My Experience of Finding A Job After My Ph.D

MY BACKGROUND

I completed my Ph.D. biochemistry in August 2011. After 4 years of hard work it felt great to be finished, in fact it feels a bit like this. I had of years of laboratory based research experience supplemented by extensive undergraduate teaching duties. I considered myself skilled and experienced in experimental design, data management/analysis, managing work flow, direct supervision of undergraduate projects, and teaching, in addition to the use of modern molecular biology techniques, and biochemistry used in the expression, purification, and characterisation of proteins. In short, I was educated, and experienced. I wanted to stay in Ireland, but I had to acknowledge most of the work for post-doctoral research was overseas.

TRANSITIONING TO POST-DOC RESEARCH

My initial job applications were focused on post-doctoral research opportunities in my field and focused mainly in the UK. While there was a constant stream of relevant positions coming online it quickly became apparent that without a firm experimental background in structural biology my current skill-set was not enough to secure a position. So I changed tactics, and began applying for research assistant positions. These positions can require less experience and expertise and are an excellent way to transition between two specialities. You become skilled in new techniques while maintaining your competency in general laboratory skills, and your employer gets an experienced scientist at low cost that will become proficient very quickly, it’s a win-win situation. However, on the few occasions where applications resulted in interviews I was dismissed as either not being skilled in what they wanted, or not being taken seriously because why would a Ph.D. apply for such a position, clearly, I was going to leave at the first opportunity contracts, responsibility and professionalism be damned!

PLAN B - INDUSTRY APPLICATIONS

So, without the right set of skills for academia, I decided to change tactics again. Clearly academia was flooded with skilled and experienced scientists, so I focused on industry applications. The major barrier for job applications in this area turned out to be recruitment agents which many companies insist on using. Through a mixture of incompetence, and simple refusal to consider any application without GMP written on it I made almost no progress while “working” with recruitment agents. The best success I’ve had with industry applications has been direct applications to the company itself, even when they are not advertising positions. I’ve received emails from the owners of smaller companies thanking me for my interest, I’ve made new contacts which may lead to work years down the line, and importantly they now know I exist, and I have skills that are useful to them.

PLAN Z - BACK TO EDUCATION...SORT OF

After nine months of applications without any success I decided to take advantage of the new government sponsored upskilling programmes run for science graduates to allow employment in the pharmaceutical manufacturing sector. Despite the government parading the term “knowledge based economy” at every opportunity, this is not backed up by private or public investment in research facilities here. Instead Ireland is used as a manufacturing hub requiring specific skills which can only be obtained through years of industry experience. In the hope of acquiring some of these skills I joined, and subsequently left a state sponsored course designed to ease the transition between academia and industry. Overall, things were beginning to feel a bit like this.

After attending the first lecture I realised I could teach the material, so I offered my services for free. I would get good lecturing experience, reduce their work load at the same time, as well as possibly leave myself in a good position for getting paid work down the line. This looked like it might go somewhere, but it turns out there are bureaucratic difficulties in turning up somewhere to work for free. Everyone involved wanted it to happen, but it couldn’t be done. Least helpful of all were the department of social welfare. Since I was on social welfare payments it would be illegal for me to volunteer for anything that was not on their list. University lecturing was not on their list, neither was laboratory work.

JOBS-BRIDGE

While attending a second state sponsored course I was called for interview for an internship I had applied for months previously. It was out of my field of expertise, but since the idea of jobs-bridge was to allow inexperienced graduates to upskill I was hopeful something would come of it, and amazingly it did. I was offered the position, a nine month contract performing research in analytical chemistry, where I would gain hands on experience with relevant techniques. I was happy to accept accept the position, 18 months after I first started applying for jobs.

THE HAPPY ENDING

My current situation is that I’m employed full time on a 5 year contract. I’m gaining relevant experience in a regulated industry setting while performing research that I find fascinating, and challenging in equal measure. For me, the jobs-bridge programme was critical to my getting a foot in the door. It allowed my employer to take a chance on me, set up an experimental research project at low cost until such time as they were in a position to hire me.

MY ADVICE

From December 2010, to September 2012 I applied for over 100 jobs mostly within Ireland and the UK, and was called for interview on 10 occasions. As a newly graduated Ph.D. I found it impossible to get my foot in the door, and for anyone to take me seriously. The tide is beginning to change now as experienced people are being snapped up, and companies are becoming more flexible on their requirements. But I don’t envy anyone looking for work over the next few years.

The best piece of advice I can give here is where at all possible bypass the recruitment agents completely. For the most part they are not scientifically literate, and they will have almost no understanding of what the job entails. Secondly, persist! Keep applying, and where possible get in touch with the company directly. Finally, join LinkedIn, and use it. Posting answers to questions on its forums is a great way to make new contacts and establish a name for yourself as someone who knows their subject matter, but also as someone that cares about their work, and act collaboratively to solve problems. Finally, get that first few months experience if you can. It might mean working for free, but it won’t be forever.

Do You Mendeley? - My Experience of a Stress Free Reference Management Tool

BACKGROUND

As an experimental biochemist embedded in a largely computational research group I was lucky enough to be exposed to some clever software tools that simplify everyday tasks such as primer design, DNA sequencing, homology modelling, and viewing protein structures. However I noticed my peers were still performing many tedious tasks by hand, or using some really terrible software. The best example of this was reference management, where Endnote was essentially ubiquitous, but everyone had problems with it. However, there is a better way. Mendeley is a free reference management tool that integrates seamlessly with MS Word, and Open Office. The developers of Mendeley have an excellent website with easy to follow tutorials on the main features, see here, but nothing beats the experiences of someone who uses it on a daily basis.

