This blog is produced by, namely,
the dedicated,
passionate,
and drosophilitic,
Lee Wei Liang and
Kenneth Koh Ren Chuan,
who attended a Drosophila Genetics elective from 1/10/07 to 9/10/07, organized by Thinksmart.
This blog is for you, the reader, to learn more about DROSOPHILA, their important uses in genetic experiments, and genetics itself. Note: this blog is partly an archive of information found on the internet. If there is anybody we forgot to thank in the making of this blog, please kindly forgive us.
Second IMPORTANT note: Please read this blog down up in (bottom post first) in order to get a more chronologically accurate account of the activities and lessons in the elective. Alternatively, and which is more conveniently, use the shortcuts on the right at the top portion of this blog (the post titles), which are in order from top to bottom. Oh and if you decide not to use the shortcuts the posts span over two pages, so click on "older posts" at the bottom to view them first.
Thank you.
Monday, October 8, 2007
Last Day!! Sob Sob
Last day of elective liao... so blog in a more relaxed and less "chim" way. So what did we do today? We learnt about this thing called BIOINFORMATICS!!!
After obtaining a portion of the protein sequence for humans (in text form of course), we then proceeded to enter this information in the GENE BANK, (http://www.ncbi.nlm.nih.gov/BLAST) which then allows us to search for "somewhat similar" genes in the whole database.
However, the database is so huge and there were so many results that we got this:
INFO: Too many HSPs to save all INFO: [blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24).
Lol.
So we only got a few results. But never mind. We still learnt that the gene name for the one we entered was the DJ-1 gene. Not Disc Jockey gene though.
.........................................nvm......................................................
Actually we were supposed to get results like mice and flies? But then, how are we similar to mice and flies??? (looks insulted). Well, this is explained in the next part of the lesson.
We learnt that in each and every living thing, there are similar genes and DNA!!! Not every one though. There is a portion of gene sequence (62 triplets of ATCG) that is similar in every organism on Earth. Cool eh? The person in the video was looking extremely awestruck. Lol.
Yeah and also the time from Gregor Mendel's theories of heredity to the time when the whole human genome was deciphered is only 150 years!!! Waah... so many smart people... some of which include THE FAMOUS Thomas Hunt Morgan who is also featured in our blog.
And things like messenger RNA are introduced to us. The video we watched really cleared my doubts about what is RNA, how it is different from RNA, etc. We learnt that MRNA (or messenger RNA) is a single strand of DNA which prevents entire DNA strands from being copied. It's like only wanting the drumstick out of the whole chicken. We don't have to buy the whole chicken to get the drumstick. (Interesting analogy eh?)
The DNA and genes of our stomach cells and our skin cells, and in fact, every cell in our body, is the same!!! Just that some parts of the genes of certain cells are turned OFF. So they don't produce RNA which gives the cell instructions for making proteins. If not, our skin will start dripping mucus and producing hydrochloric acid, pepsinogen and rennin. The pepsinogen will then be converted by the hydrochloric acid to pepsin, which can then digest stuff. Ooops a bit offtrack here.
However, the video has also sort of awakened me to the sort of tiring, monotonous, dedicated, overly-passionate work that a life scientist, or in fact, any scientist, must consign himself/herself to. Am i prepared for this? Don't know yet, but now at least i know more about this branch of work.
Haha. Actually quite like today, not becoz it's the last day, but rather, because it is so relevant to our career choice. Should have this for career guidance also. Haha. The video is good! Recommend it to anyone who likes life science. 100 greatest discoveries, genetics or sth liddat. The one with the brother of the host (not biology host). Lol. If you don't understand, IGNORE the last sentence and let your love of Biology lead you. Wahahaha.
Yeah.
What do we (auhors of this blog) love about this elective? The flies of course. They have really awakened us to the work of a life science researcher. That we have to make friends with flies to know about them. That maggots (fly larvae) are not that disgusting after all. Cute in a way. Especially wriggling under the microscope. And especially after dissection.
