Scientists Create Simple Artificial ‘Cell’ Capable Of Spontaneous Movement

photo credit: Vesicle shapes created through osmosis. Image credit: Christoph Hohmann, Nano Initiative Munich

The cells that make up all living things are in constant interaction with their environment. Most cells perform complex chemical processes to ensure the cell and the organism remain healthy. Scientists have not yet been able to replicate a fully-functional synthetic cell, but it now appears they are off to a good start. A team of biophysicists have developed basic artificial vesicles capable of changing shape and moving spontaneously. 

The vesicles created in this study will be used in future design of increasingly-complex artificial cellular structures, capable of interacting with the environment and carrying out the same processes as a natural biological cell. The research was led by Andreas Bausch from Technische Universität München, and the paper appeared on the cover of Science.

Bausch’s team went back to the basics of cell biology and used biomolecules to build the most fundamental cellular structures from the protein level up. A rudimentary cytoskeleton was constructed by adding tiny tube-shaped polymers called microtubules inside the lipid bilayer membrane that served as the vesicle’s casing. Proteins called kinesins were also added to push along the microtubules, providing movement. Kinesins require coenzyme adenosine triphosphate (ATP) to function, which was added as a source of fuel.

Within the vesicle, the microtubules formed a constantly moving flat layer of liquid crystal. Liquid crystal is a state of matter that is neither liquid nor solid, yet has properties similar to both states. 

"One can picture the liquid crystal layer as tree logs drifting on the surface of a lake," lead author Felix Keber said in a press release. "When it becomes too congested, they line up in parallel but can still drift alongside each other.”

As the 2D arrangement of the microtubule liquid crystals are trying to completely line a 3D spheroid, it cannot be done flawlessly. Think of it like trying to gift wrap a basketball. The paper can pressed mostly flat, but eventually there will be unavoidable creases and faults. The faults within the microtubules caused some to be packed in a different orientation to fit in. 

The microtubule faults had not impacted the shape or integrity of the vesicle under normal circumstances, but that changed when the vesicles were subjected to different environmental conditions. As water was extracted from the vesicle due to osmosis, the bilayer membrane deflated. Movement from the microtubules in the faults caused the sagging membrane to adopt new shapes, including some with spike-like protrusions.

"With our synthetic biomolecular model we have created a novel option for developing minimal cell models," Bausch states. "It is ideally suited to increasing the complexity in a modular fashion in order to reconstruct cellular processes like cell migration or cell division in a controlled manner. That the artificially created system can be comprehensively described from a physical perspective gives us hope that in the next steps we will also be able to uncover the basic principles behind the manifold cell deformations."

ORIGINAL: IFLScience

by Lisa Winter

September 5, 2014

Watch Proteins Do the Jitterbug

Photo

THE CROWDED CELL A jumble of proteins inside the cell, visualized in a scientific animation.Credit Harvard University, XVIVO Scientific Animation

If you could shrink down to the size of a molecule and fly into a cell, what would you see?

In 2006, a team of scientists and illustrators offered a gorgeous answer in the form of a three-minute video called “The Inner Life of the Cell.” Nothing quite like it had ever been made before, and it proved to be a huge hit, broadcast by museums, universities and television programs around the world.

The video was a collaboration between BioVisions, a scientific visualization program at Harvard’s department of molecular and cellular biology, and Xvivo, a scientific animation company in Connecticut.

Delving into the scientific literature, the scientists and animators created a video about an immune cell. The cell rolls along the interior wall of a blood vessel until it detects signs of inflammation from a nearby infection

The Inner Life of the Cell Video by XVIVO Scientific Animation

We dive into the cell to see what happens next. Molecules swim through the cell like dolphins, relaying the signal from the outside. Certain genes switch on, and the cell makes new proteins that are put into a blob called a vesicle. An oxlike protein called kinesin hauls the vesicle across the cell, walking along a molecular cable.

Once the vesicle reaches its destination, it releases its cargo. The new proteins cause the immune cell to stop rolling, and it flattens out and slips between the cells that make up the blood vessel wall so that it can seek out the infection.

“The Inner Life of the Cell” was made possible by advances on many scientific fronts.

In recent years, scientists have learned a great deal about the shapes of biological molecules, for example. They can use powerful computers to visualize the molecules in action.

GOING SMALL A dense tangle of neurons, or nerve cells.CreditHarvard University, XVIVO Scientific Animation

The video was so entrancing that it was easy to forget that it was not raw footage captured by some microscopic GoPro camera. It was a piece of art. The scientists and animators made choices about what to show, and how to show it.

For one thing, they left out just about all the proteins, giving the cell the look of a nearly empty ocean. “The interior of a cell is incredibly crowded,” said Michael Astrachan, the president and creative director of Xvivo.

Alain Viel, the director of undergraduate research at Harvard and a member of the BioVisions team, likened the inside of a cell to a rush-hour subway platform. “If there’s a big crowd in front of you, there’s a good chance you might not even see the train,” he said.

Dr. Viel and his colleagues also chose to show the proteins moving with a stately grace. Real proteins, by contrast, are perpetually quivering. They pick up bits of energy from water molecules that bump into them, and they crash into other proteins and bounce off cell membranes.

AND EVEN SMALLERA synaptic vesicle, a kind of small molecular pouch that transports neurotransmitters inside a neuron.CreditHarvard University, XVIVO Scientific Animation

Two years ago, BioVisions and Xvivo set out to upgrade their animations by capturing some of that messy complexity. They wanted to cram a virtual cell with proteins at a more realistic density, and then have them jitter and collide.

It turned out to be an enormous amount of work. The motion and appearance of each molecule had to be individually calculated, leading to a vast amount of data that put a strain on Xvivo’s computers.

Along with the scientific effort, the new video required aesthetic work. To allow viewers to distinguish among many kinds of molecules, the Xvivo animators had to search for the right scheme of colors and shadings.

Rec”:Continue reading the main story Inner Life of a Cell | Protein Packing Video by  Scientific Animationently they unveiled the result of their efforts in a video called “Protein PackingXVIVO

In this movie, we enter a neuron by diving through a channel on its surface. Once inside, we’re instantly surrounded by a swarm of molecules. We push through the crowd until we reach a proteasome, a barrel-shaped molecule that shreds damaged proteins so their components can be used to make new proteins.

