Genes and traits inherit {heredity} in patterns {genetics}|. Genetics is about genes, alleles, phenotypes, and regulation.
After DNA breakage, DNA repair can insert duplicated regions or leave out regions, resulting in more or fewer gene copies {copy number}|. Specific DNA locations can be more likely to break. Aging causes more copy-number variations. Different cells can have different gene copy numbers. Approximately 10% of genes have copy-number variations.
Inheritable proteins and RNAs regulate DNA {epigenetics}|. Chromatin has phosphate groups and ubiquitin, which can have reactions that alter gene expression. DNA methylation suppresses DNA transcription. Histones wound around DNA suppresses DNA transcription. Adding acetyl groups to histone tails allows DNA transcription. Removing acetyls suppresses DNA transcription.
Hereditary qualities can improve by preventing undesirable-trait reproduction or by encouraging desirable-trait reproduction {eugenics}|.
One gene codes for one polypeptide, which catalyzes one chemical reaction {one gene one enzyme one reaction hypothesis}.
Genes can have variations. Alternative sequences {allele}| can be at genetic loci. Bateson and Saunders invented name [1902]. Different alleles make different polypeptides and produce different phenotypes, such as blood types O, A, B, and AB. Haploid organisms have one allele at each locus. For diploid organisms, one allele is from father, and one is from mother.
For one organism, all cells have the same gene alleles {genotype}|. Johannsen invented the word [1909].
For one organism, all genes have the same gene alleles from one parent {haplotype}|. Algorithms {haplotyping} can identify such alleles.
Gene alleles can be normal most-common alleles {wildtype}|.
DNA-sequence genetic loci {polymorphic locus} can have sequence variations {polymorphism, DNA}| {polymorphic variation}. For example, genes can have different alleles. Repeated sequences can have different numbers of repeats.
Sequence positions can have different nucleotides {single nucleotide polymorphism} {single-nucleotide polymorphism} (SNP). At genetic loci, alleles can differ by one nucleotide.
Restriction endonucleases cut at different positions for different alleles at polymorphic loci, causing variations in DNA-fragment lengths {Restriction Fragment Length Polymorphism} (RFLP) (FLP). Cutting or non-cutting at restriction-endonuclease sites makes two short DNA fragments or one long DNA fragment.
Small populations, non-random breeding, and mutations can change allele frequencies in populations {population genetics}|.
In populations, heterozygous and homozygous proportion tends to stay constant {balanced polymorphism}. Balanced polymorphism uses habitat efficiently and preserves variation. In isolated groups, gene ratios stay constant even if environment favors one allele.
For genes, populations have number of one allele divided by number of all alleles {allele frequency} {gene frequency}.
Small populations can have chance allele-frequency changes {genetic drift}|.
If individuals have extreme genetic traits, general trait is in species {principle of genetic gradients} {genetic gradient principle}.
In geographic areas, allele frequencies are constant for species with stable populations {Hardy-Weinberg law}.
Allele-proportion change rate depends on allele reproductive advantage {selection pressure}| and on whether allele is recessive or dominant.
variation
Population allele ratio changes by heterozygote superiority, environmental heterogeneity, cycles, agonistic or antagonistic gene linkages, and homozygote selection.
balancing
Natural selection can maintain allele ratios {stabilizing selection} {balancing selection} to maintain variation. Balancing selection happens in large, non-isolated populations with alleles that are neither dominant nor recessive.
directional
Natural selection can change allele ratios {directional selection} {purifying selection} to reduce variation. Directional selection can happen by genetic drift or inbreeding in small isolated populations.
Homologous-chromosome genetic loci can have different alleles {heterozygous alleles}|. Population allele frequencies determine probability that individuals are heterozygous {heterozygosity}.
Homologous-chromosome genetic loci can have same allele {homozygous alleles}|.
Inheritance laws can depend on cell factors {pangenesis, cell}. Darwin invented the word [1868]. De Vries invented the word pangen.
Trait inheritance uses regular processes {Mendel's laws} {Mendel laws}: law of segregation and law of independent segregation.
For all genes, sperm and egg cells have one gene allele {segregation law} {law of segregation, Mendel}, from either father or mother.
Most gene segregations are independent {independent segregation law} {law of independent segregation}, because genes typically are not on same chromosome or are far apart on same chromosome.
For heterozygosity, phenotypes can mix two allele traits {incomplete dominance}, one allele {dominant allele}| can determine phenotype, or both alleles can cause recessive trait.
For heterozygosity, one allele can be dominant and one allele {recessive allele}| can have no affect on phenotype, or both alleles can cause recessive trait.
DNA, histone-protein, and acidic-nuclear-protein assemblies {chromosome}| contain genes and replicate. Waldeyer invented name [1888].
shapes
Prokaryotes have one circular chromosome. Eukaryotes have linear chromosomes.
pairing
In organisms with sexual reproduction, chromosomes have pairs, one from father and one from mother. Both pair members have same nucleotide sequences, except for natural allele variations or mutation damage.
number
Red blood cells have no nuclei. Germ cells have 23 chromosomes. Other human cells have 46 chromosomes, in 23 pairs. Ape somatic cells have 24 chromosome pairs. Two ape chromosomes fused to make human chromosome 2.
synteny
Different species can have chromosomes with same genes {conserved synteny}.
linkage
Different species can have same chromosome gene order {conserved linkage}.
In female cells, one X-chromosome inactivates early in embryonic development and makes a nuclear body {Barr body}|. Xist gene makes active RNA that coats that X chromosome. Coated X also methylates. The other X-chromosome makes antisense RNA that binds Xist RNA.
Stained cell-nucleus parts {chromatin}| show nucleic acid-protein complexes. Inactivated X-chromosomes have chromatin {macrochromatin} that differs in structure and appearance.
Stained chromosomes show distinctive banding patterns {cytogenic map} under light microscopy.
In diploid organisms, somatic chromosomes {homologous chromosomes}| from father and mother contain same gene sequence, except for natural allele variations or mutation damage.
Offspring from mating two different species cannot produce offspring {sterility}|, because the chromosome sets cannot interact.
In all mammals, in most animals, in some fungi, and in some protozoa, chromosome ends {telomere}| have TTAGGG repeated 2000 times. In plants, TTTAGGG repeats. In ciliates, TTTTGGGG or TTGGGG repeats. Telomeres are nucleoprotein complexes at chromosome ends and can have caps.
Chromosome copying starts just inside chromosome ends, so copies are shorter than copied chromosome. Telomeres decrease in length with each replication. Over a lifetime, humans make 150 copies and shorten telomeres by half. Telomerase enzyme restores telomere length in sperm and egg cells, and in cancer cells, using RNA as template for reverse transcriptase. Telomerase prevents shortening in human immune system, hemopoietic system, germline cells, embryonic cells, stem cells, skin cells, intestinal-lining cells, hair-follicle cells, and cancer cells.
After telomeres reach threshold length, cells can have senescence. Perhaps, telomere shortening ends at age 40, related to cell-turnover reduction.
Rodent cells do not have telomere shortening, stop dividing after 10 to 15 doublings, have telomerase, and grow indefinitely in culture.
Chromosomes {autosome}| can be all chromosomes except X and Y.
In salivary glands, fruit flies have 1000 aligned chromosome copies {polytene chromosome}|.
X-chromosomes and Y-chromosomes {sex chromosome}| determine sexual characteristics.
male
Male cells have one X-chromosome and one Y-chromosome.
female
Female cells have two X-chromosomes.
genes
Sex-chromosome genes determine sex-linked traits and diseases, such as hemophilia and color blindness. Sex hormones influence some autosomal genes, such as baldness gene and horn gene.
crossing over
X-chromosome and Y-chromosome stopped crossing over in birds and mammals.
meiosis
Tips of Y recombine with tips of X, to allow meiosis.
evolution
Reptiles that led to mammals had two X-chromosomes. SRY gene arose 350,000,000 years ago. Between 320,000,000 to 240,000,000 years ago, ancient X-chromosome larger half, containing SRY, inverted or failed to recombine, making monotreme Y-chromosome. Between 170,000,000 and 130,000,000 years ago, a region on other centromere side inverted or failed to recombine, resulting in marsupial Y-chromosome. From -130,000,000 to -80,000,000 years ago, a large region on other centromere side inverted or failed to recombine, resulting in Eutheria Y-chromosome. From -50,000,000 to -30,000,000, a large region on other centromere side inverted or failed to recombine, resulting in human Y-chromosome. During this succession, SRY gene moved to other arm.
evolution: human
Y-chromosome variations track human migrations. M91 is only in south-Africa San people. Yap, M60, M2, MT68, M89M96, M35, M172, and M304 are in Africa. M170, M343, and LLY22 are in Europe. M9, M201, M17, M173, and M69 are in Near East. M20 and M45 are in India. M175, M174, and M122 are in southeast Asia. M130, M4, and M130 are in Pacific islands. M242 and M130 are in northeast Asia and Americas.
Sex chromosomes {X-chromosome}| can have 2000 to 3000 genes. Mammals inactivate X-chromosome in females, to prevent overproduction from X genes. X-chromosome started to develop 300 million years ago.
Sex chromosomes {Y-chromosome}| can have 80 genes. Some genes are only on Y. SRY is for making testes and derived from SOX3 of X-chromosome. TTY2, CDY, PRY, DAZ, and BPY2 are for making sperm. Other genes are TTY1, TSPY, and XKRY.
Some genes are on X and Y. DBY, EIF1AY, RPS4Y, SMCY, TB4Y, USP9Y, UTY, and ZFY are for housekeeping. RBMY and VCY work only in testes. Others are PCDHY and AMELY.
One Y-chromosome end is 95% of Y-chromosome and has no functioning genes. Y-chromosome has palindrome structure.
Heredity has fundamental physical and functional units {gene}. Johannsen invented the word gene [1909]. Genes are nucleotide sequences at chromosome positions. Genes code for proteins or RNAs {gene product} for regulation, structure, or transport. Genes controlling behavior are not qualitatively different from those governing other cell functions.
Master genes {BMAL1 gene} can control timing. Superchiasmatic nucleus regulates waking and sleeping. Dorsomedial nucleus controls eating cycles.
Genes {CALHM1 gene} can regulate neuron calcium concentration.
Human DNA sequences {human accelerated region} (HAR1) (HAR2) can have rapid mutation compared to chimpanzees. HAR1 codes RNA. HAR2 (HACNS1) regulates wrist and thumb development.
Genes {IRGM gene} can act against bacteria.
Genes {Ku70 gene} can make DNA-repair Ku70 transcription factors.
Worms, insects, and vertebrates have pseudogene-regulated genes {makorin1 gene}.
Gene {MECP2 gene} mutations can cause autism Rett syndrome.
Metal-dependent endopeptidases {metalloproteinase} can break down interstitial type I, II, or III collagen, basement-membrane type IV collagen, or type V collagen. Metalloproteinases {matrilysin} {PUMP-1 gene} can split extracellular matrix. Metalloproteinases {gelatinase A} {gelatinase B} split basement membrane. MMP-1 and MMP-13 split interstitial collagen. Metalloproteinase {stromelysin-3} (MMP-3) splits extracellular matrix.
Plasminogen activators and other serine proteinases activate metalloproteinases. Cells have tissue metalloproteinase inhibitors {TIMP gene}, such as TIMP-1, TIMP-2, TIMP-3, and TIMP-4.
Genes {multidrug resistance 1 gene} {MDR1 gene} can make cell-membrane pumps that can send chemotherapy drugs out tumor cells.
Mice without a gene {Runx1 gene} do not sense heat or cold. Runx1 gene can affect neuropathic pain.
Genes {TRIM5alpha gene} can stop PtERV1 from replicating.
Drosophila genes {Yellow gene} can make black pigment. Without yellow genes, color is yellow.
Genes {AMY1 gene} can make salivary amylase to break down starch. Humans have many copies.
Genes {LCT gene} can make lactase to metabolize lactose.
Protein complexes {lac repressor} can block lactase-gene transcription. Lactose metabolites can bind to lac repressor and cause them to leave DNA, allowing gene transcription.
Genes {CETP gene} can control blood cholesterol-particle size.
Genes {CSE gene} can make enzyme that makes hydrogen-sulfide vasodilator.
Human red-blood-cell surface genes {Duffy gene} can make part of Plasmodium receptor, in brain, spleen, and kidney.
