brain, resulting in side-effects that may be helpful or harmful.

Group selection

Group selection is a proposed mechanism of evolution in which natural selection is imagined to act at the level of the group, instead of at the more conventional level of the individual. Early authors such as V. C. Wynne-Edwards and Konrad Lorenz argued that the behavior of animals could affect their survival and reproduction as […]

Group selection is a proposed mechanism of evolution in which natural selection is imagined to act at the level of the group, instead of at the more conventional level of the individual.

Early authors such as V. C. Wynne-Edwards and Konrad Lorenz argued that the behavior of animals could affect their survival and reproduction as groups.

From the mid 1960s, evolutionary biologists such as John Maynard Smith argued that natural selection acted primarily at the level of the individual. They argued on the basis of mathematical models that individuals would not altruistically sacrifice fitness for the sake of a group. They persuaded the majority of biologists that group selection did not occur, other than in special situations such as the haplodiploid social insects like honeybees (in the Hymenoptera), where kin selection was possible.

In 1994 David Sloan Wilson and Elliott Sober argued for multi-level selection, including group selection, on the grounds that groups, like individuals, could compete. In 2010 three authors including E. O. Wilson, known for his work on ants, again revisited the arguments for group selection, provoking a strong rebuttal from a large group of evolutionary biologists. As of yet, there is no clear consensus among biologists regarding the importance of group selection.

Kleiber’s law

The relationship between body mass and field metabolic rate among individual birds and mammals Lawrence N Hudson,1,1 Nick J B Isaac,2 Daniel C Reuman,1,1,3 and Daniel Ardia Allometry is the study of the relationship of body size to shape,[1] anatomy, physiology and finally behaviour,[2] first outlined by Otto Snell in 1892,[3] D’Arcy Thompson in 1917 […]

The relationship between body mass and field metabolic rate among individual birds and mammals

Allometry is the study of the relationship of body size to shape,[1] anatomy, physiology and finally behaviour,[2] first outlined by Otto Snell in 1892,[3] D’Arcy Thompson in 1917 in On Growth and Form[4] and Julian Huxley in 1932.[5] Allometry is a well-known study, particularly in statistical shape analysis for its theoretical developments, as well as in biology for practical applications to the differential growth rates of the parts of a living organism’s body. One application is in the study of variousinsect species (e.g., the Hercules Beetle), where a small change in overall body size can lead to an enormous and disproportionate increase in the dimensions of appendages such as legs, antennae, or horns. The relationship between the two measured quantities is often expressed as a power law:

y = kx^{a} ,! or in a logarithmic form: log y = a log x + log k,!

where a is the scaling exponent of the law. Methods for estimating this exponent from data use type 2 regressions such asmajor axis regression or reduced major axis regression as these account for the variation in both variables, contrary to least squares regression, which does not account for error variance in the independent variable (e.g., log body mass). Other methods include measurement error models and a particular kind of principal component analysis.

Allometry often studies shape differences in terms of ratios of the objects’ dimensions. Two objects of different size but common shape will have their dimensions in the same ratio. Take, for example, a biological object that grows as it matures. Its size changes with age but the shapes are similar. Studies of ontogenetic allometry often use lizards or snakes as model organisms because they lack parental care after birth or hatching and because they exhibit a large range of body size between the juvenile and adult stage. Lizards often exhibit allometric changes during their ontogeny.[6]

In addition to studies that focus on growth, allometry also examines shape variation among individuals of a given age (and sex), which is referred to as static allometry. Comparisons of species are used to examine interspecific or evolutionary allometry (see also Phylogenetic comparative methods).

Kleiber’s law,[1] named after Max Kleiber‘s biological work in the early 1930s, is the observation that, for the vast majority of animals, an animal’s metabolic rate scales to the ¾ power of the animal’s mass. Symbolically: if q0 is the animal’s metabolic rate, and M the animal’s mass, then Kleiber’s law states that q0 ~ M¾. Thus a cat, having a mass 100 times that of a mouse, will have a metabolism roughly 32 times greater than that of a mouse. In plants, the exponent is close to 1.

The exponent for Kleiber’s law, which is called a power law, was a matter of dispute for many decades. It is still contested by a diminishing number as being ? rather than the more widely accepted ¾. Because the law concerned the capture, use, and loss of energy by a biological system, the system’s metabolic rate was, at first, taken to be ?, because energy was thought of mostly in terms of heat energy. Metabolic rate was expressed in energy per unit time, specifically calories per second. Two thirds expressed the relation of the square of the radius to the cube of the radius of a sphere, with the volume of the sphere increasing faster than the surface area, with increases in radius. This was purportedly the reason large creatures lived longer than small ones – that is, as they got bigger they lost less energy per unit volume through the surface, as radiated heat.

