User:Sphilpo2/sandbox

Article Evaluation: Exome
Everything included in the article is relevant to the topic of the exome, however I felt that there was a large amount of information missing. With this in mind, I checked the articles ranking and it is indeed a stub. I think information regarding the importance of exome research versus full genome research would be important to add. The article is not biased, it is presented in a neutral tone, and the majority of information has a citation. I checked citations one and three to see if they were valid. I think there may be an error in the sentence validated by citation one. The sentence states that the human genome consists of roughly 180, 000 exons, however the source states that the human genome is made of roughly 180, 000 protein-coding exons. This may be an error as this count does not include non coding exons which many studies confirm are present in the human genome. The third citation appears to be accurate. Both citations sourced respected journals and were easy to access.The article is a part of the Wikiproject Genetics and Wikiproject Molecular and Cell Biology. It is ranked at mid importance for both projects. On the talk page, users have proposed adding sections on exome sequencing as well as the difference between the exome and the transcriptome.

Prophase Improvement notes:
The article I have chosen for improvement is Prophase, a stub class article in the scope of the WikiProjects Molecular and Cell Biology. Originally I had planned on improving the Interkinesis page, however when I saw the state of the Prophase page I decided to focus on this instead as Prophase is a common topic in many high school curriculums and should have a factual information source through Wikipedia. This article is missing a large amount of information, including but not limited to: substages of prophase, differences in plant and animal cells, differences in meiosis and mitosis, issues that arise with abnormalities during prophase, signalling pathways that induce prophase, cell check points in relation to prophase, and current research focusing on prophase. Structurally, the article is atrocious due to lack of subheadings and an attempt to put all information into the leading section of the article. I plan to address as many of these issues as possible in my article improvement.

Practising citations for personal improvement:

 * now understand more about how to cite textbooks
 * learned I can copy and paste citations

Notes From Textbooks and Papers
Lead Article

GAG

Chromosomes condense only in mitosis and meiosis for suitable transport into daughter cells

Mitotic Prophase

NOTES:

GAG

-      Condensation of chromosomes from undifferentiated chromatin

-      Genetic material has already been replicated in interphase and so each chromosome consists of sister chromatids joined at the centromere

-      Interphase DNA molecules as long as 4cm condensense into chromosomes measured in microns (millionths of a meter)

-      Nucleoi break down and disappear

-      Manufacture of ribosomes ceases indicating that general cellular metabolism shuts down so the cell can focus its energy on cellular division

-      Centrosomes move apart, now distinguishable as separate entities in a light microscope, propelled by intergigitated microtubules extending from both centromeres

-      Interphase microtubule scaffold disappears

-      Microtubules grow fro their centrosomal organising centers

GIM

-      Condensation of chromosomes

-      Formation of mitotic spindle, formation of a pair of centrosomes

ECB

-      Two daughter chromosomes separate and now organize their own array of microtubules

-      Begin to move to opposite side of the cell driven in part by centrosome associated motor proteins moving along the microtubules

PPAD

-      Microtubules polymerize on the surface of the nuclear envelope and begin to gather at two foci on opposite sides of the nucleus, initiating the spindle formation.

Meiotic Prophase

ECB

-Initial associate of homologs (pairing) is mediated by interation between complementary DNA base pairs at numerous sites

- bivalent: structure formed when duplicated chromosomes pair, contains 4 chromatids, maintained through long meiotic prophase that can last for years

- Recombination/crossing over: DNA helix is broken and rejoined in both a maternal and paternal chromatid, fragments of the non sister chromatids are thus exchanged in a reciprocal fashion

- By the time prophase is complete each homolog is held together by at least one chiasma 2-3 on average in humans

- Chiasma are held together until anaphase I, help stabilize bivalents on metaphase plate.

- duplicated homologs are also held together by cohesion proteins

PPAD

-      Divided into 5 phases

-      Leptotene:

o  Homologous regions within pairs begin to associate with each other

o  Meiotic recombination is initiated with the help of several specific proteins

-      Zygotene:

o  Homologous chromosomes being to pair and form synaptosomal complexes (eventually run the lengh of the chromosome pair)

o  Paired chromosomes = bivalents

-      Pachytene:

o  Chromosomes have condensed enough to be seen in a microscope as distinguishable threads

o  Crossing over starts

-      Diplotene:

o  Visible junctions can be seen (chiasmata) and are starting to be resolved (DNA exchange completed)