Enzymes {gamma-glutamyl carboxylase} can clot human blood, be in fruit flies, make cone snail venom, and participate in embryonic development. Carboxylase began at least 540 million years ago, when arthropods, mollusks, and chordates diverged, because arthropod, mollusc, and chordate gamma-glutamyl-carboxylase genes have similar introns, which direct protein folding. Therefore, introns began before 540 million years ago.
Transcription factors {hypoxia-inducible factor 1} {HIF-1 gene} can increase after hypoxia and cause increased red-blood-cell mass, blood-vessel growth, and increased ventilation.
Using sugar, proteins {selectin gene} can bind to white blood cells, to allow cells to leave blood and go into tissue.
Genes {tryptophan hydroxylase I gene} can make serotonin for blood.
Gene {AKT gene} products can aid cell suicide.
Gene {BCL-3 gene} products can regulate cell death. Mutated gene causes lymphoma.
Gene {lethal gene} mutations can kill organisms, because gene no longer produces necessary enzyme.
Transcription factors {p53 factor} {p53 protein} can start apoptosis in damaged cells. When p53 gene mutates, gene product causes cancer.
Genes {SEPS1 gene} can break down damaged proteins. Damaged proteins can cause inflammation.
Gene {archipelago gene} (ago gene) (AGO gene) products {ago protein} can regulate cell cycle, cell-differentiation Notch signaling pathway, and Alzheimer's-disease beta-amyloid precursor protein (APP) processing pathway. Ago protein contains F-box domain and seven WD40 repeat motifs. F-boxes and WD40 repeats are typically in ubiquitin-ligase complexes of ubiquitin/proteasome proteolytic pathway.
F-box
F-box domain interacts with proteins {Skp1 protein} of protein complexes {SCF complex}. Organisms have many F-box proteins, with more than 100 in Caenorhabditis elegans roundworm, for example.
WD40
WD40 repeats interact with cyclin E and cyclin F. WD40 repeats have repeating units of 40 amino acids, with tryptophan, with symbol W, and aspartic acid, with symbol D, at defined positions.
LRR repeats
Leucine-rich repeats {LRR repeat} interact with cyclin E.
cyclin E
Ago protein recognizes cyclin E and catalyzes covalent ubiquitin-to-cyclin-E attachment. Ago protein decreases cell proliferation by this mechanism.
In Drosophila cell cycle, regulatory protein {cyclin E} can increase transition from gap-1 phase to S phase, which has DNA synthesis and replication. Cyclin E genes are tumor suppressor genes. Cyclin E problems can cause cancer. Elevated intracellular cyclin E levels increase cell proliferation.
Protein-complex {ubiquitin ligase complex} substrate-recognition components are in proteolytic pathways {ubiquitin/proteasome proteolytic pathway}. Ubiquitination attaches 76-amino-acid peptides {ubiquitin, complex} to proteins. The 26S proteasome then degrades ubiquitin and protein. Ubiquitin/proteasome proteolytic pathway decreases cell-cycle-regulation, cell-proliferation, differentiation, and development proteins.
Ubiquitin/proteasome proteolytic pathway has ubiquitin-activating enzymes {E1 gene}.
Ubiquitin/proteasome proteolytic pathway has ubiquitin-conjugating enzymes {E2 gene}.
Ubiquitin/proteasome proteolytic pathway has ubiquitin ligases {E3 gene}, such as SCF types. Ubiquitin ligase connects cell-cycle protein to ubiquitin and controls protein level.
Receptors {cell-surface receptor} can use hundreds of genes.
peptides
Cell-surface receptors can bind acetylcholine, glutamate, glycine, and gamma-aminobutyric acid and endorphin and enkephalin peptides. Acetylcholine binds to sodium-ion-channel receptor. Glutamate binds to NMDA receptor. Glycine and GABA bind to chloride-ion-channel receptors. Receptor proteins using G proteins can couple to ion-channel proteins. Same-type receptors can have variable binding affinity and transport efficacy.
Alpha-adrenergic and beta-adrenergic cell-surface receptors {adrenergic receptor} can bind epinephrine and similar compounds.
membrane
Amino ends are outside membranes, and carboxyl ends are inside membranes. Seven helices pass through membrane.
functions
Adrenergic receptors can couple to G protein. Adrenergic receptors can activate or inhibit adenylate cyclase to make or decrease cAMP.
functions: phosphates
Adrenergic receptors can activate phospholipase to break down inositol phospholipids in membrane into inositol triphosphate and diacylglycerol. Inositol triphosphate makes calcium vesicles release calcium ions, which bind to calmodulin, which regulates enzymes such as protein kinase. Diacylglycerol activates protein-kinase C proteins. Phosphorylation causes conformational changes that expose active sites and activate protein kinases. Protein phosphatases, such as cytoplasmic CD45 membrane protein, remove phosphates.
Cell-surface receptor proteins {CD4 protein} can bind protein kinase at carboxyl ends inside membranes.
Cell-surface receptors {growth factor receptor} can bind growth factors. Growth factors activate 100 immediate early genes, which then make transcription factors.
structure
Growth-factor receptors pass one helix through membrane. Receptor is outside membrane. Kinase or cyclase is inside membrane.
types
Atrial naturietic peptide has protein kinase and guanylate cyclase. Activin receptor protein has serine-threonine kinase. Phosphoprotein phosphatase has tyrosine phosphatase. Growth factor receptor has tyrosine kinase.
Cell-surface receptors {hormone binding receptor} can bind hormones. Hormone-binding receptors affect G proteins inside cell membranes. G proteins use GTP to activate adenylate cyclase and make cAMP. cAMP affects protein kinase A, which then phosphorylates transcription factors, such as CRE-binding protein, that bind to cAMP response elements (CRE).
Muscle-synapse cell-surface receptors {nicotinic cholinergic receptor} can bind acetylcholine. Nicotinic receptors have membrane alpha-helix pores. Acetylcholine binds to two alpha helices. Four genes make protein receptors. Gene alleles have different mRNA splicings, making many slightly different nicotinic cholinergic receptors.
Cell-surface receptors {steroid receptor} can bind steroids. Steroids can cross membranes and bind to steroid-receptor proteins inside cells, allowing them to move to cell nucleus.
Cell-surface receptors can bind hormones and affect GTP-binding proteins {G protein} inside cell membranes. Activated G protein catalyzes its return to unactivated state, thus timing rate of G-protein processes. Immediate-early genes activated in learning use cAMP signal paths.
cyclic AMP
G protein uses GTP to activate adenylate cyclase and make cAMP. cAMP affects protein kinase A, which then phosphorylates CRE-binding protein, which binds to cAMP response elements (CRE).
senses
Olfactory sensors use G-protein transduction.
structure
G protein is similar to proteins for cross-membrane signaling, protein synthesis, cell molecule transport, and cross-membrane transport.
Steroid-receptor proteins bind to regulatory-region 15-base sequences {hormone-response element}, for activation or repression.
Chemicals {ionophore} can artificially raise cell calcium concentration.
Serine proteinases {plasminogen activator} can have cell-surface receptors. Urokinase plasminogen activator (uPA) can activate matrix metalloproteinases. Plasminogen-activator inhibitors counteract tissue plasminogen activator (tPA).
Retina rod-cell proteins {rhodopsin}| can absorb light and bind GTP to transducin, which activates phosphodiesterase, which breaks down cGMP, which closes cGMP-dependent ion channels and so causes hyperpolarization. Rhodopsin is similar to adrenergic receptor. Opsin proteins are similar to rhodopsin, because both use 11-cis-retinal as chromophore. Absorption maximum differs for opsins and rhodopsin.
GTP-binding proteins {transducin} can transduce signals in eye.
ATR protein, matrilins, integrins, and other cell-surface protein-interaction proteins have extra-cellular domains {von Willebrand factor type A}.
Genes {development genes} can control development. Serotonin affects early embryo development, and mother supplies it before fetus can make it.
Genes {histone deacetylase 4 gene} (HDAC4) can regulate muscle and bone development and maintain rod and bipolar cells.
Genes {early-response gene} {immediate early gene} can respond first to stimulation and then trigger later changes.
Homeobox and other genes {master control gene} can start gene-expression chains.
Stickleback-fish gene {Pitx1 gene} products can affect pelvic fin and other structures.
Gene {Notch gene} products can activate signaling pathways and regulate whether neural precursors become neurons or glia. Enzymes cleave Notch and APP transmembrane proteins in membrane plane {regulated intramembrane proteolysis}, to liberate cytosolic fragments, which enter cell nucleus to control gene transcription. Regulated intramembrane proteolysis is similar from bacteria to humans.
Gene {Bmi-1 gene} products can activate signaling pathways.
Gene {Wnt gene} products can activate signaling pathways.
Homeodomain binding proteins have one helix in DNA major groove and another helix across DNA that contacts other proteins. Fruitfly homeotic genes {homeobox gene} control head, jaws, teeth, thorax, and abdomen development and contain 180-base control regions {homeobox} that have helix-turn-helix {homeodomain} sequences, which are in many development genes. Regulatory region has 200,000 bases total.
retinoic acid
Extracellular-fluid retinoic acid controls homeotic-gene expression by binding to cell receptors and builds spinal cord, hindbrain, eye, and limbs. Low concentrations start gene expression at forebrain, and then higher concentrations start gene expression in sequence down to tail.
hormone
Thyroid hormone has similar receptors and controls gene expression.
Human Hox gene and other homeobox development genes {homeotic gene} can have sequences {homeotic series} along chromosomes. First gene is for mouth/nose, and last gene is for tail. Earliest homeobox genes were 1, 2/3, 4, 5, 6/7/8, and 9/10/11/12/13, in sequence. Fruit flies have 1, 2/3, 4, 5, 6, 7, 8, and 9/10/11/12/13. Fruit flies have non-homeobox region of DNA between 6 and 7. Chordates have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 13. Vertebrates have chordate-set variants on four different chromosomes.
Mammal genes {BF gene} can control gut, liver, and lungs. BF genes are similar to forkhead genes. BF-1 enlarges nasal retina and dorsal forebrain and is where neurons start dividing {germinal zone} before migrating. BF-2 enlarges ventral forebrain and temporal retina.
Mammal Emx-1 and Emx-2 genes {Emx gene} enlarge cerebrum, including corpus callosum. Fruitfly genes {empty spiracles gene} are similar.
Fruitfly genes {engrailed gene} can have homeoboxes but not be in homeotic gene sequence for body development. In most vertebrates, En-1 and En-2 genes, similar to engrailed gene, control midbrain and cerebellum growth.
Fruitfly genes {forkhead gene} can develop gut beginning and end.
Vertebrate genes {Hox gene} can be similar to fruitfly homeobox genes. If Hox genes are missing, symptoms are similar to DiGeorge congenital disease. Hox-b1, Hox-b2, Hox-b3, Hox-b4, and Hox-b5 genes enlarge hindbrain from third rhombomere down.
Genes {Lim-1 gene} can enlarge forebrain, midbrain, cerebellum, and first two or three hindbrain rhombomeres.
Genes {Otx gene} can affect brain development. Otx2 protein is for head development in embryo. After birth, it signals eye coordination.
Genes {Pax6 gene} can affect halteres balancing-wing development. Pax genes also affect eye and brain development.
Fruitfly genes {tailless gene} can develop gut beginning and end. Tailless gene enlarges forebrain, retina, and olfaction receptors.
At fertilization, genes {maternal-effect gene} from mother can code for transcription factors that establish front-to-back and top-to-bottom embryo polarity: bicoid protein, nanos protein, and dorsal gene protein transcription factor.
Proteins {bicoid protein transcription factor}, at only one pole, can make top-to-bottom gradient across embryo {morphogen, bicoid}. Nanos is at one pole, and bicoid is at other pole.
Proteins {nanos protein transcription factor}, at only one pole, can make top-to-bottom gradient across embryo. Nanos is at one pole, and bicoid is at other pole.
Maternal-effect follicle-cell genes can code for transcription factors {dorsal gene protein transcription factor} that establish front-to-back embryo polarity. Factor is similar to rel protein and NF-kappaB. Factor concentrates in cell nucleus ventrally, and cytoplasm dorsally, in all embryo cells. Cactus gene and Toll gene can partition dorsal-gene-protein transcription factor to these cell locations.
