yay, sunday.
woo.
finished all the assignments and stuff for the first half of sem 2 today. so relieved.
managed to randomly guess a question in the onlin chem quiz.. and got it right which was uber cool.
anndd i think thats all for now.
this is an AWESOME song. The Last Day on Earth, by Kate Miller-Heidke
Look down the ground below is crumbling
Look up the stars are all exploding
It's the last day on earth
In my dreams
It's the end of the world
And you've come back to me
In my dreams
Between the dust and the debris
There's a light surrounding you and me
It's the last day on earth
In my dreams
It's the end of the world
And you've come back to me
In my dreams
And you hold me closer than I can ever remember being held.
I'm not afraid to sleep now, if we can stay like this until
It's the last day on earth
In my dreams
It's the end of the world
And you've come back to me
In my head I replay our conversations
Over and over til they feel like hallucinations
You know me? I love to lose my mind
And every time anybody speaks your name I still feel the same
I ache, I ache, I ache inside.
Sunday, 30 August 2009
Saturday, 29 August 2009
havent posted in a while!
wow. havent posted in a while. being three days.
this is partly due to the fact thattt... i hv been doing my hbio essay! it was on familial hypercholesterolemia... i will attach it to the end of my little rant here..
apart from that.. i also had a hbio test on thursday.. went alright actually. i think better than my first hbio test which i epically screwed up. anyhow.. i also watched two hindi movies, salaam-e-ishq and also eklavya. both were really really good. ill attach some pics as well..
but im pretty much done assessment wise for two weeks :) besides the ongoing weekly chem quiz which i will be doin tmr.. all is well.
ohhk i think thats all for nows.
this is partly due to the fact thattt... i hv been doing my hbio essay! it was on familial hypercholesterolemia... i will attach it to the end of my little rant here..
apart from that.. i also had a hbio test on thursday.. went alright actually. i think better than my first hbio test which i epically screwed up. anyhow.. i also watched two hindi movies, salaam-e-ishq and also eklavya. both were really really good. ill attach some pics as well..
but im pretty much done assessment wise for two weeks :) besides the ongoing weekly chem quiz which i will be doin tmr.. all is well.
ohhk i think thats all for nows.
here are the pics:
annnd as promised.. here is my awesome essay:
Familial Hypercholesterolemia (FH) is a genetic disease which is characterised by an increase in blood cholesterol levels, consequently leading to atherosclerosis and an elevated risk of premature coronary heart disease (Maxwell et al. 2009). Treatment of FH is mainly composed of lifestyle factors which act as preventative measures against the onset of heart disease.
Cholesterol and lipid levels in the human body are regulated by lipoproteins, which are complexes of cholesterol and triglycerides that are transported around the body (Saladin 2007). Different types of lipoproteins exist, including low density lipoproteins (LDLs) and high-density lipoproteins (HDLs). These two lipoproteins have contrasting roles in cholesterol regulation within the body; LDLs deposit cholesterol around the body, and HDLs remove excess cholesterol from the body (Saladin 2007). Usually, LDLs are absorbed by receptor-mediated endocytosis, thus regulating the levels of LDLs within the blood (Saladin 2007) However, if the receptor on the endocytic cell is non-functional, it lacks the ability to recognise the LDL molecule, thus cannot ingest it into the cell; as a result, this leads to an increased concentration of LDLs within the blood. It is for this reason, that people with FH have a high blood cholesterol level. The genetic basis as to how this occurs will be discussed as follows.
FH is an inherited disease which is transmitted in an autosomal dominant manner (Fouchier 2001). The genetic basis from which the disorder arises is a variety of mutations on the LDL-receptor gene, which then leads to a multitude of defects in LDL-receptor synthesis (Fard-Esfahani et al. 2005). Consequently, this results in a deficiency of functional LDL receptors on the liver cellular surface, causing an increased concentration of LDL within the plasma (Alonso et al. 2009). Another genetic defect which can cause FH is a mutation in the gene responsible for the apolipoprotien which is required to ‘dock’ to the receptors surface (Schuster 2002). This affects the LDL concentration in the plasma as the apolipoprotien is non-functional, thus cannot recognise or attach to the receptor; consequently the LDL concentration in the plasma goes up.
A high concentration of LDLs in the blood suggests that a large amount of cholesterol is being deposited into the arteries, a condition known as atherosclerosis (Saladin 2007). In normal (non FH) people, LDL molecules bind to cells, and are then ingested by the cell. For example, LDL is ingested into hepatocytes in the liver, which requires cholesterol for the synthesis of bile acids (Schuster 2002). However, people with FH cannot process the LDL molecule due to mutations in the receptor or apolipoprotein genes, thus this regulation is not as controlled. Two of the main factors which cause atherosclerosis are high LDL plasma concentration and defective LDL receptors-both characteristics of FH. In atherosclerosis, the LDL receptors in the arterial cells are dysfunctional, thus continue to take up cholesterol even though the cell’s cholesterol requirements are met (Saladin 2007). This causes a deposit of cholesterol to build up, forming an atheroma, obstructing the lumen of the artery. This obstruction within the artery is a natural precursor to many heart conditions including myocardial infarction and angina pectoris (Smith 2000).