-      Diakinesis

o  Chiasmata fully resolved

o  Chromosomes further condense

o  Centromeres appear to move further away from each other

o  Chromosome ends still remain contact between homologs

o  Nuclear membrane breaks down

GIM

-      Homologous chromosomes pair and exchange genetic information

-      Zygotene:

o  Homologous chromosomes begin to align along entire length

o  Synapsis (meotic pairing) is very precise bringing corresponding DNA sequences into alignment along the length of the entire chromosome

o  Paired homologs are now called bivalents & held together by ribbonlike protenacious structure called synaptonemal complex

-      Pachytene:

o  Synapsis is complete

o  Meiotic crossing over occurs

-      Synaptosomal complex breaks down

GAG

Critical Events: condensation of chromatin, pairing of hom chroms, reciprocal exchange of genetic informationbetween paired hom chroms

Can take long time t complee. Our species and many, suspend prophase I until ovulation

-      Leptotoene:

o  Greek from thin and delicate

o  Chromosomes thicken and become visible but chromatids remain invisible

o  Each chromosome is two sister chromatids bound at the centromere (as in mitotic prophase)

o  Centromeres begin to move towards opposite poles

-      Zygotene:

o  Greek from conjugation

o  Hom chroms find partners

o  Hom Chroms enter synapsis (become attached down their lengths)

§  Synaptonemal complex is what attaches them

·      Elaborate protein structure that aligns corresponding genetic regions of hom chroms

-      Pachytene:

o  Greek from thick or fat

o  Begins at completion of Synapsis

o  Each synapsed pair = bivalent or tetrad

§  Maternal derived chromosome on one side, paternally derived chromosome on other side

§  X & Y chroms don’t synapse completely small area of homology

o  Recombination nodules appear along synaptonemal complex, exchange parts of nonsiter hom chroms

§  Called crossing over and results in recombination of genetic material

o  Each hom chrom may not longer be of purely maternal or paternal decent BUT each is still a complete entity with no gaps in genetic information

o  Crossing over (genetic exchange between nonsister chromatids of a homologous pair occurs)

-      Diplotene:

o  Greek from double or twofold

o  Synaptonemeal complex dissolves and slight sepeation of regions of hom chroms

o  A Tetrad of four chromatids is visible

o  Crossover points appear as chiasmata which holds nonsister chromatids together

§  Still tightly merged here

o  Meiotic arrest occurs at this time in many species

-      Diakinesis:

o  From greek “double movement”

o  Chromatids thicken and shorten FULL CONDENSATION HAS FINALLY OCCURRED

o  Can now clearly see that each tetrad is for separate chromatids

o  Nonsister chromatids that crossed over still tightly associated at chiasmata

o  Nuclear membrane breaks down and microtubules of the spindle begins to form

Prophase 1

Leptotene

Zygotene

Pachytene

Diplotene

Diakinesis

Prophase 2

GAG

-      If chromosomes decondensed during interphase, they will recondense

-      Nuclear envelope breaks down and spindle apparatus re-forms at the end

GIM

-      Similar to ordinary mitosis except with a haploid chromosome number.

PPAD

-      Chromosomes may decondense in telophase I requiring them to recondense in prophase II like in Arabidopsis OR they may not decondense and proceed through prophase II quickly

Mitotic Prophase
Prophase is the first stage of mitosis in animal cells, and the second stage of mitosis in plant cells. The main events of prophase are: the condensation of chromosomes, the movement of the centrosomes, the formation of the mitotic spindle, and the beginning of nucleoli break down.

Condensation of Chromosomes
DNA that was replicated in interphase is condensed from molecules with lengths reaching 4 cm to chromosomes measured in micrograms. Condensed chromosomes consist of two sister chromatids joined at the centromere.

Movement of Centrosomes
During prophase in animal cells, centrosomes move far enough apart to be be resolved using a light microscope. Replicated centrosomes from interphase move apart towards opposite poles of the cell, powered by centrosome associated motor proteins. Interdigitated interpolar microtubules from each centrosome interact with each other, helping to move the centrosomes to opposite poles.

Formation of the Mitotic Spindle
Microtubules involved in interphase scaffolding break down as the replicated centrosomes separate. The movement of centrosomes to opposite poles is accompanied in animal cells by the organization of individual radial microtubule arrays (asters) by each centromere. Interpolar microtubules from both centrosomes interact, joining the sets of microtubules and forming the basic structure of the mitotic spindle. In cells without centrioles chromosomes can nucleate microtubule assembly into the mitotic apparatus. In plant cells, microtubules gather at opposite poles and begin to form the spindle apparatus at locations called foci. The mitotic spindle is of great importance in the process of mitosis and will eventually segregate the sister chromatids in metaphase.