WHAT IS MENDELEY?

Essentially, Mendeley is iTunes for your research papers. Its allows for easy uploading, storage, and retrieval of your papers from multiple computers, in multiple formats. In addition, it automatically generates a copy of all your documents on the cloud, thanks to the free 500Mb of storage space they provide for every user. Here is what it looks like when you have built your library. 

You can see it's very well laid out. The main screen is your selection of research papers, with all the useful details listed such as title, authors, year of publication, and journal. Just having all your research papers like this makes a huge difference to how you find and use them. Mendeley is packed full of useful features, but after using this software for over two years the main features I think people will be interested in are as follows,

• cataloguing of all of your research papers visible through one portal
• super-fast library searching
• sending and receiving documents to/from other Mendeley users
• access the original website from which the article was downloaded
• digital annotation and highlighting of articles/sections of articles
• the ability to access your library from any online computer

CREATING YOUR LIBRARY

Creating your library is straightforward. I found the best way was to simply select the “Watch Folder” option from the add files menu in the main toolbar, and browse to the folder which contains your documents of interest. They can be pdf or word documents. Mendeley will now proceed to add each document to the library, scanning each for useful details such the title, the authors, the journal it was published in. In addition, any documents subsequently added to the folder will now automatically be visible in Mendeley. The documents do not need to be labelled logically for Mendeley to populate the metadata for each article. This is akin to letting iTunes fetch the details of a particular track for you, so that you have the correct album art, singer, album name etc. However, Mendeley does not always get this right, so some manual manipulation may be required to clean up the data. I consider this a small price to pay considering the benefits granted by the rest of the functions. Once you have your documents imported I recommend using the synchronisation functionality, this uploads everything to the cloud storage they provide, allowing you to access it from any computer with an internet connection.

SEARCHING YOUR LIBRARY

Once you have imported your documents the first thing you’ll notice is that double clicking on any one of the articles beings you to a full version of the document. This is fully searchable via the toolbar on the top right. It might not seem like a major feature, but when you’re trying to remember where you came across the evidence for that statement in your thesis it’s an extremely valuable and saving feature. In addition, your whole library is searchable, so you can search for authors names, or journal name, or just individual terms you are interested in. It’s happened to me before that I couldn’t remember the author, but I could remember a particular term used with the article, a few keystrokes quickly narrows down the list of possible suspects. It’s worth noting, the more effort you put into having the correct details for each article the better the results of any search will be. If you’re slightly OCD like me you’ll actually get enjoyment out of making sure everything is correct, and welcome the distraction from writing your thesis.

SENDING/RECEIVING ARTICLES

How much you use this feature depends on how collaborative your research group is, and how many other people you can convince to use Mendeley. Essentially it allows you to select any of journal articles from your library and send them to any other Mendeley user that you have invited to join Mendeley. It’s actually much quicker than email, and the document is automatically integrated to your existing library, including any notes, and annotation made by the previous “owner”. The recipient does not have to have a subscription to the online publisher of that article, so it’s an excellent way to share papers among less privileged colleagues.

ACCESS TO ORIGINAL URL

This is perhaps one of my favourite features in Mendely. It very common for the research paper you are reading to cite other articles of interest. Tracking down references can be extremely time- consuming (read pain in the ass!) depending on how the original paper referenced them. The easiest way by far is to go to the URL of the original paper, and hope that they have supplied there list of references as hyperlinks. This would allow you to get all their references relatively quickly. However, even this means you still have search for the original paper in Google Scholar, or PubMed, Mendeley can by-pass all of that time consuming nonsense by providing the URL of the source article you are reading in the right-hand toolbar. Think about what this means now. With the URL provided to you all you have to do is click on the link and you are on the correct webpage for that article! From here you can go straight to the reference section of the look for hyperlinks. It’s an extremely fast and very effective way to navigate from source to source with no typing involved. 

DIGITAL ANNOTATION AND HIGHLIGHTING

A relatively minor, but useful feature of Mendeley is that individual documents can be have “sticky notes” attached to them, essentially a collapsible text box which you can place anywhere. Generally useful for making quick notes of questions, or thoughts as you read the paper. It’s also possible to make more detailed notes in the toolbar on the right hand side, this is a better option in my opinion, since these notes are searchable, so you can actually pick out a paper based on the contents of the notes you made as you were reading it.

ACCESS, ANYTIME, ANYWHERE

Provided you have synchronised your library and you have downloaded Mendeley you will have access to your library from any computer with an internet connection. So, for example, I used to do the majority of my thesis writing in my University. But occasionally I would work from home. For me this meant I lost my access rights to the journals that supplied all those nice papers I needed. So. on these occasions I would make sure to dump any relevant research paper I could into Mendeley nd syncronise it before leaving for home. Once home, Mendeley allowed me to continue reading and inserting citations to my thesis as if I had university access. But if I ever needed something I could always get it send to me from someone who also had that document in their library. This allowed for seamless integration between multiple computers. In fact during the writing on my thesis I went through three laptops and two desktops, but it was never a problem, my library was always on the cloud, and between Dropbox and Mendeley I was back writing from where I left off within 20mins of switching to an entirely new computer I had never used before. Think about that for a moment, normally a computer failing is a massive problem mid-thesis write up. But Mendeley and Dropbox together meant I never had a single problem I could not recover from quickly. 