FH is a disease which subjects the person who has it to be predisposed to coronary heart disease. However, the incidence of heart disease in all patients is not the same. As mentioned above, the gene is inherited in an autosomal dominant manner; therefore the person with FH can be either heterozygous, or homozygous. A homozygote would produce no viable LDL receptors, whilst a heterozygote would produce half the normal amount (Saladin 2007). These production values significantly affect the incidence of myocardial infarction, due to the body’s ability to compensate to these defects. For a homozygote, the chance of heart attack in childhood is high, whilst a heterozygote is most likely to experience a heart attack by the age of 35 (Saladin 2007). Other factors which influence the formation of atheromatous plaques include anxiety, stress, obesity and bad diet. In addition, smoking, and a lack of exercise are also factors which promote the incidence of heart disease (Smith 2000). Lack of exercise increases the risk of heart disease, as it promotes LDL formation. Conversely, exercise promotes HDL formation, which lowers plasma cholesterol concentration levels, and reduces the risk of heart disease (Saladin 2007). As a result, it follows that someone who is a heterozygote, doesn’t smoke and leads a healthy lifestyle, would be unlikely to experience a heart attack.
Many preventative measures can be made when dealing with FH, along with many treatment options for coronary heart disease. As mentioned above, leading a balanced, active lifestyle delays the onset of atherosclerosis, and the resulting heart disorders which follow. Coronary heart disease can be treated in many ways, including: balloon angioplasty (whereby a catheter is introduced into the artery and the balloon inflated, such that the atheroma is either squashed or cracked, thus creating a larger lumen); laser angioplasty (whereby a laser is used to break apart and vaporise the atheroma); and coronary artery bypass surgery (whereby a section of vein or artery is used to create a bypass around the blocked section caused by the atheroma) (Saladin 2007).
FH is an inherited disease, transmitted in an autosomal dominant manner, which leads to high cholesterol level. Treatment is concerned with altering the environment of the patient to compensate for the genetic predisposition towards having heart disease.
894 words.
References
Saldin, KS 2007, Anatomy and Physiology: the unity of form and function, 4th edn. McGraw-Hill New York.
Smith, T 2000, The Human Body, Ken Fin London.
Maxwell, SJ, Molster, CM, Poke, SJ & O’Leary, P 2009, ‘Communicating Familial Hypercholesterolemia genetic information within families’, Genetic Testing and Molecular Biomarkers, vol. 13, no. 3, pp. 301-306.
Alonso, R, Defesche, JC, Tejedor, D, Castillo, S, Stef, M, Mata, N, Gomez-Enterria, P, Martinez-Faedo, C, Forga, L, Mata, P 2009, ‘Genetic diagnosis of Familial Hypercholesterolemia using a DNA-array based platform’, ClinicalBiochemsitry, vol. 42, pp. 899-903. Available from: Science Direct. [23 August 2009]
Schuster, H 2002, ‘High Risk/Priority: Familial Hypercholesterolemia-a paradigm for molecular medicine’, Atherosclerosis Supplements, vol. 2, pp. 27-32.
Fouchier, SW, Defesche JC, Umans-Eckenhausen, MAW, Kastelein, JJP 2001, ‘The molecular basis of Familial Hypercholesterolemia in The Netherlands’, Hum Genet, vol. 109, pp. 602-615
Fard-Esfahani, P, Khatami, S, Zeinali, C, Taghikhani, M, Allahyari, M 2005, ‘A modified conformation sensitive gel electrophoresis (CSGE) method for rapid and accurate detection of low density lipoprotein (LDL) receptor gene mutations in Familial Hypercholesterolemia’, Clinical Biochemistry, vol. 38, pp. 579-583. Available from: Science Direct. [24th August 2009]
Wednesday, 26 August 2009
80th
yay
80th post. apparently. according to the little post-counter thingo on the dashboard
got anhb test tmr.
argh. and also hv to write an essay. familial hypercholesterolemia. due monday.
and then im freeeeee till after the mid sem break when all the assessments will start again.
k this is all for now. need to go bak to study haha.
80th post. apparently. according to the little post-counter thingo on the dashboard
got anhb test tmr.
argh. and also hv to write an essay. familial hypercholesterolemia. due monday.
and then im freeeeee till after the mid sem break when all the assessments will start again.
k this is all for now. need to go bak to study haha.
Monday, 24 August 2009
exam!
ahh. havent posted for two days!
been studying
i got an exam tmr. its soo stupid.. its a mid-sem exam, and its not even freaking mid sem yet.
but oh wells. tmr it will be all over :D
but then i still gotta write my anhb essay. and also got an anhb test on thurs.
so much work.. but i will persevere hahaha.
and the funny thing is.. that when the mid sem study break comes around.. ill have NOTHING to study for.. just like ongoing revision.
anyhow. will post more later.
been studying
i got an exam tmr. its soo stupid.. its a mid-sem exam, and its not even freaking mid sem yet.
but oh wells. tmr it will be all over :D
but then i still gotta write my anhb essay. and also got an anhb test on thurs.
so much work.. but i will persevere hahaha.
and the funny thing is.. that when the mid sem study break comes around.. ill have NOTHING to study for.. just like ongoing revision.
anyhow. will post more later.
