On artificial and synthetic cells

Monday morning Jack Szostak talked about his ongoing work on creating artificial cells, where he is trying to create simple protocells from chemically synthesized material that in their simplest form only contain a membrane and genetic material.

Later in the afternoon Hamilton Smith gave a detailed account of the work by the J. Craig Venter Institute cumulating in the synthetic cell paper published in Science on May 20 (doi:10.1126/science.1190719, fulltext freely available).

Jack Szostak is interested to understand more about the origins of life, and for this is studying the simplest possible forms of living organisms, only containing a membrane and genetic material. A main motivation for his work has been the discovery in the 1980s that RNA is not only encoding genetic information, but can also catalyze chemical reactions inside cells – indicating that RNA might have existed before DNA and proteins. For this work, Jack Szostak and his laboratory have spent a large amount of work studying primitive membranes (e.g. Nature 2008, doi:10.1038/nature07018). Efforts to replicate genetic material using nucleic acids without the help of biologic material so far have not been successful. The work on artificial cells by Jack Szostak and others is fascinating, but extremely complicated (his lab has been working on this since the early 1990s). But we will probably learn a lot about basic biologic processes along the way.
Artificial cells are started from scratch and are completely human-made. In contrast, a synthetic cell is a cell controlled by a chemically synthesized genome and the human-made part is that genome. Hamilton Smith used the analogy from computers to explain the concept of synthetic cells: the genome is the operating system and the cytoplasm is the hardware.
The second genome ever sequenced (in 1995) is from Mycoplasma genitalium, the smallest genome (580 kB) of an organism capable of independent growth in a laboratory. In addition to 485 known coding sequences, M. genitalium contains 100 genes without known function. The synthetic biology group at the J. Craig Venter Institute started synthesizing oligos (later outsourced to several companies) that were then assembled into larger pieces by homologous recombination. It was easy to get to the quarter genome (144 kB), but assembling those last four pieces together proved difficult. The group moved to yeast in which they could assemble the full genome. The next step of transferring the synthetic genome into a receptive bacterial cytoplasm turned out to be very difficult.
After unsuccessfully working on this problem for a few months, Hamilton Smith and his group decided to use faster growing bacteria (M. genitalium has a fairly long doubling time of 16 hours). They switched to the Mycoplasma mycoides genome (1.1 MB) for the donor genome and Mycoplasma capricolum as a recipient. The process used to assemble the genome was the same (oligo synthesis, combination of fragments using homologous recombination, and final synthesis of the full genome in yeast). Hamilton Smith and colleagues then finally succeeded to transfer the synthetic genome into recipient M. capricolum. Along the way they lost three months during the assembly phase because of a single base pair deletion in an essential gene (the chromosomal replication initiator DnaA).
 
The resulting M. genitalium cells were almost indistinguishable from wild-type M. genitalium. Almost indistinguishable because the synthetic cells not only contain a tetracycline resistance to allow for selection, but also have undergone a few genetic changes in the process: 8 single nucleotide changes due to mutations, a 85 bp insertion, and a 777 bp insertion of an E. coli IS1 sequence (E. coli was used during the cloning process). 
 
TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE – James Joyce
In order to distinguish the artificial genome (and to have some fun), the synthetic M. mycoides also contains watermarks, human-readable information using a new DNA code that is biologically neutral. The scientists at the J. Craig Venter Institute encoded 46 names of people involved in the project, an email address (to contact when you cracked the code) and quotes from James Joyce, Richard Feynman and the R. Oppenheimer biography into the genome. As expected, it took less than three weeks for the code to be cracked and the names of researchers and quotes to be revealed (Using Arc to decode Venter’s secret DNA watermark). 

More than HPV: Vaccines against cancer

The late morning in Lindau was a non-stop marathon of medical researchers – first Harald zur Hausen talked about the links between infections and cancer, then Luc Montagnier gave an insight into his research that analyzes DNA under physical as well as biological aspects – venomous tongues may have linked that talk to homeopathy. At last Francoise Barré-Sinoussi talked about the discovery of HIV and how it was faciliated by global translational research.

