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Blog
Welcome to the iGEM Lund blog. Here we will post articles and other texts and media. Happy reading! Stay tuned!
2019-05-07
Synthetic Biology, The era for Engineers
Biology and its subcategories have long been an area of research dominated by theoreticians and empirical research. Darwin’s vast collection of species and Mendel’s sharp and delicate experimental technique revolutionized our understanding of biology and life itself, but how can we harvest the fruit of that knowledge? How do we innovate, develop and evolve beyond nature's own interest? Synthetic biology is the answer.
The groundbreaking discovery of the gene; the unit of ancestry, evolution, and life itself, resulted in a paradigm shift like no other. This revelation was not realized in a day but was puzzled together piece by piece for nearly a century. Even though rumbling murmurs and whispers regarding the origin of life had been around for centuries, perhaps even millennia, the idea which resulted in awe was first conceived in the middle of the 19th century. It was by Charles Darwin who established the theory of evolution and Gregor Mendel who endorsed the idea of a unit of ancestry. Together, they laid the groundwork for what came to be known as the genomic era.
In the 1950s the astonishing structure of DNA, the double-helix, was imprinted on everyone's mind. Consisting only of four nucleotides, A, T, C, and G, but able to generate the diversity of life we acknowledge on earth today. These delicate coding sequences of nucleotides come together to form genes, and enough genes come together to form a genome - the recipe for an entire organism. The recipe is transcribed and translated to form proteins and ultimately a unified organism with a specific phenotype. This recipe is, however, prone to changes. As the sequences are copied, base by base, mutations are bound to occur - nature isn’t perfect. Changes are often devastating for life however, on extremely rare occasions they improve the survivability of their hosts. An antelope may run faster or a tiger may pounce more powerfully. Thus life constantly evolves for the better, it’s a constant arms race for the survival of the fittest.
The mesmerizing structure of DNA. First described by Franklin, Watson and Crick.
Researches soon realised the power of controlling evolution. What if we could read, cut and paste genes to eliminate genetic diseases or become even stronger, smarter and faster? These questions are what fueled the following 50 years of genomics. Reading, cutting and pasting was hastily achieved and the cost of such interventions has rapidly decreased since. New techniques enable faster and simpler methods of gene-editing and the area of genomics soon became approachable by members of other sciences. As engineers began adjusting to the tools of gene-editing they soon embarked on the journey towards engineering life. Genetic engineering and synthetic biology were born.
Synthetic biology is an area of research where engineering and biology are intertwined to alter existing life forms or biological organisms with the intention to solve problems or overcome obstacles. Doing so, genetic engineering plays a vital role, enabling for easy manipulation of the genome. Since engineers entered the playing field, standardized methods and parts have been created. This way, a universal language spoken amongst synthetic biologists allow for global cooperation and understanding.
Contemporary innovations in synthetic biology are strictly regulated by laws and directives from various organizations. After all, one hiccup could be devastating for life on earth as we know it. However, these constricting regulations are causing slow and limited progress, hindering the development of new radical improvements in the field. Many researchers argue that the laws are too strict and therefore cause more harm than good. Hopefully, we’ll soon see a consensus amongst scientists and the society regarding genetic engineering.
Many organizations focus on spreading awareness and an understanding of the processes that encompass engineering life in hopes to lessen the public's fear of the research. Transparency is achieved beautifully within the scientific community, albeit transparency is often disregarded when it comes to the public. Research is often communicated using a difficult lingo, excluding the layman from the conversation. This flaw should be regarded as a sin, as science should be readily available for everyone. The concept of clarity across professions is valuable for engineers as they often work cross-professionally. The scientific competition iGEM (international Genetically Engineered Machine) embodies this concept, having all of the research open-source and available for everyone.
iGEM is a competition for university students within the field of synthetic biology. The competition began in 2003, founded and hosted by MIT (Massachusetts Institute of Technology). However, it quickly outgrew MIT and became an independent organisation. In 2018 340 teams from 42 countries competed in Boston with 340 vastly different projects. Detecting doping agents in athletes, cleaning waters from antibiotics and building fungal tents on Mars, everything is showcased in iGEM.
