Last week at the Garvan we had the privilege to attend a seminar presented by professor Michael Snyder.  His work pioneers what will hopefully soon be the future of Medicine- Personalised Medicine.  Personalised medicine means that doctors will be able to select the right treatment for your precise needs, based on information captured from your unique individual genetic make-up.

   Advances in technology such as genome sequencing have enabled the use of personalised medicine. Now we can sequence the genome faster than ever and most importantly, it is becoming affordable not only to research groups but also to individuals. The advancements in science technology have not only allowed us to gain unprecedented insight in our genome but have also have revolutionized our understanding of the cellular protein networks, metabolites and other.

   My group is making use of the new advances. We are utilising the power of a technique called Mass Spectrometry. Mass Spectrometry is one of the most powerful tools and has many applications but we will use it to enable us to look at a whole spectrum of protein interactions and modifications. In other words, within only a couple of weeks we will be able to fully reconstruct a network of proteins that are key participants in a pathway that is crucial to the survival of colon cancer cells. We hope to find those protein players, essential for colon cancer cell survival, that we can effectively ‘annihilate’ using pharmacological drugs.

   We are also making use of the new advances in technology to discover new genes responsible for chronic colon inflammatory conditions in mice (also relevant to humans). We will use fine genetic tools to pinpoint tiny genetic differences between individual mice.  These genetic differences may be responsible for some mice being more susceptible to colon inflammation than other mice.

   The discovery that DNA contains the blueprint for the making of all cellular components and for the making of a human from a single cell is absolutely extraordinary. It has also been cleverly utilised by researchers to tease out answers to their scientific quests. By introducing small pieces of DNA containing the blueprint for foreign proteins in mammalian cells, scientists can engineer cells to express proteins, which naturally do not occur in them. I use this tool in my experiments.

   I am interested to understand if an anti-cancer drug I am studying activates a certain gene in cancer cells. In order to find the answer I am using a clever method. I insert a small DNA string that contains an “activator region” for my gene of interest into some of my cancer cells. This “activator region” serves as a “green light- go ahead” to signal the cell to make a protein, attached to the “activator region”. However, in my experiments, attached to the gene “activator region” is the genetic code for a protein that does not belong to the mammalian cell- the firefly luciferase protein. It normally occurs in special abdominal cells in the firely and the insects use it in a reaction called bioluminescence in order to literally make light and attract mates. However, I will use it for a different purpose.

   If my drug activates the “activator region” in the cancer cells, then the blueprint will be read and luciferase will be synthesized in the cell. Presence of luciferase shows that my drug does activate the gene… But… How will I know luciferase is present in the cells? I will use a reaction to make bioluminescent light exactly like the firefly! Luciferase reacts with a chemical called luciferin and molecular oxygen to emit light that is pale yellow to reddish green in colour. I use a sensitive detector to detect the “brightness” of the emitted light. The brighter the light, the more luciferase is present in my engineered cells, the more the drug activates the gene.

    If the drug activates the gene I study, I will gain valuable insights about the molecular mechanism of action of the drug and the cellular pathways that it effects. Understanding the mechanism of action of a drug in detail is important in order to use the drug to its full potential to fight cancer.

2012 kicks off with new ideas, new fantastic research projects in my group and a new director for the Garvan Institute - the very inspiring and iconic Australian scientist John Mattick. 

 As a gut scientist, I would like to share with you that gut research made some of the top headlines amongst scientific breakthroughs in 2011 and these will shape the research focus in 2012.

 The human gut bacterial community was in the spotlight in 2011

   We all know that healthy bacteria in the gut aid digestion but 2011 brought new insights about the role of intestinal microbes in influencing pathological conditions such as inflammatory bowel disease, obesity, heart disease, cancer and others. It turns out that our bodies are teeming with a lot more bacteria than previously thought, the bacteria outnumbering the cells of our own body by 10 fold!

 Our diet shapes our gut microbial communities

   Remarkably in the gut, the myriad bacterial species can be clustered into just 3 types, called enterotypes. 