Once more we see a vesicle being hauled by kinesin. But in this version, the kinesin doesn’t look like a molecule out for a stroll. Its movements are barely constrained randomness.

Every now and then, a tiny molecule loaded with fuel binds to one of the kinesin “feet.” It delivers a jolt of energy, causing that foot to leap off the molecular cable and flail wildly, pulling hard on the foot that’s still anchored. Eventually, the gyrating foot stumbles into contact again with the cable, locking on once more — and advancing the vesicle a tiny step forward.

This updated movie offers a better way to picture our most intricate inner workings. For one thing, it helps us to understand why we become sick. A number of diseases, such as Alzheimer’s and Parkinson’s, are caused when defective proteins clamp onto other proteins, creating toxic clumps.

In the 2006 version of the animation, it’s hard to imagine how two proteins in such a careful dance would bump into each other. In the new version, where proteins jostle past one another like commuters in a busy train station, it’s common sense.

The new movie helps us understand biology at a deeper level, too. In the 2006 version, we can’t help seeing intention in the smooth movements of the molecules; it’s as if they’re trying to get from one place to another. In reality, however, the parts of our cells don’t operate with the precise movements of the springs and gears of a clock. They flail blindly in the crowd. Our cells work almost in spite of themselves.

“I want people to say, ‘I can’t believe this is happening at all,'” said Mr. Astrachan.

ORIGINAL: NYTimes

Carl Zimmer

April 10, 2014

A Challenge to the Supremacy of DNA as the Genetic Material

About a month ago, a news release stood out among the many I get every day: “A challenge to the genetic interpretation of biology,” from a physicist and chemist from Finland, Arto Annila and Keith Baverstock. They’d just published “Genes without prominence: a reappraisal of the foundations of biology,” in the Journal of the Royal Society Interface.

One sentence from the news release grabbed me: “The result is evolution from simpler to more complex and diverse organisms in both form and function, without the need to invoke genes.” Instead, Drs. Annila and Baverstock invoke thermodynamics.

I was mesmerized, mostly because I am immersed in writing the 11th edition of my human genetics textbook and a non-DNA-centric view got me thinking. So I read the paper and asked the authors to guest post. Their idea brought me back to pre-1953 thinking that proteins are the genetic material, mostly because we knew more about them than the mysterious goop on soiled bandages that was DNA.

Then last week I posted here about the information from a dozen sequenced human genomes not being all that clinically useful, at the same time that the blogosphere trumpeted the not-very-surprising finding that a gene attached to obesity was actually controlled by another gene. The news last week seemed to validate Drs. Annila and Baverstock’s concern about genome sequencing entering the clinic when we don’t fully understand how genes interact at the level of their products, the proteins.

Dr. Baverstock kindly agreed to post. His impressive bio is here. Most notably, he brought to global attention the increased childhood thyroid cancer incidence in Belarus caused by radioactive iodine from the Chernobyl accident. (I had thyroid cancer although I’ve never been near a leaking reactor.) Here he shares his thoughts, lightly edited, subheads added:

A VIEW FROM PHYSICS

Arto Annila and I are making the seemingly outrageous claim that mainstream biology, since around the 1920s, has pursued a course that is deeply flawed. Critical to that course is the notion that genes are Mendel’s units of inheritance and that their material realization is a DNA base sequence. We propose instead that Mendel’s unit of inheritance is a process involving the interaction of mainly activated proteins contributing to an attractor state that represents the phenotype. Many will find this language of physics unfamiliar. However, cells are complex dissipative systems (CDS) in that they consume energy and thus operate according to the 2nd law of thermodynamics as it applies to open systems.

A lily cell dividing. (Andrew S. Bajer)

First, two irrefutable facts in justification of our position:

1. When cells divide they inherit the state of the cell. If this were not the case, cancer and differentiation would have to be one-step processes. The state of the cell cannot be encoded on the DNA base sequence: it is the active proteome.
2. Key biological processes, such as development, growth and aging, are irreversible in time, whereas standard textbook physics describes time reversible deterministic dynamics.

It is very well known that at cell division the cytoplasm is partitioned between the two progeny, but not emphasized, as we propose, that it contains a coherent complex process of interacting proteins. When this state is understood as the unit of inheritance, the epigenetic memory that enables processes, like differentiation, to take place over several cell generations is a natural manifestation. In addition, CDS physics supports the phenomenon of quasi-stability – that is, stability within limits: attractors are quasi-stable states formed by the interacting proteins. This would mean that inheritance at the cellular level is not after all a matter for the nucleus, but rather for the cytoplasm.

NOT JUST THE NUCLEUS

The nucleus/cytoplasm issue was hotly debated around the turn of the century – not the last one but the one before, and eventually resolved in favor of the nucleus by the geneticist T H Morgan in 1926. It’s clear that components of the egg cytoplasm are inherited at fusion, the mitochondria for example, but it has generally been regarded that the sperm delivers only genomic DNA. However, studies on male fertility have revealed that proteins essential for successful fertilization are present in the sperm and some of the chromatin is in a non-condensed state and thus, possibly even active. Therefore, we can assume that the sperm is capable of supporting a protein-based attractor state.

One experimental way to resolve the nucleus/cytoplasm issue is cross species nuclear transfer to enucleated eggs. This has not proved possible with mammals, but has been successful with fish. Enucleated goldfish eggs transplanted with nuclei from carp eggs develop with the outward appearance of the donor carp, but with a vertebral number (26 to 31) consistent with goldfish (26 to 28) rather than the genomic DNA donor carp (33 to 36). We assume that when two dynamic attractors are placed in a common environment, as in the case of the zygote, that they will “synchronize” as, for example, with Huygens’ clocks. Therefore, we argue that biology can explain inheritance on the basis of a sound foundation in the appropriate physics, without resorting to mechanistic narratives involving genes.

Furthermore, work in the 1970s demonstrated that enucleated HPRT-competent (HPRT is an enzyme whose absence causes the awful Lesch-Nyhan syndrome, an inborn error of metabolism-RL) fibroblasts in vitro could correct HPRT deficiency in fibroblasts with an intact nucleus, by transferring molecules via gap junctions, without the need for protein synthesis. In addition, erythrocytes (red blood cells) dispose of their nuclei at the last stage of differentiation, but retain, for example, the circadian rhythm function for their lifetime.

