1. Human Metaphase Chromosomes & Karyotyping

2. Chromosome Morphology
Chromosomes are not visible under the light microscope in non-dividing cells (interphase cells).
As the cell begins to divide, the threads of chromatin (DNA-protein complex) in the nucleus begin to condense into multiple levels of coiled structures recognizable as chromosomes.
There are two modes of cell division:
Mitosis: is responsible for the proliferation of body (somatic) cells,
Meiosis: is responsible for the production of gametes.
Because mitotic cells are easy to obtain, morphological studies are generally based on mitotic metaphase chromosomes.

3. Cell division Cell division can be divided into: Interphase Mitosis
Prophase
Metaphase
Anaphase
Telophase
Cytokinesis

4. Metaphase
At metaphase the chromosomes are at their most condensed state,
Spindle fibers attaching to the area of the centromere called the kinetochore, forming pole-chromosome fibers.

5. Anaphase begins with the division of the centromere and the separation of chromatids.
Once separated, each chromatid is known as a chromosome.
The kinetochore: is the protein structure on chromatids where the spindle fibers attach during cell division to pull sister chromatids apart.

6. Chromosome Analysis
The best mitotic stage for chromosome analysis is pro-metaphase or metaphase.
A typical metaphase chromosome consists of two arms separated by a primary constriction or centromere.
Each of the two sister-chromatids contains a highly coiled double helix of DNA.
Often the sister chromatids are so close to each other that the whole chromosome appears as a single rod-like structure
A chromosome may be characterized by its total length and the position of its centromere.

7. Chromatin and chromosomes are basically the same thing
Chromatin and chromosomes are basically the same thing. The difference is that chromatin is unfolded, uncondensed, extended DNA while chromosomes are condensed DNA. Chromosomes are condensed chromatin and chromatin is unfolded chromosomes.

9. Chromosome Number
The diploid chromosome number is the number of chromosomes in the somatic cell and is designated by the symbol 2N.
The gametes, which have one half the diploid number, have the haploid number N.
Thus, there are 23 pairs of chromosomes in human cells.

10. Of these, 22 pairs are not directly involved in sex determination, and are known as autosomes.
The remaining chromosome pair consists of the sex chromosomes, and is directly involved in sex determination.
In females the two sex chromosom es are identical (XX), whereas in males the two sex chromosomes are not identical (XY).

11. Types of Tissue
A variety of tissue types can be used to obtain chromosome preparations.
Some examples include peripheral blood, bone marrow, amniotic fluid and products of conception.
In the case of blood cell culture only cells that are actively dividing can be used for cytogenetic studies.
Normally only white blood cells are used for cytogenetic analysis.
Specific techniques differ according to the type of tissue used.

12. Overview of Procedure Collection of blood Cell culture
Harvesting: stopping the cell division at metaphase
Hypotonic treatment of red & white blood cells
Fixation
Slide preparation
Staining

13. 1- Collection of blood
Draw 5 ml of venous blood into a sterile heparinized tube containing 0.1 ml of sodium heparin (500 units/ml).
Any other choice of tube is unsuitable since the sample will either arrive clotted or tube will contain EDTA which is toxic to cells and will therefore adversely affect the culture.

14. 2- Cell Culture
Sterile technique must be used throughout the cell culture preparation, because it is possible to cause major contamination during this procedure,
70% of the problems are due to a lack of good sterile technique.
Antibiotics do not eliminate problems of gross contamination which result from poor sterile technique or antibiotic-resistant mutants.
Autoclaving renders pipettes, glassware, and solutions sterile.

15. 2- Cell Culture
Medium
Pipette 10 ml RPMI 1640 medium with L-Glutamine into a 15 ml labeled sterile culture tube
Supplement the medium with the following:
Penicillin-Streptomycin Stock solution
10 µl
( u penicillin/ml – 100 mg/ml Streptomycin
Phytohemagglutinin
0.3 ml
20 µg/ml
Fetal bovine Serum 20%
2 ml
Phytohemagglutinin is A hemagglutinin extracted from a plant - A substance, such as an antibody, that causes agglutination of red blood cells.
has a number of effects on cell metabolism: it induces mitosis,
RPMI-1640 was developed by Moore et. al. at Roswell Park Memorial Institute