Us at the Lunds University iGEM team 2019 will be engineering a probiotic bacteria to bioaccumulate heavy metals. We’re going beyond what nature evolved these bacteria to handle, so that they can be used for more acute toxicities which endanger our health. To do so, we are using the same concepts conceived in the genomic era, but applying a methodology familiar to engineers. Our result will be a synthetic lifeform, unbeknownst to man up until now. We’re not playing God, we’re merely practicing engineering.
2019-05-01
A Brief History: Probiotics
Probiotics, an emerging field of medicine, has been praised and condemned by both experts and the public. It concerns the microorganisms interacting with you, their host, and the possible health benefits they may provide for you. As new research looms, we’re more and more certain that microbes cooperate with us in several ways. Perhaps we are the ones cooperating with them. After all, they were here before us.
The host-microbe interaction was first discovered by Antonie van Leeuwenhoek, a 17th-century working-man from Delft. Van Leeuwenhoek's meticulous artistry enabled him to produce refined lenses, allowing for the observation of microbes. Doing so, a whole new world opened up for the scientific community at the time. Biologist who had only been interested in the macro and comparatively colossal world of mammals and insects were now delving into the world of the miniscule. This was the beginning of the microbial era.
Symbiotic Evolution
The common viewpoint has long been that the microbes have adapted to us. We developed an intestinal tract and they inhabited it. However, this anthropocentric assumption can easily be rebutted by applying the simple statement: they were here before us. It would then seem illogical and unsatisfactory to believe that we developed an intestinal tract and they inhabited it. Instead, it would now seem obvious that a symbiotic and interdependent relationship developed and perhaps even with the microbes in the lead, we constructed an intestinal tract for them to inhabit. We evolved symbiotically.
This revolutionary understanding altered our perception of microbes. It would now seem inevitable that they influence us to an extent previously unimaginable. Richard Dawkins famously applied the following analogy to the relationship between genes and organisms in his book The Selfish Gene:
“We are survival machines — robot vehicles blindly programmed to preserve the selfish molecules known as genes”.
Perhaps, a similar analogy could be applied to the relationship between microbes and its host.
What do gut bacteria do?
Microbes have a wide variety of effects on its host. Some effects have even proven to be structural, aiding the development of organs. Others assist our metabolism or even protect us from pathogens. New research introduces the concept of microbes affecting our nervous system - ultimately altering our state of mind. Studies on the topic are constantly emerging and microbes will prove to interact with us in ways previously inconceivable.
Euprymna scolopes has an organ which growth is dependent on the presence of a special luminous bacteria. The organ illuminates the squids bottom, confusing predators on the hunt. Photo: Chris Frazee and Margaret McFall-Ngai
Today's market of probiotics
The main focus of the probiotic market is currently on gut flora. Having a poor gut microbiome entails health issues such as poor digestion, poor metabolism, an increased risk of heart disease and many more. Improving your gut microbiome would therefore prove extremely beneficial for your health, something companies quickly realised. What they didn’t realise was the complexity and intricacy of the several millions of interactions our microbiome has. This ultimately led to the demise of the reputation of probiotics as many of the promised effects were barely noticeable or even non-existent.
New companies focus on research-based formulas in a means to salvage the reputation of probiotics. As more research emerges, it seems clear to us that an unhealthy microbiome is a contributor to many diseases which prove detrimental for our health. Therefore, supplementing, altering or modifying the microbiome for the better could be a key factor in treating many of those diseases in a sustainable and effective way. Using solutions brought on by nature itself is often proven to be the most viable alternative, however, slight modifications for the better could improve on nature’s own system even more.
Our focus
iGEM Lund is a research team focusing on using synthetic biology to modify a probiotic bacteria to surpass natures innate abilities, something we’re very excited about.