Pretty sadly, though, we have to update on our results of the breeding we carried out on the first day. Thing is, they didn't breed!!! Probably accidentally put flies of the same sex together. Or perhaps they just don't like each other. Perhaps.
Yeah well shall stop here. Time to watch another video liao. Byeezzzz
After obtaining a portion of the protein sequence for humans (in text form of course), we then proceeded to enter this information in the GENE BANK, (http://www.ncbi.nlm.nih.gov/BLAST) which then allows us to search for "somewhat similar" genes in the whole database.
However, the database is so huge and there were so many results that we got this:
INFO: Too many HSPs to save all INFO: [blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24).
Lol.
So we only got a few results. But never mind. We still learnt that the gene name for the one we entered was the DJ-1 gene. Not Disc Jockey gene though.
.........................................nvm......................................................
Actually we were supposed to get results like mice and flies? But then, how are we similar to mice and flies??? (looks insulted). Well, this is explained in the next part of the lesson.
We learnt that in each and every living thing, there are similar genes and DNA!!! Not every one though. There is a portion of gene sequence (62 triplets of ATCG) that is similar in every organism on Earth. Cool eh? The person in the video was looking extremely awestruck. Lol.
Yeah and also the time from Gregor Mendel's theories of heredity to the time when the whole human genome was deciphered is only 150 years!!! Waah... so many smart people... some of which include THE FAMOUS Thomas Hunt Morgan who is also featured in our blog.
And things like messenger RNA are introduced to us. The video we watched really cleared my doubts about what is RNA, how it is different from RNA, etc. We learnt that MRNA (or messenger RNA) is a single strand of DNA which prevents entire DNA strands from being copied. It's like only wanting the drumstick out of the whole chicken. We don't have to buy the whole chicken to get the drumstick. (Interesting analogy eh?)
The DNA and genes of our stomach cells and our skin cells, and in fact, every cell in our body, is the same!!! Just that some parts of the genes of certain cells are turned OFF. So they don't produce RNA which gives the cell instructions for making proteins. If not, our skin will start dripping mucus and producing hydrochloric acid, pepsinogen and rennin. The pepsinogen will then be converted by the hydrochloric acid to pepsin, which can then digest stuff. Ooops a bit offtrack here.
However, the video has also sort of awakened me to the sort of tiring, monotonous, dedicated, overly-passionate work that a life scientist, or in fact, any scientist, must consign himself/herself to. Am i prepared for this? Don't know yet, but now at least i know more about this branch of work.
Haha. Actually quite like today, not becoz it's the last day, but rather, because it is so relevant to our career choice. Should have this for career guidance also. Haha. The video is good! Recommend it to anyone who likes life science. 100 greatest discoveries, genetics or sth liddat. The one with the brother of the host (not biology host). Lol. If you don't understand, IGNORE the last sentence and let your love of Biology lead you. Wahahaha.
Yeah.
What do we (auhors of this blog) love about this elective? The flies of course. They have really awakened us to the work of a life science researcher. That we have to make friends with flies to know about them. That maggots (fly larvae) are not that disgusting after all. Cute in a way. Especially wriggling under the microscope. And especially after dissection.
Pretty sadly, though, we have to update on our results of the breeding we carried out on the first day. Thing is, they didn't breed!!! Probably accidentally put flies of the same sex together. Or perhaps they just don't like each other. Perhaps.
Yeah well shall stop here. Time to watch another video liao. Byeezzzz
UPDATED: Saw something interesting in the video, so shall show you a picture.
Taken from www.bio.davidson.edu
Know what this is??? This is a GENE GUN!!!
Lol never heard of anything like this before. Have you? if interested there is an article on it in wikipedia. It's not used to kill genes though.
Day 6
On Day 6, we did mainly analyzing of the inheritance patterns of fruit flies, given the F1 generation (first generation of offspring) and the F2 generation (second generation of offspring). Due to the lack of flies, we used paper flies (flies printed on paper) instead.
