The Myth of Basic Science – Matt Ridley
Does scientific research drive innovation? Not very often, argues Matt Ridley: Technological evolution has a momentum of its own, and it has little to do with the abstractions of the lab.
Cells rhythmically regulate their genes
A new study from The Elowitz Lab, Caltech researchers shows that pulsing can allow two proteins to interact with each other in a rhythmic fashion that allows them to control genes. Specifically, when the expression of the transcription factors goes in and out of sync, gene expression also goes up and down. These rhythms of activation, the researchers say, may also underlie core processes in the cells of organisms from across the kingdoms of life.
“The way transcription factor pulses sync up with one another in time could play an important role in allowing cells to process information, communicate with other cells, and respond to stress,” says paper coauthor Michael Elowitz, a professor of biology and biological engineering and an investigator with the Howard Hughes Medical Institute.
The research, led by Caltech postdoctoral scholar Yihan Lin, appears in the October 15 issue of Nature. Other Caltech authors of the paper are Assistant Professor of Chemistry Long Cai; Chang Ho Sohn, a staff scientist in the Cai lab; and Elowitz’s former graduate student Chiraj K. Dalal (PhD ’10), now at UC San Francisco.
Cai, Dalal, and Elowitz reported a functional role for transcription factor pulsing in 2008. In the meantime, researchers worldwide have been steadily uncovering similar surges of protein activity across diverse cell types and genetic systems.
Realizing that many different factors are pulsing in the same cell even in unchanging conditions, the Caltech scientists began to wonder if cells might adjust the relative timing of these pulses to enable a novel sort of time-based regulation. To find out, they set up time-lapse movies to follow two pulsing proteins and a target gene in real time in individual yeast cells.
The team tagged two central transcription factors named Msn2 and Mig1 with green and red fluorescent proteins, respectively. When the transcription factors are activated, they move into the nucleus, where they influence gene expression. This movement—as well as the activation of the factors—can be visualized because the fluorescent markers concentrate within the small volume of the nucleus, causing it to glow brightly, either green, red, or both. The color choice for the fluorescent tags was symbolic: Msn2 serves as an activator, and Mig1 as a repressor. “Msn2, the green factor, steps on the gas and turns up gene expression, while Mig1, the red factor, hits the brakes,” says Elowitz.
When the scientists stressed the yeast cells by adding heat, for example, or restricting food, the pulses of Msn2 and Mig1 changed their timing with respect to one another, with more or less frequent periods of overlap between their pulses, depending upon the stressing stimulus.
Generally, when the two transcription factors pulsed in synchrony, the repressor blocked the ability of the activator to turn on genes. “It’s like someone simultaneously pumping the gas and brake pedals in a car over and over again,” says Elowitz.
But when they were off-beat, with the activator pulsing without the repressor, gene expression increased. “When the cell alternates between the brake and the gas—the Msn2 transcription factor in this case—the car can move,” says Elowitz. As a result of these stress-altered rhythms, the cells successfully produced more (or fewer) copies of certain proteins that helped the yeast cope with the unpleasant situation.
Previously, researchers have thought that the relative concentrations of multiple transcription factors in the nucleus determine how they regulate a common gene target—a phenomenon known as combinatorial regulation. But the new study suggests that the relative timing of the pulses of transcription factors may be just as important as their concentration.
“Most genes in the cell are regulated by several transcription factors in a combinatorial fashion, as parts of a complex network,” says Cai. “What we’re now seeing is a new mode of regulation that controls the pulse timing of transcription factors, and this could be critical to understanding the combinatorial regulation in genetic networks.”
“There appears to be a layer of time-based regulation in the cell that, because it can only be observed with movies of individual cells, is still largely unexplored,” says Lin. “We look forward to learning more about this intriguing and underappreciated form of gene regulation.”
In future research, the scientists will try to understand how prevalent this newfound mode of time-based regulation is in a variety of cell types and will examine its involvement in gene regulation systems. In the context of synthetic biology—the harnessing and modification of biological systems for human technological applications—the researchers also hope to develop methods to control such pulsing to program new cellular behaviors.
Original News : phys.org
Original Paper: The Elowitz Lab
Various Posts @ Dept. of Chemistry, SPPU, Pune.
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Dr. Thomas Pucadyil’s group @ IISER Pune, published in Nature Cell Biology
The plasma membrane encloses and defines a cell, the basic unit that living organisms are made of. To facilitate cellular processes like transport of metabolites or signal transmission, the plasma membrane needs to pinch off parts of itself into the cell (endocytosis). This process of membrane fission is highly regulated so that the cut allows nothing more than the intended contents into the cell. Dynamin and a few other proteins with similar characteristics represent a group of specialized protein machines that cut membranes by using energy from nucleotide hydrolysis.
A new study from Dr. Thomas Pucadyil’s group at IISER Pune, published this week in Nature Cell Biology, describes a novel model membrane assay system with which to observe the dynamin-catalyzed membrane fission reaction using a standard wide field fluorescence microscopic approach.