THE CONCLUSION

In short, I can’t recommend this software highly enough. It's fantastic. It’s intuitive, and actually fun to use. On the one occasion I had a technical issue it was resolved within 24 hours, with follow up from the support team to make sure I had what I needed. Bear in mind, this is free software, and the support they offer is far superior than anything I’ve experienced with Dell, or Microsoft. Download it, play with it, and enjoy stress free referencing! Do it now! :)

Drugs of Abuse - Amphetamines, Ecstasy and Cathinones.

BACKGROUND

People have been using psychoactive drugs for pleasure for thousands of years. From the Areca nut used as a mild stimulant in Timor over 13,000 years ago, to the coca leave cultivated in South America 5,000 years ago it seems the human brain craves stimulation, and consequently, new and interesting stimulants. Modern day humans are no exception. We're all used to hearing news stories about heroin, cocaine, ecstasy and LSD, but lately there has been an explosion in both the number and types of new drugs available.

WHAT'S THE PROBLEM?

Regulatory authorities are struggling to keep up with the number of new "illegal" drugs on the market. I say "illegal" simply because it's not clear how these compounds should be classified. The complexity in the law governing the use of drugs arises from the subtleties of the chemistry at the atom level. For instance, for any given compound, legal or not, a difference of a single atom anywhere in the structure results in a compound which is completely unique. There may not be anything known about this novel compound, and consequently, there is no legislation governing its use.

For example, let's examine the chemical composition of two drugs, one legal decongestant called pseudoephedrine, and one illegal drug called methamphetamine, (crystal meth). Pseudoephedrine is available from pharmacies as an over the counter medication. It's the active ingredient in Sudafed for example. Structurally, pseudoephedrine looks very similar to methamphetamine, see the picture below. In fact there are just two atoms in the difference.

If nothing was known about pseudoephedrine a toxicologist looking at it for the first time might expect it to have a similar effect to methamphetamine, that is, stimulatory, promoting alertness, and increasing reaction time. But it's very difficult to judge the effect of those two extra atoms. The additional (-OH) present on pseudoephedrine could make it more or less potent as a stimulant. Perhaps it's metabolised more quickly by the body? Perhaps it's more soluble in the blood now? Perhaps it has a harder time getting into the brain? A good toxicologist can make good predictions, but they are just that. Until detailed studies are performed it's really not known how a particular drug will behave.

This is the root of the difficultly for legislators. If there was a decision to make pseudoephedrine illegal this might go some way to curbing its use. However, a single atom change to its structure results in an entirely new compound. It's perfectly possible that nothing is known about the physiological effects of this compound, beyond its ability to produce a chemical high. This is exactly what happened with ecstasy (MDMA) production recently. One of the precursor ingredients for MDMA was made illegal. The idea was to make it more difficult to manufacture MDMA and ultimately make people safer.

However, far from making people safer this change in legislation resulted in the rise of a new ecstasy like compound called PMMA. Both MDMA and PMMA have similar effects, but the effects of PMMA come on much more slowly. Thinking the drugs weren't working, or that they had taken a really low dose, regular MDMA users would take more and more PMMA waiting for the effects to kick in. Needless to say, when the effects did kick in things got serious. Very quickly after the emergence of PMMA there were media reports of overdoses across Ireland and the UK. Sadly, this is a stark example of legislation that was introduced to prevent harm actually causing more harm than good.

Fuck it, lets just make everything legal!

MEDIA ATTENTION ON DRUGS

2014 saw the introduction of over 100 new synthetic drugs of abuse in Europe alone. With such a wide array of new street drugs it's no longer surprising to encounter a news story including the name of a drugs most of us have never heard before. For example, this was a recent headline in America. 

The drug being referred to here is called alpha-pyrrolidinopentiophenone, or alpha-PVP for short, street name Flakka, or Gravel. But what is this drug, and where did it come from?

ALPHA-PVP

Alph-PVP is a synthetic stimulant which belongs to a class of drugs called cathinones. Cathinone itself is naturally occurring, being found in the plant called Khat. The leaves of this plant can be chewed to produce mild stimulation. The structure of cathinone is shown below, along with the khat plant it's found in. Interestingly you can see it looks a little bit like methamphetamine, so it's not too surprising to learn that this drug is a stimulant. It also induces paranoid delusions, with users reportedly fearing for their lives after hallucinating gangs of people chasing them down!

The chemical structure of cathinone (left) and the plant which makes it Catha edulis, (right).

At this point it's important to point out here that whether or not a compound is synthetic has no bearing on its safety or toxicity. There are many synthetic compounds which are safe, and many natural compounds that are dangerous. In the case of PVP, the naturally occurring cathinone molecule was modified by a chemist to produce a novel synthetic compound. This is the case with all synthetic cathinones which include mephedrone (M-CAT, Meow, Meow), and MDPV, (Bath Salts), both of which get sporadic media attention as a result of fatal or near fatal overdoses. The structures of these compounds are shown below. If you know a little chemistry you can see they look a little like the structure of cathinone, shown above. Variants of cathinone are continously made to circumvent the laws which ban them. Thus, it is often not illegal to manufacture or sell these compounds.

