ZZZZZZZZZZZZZ watch out, genetic modified mosquitoes!

Hello again,

Having my expected number of posts, I did not have the intention of posting another synthetic biology fact, but wandering around the web I stumbled upon an interesting tidbit I definitely wanted to share with you guys! It is as the header already introduced about the genetic modified mosquito. I will shorten it to GMM in this review. These GMM are created by a company in the UK, namely Oxitec. Oxitec is a research company that tries to control different kinds of pests on a sustainable way. The GMM is one of them. All their research subjects can be found on their site: http://www.oxitec.com/

How do they try to control the little stingers? The technique on which it is based is called RIDL®, which stands for Release of Insects with Dominant Lethality. Shortly explained, they use advanced genetics to introduce a lethal gene into the genome of the mosquitoes’ larvae. The gene is passed on to the GMMs offspring. So, by releasing the male GMMs, make good use of their natural instincts to reproduce, they will mate with wild females and their offspring will inherit the lethality gene. This will result the offspring to die before reaching adulthood and therefore declining the total population of mosquitoes.

Now, where does this come in handy? Diseases like malaria or dengue fever are only transmitted through certain types of mosquitoes. Where malaria gets spread by a number of types of mosquitoes, dengue fever only gets spread by two types of mosquitoes, namely Aedes aegypti and Aedes albopictus. To use the RIDL technique, only two types of GMMs need to be created to control the population of these disease transmitters. So, with no vaccine or cure available for dengue fever, the disease can only be controlled by controlling the mosquito that spreads it. Present methods of mosquito control include spraying or fogging of chemical pesticides. These methods however have failed to stop the spread of the disease. That’s partly because the mosquitoes have developed resistance for the pesticides, but also because the mosquitoes live in and around human habitation so it can be very difficult to reach. The chemical pesticides are not really specific, so, they affect other insects as well. Not very sustainable is it?

Franken-meat, it’s “alive”!!

Hello again,

To stay into the meat-business, I found an interesting development. Can you imagine a hamburger that looks like any other burger, but is not made out of natural meat? Let me introduce to you, the synthetic hamburger!!

 

The man holding the burger is Doctor Mark Post of the University of Maastricht. Dr Post’s team developed this first synthetic hamburger out of cow stem cells. To produce such a (hopefully) tasty burger, stem cells are taken out of a living cow and cultured in a nutrient rich medium in order to produce small strands of muscle tissue. For a burger of approximately 150grams, about 20 000 of these small strands are needed. Together with some seasoning and breadcrumbs a hamburger is created. For now such a burger is not yet commercially viable. It costs around €300,000 to make one, not directly something the bigger crowd can afford.. To speak of synthetic meat in your supermarket is thus way too early. Now, the focus has to lie on scaling the process up on making such a ‘Franken-burger’. By this way, the costs can be reduced and will allow for such a burger to be affordable.

So, what are the advantages of this synthetic meat? First of all, livestock and byproducts produce billions of tons of greenhouse gasses, which contribute more than 50% of the annual emissions of it. This livestock also needs land to feed. So, a lot of precious farmland is used up on feeding these massive herds of livestock. Studies also showed that present farming methods will not be able to satisfy future demands. The growing hunger for meat in the ‘less’ developed regions cannot get satisfied. So, the livestock should get bigger and will use up even more good farmland and so on… This could all be limited by the lab grown meat. Of course it will need its supplies of nutrition, but it would be in a controlled way and the emission of greenhouse gasses would be reduced drastically.

Some people say that it would be a good alternative for vegetarians to have some meat. They can put their principles aside, because there wasn’t a cow murdered in the process of making such a burger. So, with that principle gone, why not have a juicy burger? Why stop at a hamburger? With stem cell technology everything is possible. Perhaps a tasty panda-burger, lion-steak or even a crocodile-chop? Put your feet under the table and enjoy your meal!  

The expired food snitch!

Hello faithful followers!

My latest posts were less synthetic biology oriented, although replacing DNA from one cell into another is some serious unnatural interference of the genetics! So, in the broad sense of the topic I find it is still relevant. For my new post, I let my light shine on the iGem competition. iGem stands for international genetically engineered machine and is a worldwide synthetic biology competition. A lot of interesting researches can be found on the site: https://www.igem.org/Main_Page.

