Complex Insight - Understanding our world

It is distressing, but a fact, that the more rapidly any technology is adopted by scientists the more likely it is to leave people confused, anxious, and suspicious. This week, I wrote an article for the magazine about just such a revolutionary technique, called CRISPR, that permits scientists to edit the DNA of plants and animals with an ease and a precision that even a decade ago seemed inconceivable.

CRISPR research has already begun to transform molecular biology. There have been bold new claims about its promise and powers nearly every day. Yet, for the past fifty years, at least since Watson and Crick demonstrated that DNA contained the blueprints required to build everything alive, modern science has been caught in a hype trap. After all, if we possess such exquisitely detailed instructions, shouldn’t they be able to help us fix the broken genes that cause so many of our diseases?

The assumption has long been that the answer is yes. And for decades, we have been told (by the medical establishment, by pharmaceutical companies, and, sadly, by the press) that our knowledge of genetics will soon help us solve nearly every malady, whether it affects humans, other animals, or plants.

It turns out, however, that genetics and magic are two different things. Deciphering the blueprints in the three billion pairs of chemical letters which make up the human genome has been even more complex than anyone had imagined. And even though the advances have been real, and often dramatic, it doesn’t always seem that way. This has led many people to discount, and even fear, our most promising technologies. Somehow, we take lessons more readily from movies like “Jurassic Park” and “Gattaca” than from the very real, though largely incremental, advances in medical treatments.

This dangerous disconnect between scientific possibility and tangible results has already caused great harm: a scientifically unjustified fear of G.M.O.s, for example, has prevented many potentially life-enhancing crops from even being tested, let alone planted widely. The death of one patient, in 1999, halted all human-gene-therapy experiments in the United States for several years. We should, of course, be exceedingly cautious with such research, but if the U.S. is going to stop studies that could potentially help millions of people there are costs to that, too. (It’s worth remembering that there are real risks to everything we do: aspirin kills hundreds of Americans every year, and in the first half of 2015 nearly twenty thousand people have died in car accidents.)

Because it makes manipulating genes so much easier, CRISPR offers researchers the ability to rapidly accelerate studies of many types of illness, including cancers, autism, and AIDS. It will also make it possible to alter the genes of plants so that they can resist various diseases (without introducing the DNA of a foreign organism, which is how G.M.O.s are made). With CRISPR, almost anything could become possible: You want a unicorn? Just tweak the horse genome. How about a truly blue rose? The gene for the blue pigment does not exist naturally in roses. With CRISPR, it should be a trivial matter simply to edit that gene in.

Eventually, CRISPR should also permit technicians to edit embryos, which, at least in theory, could change the genetic lineage of mankind. The prospect is at least as frightening as it is exciting, and we need to start talking about that now. In the press, at least, that conversation—about perhaps the most exciting advance in the history of molecular biology—seems to have started. Two of the researchers I focussed on in my piece for The New Yorker have also been featured in other publications in the past two weeks: the Times has a profile of Jennifer Doudna, the Berkeley biochemist who helped figure out how to program CRISPR molecules to edit DNA, and STAT, a new online health and science publication launched by the Boston Globe’s owner, has one about Feng Zhang, a pioneering biologist at the Broad Institute of Harvard and M.I.T., who first made the technology work in mammals. The subject will soon get even more attention. Early next month, the National Academy of Sciences will convene an international conference devoted to the ethical use of this powerful new tool.

Via Gerd Moe-Behrens

Bacteria adjust to different environmental conditions mainly by modulating transcription. Internal and external stimuli affect regulatory elements, all of which formulate the complex transcriptional profile of an organism at any given moment. In synthetic biology, the use of synthetic genetic circuits and metabolic pathways, which are often unresponsive to the aforementioned native regulation, is a common procedure. Such behavior can be advantageous, as it allows the organism to remain unaffected by unpredictable perturbations. In many cases, however, the lack of interaction with the internal control leads to undesired effects: metabolic intermediate accumulation, reduced fitness, and decreased product yields. This sets the framework of a recent research paper from the groups of Stephen Mayo and Richard Murray, where they describe a de novo transcription factor that is regulated by vanillin.

Vanillin is a byproduct of lignin degradation and an important substrate for the flavor industry. It is a phenolic compound with cytotoxic effects. In this article, the researchers modified qacR, a tetR-family repressor to bind vanillin, which binds to DNA via a helix-turn-helix domain. In the absence of the effector molecule, qacR physically inhibits RNA polymerase from transcribing the region downstream the binding site (see figure). The inducer causes conformational changes that prevent this binding, thus activating the gene. The procedure for qacR engineering consists of three steps:

(i) computational protein design. The researchers superimposed vanillin with the qacR crystal structure, enabling them to identify the potential binding conformations and the crucial aminoacids. They subsequently came up with a number of protein mutants that could form the correct interactions with vanillin and did not have steric clashes.

(ii) cell-free initial screening. The proteins resulting from the previous step were tested in an in vitro transcription/translation system. This methodology let the authors of the paper validate the repression qacR imposes on a reporter gene (GFP), while screening the functionality of the engineered proteins. Since all of the initial modified proteins failed to be activated by vanillin, the researchers went back to step (i) and designed more modifications. This time, two mutants showed the desired phenotype.