Each enterotype is characterised by their enrichment in either genera Bacterioides (enterotype 1), Prevotella (enterotype 2) or Ruminococcus (entero­type 3). Whether you have predominantly enterotype 1, 2 or 3 is unrelated to age, gender, nationality or body mass index. Even more interestingly, researchers have found that our long-term diet shapes the predominant enterotype in our gut, for example, a protein and animal fat diet favours a community predominantly composed of Bacteroides, while carbohydrates favours Prevotella.

   Gut immune cells can shape the composition of bacterial communities

   A deficiency in a particular receptor (TLR5) in immune system cells can cause colon inflammation, obesity and metabolic disease.

Surprisingly, these pathogenic conditions were triggered by a change in the composition of the microbial intestinal communities caused by the inability of the TLR5 deficient immune system to control the type of bacteria in intestinal microbial populations. This is one of the first pieces of experimental evidence suggesting that the cells in our body can modulate what types of microbes inhabit our intestines- healthy or pathogenic.

 Research in our group in 2012

   While we are not focusing on the bacteria within the gut (microbiome), certainly we will be leading the way in colon cancer by studying the functional role of a novel gene, which our group has found to be disrupted in more than 50% of colon cancers.

 We have designed experiments to prove that the healthy function of this gene is important to prevent early carcinogenic events in colon cells and protects the cells from switching to malignant uncontrolled growth. We will use genetic animals models and tissue culture to unravel the details of its molecular mechanism of action, an important step towards designing therapeutic approaches to help people who have a genetic disruption in this gene.

One of the hallmarks of cancer cells compared to normal cells is that malignant (cancer) cells are, at large, immortal.

Killing cancer cells through drugs, genetic manipulations or other strategies is one of the main goals in our research. When cancer cells that I grow in a petri dish are killed by the drug I study, we are all excited. But also remember that cancer cells are notoriously difficult to kill. I need to show by a scientific method that the cell is actually dead, which poses a problem; it's not easy to take the pulse of a cell.

What I do instead is to look at specific molecules that serve as biomarkers of cell death. Through years of research, scientists have found that some molecules (biomarkers) are altered when a cell dies. One of the most accurate biomarkers of cell death is the flipping of a molecule called phosphatidylserine from the inner cellular membrane to the outer part of the cell, which is exposed to the environment. We can detect this “flipping” by attaching a fluorescent dye, which affects only the flipped molecule, and thus detect the dead cells.

-  But that poses another problem...How do I count how many cells are actually dead?

I could count the cells that are marked by the fluorescent dye under the microscope but that would take really long time. Fortunately, I am really lucky because of the existence of flow cytometry (initially known as pulse cytophotometry). This spaceship control-room looking machine allows me to accurately count the number of dead cells in seconds.  Cells are carried by a stream of liquid and as they pass by, laser light is directed onto the cells. The light is scattered by the cell and the scattered and fluorescent light is picked up by detectors. Thus we can measure the size and granularity of the cell, and also the “brightness” of the fluorescent dye attached to it. In my experiment, a bright cell means a dead cell and the machine gives me the exact number of bright (dead) cells in a population of 10, 000 cells... within seconds… imagine if I was counting them manually!

 After visiting the Floriade in Canberra, I cannot stop thinking about tulips. But not because I was spellbound by their undisputable beauty. Rather, I was struck by the impressive variety of tulip colours and shapes. As a biologist, I know that these beautiful varieties are caused by mutations in the genes of a common tulip-ancestor.

 For example the variegated tulips, despite being so cherished, are a product of a genetic mutation. The Parrot tulip, so highly valued for its ruffled petals is also a product of a mutation - so forgive me for not being able to truly appreciate the beauty of these tulip varieties and simply perceiving them as mutants.

Why is this important for scientific experimentation? And what does it teach me?

 Mutations occur naturally in any population. In my in-vitro (in test tube - from Latin: “within glass”) experiments, I work with well-established cancer cell lines that grow in a Petri dish. All cells from the same cell line should be genetically identical and therefore behave in exactly the same manner. They are simply a clonal expansion of a single or a few tumorigenic (cancerous) cells.