 

Contestants at the University of Groningen won the 2012 edition with their ‘Food Warden’. (http://2012.igem.org/Team:Groningen) The food warden is an indication technique by which meat spoilage can be detected. They use the bacteria, Bacillus subtilis, as detector. This bacterium has natural genetic responses on volatiles from meat. The researchers linked a pigment production system to this natural response in order for the bacteria to change color when in contact with the rotten volatiles. So, instead of dates of the shelf life on the packaging they want these engineered bacteria to be indicators of the spoilage inside the package. I hear you thinking, I would not want these bacteria close to my nice juicy piece of meat. This is of course not the case. They use what they call ‘stickers’ (see picture), small plastic containers in which the bacteria are contained where the bacteria cannot escape from, but where the rotten volatiles can enter easily. If the meat has rotten, the plastic ‘bag’ will color purple, which is an indication that you better no longer consume it.

In a world where every year more than a billion ton of food is thrown away, the thoughts behind this research is that it could reduce this garbage load. A lot of food is thrown away because of inaccurate date stamps. This ‘sticker’ could give a live indication of how the meat quality is at that time. I find it not hard to believe that this research won the contest at 2012. It is a very promising technique that could easily be implemented in production systems. Of course, just date stamping packages will cost less than implementing such a ‘sticker’. I don’t know if it would be economically feasible. I do not think people would like to pay more for a live indicator ‘sticker’ when there is not a problem with the date stamps as it is now. So, although I really find this a good technique, it is probably yet again one to put into the fridge.. Don’t you think?

Three-Way Baby ??!!

Hello again,

I do not know why, but I happen to discover new techniques in having babies over and over again.. Hello, biological clock, is that you? But, this new technique really blows my mind, it is a three-way baby! It is called the 3-person embryo technique, developed by a group of researchers lead by Mitalipov, at Oregon Health & Science University of Portland.

So, the thoughts behind this research is that when women, who have some kind of mitochondrial disease. First, a brief explanation about mitochondria. Mitochondria are small energy-producing organelles that can be found in the plasma of the cell. These mitochondria have their mitochondrial DNA, mtDNA, by which they can duplicate and make their own proteins. Mitochondria can therefore not be built by the cell itself but is responsible for its own reproduction. So, unlike most DNA, that is located in the cell nucleus, mtDNA is only passed on by the mother and not by the fathers’ side. When the future mother has a deficit in her mitochondrial DNA, the baby is going to inherit it in all cases!

 

(http://www.dailymail.co.uk/health/article-1266000/Designer-baby-parents-hereditary-diseases-ready-years.html)

The 3-person embryo technique gives a solution in this case. The nucleus DNA of a healthy female donor egg is replaced by the nucleus DNA of the future mother. This way, after fertilization, the resulting child would inherit the mother’s nucleus DNA, with the features like hair color and height, and the donor’s healthy mitochondrial DNA (see figure). This is just amazing! So, of course there are still some ethical and legally hurdles that need to be taken, but I think this technique is really awesome for people who would like to have their own kids and have this condition. Performing this technique, five monkeys were already successfully produced. The next step is implementing in people. But first of course some heavy testing!

With all these new development in having children, it is for future parents almost unwise to not first test if you got some increased risk for certain diseases. Because who does not want a healthy kid? Now of course the ethical questions rise, but with future generations the ‘conservativeness’ of mankind will degenerate what makes that these techniques I just mentioned in my posts will become ubiquitous! What do you think? Will future generations hold less value against real natural process? Will they/we hold the same grudges against progress in this field? I, myself think this won’t be the case. Future generations will grow up with this progress and find it hard to believe that we used to hold these technologies back. Like we already think, I could not imagine a world without a mobile phone? We now even have mobile computers in our pockets. This technological evolution is unstoppable as the synthetic biology will be unstoppable as well. 

PGD – The screening of embryos for the restriction of genetic disorders

Hi everybody,

As a follow up on my latest post, because I got really interested about this screening for boy/girl and genetic disorder/healthy baby procedure, I started an internet search. The method in which this technique is bundled is called PGD. This stands for Pre-implantation Genetic diagnosis. As mentioned in my previous post, this is only legal for couples with an increased chance of passing on genetic disorders.

http://www.gezondheid.be/index.cfm?fuseaction=art&art_id=3017

So what is PGD exactly? PGD is only applicable via IVF (In Vitro Fertilization). In a first step, the ovaries get stimulated by use of hormones and eggcells are harvested. Then this eggcel gets fertilized with the donor semen. The zygote starts to divide and after 60 to 72 hours the embryo consists of about 8 daughtercells. Then, one to two cells are removed to analyze the embryos. After genetic analysis de ‘healthy’ embryos are placed in the mother’s womb.