You could argue that all that's required for legislators to get a handle on this is an outright ban of all cathinone compounds. The problem with that idea is that some cathinones are actually medicinal, and are used as antidepressants for example. Making all cathinones illegal immediately makes research into these drugs more difficult. Any research laboratory wanting to investigate these compounds would now need to apply for a licence to have them on the premises. This is a bureaucratic nightmare, enough to put off many research scientists who simply don't have the knowledge or the resources to work in such a regulated environment. Regardless of whether or not you think this is a poor attitude for a scientist to take, the reality is more barriers to research means less research is done.

Those using synthetic cathinones recreationally can be often experience far more intense "highs" than expected. Part of the problem with illegal or unregulated drug manufacture is that the contents are not tightly controlled, so the potency between batches is extremely variable. By contrast, any drug manufactured legally by a pharmaceutical company must undergo a multitude of quality control (QC) checks to ensure purity before being distributed.

SUMMARY

New drugs are being manufactured all the time. Legislation designed to protect the population from the risks and harms of drug use have actually compounded the problem resulting in deaths from the distribution of PMMA marketed as Ecstasy (MDMA). At the same time, there is increase in the number of synthetic cathinones, producing powerful psychoactive stimulants. Almost nothing is known about the physiological effects and safety of these stimulants. By contrast, the physiological effects of compounds such as amphetamine, methamphetamine and cathinone itself, are known and documented in detail. I hope this segment has given some insight into the science behind the news headlines, and the difficulties faced by regulators and scientists working in this area.

As always, comments are welcome. 

USEFUL INFORMATION

• Database on new psychoactive drugs in Europe
• Guardian Science Podcast on PMMA
• FOX news article on Alpha-PVP
• Information on Synthetic Cathinones.
• Irish Times News Story on PMMA Deaths
• Review of Flakka

Universal Blood Cells.

BACKGROUND

Some time ago, while making my way home from college I was listening to an episode of a podcast called Science Friday. It was dark and cold outside and I was keen to get home, eat and be warm, so it's safe to say my mind was not on the material at hand. Even so, what I heard blew my mind, it seemed too simple to be true, and yet it made perfect sense. I was immediately annoyed I hadn't come up with the idea myself. The idea? Universal blood cells. I'm going to keep you in suspense as to what that means while I explain more about blood in general.

BLOOD

Blood is composed of red blood cells (also referred to as RBCs, or erythrocytes), white blood cells (also referred to as WBCs, or leukocytes), and platelets. This varied composition allows it to perform a myriad of essential functions. For example, RBCs are responsible for the transport of oxygen, (O₂), from the lungs to every other organ and cell in the body. In addition, they also exchange this oxygen for a waste product of glucose metabolism, carbon dioxide (CO₂), and return it to the lungs to be expelled. Therefore there is a constant exchange of CO₂ for O₂ going on in the lungs, with blood being continually circulated around the body to remove/supply both. WBCs are a much more complicated group. There are five different subtypes of WBCs, but together they form part of our immune system, allowing us to fend of biological attacks from viruses and bacteria. Finally, plateletes are responsible for some housekeeping activities such as blood clotting, maintenance of blood vessel lining, and digestion of harmful bacteria.

The composition of blood, image taken at http://www.myvmc.com/anatomy/blood-function-and-composition/

In addition to all of the above functions blood also has the added function of regulating pH, regulating body temperature, and generally acting as a delivery mechanism throughout the body for the supply of nutrients such as glucose, amino acids, lipids, vitamins and salts. So, blood is important, and it's able to perform all of these functions because of the complex composition of RBCs, WBCs, and platelets. 

CELL BIOLOGY 101

Cells are the basic unit of life, by which I mean all living things are composed of either a single cell, or many cells, termed unicellular or multicellular respectively. But cells themselves are incredibly complex, and in the same way that we have specific organs performing specific tasks for us, our cells have tiny structures inside them called organelles performing specific tasks for them. This could be the production of protein, or conversion of sugars into cellular energy. But the complexity of a cell continues to the outside. All animal cells have a fatty cell membrane called a phospholipid bilayer separating it from the outside world. This lipid bilayer is protective, but also functional. It's scattered with protein and sugar molecules that allow it to regulate transport in/out of the cell, and generally communicate with other cells around it. Sugar and proteins sometimes combine to form what is called a glycoproteins, and these are important molecules.

BLOOD GROUPS

Most people will have heard the term blood group. But what does it actually mean? Well, there are four different blood groups called group A, B, AB, and O. It turns out that the glycoprotein surface is what determines your blood group. There are many different types of sugars, and they have names like glucose, fructose, and sucrose. In the image below "GAL", "GAL-Nac" and "FUC" are sugars called galactose, N-acetylgalatosamine and Fucose respectively. You can see how all three blood groups share the same GAL-GALNAc-GAL backbone, but differ in their terminal regions. For example, blood group A has an additional Gal-Nac sugar molecule compared to blood group O, while blood group B has an additional GAL sugar molecule compared to blood group O. Blood group A is further subdivided with blood group A₁ and A₂ being the most common.

Schematic of the A, B, and O blood groups. The red oval represents the red blood cell. The coloured hexagons represent the different sugars that attach to the blood cells to make its blood group.