In fact, the evidence clearly points to routine cellular function (apart from cell division) and regulation in somatic cells being a matter for proteins without the intervention of genes. If, for example, the dark/light rhythm changes (travel over a few time zones) then intervention involving new transcription to adjust the circadian rhythm does occur, but otherwise circadian rhythm is taken care of by protein chemistry, as has been demonstrated in vitro.

How Academia and Publishing are Destroying Scientific Innovation: A Conversation with Sydney Brenner

The LMB Governing Board, October 1967. Left to right: Hugh Huxley, John Kendrew, Max Perutz, Francis Crick, Fred Sanger, Sydney Brenner. (From the website of the MRC Laboratory of Molecular Biology)


I recently had the privilege of speaking with Professor Sydney Brenner, a professor of Genetic medicine at the University of Cambridge and Nobel Laureate in Physiology or Medicine in 2002. I had originally intended to ask him about Professor Frederick Sanger, the two-time Nobel Prize winner famous for his discovery of the structure of proteins and his development of DNA sequencing methods, who passed away in November. I wanted to do the classic tribute by exploring his scientific contributions and getting a first hand account of what it was like to work with him at Cambridge’s Medical Research Council’s (MRC) Laboratory for Molecular Biology (LMB) and at King’s College where they were both fellows. What transpired instead was a fascinating account of the LMB’s quest to unlock the genetic code and a critical commentary on why our current scientific research environment makes this kind of breakthrough unlikely today.

LMB at Cambridge. Original LMB

It is difficult to exaggerate the significance of Professor Brenner and his colleagues’ contributions to biology. Brenner won the Nobel Prize for establishing Caenorhabditis elegans, a type of roundworm, as the model organism for cellular and developmental biological research, which led to discoveries in organ development and programmed cell death. He made his breakthroughs at the LMB, where beginning in the 1950s, an extraordinary number of successive innovations elucidated our understanding of the genetic code. This code is the process by which cells in our body translate information stored in our DNA into proteins, vital molecules important to the structure and functioning of cells. It was here that James Watson and Francis Crick discovered the double-helical structure of DNA. Brenner was one of the first scientists to see this ground-breaking model, driving from Oxford, where he was working at the time in the Department of Chemistry, to Cambridge to witness this breakthrough. This young group of scientists, considered renegades at the time, made a series of successive revolutionary discoveries that ultimately led to the creation of a new field called molecular biology.

To begin our interview, I asked Professor Brenner to speak about Professor Sanger and what led him to his Nobel Prize winning discoveries.

Sydney Brenner: Fred realized very early on that if we could sequence DNA, we would have direct contact with the genes. The problem was that you couldn’t get hold of genes in any way. You couldn’t purify what was a gene. That is why right from the start in 1954, we decided we would do this by using Fred’s method of sequencing proteins, which he had achieved [proteins are derived from the information held in DNA]. You have to realise it was only on a small scale. I think there were only forty-five amino acids [the building blocks of proteins] that were in insulin. We thought even scaling that up for proteins would be difficult. But finally DNA sequencing was invented. Then it became clear that we could directly approach the gene, and it produced a completely new period in science.

He was interested in the method and interested in getting the methods to work. I was really clear in my own mind that what he did in DNA sequencing, even at the time, would cause a revolution in the subject, which it did. And of course we immediately, as fast as possible, began to use these methods in our own research.

ED: This foundational research ushered in a new era of biological science. It has formed the basis of nearly all subsequent discoveries in the field, from understanding the mechanisms of diseases, to the development of new drugs for diseases such as cancer. Imagining the creative energy that drove these discoveries was truly inspirational. I asked Professor Brenner what it felt like to be part of this scientific adventure.

SB: I think it’s really hard to communicate that because I lived through the entire period from its very beginning, and it took on different forms as matters progressed. So it was, of course, wonderful. That’s what I tell students. The way to succeed is to get born at the right time and in the right place. If you can do that then you are bound to succeed. You have to be receptive and have some talent as well.

ED: Today, the structure of DNA and how genetic information is translated into proteins are established scientific canon. Brenner joked that he “knew that molecular biology was doomed to success when [he] heard two students speaking in a bus once and asking whether they would get the genetic code in the examination. It had become an academic subject.” But in the 1950s, the hypotheses generated at the LMB were dismissed as inconceivable nonsense.

SB: To have seen the development of a subject, which was looked upon with disdain by the establishment from the very start, actually become the basis of our whole approach to biology today. That is something that was worth living for.

I remember Francis Crick gave a lecture in 1958, in which he discussed the adapter hypothesis at the time. He proposed that there were twenty enzymes, which linked amino acids to twenty different molecules of RNA, which we call adapters. It was these adapters that lined up the amino acids. The adapter hypothesis was conceived I think as early as 1954 and of course it was to explain these two languages: 
DNA, the language of information, and 
proteins, the language of work.

Of course that was a paradox, because how did you get one without the other? That was solved by discovering that a molecule from RNA could actually have function. So this information on RNA, which happened much later really, solved that problem as far as origins were concerned.

ED: (Professor Brenner was far too modest here, as it was he who discovered RNA’s critical role in this translation from gene to protein.)

SB: So he [Crick] gave the lecture and biochemists stood up in the audience and said this is completely ridiculous, because if there were twenty enzymes, we biochemists would have already discovered them. To them, the fact that they still hadn’t went to show that this was nonsense. Little did the man know that at that very moment scientists were in the process of finding the very first of these enzymes, which today we know are the enzymes that combined amino acids with transfer RNA. And so you really had to say that the message kept its purity all the way through.

What people don’t realise is that at the beginning, it was just a handful of people who saw the light, if I can put it that way. So it was like belonging to an evangelical sect, because there were so few of us, and all the others sort of thought that there was something wrong with us.

They weren’t willing to believe. Of course they just said, well, what you’re trying to do is impossible. That’s what they said about crystallography of large molecules. They just said it’s hopeless. It’s a hopeless task. And so what we were trying to do with the chemistry of proteins and nucleic acids looked hopeless for a long time. Partly because they didn’t understand how they were built, which I think we molecular biologists had the first insight into, and partly because they just thought they were amorphous blobs and would never be able to be analysed.

I remember when going to London to talk at meetings, people used to ask me what am I going to do in London, and I used to tell them I’m going to preach to the heathens. We viewed most of everybody else as not doing the right science. Like one says, the young Turks will become old Greeks. That’s the trouble with life. I think molecular biology was marvellous because every time you thought it was over and it was just going to be boring, something new happened. It was happening every day.