The problem with ? as an exponent was that it did not agree with a lot of the data. There were many exceptions, and the concept of metabolic rate itself was poorly defined and difficult to measure. It seemed to concern more than rate of heat generation and loss. Since what was being considered was not necessarily Euclidean geometry, the appropriateness of ? as an exponent was questioned. Kleiber himself came to favor ¾, and that is the number favored today by the foremost proponents of the law, despite that ¾ also does not agree with much of the data, and is also troubled with exceptions. Theoretical models presented by Geoffrey West, Brian Enquist, and James Brown,[6] – known as the WBE model – purport to show how the ¾ observation can emerge from the constraint of how resources are distributed through hierarchical branching networks. Their understanding of an organism’s metabolic/respiratory chain is based entirely on blood-flow considerations. Their claims have been repeatedly criticized as mistaken, given that the role of fractal capillary branching is not demonstrated as fundamental to the exponent ¾; and that blood-flow claims severely limit the relevance of the equation to organisms greater than e?6 (? .0025) grams when the simultaneous claim is made that the equation is relevant over 27 orders of magnitude, extending from bacteria, which do not have hearts, to whales or forests.

The pons

The pons is part of the brainstem, and in humans and other bipeds lies between the midbrain (above) and the medulla oblongata (below) and in front of the cerebellum. The pons is also called the pons Varolii (“bridge of Varolius”), after the Italian anatomist and surgeon Costanzo Varolio (1543–75).[1] This region of the brainstem includes neural […]

The pons is part of the brainstem, and in humans and other bipeds lies between the midbrain (above) and the medulla oblongata (below) and in front of the cerebellum.

The pons is also called the pons Varolii (“bridge of Varolius”), after the Italian anatomist and surgeon Costanzo Varolio (1543–75).[1] This region of the brainstem includes neural pathways or tracts that conduct signals from the brain down to the cerebellumand medulla, and tracts that carry the sensory signals up into the thalamus.[2]

The pons in humans measures about 2.5 centimetres (0.98 in) in length. Most of it appears as a broad anterior bulge rostral to the medulla. Posteriorly, it consists mainly of two pairs of thick stalks called cerebellar peduncles. They connect the cerebellum to the pons and midbrain.[2]

The pons contains nuclei that relay signals from the forebrain to the cerebellum, along with nuclei that deal primarily with sleep, respiration, swallowing, bladder control, hearing, equilibrium, taste, eye movement, facial expressions, facial sensation, and posture.[2]

Within the pons is the pneumotaxic center consisting of the subparabrachial and the medial parabrachial nuclei. This center regulates the change from inhalation to exhalation.[2]

The pons is implicated in sleep paralysis, and also plays a role in generating dreams.

The fornix

The fornix (Latin: arch) is a C-shaped bundle of nerve fibers in the brain that carries signals from the hippocampus to themammillary bodies and then to the anterior nuclei of thalamus. The fornix is part of the limbic system. While its exact function and importance in the physiology of the brain is still not entirely […]

The fornix (Latin: arch) is a C-shaped bundle of nerve fibers in the brain that carries signals from the hippocampus to themammillary bodies and then to the anterior nuclei of thalamus. The fornix is part of the limbic system. While its exact function and importance in the physiology of the brain is still not entirely clear, it has been demonstrated in humans that surgical transection – the cutting of the fornix along its body – can cause memory loss. There is some debate over what type of memory is affected by this damage, but it has been found to most closely correlate with recall memory rather than recognition memory. This means that damage to the fornix can cause difficulty in recalling long-term information such as details of past events, but it has little effect on the ability to recognize objects or familiar situations.

mitochondrial DNA

One tiny piece of our DNA is inherited only down the female line. It is called mitochondrial DNA because it is held as a unique circular strand in small tubular packets known as mitochondria that function rather like batteries within the cell cytoplasm. Some molecular biologists say that, aeons ago, the mitochondrion was a free-living […]

One tiny piece of our DNA is inherited only down the female line. It is called mitochondrial DNA because it is held as a unique circular strand in small tubular packets known as mitochondria that function rather like batteries within the cell cytoplasm. Some molecular biologists say that, aeons ago, the mitochondrion was a free-living organism with its own DNA, and possessed the secret of generating lots of energy. It invaded single celled nucleated organisms and has stayed on ever since, dividing, like yeast, by binary fission. Males, although they receive and use their mother’s mitochondrial DNA, cannot pass it on to their children. The sperm has its own mitochondria to power the long journey from the vagina to the ovum but, on entry into the ovum, the male mitochondria wither and die. It is as if the man had to leave his guns at the door.