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1. Eukaryotic chromosomes are made from a material called chromatin. Explain what chromatin is and describe the chromatin structure of eukaryotic chromosomes.
2. Describe the changes in chromatin structure that occur during mitosis.
3. Explain the mechanism of mitotic chromosome separation (anaphase), and include in your answer the following terms: centromere, centrosome, kinetochore, sister chromatids and spindle fibres.
4. Define what is interphase and explain what is happening during this part of cell cycle.
5. What can the percentage of total cells in each phase of cell cycle tell you about the duration of each phase? 

Chromatin and its Structure in Eukaryotic Chromosomes

Chromatins are a complex of nucleic acids either RNA or DNA that condenses to a chromosome during cell multiplication. In eurokaryotic (organisms with membrane bound nucleus) cells the chromatin is found within the nucleus where it helps in packaging of DNA into smaller volumes so as to fit in a cell. It also strengthens the DNA to allow for the process of meiosis and mitosis

The chromosomes contain long DNA strands that carry genetic information. The eukaryotic cells have large genomes than prokaryotes that has multiple and linear chromosomes. However, the length plus linear nature of the chromosomes increases the ability of keeping the genetic material organized as well as of passing the correct amount of DNA to every daughter cell during the process of mitosis.

During the initial phase, interphase chromatin remains in condensed form as well as appears loosely distributed in the entire nucleus. Condensation of the chromatin starts during the prophase stage where the chromosomes become visible and remains condensed in the rest of the phases of mitosis up to the final stage telophase.

Before the commencement of anaphase, a replicated chromosomes reoffered to as sister chromatids are aligned at the centre of the cell.  The sister chromatids are joined at the centromere where during this stage each chromosome pair is separated into two chromosomes that are identical and independent. The chromosomes are then separated by the mitotic spindle which is made up of microtubules that are attached to the chromosome at one pole as well as to the end of a cell at the other pole.  However, the sister chromatids are divided concurrently at the centromere where the separate chromosomes are pulled by a  spindle to the other sides of the cell.

 Interphase is a stage of the cell cycle where a cell spends most of its life. During this stage, the cell duplicates their DNA as it prepares for mitosis. Interphase can be defined as the metabolic stage of a cell where it get’s nutrients as well as metabolizes them , reads the DNA and performs other functions of the cell.  A vast number of eukaryotic cells spend most of their time in this phase where a cell gets ready for meiosis or mitosis. Diploid cells or somatic cells of the body go through mitosis so as to reproduce themselves via cell multiplication whilst diploid germ cells go through meiosis   to form gametes for reproduction.

The distribution of cells continues to decline as a cell undergoes meiosis or mitosis from the initial stage, interphase to telophase.

                         

Mitotic index for the control group    = (30/350) × 100

= 8.57%

Mitotic index for the dark cellar on earth = (12/312) × 100

      = 3.85%

Mitotic index for the sunlight on earth in babybio plant feed     = (72/480) ×100

         = 15%

Mitotic index value for sunlight in space station       = (60/480) ×100

= 12.5%

Growth condition

Interphase

metaphase

Mitotic index

Control group (in sunlight on earth)

320

7

8.75%

In dark cellar on earth

300

2

3.85%

In sunlight on earth with babybio plant feed

408

19

15%

In sunlight in space station

420

16

12.5%

                               

Changes in Chromatin Structure During Mitosis

Mitotic cells= (P+M+A+T)*100

Mitotic cells counted for dark cellar =7+2+2+1=12

Control sunlight dataset’s mitotic cells=11+7+8+4=30

 Mitotic cells counted for baby bio=30+19+15+8=72

Mitotic cells counted for space=26+16+14+4=60

Dark cellar

Control sunlight data set

Marginal tow total

Interphase

300

320

620

Mitotic cells

12

30

42

Marginal column totals

312

350

662(grand total)

Using the fisher’s exact test, the statistical p value is 0.01586.  The result is significant at p < 0.05

Babybio plant feed

Control sunlight dataset

Marginal row total

Interphase

408

320

728

Mitotic cells

72

30

102

Marginal column totals

480

350

830(grand total)

The fisher test statistical P –value is 0.00534 and the result is significant at P< 0.05                                                                                                                                                                                                      