MEDICAL RELEVANCE

Blood groups are extremely important for blood transfusions. The blood groups between donor and recipient must match otherwise the body will reject it. All blood groups can donate to themselves, so group A is compatible with A etc. However, blood group A is not compatible with blood group B, and the reverse is also true, group B is not compatible with group A. Group AB cannot be given to group A, or B. Group O however can be given to every blood type, which makes it extremely valuable. The compatibility of different blood groups can be summarised in the diagram below. Red arrows indicate blood groups which cannot be exchanged.

The compatibility of each of the blood groups, red arrows indicate blood groups which cannot be exchanged.

Invasive surgery requires blood transfusion while the operation is being performed, so if there's no time to test the blood type of your patient then you know it's safe transfuse blood O without resulting in any additional complications. Transfusing the wrong blood will lead to activation of the immune system, destruction of the new blood cells which ultimately can result in death.

UNIVERSAL BLOOD CELLS

The idea I ended up stumbling across that night while listening to my podcast was to generate blood group O cells from bags of group A, B, and AB blood. That is, the ability to take any blood type and modify it so that it's capable of being transfused without any immune response in the patient. This idea, if feasible, would make all of the current blood stocks capable of being donated to any patient! That's pretty amazing!

HOW DOES IT WORK?

The basic science behind this is involves the application of a well established biochemical technique called enzymatic hydrolysis. Enzymes are protein molecules which have the ability to add or remove chemical components to specific molecules, I've mentioned them before in a previous blogpost so I'll skip over a detailed explanation here. There are pre-existing enzymes in nature which will selectively remove the N-acetylgalatosamine and Frucose sugars from blood cells. Interestingly, the first attempts were with an enzyme found in coffee beans, but subsequent attempts using different versions of the same enzyme resulted in much better efficiency. The image below shows how these sugars actually look and demonstrates how the conversion of group A or B to group O involves the removal of just one molecule of sugar. The sugar removed in each case is highlighted by a coloured star.

Conversion of blood groups A and B to group O. Image adapted and modified from the original research paper on this topic, "Bacterial Glycosidases for the production of universal blood cells" 

There are two enzymes used for this, once called α-N-acetylgalactosaminidase for removing the sugars associated with blood group A, and a second called α-galactosidase for removal of sugars associated with blood group B. The actions of these enzymes result in blood group O cells. The structure of α-N-acetylgalactosaminidase enzyme bound to a single sugar molecule is shown below. On the left is an image of the whole enzyme/sugar complex (shown in grey, red and blue), with the sugar shown in purple. The image on the right is the same enzyme/sugar complex zoomed in to show the the complex in more detail. Enzymes often have small clefts or holes in their structure into which their substrates fit. All the chemistry associated with the removal of this sugar molecule happens in and around this small cleft area, called the active site.

The α-N-acetylgalactosaminidase enzyme, bound to a sugar residue. Image made using YASARA, and PDB ID 2IXA.

The α-N-acetylgalactosaminidase enzyme, bound to a sugar residue. Image made using YASARA, and PDB ID 2IXA. 

WHY THIS IDEA IS COOL

Biological material like blood is sensitive to large changes in pH, or temperature. In addition, it's important to keep it free from any external contamination. Biochemists are familiar with this so we add reagents to control the pH, we keep solutions cold, because it helps preserve the integrity, and slow bacterial degradation of the components and we often work in sterile conditions to prevent any contamination. This is time consuming and expensive. But one of the cool things about the procedure used to make this blood is that it is relatively easy. There are no difficult or expensive conditions required. The enzymes required were simply added to a 200mL volume of blood which had been washed with buffer solution, the solution was then mixed gently for 1 hour at room temperature, after this the blood was washed with a salty solution to remove the enzymes. In addition, even though there are different enzymes responsible for converting blood groups A and B it was possible to simply add both enzymes to a single unit of AB blood and let both of them operate together to produce a unit of blood group O.

THE DISADVANTAGES

There are some disadvantages with the enzymatic hydrolysis of blood cells. The research group responsible for demonstrating this modification of blood cells has shown it works on a small scale, but for this to be really useful it would need to be able to convert thousands of units of blood every week. Such large scale conversion would require large quantities of the enzymes used. Specifically, for the conversion of 1 unit of blood group A1 to blood group O the researchers mention they used 60mg of enzyme. Recently the Irish Blood Transfusion Service (IBTS) advertised they needed 1,500 units of group O blood each week. To convert 1,500 units of blood would therefore require 90,000mg (90g) of enzyme every week.

It's a little difficult to put this in perspective, but I used to make enzymes as part of my Ph.D work. This is done via the genetic modification of microorganisms, bacteria or yeast cells for example, which are then grown in what is called a bioreactor, or fermentation vessel. Typical yields of protein are pretty low, in the order of 100mg/L of cell culture material. So the ability to make 90g of enzyme every week is demanding, and expensive, but by no means impossible. Biotechnology companies are used to this problem, and utilise large scale bioreactors, in the order of 20,000L, to mass produce therapeutic proteins for other medical reasons. This is currently being done for diseases like diabetes, where insulin is required in large quantities for worldwide supply, so there's no technological reason why this could not be done for these enzymes.

SUMMARY

Blood donations are always needed, and in particular blood group O is in high demand because it is accepted by any blood group. Supply is always going to be restricted due to legitimate medical reasons such as disease, so anything that can be done to ease the strain on supply is definitely worth considering. The research presented here is simple, but clever, and uses well established biochemistry techniques. It might not be feasible to produce quantities of enzyme that are required, but there's a few more tricks that biochemists can perform the make it better. We can modify the protein using genetic engineering, to make it behave more efficiently, removing the sugar molecules more quickly. We can also try different ways to manufacture the enzyme which might improve the quantity we obtain. In short, this is a fantastic idea, and worth pursuing further, and I'm still annoyed I didn't think of it first!

