Saturday, 31 March 2012

Human Y Chromosome Extinction Fears Subdued


 
Human Y Chromosome Extinction Fears Subdued
Alex Schumann-Gillett
42675284

Scientists have feared the extinction of the male Y chromosome because the human male-specific region of the Y chromosome (MSY) contains only 3% of its original genetic material (Hughes et al 2012). Both the X and Y chromosomes evolved from a pair of ordinary autosomes (non-sex cells) 200 – 300 million years ago (Hughes et al 2012).


Figure 1: Chromosomal Crossing Over (University of Waikato 2011)

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The evolutionary decay of the Y chromosome was driven by 5 stratification events (Hughes et al 2012), which suppressed the exchange of genetic material between homologous chromosomes (crossing over, see figure 1) (Campbell et al 2010) within a segment, or stratum, of the chromosome (Hughes et al 2012). Because of this, genes were exposed to erosive forces associated with a lack of crossing over (Hughes et al 2012).

The fifth stratification event occurred 30 million years ago; 5 million years before the divergence of the Old World monkey human lineages (Hughes et al 2012). So, stratum 1 has the highest X-Y chromosome differentiation within the MSY and stratum 5 has the highest similarity (Hughes et al 2012).

The MSY of the rhesus macaque (Macaca mulatta) was sequenced for the first time using bacterial artificial chromosome clones and the strategy used to discover the chimpanzee and human MSY’s, and the Z chromosome of the chicken (Hughes et al 2012). Y chromosome structure was compared across humans, chimpanzees and the rhesus. The results confirmed that stratification in the three lineages finished before the divergence of apes from the Old World monkeys (Hughes et al 2012).

Protein-coding genes on the rhesus’ MSY were identified and the catalogues of the three species’ MSY were compared to gauge the levels of conservation and gene loss that have occurred over the past 25 million years (Hughes et al 2012). The rhesus and human had exactly the same 18 genes in strata 1-4 of their MSY, suggesting that the last common ancestor of humans and rhesus also had these 18 genes in strata 1-4 (Hughes et al 2012). This genetic stability is due to purifying selection, which preserves critical ancestral genes (Hughes et al 2012). There was no loss of ancestral genes in strata 5 for either lineage (Hughes et al 2012). Differences in human and rhesus MSY gene content were due to genes being added to the human MSY after separation from the Old World monkeys (Hughes et al 2012).

The number of ancestral genes at three points in the human lineage was estimated using knowledge of the five MSY strata (Hughes et al 2012). From this, the trajectory and kinematics of human MSY evolution were modelled and found to follow a path of rapid decay, deceleration and then stabilisation as in figure 2 (Hughes et al 2012). Strata 1-4 reached a stable level before the rhesus and human lineages diverged (Hughes et al 2012).


Figure 2: Models of the Trajectory and Kinematics of MSY Evolution (Hughes et al 2012)

Through the sequencing of the rhesus MSY and the comparison of its genetic material with humans and chimpanzees, it is clear that: human lineage MSY gene loss was limited to stratum 5 and gene loss in strata 1-4 finished more than 25 million years ago (Hughes et al 2012). From this, it is likely that the three per cent of the original autosome’s genes is likely to be conserved and the human Y chromosome is not going to become extinct any time soon (Hughes et al 2012).


References

Campbell, N A et al 2010, Biology, 8th edn, Pearson, Australia.

Hughes, J et al 2012, ‘Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes’, Nature, vol. 483, no. 10843, pp. 82 – 87.

University of Waikato 2011, Chromosomes Crossing Over, Sciencelearn Hub, viewed 18 March 2012, < http://www.sciencelearn.org.nz/Contexts/Uniquely-Me/Sci-Media/Images/Chromosomes-crossing-over>.  

Thursday, 29 March 2012

Gene Therapy for Cystic Fibrosis


Gene Therapy for Cystic Fibrosis


By Eleanor Sondergeld 42906401

Recently the ‘United Kingdom Cystic Fibrosis Gene Therapy Consortium’ has confirmed that in the coming months they will undertake the largest trial yet of a gene therapy treatment for Cystic Fibrosis (McKie 2012).

Cystic fibrosis (CF) is a heritable genetic disease, caused by a mutation in the gene which generates the protein; cystic fibrosis transmembrane conductance regulator (CFTR) (Yankaskas et.al 2004). This protein is involved in the transport of ions across epithelial cell membranes which line secretory cells. 

(United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012)

As the ions are not able to move freely in and out of these cells, blockage occurs and a thick salty mucus forms (National Heart Lung and Blood Institute 2011) (Yankaskas et.al 2004). 

(United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012

This cellular secretion commonly leads to severe inflammation and chronic infection in the respiratory, and gastrointestinal systems (United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012). As there is currently no cure for CF, on going treatment involves managing inflammation and infection through a combination of medication, physiotherapy and in many cases lung transplants (National Heart Lung and Blood Institute 2011).

This new treatment involves the delivery of DNA expressing a functioning CFTR gene, into cells within the respiratory tract, in the form of a nebulized aerosol (United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012). 

(BBC, 2012)


The DNA is taken up by the cell membranes and then transported to the cell’s nucleolus where it can express its copy of the CFTR gene(United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012). Through translation the CFTR gene from this DNA, the CFTR protein can be manufactured and regular lung function is returned (United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012) (McKie, 2012). This general principle of replacing non-functioning genetic material with functioning versions of that DNA is the basis of this research (Genetic Home Reference, 2012)(United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012).