Saturday, 22 August 2009
zomg awesome web thing
http://omegle.com/
this thing is awesome.
i recommend thateveryone should try it
Thursday, 20 August 2009
arcy paper!
archaeologogy paper. WTH is archaeologogy.
ARCHAEOLOGY PAPER
there we go. i was up till 2am this morning finishing this off. its due tmr morning.. and i needed to study for this other test so i made myself finish it last night haha. annnddd since i worked hard on it i shall post it here:
Tutorial paper- Australian Holocene: What is the evidence for and results of the arrival of dingoes?
The Holocene is a time period in Australian history which is associated with many changes. These changes often have a dramatic effect on the Australian ecosystem, and the evidence of these changes is apparent in the archaeological record. One such change is the arrival of the dingo. The arrival of the dingo is of great importance within the Australian Holocene as it had a marked effect on the Australian ecosystem and influenced the aboriginal culture significantly.
The dingo, or as it is taxonomically known Canis lupis dingo, is a placental, terrestrial carnivore (Gollan 1984). It has been hypothesised that the dingo is closely related to south and south-east Asian dogs, which all descend from the Indian wolf taxonomically known as Canis lupus pallipes (Flood 1995). Thus, it follows that the dingo was most likely introduced to Australia by south-east Asian sea-fearers who kept the dingoes on board as companions or as a food source. Whilst the exact date at which the species was introduced to Australia is unknown, the evidence available on the Australian mainland indicates the time period in which this introduction occurred.
The earliest evidence regarding dingoes is found at the Madura cave site, which is located in the Nullarbor Plain in Western Australia. This site is dated to 3450BP (Feder 2007). At the Mt Burr rock shelter in South Australia, dingo bone fragments have been found in the lower levels of the shelter. A date of about 7500-8500BP has been applied to the layers sandwiching this layer containing the bone fragments (Flood, 1995). However, this date has been rejected due to the presence of cracks in the upper levels of the shelter, leading to a disruption to the stratigraphical placement of fragments within that site. In essence, the bone fragments could have fallen from a ‘higher’ layer into this lower one, causing this discrepancy as to what the earliest date is regarding the dingoes existence on the Australian mainland. It is generally accepted that the dingoes first came to Australia 3500-4000 years before present, and then spread across the mainland. This idea is further supported by the abundance of dingo remains around archaeological sites all over Australia, of which many are dated to after 3000 years ago. After the dingo was introduced to Australia, it spread all over the mainland however didn’t reach Tasmania. This was because the sea levels had risen about 6000 years earlier flooding bass straight and separating Tasmania from the Australian mainland (Johnson & Wroe 2003). Thus, many of the changes which occur on the Australian mainland after the arrival of the dingoes are not evident in Tasmania.
One such change which only occurred on the Australian mainland after the arrival of the dingoes is the change in the ecosystem. The arrival of the dingoes coincided with the extinctions of three Australian faunal species: the thylacine, Tasmanian devil, and the Tasmanian native hen. Whilst the dingoes cannot be solely held responsible for these extinctions, the lack of change in abundance of these three species in Tasmania suggests that the dingoes had a significant influence in the extinctions which occurred on the mainland. In addition, within the last 8000 years, the climate has been relatively stable throughout Australia, therefore ruling out the possibility that the extinctions occurred due to climatic instability or change (Johnson & Wroe 2003). There are many hypotheses explaining as to how these three extinctions occurred, and the role that the dingo played in each of these extinctions. As there is a lack of evidence surrounding each of the hypotheses it should be noted that they aren’t definitive, but rather serve as a possible plausible explanation.
The hypothesis regarding the extinction of the thylacine stems from the belief that there was a substantial overlap in the diet of the dingo and the thylacine, thus the thylacine was outcompeted (Johnson & Wroe 2003). In addition, it has also been suggested that the dingo was a superior competitor as it possessed a complex social organisation allowing it to hunt in groups or defend resources; a skill which the thylacine lacked as a more solitary animal. Whilst these theories are mostly correct, further research has suggested that the overlap in diet was overstated; the dingo had access to a wide variety of food sources, whilst the thylacine had a more restricted diet. Consequently it seems unlikely that the dingo was the sole reason behind the depletion of the Thylacine’s food sources, but rather there was another factor.
The Tasmanian devil fed mainly on carcasses and carrion of the large bodied fauna such as the macropods and wombats. In addition, it was able to capture smaller animals as prey (Johnson & Wroe 2003). As mentioned before, the dingoes possessed a complex social organisation, so were able to deny Tasmanian devils access to carcasses with their superior defending skills, and out compete them when capturing small prey. Furthermore, dingoes are better anatomically equipped as scavengers. For example, they can crack bones with their jaws to retrieve the marrow inside. As a result, the dingoes would have left no viable resources for the Tasmanian devils to survive on. Whilst this premise seems possible, it also has some discrepancies associated with it. As the Tasmanian devil fed predominantly on carcasses, it would make sense that the effect of the dingoes on Tasmanian devils would be greater than that on the thylacine as less energy is required to defend a carcass when compared to defending live prey. However, this is not so. Additionally the Tasmanian devil and the dingo coexisted for approximately 3000 years so it seems strange that the extinction took so long to occur.