How Does Penicillin Work?

ANTIBIOTICS

The first antibiotic, penicillin, was discovered serendipitously in 1928 by Alexander Fleming. A medic by training Fleming went on to specialise in bacteriology before leaving his comfortable lecturing position for the trenches of World War I. He served as a medic in French field hospitals on the western front. There's no doubt that during his military service Fleming was exposed to the horrific toll that bacterial infection caused wounded troops. Many amputees died from non-life threatening surgery due to infections obtained in unsanitary field hospitals. But the discovery of penicillin revolutionised surgery, allowing patients to recover from infections that could otherwise kill them.

Alexander Fleming, perhaps not the happiest scientist there ever was. 

So effective was this wonder drug that Fleming was awarded the Nobel prize for Medicine in 1945. By this point, penicillin had saved thousands of lives both on and off the battlefield.

So how does Penicillin work? Well, to understand that one needs to understand the basics of cell biology. Cell biology studies with what cells are made of, and how they operate. A detailed understanding of cell biology is beyond the scope of this post, but it is useful to understand bacteria in the context of other forms of life. 

TYPES OF LIFE

It might seem surprising, but every living thing on the planet can be categorised into just there different branches on the complex tree life. These branches of life are called Prokaryotes, Eukaryotes, and Archaea. In addition there are also viruses. Viruses are often difficult to introduce when discussing simple life-forms because while they are much more simple than a bacteria cell, they are not always considered living cells. They have many of the characteristics of life, movement, sensitivity to their surroundings and so on, but unlike living cells they are unable to reproduce without a host cell. That is, they rely on infecting a bacteria or human cell to make more copies of themselves. For this reason, viruses are often considered nothing more than assembles of biomolecules, albeit, very interesting and often dangerous assemblies of biomolecules.

THE ARCHAEA

The Archaea branch of life contains the simpler organisms, the early forms of bacterial life on earth. They are single celled with an amazing ability to survive and adapt, often living in environments that we would consider hostile. For example, there are some Archaea bacteria that live in the very darkest depths of the ocean, in close proximity to hydrothermal vents. These living conditions contain extreme pressures and temperatures and there no sunlight. However, this proves to be no obstacle to these hardy organisms who thrive on the constant supply of noxious chemicals released from deep below the surface of the earth. 

THE PROKARYOTES

Like the Archaea, these are simple, unicellular organisms, but they tend to live in less hostile environments. These are the bacteria you are more likely to have heard of. The E.coli bacteria associated with food poisoning for example, or MRSA infections commonly contracted in hospitals. Prokaryotes are tough, adaptable, and capable of reproducing quickly making them potentially very dangerous. However not all of them cause disease in human (a quality known as pathogenicity). Some are actually beneficial to us, bacteria in our intestine actually help us digest food we eat, and produce vitamins for us in return.

THE EUKARYOTES

Finally, the eukaryotes. These are the most complicated organisms, and include some unicellular life such as yeast cells, but also the more complicated multicellular organisms. This includes everything from sponges to worms to humans. The individual cells that make up a human are much more complicated than an individual bacterial cell. This complexity comes at a price, namely the speed at which a human cell can make more of itself. Bacteria are very quick to reproduce but human cells, by comparison, are slow but make a more faithful copy of themselves. 

THE ANATOMY OF BACTERIAL CELLS

Bacteria themselves are incredibly interesting lifeforms. Although more simple than us they are  still very complex. They consist of a bunch of cell organelles, and some DNA wrapped up in a fatty skin called the cell membrane. Surrounding this cell membrane is a tougher shell called the cell wall. The cell wall is made of a tough material called peptidoglycan, and offers the bacteria some protection from the outside world. You can think if it as multiple layers of wire mesh; rigid, strong, but also flexible.

The anatomy of a bacterial cell. The yellow "skin" on the outside represents the cell membrane, and the cell wall. 

This peptidoglycan mesh is a composite of sugars and amino acids. The sugar components have the unwieldy name of N-acetylglucosamine, and N-acetylmuramic acid so for ease, biologists abbreviate these to simply NAG and NAM. NAG and NAM sugars are joined together in a chain, and individual chains become cross-linked with small protein molecules for extra strength and rigidity. As with many processes in biology the formation of a bacterial cell wall is facilitated by an enzyme, in this case, an enzyme called transpeptidase.

This image shows the function of the transpeptidase enzyme in making bacterial cell walls. The red and orange hexagons represent the individual NAG and NAM sugars that combine in long chains. The chains have small pieces of sticky protein (peptides)  hanging from every NAM molecule. The transpeptidase stitches each NAG-NAM chain together by fusing the peptides molecules together. These fused chains are the basic structure of a bacterial cell wall. 

Bacteria are constantly making and degrading their peptidoglycan cell walls during the process of cell division. It's a necessary part of how the divide and make more of themselves. Without the ability to make and repair their cell walls bacteria become flooded with water from outside the cell, and burst. A process called cytolysis. Therefore, the transpeptidase enzyme is essential for the survival of bacterial cells. Some antibiotics work by inhibiting the action of this essential enzyme. But how?