The immune systems of CF patients are highly developed due to the constant infections that accompany the disease; thus introducing foreign bodies, particularly into the respiratory system is problematic (Hickman, 2012). Viral vectors that have been successfully developed as a carrier of DNA in other gene therapy treatments (Genetics Home reference, 2012) are targeted by the immune system and are therefore largely ineffective in delivering genetic material into the cells of CF patients (Hickman, 2012). For this reason, non-viral vehicles were developed; in this case liposomal transport has been shown in preliminary research to be the most effective vector for the CFTR gene (United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012).

The product used in this trial is GL67A/pGM169, a mixture of the cationic liposome GL67A and the plasmid DNA which expresses CFTR pGM169 (United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012). This is delivered into the lungs of patients when they inhale this product as an aerosol through a jet nebulizer(United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012).

The plasmid used is a single stranded “complimentey” DNA (cDNA) and is used because the entire CFTR gene contains DNA that is not essential to CFTR synthesis and can interrupt the protein coding sequence (Hickman, 2012)(United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012). It is then mixed with the compound hCEFI which has been shown to promote the longest period of CFTR expression in cells reached by the treatment (Hyde et.al 2008) as well as the liposomal GL67A vector (United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012).


A western blot to detect CFTR protein expression from human cell lines. pGM169 is in the two right hand lanes.

(United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012)


Liposomes comprise a synthetically manufactured fatty substance which is able to encapsulate aqueous solutions (the cDNA plasmid pGM169) (United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012), and which can be designed to include ligands on its surface (Mady, 2011). According to Prokop; the addition of specific ligands to these molecules allow for the more exact targeting of specific cell types (which for CF sufferers are epithelial cells) as well as a ‘stealth’ like property which prevents the immediate engulfment of the molecule by phagocytic cells (Prokop, 2012). Furthermore the liposomes are able to mix with the phospholipid cell membrane (Prokop, 2012) and efficiently deposit the genetic material into the cell, which can then be taken into the cell’s nucleus (Mady, 2011)(United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012).

When mixed, the positively charged fatty liposomes (GL67A) and negatively charged plasmid cDNA form small, strongly bound particles; stable enough to resist aerosolisation and pass through the mucus covered membrane of cells of the respiratory tract (United Kingdom Cystic Fibrosis Gene Therapy Consortium, 2012).

This study is based the culmination of findings from numerous preliminary studies using the most current techniques and products available. If successful it potentially may lead to the development of a treatment that can be made available to the thousands of CF sufferers globally.











 BBC, 2012, Cystic Fibrosis, Viewed 16 March 2012
 <http://www.bbc.co.uk/learningzone/clips/gene-therapy-and-cystic-fibrosis/6014.html>


Yankaskas, JR; Marshall, BC; Sufian, B; Simon, RH; Rodman, D 2004, ‘Cystic Fibrosis Adult Care Consensus Conference Report’, Chest, vol.125, no.1, viewed 16th March 2012,
<http://chestjournal.chestpubs.org/content/125/1_suppl/1S.long>

McKie, R 2012, Cystic fibrosis treatment saved by last-minute £4 bailout, The Guardian, viewed 18th March 2012,
<http://www.guardian.co.uk/science/2012/mar/18/cystic-fibrosis-research-saved>

Mady, MM 2011,’Cationic liposomes as gene delivery system’, African Journal of Pharmacy and Pharmacology, vol. 5, no.17, pp. 2008-2012

UK Cystic Fibrosis Gene Therapy Consortium, 2012, Multi-dose Clinical Trial, viewed 16 March 2012, <http://www.cfgenetherapy.org.uk/clinical/multidose.html>

Prokop, A 2011, Intracellular Delivery: Fundamentals and Application, Springer Publishing, New York.

Hyde, SC, Pringle, IA, Abdullah, S, Lawton, AE, Davies, LA, Varathalingam, A, Nunez-Alonso, G, Green, AM, Bazzani, RP, Sumner-Jones, SG, Chan, M, Li, H, Yew, NS, Cheng, SH, Boyd, AC, Davies, JC, Griesenbach, U, Porteous, DJ, Sheppard, DN, Munkonge, FM, Alton, EW & Gill, DR 2008, ‘CpG-free plasmids confer reduced inflammation and sustained pulmonary gene expression’, Nature Biotechnology, vol.26, pp. 549-551

National Heart Lung and Blood Institute 2011, What is Cystic Fibrosis?,  viewed 16 March 2012,
< http://www.nhlbi.nih.gov/health/health-topics/topics/cf/> 

Genetics Home Refference 2012, What is gene therapy?, viewed 16 March 2012
<http://ghr.nlm.nih.gov/handbook/therapy/genetherapy>

Hickman, M 2012, Cystic Fibrosis in Detail, Podcast, Changing Futures, viewed 16 March 2012,
<http://www.youtube.com/watch?v=z7tbEuYS1JY>