After first cell divisions, genes {gap gene} {hunchback gene} {hunchback-maternal gene} {knirps gene} {Kruppel gene} can code zinc-finger transcription factors that make bands along embryo and body regions by working with maternal-effect genes and by repressing each other. Gap genes also regulate genes expressed later. Transcription-factor binding sites are high-affinity or low-affinity, so transcription-factor concentration affects which genes transcribe and how much, leading to gradients and bands. In small regions, same chemicals cause different effects.
After gap-gene expression, genes {segmentation gene} can code for transcription factors that segment body, pair segments, and make segment polarity. Segmentation genes work with gap-gene products, and interact with each other using autofeedback, to sharpen segment boundaries. Segmentation genes include pair-rule genes, such as fushi tarazu gene, even-skipped gene, hairy gene, runt gene, and eve gene.
Segmentation genes {pair-rule gene} {eve gene} {even-skipped gene} {fushi tarazu gene} {hairy gene} {runt gene} can be about splitting body regions. In small regions, same chemicals cause different effects.
Genes {segment polarity gene} can be about front and back. In small regions, same chemicals can cause different effects.
Genes {FTO gene} can have alleles related to obesity.
Gene {NCoR gene} products can regulate fat-metabolism genes.
Hypothalamus proteins {PTP1B gene} can affect leptin signaling inside cells.
Hypothalamus proteins {SOC3 gene} can block leptin receptors.
Gene products {ERK factor} can be for cell growth.
Gene products {MEK factor} can be for cell growth.
Genes {NEGR1 gene} can affect hypothalamus neuron growth.
Transcription factors {NF-kappaB} can be for cell growth and cytokine production.
Mice genes {p16INK4a gene} can regulate cell growth and regeneration. With age, protein increases, and cells regenerate less.
Transcription factors {RSK factor} can be for cell growth.
Gene {SOS gene} products can be for cell growth.
Fox-01, Fox03, and Fox04 transcription factors {fox factor} {Fox gene} are for glucose metabolism and cell defense.
Gene products {orai 1 protein} can be in T-cell calcium-ion channels.
Proteins {siglec proteins} can prevent immune-system cells from activation.
Genes {intoxication genes} can affect intoxication.
Genes {ADH2 gene} can prevent alcoholism in some East Asians by affecting alcohol metabolism.
Genes {ALDH2 gene} can prevent alcoholism in some East Asians by affecting alcohol metabolism.
Alcohol affects fruitfly genes {cheap date gene}.
Genes {CHRM2 gene} can affect alcohol use.
Genes {DRD2 gene} can relate to alcoholism.
Genes {GABRA2 gene} can affect alcohol use.
C. elegans genes {slo-1 gene} can code for neuron, muscle-cell, and gland-cell BK potassium-ion-channel proteins. Alcohol affects BK-channel.
Genes {ATP1A2 gene} can code for membrane sodium-pump and potassium-pump proteins.
Genes {CACNA1A gene} can code for P/Q calcium-channel protein.
Gene {SCN1A gene} codes for sodium-channel proteins.
Transcription factors {MyoD gene} can be for muscle development and repair.
Genes {POP3 gene} can build striated muscle. POP2 and POP3 are also in plants.
Immediate-early genes {cFos gene} can make proteins that are neuronal activation markers.
Trimer proteins {clathrin triskelion} {clathrin gene} can have tetrahedron shapes at corners of presynaptic-nerve-ending icosahedral neurotransmitter-release structures.
Genes {Dscam gene} can guide axon growth.
Genes {Eph gene} can build brain topographic maps.
Notch, split enhancer, big brain, mastermind, and neuralized genes {neurogenic gene} can make cell-adhesion, signal-transduction, membrane-channel, and transcription-factor cell-to-cell signal proteins, to develop cells and inhibit nearby cells.
After making neurons, genes {neurotrophic gene} can code for secreted proteins {neurotrophic factor} that keep neurons alive, differentiate neurons, and make neurotransmitters, such as nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), CNTF, and NT-3. Other genes code for neurotrophic-factor receptor proteins.
After head and tail develop, daughterless and achaete-scute genes {proneural gene} can code for helix-loop-helix transcription factors that make neural precursor cells to start brain development. da enhances achaete-scute, and emc inhibits it.
Vertebrate genes {reelin gene} can affect axon branching and synapse creation.
Genes {Robo gene} can affect axon travel between hemispheres.
Cut and other genes {selector gene} can code for homeobox transcription factors that make neuron types.
Chromosome-7 genes {Forkhead box P2 gene} {FOXP2 gene} can have a mutation [-100000] associated with speech and language problems. Neanderthals also have this allele.
Fruitfly genes {Fru gene} can affect courtship rituals.
Amygdala proteins {stathmin} can affect fear.
Genes {ASPM gene} can help control brain size.
Genes {MCPH1 gene} can help control brain size.
Genes {CDK5RAP2 gene} can help control brain size.
Genes {CENPJ gene} can help control brain size.
One base change in a recessive gene {hothead gene} can cause fused petals, but Arabidopsis thaliana mustard plant can revert to wild type.
Plants have POP2 and POP3 genes {POP gene}.
Genes {terminator gene} can make proteins {ribosome inhibitor protein} that kill seeds.
Nuclear genes {cytochrome b gene} can make mitochondrial respiratory-chain proteins.
cybS
Nuclear genes {cybS gene} {SDHD gene, cytochrome} can make small cytochrome-b subunits. cybS protein is in mitochondria protein complexes {mitochondrial complex II} {succinate-ubiquinone oxidoreductase}, which are in electron transport chains.
Perhaps, cybS genes are tumor suppressor genes, because they are typically not in bladder, breast, cervix, stomach, lung, and ovary cancers or in melanomas. Perhaps, cybS protein is in carotid-body oxygen-sensing system. Without cybS protein, chronic hypoxic stimulation causes cell proliferation. Solid tumors are typically hypoxic compared to normal tissues.
Regulators {PGC-1alpha regulator} {PGC gene} can develop muscles by controlling respiration.
Nuclear genes {SDHD gene, mitochondria} can make mitochondrial respiratory chain proteins, which are small cytochrome-b subunits.
Genes {RNA gene} can make rRNA, tRNA, microRNA, RNA-protein enzyme complexes such as RMRP, and riboswitches.
In bacteria, long RNAs {riboswitch} have aptamer ends that bind to other molecules to act as sensors and other ends {expression platform, riboswitch} that change structurally, by making and unmaking hairpins, to affect protein translation or RNA transcription.
Protein complexes {TRAP complex} can bind tryptophan mRNA and inhibit tryptophan-gene transcription and mRNA translation.
X-chromosome genes {DAX gene} can tend to suppress SRY gene {sex-chromosome drive}. Y-chromosome is too small to reduce such suppression.
Maleness or femaleness genes {sexually antagonistic gene} cluster together and do not work in other sex. Maleness or femaleness genes are in different chromosomes in birds and mammals.
Y-chromosome genes {Sry gene} can control testes development and so testosterone production. Sry gene starts masculinization. Human SRY differs greatly from ape SRY, but has had few mutations.
Nematodes transcription-factor ELT-3, ELT-5, and ELT-6 genes {ELT gene} are active in youth. ELT genes are more active in old age. ELT genes are similar to human GATA transcription factors.
Human transcription-factor genes {GATA gene} can be active in youth. Nematode ELT genes are similar to GATA transcription factors.
Transcription-factor genes {c-myc gene} can restore pluripotency to cells.
Transcription-factor genes {Klf4 gene} can restore pluripotency to cells.
Transcription-factor genes {Oct4 gene} can restore pluripotency to cells.
Transcription-factor genes {Sox2 gene} can restore pluripotency to cells.
Individuals have ancestors {pedigree} {family tree} {geneaology}|.
Children or grandchildren can breed with parents {back cross}|.
In isolated populations, genetically similar individuals can breed {inbreeding, population}|. Continual inbreeding can result in species varieties in which all individuals are essentially genetically identical. 10% gene flow prevents too much inbreeding and keeps human populations from differentiating into new species.
Geographic isolation {isolating mechanism}, ecology, and genetic factors can increase interbreeding.
First filial generation {F1 generation} is children of parents.
Second filial generation {F2 generation} {grandchildren} is children of children.
Parental generation can have children {filial generation}, grandchildren, and so on.
Males and females {parental generation} can start reproductive lines.
Organisms have all genetic material in chromosomes {genome, genetics}|. Typical animal cells express 4,000 to 10,000 genes. Humans have more than 30,000 genes. Two unrelated people differ in 100 to 5000 genes. Human genes differ from chimpanzee genes by one percent. Humans have 85,000 different mRNAs.
Transposable elements are 45% of human DNA. Non-coding DNA is 24% of human DNA. Structural DNA is 20% of human DNA. Repeated sequences are 10% of human DNA.
Protein coding genes are 1% of human DNA. 42% of genes have not been characterized. 14% are nuclear transcription factors. 12% are messengers. 10% are enzymes. 5% are miscellaneous. 5% are structural. 5% are for molecular transport. 3% are cell-surface proteins. 3% are tumor-suppressor genes. 1% are immune-system proteins.
People have 5 x 10^9 nucleotides. Unrelated people differ by 5 x 10^5 nucleotides.
Genes have sequences, functions, regulation, and interactions with themselves and environment {genomics}|. Computational tools can identify genes, inducers, binding sites, structures, and relations between nucleic acid and protein sequences.
Protein study can depend on genes {proteomics}|. Proteomics involves post-translational modification, protein folding, and protein-protein interactions. 10 to 20 million different human proteins are possible.
Human bacteria and humans make many chemicals {metabolomics}. Human bacteria and humans make many chemicals in response to stress {metabonomics}.
Projects {genome, human} {Human Genome Project} sequenced human DNA.
purposes
From nucleotide sequences, experimenters can determine gene number, types, and relations. They can identify functional regions, coding regions, pseudogenes, and loci. They can identify regulatory regions, such as promoters, enhancers, silencers, trans-activating factors, transcription factors, and transcription-factor receptors. They can identify splicing sites, such as RNA splicing sites and alternative splicing sites. They can identify repeat regions, such as simple repeats like STR, complex repeats like Alu, or coding-triplet repeats. They can identify translocations and DNA-rearrangement signals. They can identify three-dimensional structure sites. They can identify antigen response sites. They can identify sites involved in polymorphism, disease, and development.
evolution
Experimenters can find racial, cultural, geographic, and individual variations. They can identify evolutionary regions, such as orthologues or dot matrices. They can trace human DNA evolution. They can define heredity traits and study questions about environment role {nature vs. nurture debate}.
questions
Should fetal tissues be research tools?
Should society allow changes to germ cells? How much diversity should society maintain and how much should society try for perfection? Which eugenics program is best, if any? Do parents have right to choose children gender?
Who owns information about genes, regions, or proteins, and is it patentable? Who owns genetic materials and data?
Who can access genetic information: relatives, governments, insurance, and/or employers? How can people have privacy?
Should gene therapies modify behavior? Should society screen everyone for genetic diseases or traits? Is it ethical to have disease diagnosis without available treatment? Should society allow children to have genetic defects, and what are defects? Are treatment costs important factors?
Is anyone liable for genetic makeup or behavior consequences? Does or will genetic defects cause social stigma?
How much education about genetic issues is practical and/or useful?
Genomes have numbers of homologous somatic chromosomes {ploidy}, such as haploid and diploid. Triploid organisms have three. Tetraploid organisms have four. For sex-linked chromosomes, ploidy can differ between males and females.
Cells {haploid}| can have one chromosome set, rather than two. Sperm and egg cells {germ cell} are haploid. Bacteria have one gene copy, because they are asexual. However, they have as many different traits and trait variations as sexual organisms.
Somatic cells {diploid}| can have two chromosome sets. Sexual reproduction contributes one chromosome set from each parent.
Many organisms have more than two chromosome sets {polyploidy}|. Haploids and diploids can make extra chromosomes or chromosome parts. Insects typically have more than two chromosome sets.
Same-chromosome alleles or RFLP markers tend to inherit together {linkage}| {genetic linkage} {linkage group} in meiotic recombination, mitotic replication, and prokaryote binary fission. Closer markers are less likely to separate during DNA recombination and so are more likely to inherit together. Linkage frequency depends on distance between loci.
finding distance from linkage
Known genetic linkages show relative loci distances. Distances are in centimorgans. Markers less than five centimorgans have less than 1 in 20 chance to separate.
Alleles at neighboring genetic loci can more frequently associate than expected from allele frequency and genetic linkage {linkage disequilibrium} {allelic association}. Algorithms can identify linkage disequilibrium.