The membrane system the team has devised comprises of an array of narrow ~40 nm wide supported membrane tubes, dubbed SMrT templates, laid out on a non-reactive glass surface. This system allowed them to visualize dynamin-catalyzed membrane fission reaction as a single membrane tube getting cut at multiple independent sites.
The advantage of this assay system amenable to fluorescence microscopy is that a single experiment allows the analysis of scores of independent membrane fission events along with potential information on membrane intermediates generated during the membrane fission reaction. Using this assay system, the Pucadyil lab has proposed a mechanism by which the dynamin scaffold assembly only imposes a moderate degree of curvature stress on the underlying membrane tube. Their analysis suggests GTP hydrolysis to be necessary to further constrict the membrane tube down to dimensions that cause the generation of tube intermediates, which resolve spontaneously into cuts on the tube.
The paper titled “A high-throughput platform for real-time analysis of membrane fission reactions reveals dynamin function” and authored by Srishti Dar, Sukrut Kamerkar and Thomas Pucadyil has appeared as an advance online publication of Nature Cell Biology.
This work received funding from the Wellcome Trust-DBT India Alliance and CSIR India.
Original News : IISER,Pune News
Peter Walter (UCSF, HHMI) : Harnessing Serendipity
– In Conversation With Claudia Dreifus, New York Times.
Peter Walter, a professor of biochemistry at the University of California, San Francisco, studies how proteins within cells communicate with one another. His contributions have been instrumental in shaping scientific understanding of how cells are organized and how they function.
While still a graduate student, Dr. Walter discovered the signal recognition particle, which guides proteins to their correct locations within cells. At U.C.S.F., his laboratory identified the inner workings of the unfolded protein response, which helps cells maintain properly configured proteins. Improperly folded proteins have been implicated in a variety of diseases, among them Alzheimer’s disease and cancer.
We spoke for two hours in February at his San Francisco home and more recently when he came to New York City to accept the Vilcek Prize, which honors the work of immigrant scientists and artists.
A condensed and edited version of the two conversations follows.
Q. Where did you grow up? Do I hear a Berliner accent?
A. Yes. I grew up in West Berlin during the Cold War years. My parents had a little chemists’ shop, which was like a second home to me. I think, in part, my scientific inclination was born in being around the fantastic materials there. That, and experimenting in the house.
It seemed natural for me to pick the chemistry track at university.
Unfortunately, the science instruction at the Free University of Berlin was, in the early 1970s, extremely proscribed. There was no room to discover the unknown, which to me is the essence of scientific inquiry. You were given protocols to follow. It was always clear what would happen at the end. You were graded on getting the expected outcome.
This did not engage me. What interested me more was something developing in America, a new field where people studied the chemistry of cells and how life worked. I tried to read all I could about this biochemistry. But I was hindered because most of the important papers were published in English.
So to improve my English, I did something audacious. I signed up as an exchange student at Vanderbilt University in Nashville.
What’s audacious about that?
Well, we Germans don’t tend to migrate — we stay pretty much in the place we come from. At 22, I’d never lived anywhere but Berlin. I told my mother I’d be back in nine months.
How did you like Nashville?
It was absolute culture shock — a very small town with a church on every corner. My host family, lovely people, believed that America had won the war in Vietnam.
The university, however — Vanderbilt was a revelation. At the laboratory of Professor Tom Harris, I was allowed to do real research. Here I was, this lowly exchange student, and I was given use of the most expensive equipment and complete freedom to design my own experiments.
At Vanderbilt, I began to appreciate something uniquely American: the possibility of personal reinvention.
And so, when one of the Vanderbilt trustees suggested I apply for my doctoral studies to Rockefeller University, where the students were free to design their own curriculum, I didn’t hesitate. And when I only made it to the Rockefeller wait list, I still hoped.
But then came some serendipitous luck: At the last moment, an accepted student opted for Harvard, and I was offered his place. So I told my mother that the nine months would be a little longer.
At Rockefeller, you ended up working in the laboratory of Gunter Blobel, who won the 1999 Nobel Prize in Medicine. What was he researching when you joined his group?
He was trying to understand how the protein machines inside the cells organized themselves, and how they knew where to go within the cells to perform their functions. Gunter’s idea was that, in nature, things don’t just happen. There’s a machinery inside the cell that’s important to its organization.
He proposed that the proteins had these chemical ZIP codes that directed them to their destinations. At the time, this was unproven, and many of Gunter’s rivals disparaged it.
I spent four years taking the process apart biochemically and discovered this signal recognition particle that directs the proteins to their correct location. This was an important step in proving the validity of Gunter’s ideas.
Few graduate students get to make such a significant discovery. Did the experience give you confidence?
I think it gave me the confidence to, in 1983, open my own lab shortly after graduate school. Once you realize you’re good at looking into the unknown, it no longer scares you. In my lab at the University of California, San Francisco, we took some of the research that Gunter pioneered further by studying the folded protein response of cells.
A cell is more than a bag of chemicals. It has a power plant, garbage disposal units, libraries, the genome, roads and traffic lanes. All the protein components produced have to fold up correctly within the cell. Proteins that are not properly folded can be toxic.
