Genomics week 9

winniesmith2's version from 2017-12-31 15:11

Section 1

Question Answer
Direct Methods of gene mapping ; original methodLocation of particular gene on a chromosome. Original method= chromosomal analysis (chromosomal number, visible deletions, inversions, translocations). Starting point of looking at genes.
What is situ hybridisation; direct visualisation of a DNA probe hybridised to chromosomal preparations. Such as FISH (Fluorescent in-situ hybridisation).
Cytogenetic- Karyotyping ; what is itThe microscopic examination of chromosome shape, size, structure and function. Chemical treatment (colchicine) used to arrest cells during metaphase. Metaphase chromosomes differ from each other in size and shape. Length of any one chromosome will depend on when it was fixed during mitosis. Relative position of the centromere is constant, which means that the ratio of the lengths of the 2 arms is constant for each chromosome. Banding pattern is unique to each chromosome.
How do you create a karyotype - summaryBlood culture is centrifuged to separate the white blood cells. Fix white blood cells on a slide, take a picture of it, picture studied under microscope, karyotype developed, by looking at chromosome size, shape and banding pattern. (blood culture, centrifuge to separate fluid and cells, Hypotonic solution added to burst RBCs, white blood cells taken, fixative added, stain added).
Karytyping- what do you look at? first step Giemsa stand will separate gene containing areas (light) and no coding dna areas (dark).Banding pattern of each chromo depicted on an ideogram. Studied by number. . First level is position or size of chromosome. Then look at centromere position.
chromosome banding patterns allow what us to look at the location of those genes and location of genetic variation in that process and between populations/ different animals.
Describe basic chromosome structure The centromere is a distinctive feature of chromosomes and plays an important role during mitosis. On either side of the centromere are “arms” that extend to terminal regions, known as telomeres. The short arm of a chromosome is designated as “p” while the long arm is referred to as “q”.
Describe basic chromosome nomenclature The band nomenclature refers to physical staining with a Giemsa dye (G-banded). Band localization is determined by G-banding the image of a metaphase spread during cell division. Bands are numbered outward from the centromere with the largest values near the telomeres.

Section 2

Question Answer
Human cytogenetics, 2 levels of analysis. 1: Numerical cVariation from 46 chromosomes. such as; -Aneuploidy (result from errors occurring during meiotic or mitotic segregation). -Trisomy: the presence of an extra chromosome. -Monosomy: the absence of a whole chromosome.
Human cytogenetics, 2 levels of analysis. 2: structural changessuch as; -Translocation: the breakage and rejoining of parts of two, non-homologous chromosomes. -Inversion: the 180 rotation of a part of a chromosome. -Insertions -Deletion: the absence of a part of a chromosome. -Duplications
Down's syndrome Triploid 21. Most common chromosomal disorder 1/1000 births. Mental retardation. Small, round, flat face, small mouth, protuding tongue. Eyes slant up and out (epicathal fold) Enlarged tongue, spleen, liver, heart and asthma.
Klinefelters syndromeXXY. General male phenotype, external genitalia are normal. Testes small (no sperm). arms longer than average. High pitched voice. Breast development, sex chromatin positive.
Patau syndrome 47, XY, 13+. Rare 1/15000. Much more severe than downs. Microcephaly (small brain size) cleft lip, small jaw, mental/growth retardation. Deformed low-set ears. Polydactyly. Congenital heat defects. Seizures. Low birth weight.
Turners syndrome45XO. Female phenotype. short (less than 5ft) sexually underdeveloped. infertility. malformed elbows. shield shaped chest, webbing at back of neck, Normal intelligence, reduced lifespan.
Cri-du-chat syndrome 46XX/Y, 5p- . Deletion of short arm (p) of chromosome 5. High pitched cat-like cry. Mental retardation, poor muscle tone.

Section 3

Question Answer
Molecular cytogenetics. Deletions of part of the chromosome so it becomes smaller. Insertion; ex. part of chromosome 4 moving to chromosome 20 (4 shorter, 20 longer). Translocation; swapping of parts. Chromosome 4 gets small part of 20, 20 gets bigger part of 4. Here it is important to understand banding pattern
Molecular mechanisms for chromosomal rearrangements Exogenous and endogenous causes of structural aberrations.
Exogenous causes of structural aberrations Viral infections. Lesions may undergo repair or misrepair by a wide range of DNA repair systems. Chemicals; alkylating agents, purine/pyrmidine analoges. Alkyl epoxides, aromatic amines and heavy metals. Can be slightly controlled.
Endogenous causes of structural aberrations Rare autosomal recessive chromosome breakage syndromes caused by defective DNA repair enzymes. Transposable elements (LINE, SINE), segmental duplication, gene duplication, fragile sites.
How do you study molecular mechanisms for chromosomal rearrangements Fluorescence in situ hybridization (FISH) .
What does FISH do paints chromosomes or portions of chromosomes with fluorescent molecules. Identifies chromosomal abnormalities. Aids in gene mapping, toxicological studies, analysis of chromosome structural aberrations. Used to identify the presence and location of a region of DNA or RNA within morphologically preserved chromosome preparations, foxed cells or tissue sections. View a segment or entire chromosome with your own eyes. Mostly metaphase but now used on interphase as well.
FISH procedure locate gene sequence you are interested in. Denature the chromosome. Denature the probe/piece of DNA of interest. Hybridisation. Fluorescence staining. Examine slides or store in the dark.
FISH results can look at where the probe attached. hybridisation results.
SKY (spectral karyotype) what is itExtension of in situ hybridisation; Allows you to paint different chromosomes with different dyes. Can see where chromosomes have exchanged or translated by colours on the chromosome. Expensive technique but good.
Comparative genome hybridization (CGH)we are comparing one normal genome and one effected genome. First we extract and label DNA. Then we mix the dna+cot1 (facilitator). Denature dna, hybridize DNA. Allows us to see which chromosomes are still present, which are changed, which are normal, and where there is a chromosome loss or gain.
if you want to study any diseasestart with (pedigree and then) chromosomal analysis.