Human and dolphin genomes


By Charlotte Dudal - 42832845




Humans and dolphins, what do these two animals have in common? You might think that the only thing they could have in common is that they are both mammals. You’re right, but there is a much more interesting fact. Dolphin and human genomes are almost the same. Dr. David Busbee from the Texas A&M University has been involved in a project that studies the genome of dolphins (Kolber, 2010). His team did a number of experiments using hybrid chromosomes combining human and dolphin chromosomes to identify the homologous traits. The results showed that 36 blocks were matching on both species (Fig.1&2). The experiment consisted in “painting” the chromosomes with a fluorescent chemical that would show the homologous traits (Fig.3). Busbee said that he was very surprised when he got to see the results. Because dolphins seem so different animals compared to humans, they live in oceans, eat fish and their physiology is far from ours. However, scientists believe that at some point humans and dolphins came from the same branch of the evolutionary tree. This is shown by the fact that dolphins are mammals that breathe air just like us, so it is believed that initially they were living on land and moved back to the oceans at a later time.
Fig.1: Homologies between human and dolphin chromosomes detected by chromosome painting.
Fig.2: Matrix showing the distribution of conserved chromosome segments between dolphin (left) and human (top).
Fig.3: Painting of dolphin chromosomes with biotinylates human chromosome-specific paints. Yellow are matching traits.

But how is this discovery useful to science and to us? Evans (2010) discussed that because dolphins have such similarity, they are affected by the same toxins and diseases that affect us. For example, they are affected by red tide toxins, chemicals that are present in wastes which we dump in the sea and other toxins that are present in ocean life. Furthermore, not only have dolphins been affected by the same toxins but they also have learned how to fight or block the effects of these dangerous chemicals. So in other words, if we were able to find out how they are able to have immunization to what affects us, we could use this information to cure or fight the diseases that are caused in humans! For example, we could synthetize a vaccine for diseases. Another important fact is that dolphins can fight type 2 diabetes by simply “switching off” the gene that is affected by the illness and so block the effects of it (Gill, 2010). That would mean that we could cure thousands of people much faster. Another way in which this discovery could help science is that scientists have been studying the dolphin’s genome for years, but with little progress because of lack of resources. But with knowing that it is so similar to our genome it would speed up research by up to 20 years! That would save up a lot of time and money.

References:


Evans, M., 2010, Human genes are helping Texas A&M veterinarians unlock the genetic code of dolphins, viewed 18th March 2012, <http://www.oar.noaa.gov/spotlite/archive/spot_texas.html>
Gill, V., 2010, Dolphins have diabetes off switch, viewed 18th March 2012, < http://news.bbc.co.uk/2/hi/8523412.stm>
Kolber, J., 2010, Dolphin DNA very close to human, viewed 18th March 2012, < http://www.articlesafari.com/2010/10/dolphin-human-dna/>
Kumar, S., 2010, Human genes closer to dolphin’s than any land animal, Discovery Channel Online, viewed 18th March 2012, < http://dsc.discovery.com/>

Compulsive Behaviours in Dogs: Not as lolz as YouTube thinks.


This is Oliver.


He’s pretty cute, right? (Right.)

Unfortunately, Oliver spent the first few months of his life wandering the streets, going from shelter to shelter, and generally having a rough time. As a consequence of these highly stressful formative experiences, Oliver developed a compulsive disorder, which manifested as serious tail chasing. Like, seriously bad tail chasing. Poor guy would tear out the hair and chew on his tail until it was raw and bleeding. Not pleasant. What’s interesting, though, is that while lots of dogs have stressful early experiences, not all of them develop these compulsive behaviours.

Though the video is titled ‘funny dog chases tail’, this condition is actually the start of something pretty serious, behaviourally speaking.

Recent scientific advances have shown that there are certain genes that are far more common in dogs that develop Canine Compulsive Disorder (CCD) than those who do not, which indicates that some animals have a genetic predisposition to respond to anxiety, frustration or stress in this way. There are several recognised manifestations of CCD, including tail-chasing, pacing, and over-grooming. A specific kind of over grooming is called ‘flank-sucking’, and is particularly common among Doberman Pinschers. Flank-sucking is pretty much what it sounds like: the dog compulsively licks, bites and sucks on its hind quarters and back until the area becomes irritated, and in many cases develops dermatitis and infection. Another common affliction for Dobies is blanket-sucking, which can lead to ingestion of massive amounts of fabric,  causing choking and blocked digestive tracts.

You can see in this clip the fervour with which this little guy is grooming himself. This is not a response to an itch or bite, but a compulsive behaviour.

The research is a joint effort of Tufts University and the Broad Institute at MIT, and outlines lots of complicated things about how they identified this gene that looks to be responsible for CCD. Essentially, they mapped the genome of a bunch of Doberman Pinschers, both those affected by CCD and not, It pretty quickly became apparent that one gene, CDH2, was appearing commonly in dogs with CCD, and rarely in those without it. (About 60% of the time in those dogs with serious CCD, and only about 20% of the time in those without the disorder.)

This discovery has implications for medical as well as veterinary science. It is estimated that anywhere up to 8% of the human population suffers from Obsessive Compulsive Disorder (OCD). This disorder manifests in similar ways as CCD, including hair pulling and pacing, and also in activities such as excessive hand-washing or counting of objects.

Scientists who were not directly involved in the study are examining the CDH2 gene in humans, and investigating any links it might have with OCD. Further results of this type of research will hopefully lead to the development of drugs that can target this gene, and allow both animal and human sufferers of compulsive disorders to return to a normal life.