So I don’t know if you can ride on the crest of a wave; you can ride on it, I believe, forever. I think that being in science is the most incredible experience to have, and I now spend quite a lot of my time trying to help the younger people in science to enjoy it and not to feel that they are part of some gigantic machine, which a lot of people feel today.

ED: I asked him what inspired them to maintain their faith and pursue these revolutionary ideas in the face of such doubt and opposition.

SB: Once you saw the light you were just certain that you had to be right, that it was the right way to do it and the right answer. And of course our faith, if you like, has been borne out.

I think it would have been difficult to keep going without the strong support we had from the Medical Research Council. I think they took a big gamble when they founded that little unit in the Cavendish. I think all the early people they had were amazing. There were amazing personalities amongst them.

This was not your usual university department, but a rather flamboyant and very exceptional group that was meant to get together. An important thing for us was that with the changes in America then, from the late fifties almost to the present day, there was an enormous stream of talent and American postdoctoral fellows that came to our lab to work with us. But the important thing was that they went back. Many of them are now leaders of American molecular biology, who are alumni of the old MRC.

ED: The 1950s to 1960s at the LMB was a renaissance of biological discovery, when a group of young, intrepid scientists made fundamental advances that overturned conventional thinking. The atmosphere and camaraderie reminded me of another esteemed group of friends at King’s College – the Bloomsbury Group, whose members included Virginia Woolf, John Maynard Keynes, E.M. Forester, and many others. Coming from diverse intellectual backgrounds, these friends shared ideas and attitudes, which inspired their writing and research. Perhaps there was something about the nature of the Cambridge college systems that allowed for such revolutionary creativity?

SB: In most places in the world, you live your social life and your ordinary life in the lab. You don’t know anybody else. Sometimes you don’t even know other people in the same building, these things become so large.

The wonderful thing about the college system is that it’s broken up again into a whole different unit. And in these, you can meet and talk to, and be influenced by and influence people, not only from other scientific disciplines, but from other disciplines. So for me, and I think for many others as well, that was a really important part of intellectual life. That’s why I think people in the college have to work to keep that going.

Cambridge is still unique in that you can get a PhD in a field in which you have no undergraduate training. So I think that structure in Cambridge really needs to be retained, although I see so often that rules are being invented all the time. In America you’ve got to have credits from a large number of courses before you can do a PhD. That’s very good for training a very good average scientific work professional. But that training doesn’t allow people the kind of room to expand their own creativity. But expanding your own creativity doesn’t suit everybody. For the exceptional students, the ones who can and probably will make a mark, they will still need institutions free from regulation.

ED: I was excited to hear that we had a mutual appreciation of the college system, and its ability to inspire interdisciplinary work and research. Brenner himself was a biochemist also trained in medicine, and Sanger was a chemist who was more interested in chemistry than biology.

SB: I’m not sure whether Fred was really interested in the biological problems, but I think the methods he developed, he was interested in achieving the possibility of finding out the chemistry of all these important molecules from the very earliest.

ED: Professor Brenner noted that these scientific discoveries required a new way of approaching old problems, which resist traditional disciplinary thinking.

SB: The thing is to have no discipline at all. Biology got its main success by the importation of physicists that came into the field not knowing any biology and I think today that’s very important.

I strongly believe that the only way to encourage innovation is to give it to the young. The young have a great advantage in that they are ignorant. Because I think ignorance in science is very important. If you’re like me and you know too much you can’t try new things. I always work in fields of which I’m totally ignorant.

ED: But he felt that young people today face immense challenges as well, which hinder their ability to creatively innovate.

SB: Today the Americans have developed a new culture in science based on the slavery of graduate students. Now graduate students of American institutions are afraid. He just performs. He’s got to perform. The post-doc is an indentured labourer. We now have labs that don’t work in the same way as the early labs where people were independent, where they could have their own ideas and could pursue them.

The most important thing today is for young people to take responsibility, to actually know how to formulate an idea and how to work on it. Not to buy into the so-called apprenticeship. I think you can only foster that by having sort of deviant studies. That is, you go on and do something really different. Then I think you will be able to foster it.

But today there is no way to do this without money. That’s the difficulty. In order to do science you have to have it supported. The supporters now, the bureaucrats of science, do not wish to take any risks. So in order to get it supported, they want to know from the start that it will work. This means you have to have preliminary information, which means that you are bound to follow the straight and narrow.

There’s no exploration any more except in a very few places. You know like someone going off to study Neanderthal bones. Can you see this happening anywhere else? No, you see, because he would need to do something that’s important to advance the aims of the people who fund science.

I think I’ve often divided people into two classes: Catholics and Methodists. Catholics are people who sit on committees and devise huge schemes in order to try to change things, but nothing’s happened. Nothing happens because the committee is a regression to the mean, and the mean is mediocre. Now what you’ve got to do is good works in your own parish. That’s a Methodist.

ED: His faith in young, naïve (in the most positive sense) scientists is so strong that he has dedicated his later career to fostering their talent against these negative forces.

SB: I am fortunate enough to be able to do this because in Singapore I actually have started two labs and am about to start a third, which are only for young people. These are young Singaporeans who have all been sent abroad to get their PhDs at places like Cambridge, Stanford, and Berkeley. They return back and rather than work five years as a post-doc for some other person, I’ve got a lab where they can work for themselves. They’re not working for me and I’ve told them that.

But what is interesting is that very few accept that challenge, providing what I think is a good standard deviation from the mean. Exceptional people, the ones who have the initiative, have gone out and got their own funding. I think these are clearly going to be the winners. The eldest is thirty-two.

They can have some money, and of course they’ve got to accept the responsibility of execution. I help them in the sense that I oblige them and help them find things, and I can also guide them and so on. We discuss things a lot because I’ve never believed in these group meetings, which seems to be the bane of American life; the head of the lab trying to find out what’s going on in his lab. Instead, I work with people one on one, like the Cambridge tutorial. Now we just have seminars and group meetings and so on.

So I think you’ve got to try to do something like that for the young people and if you can then I think you will create. That’s the way to change the future. Because if these people are successful then they will be running science in twenty years’ time.