Units {centimorgan} (cM) can measure recombination frequency. One centimorgan is 1% chance that, at one crossing over, marker at one genetic locus separates from marker at second locus. In humans, one centimorgan is one million base pairs.
Chromosomes have gene locations {DNA mapping}.
chromosome separation
Cell-sorting machines can sort chromosomes. Alternatively, people can separate chromosomes using microscopes and fine instruments. Human cells treated with x-rays can fuse with mouse cells to isolate chromosome pieces, to map with markers {radiation hybrid mapping}. Two-dimensional electrophoresis using variable fields can separate DNA fragments up to three million bases {pulsed field gel electrophoresis} (PFGE), over several days.
protein removal
Proteolytic enzymes remove protein from chromosomes held in gels, leaving DNA.
DNA fragments
NotI, MluI, NruI, and SfiI restriction enzymes have eight-base sites and cut DNA in few places, to make million-base DNA fragments.
methylation
Tissues can have methylated sites, allowing fewer cuts and larger fragments, so researchers must compare different tissues. Large fragments have further processing.
cloning
YACs allow cloning hundred-kilobase DNA fragments. Phages and cosmids allow cloning 40000-base DNA fragments, for genomic libraries.
separation
From clones, electrophoresis separates restriction fragments by size.
markers
Genetic markers can find loci.
hybridization
20-base oligonucleotide probes can hybridize with DNA. Probes can have minor-groove binder to enhance exact hybridization, allowing shorter probes. Probes hybridize with clone DNA fragments. Overlapping DNA fragments hybridize to same probe. Clone-fragment sequence-tagged connector ends hybridize to probes.
sites
Using unique primers, processing identifies unique 200-base to 500-base sequence-tagged sites, which have known locations.
overlapping
DNA fragments overlap to build longer sequences {contig, DNA}, to sequence chromosome DNA.
Neutral or disadvantageous gene mutations can survive if they are adjacent to advantageous genes {hitch-hiking natural selection}.
Complex genetic diseases divide into different onset ages and/or different disease severities {liability class}. This can increase genetic-linkage information by accounting for phenocopy traits, whose appearances are similar but have different causes. Categories have different phenocopy rates. Phenocopy rates increase as onset age increases and as severity decreases.
Genes and other markers are at relative or absolute chromosome positions {locus, gene}| {loci} {genetic locus}.
Individual marker traits have probabilities. Probabilities differ for linkage or no linkage. Values {LOD Score} can measure linkage degrees in families by estimating recombination fraction: base-10 logarithm of ratio between probability assuming linkage and probability assuming no linkage. In LOD-score analysis, disorders can make complex patterns.
Testing father, mother, and child to establish genetic linkage and association {Transmission Disequilibrium Test} (TDT) can find linkage disequilibria.
Chemicals, radiation, and copying and repairing errors can cause chromosomal DNA-sequence damage {mutation}|. People can inherit changed genotypes.
types
Single nucleotides, short regions, genes, and chromosomes {muton} can mutate. Mutations include nucleotide deletions, insertions, and changes {point mutation}. Mutations include chromosome number or structure changes. DNA regions can delete, insert, invert, double, and alter.
rate
Trait mutation rate is 10^-4 to 10^-6 per generation. One to ten percent of cells have mutations.
affects
Mutations are typically bad, but bad mutations can be good in new environments. Mutations degrade good, working genetic code to make it more variable, and this process adds to genetic variability. Higher mutation rates affect organisms with more genes more.
experiments
In animals or plants, to discover if genes {candidate gene} relate to diseases, researchers mutate genes to see if mutation causes disease symptoms.
Higher mutation rates typically cause poorer adaptation {error catastrophe, mutation}.
Modified plant genes can go only to ovules {maternal inheritance}, not to pollen.
Codons, with same first two bases but different third base, can code for the same amino acid. For those codons, third-base mutations {silent mutation} do not make any difference to survival.
However, different codons bind to different t-RNAs, and some t-RNAs are more abundant than others. Times to bind scarcer t-RNA are longer than times for more abundant t-RNA. Time differences can affect protein folding, change protein structure, and affect function.
Silent mutations can accumulate and eventually encode new proteins. For example, mutations can cause body-part replication. Subsequent generations can modify replicated parts to make new structures and functions.
Gene changes can help identify which genes are performing which functions.
process
Plasmids and other vectors can have genes. Added chemicals or enzymes can mutate genes {in vitro mutagenesis}. Vectors go into hosts, express genes, and make protein.
methods
Gene changes can be at restriction endonuclease sites. If sites have overhanging strands, S1 nuclease can remove overhanging single-strand DNA, or DNA polymerase can extend shorter strands, to make blunt ends. Linkers can attach to blunt ends.
Chemicals can alter gene nucleotides. Sodium bisulfite makes C into U. Hydrazine and formic acid delete nucleotide nitrogenous base, leaving sugar and phosphate. At low nucleotide concentrations or in harsh chemical conditions, DNA polymerase can add wrong nucleotides during DNA synthesis.
In vitro mutagenesis {site-directed mutagenesis} can study binding sites and functional regions. Site-directed mutagenesis hybridizes synthetic 10-base to 15-base oligonucleotides to DNA sites. Oligonucleotides differ from original sequences by one nucleotide at end. Oligonucleotides hybridize well to original sequences, because they differ by only one nucleotide. Hybridized sequences replicate to make mutated genes.
enzymes
DNA ligase connects perfectly aligned DNA strands. Mutated ends do not ligate {ligase-mediated}, showing mutation locations. RNase A cuts DNA-RNA complexes where sequences mismatch and can detect mutation locations. Osmium tetroxide and hydroxlamine cut at unmatched C or T bases. Restriction enzymes fragment single-strand DNA. Different DNA fragments have different conformations and so different mobilities {single-stranded conformation polymorphism} (SSCP).
Near synapses, neurons have granules {mRNA storage granule} to provide mRNA for synapse connections. Animal egg-cell mRNA storage granules provide mRNA for early development.
RNA {small nuclear RNA} (snRNA) can have sequences complementary to intron 5' sequences.
RNA interference, microRNA, and piRNA {small silencing RNA} silence genes.
After viral genes or mobile genetic elements express, double-stranded RNA can catabolize their mRNA {RNA interference} {RNAi}. When extra gene copies insert into organisms, double-stranded RNA suppresses expression.
short interfering RNA
Dicer enzyme hydrolyzes double-stranded RNA to make 22-base-pair double-stranded RNA {short interfering RNA} {small interfering RNA} (siRNA). siRNA has unpaired nucleotides at ends. Proteins {Argonaute protein} can bind to siRNA ends. siRNA unlinks its two strands. One strand binds to proteins {RNA-inducing silencing complex} (RISC). RISC tries to bind to mRNA. If binding is good, Slicer enzyme splits mRNA, which leaves RISC. If binding has short mismatched regions, mRNA stays bound to RISC. Both cases have no translation.
evolution
RNAi began in plant, animal, and fungi common ancestor, one billion years ago, to protect against viruses and mobile genetic elements.
experiments
Using RNAi, researchers can destroy gene mRNA and study results.
RNAi can regulate growth and development using regulatory double-stranded RNA {microRNA} precursors, which Dicer makes into microRNA. MicroRNA has same metabolism as siRNA. Two hundred microRNA genes include JAW, lin-4, and let-7. Small RNA and protein numbers are approximately the same.
RNA {piRNA}, with 25 to 30 nucleotides, binds to Piwi protein in mammal male germ cells, especially at meiosis, making 20000-base to 90000-base clusters {piRNA complex} (piRC). Piwi protein is homologous to Argonaute protein.
DNA-sequence ends {3' end} can have expressed sequence tags. At 3' ends, ESTs accumulate, end within 10 bases of each other, and overlap near polyadenylation consensus sequence, after coding region and before polyA terminus. 3' ends are within last 1500 bases of transcript 3'-UTR.
Nucleic acids have 5' ends {cap, nucleic acid}.
DNA sequences {cistron}, typically having several genes, can underlie biochemical functions.
Messenger RNA can be templates for single-stranded DNA synthesis {complementary DNA} (cDNA). cDNA corresponds to cell-DNA exons.
RNA {complementary RNA} (cRNA) can transcribe from single-stranded DNA.
Gene regions {exon} transcribe as mRNA sequences. Exons are not introns. Functional mRNAs have spliced exons, with intron regions removed.
Genes have regions {intron} that are not for translation. Introns can affect protein folding.
DNA sequences {open reading frame} can code for one mRNA, because they have no stop codons until end.
Poly(A) polymerase adds 100 to 300 adenosines {polyA tail} to 3' ends. Perhaps, polyA tails block RNAse.
DNA contains repetitive sequences, introns in gene-coding regions, untranslated sequences 5' and 3' to gene-coding regions, pseudogenes, and transposed regions {junk DNA} {selfish DNA}. Almost all DNA is non-coding junk DNA. Over time, species can gain and lose junk DNA.
repeats
Most junk DNA is repetitive. Species have distinctive repetitive sequences. Repetitive regions change in cancer and cell growth.
Satellite DNA has 100 bases. Minisatellite DNA, such as GGGCAGGAXG, has 10 to 20 bases, is at 1000 loci, has 5 to 50 repeats, and initiates gene swapping. Microsatellite DNA has less than 20 bases.
Alu repeats are only in primates, repeat million times in different locations, are 10% of DNA, have internal promoter, and are similar in sequence to ribosome gene.
B1 repeats are in mice.
LINE-1 repeats contain reverse transcriptase, are 15% of DNA, and have a hundred thousand copies.
introns
Humans and other highly evolved species tend to have more, longer, and more-complex introns.
untranslated regions
5' and 3' untranslated regions contain enhancers and suppressors and regulate protein translation. Humans and other highly evolved species tend to have longer and more-complex 5' and 3' untranslated regions.
transposition
Retroviruses and bacteria cause transposition. DNA transposition rate in primates is lower than in mice. Immune responses use transposition.
language
Junk DNA statistically appears to have sequence patterns with characteristics similar to patterns in language. Junk sequences can be codes for processes that control signal transmission, gene expression, protein alteration, or other processes that use information.
Many non-functional DNA regions {pseudogene} are similar in sequence to actual genes, such as ribosome genes. Reverse transcription can incorporate host or foreign mRNA into DNA {processed pseudogene} {retropseudogene}, using RNA-mediated retroposon transposition. Mutations can make pseudogenes. Pseudogenes can have copies and repeats. They can harbor RNA sequences. Pseudogenes can represent information to turn off or turn on. Species have distinctive pseudogene patterns.
In eukaryotes, important genes and satellite DNAs repeat {DNA repeat, genetics}. Eukaryotes have many repeated or duplicated DNA regions. Histone, rRNA, tRNA, and other genes that are fundamental to cell processes repeat many times in same chromosome regions {clustering, chromosome}.
gene duplication
Gene duplication allows variant protein forms to arise. Original gene still provides needed protein. Duplicate gene can mutate and recombine to make variant protein, such as globin chains. Duplication can revert, by gene conversion after sequence break, using normal sequence as template to repair mutant sequence.
Besides repeated and duplicated genes, eukaryote genomes have many short, often tandemly repeated sequences {single-sequence DNA} {satellite DNA} of 5 bases to 200 bases.
Yeast has retrotransposon Ty elements, which contain reverse transcriptase, whose direct repeats or long terminal repeats {delta element} have promoters.
Simple tandem repeats {simple tandem repeat} (STR) {microsatellite DNA}, like repeated CA, vary in repeat number. Mononucleotide, dinucleotide, trinucleotide, or tetranucleotide tandem repeats, such as CA dinucleotide repeats, with differing lengths, are in all chromosomes. DNA markers can have mononucleotide, dinucleotide, trinucleotide, or tetranucleotide repeats in tandem arrays, such as CA or GT dinucleotide repeats. Perhaps, they distribute throughout genomes. Microsatellites can aid genetic mapping. Simple tandem repeats can have polymorphism.
Minisatellite DNA tandem repeats {variable-number tandem repeat} (VNTR) between restriction sites {hypervariable loci} can vary in repeat length and repeat number and are useful for DNA fingerprinting. Forensics, cell cultures, and family relationship tracing can identify individuals. Large-enough polymorphism sets can provide high probabilities that identifications are unique. Myoglobin-gene introns, mitochondrial DNA, and class II HLA gene DQalpha test for polymorphisms in forensics.