The final animal whose extinction is associated to dingo is the Tasmanian native hen; a ground dwelling bird whose habitat is limited to being in the vicinity of a permanent water source (Johnson & Wroe 2003). The theory suggests that in the last glacial maximum, the habitat in which these birds could live contracted significantly. As a result, the hen continued to live within this contracted locality, where it became an easily acquirable food source for the dingo. Whilst this theory also seems reasonable, a problem does exist. As the hen was able to coexist with the Thylacine and Tasmanian devil for thousands of years before the arrival of the dingo, it seems strange that it couldn’t coexist with the dingo. As the dingo, thylacine and Tasmanian devil all share some similarities in their diets, it would be expected that the hen would have become extinct a lot earlier.
Each of these hypotheses offers an explanation of the role that the dingo played in the extinction of these animals. However, there is still a lot which is not accounted for. As these extinctions only occurred on the Australian mainland, the significance of the dingo in these extinctions cannot be denied. During this time, there was also a period of intensification in the use of specific food resources by the Australian people (Lourandos & Ross 1994). As a result, it is generally accepted that the extinctions of these three faunal species was a result of both dingoes and humans’ influence.
The arrival of the dingo didn’t just have a biological impact on Holocene Australia, but also seems to have had an impact on the Australian aboriginal people’s culture. Dingo burials have been found at the Werribee River site, which has been dated to 7300BP. The presence of such burials suggests a close relationship between the aboriginal people and dingoes as these animals were regarded highly enough to deserve a burial. In addition, dingo remains have been found with human burials which further reinforces this idea that the Australian aborigines shared a close relationship with the dingoes. The dingo also appears in rock art paintings, such as the painting at Kunminyini Springs in the Northern Territory. This painting portrays a woman alongside a figure which is thought to be a dingo. The presence of dingoes within these paintings supports the suggestion that the aboriginal people and dingoes shared a close relationship. Moreover, the dingoes had a significant influence on the Australian aboriginal people’s way of life. They were used as a source of warmth, and also had an important place in the rituals and mythology of the Australian Aboriginal people’s culture (Flood 1995).
The dingo is an animal which has considerable significance within the Australian Holocene. After its arrival into the country around 3500 years ago, the dingo spread all over the mainland, in habiting much of it. As the dingo had to compete with the already existing fauna, it caused significant disruptions to the already existing ecosystem. In addition, the arrival of the dingoes also had a significant impact on the Australian Aboriginal people’s culture; both as a companion in their everyday life, to finding its way into their rituals and mythology.
ARCHAEOLOGY PAPER
there we go. i was up till 2am this morning finishing this off. its due tmr morning.. and i needed to study for this other test so i made myself finish it last night haha. annnddd since i worked hard on it i shall post it here:
Tutorial paper- Australian Holocene: What is the evidence for and results of the arrival of dingoes?
The Holocene is a time period in Australian history which is associated with many changes. These changes often have a dramatic effect on the Australian ecosystem, and the evidence of these changes is apparent in the archaeological record. One such change is the arrival of the dingo. The arrival of the dingo is of great importance within the Australian Holocene as it had a marked effect on the Australian ecosystem and influenced the aboriginal culture significantly.
The dingo, or as it is taxonomically known Canis lupis dingo, is a placental, terrestrial carnivore (Gollan 1984). It has been hypothesised that the dingo is closely related to south and south-east Asian dogs, which all descend from the Indian wolf taxonomically known as Canis lupus pallipes (Flood 1995). Thus, it follows that the dingo was most likely introduced to Australia by south-east Asian sea-fearers who kept the dingoes on board as companions or as a food source. Whilst the exact date at which the species was introduced to Australia is unknown, the evidence available on the Australian mainland indicates the time period in which this introduction occurred.
The earliest evidence regarding dingoes is found at the Madura cave site, which is located in the Nullarbor Plain in Western Australia. This site is dated to 3450BP (Feder 2007). At the Mt Burr rock shelter in South Australia, dingo bone fragments have been found in the lower levels of the shelter. A date of about 7500-8500BP has been applied to the layers sandwiching this layer containing the bone fragments (Flood, 1995). However, this date has been rejected due to the presence of cracks in the upper levels of the shelter, leading to a disruption to the stratigraphical placement of fragments within that site. In essence, the bone fragments could have fallen from a ‘higher’ layer into this lower one, causing this discrepancy as to what the earliest date is regarding the dingoes existence on the Australian mainland. It is generally accepted that the dingoes first came to Australia 3500-4000 years before present, and then spread across the mainland. This idea is further supported by the abundance of dingo remains around archaeological sites all over Australia, of which many are dated to after 3000 years ago. After the dingo was introduced to Australia, it spread all over the mainland however didn’t reach Tasmania. This was because the sea levels had risen about 6000 years earlier flooding bass straight and separating Tasmania from the Australian mainland (Johnson & Wroe 2003). Thus, many of the changes which occur on the Australian mainland after the arrival of the dingoes are not evident in Tasmania.