Now, what are actually possible conditions on which the embryos can be screened? First of all, PGD is only applied when in advance is known for which disorder an increased risk is present. And there is only screened for these possible disorders! Possible disorders are certain gender related disorders like hemophilia, syndrome of Duchenne and others.. Here, there only has to be looked of the embryo will turn out to be a boy or a girl. Other, not gender related genetic disorders are also possible, like the disease of Huntington. With these non-gender related PGD-screening, the semen gets screened and the one that do not contain the disorder are injected directly in an eggcell.

This is not really synthetic biology related, but it was something I got interested in. I hope you picked up something about it! I think it is handy to know that this kind of technique is already available. It is in the child’s best interest that it does not have to live with such life degrading conditions. Life should be enjoyable for both the child and the parents. But do not understand me wrong, I too think that it should only be applied in serious cases.

To end with a synthetic biology note:  I do not think it is unimaginable that with IVF techniques it can be an easy way in controlling the outcome of the baby. When you can adjust some genes in both the eggcell and the semen, the engineered infant is closer by than you know, don’t you think?

The better baby! How much would you want to tinker with your offspring?

Hello again!

Recently, I read an interesting article in the scientific magazine ‘Quest’(November 2013, 117) which subject was the designbaby.

 

Talking about a designbaby, everybody would like to have the perfect child is it not? Who would not want a perfectly healthy, genius kid with blue (or like myself: green) eyes? How would it proceed? A little swimmer, the spermatozoid, fertilizes an eggcel in a test tube.  Geneticists remove the unhealthy genes and replace them with the healthy ones and meanwhile tinker some on the intelligence and look. Then put this ‘superzygote’ in to the mother’s womb and nine months later… Tadaaaaa, there he is, the perfect baby! Scientific progress on this matter however is not even in its infancy. Currently, techniques are being developed by which the genes of an embryo can be entirely seen. So, when the techniques of overlooking the embryo’s genome is not yet entirely available, one does not even dare speaking of the possibility of remodelling the genome as if it was nothing. Nevertheless, with the progress researchers make, it is not unwise to already have some thoughts about it! If this was possible, would you dare to make use of this technique? Will people still recognize their own child? Is it not in our instinct that we would like to pass on our own genes to our offspring? Like maybe one is not that smart or handsome, but at least the baby is theirs. Or you rather don’t want your child to have your big nose or flappy ears? Another thought, with the adaptation on the baby appearances, will visitors still say: Ooooooh he has your eyes/nose/chin. Or rather say well that was not the best geneticist that you hired, what a shrivelled little guy!

Food for thoughts is it not?

LUMINESCENT PLANTS –> STEP FORWARD TO A SUSTAINABLE FUTURE

Hello everybody,

It has been a while since my latest post, but here I am again with some new discoveries in the field of synthetic biology. Are you sick and tired of your high energy bill? Do you hate driving on non-illuminated roads? Or you just cannot appreciate the design or view of a lamp or lighting post? I present to you the glowing plant!

 

A couple of years ago, Taiwanese scientists were able to implant glowing gold nanoparticles into an aquatic plant. These glowing particles were called bio-LEDS. The whole idea about this research was to develop glowing trees! Can you imagine driving down a road illuminated by trees? Not only would this be saving a huge amount of electricity, it would certainly help the greening of industrialized cities! We are off course not there yet.

Now for a closer by future, I found some good guy scientists that are open source researchers. This means they share every discovery in order to develop a new sustainable energy source. They are making the glowing plant. Say goodbye to your bedside nightlight and see hello to the bedside luminescent plant! In order to achieve this plant they use an iterative design-print-transform cycle. First step is sequencing DNA using specific software. Than the DNA is made using a new technique called DNA laser printing (for more info on this technology visit: http://cambriangenomics.com/) and after collecting the DNA, the gene gun (still loving it!) cares for the insertion of the DNA in the plant. This process is iterated to get a brighter plant.

