A Slice of Science

I had quite a blast this week. The workload was chill despite having a plant exam last Wednesday that took me around three days to study since I literally had to take a break every 30 minutes. Joking aside, I’m incredibly happy that more than half of my batchmates ate at Sbarro in UP Town Center yesterday.

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So more than half of MBB 2016 ate at #Sbarro this lunch 😀 #DamingTime

A post shared by JP Chan (@chanocyte_) on Feb 13, 2015 at 5:38am PST

Yes, that’s right. 21 of us invaded and claimed dominion over that restaurant for more than an hour. I think the manager was very pleased to see that many customers in the morning.

As I was eating my slice of delicious pizza, I suddenly had the urge to share the things I’ve read about for the past few months. Perhaps it’s the rich variety of toppings that inspired me to blog about the latest life science related news. Maybe it’s just an epiphany via pepperoni. Nonetheless, I’m giving you a glimpse of Science in this short post. I’ve provided many clickables in order to keep this entry from becoming boringly long. Like a slice of pizza, I wanted to give an explosion of flavors in one tasty bite.

1.) Antibiotics as Anticancer drugs. In one of the most surprising news out there, a group of medical doctors tested the efficacy of antibiotics to treat cancer. This is rather counterintuitive because antibiotics specifically kill bacteria (duh). But because of a fortuitous side-effect of some antibiotics that prevent mitochondria production, cancer cells effectively get deprived of surplus energy to wreck havoc in the body. Hence, these cancer cells can’t live the thug life.

Here’s a cute video on antibiotics hehe

2.) Novel class of Antibiotics found. I’ve posted a link about this before but I didn’t expound much about it. The fact that they discovered a 100% effective antibiotic is newsworthy enough. These Scientists also figured out a way to grow previously “unculturable” bacteria in the lab. Their method is a conceptually simple one which I might discuss in a future blog (hehe)

3.) GMO Biocontainment. There’s whole host of people out there who hate GMOs with such fiery passion but don’t even know what the acronym means. If I get a coin every time I hear people say they don’t like food with chemicals, I’ll be drowning in money. If you don’t like food with chemicals, don’t eat at all because all food are made of chemicals (do me a favor and don’t breathe as well because air is made of chemicals too).

WARNING: 100% of people who have come in contact with dihydrogen monoxide has died. Drink dihydrogen dioxide instead as it has been proven to kill all bacteria.

Ranting aside, there is a very small chance that genetically modified organisms (take note h8trs) might exchange DNA with wild organisms thereby polluting the gene pool. Thus, a group of scientists created organisms that rely on synthetic amino acids for their survival. At any rate, it prevents modified organisms from surviving outside the lab where these nutrients are not supplied.

4.) Using Smartphones to diagnose HIV. The incidence of sexually transmitted disease is increasing worldwide. Perhaps it’s a function of increased promiscuity among the youth coupled with a reluctance to practice safe sex. I’m personally not an advocate of pre-marital sex but if you gotta do it, put some protection on that erection. I recently had dinner with a good friend from mass comm and damn, STD in the Philippines is frekin’ real. Many college people nowadays seem to be getting a lot of action too. The threat is very real.

My friend gave me this sticker yesterday. I don’t know why but now I understand that it was destined for this blog

While a cure for HIV is probably decades away (’cause viruses are fucking crazier than kids on weed), at least we can prevent HIV from spreading by detecting them early on. This piece of tech is promising but the 14% false alarm rate is pretty insane. In a group of 100, you can get 14 people to think they’re HIV positive even if they’re not. Imagine the stress these unfortunate souls will get. However, I’m confident that bioengineers will be able to improve on this technology and increase the accuracy of the device.

5.) Photosynthesizing sea slugs. I know what you’re thinking; this is damn crazy to be true. But apparently, these critters have been known to bask in the summer sun since their discovery in the 70s. I’m sharing this largely because I don’t think many people know that these awesome sea slugs even exist. In a nutshell, this sea slug (Elysia chlorotica) incorporates chloroplasts into its digestive cells. And apparently, they also exchange DNA with their algal prey to maintain their captive chloroplast organelles. It’s quite literally an animal-plant hybrid. My Bio 12 profs (Mamaril x Roderos OTP) will be proud.

I would have mistaken it for a leaf myself 

6.) Light-activated CRISPR-Cas9. I’ve dedicated my previous post on the brief history of CRISPR and its therapeutic potential. Now here’s a new development that features my favorite biological system! By attatching it floral proteins sensitive to light, Scientists from Duke university were able to make a light controlled CRISPR-Cas9 system. This means that they can exercise spatiotemporal (space and time) control over the mechanisms of gene editing. It’s not only useful in tissue engineering but it’s also pretty cool on its own 😀

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The last two entries are news that I don’t expect most people to appreciate because they’re hardcore research tools. Hence, I’m writing this for the biologists, chemists, and people in between to get them excited about these new tech.

7.) DNA nanoswitches.  It’s basically a tool for studying molecular interactions at a cost of pennies per sample. If I recall my MBB 130 correctly, people typically use expensive equipment and reagents, like Fluorescent probes that employ FRET, to monitor protein-protein interactions. With this system, you only need to buy a couple of oligomers that attach to your proteins of interest.