Satellite DNA, found only in vertebrates, can have 130-base to 300-base repeats that are not tandem {short interspersed element} (SINE). RNA polymerase III transcribes SINEs. SINEs include Alu repeats. Human genome has one million Alu repeats. SINE-repeat sequences entered genomes by transposition.
Satellite DNA, found only in vertebrates, can have long repeats {long interspersed element} (LINE) that are not tandem. LINE repeat sequences entered genomes by transposition.
Satellite DNA {minisatellite DNA} can have 10-base to 100-base sequence that tandem repeats 20 to 50 times. In all chromosomes, 10-nucleotide tandem repeats, with differing lengths, often cluster near telomeres. Minisatellite DNAs do not transcribe. At genome locations, repeat number gradually evolves, so individuals have different repeat numbers.
uses
Minisatellite DNA can be for genetic mapping. Minisatellite DNA lengths are unique to individual and can be for identification by DNA fingerprinting.
Minisatellite DNA lengths are unique to individuals {DNA fingerprinting}, for identification. At genome locations, repeat number gradually evolves, so individuals have different repeat numbers.
Genes and cistrons have control regions {operon}, where repressors bind to prevent transcription.
Genes {repressor gene} can make repressors, which bind to operator regions.
Repressors bind to operon regions {operator region} that precede coding regions.
RNA polymerase binds to regions {promoter region} just before coding regions. Repressors block RNA polymerase binding. Derepressors can bind to repressors at allosteric sites to release repressors from operators. Corepressors can bind to repressors to aid repression. Inducers can bind to repressors to block repression.
RNA-polymerase-III 50-base internal-control regions have two regions {zinc finger} that bind zinc.
Oligonucleotides {primer DNA} can start polymerization by DNA polymerase.
Repeated CGs {CpG island} can be in regulatory DNA.
Organism physical, biochemical, and physiologic traits {phenotype}| result from genotype and environment interactions. Johannsen invented the word [1909]. Organisms can express behavior and structure genes. Some phenotypes confer better fitness and adaptation. Offspring phenotypes are typically intermediate between parent phenotypes.
roles
Phenotypes can have adaptations, be pleiotropes, have neutral fitness, or have exaptations.
Gene phenotypes vary in expression {expressivity}.
New species come from repeated-body-segment structure and number changes. Modifications are similar to existing parts {homeosis} {homeotic transformation}. Parts can have jumps. For example, upper thoracic vertebrae can have no ribs, or lower cervical vertebrae can have ribs.
Gene phenotypes have expression ranges {penetrance}.
Traits {phenocopy} can have appearance similar to other traits but have different causes. Phenocopy rate increases as onset age increases and as severity decreases.
Genotypes and environments vary phenotypes {phenotypic variance}.
One gene can control more than one phenotype {pleiotropism}|.
Organism functions and behaviors {trait}| have genetic determinants. Tasting phenylthiocarbamide and other traits can depend on only one gene.
Structures can arise and then later have purposes {exaptation, role}.
Phenotypes can be adaptation side effects {spandrel, phenotype}, because they are pleiotropic.
Genetic traits typically interact {gene interaction}, allowing different optimum conditions or gene combinations. Environments and other-gene effects can suppress gene potentials. Most genes act differently depending on other-gene actions. Gene changes can affect individuals, families, troops, groups, demes, populations, and species. Genes that favor adaptability at more than one level are reinforcing. Genes that favor one level but harm another level are counteracting.
Most traits {polygenetic trait}, such as intelligence and personality, depend on multiple genes. Learning and environment affect polygenetic phenotypes more.
Independent genes can add {polygenic inheritance} effects to make phenotypes, such as skin color and height.
Independent genes can interact to produce phenotypes. Independent dominant genes {complementary genes} can interact to determine phenotype.
Independent genes can interact so one dominant allele is complementary but other dominant allele is not complementary {supplementary genes}, such as in albinism or skin color.
Earlier traits can reappear in modern organisms {atavism}|.
Animals {chimera}| can have parts or genes from other animals.
In individuals, different phenotypes can express at different body locations {mosaicism}| {mosaic, genetics}. Individuals can have male or female tissues, where one allele prevails.
Lower-organism phenotypes can appear in individuals {recidivism}|.
individual regularity {idiographic law}.
species regularity {nomothetic law}.
Plants have asexual and sexual reproduction, and plant cells have chromosomes {plant genetics}. Plants make many seeds, so seed generations have many mutations and recombinations. Many plants have polyploidy, allowing more variation.
cloning
Electroporation and tungsten bullets can introduce DNA fragments into plants. The small flowering-plant weed Arabidopsis thaliana can clone genes.
cloning: expression
Plants can express oils and seed proteins. Plants can add drought and frost resistance. Plants can become able to fix nitrogen.
insects
Plants can protect themselves from insects. Bacillus thuringiensis sporulation makes protein crystals that kill many insect larvae. Tomato, potato, and cowpea serine-protease inhibitors inhibit serine protease in insect intestines.
weeds
Weeds grow faster and so use more chemicals than regular plants. Plant-killing chemicals inhibit growth mostly in weeds, but other plants have affects. Herbicide-tolerant plants have enzymes that break down herbicides, increase herbicide-targeted enzymes, or have mutated enzymes that herbicides cannot affect. Bacteria can have enzymes that break down herbicides.
Ultrapetala gene {petal gene} controls petal number by modifying meristem cell number.
Double-stranded plant DNA viruses {geminivirus} can hold foreign genes for cloning in plants.
Agrobacterium-tumefaciens Ti plasmids cause tumors {crown gall tumor} in dicot plant cells. Agrobacteria have genes that make proteins that hold bacteria on plants.
Agrobacterium-tumefaciens large, circular, DNA plasmids {Ti plasmid} can cause crown gall tumors. Ti plasmids carry genes and antibiotic marker genes into plant leaf cells, in the leaf-disk technique. Ti-DNA sequences can insert into dicot-plant-cell chromosomes. Ti DNA codes auxin enzyme.
Regenerating-plant-cell molecules activate Ti-plasmid genes {vir gene}, which make trans-acting proteins to transform cells to tumors. After vir genes start making proteins, cells release transposable elements with 25-base border ends as single-strand DNAs {T-DNA}.
T-DNA codes for special amino acids {opine, amino acid} that other Ti enzymes break down for food.
Ti DNA codes enzymes and hormones {auxin enzyme} {phytohormone} that together cause tumor-cell division.
Plant tissue {callus, plant}| can cover wounds. Callus cells can make new plants. Different callus cells from the same plant callus make different plants {somaclonal variation}, because gene expression differs.
After cutting leaves, edges regenerate using special cells {edge cell}.
Removing cell walls from plant embryo cells, with fungal cellulase, leaves cells {protoplast}| surrounded only by plasma membrane. Protoplasts can start new plants.
One plant can make new plants {selfed}|, because plants can self-fertilize.
After transcription {post-transcription}, eukaryotic mRNA can change. For example, poly(A) polymerase adds 100 to 300 adenosines as a polyA tail to RNA 3' ends. Methylated guanosine can add to RNA 5' ends.
RNA can alter {adenosine-to-inosine editing} (A-to-I editing), especially in primate Alu repeats.
To regulate gene expression, cell or virus mechanisms can add methyl groups {DNA methylation} {methylation} to cytosines preceding guanines {CG pair}.
virus
Virus can methylate host genes to inactivate them.
cancer
Cancer genes often have demethylated cytosines in promoters.
drugs
Valproic acid tranquilizer and decitabine chemotherapy agent remove methyl groups from DNA or prevent methylation. Procaine affects DNA methylation.
purposes
Researchers methylate nucleotides to prevent cutting by restriction enzymes. Promoter methylation can suppress gene expression.
After translation {post-translation}, proteins can add side groups, go to special locations, and bind to lipids, sugars, and proteins.
Cells, perhaps only neurons, can substitute RNA bases at three-dimensional loops {recoding}.
Enzymes {reverse transcriptase} can make DNA from RNA, typically making mRNA into cDNA. Hundreds of genes code enzymes that can make DNA from RNA.
RNAs can be catalysts {RNA catalyst}.
RNase-P RNA part splits tyrosine-tRNA precursor to make tRNA.
Fungus-mitochondria mRNA and rRNA precursors, and bacteriophage mRNA precursors {Class I self-splicing}, can catalyze themselves to remove introns, using guanosine as cofactor. Introns have further processing to make different RNA catalysts.
Yeast and fungus mitochondria mRNA precursors, and Chlamydomonas chloroplast mRNA precursors {Class II self-splicing}, can catalyze themselves to remove introns, using no cofactors.
Some protozoa edit transcribed RNA to make correct reading frames, possibly using RNA catalysts.
Mammals edit intestine transcribed apolipoprotein B mRNA, possibly using RNA catalyst.
Enzymes {restriction enzyme} can cleave nucleotide sequences at sites. 150 enzymes {endonuclease}, such as FokI and NotI, cut DNA near 4-base to 8-base recognition sequences.
ends
Restriction enzymes can leave ends {blunt end} with paired bases or ends {sticky end} with overlaps. Sticky ends can bind to other sticky ends and then DNA ligase can seal them, allowing splicing with other DNA fragments. Blunt ends can become sticky by terminal transferase, which adds polyA or polyT to one strand. Blunt ends can become sticky by attaching a DNA linker, with recognition sites, to blunt ends and then cleaving with restriction enzyme.
middle
Endonucleases cut nucleic acids at sequence sites not at end. Pancreatic ribonuclease, T1 ribonuclease, and other ribonucleases cut only RNA. Bacterial restriction endonucleases and other deoxyribonucleases cut only double-stranded DNA.
S1 nuclease {exonuclease} pares back RNA and single-stranded DNA ends. Sticky ends can become blunt ends by removing single-stranded DNA using S1 nuclease.
Genes that make mRNA have exon regions for translation and intron regions not for translation.
introns
RNAs typically have several introns. Introns came from bacteria or, if protein folding requires them, have always been in genes. After transcription, mechanisms {RNA splicing}| splice introns out.
exons
Exons typically are functional domains, and proteins have different functional domains. Exons can mix in different ways to make membrane-bound or secretable proteins or to make proteins for different development stages or different tissues.
process
After mRNA leaves cell nucleus, cell processes splice out introns and join exons {mRNA splicing}, to make mRNA for translation. Introns have 5' sequences and 3' sequences.
Large ribonucleotide and protein particles {spliceosome} perform splicing. Spliceosomes have U1 and U2 small nuclear ribonucleoproteins, U1 and U2 small nuclear ribonucleic acids, and SF2, U2AF, and other proteins. Intron 5' ends split first. Intermediate RNAs have lariat shapes, because introns bind to themselves with 2'-5' bonds. Enzymes cut 3' ends, and other enzymes join exon ends. Introns leave as lariats, because introns bind to themselves with 2'-5' bonds to make circles.
Proteins {splicing regulatory protein} (SR protein) can determine which exons to keep, by binding to exonic splicing enhancer (ESE) or exonic splicing suppressor (ESS). SR protein is for fruitfly sex determination.
Protein actions can block RNA 5' sites after transcription, allowing only other splicing sites {alternative splicing}. Alternative splicing results in different-size and different-function proteins.
RNAs can splice pieces together, using mechanisms {self-splicing RNA} different than spliceosomes.
DNA sequences {transposon, DNA} can excise themselves and then insert at other genome locations {transposition, DNA}|. Transposons code for enzymes that recognize DNA splice sites.
methylation
Methylation inactivates transposons.
bacteria
Bacteria have Tn3 and Tn10 transposons with DNA insertion sequences (IS). Tn3 transposons code enzymes that act at transposon-resolvase sites to allow recombination, so they copy themselves, place copies at new sites, and leave originals.
bacteria: Agrobacterium
Agrobacterium infects plants with Ti plasmid.
yeast
Yeast has Ty elements, whose delta-element direct repeats have promoters. Ty elements contain reverse transcriptase.
Yeast MAT genes have mating-type alleles. Yeasts have two mating types, a and alpha. After mating, mating type changes to opposite mating type, as HO endonuclease cuts MAT site. a-gene and alpha-gene copies are far from MAT sites. Copies are templates to reconstruct MAT site as opposite mating type {gene conversion} {replicative transposition}.