A lot of questions pop up in my head about this technology. Will we be able to turn this plant off? I hate sleeping with light. Will it survive long enough? The illumination is very energy consuming for the plant I guess. Will it be still decomposable? Can you think of some extra concerns on this topic?

All in all, I think this field should be intensively explored. If these bio-lamps could replace the present bulbs and street lights I would sign for it immediately! When you have the knowledge that lighting nowadays produces as much CO2 as cars it would be a tremendous step forward in reducing our environmental impact and one step closer to a sustainable future.

SYNTHETIC BIOLOGY REINVENTED

Here I am again with some interesting new study I found!

Since my last post I encountered some new truly interesting research in a science magazine. It refers to a implementing synthetic biology on a whole new level. To fully understand this new concept, I will first repeat some basic biological knowledge so the clouds in your mind will vanish.

As I already showed in my second post (DNA EXPLORATION), proteins are coded in the DNA in specific regions, called the genes. The genes are built of sequences of bases and it is the sequence of these bases that hold the genetic code. There are four bases in the DNA, namely thymidine, cytosine, guanine and adenine. The collection of three following bases is called a codon and eventually will stand for one amino acid, which is a building block of proteins. Going from DNA towards proteins does not happen directly. First, the coding sequence for a protein is transcripted from DNA to mRNA (messenger RNA) and further by attaching ribosomes it is translated into a protein. This translation happens under influence of tRNA (transport RNA) that holds the complementary codon, the anti-codon, and the corresponding amino acid.

RNA is a homologue molecule of DNA in which thymidine is switched by uracil. So, thymidine is a base that only occurs in DNA and uracil is only present in RNA. When DNA is transcripted towards mRNA, the base thymidine gets exchanged with uracil. The corresponding RNA-codons will eventually get translated to amino acids and proteins.

The protein synthesis stops when a STOP-codon appears, by which the protein is released from the ribosome. There are 3 STOP-codons, namely the combination of bases, UAA, UAG and UGA. When we look at the possible codons and the available amino acid, it is notable that different codons encode the same amino acid. On how many ways can a codon exist? It is a simple statistical calculation. There are 3 places with 4 possibilities on each place: 4³ or 64 ways! There are only 20 amino acids available for translation. This means with the 3 STOP-codons, there are still a lot of codons that  encode the same amino acid.

Researchers have now succeeded to recode this natural way of protein synthesis. They remade a whole genome of E. coli and replaced every UAG STOP-codon with its equivalent UAA and they also deleted the instructions for making the release factor, that usually binds UAG to release the protein from the ribosome. With these changes UAG becomes meaningless.

Now that UAG holds no real function, the next step was to assign a new meaning to UAG during the protein production. The design stage of this new approach is off course not to held lightly. tRNAs with accompanying enzymes that would attach unnatural amino acids had to be created and brought inside the cells. UAG was reintroduced on specific places and now the unnatural amino acids could be built into proteins at will. By recoding this little piece of information a whole new world of chemical diversity of proteins can be entered.

For example, artificial amino acids could be added that give proteins unusual properties, such as the ability to bind to metals. This would result in novel ways of binding heavy metals in the environment, or in the development of new adhesives or dye. In pharmaceuticals, enzymes could be developed with specific binding places for malignant cells.

The introduction of these man-made proteins is obviously a fundamental step forward. It is even expandable, because so much of the genetic code is redundant (more codons encode the same amino acid) there might be other codons that could be reassigned. The possibilities with this new approach are unlimited once multiple codons can be recoded to translate into alien amino acids.

You might think, hey where is the catch with these GRO’s (genetically recoded organisms). Do they hold any threat towards the environment or healthcare? On first notice it is unlikely, the new created GRO’s even hold resistance towards viruses. Because when this virus uses the UAG stop codon, this can no longer be read. Too bad little virus, your days are over! Even an accidental release of these GRO’s holds no threat. When in contact with wild-type organisms, the recoded stop codons will be read as normal stop codons in natural cells, terminating the protein synthesis prematurely.

So, what would you say on this matter? Are these GRO’s innocent? Will they be harmless and stay harmless? Or would you say innocent until proven guilty? It is your choice!

SYNTHETIC BIOLOGY PEEKABOO

Here I am again!