Student 42059549

Wednesday, 28 March 2012

Genetics in Neurological Medicine

Figure 1: Focal Point of  Upper Motor Neurons
Neurological disorders are those caused by abnormalities within the body’s nervous system. This includes the nerves and their components, the brain and the spinal cord. These disease’s can be caused by defective genes (as in muscular dystrophy), incorrect development or through injury among others. Another category of neurological disorders are the degenerative diseases. Degenerative diseases either cause damage or the loss of neurons. One such disorder is Amyotrophic Lateral Sclerosis (National Library of Medicine – National Institutes of Health, 2011).








Figure 2: Typical Mobility Problems due to ALS


Amyotrophic Lateral Sclerosis (ALS) affects approximately three people in a hundred thousand. It is a progressive neurological  disorder that attacks both upper and lower motor neurons. Upper motor neurons are those located within the brain and have no direct contact with muscle fibers whilst lower motor neurons attach directly to muscle fibers and act due to upper motor neuron impulses. ALS is characterised by a gradual decline in muscle strength with sufferers often experiencing respiratory, vocal and swallowing difficulting. Lower limb spactisity is also common. The health of those afflicated degenerates steadily with paralysis common in the later stages, before death, usually from respiratory failure(Armon C, 2011). ALS generally affects the middle-aged, with patients averaging from 40-70 years. Death normally occurs within five years of diagnosis.




Figure 3: Stephen Hawking
Amyotrophic Lateral Sclerosis is classified as juvenile when it affects subjects younger than 25. Juvenile ALS can be found in subjects as young as 2 years of age.  It is most famously seen in renowned physicist Steven Hawking (pictured left). A recent investigation into juvenile ALS has suggested that ALS is caused by a missense mutation of the Sigma1 receptor (Science Daily 2011) . A missense mutation is when a single nucleotide is substituted for another causing a different amino acid to be produced, and thus an altered protein. This protein can either be the same protein, but a different shape, which would affect its functionality or a different protein altogether. In this case the mutation appears to prevent the Sigma1 receptor from functioning. This is thought to cause an accumulation of miss folded proteins upon motor neurons, causing their degeneration.  This breakthrough was made possible by the use of homozygosity mapping and gene sequencing.
Figure 4: Missense Mutations
 
Figure 5: Sigma 1 Receptor
Homozygosity mapping is a computational genetic   technique used to identify and accurately detect homozygous genes. This would appear to be a severe limitation however researchers from Michigan and Germany have suggested that mutations that cause disease are homozygous in 93% of cases. In the case of the ALS study homozygosity mapping revealed a shared zone between those with ALS which was lacking in those without (Biotech About 2009). This zone contained nine genes, each of which was sequenced. The Sigma1 receptor showed the mutation which is believed to cause ALS.  This is just another case where a noteworthy discovery was made in another field thanks to a new application of genetic technology. In this case, the discovery of this mutation should allow an accurate and complete diagnosis, especially with the recent advances in the human genome project. It could also possibly lead to a cure, with the correction of this mutation.



By Roger Goodyear - 42884255   

References
·         National Library of Medicine – National Institutes of Health 2011, Neurologic Diseases, viewed 19th March 2012, <http://www.nlm.nih.gov/medlineplus/neurologicdiseases.html>
·         Armon C, 2011, Amyotrophic Lateral Sclerosis, MD, MSc, MHs, viewed 19th March 2012, <http://emedicine.medscape.com/article/1170097-overview>
·         Science Daily 2011, Mutation in SIGMAR1 Gene Linked to Juvenile Amyotrophic Lateral Sclerosis: Sigma-1 Receptor Offers Potential Therapeutic Target, viewed 16th March 2012, < http://www.sciencedaily.com/releases/2011/08/110812091545.htm>
·         Biotech About.com, 2009, Homozygosity Mapping for Outbred Individuals, viewed 18th March 2012, < http://biotech.about.com/b/2009/01/26/homozygosity-mapping-for-outbred-individuals.htm>

Images (in order of appearance)


Researchers discover hidden pieces to the MS puzzle


Could you imagine your own body’s defence system targeting the very thing it is designed to protect?


(Granovsky, D 2011)


Unfortunately this is the reality for many people diagnosed with the disease, Multiple Sclerosis (MS). Over 20,000 people in Australia and 2.5 million worldwide have MS (MS Research Australia 2012).  It’s an autoimmune disease, where the immune system attacks the central nervous system (CNS), causing inflammation and damage to the insulating tissue layer of nerve fibres called myelin. The myelin facilitates the communication between nerve cells. Once this layer is damaged a build up of plaque forms, impairing the signal along the nerve pathway to the brain. The health problems associated with MS are therefore dependant on the area and extent of damage to the CNS. Additionally, the effects of the disease can come and go sporadically making it difficult to manage and understand for both researchers and sufferers alike (Kalb 2011, pp. 7-9).




(MS Research Australia 2012)

                                                                           
A study undertaken by the International Multiple Sclerosis Genetics Consortium (IMSGC), has lead a collaboration of 250 scientists, from 15 countries, to the discovery of 57 genes which play a major role in MS. A trend seen throughout the study highlights the activity these genes have in the immune response (most importantly T cells) and that the reasons for getting the disease mainly results from inherited changes in the immune system (The University of Melbourne 2011).


T Cells are known as the directors of the immune system. They can function in two ways, one as killer cells by releasing toxic chemicals directly into invading cells, or two they can talk to other cells involved in the immune response, initiating the start and end of an attack on foreign cells. Although the destruction of normal cells by processes of the immune system is not fully understood (Iezzoni, LI 2010, p.44), the link from the consortiums research to specific genes in this stage offers a stepping stone to further studies in the future.