Concerning the history of the relationship between infections and cancer, Martin has already written a great article a few weeks ago. Professor zur Hausens lecture let the audience awestruck by the Laureate’s quick and clever demonstration of how much cancer can possibly be caused by infections. As such he mentioned of course the papilloma virus (HPV), for whichs role in cervical cancer he was awarded with half the Nobel Prize in 2008 (the other half went to Montagnier/Barré-Sinoussi). But there are several further viruses and bacterias that can be indirect causes to human cancers, as for example helicobacter pylori is linked to gastric cancer, HIV 1 and 2 increase several cancer risks due to weakening the entire immune system, tuberculosis increases the risk of developing a later lung cancer and borrelia burgdorferi is known to increase the risk of b-cell lymphomas. Zur Hausen explained how many of those viruses even introduct oncogenes into their host cells. In some cases even parasites can lead to cancers, as for example schistosoma is associated with bladder cancer – in Egypt the parasite is one of the main causes of this type cancer. Alltoghether zur Hausen estimated that 21 percent of all global cancer incidents are linked to infections – and many of them are preventable.

And zur Hausen also showed another interesting aspect that might lead to new ways to reduce cancer prevalences. In comparing risk factors for early-childhood leukemia, he pointed out that infections during our childhood in general lower the risk of developing such a cancer. However, if a high number of infections occur in the first year of life, the risk of leukemia is increased – supposedly the immune system can’t mature efficiently. This example also explained how children with a higher socioeconomic status are under this aspect disadvantage.

To prevent such infection-induced cancers he suggested to develop further vaccines so that infections can be prevented. Toghether with Prof. Ethel-Michele de Villiers he currently does research on the TT-Virus – a virus that for itself “just” harms the liver but is linked to causing brain tumours as well as promoting autoimmune diseases such as asthmatic conditions and multiple sclerosis.

The past decades have been filled with discoveries of links between cancer and infections. Not only did zur Hausens lecture encourage young medical researchers to focus on vaccines – but it also showed that there are a lot more viruses, bacterias and parasites to explore.

Historical lectures I: Rita Levi-Montalcini

I am one of the lucky people who may attend the Lindau Nobel Laureate Meeting several times. This will be my third time. But there’s a big BUT: The more often I have been, the more sad I am about all the other meetings I have missed. This year, the Lindau meetings celebrate their 60th anniversary and the list of Laureates and lectures is the largest in the history of the meeting. One of the most outstanding persons I have never had chance to listen or even talk to at Lindau is the Grand Dame of Sciences Rita Levi-Montalcini (101).

Miraculously the Lindau colleagues brought some golden treasures from their archives to the public. On their online platform, we can listen to Rita Levi-Montalcini’s lecture from 1993. If I counted correctly, there are currently over 130 lectures available in this online library in form of podcasts and videos (since 2004). I want to mention just a few of them to give you an idea to whom one might listen: Otto Hahn, Werner Heisenberg, Sir Chandrasekhara Raman, William Bragg, Paul Dirac… It is difficult to decide to whom you want to listen first, isn’t it? You want to hear them all!

To help you, I will introduce to you my favourite lectures, beginning with the Grand Dame I adore : Rita Levi-Montalcini. I adore this 101 year-old medical doctor…

  • for her achievements – the Nobel Prize in Physiology or Medicine, which she received in 1986 together with Stanley Cohen for their discoveries of growth factors, especially the nerve growth factor neurotrophin, is just one example;
  • because of her strong will – under Mussolini, she was refused access to the academies due to her status as an ‘non-Aryan’ woman, yet she did not give up and continued her research;
  • because of her commitment to others and much more. I recommend to read this article celebrating her 100th birthday by Nature.
  • And not least I adore her because of this lecture, “The Magna Charta of Duties” in which she reminds humanity to act responsibly.

Levi-Montalcini refers in her presentation to various declarations such as the Stockholm Declaration of the United Nations Conference on the Human Environment and tells the young generation of researchers of their duty to be aware of their responsibility for the survival of mankind and the preservation of the environment. For me, it is a duty to listen to her lecture and to pursue her appeals.

Levi-Montalcini

The Magna Charta of Duties

Rita Levi-Montalcini, 1993 – 43th Meeting of Nobel Laureates

 

Appetizers

38:20 Young people here should be well aware of the importance of science and the necessity of science to go on. We cannot stop it unless we want to kill homo sapiens themselves

23:04 The main thesis is something rather new – that is just for young people: The stipulation of a new moral contract between the older and the younger generations based on the principle of the total equality and not as presently based on a paternalistic or hierarchical system and on a worldwide resolution to uphold this contract in view of the above mentioned obligation.

20:52 Scientists we believe are henceforth obligated to pay a third of their knowledge by sacrificing a portion of their careers in order to make an informative contribution to the public debate on wider issues of our times on which depends the survival of mankind.

100 years infection and cancer

There are many reasons to get excited in anticipation of this year’s Lindau Nobel meeting that is now less than two weeks away. One aspect of the meeting I personally enjoy is the appreciation for the historical perspective of science. One recurring theme of many Nobel laureates in Medicine or Physiology during the last 50 years is the fascinating relationship between infections and cancer, and in fact this year marks the 100th anniversary of one of first important discoveries in the field.