To not get ahead of myself (dixit previous post, final movie) let us start with the beginning of the synthetic biology. They didn’t just made a whole genome out of nothing and inserted it in a micro-organism. The first big breakthrough for synthetic biology was the discovery of restriction-enzymes.  These little fellows were able to cut DNA into fragments on specific locations in the code. Now they were able to extract genes out of DNA that, in turn,  opened perspective towards synthetic biology.

A very nice feature of micro-organisms are their ability to multiply at a very high rate. When we would like to produce certain interesting proteins, they can be built in a, for example, yeast and let that yeast grow in a very rich media. Afterwards the protein can be extracted from the yeast and purified.

How can these DNA-fragments be put inside a host? There are different ways on solving that problem. A first way is to take DNA-fragments and insert them in a plasmid. A plasmid is a ring-shaped DNA molecule that occurs in some unicellular organisms and can be exchanged in between mutual bacteria or even different family of bacteria. By cutting these plasmids with the same restriction-enzymes, new DNA-fragments can be built inside the plasmid. By bringing these plasmids in a host-cell you can introduce new features inside the host.

 

The plasmids always has a unique marker that can identify a cell that was successfully transfected. In most cases this marker is an antibiotic resistance so the organism could grow in a growth medium that contained that antibiotic.

Another way is by bringing in the big guns! Say hello to my little friend!

 

They literally shoot some golden bullets, with plasmid DNA-fragments on, in the cell. This technique is referred to as bio-ballistics or as gene gun. It is often used in plant cell synthetic biology. A schematic overview will give some insight in the technique!

Now we know how a gene can be brought inside a cell and can be identified. Time to share the first real product made by this protocol. I am talking about the production of Insulin. In the late seventies, a synthetic version of the human insulin gene was brought in the bacteria Escherichia coli. Diabetics who have a dysfunction of the insulin production rely on insulin that they can inject when there blood level of sugar swings through the roof. With this new technique there was an easy way of producing insulin for the diabetics.

Since this initial success, the application of synthetic biology in human medicine has taken a phenomenal flight! Nowadays one can no longer imagine medicinal science without the use of synthetic organisms.

Synthetic biology seeks to apply the principles of engineering to the practice of biology. Therefore they try to develop biological systems, even entire organisms, that maybe cannot be found in nature and with the sole purpose to serve humane needs. With the constant evolution in biological knowledge and creation of new techniques, the goal of making synthetic organisms is step by step coming closer. However, getting there also rises ethical questions and issues.

Will these synthetic organisms cause severe danger to our public health? Won’t they contaminate our environment? Don’t forget our human nature to try to make weapons out of everything.. What do you think will happen when all life processes were known and people could build any type of organism? Ready to live like this?

Time for some self-reflection!

DNA exploration!

As Francis Crick and James Watson mentioned when walking into their local pub: “We have found the secret of life”, they were not even exaggerating. We can subscribe DNA as a large double stranded polymer of a carbohydrate, called ribose, on which every time one of four bases is connected. These four bases are adenine, thymine, cytosine and guanine. It is the sequence of this bases that hold the information of all life processes. A codon is composed out of three bases and it is the sequence of this codons that are translated into amino acids, which are on their turn the building blocks of proteins. Proteins can be found all over the body and have all different types of functions on which life depends. So, It is the transcription and then the translation of this code on DNA that forms the cells necessary proteins.

As a nice picture always tells more than a thousand words let me show you one!

Figure 1: Structure of DNA (http://katienelson4b.edublogs.org/tag/nucleotide/)

Also for the translation of the code, following link says a lot! Feel free to take a look!

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter3/animation__how_translation_works.html

As can be deduced from this animation, if you understand the code and can sequence the DNA you have the power to build organisms at your will, with the functions you desire! With the non-stop evolution of human knowledge on this subject, a lot of proteins have been sequenced and with reversed transcriptions it is easy to find out the corresponding DNA-sequence.

Now it is the job of synthetic biologists to try to make these DNA-fractions and built it in the organisms to get specific features. Is it you would like to synthetize a metal eating, garbage loving specimen or maybe a highly alcohol persistent yeast which can produce a higher amount of alcohol. Anything is possible once you can find a way to create the right genetic code.
In the following movie scientist reveal their scientific breakthrough of the first self-regenerating synthetic cell.