What did we have to do? Mainly it was just seperating the paper flies into males and females, and red eyed and white eyed flies (for F1 generation) and short wingspan and long wingspan flies (for the F2 generation). After we got the numbers right, we had to use these statistics to predict the genotypes of the parents from the numbers and proportions of the different offspring.
Nothing much, but it can get quite confusing, especially when we had to use W and W+ to represent the red eyed and white eyed flies respectively. and Vg and Vg+ to represent the vestigial wing and normal wing variety of flies respectively. We had to use these symbols to draw four Punnet's Squares that we could use to help us in our analysis.
Some terms that we learnt:
1. autosomal recessive gene
2. autosomal dominant gene
3. sex-linked recessive gene
4. sex-linked dominant gene
What do they mean?
1. occurs on the autosomes and the phenotype it gives will be expressed even in the gene is heterozygous.
2. occurs on the autosomes and only become phenotypicaly apparent when 2 copies of the same gene is present (needs to be homozygous for it to be expressed)
3. occurs on the sex chromosomes and only becomes phenotypically apparent when 2 copies of the gene are present (needs to be homozygous for itto be expressed)
4. occurs on the sex chromosomes and the phenotype it gives will b e expressed even if the gene is heterozygous.
What did we have to do? Mainly it was just seperating the paper flies into males and females, and red eyed and white eyed flies (for F1 generation) and short wingspan and long wingspan flies (for the F2 generation). After we got the numbers right, we had to use these statistics to predict the genotypes of the parents from the numbers and proportions of the different offspring.
Nothing much, but it can get quite confusing, especially when we had to use W and W+ to represent the red eyed and white eyed flies respectively. and Vg and Vg+ to represent the vestigial wing and normal wing variety of flies respectively. We had to use these symbols to draw four Punnet's Squares that we could use to help us in our analysis.
Some terms that we learnt:
1. autosomal recessive gene
2. autosomal dominant gene
3. sex-linked recessive gene
4. sex-linked dominant gene
What do they mean?
1. occurs on the autosomes and the phenotype it gives will be expressed even in the gene is heterozygous.
2. occurs on the autosomes and only become phenotypicaly apparent when 2 copies of the same gene is present (needs to be homozygous for it to be expressed)
3. occurs on the sex chromosomes and only becomes phenotypically apparent when 2 copies of the gene are present (needs to be homozygous for itto be expressed)
4. occurs on the sex chromosomes and the phenotype it gives will b e expressed even if the gene is heterozygous.
Saturday, October 6, 2007
Knowing more about fruit flies
1. Pictures
Some of the different stages of the fruit fly we looked out for on Day 5 of the module. We learned how to differentiate between the different stages of the larvae, and how to tell between newly formed pupae and "older" pupae, and how to tell if pupal cases were empty or not.
A Drosophila egg under the microscope. Taken from http://www.biologydaily.com/
A 1st-instar Drosophila larva under the microscope. Taken from http://www.ratical.org/co-globalize/MaeWanHo/fruitfly.jpg
first instar (extreme left), 2nd instar (extreme right) and 3rd instar larva (middle) of the fruit fly. Note the differences in length and width. First instar larvae are usually 1-2 mm long, 2nd instar larvae are usually 2-3 mm long, and 3rd instar larvae are around 4 mm long. Also, more developed larvae are usually found higher up in the flask as they are preparing to pupate. The recently hatched larvae would be found nearer the bottom, in the food. Taken from http://www.biology.clc.uc.edu/
Third instar larva (left) and pupa of the fruit fly. Taken from http://www.quest.nasa.gov/
Needless to say, pupa of the fruit fly. The one on the left is a less developed pupa, the prepupa, while the one on the right is in its later stages of metamorphosis. Taken from http://www.openscience.it/
Info about pupa: Sometimes it can be hard to differentiate between pupa and empty pupal cases. Well, there is a simple method to distinguish between the two. Just hold the pupa up to the light. If it allows light to pass through, then it is just an empty pupal case.