(Skutelnik, N 2012)

In previous studies carried out in Australia a correlation between low levels of Vitamin D and a high risk factor of MS has been found. The IMSGC discovered another vitamin D gene, further supporting the idea that MS is not only controlled by genetics but also the environment (The University of Melbourne 2011). Researchers have found the number of people affected by MS drops off, the closer to the equator they live, possibly due to more time spent in the sun and higher levels of ultra violet radiation. Given the body synthesises vitamin D when the skin comes into contact with the sun, this could therefore assist in the prevention of MS (Iezzoni, LI 2010, p.37).


There are still so many hidden reasons to the cause of MS and the role the recently discovered genes will play in the disease could take some time to reveal. This presents many opportunities for the future treatment of patients currently suffering from MS and generates a new focus for clinical trials. Hopefully the key to unlock the answers to MS is found within the genes in the not too distant future.

Reference List

Granovsky, D 2011, The Stem Cell Blog, viewed 18 March 2011, http://repairstemcell.wordpress.com/tag/ms/

Iezzoni, LI 2010, Multiple Sclerosis, Greenwood, California.

Kalb, R 2011, Multiple Sclerosis: The Questions You Have-The Answers You Need, 5th Edn, Demos Health, New York.

MS Research Australia 2012, Living with MS: Quick Facts about MS, viewed 18 March 2011, http://www.msra.org.au/living-ms

Skutelnik, N 2012, Suntan, Kidzworld, viewed 18 March 2011, http://www.kidzworld.com/article/4465-the-science-of-tanning

The University of Melbourne 2011, Breakthrough research holds clues about MS cause, Viewed 16 March 2011, http://newsroom.melbourne.edu/news/n-600

Genetic Engineering - Diabetes

Phoebe Rutter 42885551

Genetic Engineering – Finding a Cure for Type 1 Diabetes


Diabetes is a serious condition, whereby the beta cells in the pancreas fail to produce insulin, the hormone that is responsible in maintaining regular blood glucose levels in the body (National Health Cail Centre , 2012). The disease, if undetected or poorly managed can result in kidney failure, blindness, strokes, heart failure, lower limb amputation and impotence. It has been recently estimated that approximately one million Australians have been diagnosed with the disease (National Health Cail Centre , 2012).

It is recognised that underlying all presentations of diabetes, there is impaired insulin response, due to dysfunction or loss of the beta cells (Fu, et al., 2007). It is the regulation of insulin secretion (by the beta cells) that is vital for glucose homeostasis (Fu, et al., 2007).
Research into Type 1 Diabetes focuses on both cures and treatments. One area of “cure research” involves Beta Cell therapy. Beta cell therapy is directed at replacing or regenerating the insulin producing beta cells, thereby restoring the body's ability to produce insulin (Junior Diabetes Research Foundation, 2012).
Scientists have recently made significant advances in the search for a cure of Type 1 Diabetes, employing genetic engineering. Through the use of genetic engineering, scientists manipulate an organism’s genome and create a DNA sequence with the required genetic elements (Fu, et al., 2007). This is then introduced into the host organism either indirectly through a vector system or directly through injection techniques.
Another form of genetic engineering involves removing genetic material from the target organism, creating what is known as a ‘knockout’ organism (Children's Hospital Eastern Ontario Research Institute, 2009).


Recently investigations undertaken by a specialised team, lead by Dr. Robert Screaton at the Children’s Hospital of Eastern Ontario (CHEO) Research Institute, have identified a protein known as the Lbk1 gene, that restricts insulin production. By using sophisticated genetic engineering in laboratory mice, the scientists removed the Lkb1 gene. (Children's Hospital Eastern Ontario Research Institute, 2009). The procedure resulted in the beta cells in the ‘knock out’ organisms both increasing in size and proliferation, as well as the cells storing and releasing greater quantities of insulin; thus improving glucose tolerance and protection against diet-induced hypoglycaemia. Significantly, this enhancement in the function of the beta cells of the lab mice was maintained for five months minimally (Union of Concerned Scientists, 2012).

Genetic engineering represents an artificial manipulation of the genetic code and has met with criticism of scientists “playing God” (Union of Concerned Scientists, 2012). However, as modern scientific investigation has shown, genetic engineering has the potential to eradicate disease and save lives. As discussed in Science Daily, sophisticated genetic engineering has lead to improvement in insulin-producing beta cells in diabetes and new knowledge in the understanding of Type 1 diabetes potentially leading to a cure. 



Source List


Children's Hospital Eastern Ontario Research Institute 2009, Genetic Engineering Improves Insulin-producing Beta Cells, Science Daily, viewed 19 March 2012, http://www.sciencedaily.com­ /releases/2009/10/091007124727.htm.

Fu, A., Cheuk-Him Ng, A., Depatie, C., Wijesekara, N., He, Y., Wang, G., et al. 7 October 2007, 'Loss of Lkb1 in Adult β Cells Increases β Cell Mass and Enhances Glucose Tolerance in Mice', Cell Metabolism , pp. 269-308.

Junior Diabetes Research Foundation 2012, Research Pathways, viewed 20 March 2012, JDRF: http://www.jdrf.org.au/type-1-diabetes-research/research-pathways.