THE STRUCTURE AND FUNCTION OF ANTIBIOTICS

There are many different types of antibiotics, and they can be classified on the basis of their chemical structure, mode of action, or spectrum of action. As mentioned, Penicillin works by inhibiting bacterial cell wall synthesis, but other antibiotics work in different ways. What is it about penicillin that makes it work the way it does? Well, like a lot of biochemistry, it all comes down to to the atomic structure of the penicillin molecule. Fleming did not know this at the time of his discovery, but penicillin actually looks very like the peptide molecules used to strap the peptidoglycan chains together.

So, when we take penicillin to treat a bacterial infection we are presenting the bacterial transpeptidase enzyme with a choice. The enzyme can either, grab hold of the peptide molecule (D-Ala-D-Ala) like it's supposed to, or it can grab a molecule of penicillin. If it grabs a molecule of D-Ala-D-Ala then everything goes to plan, at least as far as the bacteria are concerned. Cell wall biosynthesis occurs normally, and the bacteria happily go about reproducing. However, if the transpeptidase enzyme grabs a molecule of penicillin instead of D-Ala-D-Ala, then the bacteria are in trouble. Penicillin will bind strongly to transpeptidase enzyme, effectively gumming up the works. We now have a situation much more like the image shown below.

Here, the penicillin molecule is represented as the yellow and black circle, jammed in the mechanism of the transpeptidase enzyme.

Here, the penicillin molecule is represented as the yellow and black circle, jammed in the mechanism of the transpeptidase enzyme. With penicillin gumming up the works it is not possible for transpeptidase to do it's job. The more penicillin we take the more this situation occurs, making it very difficult for the bacteria to reproduce. This mechanism of actions applies only to penicillin and antibiotics that look like penicillin such as amoxicillin. Different antibiotics work in slightly different ways, targeting different proteins that are important for bacterial cell survival.

ANTIBIOTIC RESISTANCE

Antibiotic resistance is becoming an increasing problem. It refers to the ability of some bacteria to keep reproducing despite the presence of antibiotics designed to kill them. So, how have these crafty bacteria overcome our sophisticated chemical weapons? The answer is evolution. Every generation of bacteria results in a slightly new organism. It's still a bacteria, but it's ever so slightly different from the "parent" that made it. Sometimes these differences are enough to result in interesting properties such as antibiotic resistance.

Antibiotic resistance stems from an overuse of antibiotics in medicine. This could be over-prescription by doctors, or people administering for diseases not associated with bacteria, such as colds, or flu, caused by viruses.  For any given infected individual it is unlikely that a single dose of antibiotics will wipe out every single bacterial cell in the body. Any cells that are left will produce offspring which become resistant to their hostile environment, and thrive in their new competition free zone. Next time these bacteria encounter this antibiotic they have already adapted to it, and produce their own chemical weapons to destroy ours.

CONCLUSION

So, there you have it. Penicillin works by preventing the construction of bacterial cell walls, causing bacteria to explode via an intake of water. Penicillin is just one of many types of antibiotic, which can produce their effects in different ways. Bacteria are adapting to these chemical weapons by producing chemical weapons of their own, destroying of the antibiotics before they can take effect. This has resulted in an literal arms race between us and the bacteria, but we are losing. The result is multidrug resistant bacteria such as MRSA which is having a pronounced effect on hospital patients worldwide. If we are to win this arms race we need think differently, and stop relying on brute force approaches. 

Genetically Modified Organisms

BACKGROUND
This is a post about genetic modification, and genetically modified organisms, or GMO's for short. Using farming as an example I will discuss how genetics can be used to improve traits such as milk production in cows, and disease resistance in potato crops. The aim of this post is to show how genetics has some real-world applications that affect all of us.

THE ORIGINS OF GENETICS

Although farmers across Europe have been breeding their cattle and crops selectively for centuries, it was a nineteenth century Augustinian monk who first realised the power of genetics. Friar Gregor Mendel used his monastery's pea garden to study the size, shape and colour of pea plants and their seeds. This unassuming research allowed him to identify the root of how individual traits are passed from parents to offspring, a term now named in his honour as Mendelian inheritance. The term “Mendelian Inheritance” refers to the transfer of genetic material, DNA, from parent to offspring. Centuries of research since Mendel’s humble beginnings in his pea garden has shown that many characteristics of plants and animals are determined by small packages of DNA called genes.  I have discussed, genes, and DNA in detail in a previous post so I won't go into detail here.

THE IMPORTANCE OF GENETICS

In the 150 years since Mendel our understanding of genetics has developed enormously, and modern scientists have now gained more precise control over the characteristics that can be added or removed from a variety of plants and animals. With the help of Teagasc, an independent state-funded agricultural research body, we are moving away from older and more costly methods of crossbreeding. Modern genetic manipulation now means that desirable traits can be selected for while undesirable ones can be left behind. This means that today’s farmers can save both time and money crossbreeding cattle and crops and increase crop yields for an ever expanding food market.

WHAT ARE GMOs?

Genetically modified organisms, or GMOs are organisms which have been altered through the addition or removal of individual genes. Human beings have been living in harmony with genetically modified food since the beginning of agriculture in the form of disease-resistant crops or bulkier cattle for better meat production. Although sensationalised media reports sometimes paint GM food as unnatural “Frankenstein food” that may pose a risk to our health or the environment, the reality is much less sinister. In fact, modern genetic modification techniques allow farmers to better control desirable gene inheritance in a fraction of the time traditional methods would have required.