One such change which only occurred on the Australian mainland after the arrival of the dingoes is the change in the ecosystem. The arrival of the dingoes coincided with the extinctions of three Australian faunal species: the thylacine, Tasmanian devil, and the Tasmanian native hen. Whilst the dingoes cannot be solely held responsible for these extinctions, the lack of change in abundance of these three species in Tasmania suggests that the dingoes had a significant influence in the extinctions which occurred on the mainland. In addition, within the last 8000 years, the climate has been relatively stable throughout Australia, therefore ruling out the possibility that the extinctions occurred due to climatic instability or change (Johnson & Wroe 2003). There are many hypotheses explaining as to how these three extinctions occurred, and the role that the dingo played in each of these extinctions. As there is a lack of evidence surrounding each of the hypotheses it should be noted that they aren’t definitive, but rather serve as a possible plausible explanation.
The hypothesis regarding the extinction of the thylacine stems from the belief that there was a substantial overlap in the diet of the dingo and the thylacine, thus the thylacine was outcompeted (Johnson & Wroe 2003). In addition, it has also been suggested that the dingo was a superior competitor as it possessed a complex social organisation allowing it to hunt in groups or defend resources; a skill which the thylacine lacked as a more solitary animal. Whilst these theories are mostly correct, further research has suggested that the overlap in diet was overstated; the dingo had access to a wide variety of food sources, whilst the thylacine had a more restricted diet. Consequently it seems unlikely that the dingo was the sole reason behind the depletion of the Thylacine’s food sources, but rather there was another factor.
The Tasmanian devil fed mainly on carcasses and carrion of the large bodied fauna such as the macropods and wombats. In addition, it was able to capture smaller animals as prey (Johnson & Wroe 2003). As mentioned before, the dingoes possessed a complex social organisation, so were able to deny Tasmanian devils access to carcasses with their superior defending skills, and out compete them when capturing small prey. Furthermore, dingoes are better anatomically equipped as scavengers. For example, they can crack bones with their jaws to retrieve the marrow inside. As a result, the dingoes would have left no viable resources for the Tasmanian devils to survive on. Whilst this premise seems possible, it also has some discrepancies associated with it. As the Tasmanian devil fed predominantly on carcasses, it would make sense that the effect of the dingoes on Tasmanian devils would be greater than that on the thylacine as less energy is required to defend a carcass when compared to defending live prey. However, this is not so. Additionally the Tasmanian devil and the dingo coexisted for approximately 3000 years so it seems strange that the extinction took so long to occur.
The final animal whose extinction is associated to dingo is the Tasmanian native hen; a ground dwelling bird whose habitat is limited to being in the vicinity of a permanent water source (Johnson & Wroe 2003). The theory suggests that in the last glacial maximum, the habitat in which these birds could live contracted significantly. As a result, the hen continued to live within this contracted locality, where it became an easily acquirable food source for the dingo. Whilst this theory also seems reasonable, a problem does exist. As the hen was able to coexist with the Thylacine and Tasmanian devil for thousands of years before the arrival of the dingo, it seems strange that it couldn’t coexist with the dingo. As the dingo, thylacine and Tasmanian devil all share some similarities in their diets, it would be expected that the hen would have become extinct a lot earlier.
Each of these hypotheses offers an explanation of the role that the dingo played in the extinction of these animals. However, there is still a lot which is not accounted for. As these extinctions only occurred on the Australian mainland, the significance of the dingo in these extinctions cannot be denied. During this time, there was also a period of intensification in the use of specific food resources by the Australian people (Lourandos & Ross 1994). As a result, it is generally accepted that the extinctions of these three faunal species was a result of both dingoes and humans’ influence.
The arrival of the dingo didn’t just have a biological impact on Holocene Australia, but also seems to have had an impact on the Australian aboriginal people’s culture. Dingo burials have been found at the Werribee River site, which has been dated to 7300BP. The presence of such burials suggests a close relationship between the aboriginal people and dingoes as these animals were regarded highly enough to deserve a burial. In addition, dingo remains have been found with human burials which further reinforces this idea that the Australian aborigines shared a close relationship with the dingoes. The dingo also appears in rock art paintings, such as the painting at Kunminyini Springs in the Northern Territory. This painting portrays a woman alongside a figure which is thought to be a dingo. The presence of dingoes within these paintings supports the suggestion that the aboriginal people and dingoes shared a close relationship. Moreover, the dingoes had a significant influence on the Australian aboriginal people’s way of life. They were used as a source of warmth, and also had an important place in the rituals and mythology of the Australian Aboriginal people’s culture (Flood 1995).
The dingo is an animal which has considerable significance within the Australian Holocene. After its arrival into the country around 3500 years ago, the dingo spread all over the mainland, in habiting much of it. As the dingo had to compete with the already existing fauna, it caused significant disruptions to the already existing ecosystem. In addition, the arrival of the dingoes also had a significant impact on the Australian Aboriginal people’s culture; both as a companion in their everyday life, to finding its way into their rituals and mythology.