Yeast sterile (STE) genes code for a and alpha pheromones, which stop cell growth and change cell shape. Pheromones combine both mating types to form diploids, causing yeast to mate. STE proteins are G-protein subunits (STE4) (STE18), protein kinases, and transcription factors (STE12). STE proteins (STE2) (STE3) can bind factors.
maize
Maize has Ac and Ds transposable elements.
retrovirus
Retroviruses have direct repeats with promoters and contain reverse transcriptase to allow transposition.
trypanosome
Trypanosomes use gene conversion to vary surface glycoproteins (VSG).
fruitfly
Drosophila have P elements. Drosophila have copia elements, which have direct repeats with promoters.
Fruitfly P elements and other transposition elements can code for enzymes that recognize DNA splice sites. By opening and closing splice sites, genes {transposon, genetics} {jumping gene} can excise and insert between any two splice sites.
Reverse transcriptase can make DNA {retrotransposon} {retroposon} from RNA, and DNA can insert back into genome at special sites. Virus-gene fragments can copy themselves and insert in genomes. DNA from retrovirus RNA {human endogenous retrovirus} (Hervs) is 1% of human genome.
All species have 750-base to 5000-base sequences that code for enzymes {transposase} that recognize DNA sites just beyond both transposase-gene ends.
process
Sites have 10-base to 40-base inverted repeats. Transposase enzymes recognize inverted repeats and cut out transposase-gene sequence between sites. Transposases recognize inverted repeat at other locations in genomes, plasmids, or phages and cut sequence to place transposase-gene sequence in those locations. If two transposons are near each other, transposases can cut at the farthest ends and both transposons, and any DNA between them {complex transposon}, can transpose as one sequence to inverted repeats at other locations.
Gene arrays can test for gene expression {gene expression, algorithms}.
array algorithms
Gene-expression-array algorithms automatically find background, errors, fiducials, normalization, signal values, spatial cross-talk, spots, replicate aggregates, and clustering.
gene expression analysis
Gene-expression analysis compares different tissues or conditions to find gene-expression patterns. Genes in the same biochemical pathways, genes with similar chemical reactions, and genes for similar cell processes have similar regulation and have similar gene-expression patterns.
gene expression visualization
To visualize expression patterns, expression spaces can have dimension number equal to experiment number. Experiments determine gene-expression ratios, which are expression-space points or vectors. Similar genes have points that cluster near each other in expression space.
Expression matrices have column number equal to experiment number. Gene-expression ratios are expression-matrix rows. Algorithms sort rows and columns to cluster up-regulated and down-regulated genes and/or experiments. Expression-matrix cells can have colors, such as red for up-regulated, green for down-regulated, and black for control levels.
cluster analysis
Using distance measures, genes and/or experiments can cluster. Clustering algorithms include hierarchical, self-organizing maps, K-means, fuzzy C-means, and expectation maximization. Statistical techniques identify gene classes and/or experiment classes and assign shared features. Hierarchical clustering makes hierarchies. Self-organizing maps group equal categories. Error-weighted gene-expression clustering retrofits clustering algorithm information to use error-propagation information.
assay multiplexing
Several assays can be simultaneous, or several samples can be in same wells {multiplexing, assays}.
Basic Local Alignment Search Tool {BLAST algorithm} searches sequence databases for similar sequences.
Algorithms {ClustalW algorithm} can align multiple sequences.
Nucleotide or amino-acid sequences can align {Comparative Sequencing Analysis} (CSA).
Algorithms {FASTA algorithm} can search sequence databases for similar sequences.
Algorithms {MSA2.1 algorithm} can align multiple sequences.
Nucleotide and amino-acid sequences can align using algorithms {Smith-Waterman algorithm} {Gotoh-Smith-Waterman algorithm} or filtering algorithms {Chang-Marr algorithm} {Filtered Smith-Waterman algorithm}.
Restriction-enzyme techniques can recombine nucleic-acid sequences {recombinant DNA}|.
Experiment assays can analyze physical substances {sample, DNA}. Samples come from subjects.
Diluting main sample {aliquot}| creates secondary samples.
Samples {parent sample} can make aliquots.
Sample information is in databases {logging}.
Most experiments test samples by the same method more than once {replicate, sample}|.
Techniques {amplification, DNA} {DNA amplification} can increase number of DNA-fragment copies. In vivo amplification amplifies repeat sequences in fragile X syndrome. In vitro amplification uses cloning or polymerase chain reactions.
purposes
Amplified DNA indicates mutations, translocations, viral and bacterial infections, sex, genealogy, living and extinct species differences, and forensic identification.
DNA synthesis
To make probes or primers, first blocking-group covers 5' or 3' hydroxyl groups of two nucleotides. Then other two hydroxyl-groups react to make phosphodiester bonds. Then acid or base removes blockers. Process repeats to elongate chain.
After restriction-enzyme digestion, DNA fragments can amplify, and relative lengths indicate polymorphisms {Amplified Fragment Length Polymorphism} (AFLP).
After electrophoresis, DNA fragments flow in transparent tubes {cuvette}|, and lasers excite dyes.
Two complementary DNA or RNA single strands can form a double-stranded molecule {hybridization, DNA}|. Two nucleic-acid strands can pair by hydrogen-bonding A and T, or A and U in RNA, and C and G. DNA or DNA and RNA complementary-strand nitrogenous bases can have hydrogen bonding.
arrays
All array spots have hybridization, as cartridge holds array in position. Hybridization measurement depends on dye sensitivity and dynamic range. If array spots are close together, they can cross-hybridize. Evaporation also causes problems, so arrays have humectants, lids, or dewpoint controls. Spotting pins must be 0.2 mm small and clean. Alternatives to spotting include acoustic focusing, multi-nozzle piezoelectric jets, and continuous solid pin spotting. Probes, cDNA arrays, and oligonucleotide arrays are alternative hybridization methods.
Methods {polymerase chain reaction}| (PCR) can make many DNA-sequence copies using heat-stable polymerase, 20-base primers complementary to + strand at one sequence end, and 20-base primers complementary to - strand at other end. Synthesized strands are additional templates, so process doubles copies each primer-annealing, strand-elongation, and dissociation cycle.
purpose
PCR can detect defined sequences in DNA samples. PCR can make stutter bands and add bands resulting from extra nucleotide addition by Taq polymerase.
mRNA amplification
DNA has small amounts, but mRNA has much larger amounts. First, reverse transcription converts mRNA to cDNA and then PCR amplifies cDNA (RT-PCR).
DNA amplification
Machines heat DNA double helix to 94 C for several minutes to make single-stranded DNA. Solution contains DNA polymerase from heat-tolerant organisms and the four bases.
When temperature lowers to 30 C to 65 C for 30 seconds, 20-nucleotide primer DNA binds to DNA, outside region to copy. One primer is for 5' strand, and one primer is for 3' strand. Annealing puts complementary 20-base primer at both ends.
Machines raise temperature to 72 C for some minutes, to allow DNA polymerase and bases to extend both primers beyond other primer region. Now both double-helix molecules have primer on one end and extend beyond other primer on other end. Elongating both strands uses heat-stable DNA polymerase, which synthesizes DNA.
Machines heat DNA to 94 C for several minutes again to extend same primers through other primer at strand ends. Now all synthesized-strand lengths are the same, from one primer through other primer. There are now four DNAs.
Cycles make twice as many DNA strands, and process uses new and old strands again, making chain reactions. Repeating process 30 to 60 times makes millions of copies.
primers
Primers can be genome repetitive sequences, such as Alu repeats. Alu repeats are 300 bases, but smaller region varies little in humans. Alu repeats are in both directions.
primers: nested
After one PCR, second primer that binds inside copied sequence {nested primer} can amplify shorter sequences.
primers: concentration
If one primer has high concentration and one has low, system makes mostly single-stranded DNA {asymmetric PCR}, with no chain reaction.
contamination
Contamination with wrong DNA is common. Negative controls make sure correct DNA amplifies.
Sequence tags {adapter sequence} are in probes.
Single-stranded DNA sequences {oligonucleotide}| {oligo} can have less than 61 bases.
To add deoxyribonucleotides to nucleic acid by DNA polymerase requires oligonucleotides {primer, DNA}|.
Short RNAs or single-stranded DNAs {probe, DNA} {DNA probe} can detect complementary base sequences by hybridization. Probes have 25 to 60 bases and can have 3'-hexyl-amine. Probes attach to last 1500 base pairs closer to transcript 3' ends, where genes have unique short DNA regions. Bacteria and yeast genes have unique primers. Higher organisms have three million different expressed sequence tags (EST).
process
High-concentration purified probes are in 96, 384, or 1536 wells on plastic microtiter plates. Robots take probes from microtiter plate to make same number of spots on glass slides, one slide for each RNA sample to test. Multiple probes test each gene.
Nucleotide sequences {zipcode} can attach to molecules to allow probe complementary nucleotide sequence {zipcode complement} to hybridize.
Genomes can have known sequences {DNA sequencing}. H. influenzae has 1.8 million bases and 800 genes. E. coli has 4.5 million bases and 2000 genes. Saccharomyces yeast has 12 million bases and 6000 genes. P. falciparum has 30 million bases and 6500 genes. Caenorhabditis elegans roundworm nematode has 100 million bases and 10000 genes. Arabidopsis thaliana weed has 120 million bases and 20000 genes. Drosophila melanogaster fruitfly has 165 million bases. Fugu rubripes is zebrafish. Mus musculus mouse has 3000 million bases. Humans have 3500 million bases and 30000 genes.
methods
Sequencing {plus-minus method} can elongate DNA sequences using DNA polymerase.
Sequencing {Maxam-Gilbert sequencing method} can chemically degrade labeled, short DNA chains at G, C, A and G, and T and C to make fragments and then electrophorese all four, separately or together, to separate by size.
Sequencing {Sanger sequencing method} can elongate DNA chains and randomly terminate them with nucleotides that cannot bind to next ribose, using A, G, T, and C 2',3'-dideoxynucleoside triphosphates, and then electrophoreses all four, separately or together, to separate by size.
Mixing differently labeled clones {multiplex DNA sequencing} allows easier processing. Labels identify clones.
DNA-fragment ends can have fluorescent dyes, which respond to laser light. Dye terminator attaches to nucleotide 3' ends. Dye primer attaches to 5' ends. Longer fragments have higher signals. Fragments separate by electrophoresis in gels {horizontal ultrathin gel electrophoresis} (HUGE) or capillary tubes {capillary gel electrophoresis}. Because charges are equal, fragments leave gel or tube by size.
Scanning tunneling electron microscopes can sequence DNA strands by wand distance needed to maintain constant voltage. They can sequence 40000-base DNA fragments one base at a time. Exonuclease removes end nucleotide. Shining laser light and recording with photomultiplier reads nucleotide type.
Gas or liquid mixtures can separate using gas chromatography, liquid chromatography, supercritical fluid chromatography, or capillary electrophoresis.
Computers overlap sequence information about DNA fragments {contig, sequencing} to build longer sequences, to map large fragments and then chromosomes.
Cluster hierarchies can look like tree diagrams {dendrogram, sequencing}.
If many DNA fragments insert into many bacteria, plate colonies can account for all DNA fragments {DNA library} from foreign organisms.
DNA analyses include comparing DNA sequences. Sequences of same gene from different organisms can align somewhat {homology, DNA}| {homologous sequences}.
Probes hybridize with clone and fragment regions. Overlapping DNA fragments hybridize to same probe. 20-base oligonucleotides can be probes to find overlapping DNA fragments. For clone ends, random sequences can be probes {sequence-tagged connector} (STC). Probes can have minor-groove binder to enhance exact hybridization, allowing shorter probes.
Processing identifies unique 200-base to 500-base sequences, with unique primers, from known locations {sequence-tagged site} (STS). Perhaps, clones share STS.
After DNA fragments exit capillary, plot {electropherogram} shows relative dye concentration versus time expressed as frame number. In electropherograms, small peaks {pull-up peak} can appear under main dye peaks. Incorrect dyes, dye contamination, or capillary or fluid-property changes after spectral calibration can cause pull-up peaks.
In direct methods, mRNA-AAAAA + reverse transcriptase + Oligo-dT Primer + dNTPs + Cy3 and Cy5 or SymJAZ dye-dNTP -> Dye-cDNA {DNA labeling}.
In random priming methods, mRNA + reverse transcriptase + T7-T20-24 + MuLV -> DNA/RNA + hydrolysis -> cDNA first strand + Bst DNA polymerase + ligase + pN8-9 -> T7-ds cDNA + dye-UTP + T7 RNA polymerase + IVT -> labeled cRNA.