 When I give the cells an anti-cancer drug, they respond in a certain way. For example, in my experiments, they start producing large amounts of inflammatory molecules. I quantify the amount of inflammatory molecules produced by performing Polymerase Chain Reaction on specialised equipment, which “counts” the relative number of inflammatory molecules in my samples.

However, I find when I repeat the experiment, the amount of inflammatory molecules produced is different - even though I keep all parameters exactly the same and observe a similar overall trend.

 This is very frustrating because I am desperately trying to minimise any experimental variation by keeping all conditions of the experiment constant. Despite my frustration however, it also demonstrates a very interesting and important fact: cells accumulate spontaneous mutations. Not all cells in a population behave in the same manner. And although it is frustrating for me, these mutations drive evolution: the striking tulip varieties and… unfortunately cancerous changes.

 The older my cells grow and the longer they propagate, the more spontaneous mutations they accumulate and the more differently they behave. After a certain period of time using a particular set of cells I go back to my original frozen stock of cells to try to minimise variation.

 By repeating the experiment many times I get a mean (average) value for the number of inflammatory molecules produced. This average of all responses I have observed gives me a more accurate insight into the general response to the drug. Some cells will respond stronger, some weaker. The really difficult part is to obtain a result that is statistically significant when the variations I observe in my experiments are very large.

Well, a long day again ahead of me…repeating, repeating.

In my previous blog I discussed the use of a technique called immunohistochemistry  (IHC), which will enable us to identify the precise location of our gene of interest.

This technique is simple to explain. Genes code for (or provide the blue prints for) proteins. Proteins are the building blocks of our cells. However, when we introduce small parts of a protein from one species to another, the recipient species reacts by mounting an immune response and generating antibodies. We use this fact to our advantage.

The antibodies generated against a specific protein can be collected and labelled in such a way that they can be visualized later. Labelling the antibody is like painting a whole bunch of hats yellow - then they attach themselves to certain people in a crowd (the proteins) and allow us to see where those people are. When we expose tissue to the labelled antibody, the antibody binds to the protein of interest and then we detect the antibody label, thus visualising where the protein of interest is located.

Look at the example below:

Image A shows a schematic of human lungs and a photomicrograph showing the microstructure of mouse lungs stained with tissue dyes. Each blue dot represents a cell nucleus. The big oval shapes are the bronchi and the small ones are the alveoli. Image B shows mouse lungs stained with antibody recognising a protein called Ki67. You can see that the labelled antibody bound to Ki67 appears brown (arrows) while the rest of the tissue which does not contain Ki67 is blue.

Thus we can determine in which lung cells Ki67 is present.

We used the same technique for our protein of interest but as this material is not published yet, I will not be able to show an image.

We are studying a gene that is often not functional in colon cancer patients. Our aim is to identify whether mutations in the gene drive the onset of colorectal cancer. In order for us to understand the importance of the gene in colon cancer, we must first understand its physiological function - which process in our bodies is regulated by this gene.

We have found that this gene is highly expressed (abundant) in the lung and in the colon. Cells from different tissues sometimes share common functions. For example, specialised cells in the lungs and in the colon produce mucous to lubricate the organ.

Although the research we perform is geared towards understanding colon cancer, by studying the function of this gene in the lung tissue we can gain valuable insights about its physiological role - what is it important for? We have no idea what this gene does and we are interested in any and all clues we can get.

Understanding the miraculous lungs

The first step is to determine in which specific cells of the lung tissue our gene of interest is most abundant. For this purpose we must get familiar with the microscopic structure of the lungs.

The most prominent structure within the lungs are the alveoli - the air sacks, which take up oxygen - and the airways (bronchi) which are the branched tree structures that deliver the air we breathe to the alveoli. The alveoli are one of the most important physiological adaptations for life on Earth, a product of millions of years of evolution. Three hundred million alveoli (300,000,000) in the lung are covered with a special substance (a surfactant), allowing the lungs to open easily when we breathe in and not collapse during exhalation. Next week I will perform a technique called immunohistochemistry (IHC) in order to detect the precise location of the expression of our gene in the lungs and in the colon.

I have studied chronic inflammatory conditions in mice for over 4 years and this week in the lab I was required to assess whether a mouse had developed chronic gut inflammation. In people, chronic intestinal inflammation is not only a cancer risk factor but also has a negative impact on daily activities, mood and energy levels.