National Health Cail Centre, January 2012,  Diabetes, Health Insite, viewed  March 19, 2012,  http://www.healthinsite.gov.au/topics/Diabetes.

Union of Concerned Scientists. (2012). What Is Genetic Engineering?, Food and Agriculture viewed 20 March 2012, http://www.ucsusa.org/food_and_agriculture/science_and_impacts/science/what-is-genetic-engineering.html.










Changing the Gentic Code

Ebrahim Ghasemi, 42650227

All life possesses a genome and the nature of that life is determined by it's genome. The genome consists of DNA which is made up of four nucleotides (Adenine, Cytosine, Guanine, Thymine), a series of three of these nucleotides is called a codon (64 codons in total) with each of these codons corresponding to one of the 20 amino acids or one stop codons. These codons are then translated into their respective amino acids until a stop codon is reached. Now what would happen if an organism had a codon that it did not normally have?
E coli just chiling

In theory an organism with non-naturally occurring amino acids could be made immune to viruses at the very least. Viruses replicate basically by commandeering a cell's ribosome and the other components used for replication.“Viruses depend on the fact that their proteins are encoded by the same codons as those of their hosts”(Young, Discover magazine 2011) If the organism has unnatural codons the viruses are almost certainly not going to have those codons and as such be unable to take over.

A team led by Farren Issacs at Yale University is attempting to answer that question. To do this they have edited the genome of Escherichia coli replacing the E coli's TAG stop codon with TAA another stop codon. First the team identified all 314 TAG codons in E coli, they then created small segments of DNA that had TAA instead of TAG which they mixed into a nutrient rich solution that was swimming with viral enzymes then submerged around a billion E coli in this solution.

The first of two processes MAGE was then used. MAGE or multiplex automated genome engineering, was first used a few years ago and allows bioengineers to do in days what would have previously taken them years. Essentially a specially prepared segment of DNA is placed in a solution with the cell and then electricity is run through the solution. This causes the cell to open pores in it's membrane allowing the DNA inside. Then when the cell next undergoes mitosis it will use this new DNA in the process. The DNA can then be found in the genome of the daughter cells.

MAGE gave the researchers E coli that had some TAA codons, however to create E coli that only had TAA they would have to use another process call CAGE. CAGE or conjugative assembly genome engineering relies on the bacterial form of sex, Bacterial conjugation, where one bacteria transfers genetic material (in this case the TAA codons) to another. The researches separated the E coli into 32 groups then used CAGE until they had a strain with almost entirely TAA codons.

Once the process is complete, the researchers could assign the now unnecessary TAG codon to an amino acid (natural or otherwise) instead of a stop codon. As mentioned before this could make bacteria immune to viruses, (a great thing if that bacteria is used in the production of medicine), what else this could potentially do we can at the moment only speculate. . It should be noted that the E coli seem to suffer no effects from their lack of TAG codons, raising the question what effects the stop different codons have.



References

E.coli's genetic code has been rewritten, 2011, viewed 19th March 2012, http://www.newscientist.com/article/dn20698-e-colis-genetic-code-has-been-rewritten.html

Hacking the genome with MAGE and CAGE, 2011, viewed 19th March 2012,
http://blogs.discovermagazine.com/notrocketscience/2011/07/14/hacking-the-genome-with-a-mage-and-a-cage/

Genoms edited to free up codons, 2011, viewed 19th March 2012,
http://www.nature.com/news/2011/110714/full/news.2011.419.html

Genome engineering goes high speed, 2009, viewed 19th March 2012
http://www.wired.com/wiredscience/2009/07/cellfactories/

Advances in genetic sequencing


Advances in genetic sequencing

The article “Exome sequencing identifies the cause of a mendelian disorder” published in January of 2010 has identified new ways of researching genetics especially those of rare diseases. This is exactly what a mendelian disorder is, an abnormality or mutation of the human genome (Reece J.B, p313-315). The aims and concepts discussed were the discovery of being able to distinguish these genes using the exome. As stated in the article “the exome sequencing of a small number of affected family members or affected unrelated individuals is a powerful, efficient and cost-efficient strategy.”


The research was to reveal which gene was causing Miller syndrome. This being a very rare disease, the number of subjects is limited the study only containing five, two sibling kindred’s and three other unrelated cases. Due to the large amount of information in genetics it was focused on the nonsynonymous variants, splice and donor site mutations and short coding insertions. It focused on these because they are notorious for creating issues like mutations and disease.

Findings:
What was found was that the two sibling kindreds had several variants associated with the disorder; these were then compared to the other unrelated cases in which the gene DHODH was highlighted. Due the small amount of subjects it was needed to prove this finding, the null hypothesis was used to create a comparison. The null hypothesis would state that this specific gene was highlighted only by chance or coincidence. The p-value found was 0.000015 which makes it highly unlikely this would happen by chance in fact a 0.0015% chance of occurrence.


 What does this mean?

The gene DHODH encodes the enzyme dihydroorotate dehydrogenase. This enzyme is used to oxidize dihydroorotate to orotate. This is linked to the short-term energy supply and interrupts the normal growth of a fetus. It is not known how or why the mutation of this gene causes these specific abnormalities but with this knowledge, science is a step closer to clarifying this picture. It is believed that even if only one genome is mutated it results in the change of the entire genetic makeup (Chen J, M). Yet again another mystery about genetics.


Why is this important?