In RNase H methods, mRNA + reverse transcriptase -> DNA/RNA + RNase H -> DNA/RNA + DNA polymerase + ligase -> T7-ds cDNA + dye-UTP + T7 RNA polymerase + IVT -> labeled cRNA.
purposes
DNA labeling can measure labeled-cRNA dye incorporation, reverse-transcriptase conversion, fluorescence-specific activity, minimum RNA, maximum RNA, IVT amplification, total amplification, and length.
controls
Control reagents aid spot finding, image analysis, and signal quantification. Array probes monitor spotting, labeling, hybridization, printing, attachment, and features. Labeling controls monitor enzyme activity, target stability, and dye incorporation during labeling protocols. Hybridization controls monitor mixing, stringency, and washing during array-hybridization protocol. Printing and attachment controls monitor array manufacturing, probe attachment, and lot-to-lot variability. Feature controls normalize signal variability.
DNA analyses include finding sequences longer than cloned DNAs by looking for their overlaps. First clone can screen whole-genome clone library for overlapping sequences. If overlap, second clone can screen, and so on, to build longer and longer sequences {chromosome walking}.
DNA sequencing can use modified shotgun methods {polony sequencing}.
DNA-fragment mixtures can separate fragments by lengths {fragment analysis}.
Electrophoresis gels have band sequences {lane}, starting from top sample bands.
Electrophoresis separates eluted DNA fragments, to compare peak separations, spectral separations, and spatial separations {fragment separation}.
Compounds less soluble in stationary phase elute faster {retention time, elution}.
DNA analyses can separate cell RNAs or mRNAs on gels and transfer gel-band contents to filters, where RNAs can hybridize to known RNA or cDNA sequences {Northern blotting}. Northern blotting compares mRNAs to cDNAs to study gene expression.
DNA analyses can separate DNA fragments on gels and transfer gel-band contents to filters, where DNA fragments can hybridize to known DNA sequences {Southern blotting}. Southern blotting can detect gene rearrangements that make antibodies and T-cell receptors. It can detect disease-caused gene rearrangements and deletions. It can detect related genes in organisms and homologous genes from different species. It can detect mRNA-splicing-caused intron removal and exon use. It can detect mRNA splicing to make alternative proteins. It can detect nested genes.
DNA transcription makes tRNA, rRNA, and mRNA {gene expression}|.
purposes
Gene expression studies gene functions, regulation, and interactions. Hybridization measures gene expression for gene discovery, gene identification, biochemical pathways, and disease mechanisms.
probes
Human-genome arrays have probes for all genes. Human-transcriptome arrays have probes for all transcripts. SNP arrays have all SNPs. Arrays can have immune, toxicity, or cancer-gene probes.
RNA or single-strand DNA oligonucleotides {antisense RNA}|, complementary to cell mRNAs, can bind to mRNA and prevent gene expression. Antisense RNAs can be in vectors, or techniques can inject them into cells.
300-base to 500-base sequences {expressed sequence tag} (EST) are specific to expressed gene regions, typically at 3' ends. ESTs map gene chromosomal locations from several tissues, recover corresponding gene sequences by electronic-database similarity searching, and retrieve complete cDNA clones for further analysis. Whole-genome shotgun sequencing using EST assembly reduces redundancy and creates longer consensus sequences.
For gene-probe spots and dyes, software calculates ratios {expression ratio} {gene expression ratio}: normalized expression level divided by normalized expression level for control gene. Average expression ratio is 1. If expression ratio is greater than or equal to 2 {up-regulated, expression} or less than or equal to 0.5 {down-regulated, expression}, genes have significant expression {differentially expressed}. Expression-ratio base-two logarithm averages 0, is +1 if expression ratio is 2, and is -1 if expression ratio is 0.5.
Gene similarity measures can be distances {gene distance} between expression vectors in expression space.
metric
Distances can have metrics {metric distance}. Distance can always be positive. Distance between point and itself can always be 0. Euclidean distance between two points can always be less than or equal to sum of distance from first point to third point and distance from third point to second point {triangle rule}.
metric: Euclidean distance
Euclidean distances can be differences in point coordinates. Euclidean distances are metric.
semi-metric
Distance measures {semi-metric distance} can be always positive and have distance between point and itself always zero, but not obey triangle rule.
To emphasize variation amounts, especially for timed experiments, methods {scaling method} can reduce large expression-ratio values by changing expression-ratio range. Scaling can set average logarithm to zero {mean centering}, by subtracting baseline value. Scaling can adjust logarithm range to -1 to +1. Scaling can normalize expression-vector magnitudes to 1.
Gene-expression technologies can use cell extracts from different tissues, same tissues under different conditions, or same tissues under same conditions, over time sequences {serial analysis of gene expression} (SAGE) {expressed RNA}. From RNA, two cell extracts from same tissues under same conditions can make first-strand cDNA labeled with fluorescent dye, one with Cy3 and one with Cy5. Purified labeled cDNA solution soaks slides at optimum temperatures for times. Robots measure slide-spot probe-DNA and labeled-cDNA hybridization.
Compared to control level, genes can have less expression {down-regulated, gene}. Less expression under same conditions indicates similar biological functions.
Compared to control level, genes can have more expression {up-regulated, gene}. More expression under same conditions indicates similar biological functions.
Artificial situations {experiment} can test hypotheses or answer questions. Genomics experiments use one or more assays, samples, and markers.
Arrays can have random sets of spots with various concentrations and known green-intensity vs. red-intensity ratios {Random Ratio Dilution series test} (RRD). Automated spot finding works at the 85% level. Variation coefficient {coefficient of variance} (CV) is less than 20%.
Lasers can fluoresce microarray to read sample results {reader, microarray} {microarray reader} {scanner, microarray} {microarray scanner}. Displays can zoom, track, and normalize arrays or array sets. Dual red/green lasers need constant laser-spot size and large field depth. Scanning simultaneously minimizes spatial crosstalk. Microarrays are in automatic loaders to maintain positions.
Control samples {standard sample} calibrate instruments or methods.
Oligonucleotides attach to plates {array} in rectangular patterns, to test one sample for hybridization.
plates
Plates can be silicon chips {DNA chip}, plastic blocks with small wells {microarray, plate}, optical-fiber tips {bead array}, or glass slides {planar array}.
process
For example, plastic blocks have wells. Wells have reactive-chemical solutions to assay samples. Array probes samples by hybridizing oligonucleotides to sample RNAs or cDNAs. Reader detects hybridization amount using light. Statistical and comparative calculations follow.
Sample plates {master plate} stored in freezers can make daughter plates.
Master plates supply other plates {daughter plate}.
Arrays {microarray} can have 9x9-spot matrices at hundreds of positions, to test many genes against one or more test oligonucleotides, plus controls and fiducial-probes.
Plates {microtiter plate} can have small wells.
Sample plates contain pits {well, array} that can hold one or more samples.
DNA fragments inserted into host nucleic acids can replicate in host organisms {cloning}|.
hosts: bacteria
Plasmids can insert up to 1000 bases. 50,000-base bacteriophage viruses can infect bacteria and can insert up to 15,000 bases. 300,000-base bacterial artificial chromosome DNA can have all bacterial-chromosome functional regions. Cosmids can hold 45,000 bases between cos sites. Gene-product secretion is preferable to harvesting cells.
In bacteria hosts, eukaryote proteins do not fold properly. Foreign proteins can kill bacteria. Bacteria have no post-translation enzymes.
hosts: yeast
Gene-product secretion is preferable to harvesting cells. In yeast hosts, proteases can destroy generated proteins.
For yeast hosts, replicating nucleic acid can be yeast artificial chromosomes.
Two-micron-circle yeast plasmid has replication origin that makes many copies per cell cycle. Other plasmids that use autonomously replicating sequence, sometimes helped by centromere sequence, make one or two copies per cell cycle. Yeast plasmids {shuttle vector} can work in bacteria.
Yeast vectors {integrating vector} with no replication origin integrate gene into yeast genome.
hosts: plants
For plant hosts, replicating nucleic acid can be Ti plasmid.
hosts: insects
For insect hosts, replicating nucleic acid can be baculovirus. Insect cell cultures have high costs. Gene-product secretion is preferable to harvesting cells.
hosts: mammals
For eukaryotic hosts, replicating nucleic acid can be virus or retrovirus. Mammalian cell culture has highest costs. Gene-product secretion is preferable to harvesting cells.
DNA fragment
DNA fragments can come from foreign organisms by cutting chromosomal DNA into DNA fragments using restriction enzymes. DNA fragments can come from mRNA by making cDNA from mRNA using reverse transcriptase and then making double-stranded DNA from cDNA. Synthesis methods can synthesize DNA.
polylinker
DNA fragments have polylinkers added at both ends, to allow nested cuts by different restriction enzymes.
insertion
DNA fragments can link into replicating nucleic acids using restriction enzymes to cut both nucleic acids and then allowing recombination.
selection
After replicating nucleic acids go into hosts, agents kill hosts if they do not have protecting genes in replicating nucleic acids. For example, bacteria with no plasmids die, because plasmids have genes to protect against antibiotics.
DNA
Host cells that live have DNA fragments, for extraction or secretion. Hybridization can test extracted or secreted DNA for DNA fragments. DNA sequencing can test for DNA fragments. Antibody binding or direct protein assays can test extractions or secretions for DNA-fragment gene products.
Toxic changed or foreign genes destroy tissue {cell ablation, cloning}.
Organisms, cells, and molecules can duplicate {clone}|.
Bacteria {colony, bacteria}| can grow on media.
DNA analyses can cleave chromosomes by restriction enzymes to make DNA fragments, separate fragments by size, and use fragment overlaps to mark relative restriction-enzyme-site positions {restriction map}.
Blunt ends can become sticky by attaching DNA {linker} containing recognition sites to blunt ends and then cleaving with restriction enzymes.
DNA fragments inserted into replicating nucleic acids can have many possible restriction enzyme sites {polylinker}, to allow nested cuts by different restriction enzymes.
Inheritable DNA-sequence positions {marker}| are restriction-enzyme cutting sites, fragment-length polymorphisms, genes, minisatellite DNAs, or microsatellite DNAs. Markers have inheritance patterns.
Replicated nucleic acids have added genes {marker gene}, to indicate foreign-DNA insertion and DNA replication.
bacteria
Hosts with added antibiotic resistance genes make proteins that resist antibiotics, whereas hosts with no such genes die. Beta-galactosidase gene makes protein that metabolizes galactose and makes color. Hosts with no beta-galactosidase gene have no color.
yeast
Yeast can grow without leucine if they have LEU gene, without histidine if they have HIS3 gene, without lysine if they have LYS2 gene, without tryptophan if they have TRP1 gene, and without uracil if they have URA3 gene.
plants
Genes {beta-glucuronidase gene} {GUS gene} can make protein that makes glucuronides. Plants have no glucuronides, so E. coli GUS genes can be markers for plants. Firefly luciferase gene makes light. Luciferase genes can be reporter genes for plants.
mammals
Thymidine kinase (tk) gene makes protein that makes thymidine triphosphate {thymidylate}. Mammalian cells (tk-) can have no thymidine kinase gene, so thymidine kinase genes can mark cells (tk+). Aminopterin inhibits all other thymidylate synthesis pathways, so only thymidine kinase gene can make thymidylate.
drugs
G418 inhibits protein synthesis and causes cell death. Aminoglycoside phosphotransferase (APH) gene makes protein that inactivates G418.
Methotrexate inhibits dihydrofolate reductase and causes cell death. Methotrexate-resistant dihydrofolate reductase (DHFR) gene makes protein that resists methotrexate.
Hygromycin-B inhibits protein synthesis and causes cell death. Hygromycin-B-phosphotransferase gene makes protein that alters hygromycin-B.
Mycophenolic acid inhibits GMP synthesis and causes cell death. Xanthine-guanine phosphoribosyltransferase (XGPRT) gene allows GMP synthesis from xanthine.
9-beta-D-xylofuranoyladenine (Xyl-A) damages DNA and causes cell death. Adenosine deaminase (ADA) gene metabolizes Xyl-A.
Replicating nucleic acids can have added genes {reporter gene} that catalyze reactions used to report that promoters are working or not, for gene-expression or transcription-factor studies. For example, chloramphenicol acetyltransferase gene (CAT) reacts with chloramphenicol. Reporter genes are after promoters, to provide direct promoter-activity assays.
If electric fields make holes in bacterial membranes {electroporation}, plasmids can enter bacteria.