So how did I assess gut inflammation in the lab?

Inflammation on cellular level

I looked for signs of inflammation in mouse colon biopsies under a microscope. Infiltration of immune system cells in the gut lining and wall indicated there might be an inflammatory process present. I could also distinguish between different types of immune cells present. A large number of macrophages (cells that engulf other cells and pathogen particles), for example, indicate that there is chronic inflammation present.

Some breast cancer patients become resistant to treatment

Dr Andrew Stone’s research tackles an important question that doesn’t have an easy answer. For more than 30 years, women suffering from breast cancer have benefited from the drug tamoxifen. Tamoxifen, an anti-hormone treatment, is remarkably effective in treating patients with a subtype of breast cancer, known as Estrogen Receptor positive cancer (ER-positive).

While women with ER-positive tumours benefit enormously from the therapy, 40% of women that suffer from this type of breast cancer either do not initially respond, or become resistant to this form of treatment during the five years it is prescribed. Currently, anti-hormone resistant breast cancer has yet to effectively challenged in the clinic, thus tumours inevitably progress, often metastasising to other sites around the body and invariably claiming the lives of the patient. The mechanisms that underlie intrinsic and acquired resistance to tamoxifen are therefore being researched intensively.

Just like millions of women around the world, Andrew’s mother was diagnosed with ER-positive breast cancer ten years ago. This inspired him to find out more about the disease and the treatments available and eventually led him to pursue career in cancer research. Andrew’s mother was successfully treated with tamoxifen, and his research is now focused on determining what molecular factors contribute to tamoxifen resistance.

It’s not all in the genes

Andrew thinks that the answer lies in epigenetics. Epigenetics is the study that extends beyond our genome or simply said beyond our DNA sequence. It researches the “chemical coating” of our genes, which, unlike the genetic code is not inherited but can be modified by certain factors such as environmental changes and can cause altered gene behaviour.

In order to decipher the epigenome of cancers resistant to tamoxifen, Andrew will apply cutting edge techniques that will map the epigenetic changes that take place in breast cancer cells following the acquisition of tamoxifen resistance. This technique will generate a huge amount of data which will help further the understanding of anti-hormone resistance and could potentially lead to new therapeutic opportunities.

The lengthy process requires multiple steps. In order to study the epigenetic changes of DNA, the first step is to extract DNA from cell lines. A human cell’s DNA when stretched out will be at least a meter long. In order to get shorter fragments of DNA, Andrew will shear it to pieces through sonication (applying ultrasound).

From old South Wales to New South Wales

Much of the developmental work that saw tamoxifen become the gold-standard therapy for ER-positive breast cancer was carried out in the Tenovus laboratories at Cardiff University. This was achieved with the aid of many collaborators including Professor Robert Sutherland, who is now head of the Garvan’s Cancer program. Both institutions have since contributed enormously to the understanding of anti-hormone resistant breast cancer. Andrew completed his doctorate in 2009 at Cardiff University, and is now lucky enough to join the Garvan Institute, to continue the collaborative work on tamoxifen and its role in the clinic.

Our life without oxygen is unthinkable. But you may be surprised that a lot of cells in our bodies survive in hypoxic (low oxygen) conditions. This is possible because cells in our body have mechanisms to adapt to life in environments with very little oxygen.

In normal conditions, cells produce energy for their every-day needs with the help of oxygen. However, the oxygen we breathe in does not reach every cell of the body equally. Sometimes conditions such as chronic inflammation can dramatically reduce tissue oxygen concentration at the site of the disease. Luckily, cells have an alternative mechanism of producing energy independent of oxygen. This ancient mechanism, conserved in our evolution is, however, very inefficient - it uses a lot of food to produce very little energy. The positive side though is that it produces energy much quicker than the oxygen dependent mechanism.

The low oxygen levels, combined with the switching on of the oxygen -independent energy producing mechanism hold a hidden danger for our cells. Cells start producing molecules to help them survive in the very harsh body microenvironment. However, these molecules can easily become out of control and influence healthy cells to turn into cancer cells.  Cancer cells thrive in an oxygen-starved environment, they exploit the fact that they can produce energy quickly and use it for uncontrolled growth.

