Tag Archives: molecular biology

The CRISPRs Fever

You may remember from biology textbook that we can edit genetic material using restriction enzymes, a DNA-cutting protein structure. Using this we can learn about gene functionalities, search for disease treatments or increase yields of crops. Controversially, it also made unnatural creations possible. However, different gene targets require different enzyme structures, just like to open different doors you need different keys, and making these “keys” turns out to be complicated, expensive and time-consuming, which might have kept most of the “fantasies”, such as “super human” or other wired things, away from reality for now for better or worse.

by PuraVida_Fotografie from Google Image "genetic mutation" Labeled for reuse

by PuraVida_Fotografie from Google Image search “genetic mutation”, labeled for reuse.

However, what if all the “doors” also have the same type of “digital locks”, and all you need to change is the password? CRISPRs (clustered regularly interspaced short palindromic repeats) turns out to be this “lock”. It contains repeated sequences sandwiched with spacers (unique genetic information) in between. The spacers are external virus genes kept in bacterias and served as the “criminal records” so that when invasion happens again, the bacteria can send an “army” of gene-cutting enzymes, called Cas9, to cut the recognized viruses’ DNA apart.

"Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA" by Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki - Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA http://dx.doi.org/10.1016/j.cell.2014.02.001. Licensed under CC BY-SA 3.0 via Commons

“Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA” by Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki – Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA http://dx.doi.org/10.1016/j.cell.2014.02.001. Licensed under CC BY-SA 3.0 via Commons

In 2012, scientists have proven that instead of making restriction enzymes for different genes, we can simply replace these “criminal records” and use the same Cas9 “armies” to cut desired genes with much less time and cost. You can find the details in this following video.

YouTube Preview Image[by McGovern Institute for Brain Research at MIT]

Nature , Science and many major media have unanimously deemed CRISPRs to be a revolution. Radiolab has discussed its ethical controversies as if the realization of the technology is right around the corner. It has been portrayed as such a simple and approachable method that people even claim to provide CRISPR DIY kit for experiments at home.

However, I think despite these attentions,  the reality is that we are still far from ready to harness CRISPRs. Although many researches has already been using it to edit genes in a variety of bacterias, plants, and animals within a short 3-year period, few studies focused on the limitations and functions of CRISPR itself. Some research was done too early without waiting for the technology to mature, such as the research using human embryos, which has resulted in a less satisfactory result. Some researchers commented that CRISPR can be less accurate than expected and may not be the most efficient and cost-effective solution for certain problems on Quora. Scientist Konstantin Severinov on Quanta Magazine also pointed out that it is still unknown whether defending invaders is the major usage of CRISPRs since many of these spacers appear to be genes of viruses that are long gone. It might be a good time now to slow down and maybe build the technique from ground up concretely first.

by Sainan Liu

Jelly-like Features of Disease-causing Proteins

I remember when I was a kid (or even now), one of my all time favourite snack is strawberry flavoured Jell-O (or jelly). Not to mention, making it was so easy and so much fun, as the strawberry aroma would fill the kitchen.

C. elegans worm used in the study. Source: Wiki Commons

C. elegans worm used in the study. Source: Wiki Commons

Scientists at the University of Cambridge, led by Peter St George-Hyslop used nematode worm C. elegans as a model for amyloid lateral sclerosis (ALS) and frontotemporal dementia to study the physical properties of FUS, an essential RNA-binding protein in the body. The behaviour and physical properties of FUS can be closely compared to that of jelly. All RNA-binding proteins have two common domains: one for binding RNA and the other where the protein appears to be unfolded. It is at this unfolded region that the FUS undergo a process of reversible ‘phase transition’, which closely resembles the formation of jelly.

Comparison of ALS-affected and normal nerve cell. Source: Sarah Scoles

Comparison of ALS-affected and normal nerve cell. Source: Sarah Scoles

One common characteristic of all neurodegenerative disease is the irreversible accumulation of misfolded or mutated proteins aggregates in the brain, which as a result causes damage to the brain and disrupts communication between brain cells.  FUS is one of many types of RNA-binding proteins that is essential to the brain. It is essential in the regulation of protein synthesis, with functions in the nucleus and cytoplasm of a cell. However, the accumulation of mutated FUS and other associated proteins is also the underlying cause of the neurodegenerative diseases such as ALS and frontotemporal  dementia. Until recently, the significance and how FUS proteins affects the development of these neurodegenerative disease has been unclear.

YouTube Preview Image

[Video courtesy of C.D. Net]

FUS starts out as soluble monomers (like the initial powered-form of jelly), and forms distinct localized accumulations. As it further condenses, a thick gel-like hydrogel structure is formed (like the formation of jelly after it cools in the fridge). This process can be reversible (like warming and cooling jelly repeatedly). Furthermore, during these transitions, RNA and proteins are continuously released from protein assemblies (like suspended fruits in the jelly as it is re-warmed and re-cooled).

The above processes are beneficial because it allows the cells to accumulate cellular machinery in a confined three-dimensional space (with no cell membrane required)  when needed to perform key tasks, but also disassemble when not needed. In addition, it is also faster and less-energy costly compared to the formation of a membrane-bound vesicle.

Although FUS is able to carry out vital cell processes by interchanging between different states, “this essential property also makes them vulnerable to forming more fixed structures if mutated, disrupting their normal function and causing disease” says Professor St George Hyslop. Mutation of FUS causes it to over-condense and become a thick fibrous gel, irreversibly trapping the essential RNA and proteins required for protein synthesis. It is the accumulation of misshaped FUS and other RNA-binding proteins that causes serious neurodegenerative diseases. However, further research and understanding of what are in these assemblies can bring us one step closer to curing ALS and other neurodegenerative diseases.