DNA forming a closed loop due to interactions between conjugated groups

Interaction between these proteins would cause the DNA to form a loop-like structure. If you run this sample in a conventional agarose gel, you’ll get a band that’s slightly higher than a band if no interaction took place. This is because the looped DNA conformation retarded movement in the gel. Wyss has an amazing video series about this new technology that is freely available for viewing.

8.) Aptamers. They’re the nucleic acid cousins of antibodies who aren’t as picky as their protein counterparts. Aptamers are sequences of DNA/RNA that have been selectively chosen to bind to a particular ligand. DNA/RNA are ran through a column to remove non-specific sequences while those that do adhere to the substrate are amplified through PCR. This cycle is repeated until you get very specific aptamers. It’s a relatively young field but I find it interesting how nucleic acids can be used instead of proteins in performing canonical antibody functions in the lab 🙂

Fig. Aptamer selection. Learn more here

A CRISPR Way of Looking at DNA

[This entry is inspired by a Quanta magazine post. QM is hands down my favorite source of well-written popular science treatises. And I only loved the website more when they wrote about CRISPR. Click on the image above to direct you to a video on CRISPR]

My goal is to get you excited about CRISPR by the end of this article. It is a daunting duty to get people interested in a scientific discovery. The immediate reaction of most people is to dismiss it as boring or too hard to comprehend. I sincerely believe it’s due to a lack of scientific communicators out there to stoop down to the level of the common person. This is my contribution to the thankless task of translating science for the general audience. I hope that I will not only help you understand this discovery but infect you with my enthusiasm as well.

CRISPR is an acronym for “clustered regularly interspaced short palindromic repeats.” I know this sounds intimidating for people without a background in biology but I will try my best to dissect this term for you. DNA is the material in cells that encodes information in all living organisms. Unlike the 26 letters that make up the English language, this nucleic acid language is made up of only 4 letters (A,C,T,G) called bases. Now these bases are lined up together in sequences that compose the cell’s repository of information. CRISPR simply refers to DNA sandwiches of repeating (AGAGAG, for instance) and “random” sequences scientists have found in bacterial genomes.

At first, nobody really knew what they were for. It was just that these DNA sandwiches are found in many microorganisms whose genomes have been sequenced. Their ubiquity, however, hints on a crucial biological function yet to be determined. It is the first clue to the interesting mystery that biologists want to solve. Further comparisons among the sequences led to the observation that CRISPR is always found near a Cas gene.

The Cas gene encodes for an endonuclease protein. From the terms “endo-” and “nuclease”, it means that it cuts within inside a DNA sequence. So scientists had a hunch that perhaps CRISPR is involved in cutting up DNA sequences. Naturally, this leads to the question of what does it cut? The answer to this question came when other scientists studying CRISPR realized that the ” random” sequences looked a lot like viral DNA.

The hypothesis formed from this observation was that bacteria use CRISPR like a target list of criminals to kill. It is a list generated when Cas protein gets the DNA of an invading virus. Once it has the DNA of the virus, the bacteria can recognize that sequence and destroy the viral DNA. Experiments confirmed this hypothesis and eventually found that the Cas protein uses the CRISPR sequence for specificity. It locks in like a guided missile headed towards an invading pathogenic DNA to neutralize the threat.

If you have some knowledge of immunology, you’d realize that this is analogous to the active immune response in animals. In the context of basic biology, the discovery that single-celled organisms have a complex system of detecting and destroying specific viral pathogens is mind-blowing. It questions the paradigm that microorganisms are primitive creatures capable only of simple processes.

But that’s not the end of the story. Once you comprehend how this system works, it’s easy to imagine its wide application in biotechnology. This is essentially a system that could be utilized with unlimited potential. To help you understand the implication of this discovery, remember that it’s the CRISPR that gives target specificity to the Cas protein. CRISPR is a nucleic acid sequence that we can easily change with readily available laboratory techniques. By conjugating the Cas protein with different CRISPRs, we can target any DNA sequence we want. Anything from fruit fly wings to human cancer cells is fair game for CRISPR-Cas because all organisms use DNA to store their genetic information.

Thus, CRISPR provides a precision tool for molecular manipulation. This is not just a groundbreaking theory, it has actual clinical and industrial applications that are actively being researched right now. For instance, HIV viral DNA was snipped off an infected cell using a CRISPR-Cas system. While actual clinical trials are still far off in the future, it is an important proof-of-concept that may lead to an effective cure for AIDS. Since the CRISPR-Cas system is found in many bacterial species, there are numerous variations to work with when optimizing its applications. The potential is even greater now because scientists have recently discovered a method of culturing previously unculturable cells, expanding the repertoire of microorganisms available for experimentation.

Applications aside, CRISPR illustrates a recurring theme in the Scientific research process that I want you to remember. Everything starts with a basic research that attempts to solve a seemingly uninteresting topic. Scientists initially just wanted to know why they kept seeing these DNA sandwiches in the different microorganisms they sequenced. Now we have a novel method for precision genetic engineering. The discovery of restriction enzymes follows a similar story and these enzymes led directly to a range of researches that gave us the injected insulin used by diabetics worldwide.

So the next time you hear of a boring research conducted by local scientists in your nearby university, don’t think of it as a waste of public funds. Think of it as an exercise of the primal human instinct for the pursuit of knowledge.Think of it as a potential game changer in public health and industrial development. Think of it as an investment for a better and brighter future.