I study hypoxia in the mouse colon in order to find out if hypoxia contributes to cancer promotion in the colon. The first step though is to find a technique that can detect hypoxia in the colon. Luckily, researchers have made a chemical, which can be injected in the body and can be delivered to every organ and cell through the bloodstream. When it reaches a site with low oxygen, the chemical changes its structure. We have techniques which detect this changed structure and that help us recognise tissues with low oxygen.

I have spent a long time optimizing it but now that it works I will start getting some results.

Cellular master genes

During embryological development, our cells are very young and some of them do not have an assigned function yet - they are neither skin, nor eye or any other tissue. These cells are waiting for their fate to be decided.

There are extremely powerful genes in our cells that coordinate the activity of thousands of other genes. These master genes can help young embryonic cells mature and find their purpose in the body - skin, eye or any other organ.

The master genes do this by providing cells with essential “instructions” for their function from the genome - the DNA code library that we all carry in each single cell. So these master genes are extremely efficient “librarians”, who have memorized where all different “books” with instructions are kept. They organize and compartmentalize all the genome information.  Sometimes they have to archive some “books” deep in the archival library because accessing these sets of instructions becomes dangerous in certain stages of our life.

Master genes and cancer

Some master genes can become dysfunctional themselves and this is a major danger. If an event like this happens, we are at risk of developing cancer.

In a highly publicized study, it has been shown that a particular master gene is over-active in breast cancer and is linked to a decrease in patient survival.

What is true for one cancer type though is not true for all cancer types. A brilliant research fellow in our group, Dr. Tina Selinger, has recently demonstrated that the same master gene is under-active in lung tumours and its inactivity is associated with poorer patient survival.

Why is there difference between the two types of cancer, why is a functional master gene needed in the lung but not the breast?  It is probably because breast and lung are tissues with very different functions so they need access to different “libraries” with instructions for their function. The master gene may organize the library archive in a different way in the breast versus in the lung tissue - and the master gene function is needed in one but not the other.

From bone to lung cancer

Dr. Selinger’s interest in this particular gene started while she was doing her doctorate on bone research. She noticed that this master gene is very important for bone cell maturation. She also noticed that the gene controls the activity of myriad of genes, implicated in cancer. Dr. Selinger is particularly motivated to research lung cancer, because lung cancer kills more people each year than any other type of cancer but our knowledge about the molecular mechanisms of the disease are still limited. Dr. Selinger is currently finalizing a scientific paper and will submit a publication.

Dr. Sam Al-Sohaily will try to find out whether the same master gene plays a role in colorectal cancer.

To smoke or not to smoke

Although not all lung cancer cases can be attributed to smoking, the overwhelming majority of lung tumours are related to smoking. Dr. Selinger believes that the best cure is prevention and it’s never to late to quit smoking.

The real cost of research

This week in the lab we had a lab meeting in order to summarize all recent research progress and plan for the future direction. When we plan future experiments, one of the most discussed issues is the cost of equipment and chemicals.

Such discussions make me realize the crucial role of donations and government funding for our research.

When I was calculating my budget, I quickly realized that science is a lot more expensive than other “industries”. You, as past, present or future donors may be wondering where does money in science go and why do we need so much money in research?

Return on investment

To start with, our daily lab activities require substantial funding. For example, the plastic flasks, in which we grow human cancer cells in special liquid, look like simple Tupperware, but they are very expensive to purchase. Why is that? It is because biotechnology companies invested a lot of time and resources designing and optimizing the most suitable material for these flasks: the perfect shape, the most suitable coating… in other words, a flask that creates the optimal conditions for cell growth.

Similarly, years and years of research have been involved in formulating the special liquid, which maintains the growth and life of cells. Without these simple tools we cannot do any experiments.

Patenting

In order to secure the intellectual property of a given product and make sure no other company takes free advantage of the fruits of the painful and time-consuming product development process, companies patent their inventions. Patenting can be extremely expensive because of patent fees and fees charged by patent attorneys.