.jpg)
And not forgetting the main star itself: the ADULT DROSOPHILA MELANOGASTER, a.k.a FRUIT FLY!!! Taken from http://www.notexactlyrocketscience.wordpress.com/
2. How long?
Well, now that we have since the different stages of growth of the fruit fly, there is still a nagging question: how long does it take for each of the stages of growth? The answer is revealed below:
egg to larva--- 1 day
first instar larva to second instar larva---2 days
second instar larva to third instar larva---2 to 3 days
third instar larva to pupa--- 2 days
pupa to adult--- 6 days
So, adding up the above numbers, it takes a total of 14 days (estimate) for the egg to become an adult drosophila. Compare that to 20 years that a human takes.
3. Experiments
It is now time to explore!!! Explore what? The growth of the fruit fly!!! This is for interested people who would like to know more about the Drosophila Melanogaster (a.k.a fruit fly), and how different conditions can affect their growth through the different stages, particularly through the larval and adult stages.
Firstly, there will be four different set-ups, each with 5 containers of fruit fly larvae with varying compositions of food inside the containers. To prevent inaccuracies, all the larvae used should be newly hatched. There should be around 10-15 larvae in each container (number of larvae used should be the same) The experiment will be carried out for 20 days, which is enough time for the larvae to grow to maturity as adult fruit flies. At the end of the experiment, all the flies in each container will be measured and the average length of the flies will be taken. (Note: A product, FlyNap, can be used to anesthetize the flies to knock them out before measurement)
The results will show which conditions are best for the optimum growth of fruit flies. The below summarization will show the conditions of the various set ups, followed by the 4 different compositions of food in 4 different containers of fruit fly larvae. (Discounting agar powder, water and vinegar). So together, there will be 16 different conditions for the fruit flies (4x4) which can be the best condition for the growth of fruit flies. The best condition will, of course, yield flies which are longer and bigger.
SET-UP 1: Dry conditions, 20 degrees celsius
1. Milo powder, banana, yeast in equal amounts
2. More milo powder, less mashed banana, less yeast
3. More mashed banana, less milo, less yeast
4. more yeast, less banana, less milo
SET-UP 2: Dry conditions, 28 degrees celsius
*same four compositions*
SET-UP 3: Moist conditions, 20 degrees celsius
*same four compositions*
SET-UP 4: Moist conditions, 28 degrees celsius
*same four compositions*
Note: Conditions should be maintained for the whole of the experiment, and there should be no disruptions or external stimulus. The use of thermostats can be used to adjust the different temperatures for the different set-ups. Temperatures should be adjusted beforehand.
Second note: The amount of agar powder and vinegar added should be THE SAME. The amount of water will vary due to the need for moist and dry conditions. However, for each condition (dry or moist), the amount of water should be THE SAME.
HAVE FUN!!!
Some of the different stages of the fruit fly we looked out for on Day 5 of the module. We learned how to differentiate between the different stages of the larvae, and how to tell between newly formed pupae and "older" pupae, and how to tell if pupal cases were empty or not.
A Drosophila egg under the microscope. Taken from http://www.biologydaily.com/
A 1st-instar Drosophila larva under the microscope. Taken from http://www.ratical.org/co-globalize/MaeWanHo/fruitfly.jpg
first instar (extreme left), 2nd instar (extreme right) and 3rd instar larva (middle) of the fruit fly. Note the differences in length and width. First instar larvae are usually 1-2 mm long, 2nd instar larvae are usually 2-3 mm long, and 3rd instar larvae are around 4 mm long. Also, more developed larvae are usually found higher up in the flask as they are preparing to pupate. The recently hatched larvae would be found nearer the bottom, in the food. Taken from http://www.biology.clc.uc.edu/
Third instar larva (left) and pupa of the fruit fly. Taken from http://www.quest.nasa.gov/
Needless to say, pupa of the fruit fly. The one on the left is a less developed pupa, the prepupa, while the one on the right is in its later stages of metamorphosis. Taken from http://www.openscience.it/
Info about pupa: Sometimes it can be hard to differentiate between pupa and empty pupal cases. Well, there is a simple method to distinguish between the two. Just hold the pupa up to the light. If it allows light to pass through, then it is just an empty pupal case.