CASE STUDY 1: THE HOLSTEIN-FRIESIAN/NEW ZEALAND JERSEY MIX

In 2013, for the first time in our history, Irish food and drink exports approached €10 billion and the dairy industry accounted for almost a third of this. Dairy exports in 2013 amounted to €3 billion, up 15% from 2012, and are expected to rise again this year. This is a testament to the high standards Ireland sets and maintains in this sector. The majority of Irelands milk production and calving is seasonal, with over 75% of milk production occurring from April to September, whilst 79% of calves are born between January and April.

The Irish dairy herd is dominated by the Holstein-Friesian breed, which makes up 63% of the national herd. Our farmers favour this breed because of its exceptional milk yields, a characteristic arising from breeding programmes in the US. When we consider that Ireland has a limited calving season of only four months, we can see that improving our herds reproductive success would have a knock-on gain in the milking season and allow farmers to boost their profit margins. Until recently, any potential gains to be had from cross-breeding the Holstein-Friesian with a more fertile breed were disregarded by farmers wary of tampering with the Holstein-Friesian’s milk yield. But all that changed when the Holstein-Friesian was crossbred with the New Zealand Jersey.

The Holstein-Friesian (left)  and New Zealand Jersey (Right)

Although the New Zealand Jersey has slightly inferior milk production properties compared to the Holstein-Friesian, it does have superior reproductive qualities and tends to live longer. A recent Teagasc study showed that the offspring of the Holstein-Friesian and New Zealand Jersey, called F1, had the characteristics required to improve the overall profitability of the Irish herd.

The results of the Teagasc study, with all values displayed relative to the Holstein-Friesian breed.

The Teagasc study revealed that the quantity of milk produced by the F1 crossbreed was marginally lower than the Holstein-Friesian, but this issue was compensated for with higher fat and protein content. The results also showed a modest improvement in turnaround time from calving to conception compared to the Holstein-Friesian. On top of this, the significantly hardier body condition of the F1 means lower maintenance costs for the farmer. When we add up the findings of this study, it clear that the benefits far outweigh the negligible disadvantages of crossbreeding these two strains. It’s no wonder then that New Zealand has already begun adopting this breed, with the F1 making up 33% of their national herd.

CASE STUDY II - GENETICALLY MODIFIED POTATOES

Potatoes are a staple ingredient on dinner tables all over Ireland, but it’s hard to mention this delicious starch without thinking about the Great Famine of 1845. This tragic episode in Irish history was caused by a fungus called Phytophthora infestans, commonly known as potato blight. Incredibly, over 150 years on, blight continues to be a serious concern for present day potato farmers.

In the battle against blight, fungicide remains our main weapon of choice. Fungicide is effective, but it requires as many as 15 to 20 sprays a year to secure a good potato crop. European regulations on fungicides are becoming more restrictive and, although many welcome this decision from an environmental perspective, potato farmers will need new weapons to protect their crop. As yet there are no blight-resistant strains of potato in Ireland but genetic modification may hold the key.

Some Central America potato strains possess genes known to provide protection against blight. Traditional methods of cross-breeding potatoes are both time consuming and inefficient, but new genetic modification methods have had great success in introducing these genes to European strains of potato. Teagasc collaborations on an international level have led to possibility of blight-resistant potatoes being developed in Ireland. The picture below highlight the significance of their efforts.

The image on the left shows a GM potato line (A15-031) containing genes for blight-resistance, while that on the right shows a unmodified potato crop

The effects of blight on both strains can be seen, with the GM potato crop remaining healthy despite the presence of blight, while the unmodified crop succumbs to the disease. This development provides farmers with new options going forward. However Ireland proceeds, the decisions made by this generation is likely to have very real and long-lasting consequences to future generations.

CURRENT OPINION GMOs

As with any new technology, a decision needs to be made on how and when it should be implemented. Those in favour of GMOs will urge for an early adoption to get ahead of European fungicide restrictions as well as to take advantage of any financial gains that can be made. Those who favour caution will prefer to wait and see how GMOs pan out for other nations. Teagasc is very clear about its stance on the issue of GMOs, making sure to distance itself from the commercial profit-oriented organisations and instead favouring unbiased publically-funded research. Dr. Ewen Mullins, Senior Research Officer of the Crop Science Department at Teagasc says, “We can’t rely on research done outside of the country by groups that are either for or against the technology”. Ireland has a lot to gain from probative research like this, but we need to be sure we are acting on the best available evidence. Teagasc is cautiously optimistic about introducing this GM potato crop in the field, stating, “Arising from the preliminary study completed in 2012, we now know that the GM potato variety we are researching has the potential to resist Irish blight strains but much more work is required and this will commence in 2013.”

THE FUTURE OF GMO IN IRELAND

Genetic modification will play an ever-increasing role in the growth and development of Irish agriculture. Ireland is fortunate to have a unique blend of traditional farming experience and a highly-developed scientific sector, allowing us to integrate old and new expertise to our benefit. The ability to skillfully handle GMOs will mean we can find tailor-made solutions to the various challenges facing the Irish agricultural sector. We can only speculate what Mendel would make of these modern advance, but I’d think he’d agree it’s not exactly “easy peasy” work.

REFERENCES

• Radio interview with Dr. Ewen Mullins: http://www.teagasc.ie/news/GMspud1.mp3 
• Blight research article, http://www.teagasc.ie/crops/potatoes/gm.asp