Tuesday, 18 August 2009
long time!
holy-moly havent posted in a long time..almost a week o.o i think...
well.. alot has happened. i am officially fully-fledged in the midst of my 'stressfull period of assignments.' hbio test, chem quiz 3 and the mbc lab report are done with.. now just gotta do my archaeology paper due for friday, and then mbc MID SEMESTER EXAM next week T_T annndd then hbio essay as well. oh and there is also chem quiz number FOUR. so yeaah, lots of stuffs to do.. however, after the end of aug (when my hbio essay is due) its gonna be nice and calm with basically no assignments.. just the usual ongoing study. and then the mid sem break will come which will be uber joyous.
but seriously cannot wait till this month is over. im happy just thinking about it lol. last night i was up till about 1:30 am (this morning) doing my mbc lab report. its amazing how much effort we put into something which only has a weighting of like 2% haha. hmm since im bored i shall post it here hahaa. i cbf uploading all the appendices and figures and stuff so its just the report part. (ill post it below)
hmm what else.. oh AWKWARD situation today. i was walking across the uni today and i saw these two ppls i know (lets call them A & B) together.. who were supposedly going out.. soo.. i saw these two ppls together so i texted my friend with a message saying something like this: just saw Person A and Person B sitting together on the oval.. NAAAWWWWW LOL.
i then preceded to recieve a text from my friend which said.. ohh they were breaking up.i was like O.O so it was rather awkward.. im just glad i didnt go upto person A and B when they were sitting 'together' to say hi. THAT would have been BAD.
Introduction
All living cells contain deoxyribonucleic acid (DNA) as it is used to store genetic information within the cell (Alberts et.al.2008). All cells are enclosed by a plasma membrane, and within this cell membrane, proteins are embedded (Alberts et.al.2008). Thus, by disrupting this membrane and solubilising the proteins, the DNA can be isolated and extracted. To quantify DNA, many different methods exist, such as using UV spectrophotometry, light spectrophotometry and the wet-weight to dry-weight ratio. A spectrometer is an instrument for producing and examining spectra (Turner 1987). Thus a spectrophotometer is one which does so within or near the visible spectrum. This instrument can then be used to determine the concentration of DNA present within a sample. The wet-weight/dry-weight method is used as there is a known ratio which exists between the weight of ‘wet’ and ‘dry’ DNA, thus the initial concentration of dry DNA can be calculated if the ‘wet’ weight of the DNA is obtained, and the initial volume of the sample is provided.(Appendix A).
The first objective of this experiment was to extract DNA from a chicken liver cell homogenate by exploiting the various solubility properties of the cellular macromolecules. After doing this, the objective was to then quantify the DNA using three different methods; using wet-weight/dry-weight calculations, UV spectrophotometry, and using a light spectrophotometer after treating the DNA sample with diphenylamine.
Materials and Methods
The experiments were carried out as written in the SCIE1106 unit manual (pages23-30). A deviation from the procedure was made in step 8 of laboratory 2, whereby the tubes were cooled in an ice bath for ten minutes, as opposed to being left at room temperature to cool down.
Results
The results for the experiments were as follows:
After centrifugation in step 5 of Lab 1, three separate layers were observed; a bottom organic layer, a middle protein layer, and a upper aqueous layer which contained the dissolved DNA. Upon extraction of the uppermost layer in step 7 of Lab 1, 3.5 ml’s of the aqueous layer was collected without disturbing the underlying protein layer. In step 8 of Lab 1, after the ethanol was carefully added to the 3ml of aqueous DNA solution which was isolated in the previous steps, two distinct layers were observed. The ethanol was added by using a Pasteur pipette to introduce the ethanol down the side of the tube, such that it could flow down onto the aqueous DNA layer. In step 9 of Lab 1, the DNA became visible when the two layers were mixed, thus it could be wound onto the end of the Pasteur pipette. After the DNA was left to drain, the wet weight of the DNA was 29.00mg. This wet weight was converted to a dry weight as shown by the calculation in Appendix A. The dry weight of the DNA was 1.827mg. This dry weight of DNA was then used to calculate the concentration of DNA present in the liver-cell homogenate. A concentration of 4.035mg dry DNA/g of liver was obtained. The calculations are attached as Appendix B. An UV spectrophotometer was also used to quantify the concentration of the DNA and RNA in the solution, along with the concentration of proteins. The readings are as follows:
260nm=0.0672 (concentration of DNA, RNA and other free nucleotides)
280nm=0.315 (concentration of proteins)
In laboratory 2, the DNA was treated with diphenylamine, and a standard curve produced. This curve is included as Figure 1. The table from which this standard curve was produced is attached as Table 1. Upon consultation of the graph, the ½ dilution and undiluted DNA values were observed as follows:
½ dilution: ~0.015mg in 500μl
Undiluted: ~0.030mg in 500μl
As the amount of DNA in the ½ dilution corresponded to approximately half of the DNA present in the undiluted sample, the initial pipetting and dilutions were observed as being accurate. Using the standard curve, the concentration of DNA in the initial liver cell homogenate was calculated to be 0.33125mg dry DNA/g of liver. The calculations are attached as Appendix C.
Discussion
As the results of these experiments demonstrate, the primary objectives to extract DNA from a chicken liver cell homogenate and then quantify it using the three different methods were met. However, the three different quantification methods resulted in three very different DNA concentration values due to the different nature of the quantification methods. In the quantification method in Laboratory 1 (in which the wet-weight/dry-weight ratio was used) the ‘wet-weight’ of the DNA would have also included ribonucleic acid (RNA) and other free nucleotides, thus contributing to a heavier wet-weight. Furthermore, as the ‘wet’ DNA was only left to drain off the excess ethanol for ten minutes, a large quantity of ethanol would still have been present when the wet DNA was weighed, thus also contributing to this inaccuracy. As this wet-weight served as the basis for further calculations, this resulted in the significant difference in the concentration values obtained.