Plasmids can enter bacteria during short high-heat periods {heat shock}|, in concentrated calcium-chloride solution.
Lipid vesicles {liposome}| with DNA or protein can fuse with cell membranes and enter cells.
Replicating nucleic acids can go into host organisms to make different organisms {transformation, DNA}|. Plasmids can enter by heat shock or electroporation. Bacteriophages can infect bacteria naturally. Transforming prokaryotic cells has high success rate.
Soy, maize, and other organisms {genetically modified organism} (GMO) can have deliberate genetic changes by genetic engineering.
Replacing genes with bad genes {knockout gene} makes animals that lack proteins. Transgenes can insert into normal gene positions, causing gene-function loss and affecting development.
Genes can transfer into eukaryotic-cell genomes {transfection}|. Mice, plants, and yeast have only one transfection per thousand cells. DNA can go to cell nucleus but not enter genome, so gene expresses until DNA breaks down {transient expression}. Transfection takes time. Mammalian cell lines must be immortal. Cell culture requires many cells.
types
Inject DNA fragments into cell nucleus {microinjection}. Precipitate DNA fragments with calcium phosphate, so cell-culture cells absorb precipitated DNA by endocytosis. Make liposome lipid vesicles, with DNA inside, that can fuse with cell membranes and enter cells. Fire tungsten microbullets, with DNA fused to them, into plant cells, to penetrate cell wall.
types: virus
Viruses can transfect. Omitting coat proteins prevents virus formation, so cells do not die.
Monkey COS cells include most SV40-virus DNA and make T antigen, which binds to SV40 replication origin. Plasmids with SV40 replication origin can transfect COS cells. Vaccinia virus is large and can hold bacteriophage RNA polymerase. Plasmids with bacteriophage promoter can transfect cells and suppress cell mRNAs. Insect baculovirus DNA is large and can hold genes in coat-protein DNA.
types: retrovirus
Retroviruses can go into all mammalian cells. Retroviruses first place provirus DNA sequence in genomes and then make retroviral RNA. The next stage {packaging, virus} makes complete viruses by adding coat proteins. Then cells die and release viruses. For transfection, experimenters remove packaging genes from retrovirus {helper-free}, to prevent making complete viruses, so cells live.
Changed or foreign genes can enter mouse embryo cells {transgenic mice} at chromosomal positions. Transgenic-mice descendants have changed or foreign genes and have new proteins.
organism
Mammals have cell and tissue interactions, so testing requires whole organisms.
process: injection
SV40, Moloney murine leukemia virus (MoMLV), or mouse mammary tumor virus (MMTV) microinjection can put changed or foreign DNA into cells. Cloned-gene microinjection into fertilized egg pronuclei can put changed or foreign DNA into cells.
process: cell addition
Mice embryos can change by adding altered cells. Mouse blastocysts have inner-cell {embryonic stem cell, blastocyst} (ES cell) layers, which can culture with fibroblasts or with leukemia inhibiting factor to prevent further differentiation. Embryonic stem cells can uptake and insert genes by homologous recombination. Then ES cells go into mouse embryos.
marker
Neo gene resists G418. ES cells with neo gene resist G418 and live.
embryonic development
In embryos, tissue-specific regulators express changed or foreign genes in one tissue but not different tissues. If changed or foreign genes are toxic, they destroy tissue {cell ablation, toxin}. Ablated cells prevent subsequent tissue development, allowing embryo location and function tracking {cell lineage study}. Retrovirus with E. coli lacZ reporter can trace tissue differentiation and cell migration.
Chinese-hamster ovary (CHO) cells {transgenic tissue} can track transgenic effects. Mammary glands can express transgenes.
DNA or RNA sequences {cloning vector}| can contain DNA or RNA from other sources and can replicate in host organisms. Vectors include plasmids, phages, retroviruses, cosmids, baculoviruses, bacterial artificial chromosomes, and yeast artificial chromosomes.
Cauliflower-Mosaic-Virus promoters {35S promoter} can be in soy, maize, and other genetically modified organisms.
Vectors {Bacterial Artificial Chromosome} (BAC) derived from F-factor plasmids can clone 100,000-base to 300,000-base DNA fragments in Escherichia coli.
Cloning-vector plasmids {cosmid} can contain lambda-phage cos gene, infect E. coli, and clone DNA fragments up to 45,000 bases between phage-end cos sites.
Bacteria can have 5000-base circular DNAs {plasmid}| that can insert up to 1000 bases. Cells can have 10 to 200 independently replicating plasmids {relaxed-control plasmid}. Plasmids {stringent-control plasmid} can replicate together with bacterial chromosomes. Artificial plasmids can be cloning vectors.
For yeast hosts, replicating nucleic acids can be artificial DNA with all yeast-chromosome functional regions {yeast artificial chromosome} (YAC). YAC replicates like yeast chromosomes.
parts
Yeast artificial chromosomes contain autonomously replicating sequence, centromere (CEN), and telomeres.
gene size
YAC can hold 100,000 bases. Several YACs can undergo homologous recombination to create complete genes from fragments.
Yeast artificial chromosomes contain sequences {autonomously replicating sequence} (ARS) for replication.
Factors that bind to DNA-control-region binding sites can regulate gene expression {regulation, DNA}| {DNA regulation}. Carbon-atom methylation regulates gene expression by changing binding sites. Environmental factors methylate or demethylate gene-control regions by affecting transmethylase enzymes.
Genes {chromatin remodeling gene} can control transcription by allowing transcription factors to reach DNA. They can be tumor suppressor genes {hSNF5/INI1 gene} for malignant rhabdoid tumors (MRT) and central-nervous-system cancers {CNS cancer}, such as choroid plexus tumors, medulloblastomas, and central primitive neuroectodermal tumors (cPNET).
Genes can produce repressors and derepressors to make effect patterns {genetic circuit, biology}. Differing gene repression and derepression causes cell differentiation.
In bacteria, long RNA riboswitches have ends {aptamer} that bind to other molecules to act as sensors and have ends {expression platform, RNA riboswitch} that change structurally by making hairpins, or not, to affect protein translation or RNA transcription.
Cathepsin S and other proteases {cysteine protease} can cleave proteins to activate pathways. Cysteine proteases have poor regulation in some diseases. Cathepsin S activates antigen receptor MHC-II, which initiates T-cell immune responses. Eph receptor kinases and ephrins affect cardiovascular function, nerve regeneration, and cancer.
Nuclear acidic proteins can bind to histones to unblock DNA reading {derepression}.
Techniques {DNA footprinting} can measure protein binding to DNA without measuring gene expression or protein synthesis. Protein binding to DNA sites prevents DNAase enzyme from cutting DNA. If protein binds to DNA, protein-DNA complex moves more slowly in gels than DNA with no protein {mobility-shift assay}, so slower moving fragments have bound proteins.
Myxobacterium S. cellulosum epothilone A, epothilone B, and epothilone D polyketides {epothilone} stabilize microtubules and interfere with cell division. They are like Taxol but more water-soluble.
Factors {hepatic nuclear factor-1-alpha} {HNF-1-alpha} can have dimerization domains, which have mini-zipper four-helix-bundle (4HBs) superfamilies. Low transcription factor affects glucose-metabolism regulation, because dimers bind anti-parallel to coactivator protein {DCoH protein} to start insulin secretion in response to glucose.
Basic proteins {histone}| can bind to DNA to make chromosome chromatin structure. Histones can methylate to regulate DNA expression.
Enzymes {ligase} can join slightly-separated DNA-fragment ends already hydrogen-bonded to other strands, using other strands as templates to add missing bases.
Proteins {mutS protein} can find imperfect DNA helices and uses mutH and mutL proteins to correct them.
Proteins {nuclear acidic protein}| can bind to histones to unblock DNA reading for derepression.
Regulators {P300 protein} can add acetyl groups to histones.
Histones surround chromosomal DNA and block polymerase DNA reading {repression, DNA}| {DNA repression}.
Enzymes {RNase} can cut RNA. RNase A cuts hybridized DNA-RNA at mismatched bases.
Regulatory proteins or ribonucleic acids {transcription factor}| bind before and after genes. Transcription factors and DNA regions differ for different genes. Typically, genes have several regions, for transcription-factor sets. Eukaryote DNA has transcription-factor recognition sites at gene 5' and 3' ends.
Fos
C-fos genes make Fos protein transcription factors.
TATAA
TATAA sites are at 5' ends, just before mRNA transcription-start sites.
GC box
GC boxes are at 5' ends, just before mRNA transcription-start sites.
CCAAT
CCAAT sites are at 5' ends, just before mRNA transcription-start sites.
mRNA enhancer
50-base to 150-base mRNA-enhancer sites can be at 3' ends, 5' ends, or anywhere. They have redundant regions. They react to signal molecules, heat, metal ions, growth factors, or hormones. They contain regions that suppress other-cell-type transcription.
AAUAAA
AAUAAA sites at 3' ends act as signals to cut mRNA 10 to 30 bases away and then add polyA tails.
zinc finger
RNA-polymerase-III 50-base internal-control regions have two regions that bind zinc.
transcription factors: classes
Eukaryotes have transcription-factor classes that bind to DNA-regulatory-region sites: RNA polymerase II promoter, homeodomain, zinc finger, leucine zipper, and helix-loop-helix.
transcription factors: RNA polymerase II promoters
Eukaryotes have transcription factors that bind to RNA polymerase II promoters. Eukaryote promoters have DNA-binding sites and transcriptional-activation sites. Transcription factors help RNA polymerase bind to promoters or change reaction rates. TFIID binds to TATAA sites. TFIIA binds before TATAA sites. TFIIB works with RNA polymerase II. TFIIE binds after RNA polymerase II sites.
transcription factors: homeodomain binding proteins
Homeodomain binding proteins have one helix lying in DNA major groove and another helix lying across DNA to contact other proteins. Fruitfly homeotic genes control body development and contain 180-base homeobox control regions that have helix-turn-helix homeodomain found in most development genes. Vertebrate Hox genes are similar.
400 million years ago, Hox Ubx regulatory-gene mutations caused sea-dwelling arthropods with limbs on all body segments to evolve into terrestrial six-legged insects. Ubx regulates many other genes to prevent fruitfly (Drosophila) thorax-limb development, allow some brine-shrimp (Artemia) thorax-limb development, and allow other-crustacean thorax limbs.
transcription factors: zinc finger
Zinc-finger binding proteins {Kruppel protein} have repeated cysteines and histidines involved with zinc, as in SV40 early-gene GC-box Sp1, steroid-receptor proteins, and gap-gene proteins.
transcription factors: leucine zipper
Leucine-zipper binding proteins, such as FOS oncogene and JUN oncogene proteins, have four or five leucines, seven amino acids apart and just after arginine and lysine regions, that make dimers that bind to DNA.
transcription factors: helix-loop-helix
Helix-loop-helix binding proteins have regions, with arginine and lysine, that bind to DNA and make dimers, as in MyoD-gene and Myc-gene proteins.
Small molecules {corepressor} can bind to repressors to aid repression.
Molecules {derepressor} can bind to repressors at allosteric sites to release repressors from operators.
Small molecules {inducer} can bind to repressors to block repression.
SV40 monkey virus and mouse polyoma virus {virus, genetics}| have circular DNA with 10 genes.
replication phases
In replication early phase, cells make T antigen. In late phase, viral DNA replicates, and cells make coat proteins.
complementary DNA
RNA tumor viruses make complementary DNA by reverse transcriptase. Complementary DNA makes double-stranded DNA that enters host genome and makes RNA virus.
RNA
Tobacco mosaic virus, influenza virus, poliovirus, RNA phages, and other RNA viruses have single-stranded RNA, which replicates using RNA replicase. Single-stranded RNA also acts as mRNA to make viral proteins.
coat protein
Coat proteins surround virus and phage nucleic acid. M13-phage gene III codes coat protein. Genes cloned into Gene III appear on phage surfaces {phage display}. Tobacco mosaic viruses and other mild plant viruses have coat proteins that protect against worse viruses.
In replication early phase, cells make viral proteins {T antigen} {tumor protein} for virus DNA replication.
Circinoviridae single-stranded circular DNA {TT virus} (TTV) is similar to Circoviridae DNA.
Virus structural proteins can arrange to make particles {virus-like particle} (VLP) with virus shapes and sizes.
Outline of Knowledge Database Home Page
Description of Outline of Knowledge Database
Date Modified: 2022.0225