.jpg)
And not forgetting the main star itself: the ADULT DROSOPHILA MELANOGASTER, a.k.a FRUIT FLY!!! Taken from http://www.notexactlyrocketscience.wordpress.com/
2. How long?
Well, now that we have since the different stages of growth of the fruit fly, there is still a nagging question: how long does it take for each of the stages of growth? The answer is revealed below:
egg to larva--- 1 day
first instar larva to second instar larva---2 days
second instar larva to third instar larva---2 to 3 days
third instar larva to pupa--- 2 days
pupa to adult--- 6 days
So, adding up the above numbers, it takes a total of 14 days (estimate) for the egg to become an adult drosophila. Compare that to 20 years that a human takes.
3. Experiments
It is now time to explore!!! Explore what? The growth of the fruit fly!!! This is for interested people who would like to know more about the Drosophila Melanogaster (a.k.a fruit fly), and how different conditions can affect their growth through the different stages, particularly through the larval and adult stages.
Firstly, there will be four different set-ups, each with 5 containers of fruit fly larvae with varying compositions of food inside the containers. To prevent inaccuracies, all the larvae used should be newly hatched. There should be around 10-15 larvae in each container (number of larvae used should be the same) The experiment will be carried out for 20 days, which is enough time for the larvae to grow to maturity as adult fruit flies. At the end of the experiment, all the flies in each container will be measured and the average length of the flies will be taken. (Note: A product, FlyNap, can be used to anesthetize the flies to knock them out before measurement)
The results will show which conditions are best for the optimum growth of fruit flies. The below summarization will show the conditions of the various set ups, followed by the 4 different compositions of food in 4 different containers of fruit fly larvae. (Discounting agar powder, water and vinegar). So together, there will be 16 different conditions for the fruit flies (4x4) which can be the best condition for the growth of fruit flies. The best condition will, of course, yield flies which are longer and bigger.
SET-UP 1: Dry conditions, 20 degrees celsius
1. Milo powder, banana, yeast in equal amounts
2. More milo powder, less mashed banana, less yeast
3. More mashed banana, less milo, less yeast
4. more yeast, less banana, less milo
SET-UP 2: Dry conditions, 28 degrees celsius
*same four compositions*
SET-UP 3: Moist conditions, 20 degrees celsius
*same four compositions*
SET-UP 4: Moist conditions, 28 degrees celsius
*same four compositions*
Note: Conditions should be maintained for the whole of the experiment, and there should be no disruptions or external stimulus. The use of thermostats can be used to adjust the different temperatures for the different set-ups. Temperatures should be adjusted beforehand.
Second note: The amount of agar powder and vinegar added should be THE SAME. The amount of water will vary due to the need for moist and dry conditions. However, for each condition (dry or moist), the amount of water should be THE SAME.
HAVE FUN!!!
Friday, October 5, 2007
Getting To Know The Flies Better
On Day 4 we had to dissect the fruit fly larvaes in order to look at their polytene chromosomes. It was a totally new and cool experience and we realised that it was not as easy as it seemed. We actually had to "pull" the larvae apart using a disecting needle and a focep to get its salivary glands which contain the polytene chromosomes. It was really difficult to do that as we encountered problems like locating the larvae's head as well as the pinning down of the head and the removal of its body. We failed many times as we were either not able to locate the salivary glands or we were unable to separate the salivary glands from the other body parts. Even though we failed to extract the chromosomes in the end, we learnt about the importance of perseverance and not giving up no matter how tough the challenge is.