16. 2- Cell Culture Incubation
Add 1 ml of whole heparinized blood into the tube containing the supplemented medium
Mix contents of tube with gentle inversion
Incubate in 5% CO2 incubator at 37oC for 72 hours
- CO %, المحافظة على ph للخلايا من الشروط المهمة لنجاح نمو الخلايا بشكل طبيعي

17. 3- Harvesting
Harvesting: mitotic spindle formation is blocked: usually by adding colcemide to the culture, and the cell division is stopped at the metaphase level.
Pre-warm the Colchicine (0.04 mg/ml) in incubator at 37oC.
Add 25 µl of pre-warmed Colchicine to the culture.
Mix gently and incubate at 37oC for minutes.
Note: Colchicine inhibits microtubule polymerization by binding to tubulin, one of the main constituents of microtubules
Availability of tubulin is essential to mitosis, and therefore colchicine effectively functions as a "mitotic poison" or spindle poison
A Tubulin is one of several members of a small family of globular proteins. α-tubulin and β-tubulin, the proteins that make up microtubules
colchicine also inhibits neutrophil motility and activity, leading to a net anti-inflammatory effect

18. 4- Hypotonic treatment of red & white blood cells
Centrifuge for 10 minutes at 2000 rpm.
Discard supernatant without disturbing the cells leaving 0.5 ml of fluid.
Add 1 ml of pre-warmed hypotonic solution (0.075 M KCl) at 37oC.
Mix and then add 9 ml of hypotonic solution.
Mix well by Pasteur pipette.
Incubate at 37oC incubator for 17 minutes,
hypotonic solution should not be in contact with cells more than 27 minutes (may cause rupture of WBCs).

19. 5- Fixation Fixative must be prepared fresh
Add 3 parts of chilled absolute methanol:1 part glacial acetic acid.
Centrifuge for 10 minutes at 1000 – 1500 rpm.
Remove supernatant leaving about 0.5 ml of fluid on top of cells.
At this time there is probably a small whitish or reddish film at the bottom of the tube.
The film contain red blood cell debris and enlarged WBCs.

20. 5- Fixation Add 5 ml of fixative to the tube.
Mix with a Pasteur pipette 3-4 times.
Place in refrigerator for 30 minutes.
Centrifuge the tube for 10 minutes at rpm.
Remove supernatant and add another 6 ml of cold fixative, & mix well.
Repeat the last two steps.
Remove the supernatant leaving 1 ml of fluid at the bottom.
The remaining material will be used to make the slides.

21. 6- Slides Preparation The slide must be exceptionally clean
Lay slides on a paper towel
Withdraw a few drops of cell suspension into a pipette
From a height of 20 cm, drop 2 or 3 drops of fluid on each slide
Allow the slides to dry

22. 7- Staining
Stain the slides by immersion in fresh Giemsa stain for 7-10 minutes
Remove slides from stain & rinse in distilled water
Observe under microscope 40X then under oil immersion

25. Karyotyping

26. What is a Karyotype?
A display or photomicrograph of an individual’s somatic-cell metaphase chromosomes that are arranged in a standard sequence (usually based on number, size, and type)

27. Why do scientists look at chromosomes?
Scientists can diagnose or predict genetic disorders by looking at chromosomes.
This kind of analysis is used in prenatal testing and in diagnosing certain disorders, such as
Down syndrome,
or in diagnosing a specific types of leukemia.

28. Chromosome abnormalities
Chromosome abnormalities can be
numerical, as in the presence of
extra
or missing chromosomes
Structural as in translocations, inversions, large scale deletions or duplications.

29. Chromosomal Abnormalities
Alterations in chromosome number.
Euploid - normal set (2n)
Polyploidy – extra set of the entire genome.
(3n, 4n, ……….etc)
Aneuploidy – the number of chromosomes is not a multiple of the normal haploid number.
Monosomy
one member of a chromosome pair is missing, (2n-1)
Trisomy
one chromosome set consists of 3 copies of a chromosome, (2n+1)

30. Turner syndrome results from a single X chromosome (45, X or 45, X0).
Klinefelter syndrome, the most common male chromosomal disease (47, XXY)
Down syndrome, a common chromosomal disease, is caused by trisomy of chromosome 21.