ED: Our discussion made me think about what we consider markers of success today. It reminded me of a paragraph in Professor Brenner’s tribute to Professor Sanger in Science:

“A Fred Sanger would not survive today’s world of science. With continuous reporting and appraisals, some committee would note that he published little of import between insulin in 1952 and his first paper on RNA sequencing in 1967 with another long gap until DNA sequencing in 1977. He would be labelled as unproductive, and his modest personal support would be denied. We no longer have a culture that allows individuals to embark on long-term—and what would be considered today extremely risky—projects.”

I found this particularly striking given that another recent Nobel prize winner, Peter Higgs, who identified the particle that bears his name, the Higgs boson, similarly remarked in an interview with the Guardian that, “he doubts a similar breakthrough could be achieved in today’s academic culture, because of the expectations on academics to collaborate and keep churning out papers. He said that: ‘it’s difficult to imagine how I would ever have enough peace and quiet in the present sort of climate to do what I did in 1964.’”

Fellowships in Biochemistry, Cell Biology, Developmental Biology, Epigenetics, Immunobiology and Molecular Biology. Max Planck Institute

PhD overview

Our programme provides outstanding students with excellent research-oriented interdisciplinary training in Biochemistry, Cell Biology, Developmental Biology, Epigenetics, Immunobiology and Molecular Biology. We train students to become self-reliant and to acquire and utilize the knowledge necessary for their research project. Students have the chance to interact with experts in various fields both to extend their scientific knowledge and to learn critical thinking as well as acquire problem-solving skills.

The IMPRS-MCB fellows have 3 to 4 years to obtain their degree. Most of this time they work on their individually supervised research project. In addition to the experimental part all fellows have a possibility and are obliged to participate in curricular activities of the programme. These are:

• scientific and soft skills courses offered by the programme (see Curriculum)
• institute seminars
• PhD retreat
• supervision of junior students (master students or summer trainees)
• conference attendance
• career evenings

Our students are funded during the whole time of their PhD (3-4 years). The payment is sufficient for monthly living costs in Freiburg to be covered. There are no tuition fees to be paid.

Graphical overview of the curricular activities during your PhD

Figure Legend: Orange - activities related to research and the PhD project; Blue - courses; Green - scientific conference/retreats

ORIGINAL: Max Planck Institute

The gold standard for cell penetration

ORIGINAL: MIT
David L. Chandler, MIT News Office
August 23, 2013

Gold nanoparticles with special coatings can deliver drugs or biosensors to a cell’s interior without damaging it.

Illustration shows the passage of a gold nanoparticle (in orange) covered with a monolayer of hydrophobic/hydrophilic material (shown in blue-green, yellow and red), passing through a cell membrane composed of lipids (white and blue). Graphic courtesy of Reid Van Lehn

Cells are very good at protecting their precious contents — and as a result, it’s very difficult to penetrate their membrane walls to deliver drugs, nutrients or biosensors without damaging or destroying the cell. One effective way of doing so, discovered in 2008, is to use nanoparticles of pure gold, coated with a thin layer of a special polymer. But nobody knew exactly why this combination worked so well, or how it made it through the cell wall.

Now, researchers at MIT and the Ecole Polytechnique de Lausanne in Switzerland have figured out how the process works, and the limits on the sizes of particles that can be used. Their analysis appears in the journal Nano Letters, in a paper by graduate students Reid Van Lehn, Prabhani Atukorale, Yu-Sang Yang and Randy Carney and professors Alfredo Alexander-Katz, Darrell Irvine and Francesco Stellacci.

Until now, says Van Lehn, the paper’s lead author, “the mechanism was unknown. … In this work, we wanted to simplify the process and understand the forces” that allow gold nanoparticles to penetrate cell walls without permanently damaging the membranes or rupturing the cells. The researchers did so through a combination of lab experiments and computer simulations.

The team demonstrated that the crucial first step in the process is for coated gold nanoparticles to fuse with the lipids — a category of natural fats, waxes and vitamins — that form the cell wall. The scientists also demonstrated an upper limit on the size of such particles that can penetrate the cell wall — a limit that depends on the composition of the particle’s coating.

The coating applied to the gold particles consists of a mix of hydrophobic and hydrophilic components that form a monolayer — a layer just one molecule thick — on the particle’s surface. Any of several different compounds can be used, the researchers explain.

“Cells tend to engulf things on the surface,” says Alexander-Katz, an associate professor of materials science and engineering at MIT, but it’s “very unusual” for materials to cross that membrane into the cell’s interior without causing major damage. Irvine and Stellacci demonstrated in 2008 that monolayer-coated gold nanoparticles could do so; they have since been working to better understand why and how that works.

Since the nanoparticles themselves are completely coated, the fact that they are made of gold doesn’t have any direct effect, except that gold nanoparticles are an easily prepared model system, the researchers say. However, there is some evidence that the gold particles have therapeutic properties, which could be a side benefit.

Gold particles are also very good at capturing X-rays — so if they could be made to penetrate cancer cells, and were then heated by a beam of X-rays, they could destroy those cells from within. “So the fact that it’s gold may be useful,” says Irvine, a professor of materials science and engineering and biological engineering and member of the
Koch Institute for Integrative Cancer Research.

Significantly, the mechanism that allows the nanoparticles to pass through the membrane seems also to seal the opening as soon as the particle has passed. “They would go through without allowing even small molecules to leak through behind them,” Van Lehn says.

Irvine says that his lab is also interested in harnessing this cell-penetrating mechanism as a way of delivering drugs to the cell’s interior, by binding them to the surface coating material. One important step in making that a useful process, he says, is finding ways to allow the nanoparticle coatings to be selective about what types of cells they attach to. “If it’s all cells, that’s not very useful,” he says, but if the coatings can be targeted to a particular cell type that is the target of a drug, that could be a significant benefit.

Another potential application of this work could be in attaching or inserting biosensing molecules on or into certain cells, Van Lehn says. In this way, scientists could detect or monitor specific biochemical markers, such as proteins that indicate the onset or decline of a disease or a metabolic process.

In general, attachment to nanoparticles’ surface coatings could provide a key to cells’ interiors for “molecules that normally wouldn’t have any ability to get through the cell membrane,” Irvine says.

Vince Rotello, a professor of chemistry at the University of Massachusetts at Amherst who was not involved in this research, says this work is “careful, well thought out and elegantly presented.” He adds, “This study provides a very interesting alternative mechanism to cell uptake of nanomaterials that could open up new therapeutic pathways.”