Procedures for Polytene chromosomes extraction and staining
- Remove a larvae from the vial provided and place it onto a drop of 0.7% saline solution
- Using a sharp forcep, a sharp needle, dissect the larvae and look for the salivary glands as shown in the pictures below.
- Tease out all other tissues and take only the salivary glands.
- Drain the saline off the slides and replace with HCL( Fixation of chromosomes; preserve the integrity of the structure) for a minute.
- Drain the HCL and replace with aceto-orcein stain(stain the cells). Let it stand for 10 minutes.
- Drain the stain and replace with acetic acid(fill the stain permanently). Let it stand for 1-3 minutes.
- Drain and replace with saline.
- Place a coverslip over the glands, using the thumb and a paper towel, push down on the slide. The pressure applied will squash the glands, rupture the nuclear membrane and free the chromosomes.
- Using a compound microscope, observe the slide at the different magnifications to check for the stained chromosomes.
- Make the slide permanent by brushing along the edges of the coverslip with nail polish.
More on Polytene Chromosomes
How are they formed?
Polytene chromosomes are formed when some specialized cells undergo repeated rounds of DNA replication without cell division (endomitosis), producing chromatids that remain synapsed together in a haploid number of chromosomes.
Characteristics
They have light and dark banding patterns which can be used to identify chromosomal rearragements and deletions.
Functions
They can increase the volume of the cells nuclei, cause cell expansion and polytene cells may also have a metabolic advantage as multiple copies of genes permits a high level of gene expression.
Taken from http://en.wikipedia.org/wiki/Polytene_chromosome
Banded chromosomes from http://biology.clc.uc.edu/fankhauser/Labs/Genetics/Drosophila_chromosomes/Drosophila_Chromosomes.htm
Thursday, October 4, 2007
The fly man: Thomas Hunt Morgan
1. Who is he?
Thomas Hunt Morgan, taken from www.wikipedia.org/thomashuntmorgan
He was a famous American geneticist and embryologist, born on September 25, 1866, and died on December 4, 1945. He is widely acknowledged as the "founder" of using fruit flies to study heredity in breeding experiments.
Information taken from www.wikipedia.org/thomashuntmorgan
2. What did he do?
Using the fruit fly for his experimental research, he showed that genes are linked in a series on chromosomes, and are responsible for identifiable, hereditary traits. His work played a key role in establishing the field of genetics.
It was in his lab, in one of the many breeding experiments that he carried out, that the first mutant fruit fly, with white eyes instead of red eyes, was first discovered.
White eyes (left) and red eye (right) fruit flies, taken from http://www.exploratorium.edu/exhibits/mutant_flies
3. His achievements
Thomas Hunt Morgan was awarded the Nobel Prize in Physiology or Medicine in 1933. The work for which the prize was awarded was completed over a 17-year period at Columbia University, commencing in 1910 with his discovery of the white-eyed mutation in the fruit fly, Drosophila. He was the first to win the Nobel Prize for genetics.
Information taken from http://nobelprize.org/nobel_prizes/medicine/articles/lewis
Tuesday, October 2, 2007
Flies through the years
1. History
When were flies first used in genetic breeding experiments? It is an enormous research tradition that dated to more than a century ago! Even though he was not the first person to grow flies, Thomas Hunt Morgan was definitely the founder of fly genetics. The first mutant fruit flies (with white eyes instead of the usual red) were discovered in his lab in Columbia University in 1910.
Information taken from http://flymove.uni-muenster.de/Tour/history/Hispage.html?http&&&flymove.uni-muenster.de/Tour/history/HisTxT.html
2. The fly now
Today, the Drosophila field has a large research community, its own conferences and databases like FlyBase, Interactive Fly, Bloomington stock center, BDGP and FlyView. The genomic sequence of Drosophila is now completely resolved.
This information is taken from http://flymove.uni-muenster.de/Tour/history/Hispage.html?http&&&flymove.uni-muenster.de/Tour/history/HisTxT.html
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