31. Chromosomal abnormalities (can be detected by karyotyping)

32. Chromosomal abnormalities (can be detected by karyotyping)
The Ph chromosome is an abnormally short chromosome 22 that is one of the two chromosomes involved in a translocation (an exchange of material) with chromosome 9: t(9;22)(q34;q11). This translocation takes place in a single bone marrow cell and, through the process of clonal expansion (the production of many cells from this one mutant cell), it gives rise to the leukemia (CML). 
ABL and BCR are normal genes on chromosomes 9 and 22, respectively. The ABL gene encodes a tyrosine kinase enzyme whose activity is tightly regulated (controlled). In the formation of the Ph translocation, two fusion genes are generated: BCR-ABL on the Ph chromosome and ABL-BCR on the chromosome 9 participating in the translocation. The BCR-ABL gene encodes a protein with deregulated (uncontrolled) tyrosine kinase activity. 
Philadelphia Chromosome - CML

33. Situations where analysis is strongly recommended
Problems with early growth & development
Fertility problems
Neoplasia
Pregnancy in older women
Chorionic villus sampling (CVS) is a form of prenatal diagnosis to determine chromosomal or genetic disorders in the fetus. It entails getting a sample of the chorionic villus ( placental tissue) and testing it. The advantage of CVS is that it can be carried out weeks after the last period, earlier than amniocentesis (which is carried out at weeks).

34. How Do Scientists Identify Chromosomes?
Three key features to identify their similarities and differences:
Size. This is the easiest way to tell two different chromosomes apart.
Banding pattern. The size and location of Giemsa bands on chromosomes make each chromosome pair unique.
Centromere position. Centromeres are regions in chromosomes that appear as a constriction.
Using these key features, scientists match up the 23 pairs

35. In metacentric chromosomes, the centromere lies near the center of the chromosome. Submetacentric & very Submetacentric chromosomes, have a centromere that is off-center, so that one chromosome arm is longer than the other. In acrocentric chromosomes, the centromere resides very near one end.

36. Chromosome banding
Chromosomes are stained with various dyes enabling the chromosome segments to be identified
Most methods can distinguish 550 bands/ haploid set
High resolution methods can distinguish up to 850 bands/ haploid set that can allow identification of small interstitial deletions
G-Banding, C-Banding, Q-Banding, R-Banding, T-Banding
G banding - Giemsa
Q banding - Quinacrine “Used especially for Y chromosome abnormalities or mosaicism ”
R banding - Reverse “Used to identify X chromosome abnormalities”
C banding - Centromeric (heterochromatin) “Used to identify centromeres / heterochromatin”

37. G-Banding
Regions that stain as dark G bands replicate late in S phase of the cell cycle and contain more condensed chromatin,
While light G bands generally replicate early in S phase, and have less condensed chromatin.

38. The difference between dark- and light-staining regions was believed to be caused by differences in the relative proportions of bases:
G-light bands being relatively GC-rich
G-dark bands AT-rich

39. Chromosome Groups Group Chromosomes Description A 1–3
Largest; 1 and 3 are metacentric but 2 is submetacentric B
4,5
Large; submetacentric with two arms very different in size C
6–12,X
Medium size; submetacentric D
13–15
Medium size; acrocentric with satellites E
16–18
Small; 16 is metacentric but 17 and 18 are submetacentric F
19,20
Small; metacentric G
21,22,Y
Small; acrocentric, with satellites on 21 and 22 but not on the Y
Autosomes are numbered from largest to smallest, except that chromosome 21 is smaller than chromosome 22.

40. Overview of Procedure Collection of blood Cell culture
Stopping the cell division at Metaphase
Hypotonic treatment of red & white blood cells
Fixation
Slide preparation
Slide dehydration
Treatment with enzyme
Staining

41. 7- Slide dehydration
Place fixed, dry slides on slide rack in 60oC oven
Bake for 3 days
Allow to cool before proceeding to the next step

42. 8- Treatment with enzyme
Prepare 0.025% trypsin solution fresh, by mixing 5 ml of 0.25% trypsin with 45 ml Hank’s solution
Immerse slide in % trypsin for seconds
Remove slide from trypsin and immediately immerse in phosphate buffer to stop trypsin action

43. 9- Staining
Prepare a dilution of Giemsa stain by mixing 1 part of Giemsa stain with 3 parts of Phosphate buffer
Flood slide with Giemsa stain for 2 minutes
Rinse slides thoroughly with distilled water
Allow slides to drain, then place on 60oC slide warming tray until completely dry

44. x y

47. Exercise

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