The discovery in using this method aids the research into rare diseases and makes it more cost efficient. Genomes hold so much information the easier it is for us to extract the more knowledge we can gain and improve our way of life.  Although there is still a lot we don’t know, each small discovery brings science one steps closer to an answer or another discovery in which will arise more and new questions.

References

Chen J, M. Frec C  et al. 2010 ‘Revealing the human mutome’ Clinical Genetics, vol. 78, p310-320

Ng S, B, Buckingham K, J. et al. 2010 ‘Exome sequencing identifies the cause of a mendelian disorder’, Nature Genetics vol. 42, no. 1, p30-36

Reece, Jane B; Meyers, Noel; Urry, Lisa A; Cain, Michael L; Wasserman, Steven A; Minorsky, Peter V; Jackson, Robert B; Cooke, Bernard N, 2012; Campbell Biology, Australian 9th Edition, Pearson, Australia p309-340


 By M. Yelorm

The Ebola Virus and Niemann-Pick C1: Towards the Synthesis of a Cure?


By Kim Hanna (41387432)

An electron-microscope image of Ebola-Zaire
(Centers for Disease Control and Prevention 2009)
Ebola is the generic title given to very five similar subtypes of virus, the first of which was discovered during an outbreak in the mid '70s throughout continental Africa. Though the microbiology of Ebola is really quite simple - the virus' genome consists only of a single strand of ribonucleic acid - it has still managed to generate a significant amount of notoriety within the medical and virological worlds as one of the most virulent of diseased that has ever been recorded (Reece et al. 2012).

Three of the five subtypes of Ebola have lead to cases of human death, with these subtypes having a mortality rate of up to ninety percent per individual outbreak, due to the incredibly deleterious effects of viral hemorrhagic fever (Google at your own risk!) The symptoms of an infection are quite varied, but may include both internal and external bleeding, nausea, and muscular pain.   

Perhaps the hardest pill to swallow about Ebola is that there actually is no pill to swallow; there is currently no anti-viral treatment available to combat an infection. However, while a huge amount remains unknown about the ways in which the virus infects host cells, a number of very promising breakthroughs in virological research could potentially lead us towards the synthesis of a future vaccine or cure. 

In early January of this year, medical columnist for The New York Times, Amanda Schaffer, summarised a paper that appeared in Nature, titled "Ebola virus requires the cholesterol transporter Niemann-Pick C1" (Carette et al. 2011). Schaffer's article, "Key protein may give Ebola virus its opening," provides a basic description of the paper's findings, which suggest that the infection mechanism of the Ebola virus has intrinsic links to the cellular presence of a rather unremarkable protein. 

According to Schaffer, researchers working upon a biologically altered, non-lethal form of Ebola have discovered that mice lacking a particular protein known as Niemann-Pick C1 (NPC1) appear entirely immune to the lethal effects of the virus, even after direct exposure. Furthermore, mice that have been genetically engineered to be partially deficient in NPC1 appear far more likely to survive a bout of Ebola infection.

So, what does this all mean?

The Precession of the Trojan Horse in Troy,
Domenico Tiepolo, 1773.
Though the exact molecular interaction between NPC1 and Ebola has not been established, it has been suggested by Dr Karthik Chandran that the protein is required to shuttle the virus from the lysomal membrane into the cytoplasm of the cell, where it can begin replication (Albert College of Medicine 2011). Those that are familiar with the epic poems of Ancient Greece may think of NPC1 as the Trojan horse that appears to bear gifts, but actually harbours great malevolence.

The findings are quite exciting! They provide us with a much clearer image of the ways in which Ebola penetrates into and eventually decimates host cells. Armed with this knowledge, scientists can now target an exact molecule that seems to be key to Ebola infection, and begin some novel research.

For instance, I have since discovered a very recent paper that further proves the link between Ebola and NPC1. Here, the authors propose that a compound which modifies NPC1 within human cells could potentially thwart an otherwise inevitable infection of the virus (Hunt, Lenneman & Maury 2012). This is, of course, much easier said than done, but I find it fascinating to think that changing the transcription, availability or even expression of NPC1 could eventually save countless lives.

Ultimately, while it will be quite some time before we have an effective method to treat Ebola infection, it's reassuring that there have been such critical breakthroughs in the research. Furthermore, for those of us enrolled in BIOL1030, it's great to see that these breakthroughs are being properly communicated to the wider, non-scientific communities through the various forms of mass media.

References

Albert Einstein College of Medicine 2011, Researchers find ‘key’ used by Ebola virus to unlock cells and spread deadly infection, viewed 18 March 2012, http://www.einstein.yu.edu/home/news.asp?id=695.

Carrette, JE, Raaben, M, Wong, AC, Herbert, AS, Obernosterer, G, Mulherkar, N, Kuehne, AI, Kranzusch, PJ, Griffin, AM, Ruthel, G, Dal Cin, P, Dye, JM, Whelan, SP,

Chandran, K & Brummelkamp TR  2012, “Ebola virus entry requires the cholesterol transporter Niemann-Pick C1,” Nature, vol. 477, no. 7364, pp. 340-343.

Hunt, CL, Lennemann, NJ, & Maury, W 2012, “Filovirus entry: a novelty in the viral fusion world,” Viruses, vol. 4, no. 2, pp. 258-275. 