The work was supported by the National Science Foundation, the National Cancer Institute and the U.S. Army Research Office.

Learning from a Virus: Keeping Genes Under Wraps

ORIGINAL: University of Arizona

Cytomegalovirus particles as seen through an electron microscope: While some of the protein capsules are empty, others contain tightly packaged DNA, visible as dark structures. The diameter of a human hair would cover a line of about 600 virus particles. (Photo: Farah Bughio, Felicia Goodrum)

July 30, 2013 — An international collaboration of researchers including Felicia Goodrum of the University of Arizona's immunobiology department has studied how a human herpes virus carried by the majority of the population packages its genetic information during infection.

The discoveries improve the chances of developing more targeted therapies in place of existing drugs, which do not always work or come with side effects.

Experts estimate that 60 to 90 percent of the world's population carry the human cytomegalovirus, or CMV, which is one of the eight herpes viruses that infect humans.

In healthy individuals, the virus lies dormant and does not cause overt disease. However, it poses a significant risk when contracted by unborn children -- whose immune system has not matured yet -- and individuals with compromised immune function.

CMV is the leading cause of birth defects resulting from any infectious agent. It affects one in 150 births in the US and most commonly results in hearing loss, but can also cause cognitive or physical anomalies and cerebral palsy. Once infected, the virus stays in the body for life and flares up only when the immune system is suppressed, for example in AIDS patients, transplant patients and cancer patients undergoing intensive chemotherapy.

For the study, published in the scientific journal Proceedings of the National Academy of Sciences (PNAS), Goodrum teamed up with collaborators in Germany and Israel.

The researchers investigated how a fundamental aspect of the human cell regulates the virus: the mechanism by which genetic information is packaged and stored. Understanding how the viral DNA behaves in the human host cells during dormancy and reactivation of the virus provides the basis for the development of drugs that could prevent the virus from "waking up" and causing disease.

"The human immune system is very sophisticated, and the way this virus has managed to stealthily integrate into our biology to ensure its own survival is no small feat," said Goodrum, also a member of the UA's BIO5 Institute.

"CMV is a master of human cell biology. From transcribing DNA into blueprints for proteins to the manufacturing of those proteins, from cell division to cellular metabolism, there is not a process this virus has not tweaked," Goodrum also said.

Virus factory: The top image shows uninfected, normal human cells with cell nuclei in blue and the cellular protein processing apparatus in red. In the infected cells (bottom image), the virus has produced proteins (green) that take over and reorganize the cellular processing apparatus into a virus factory. (Credit: Photo: Farah Bughio, Felicia Goodrum)

That mastery, she explained, is the reason the virus is so elusive to vaccine, and there currently is no way to eradicate it. Goodrum noted that with other herpes viruses, like Epstein-Barr or chicken pox, the infection is obvious. But that is not the case with CMV.

"From the perspective of a virus, that is the pinnacle of mastery -- to infect without ever making its presence known," Goodrum said.

"To develop more effective antiviral strategies, we must understand the biology of the virus infection and how the virus manages to persist for our lifetimes," she said. "We are trying to understand how our cellular mechanisms are being used by this virus and discover targets for drugs to control it."

Each human cell contains a thread of DNA that is about 6 feet long, stowed away in its nucleus and tightly packaged by proteins called histones. One such package of genetic material is called a chromosome.

"You can imagine histones as a spool, and the thread is DNA that wraps around the spool," Goodrum said. "This accomplishes two important objectives: first, it condenses DNA so that it can be packed into the cell nucleus and second, it provides the cell with a mechanism to regulate the activity of the genes encoded on that DNA."

The association between histones and DNA is very dynamic and acts as a key mechanism used by cells to control which genes are expressed and which are not, Goodrum explained.

For example, when DNA is wound tightly around histones, it is not accessible to enzymes specializing in making copies of genes in a process called transcription, which subsequently serve as blueprints to manufacture proteins.

"When a virus like CMV infects our cells, its DNA is packaged by histones just as if it were the cell's own DNA," Goodrum said.

"The question is, how does this happen, and does the virus have any choice in the matter? Our work maps the deposition of histones across the viral DNA chromosome and shows that the virus encodes a mechanism to reorganize these histones to favor the expression of genes from the viral chromosome."

Michael Nevels of the Institute for Medical Microbiology and Hygiene at the University of Regensburg, Germany, said: "Now that we have determined the positions of the nucleosomes, we can study how transcription is regulated, and from that others can start developing therapies."

For example, if researchers can identify molecules that play key roles in the process, they can design new drugs that target those molecules.

"Since we can't eliminate the virus, the goal is to keep it in check," said Nevels, who led the study together with Eran Segal and Einat Zalckvar of the Weizmann Institute of Science in Rehovot, Israel.

"The idea is to target the virus on the level of its DNA structure and to reduce the gene activity back to the dormancy levels," Nevels said.

One such molecular target identified in this study is a viral protein called IE1. Because it regulates the packaging and unpacking of the viral DNA, it could potentially be a target for new therapies.

Cautioning that many more steps will be necessary before this could be achieved, Nevels said that "if we could inhibit IE1, the virus genome would be packed more tightly with histones, which leaves less DNA accessible and prevents genes from becoming active."

Another strategy takes the opposite direction by deliberately awaking the virus from its dormant state so it becomes vulnerable to antiviral drugs. This could be an option for patients about to undergo an organ transplantation, which requires immune-suppressing drugs to prevent the new organ from being rejected. Suppressing the immune system allows the virus to reactivate.

"There are antivirals that target the active, replicating virus but they can't target latent virus because in that state, it's really just a piece of DNA in the cell nucleus," Goodrum said. "Before those patients enter a immunosuppressed state, you would target the viral reservoirs and force the virus out of latency."