Space station

Control sunlight dataset

Marginal row total

Interphase

420

320

740

Mitotic cells

60

30

90

Marginal column totals

480

350

830 (grand total)

The fishers exact test statistical value is 0.089529. The result is not significant at P< 0 .05

A table of the resulting P values

In the dark cellar category, the p value is 0.01586 which is significant at p < 0.05 while in the babybio plant feed, the resulting P value is 0.00534 which is significant at  P<0 .05. Lastly, in the space station the P value is 0.089529 which is not significant at p<0.05

Categories

Resulting P-value

Dark cellar

0.01586

Babybio plant feed

0.00534

Space station

 0.089529

The smaller the mitotic index the more significant the p value. From the dark cellar condition , it can be deduced that the smaller the ratio between the number of cells undergoing mitosis versus those not undergoing  leads to an increase in the growth of onion roots where the calculated p value is less than the critical value.

The larger the mitotic index, the smaller the p value becomes. From the sunlight with babybio plant feed condition , it can be concluded that the larger the ratio between number of cells in a population undergoing mitosis and those not undergoing will lead to a decreased p value which is less significant to the critical value

In space station, the larger the mitotic index the larger the value of P which is not significant. this is because the calculated p value is larger compared to the critical p value hence the faster growth of onion  roots due to rapid cell division.

References:

Bueno, Danilo, Octavio Manuel Palacios-Gimenez, and Diogo Cavalcanti Cabral-de-Mello. "Chromosomal mapping of repetitive DNAs in the grasshopper Abracris flavolineata reveal possible ancestry of the B chromosome and H3 histone spreading." Plos one 8.6 (2013): e66532.

Cao, Hui, et al. "Prognostic analysis of patients with gastrointestinal stromal tumors: a single unit experience with surgical treatment of primary disease." Chinese medical journal 123.2 (2010): 131-136.

Chénais, Benoît, Aurore Caruso, Sophie Hiard, and Nathalie Casse. "The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments." Gene 509, no. 1 (2012): 7-15.

Dhall, Deepti, et al. "Ki-67 proliferative index predicts progression-free survival of patients with well-differentiated ileal neuroendocrine tumors." Human pathology 43.4 (2012): 489-495.

Figarella-Branger, Dominique, et al. "Mitotic index, microvascular proliferation, and necrosis define 3 groups of 1p/19q codeleted anaplastic oligodendrogliomas associated with different genomic alterations." Neuro-oncology 16.9 (2014): 1244-1254.

Hadfield, J. D., and S. Nakagawa. "General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi?trait models for continuous and categorical characters." Journal of evolutionary biology 23.3 (2010): 494-508.

Hazkani-Covo, Einat, Raymond M. Zeller, and William Martin. "Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes." PLoS genetics 6.2 (2010): e1000834.

Martis, Mihaela Maria, et al. "Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences." Proceedings of the National Academy of Sciences 109.33 (2012): 13343-13346.

Roa, Fernando, and Marcelo Guerra. "Distribution of 45S rDNA sites in chromosomes of plants: structural and evolutionary implications." BMC evolutionary biology 12.1 (2012): 225.

Rustenholz, C., Choulet, F., Laugier, C., Šafá?, J., Šimková, H., Doležel, J., Magni, F., Scalabrin, S., Cattonaro, F., Vautrin, S. and Bellec, A., 2011. A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. Plant physiology, 157(4), pp.1596-1608.

Tiang, Choon-Lin, Yan He, and Wojciech P. Pawlowski. "Chromosome organization and dynamics during interphase, mitosis, and meiosis in plants." Plant physiology 158.1 (2012): 26-34.

Varshney, R.K., Chen, W., Li, Y., Bharti, A.K., Saxena, R.K., Schlueter, J.A., Donoghue, M.T., Azam, S., Fan, G., Whaley, A.M. and Farmer, A.D., 2011. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature biotechnology, 30(1), pp.nbt-2022.

Wang, Baojun, et al. "Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology." Nature communications 2 (2011): 508.

Wicke, Susann, et al. "The evolution of the plastid chromosome in land plants: gene content, gene order, gen

Growth condition

Mitotic index

p-value

In dark cellar

3.85%

0.01586

Sunlight with babybio plant feed

15%

0.00534

In space station

12.5%

0.089529

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