Scientists can also patent intangible inventions or ideas, for example, new therapeutic approaches. Pharmaceutical companies usually welcome such patents. If Pharmaceutical companies see enough potential in the patented research, they can buy the license from the scientists and develop a new drug or treatment.

Pharmaceutical companies will produce a drug only if they see a potential for profit. Some patients may think such an approach is business-as-usual and is not altruistic and does not serve the credo of science - helping people. However, pharmaceutical companies will need to run at least three very costly clinical trials, involving thousands of patents, in order to prove that their newly developed drug is safe and effective. If they can’t cover the costs of the clinical trials through future profits, the drug will never get to the market and people will never benefit from it.

From bench to bedside

The most effective way to put our research into practice and help people is to commercialize it, an initiative that requires a magical mixture of technical and managerial skills, vision and a lot of initial funding.

What remains hidden behind the scenes though, is that usually scientists invest a considerable amount of time and effort, without profit. In my lab it is commonplace to see people working at 11 pm on Saturday or Sunday night, driven by personal motivation and curiosity. It is this dedication without the thought of personal gain that brings new treatments and therapeutics to life.

Good science is good observation

Anyone who has good observation skills can contribute to science.

Leonardo Da Vinci, regarded as the best modern scientific mind, was not trained as a scientist. He started earning his living as an artist but he loved observing nature and nature inspired some of his greatest discoveries and inventions.

The father of genetics, Gregor Mendel, was not a scientist either. He was a monk, who noticed that pea plants inherit certain traits from their parents.

Copernicus and Galileo rebelled the church-enforced dogma that the Sun rotates around the Earth and proved that in fact, the Earth rotates around the Sun. They came to this conclusion by simply observing the celestial motion of planets. 

What do all these people have in common? What makes them brilliant scientists?

1. To observe carefully;
2. To trust your observations, nothing else.

Treading unknown grounds

This week in the lab Dr. Pangon observed some protein interactions that defy logic and have not been described before. Are his experiments wrong or has he stumbled across a new discovery? What is he going to do?

The only way for him to prove or disprove his observations is to repeat the experiment many times. He also has to change the conditions in his experiments and prove that he can observe the same effect in different conditions. He can also perform a familiar technique of removing the protein of interest from the cell and then putting it back in the cell in order to observe how it affects the protein interactions.

It may seem like a small discovery, but in science they are not small discoveries. In fact, Dr. Pangon’s discovery may have enormous implications for understanding how his protein of interest contributes to colon cancer. 

The Formula 

Sometimes we have to trust our senses and intuition. So did Einstein when he came up with the famous equation of energy and mass (E=mc²). This equation was not based on any scientific proof or evidence.

It seems the best formula to be a good scientist is to observe nature and trust your intuition. And anyone can do it.

Are you ready to discover?

In the lab, when you reach the point where you cannot make a conclusion from a set of experiments,  it is a deadlock situation.

This week, my research in the lab reached a deadlock as though to reflect on the political situation in Australia at the moment - no political party has won the majority of seats in order to form a government after the Saturday elections. The country is waiting for some political solution. I am waiting for some solution on my research.

The unfolding of events

The drug on which I perform my research is a potent colorectal cancer drug and it induces reactive oxygen species in the cell. Reactive oxygen species are a dangerous form of oxygen, which can seriously damage healthy cells but can also kill cancer cells.

In order to prove that my drug kills cancer cells through increasing reactive oxygen species, I performed a somewhat backwards experiment and neutralized them to prove that there would be less damage to the cell without their presence.

To my surprise, there was absolutely no effect, as though the reactive oxygen species did not play any role in the process of killing cancer cells whatsoever.

So what is happening? Why did my conventional neutralizers fail to produce any effect?

The decision

A deadlock. I have to design a whole array of new experiments, using more reactive oxygen species neutralizers in order to start solving the puzzle.

Just as in the parliament situation, now every experiment is decisive.

It will take months to come to a definite conclusion. Let’s hope the political situation is resolved faster and  we won’t stay more than a month without a new government.