The three different methods of DNA quantification which were used in these experiments each had their own advantages and disadvantages. Whilst the wet-weight/dry-weight method was a quick and easy method, it had many disadvantages, as discussed above. In addition to these, the use of a lab scale meant that only very large quantities of DNA could be quantified, as the weight of the DNA must have been large enough to register on the scale. Likewise, the UV spectrophotometry method is a quick and simple method; however the absorbance at 260nm also measured the concentration of RNA and other nucleotides. In addition, an UV spectrophotometer is expensive. The final method used in these experiments was the use of diphenylamine reagent, which also had its merits. As diphenylamine reacts solely with the deoxyribose sugar, the spectrophotometer detected only the DNA, and not other nucleotides; thus giving the most accurate quantification. Furthermore, as the diphenylamine reacted within the visible spectrum, a cheap light spectrophotometer was all that was required. A disadvantage for this method was the labour-intensive, time consuming procedure in which precise pipetting was required when creating the microtitre plate. In addition, the handling of hot acids and use of other dangerous chemicals could have lead to a laboratory hazard if precautionary steps were not adhered to.
The use of UV and light spectrophotometry has been used to quantify DNA in other experiments, such as the one explained within the journal article ‘Comparison of fluorometric and spectrophotometric DNA quantification for real-time quantitative PCR of degraded DNA’ (Shokere, Holden & Jenkins 2009). As explained within the article, DNA was quantified using a spectrophotometry machine at 260nm, and by using flourometry. The results from this experiment concluded that the flourometry method provided a more accurate quantification of the DNA; similarly in our laboratory experiments, it was concluded that the diphenylamine method was the most accurate method of quantification. In accordance to the experiment explained within this article and many similar experiments in other journal articles, our results are reflective of the ones which have been obtained within these experiments, thus seem to be valid.
In conclusion, the diphenylamine method of quantification was regarded as being the most accurate method due to the use of the deoxyribose-specific reagent. The A260nm method and the wet-weight/dry-weight method were considered inaccurate as the quantified amount included the concentration of RNA and other free nucleotides. In addition, the presence of ethanol in the latter method lead to further inaccuracies when calculating the concentration from the wet weight. As our results and conclusions were consistent with other scientific literature, the experiments’ results were regarded as legitimate.
well.. alot has happened. i am officially fully-fledged in the midst of my 'stressfull period of assignments.' hbio test, chem quiz 3 and the mbc lab report are done with.. now just gotta do my archaeology paper due for friday, and then mbc MID SEMESTER EXAM next week T_T annndd then hbio essay as well. oh and there is also chem quiz number FOUR. so yeaah, lots of stuffs to do.. however, after the end of aug (when my hbio essay is due) its gonna be nice and calm with basically no assignments.. just the usual ongoing study. and then the mid sem break will come which will be uber joyous.
but seriously cannot wait till this month is over. im happy just thinking about it lol. last night i was up till about 1:30 am (this morning) doing my mbc lab report. its amazing how much effort we put into something which only has a weighting of like 2% haha. hmm since im bored i shall post it here hahaa. i cbf uploading all the appendices and figures and stuff so its just the report part. (ill post it below)
hmm what else.. oh AWKWARD situation today. i was walking across the uni today and i saw these two ppls i know (lets call them A & B) together.. who were supposedly going out.. soo.. i saw these two ppls together so i texted my friend with a message saying something like this: just saw Person A and Person B sitting together on the oval.. NAAAWWWWW LOL.
i then preceded to recieve a text from my friend which said.. ohh they were breaking up.i was like O.O so it was rather awkward.. im just glad i didnt go upto person A and B when they were sitting 'together' to say hi. THAT would have been BAD.
well i think thats all for nows... cant really think of much else..i shall post my lab report as promised:
Introduction
All living cells contain deoxyribonucleic acid (DNA) as it is used to store genetic information within the cell (Alberts et.al.2008). All cells are enclosed by a plasma membrane, and within this cell membrane, proteins are embedded (Alberts et.al.2008). Thus, by disrupting this membrane and solubilising the proteins, the DNA can be isolated and extracted. To quantify DNA, many different methods exist, such as using UV spectrophotometry, light spectrophotometry and the wet-weight to dry-weight ratio. A spectrometer is an instrument for producing and examining spectra (Turner 1987). Thus a spectrophotometer is one which does so within or near the visible spectrum. This instrument can then be used to determine the concentration of DNA present within a sample. The wet-weight/dry-weight method is used as there is a known ratio which exists between the weight of ‘wet’ and ‘dry’ DNA, thus the initial concentration of dry DNA can be calculated if the ‘wet’ weight of the DNA is obtained, and the initial volume of the sample is provided.(Appendix A).
The first objective of this experiment was to extract DNA from a chicken liver cell homogenate by exploiting the various solubility properties of the cellular macromolecules. After doing this, the objective was to then quantify the DNA using three different methods; using wet-weight/dry-weight calculations, UV spectrophotometry, and using a light spectrophotometer after treating the DNA sample with diphenylamine.
Materials and Methods
The experiments were carried out as written in the SCIE1106 unit manual (pages23-30). A deviation from the procedure was made in step 8 of laboratory 2, whereby the tubes were cooled in an ice bath for ten minutes, as opposed to being left at room temperature to cool down.