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference: E. Zalckvar, C. Paulus, D. Tillo, A. Asbach-Nitzsche, Y. Lubling, C. Winterling, N. Strieder, K. Mucke, F. Goodrum, E. Segal, M. Nevels. Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein. Proceedings of the National Academy of Sciences, 2013; DOI: 10.1073/pnas.1305548110

The Mechanism Determining Plant Height and Leaf and Seed Size - Balance between three proteins controls plant-cell elongation -

ORIGINAL: AIST

- Balance between three proteins controls plant-cell elongation -
(Translation of AIST press release on November 19, 2012) Points
Identification of three types of protein controlling plant-cell elongation
Elucidation of a new mechanism by which each of the three types of protein antagonistically affects the activity of others
Expectations of the development of new crops and garden plants with modified plant height, leaf and seed size, and morphology Summary

Masaru Ohme-Takagi (Invited Senior Researcher), Miho Ikeda (Collaborative Researcher, Restart Postdoctoral Fellow of Japan Society for the Promotion of Science), and co-workers of Plant Gene Regulation Research Group, the Bioproduction Research Institute (Director: Yoichi Kamagata) of the National Institute of Advanced Industrial Science and Technology (AIST; President: Tamotsu Nomakuchi), have confirmed that the length of a plant cell is controlled by the antagonistic actions of three types of protein.

Cell length directly affects plant height and leaf and seed size. The researchers have identified two proteins, PRE1 and ACE, which act as a positive regulator for cell elongation, and one protein, AtIBH1, which inhibits cell elongation. They have found that ACE directly induces cell elongation, whereas AtIBH1 inhibits the activity of ACE by interacting with it. PRE1 indirectly promotes elongation by interfering the activity of AtIBH1. Final cell length is determined by the balance between the three proteins.

These proteins are transcription factors controlling functions of several genes. Use of these transcription factors would make it possible to modify plant height, leaf and seed size, flower and plant morphology, etc. They are expected to be applicable to a variety of areas, including improvement in the efficiency of farming, creation of large plants suitable for biofuel production, and development of unique garden plants.

Details of the results will be published in a US scientific journal, The Plant Cell.

Effect of differences in cell length on plants (Arabidopsis thaliana).

Social Background of Research

Plants, which are important resources, have been traditionally used as food, clothing, and home-building materials, and have comforted people as garden plants. Recently plant-based pharmaceuticals, biofuels, and industrial materials become popular and their application has been increasing. Modifying plant morphology and size to suit different applications should increase the efficiency of production.

From this perspective, modification of plant-cell length is an important subject of breeding studies because it directly affects tree and plant height and leaf and seed size. There are various environmental factors that determine cell length, including sun exposure, temperature, water contents, and nutrient ratios. It is not known how a plant determines its cell length in response to these environmental conditions.

History of Research

AIST has been studying plant genes, particularly the transcription factors that control the actions of many genes, in order to apply them to the production of industrial materials, medicines, and food. The Chimeric REpressor Gene Silencing Technology (CRES-T) and the transcription factor library developed in these studies are being used worldwide as general-purpose tools for a variety of basic and applied transcription factor studies. In addition to the development of such general-purpose tools, AIST is also studying functions of individual transcription factors involved in various phenomena, such as plant morphology, size, and substance production. In the present study, the researchers investigated the mechanism by which plant-cell elongation is controlled.

This study was supported by a grant-in-aid for JSPS Fellows, titled “Isolation of Transcription Factors Controlling Branching, Dwarfing, and Differentiation Potency Applicable to General Crops and their Use (FY2011–2013).”

Details of Research

Plants control cell elongation in response to various environmental conditions, such as sun exposure, temperature, water, and nutrient ratios, and to grow into forms adapted to their environment (e.g. a sunny or a shady location). When, and which, cells are to be elongated is related to seasonal differences in growth (e.g. the elongation of shoots in spring) and to changes in growth over time (e.g. young plants grow vigorously, whereas old plants grow very little). In addition, plant-cell elongation is involved not only in simple growth but also in important plant functions, such as the blooming of a flower and the turning of a flower toward the light when a plant falls over (Fig. 1).

Figure 1 : Examples of phenomena in which plant cell elongation is involved

The researchers have identified three transcription factors from a model plant, Arabidopsis thaliana: PRE1 and ACE, which enhance cell elongation, and AtIBH1, which inhibits cell elongation. These three transcription factors control plant size by regulating cell elongation, without affecting the number of cells. ACE activates the expression of enzyme genes that promote cell elongation. AtIBH1 inhibits cell elongation by interacting with ACE and interfering with its function. PRE1 interacts with AtIBH1 and thus interferes with its inhibition of ACE, thus promoting cell elongation. The researchers named the mechanism of this antagonistic inhibition by ACE, AtIBH1, and PRE1 a tri-antagonistic bHLH system (Fig. 2). Similar mechanisms of antagonistic inhibition, but between only two factors, have been reported in human beings, but mechanisms of antagonistic inhibition by three factors have not been reported before in plants or animals. The tri-antagonistic system is thus a new control mechanism.

Of the three types of transcription factor that were discovered, PRE1 was abundant in stem tips and young leaves and seeds, whereas AtIBH1 was abundant in hardened stem bases, old leaves, and mature seeds. This suggests that the antagonistic inhibition by the three factors, ACE, AtIBH1, and PRE1, regulates the elongation of various cells in each growth stage of the plant.

Figure 2 : Tri-antagonistic bHLH system controlling plant-cell elongation

Future Plans
The researchers aim to develop a technology for modifying plant height and leaf, flower, and seed size by partially enhancing or inhibiting with the functions of PRE1, AtIBH1, and ACE. They will then apply the technology to crop breeding. It is expect that manipulation of these three factors will change plant morphology, as well as its metabolism. They intend to conduct research in the effect of these factors on the metabolic system of plants.

Scientists uncover the nuclear life of actin

ORIGINAL: Physorg

First discovered in muscle cells more than 70 years ago, actin has a well-established identity as a cytoplasmic protein that works by linking itself in chains to form filaments. Fibers formed by these actin polymers are crucial to muscle contraction.

Figure 1: F- actin, a controller of organism motion. F-actin acts as a motor for movement in one direction. As the filament pushes the cell membrane from inside the cell, cell projections are formed, and cells move. ORIGINAL: Riken Research

Figure 3: F-actin structure. G-actin consists of two twisted domains. When constructed into F-actin, the domains of G-actin untwist into a flat comformation.
Figure 4: Structural change in actin and hydrolysis of ATP. The hydrolysis of ATP is hypothesized as follows. G-actin (upper) polymerizes to form F-actin and assumes a flat comformation (lower). A region around the amino acid anchoring a water molecule deforms to allow the water molecule to approach the ATP. Upon rotation of the ATP-bound domain (yellow), the ATP approaches the water molecule, allowing the ATP and water molecule to react leading to ATP hydrolysis. ORIGINAL: Riken Research

So it came as a surprise when scientists discovered actin in the nucleus. Labs have been working for the past few decades to figure out exactly what it's doing there.