Reece, JB, Meyers, N, Urry LA, Cain, ML, Wasserman, SA, Minorsky, PV, Jackson, RB, & Cooke BN 2012, Campbell Biology, 9th edn, Pearson Australia Group, 

Schaffer, A 2012, Key protein may give Ebola virus its opening, The New York Times, 16 January, viewed 17 March 2012, http://www.nytimes.com/2012/01/17/health/npc1-protein-may-give-ebola-its-opening.htm


World Health Organisation 2012, Ebola haemorrhagic fever, viewed 18 March 2012, http://www.who.int/csr/disease/ebola/en/



SEX DEPRIVED FRUIT FLIES & ALCOHOL

By Robin-Lee Troskie

It would be extremely naive and ignorant to regard Homo sapiens as a ‘higher species’ especially when our often troubled and senseless behaviour says otherwise. Our over zealousness can be demonstrated by modelling one of societies greatest and most complex crisis’s – drug abuse – and testing it in an experiment using
Fruit flies (Miller 2003).


The experiment, undergone by neurologist Ulrike Heberlein at the University of California, and researchers from Howard Hughes Medical Institute Research Centre showed the similarities of alcoholism between humans and fruit flies (Drosophila melanogaster) (Ledford 2012) with regard to sexual rejection and the over sexed nature brought about when an excess of alcohol was consumed.
It should be noted that two thirds of fruit fly genes are identical to that of humans and are the basis of many experiments because they are “cheap, prolific, simple to breed, and perhaps most significant, their genes are easy to examine and manipulate” (Miller 2003). This ease of manipulation made them the perfect experimental organism for Heberlein’s research.
Neurologist Galit Shohat-Ophir from Howard Hughes Medical Institute Research Centre carried out an experiment which “subjected male flies to four days of repeated rejection by pairing them with females who had already mated” (Yong 2012). She discovered that male fruit flies were more likely to consume food injected with alcohol when sexually rejected by females.

They revealed a neurotransmitter called neuropeptide F, or NPF, which is responsible for this behaviour in the flies. Males exhibited low levels of neuropeptide F when refused sex by females, ultimately “driving them to seek rewards in alcohol” (Yong 2012).  It was also observed that when flies were artificially given neuropeptide F, boosting their levels, no interest in alcohol was showed even if the fly was denied sex.  Also flies that were rejected but then shortly allowed to mate afterwards showed no appeal in the alcohol infused food (Yong 2012).

In the experiment, the higher exposure to ethanol the more similarities flies demonstrated to humans. “
As the concentration of ethanol in the body rises, flies begin to become uncoordinated and oblivious to their surroundings: they get tipsy. “They bump into each other. They bump into the walls,” says Heberlein” (Ledford 2012). Amazingly, the alcohol concentration in flies that induced these drunken actions was almost identical to the amount seen in humans. Shohat-Ophir noted that the more alcohol the male flies were exposed to the less discriminating they became of their mates gender. Soon male flies were chasing other male flies while serenading each other “with a traditional fruitfly courtship song played on vibrating wings” (Lee, Kim, Dunning, Han 2008).
The experiment showed that neuropeptide F is directly linked with the brains neural pathways of the reward system, which brings pleasure from consuming food and having sex. These pathways however, when subject to a negative experience like sexual rejection, can be taken over by alcohol, biasing them towards the addictive substance and causing “an outcome that may lead to alcohol dependence” (Thiele, Marsh, Ste Marie, Bernstein, Palmiter 1998).   
This ‘cycle of alcoholism’ in flies can also be seen in humans; however, the neurotransmitter responsible for the rewards system in animals is called neuropeptide Y or NPY. “NPY could be the connection between negative experiences
and humans seeking rewards in drug dependence. If so, Heberlein says, it might be possible to break this link by boosting levels of the neurotransmitter — like feeding NPF to flies to stop them turning to alcohol” (Yong 2012). Heberlein also describes that low levels of neuropeptide Y are strongly related with not only excessive alcohol consumption but also with suicides, post-traumatic stress disorders, anxiety and obesity (Rasmusson 2000).
These experiments are still continuing as scientists search for a definite link between alcoholism and negative experiences in the rewards system. With the combination of modern technology and advances in genetics, scientists can continue to experiment on flies to understand the genetic makeup of humans that causes drug addictions and discover ways to prevent it. Genetics opens up a whole new world of discoveries and each time brings us one step closer to understanding the mysteries of evolution and the way the world and everything on it functions in complete equilibrium.
References
1. Miller, J., 2003, Ulrike Heberlein: High Flies Have Heberlein Hopeful, viewed 17 March 2012 < http://pub.ucsf.edu/magazine/200305/heberlein.html >
2. Yong, E., Nature Publishing Group, 2012, Rejected flies turn to booze, viewed 17 March 2012, < http://www.nature.com/news/rejected-flies-turn-to-booze-1.10227 >
3. Ledford, H., Nature Publishing Group, 2012, Drunken flies get hypersexual, viewed 16 March 2012, < http://www.nature.com/news/2008/080103/full/news.2007.402.html >
4. Lee, H. G., Kim, Y. C., Dunning, J. S. & Han, K. A. PLoS ONE 3, e1391 (2008)
5.  Thiele, T. E., Marsh, D. J., Ste Marie, L., Bernstein, I. L. & Palmiter, R. D. Nature 396, 366369 (1998)
6. Rasmusson, A. M., et al. Biol. Psychiatry 47, 526539 (2000)