Results
The results for the experiments were as follows:
After centrifugation in step 5 of Lab 1, three separate layers were observed; a bottom organic layer, a middle protein layer, and a upper aqueous layer which contained the dissolved DNA. Upon extraction of the uppermost layer in step 7 of Lab 1, 3.5 ml’s of the aqueous layer was collected without disturbing the underlying protein layer. In step 8 of Lab 1, after the ethanol was carefully added to the 3ml of aqueous DNA solution which was isolated in the previous steps, two distinct layers were observed. The ethanol was added by using a Pasteur pipette to introduce the ethanol down the side of the tube, such that it could flow down onto the aqueous DNA layer. In step 9 of Lab 1, the DNA became visible when the two layers were mixed, thus it could be wound onto the end of the Pasteur pipette. After the DNA was left to drain, the wet weight of the DNA was 29.00mg. This wet weight was converted to a dry weight as shown by the calculation in Appendix A. The dry weight of the DNA was 1.827mg. This dry weight of DNA was then used to calculate the concentration of DNA present in the liver-cell homogenate. A concentration of 4.035mg dry DNA/g of liver was obtained. The calculations are attached as Appendix B. An UV spectrophotometer was also used to quantify the concentration of the DNA and RNA in the solution, along with the concentration of proteins. The readings are as follows:
260nm=0.0672 (concentration of DNA, RNA and other free nucleotides)
280nm=0.315 (concentration of proteins)
In laboratory 2, the DNA was treated with diphenylamine, and a standard curve produced. This curve is included as Figure 1. The table from which this standard curve was produced is attached as Table 1. Upon consultation of the graph, the ½ dilution and undiluted DNA values were observed as follows:
½ dilution: ~0.015mg in 500μl
Undiluted: ~0.030mg in 500μl
As the amount of DNA in the ½ dilution corresponded to approximately half of the DNA present in the undiluted sample, the initial pipetting and dilutions were observed as being accurate. Using the standard curve, the concentration of DNA in the initial liver cell homogenate was calculated to be 0.33125mg dry DNA/g of liver. The calculations are attached as Appendix C.
Discussion
As the results of these experiments demonstrate, the primary objectives to extract DNA from a chicken liver cell homogenate and then quantify it using the three different methods were met. However, the three different quantification methods resulted in three very different DNA concentration values due to the different nature of the quantification methods. In the quantification method in Laboratory 1 (in which the wet-weight/dry-weight ratio was used) the ‘wet-weight’ of the DNA would have also included ribonucleic acid (RNA) and other free nucleotides, thus contributing to a heavier wet-weight. Furthermore, as the ‘wet’ DNA was only left to drain off the excess ethanol for ten minutes, a large quantity of ethanol would still have been present when the wet DNA was weighed, thus also contributing to this inaccuracy. As this wet-weight served as the basis for further calculations, this resulted in the significant difference in the concentration values obtained.
The three different methods of DNA quantification which were used in these experiments each had their own advantages and disadvantages. Whilst the wet-weight/dry-weight method was a quick and easy method, it had many disadvantages, as discussed above. In addition to these, the use of a lab scale meant that only very large quantities of DNA could be quantified, as the weight of the DNA must have been large enough to register on the scale. Likewise, the UV spectrophotometry method is a quick and simple method; however the absorbance at 260nm also measured the concentration of RNA and other nucleotides. In addition, an UV spectrophotometer is expensive. The final method used in these experiments was the use of diphenylamine reagent, which also had its merits. As diphenylamine reacts solely with the deoxyribose sugar, the spectrophotometer detected only the DNA, and not other nucleotides; thus giving the most accurate quantification. Furthermore, as the diphenylamine reacted within the visible spectrum, a cheap light spectrophotometer was all that was required. A disadvantage for this method was the labour-intensive, time consuming procedure in which precise pipetting was required when creating the microtitre plate. In addition, the handling of hot acids and use of other dangerous chemicals could have lead to a laboratory hazard if precautionary steps were not adhered to.
The use of UV and light spectrophotometry has been used to quantify DNA in other experiments, such as the one explained within the journal article ‘Comparison of fluorometric and spectrophotometric DNA quantification for real-time quantitative PCR of degraded DNA’ (Shokere, Holden & Jenkins 2009). As explained within the article, DNA was quantified using a spectrophotometry machine at 260nm, and by using flourometry. The results from this experiment concluded that the flourometry method provided a more accurate quantification of the DNA; similarly in our laboratory experiments, it was concluded that the diphenylamine method was the most accurate method of quantification. In accordance to the experiment explained within this article and many similar experiments in other journal articles, our results are reflective of the ones which have been obtained within these experiments, thus seem to be valid.
In conclusion, the diphenylamine method of quantification was regarded as being the most accurate method due to the use of the deoxyribose-specific reagent. The A260nm method and the wet-weight/dry-weight method were considered inaccurate as the quantified amount included the concentration of RNA and other free nucleotides. In addition, the presence of ethanol in the latter method lead to further inaccuracies when calculating the concentration from the wet weight. As our results and conclusions were consistent with other scientific literature, the experiments’ results were regarded as legitimate.
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