A new study published this week in Nature Structural & Molecular Biology reveals that actin has a new and fundamental nuclear function, and that surprisingly, it accomplishes this task in its single-molecule (monomeric) form – not through polymerization.

Senior author of the study Xuetong "Snow" Shen, Ph.D., associate professor in The University of Texas MD Anderson Cancer Center Department of Molecular Carcinogenesis, has been fascinated by the mystery of nuclear actin. In collaboration with researchers from Colorado State University, his lab developed a unique model system to nail down actin's function in the nucleus by studying the actin-containing INO80 chromatin remodeling complex.

In 2000, as a postdoc at NIH in Carl Wu's lab, Shen identified actin as a component of the INO80 complex, adding to the growing list of evidence that actin indeed has a life in the nucleus. However, how actin actually works in the nucleus remains fuzzy due to lack of clear experimental systems.

"Our model system opened up a new opportunity to look in depth at the function of nuclear actin as it relates to gene regulation, genome stability, and ultimately cancer," Snow said.

A nuclear role for monomeric actin

Because yeast have only a single actin gene, the authors reasoned that studying INO80 in yeast cells would allow a direct assessment of the protein's nuclear function. In contrast, mammals have at least six forms of actin coded by separate genes, making their study more difficult.

The researchers used both genetic and biochemical methods to dissect actin's role in the INO80 complex. The INO80 complex normally functions in the nucleus to rearrange chromatin ¬– the intertwined proteins and DNA that are packaged into chromosomes – regulating the expression of many different genes.

The authors found that a mutant form of actin impairs the ability of INO80 to function correctly, implicating actin in the process of chromatin remodeling – an exploding field of research with applications in cancer diagnosis and treatment.

In the cytoplasm, actin functions primarily as a polymer. Cytoplasmic actin is a component of the cytoskeleton and the muscle contractile machinery, and is essential for cell mobility, including cancer metastasis. Actin inside the INO80 complex is arranged in a clever way such that it cannot polymerize; instead, actin's monomeric form appears to interact with chromatin.

"Our study challenges the dogma that actin functions through polymerization, revealing a novel and likely a fundamental mechanism for monomeric nuclear actin," Shen said.

New findings for an ancient complex

Because actin and several of the other INO80 components are so highly conserved, even in human cells, this mechanism likely represents an ancient, fundamental role of actin, which has been preserved through evolution.

Shen's group is now teasing out the exact mechanism by which nuclear actin interacts with chromatin. They also hope to extend the results to human cells and to identify potential ways by which nuclear actin could be involved in cancer.

Chromatin is critical for maintaining the delicate balance between gene activation and repression, Shen said. "Disrupting this regulation can lead to cancer, and it remains to be seen whether nuclear actin has a role in this process."

Journal reference: Nature Structural & Molecular Biology

Provided by University of Texas M. D. Anderson Cancer Center

Most popular human cell in science gets sequenced

ORIGINAL: Nature

Ewen Callaway

15 March 2013

The HeLa cell genome is riddled with errors, raising questions about its continued use.

HeLa cells have contributed to work in thousands
of research papers but sequencing shows their genome
to be full of errors.
 THOMAS DEERINCK,
NCMIR/SCIENCE PHOTO LIBRARY

The research world’s most famous human cell has had its genome decoded, and it’s a mess. German researchers this week report the genome sequence of the HeLa cell line, which originates from a deadly cervical tumour taken from a patient named Henrietta Lacks.

Established after Lacks died in 1951, HeLa cells were the first human cells to grow well in the laboratory. The cells have contributed to more than 60,000 research papers, the development of a polio vaccine in the 1950s and, most recently, an international effort to characterize the genome, known as ENCODE.

Previous work showed that HeLa cells, like many tumours, have bizarre, error-filled genomes, with one or more extra copies of many chromosomes. To get a closer look at these alterations, a team led by Lars Steinmetz, a geneticist at the European Molecular Biology Laboratory in Heidelberg, Germany, sequenced the popular 'Kyoto' version of the cell line and compared the sequence with that of a reference human genome. The team's results are published in G31.

Steinmetz’s team confirmed that HeLa cells contain one extra version of most chromosomes, with up to five copies of some. Many genes were duplicated even more extensively, with four, five or six copies sometimes present, instead of the usual two. Furthermore, large segments of chromosome 11 and several other chromosomes were reshuffled like a deck of cards, drastically altering the arrangement of the genes.

Without the genome sequence of Lacks’ healthy cells or that of her original tumour, it is difficult to trace the origin of these alterations. Steinmetz points out that other cervical tumours have massive rearrangements on chromosome 11, so the changes in the HeLa cell may have contributed to Lacks’ tumour.

Henrietta Lacks, whose cancer
gave rise to HeLa cells. 
OBSTETRICS & GYNAECOLOGY/SCIENCE
PHOTO LIBRARY

Potential uses

Having been replicating in labs around the world for six decades, HeLa cells have also accrued errors not present in the original tumour DNA. Moreover, not all HeLa cells are identical, and Steinmetz says that it would be interesting to chart the cell’s evolution.

Whatever their origin, the genetic changes raise questions over the widespread use of HeLa cells as models for human cell biology, Steinmetz says. For instance, his team found that around 2000 genes are expressed at levels higher than those of normal human tissues because of the duplications. Alternative cell lines, such as induced pluripotent stem cells generated from patient skin cells, offer a more accurate window on human biology, he says.

Mathew Garnett, a cancer biologist at the Wellcome Trust Sanger Institute near Cambridge, UK, says that HeLa cells could prove useful for studying aspects of the biology of cervical tumours, such as their response to cancer drugs.In recent years, the genomes of many cervical tumours have been sequenced, and so it should be possible to see how these compare with the HeLa genome.

Steinmetz also points out that thousands of research papers based on HeLa cells, along with HeLa resources such as genetically manipulated lines and now a genome, means that labs will continue to stock the cells, even if they are not a perfect model of human biology. “These are not going to go out of fashion over the next 10 years,” he says. "I’m not sure where we’re going to be 20 years from now."Nature doi:10.1038/nature.2013.12609

References

Landry, J. et al. G3 http://dx.doi.org/10.1534/g3.113.005777 (2013).