We discovered how cells determine if they have sufficient capacity to fold proteins into their appropriate three-dimensional shapes. Not having enough capacity to do this triggers the unfolded protein response.
Why is this important?
If cells can’t do it, they die. Thus, the unfolded protein response makes life-or-death decisions. It is connected to numerous human diseases like diabetes, neurodegeneration, cancer.
You had cancer six years ago. What did your time as a patient teach you about your lab work?
The treatment I got was pretty generic. It made me feel what an extreme dearth of knowledge we have about why cancer cells grow out of control and what we can do about it.
I am happy to say I’m disease free as I sit here. But I’ve had friends die because there was no treatment possible. So, we really need to understand what fundamentally goes wrong in these cells and how we can correct the defect. I think from that angle, yes, it gave my research a very strong new motivation.
Original Source : New York Times (NYT)
More Story : HHMI Bulletin
Video : Click
Homi Bhabha Centre for Science Education (HBCSE) : Need for more like this.
1) Teacher Education is one of the major activities of the Centre.
2) Centre of the country for Olympiad programmes.
3) R & D
Mysteries of misfolding: how does the prion protein misfold?
– Anusha Krishnan
Prions are strange, even by the standards of the biological world which regularly throws up bizarre creations. They are the agents that cause mad cow disease in cattle, scrapie in sheep, Creutzfeldt- Jakob disease (the equivalent of mad-cow in humans) and fatal familial insomnia. The term prion was coined from the words “protein” and “infection” to reflect its unique nature – an infectious protein, which does not require the all-important DNA or RNA molecules to copy and transmit biological information.
Prions are misfolded forms of regular cell proteins with a distinctive ability to convert their normally folded counterparts into more prions. If prions are deviant forms of normal proteins, sheer curiosity prompts one to ask – how are they formed? What causes these normal proteins to contort themselves into the prion form? Scientists Jogender Singh and Jayant Udgaonkar from the National Centre for Biological Sciences (NCBS, Bangalore) have a partial answer to this. Their work on the prion protein demonstrates that certain genetic mutations can destabilise the structure of the proteins and set it onto a “misfold path” leading to the aberrant 3-D conformation of a prion.
As with all proteins, prions are made of amino acids (the fundamental building blocks of proteins) that are chemically bonded to each other in a specific sequence. A simple analogy can liken them to beads of different sizes and shapes strung together. The ability to fold into a 3-dimensional structure such as a helix or a sheet depends on its constituent amino acids – much like how the physical and chemical attributes of the component beads allow the arrangement of such a string into a 3-D shape. Changing a single amino acid could drastically alter the folded form of a protein, just as changing a bead could affect the final form of a bead sculpture. Singh’s and Udgaonkar’s work shows that such single amino acid mutations in particular stretches of the normal protein sequence can spontaneously initiate misfolding into a prion.
The study utilised one of the first known prion proteins – simply dubbed “Prion Protein” or PrP – as a model to examine how naturally occurring amino acid mutations could disrupt normal protein structure to induce it to misfold. “We know that genetic or familial instances of prion diseases could be caused by single amino acid mutations in prion proteins. What we have tried to understand here is the mechanism of misfolding of the prion protein by studying the effects of familial mutations on the structure of the protein”, says Dr. Singh, the lead author in this investigation. The answer lies in a section of PrP named “α-helix 1” – a segment that is shaped like a helix. When this structure and an adjacent loop are destabilised due to pathogenic mutations, misfolding is facilitated in other parts of the prion protein, and the rates of PrP’s normal-to-prion conversion are increased. The instabilities cause the formation of flat sheet-like structures which further drive the transition of other helices within the protein into sheets.
“What is even more interesting is that none of the mutations we have studied are actually in the α-helix 1 region; but all of them destabilise this region”, says Dr. Singh. The results of this work also showed that the extent of misfolding in a mutant PrP was highly correlated with the extent of destabilisation in the α-helix 1 region wrought by the mutation.
The misfolded proteins now stick together to form spherical “oligomers”, whose subunits consist of the misfolded prions. The accumulation of such protein oligomers in nerve cells is the main cause of neuro-degenerative symptoms and ultimately, death, in patients with prion diseases. Research on other neurodegenerative disorders such as Parkinson’s and Alzheimer’s have noted a striking similarity between the toxic protein clumps (called amyloid plaques) within neurons found in these conditions and the prion oligomers in prion diseases. Therefore, these conditions are also increasingly being thought of as prion diseases or “prion phenomena”.
The research highlighted in this article elucidates the initiating steps of prion formation. This knowledge is of immense practical value as arresting these steps can stall the progress of prion formation and hence the disease it causes. Intriguingly, in another study Singh and colleagues showed that specific stabilization of the prion protein by mutation could completely inhibit its misfolding. Current therapies for prion diseases have taken the form of antibodies and other molecules that stabilise the helical structures in normal forms of potential prion proteins. These anti-prion drugs are highly potent in blocking further prion formation – they offer hope in not only surviving prion diseases, but may also prove therapeutic for Alzheimer’s or Parkinson’s.
About the study:
The paper appeared in the journal Angenwandte Chemie on 8th May 2015, and can be accessed here.