(iii) in vivo validation. As a last step, the two proteins from step (ii) were tested in E.coli. Both were able to suppress GFP expression in the lack of activator. One of them responded positively to increasing concentrations of vanillin, resulting in increased fluorescence.

Via Gerd Moe-Behrens

cientists have made an amplifier to boost biological signals, using DNA and harmless E. coli bacteria.

 Conventional amplifiers, such as those that are combined with loudspeakers to boost the volume of electric guitars and other instruments, are used to increase the amplitude of electrical signals. Now scientists from Imperial College London have used the same engineering principles to create a biological amplifier, by re-coding the DNA in the harmless gut bacteria Escherichia coli bacteria (E. coli). 
Via Gerd Moe-Behrens

The full lecture title is "Cancers - Their Genomes, Microenvironments, and Susceptibility to Bacteria-based Therapies" by Bert Vogelstein. The Johns Hopkins Center for Biotechnology Education and the Department of Biology in the Krieger School of Arts and Sciences hosted the American Society for Microbiology's Conference for Undergraduate Educators (ASMCUE) on the Homewood campus. Bert Vogelstein gave the closing plenary lecture, "Cancers - Their Genomes, Microenvironments, and Susceptibility to Bacteria-based Therapies". He teaches at John Hopkins University.

ASMCUE, now in its 18th year, is a professional development conference for approximately 300 educators. Each year, its steering committee organizes a program that offers access to premier scientists in diverse specialties and to educators leading biology education reform efforts. For more information on the conference, go to http://www.asmcue.org/page02d.shtml

Via Dr. Stefan Gruenwald

New computer technology cracks the age-old riddle, demonstrating how a protein kickstarts eggshell formation. Researchers at the Universities of Sheffield and Warwick, in northern and central England, demonstrate how vocledidin-17 (OC-17), plays a part in eggshell formation. In a computer simulation, the OC-17 protein acted as a catalyst to kickstart the formation of crystals that make up an eggshell by clamping itself on to calcium carbonate particles. In otherwords the chicken came first. Click on image or title to learn more...

University of Texas Medical Branch at Galveston researchers have found a surprising connection between a key DNA-repair process and a cellular signaling network linked to aging, heart disease, cancer and other chronic conditions. The discovery promises to open up an important new area of research — one that could ultimately yield novel treatments for a wide variety of diseases. Learn more...

Via Dr Richard Badge

There is currently a great deal of concern about population declines in pollinating insects. Many potential threats have been identified which may adversely affect the behaviour and health of both honey bees and bumble bees: these include pesticide exposure, and parasites and pathogens.

 

Whether biological pest control agents adversely affect bees has been much less well studied: it is generally assumed that biological agents are safer for wildlife than chemical pesticides. The aim of this study was to test whether... nematodes sold as biological pest control products could potentially have adverse effects on the bumble bee... One product was a broad spectrum pest control agent... the other product was specifically for weevil control...

 

Both nematode products caused ≥80% mortality within the 96 h test period when bees were exposed to soil containing... nematodes at the recommended field concentration... Of particular concern is the fact that nematodes from the broad spectrum product could proliferate in the carcasses of dead bees, and therefore potentially infect a whole bee colony or spread to the wider environment.

 

https://dx.doi.org/10.7717/peerj.1413

 

Via Alexander J. Stein

New imaging technology has revealed how the molecular machines that remodel genetic material inside cells 'grab onto' DNA like a rock climber looking for a handhold.

 

The experiments, reported in this week's Science, use laser light to generate very bright patches close to single cells. When coupled with fluorescent tags this 'spotlight' makes it possible to image the inner workings of cells fast enough to see how the molecular machines inside change size, shape, and composition in the presence of DNA.

 

The Oxford team built their own light microscopy technology for the study, which is a collaboration between the research groups of Mark Leake in Oxford University's Department of Physics and David Sherratt in Oxford University's Department of Biochemistry.

 

The molecular machines in question are called Structural Maintenance of Chromosome (SMC) complexes: they remodel the genetic material inside every living cell and work along similar principles to a large family of molecules that act as very small motors performing functions as diverse as trafficking vital material inside cells to allowing muscles to contract.

 

The researchers studied a particular SMC, MukBEF (which is made from several different protein molecules), inside the bacterium E.coli. David Sheratt and his team found a way to fuse 'fluorescent proteins' directly to the DNA coding for MukBEF, effectively creating a single dye tag for each component of these machines.

 

Up until now conventional techniques of biological physics or biochemistry have not been sufficiently fast or precise to monitor such tiny machines inside living cells at the level of single molecules.

 

'Each machine functions in much the same way as rock-climber clinging to a cliff face,' says Mark Leake of Oxford University’s Department of Physics, 'it has one end anchored to a portion of cellular DNA while the other end opens and closes randomly by using chemical energy stored in a ubiquitous bio-molecule called adenosine triphosphate, or 'ATP': the universal molecular fuel for all living cells.

 

'This opening and closing action of the machine is essentially a process of mechanical 'grabbing', in which it attempts to seize more free DNA, like the rock-climber searching for a new handhold.'

 

It is hoped that pioneering biophysics experiments such as this will give fresh insights into the complex processes which are vital to life, and pave the way for a whole new approach to biomedical research at the very tiny length scale for understanding the causes of many diseases in humans, and how to devise new strategies to combat them.