Peyton Rous (Nobel Prize for Physiology or Medicine in 1966) in 1910 described a malignant chicken sarcoma which could be propagated by transplanting its cells, forming new tumors in other chicken. He also showed that these tumors were caused by a virus (the Rous Sarcoma Virus), but it took 15 years of discussions before the scientific community unanimously accepted this connection. In the 1930s Rous discovered that the giant warts (benign tumors of the skin that can progress to cancer) of rabbits in the Southwestern US were caused by papilloma viruses.

It took another 30 years until viruses were found to also cause tumors in man. By the late 1960s the first oncogenes were discovered: part of the genetic material of viruses and able to induce tumors in human cells. David Baltimore, Renato Dulbecco and Howard M. Temin (Nobel Prize for Physiology or Medicine in 1975) studied the mechanisms of how viruses transform normal cells into tumor cells, including the enzyme reverse transcriptase that transcribes the genetic information of RNA viruses into DNA.

Michael Bishop and Harold Varmus (Nobel Prize for Physiology or Medicine in 1989) discovered that most oncogenes are in fact of cellular and not viral origin, acquired by viruses during replication in the host cell. 

BaruchBlumberg (Nobel Prize for Physiology or Medicine in 1976) began working on serum protein polymorphisms and inherited susceptibility to disease in the late 1950s. This work led him to the discovery of the Australia Antigen (now called Hbs Antigen) in 1963 and by 1967 the Hepatitis B virus was isolated. By 1969, blood donors were tested for Hepatitis B virus and rates of post-transfusion hepatitis soon soon decline.

After testing for Hepatitis B virus became available, it became obvious that there is a strong the geographical correlation between chronic Hepatitis B infection and liver cancer. A first vaccine against Hepatitis B virus was approved in 1982, and a decrease in liver cancer was first detected in 1990. Since 2003, vaccination for Hepatitis B is in use worldwide.

Harald zur Hausen (Nobel Prize for Physiology or Medicine in 2008) in the late 1960s started to study the role of the newly discovered Epstein-Barr virus in causing Burkitt’s lymphoma. He showed that Epstein-Barr virus DNA was integrated into the genome of these tumors, rather than causing a chronic infection.

In the mid 1970s he switched to searching for an infectious agent causing cervical cancer. Cervical cancer was long thought to be related to an infection, starting with the observation in 1842 by Rigoni-Stern that this cancer is more common in married women, widows and prostitues than in virgins and nuns. After initially trying to detect herpes simplex virus in cervical cancer tissue, zur Hausen switched to studying human papilloma viruses. In 1983 he and his coworkers successfully isolated HPV-16, and later detected DNA from this virus in half of all cervical cancer biopsies. HPV-18 was isolated in 1984 and in the following years his laboratory studied the mechanisms by which human papilloma viruses induce cervical cancer. A causal relationship between human papilloma viruses and a subset of oral cancers was discovered in 2000. The first vaccine against human papilloma virus infection was approved in 2006 with the expectation to decrease the rate of cervical cancer in the coming decades.

Françoise Barré-Sinoussi and Luc Montagnier received the Nobel Prize for Physiology or Medicine in 2008 for their work on the human immunodeficiency virus that is causing the aquired immundeficency syndrome (AIDS). Patients with AIDS have a dramatically increased risk to develop lymphomas associated with Epstein-Barr virus infection. The rare tumor Kaposi sarcoma is also much more common in AIDS patients, but it soon became clear that it is not HIV itself that is causing the tumor – no HIV proviral DNA was detected in Kaposi sarcoma samples, and the risk for Kaposi sarcoma was not the same for every HIV-infected person. This led to the search for another infectious agent, and in 1994 Kaposi-sarcoma associated herpesvirus was discovered by Yuan Chang, Patrick Moore and colleagues. This virus is required for Kaposi sarcoma to develop, and is also responsible for two other rare cancers.

The pathologist Robin Warren was studying gastritis-causing bacteria in the late 1970s, and in 1981 was joined by the gastroenterologist Barry Marshall (shared Nobel Prize for Physiology or Medicine in 2005). Their work not only showed that the bacterium Helicobacter pylori is involved in most cases of gastritis and peptic ulcer, but also that chronic H. pylori infection increases the risk of gastric cancer and lymphoma of the stomach. This makes H. pylori one of the few infectious agents that are not viruses to be implicated in causing tumors in man.