Beginning of Nucleoli Breakdown
The nucleoli begin to break down in prophase, resulting in the discontinuation of ribosome production. This indicates a redirection of cellular energy from general cellular metabolism to cellular division. The nuclear envelope stays intact during this process.

Meiotic Prophase
Meiosis involves two rounds of chromosome segregation and thus undergoes prophase twice, resulting in prophase I and prophase II. Prophase I the most complex phase in all of meiosis because homologous chromosomes must pair and exchange genetic information. Prophase II is very similar to mitotic prophase.

Prophase I
Prophase I is divided into five phases: leptotene, zygotene, pachytene, diplotene, and diakinesis. In addition to the events that occur in mitotic prophase, several crucial events occur within these phases such as pairing of homologous chromosomes and the reciprocal exchange of genetic material between these homologous chromosomes. Prophase I occurs at different speeds dependent on species and sex. Many species arrest meiosis in diplotene of prophase I until ovulation. In humans, decades can pass as oocytes remain arrested in prophase I only to quickly complete meiosis I prior to ovulation.

Leptotene
In the first stage of prophase I, lepotene (from the Greek for “delicate”), chromosomes begin to condense. Each chromosome is in a haploid state and consists of two sister chromatids; however, the chromatin of the sister chromatids is not yet condensed enough to be resolvable in microscop y. Homologous regions within homologous chromosome pairs begin to associate with each other. PPAD

Zygotene
In the second phase of prophase I, zygotene (from the Greek for “conjugation”), all maternally and paternally derived chromosomes have found their homologous partner. The homologous pairs then undergo synapsis, a process by which the synaptonemal complex (a proteinaceous structure) aligns corresponding regions of genetic information on maternally and paternally derived non-sister chromatids of homologous chromosome pairs. The paired homologous chromosome bound by the synaptonemal complex are referred to as bivalents or tetrads. Sex (X and Y) chromosomes do not fully synapse because only a small region of the chromosomes are homologous.

Pachytene
The third phase of prophase I, pachytene (from the Greek for “thick”), begins at the completion of synapsis. Chromatin has condensed enough that chromosomes can now be resolved in microscopy. Structures called recombination nodules form on the synaptonemal complex of bivalents. These recombination nodules facilitate genetic exchange between the non-sister chromatids of the synaptonemal complex in an event known as crossing-over or genetic recombination. Multiple recombination events can occur on each bivalent. In humans, an average of 2-3 events occur on each chromosome.

Diplotene
In the fourth phase of prophase I, diplotene (from the Greek for “twofold”), crossing-over is completed. Homologous chromosomes retain a full set of genetic information; however, the homologous chromosomes are now of mixed maternal and paternal descent. Visible junctions called chaismata hold the homologous chromosomes together at locations where recombination occurred as the synaptonemal complex dissolves. It is at this stage where meiotic arrest occurs in many species.

Diakinesis
In the fifth and final phase of prophase I, diakinesis (from the Greek for “double movement”), full chromatin condensation has occurred and all four sister chromatids can be seen in bivalents with microscopy. As in mitotic prophase, meiotic prophase ends with the spindle apparatus beginning to form, and the nuclear membrane beginning to break down.

Prophase II
Prophase II of meiosis is very similar to prophase of mitosis. The most noticeable difference is that prophase II occurs with a haploid number of chromosomes as opposed to the diploid number in mitotic prophase. In both animal and plant cells chromosomes may de-condense during telophase I requiring them to re-condense in prophase II. If chromosomes do not need to re-condense, prophase II often proceeds very quickly as is seen in the model organism Arabidopsis.

Differences in Plant and Animal Cell Prophase
The most notable difference between prophase in plant cells and animal cells occurs because plant cells lack centrioles. The organization of the spindle apparatus is associated instead with foci at opposite poles of the cell or is mediated by chromosomes. Another notable difference is preprophase, and additional step in plant mitosis that results in formation of the preprophase band, a structure composed of microtubules. In mitotic prophase I of plants this band disappears.

Cell Checkpoints
Prophase I in mitosis is the most complex iteration of prophase that occurs in both plant cells and animal cells. To ensure pairing of homologous chromosomes and recombination of genetic material occurs properly, there are cellular checkpoints in place. The meiotic checkpoint network is a DNA damage response system that controls double strand break repair, chromatin structure, and the movement and pairing of chromosomes. The system is comprised of multiple pathways (including the meiotic recombination checkpoint) that prevent the cell from entering metaphase I with errors due to recombination.

Genetic Abnormalities
Arrest at dictyotene in Prophase I