This week in the lab I was completely devoted to writing a scientific paper manuscript with my supervisor which has been very long and tedious process. A scientific paper is a publication that summarizes and explains the results to a scientific question – or ‘hypothesis’.

How long does it take to prepare a scientific publication?

The writing part takes between 1 and 2 months, including hundreds of revisions. Producing the original results for the paper takes years, sometimes as little as 1 year, sometimes more than 3 years.

The most important part of the manuscript, or the scaffold, is the figures. The figures present our experimental results in a concise and clear manner.The body of the text describes the results and discusses them critically.

All results have the form of pictures or charts. While we are scientists and not graphic designers, nowadays we are expected to produce high quality images which necessitates preparation of these images in programs such as Adobe Illustrator.

We are also required to report the statistical significance of our results or in other words, to demonstrate that our observations are not due to chance and error, but they are reproducible and reliable. So this week I have been a scientist, a writer, a graphic designer and a statistician.

What is the next step for our paper?

We will submit it to our preferred scientific journal for assessment from a panel of three independent scientists, working in a similar field to our own. They will find any flaws of the paper and criticize it or give useful suggestions. Sometimes they will reject it and we have to submit to a different journal and go through the same process again.

Wish us luck!

It has been a lot of effort and years of research!

As far as our group’s protein is concerned, we don’t have the tools to actually “see” its shape, however we can somehow predict its shape based on our knowledge about the composition of its building blocks - the amino acids.>

During the week, Dr. Pangon and research assistant Melissa Abas successfully performed the experiment.

Within the cell, proteins are not stationary; they are not tethered to their mini-production line all the time. Sometimes a production line will be operational only if there is a stimulus outside the cell, like a meal we have just eaten.

However, in order to serve their function, proteins need to meet with their appropriate partners. Sometimes they travel enormous distances in milliseconds and find their partner in a vast space. How they manage to do this is a mystery for us but we do know that they do it with amazing speed and precision.

Dr. Pangon found that our protein interacts with three other proteins, which all meet together to form a group (complex) together. However, the most remarkable discovery was that our protein was essential for this complex to form.

This means that if our protein does not arrive, the other three proteins will not bind together to form a group (complex). The consequences for the cell are enormous. These proteins are a part of an essential production line that “senses” changes in the external environment and is responsible for producing signals (instructions) that will speed up, slow down or shut off other production lines. This is how the cell adapts to changes in the environment. In cancer cells, sometimes the particular protein that we are studying is missing or is faulty which results in the interruption of important messages to other production lines resulting in the cell becoming unable to respond correctly to external changes.

Next, Dr. Pangon will find out which part of the protein is required for the group (complex) of our four proteins to form. This is very important because we need to have a detailed and accurate understanding of the mechanism of interaction in order for us to best design intervention (treatment) strategies.

Cancer behaves differently from healthy tissue because in cancer cells the programming has changed in such a way that it no longer follows the “blueprints” of the body. Cells are like mini-factories with thousands of production lines and conveyor belts, every of them with specific important task.

Often in cancer cells some “conveyor belts” are broken or altered. We need to understand in detail which “conveyor belt “is damaged so that we can fix it. Cellular production lines are serviced by the cell mini-workers- proteins. The colorectal and lung cancer group has found a particular protein, which we believe is implicated in colorectal cancer, which means that its function may be important for a particular “production line”. The problem is that we have very limited information about its role in the cell. Dr. Pangon from our group has undertaken the enormous task to try and understand its function. First, Dr. Pangon and group members will try to find its partner proteins or in other words, proteins which are in very close proximity to it. By finding partner proteins with known functions, Dr. Pangon will get a better idea which “production line” the protein might play a role in. This is the first clue about its function.

He has designed a very clever experiment to answer this question. The results should come next week! It is exciting!

Dr Pangon and the group team will fish for the protein partners in the cell by using the protein itself as a bait. The protein is immobilized in tiny synthetic beads, which will serve as a fishing rod. This method will allow Dr. Pangon to "catch" several partner proteins which "bite" the bait.

Then the reverse experiment will be performed. The newly discovered partner proteins, which have been pulled out will be used as a bait and we expect that this time our protein will be pulled out. In that way we have double confirmation about the interaction between the proteins.