A Vaccine for HIV?

Let’s face it. HIV is a pretty scary virus. There is no cure or vaccine available in the market to help you. It doesn’t matter whether you’re a hotshot businessman loaded with cash or a homeless dude begging in the streets. Once you get infected, you’re in for a lifetime of medication. The only way be free of HIV is to prevent infection in the first place.

20150214_071714Don’t let your affection give you an infection. (yes, I’m using this photo again)

Given the prevalence of HIV infection around the world, research is actively being done to combat this virus. You’d think that scientists should have figured out this problem long ago and that the only reason people are not getting a cure is because of Big Pharma. But before you scare the shit out of people with conspiracy theories, consider that the biology of the HIV makes it incredibly hard to defeat.

HIV mechanism

HIV is one slippery son of a gun. First, it’s a virus that attacks your immune cells. In particular, it preferentially targets your helper T cells (CD4+ lymphocytes in nerd speak) responsible for mounting an effective immune response. That’s right, it screws you over by turning cells sworn to protect you into HIV making machines. Second, it mutates so easily that the body is essentially blind to the HIV infection. For instance, the envelope glycoprotein that surround the viral genetic material changes rapidly. It’s so prone to changes that antibodies used to bind to them are rendered useless after a while.

hiv_virus

HIV THUG LYF. HUSTLE HARD OR DIE HARD

Potential Vaccine?

Now, scientists from The Scripps Research Institute (TSRI) have announced the creation of a novel drug candidate that blocks every strain of HIV including the hardest-to-stop variants. In their study published in Nature, they reported that the drug candidate efficiently neutralized 100% of all tested viral isolates.

This drug was created by fusing the proteins,CD4-Ig and a modified CCR5 co-receptor, into a protein called eCD4-Ig that selectively bind to two conserved regions within the viral envelope glycoprotein, Env.

Whew, that was a mouthful. But that sentence effectively summarizes what the scientists have done. For the sake of a conceptual overview, it doesn’t matter what those two proteins are. What matters is that they bind to conserved regions within Env. It’s important because I’ve mentioned earlier that this envelope is highly prone to mutations.

WAIT, WHAT?

I understand that the sentence summary above is complicated for non-technical readers out there. So let’s bring the news to a comfortable level of comprehension. To understand how this vaccine is such a breakthrough, imagine that HIV is an elite force of a global terrorist group. Think of HIV as a highly trained infiltration unit who are masters in the art of disguise. The police have such a hard time of tracking these terrorists because they keep changing their appearance.

It can be argued how a terrorist looks like but here’s what the media is feeding us. That’s also a social science topic lol

Through painstaking investigation, let’s say that the police has established that the HIV terrorists have two tattoos in their body that mark them as HIV members; one in each thigh. These tattoos are definitive markers because it’s what identifies them as part of the HIV terrorist arm. They’re hidden from view but the police can easily check for these tattoos.

In a nutshell, eCD4-Ig targets these “tattoos” of the HIV. Stretching our analogy further, you can think of the “tattoos” as the conserved regions crucial to the entry of the HIV virus to its host cell. Obviously, if the virus mutates critical elements of Env too much then it couldn’t enter the cell. eCD4-Ig effectively targets not just one but two conserved regions of Env thereby ensuring its binding. When the binding event happens, they’re marked as HIV and are now on the hit list of the police (the immune system).

Gene Therapy

The Scientists didn’t just stop with the production of the fusion protein. It’s a very effective agent against HIV but it wouldn’t work in a vaccine-like manner if your body can’t produce it on its own. How do you insert a gene sequence that instructs cells to produce the fusion protein?

You use a virus.

Paradoxically, the scientists used a virus to prevent the Rhesus macaques in the study from getting infected by HIV. Of course, this wasn’t an ordinary virus. It’s an engineered adenovirus that has been modified to deliver a genetic payload without causing harm to a cell.And for at least 34 weeks, the Rhesus macaques in the experiment were protected from HIV infection even after getting injected by amounts of the virus too high to be transmitted naturally.

WHAT AGAIN?

Okay, that sounds complicated as well. But the adenovirus simply just gave instructions to your cell on how to look for the HIV. To stretch our terrorist analogy even further, imagine that the adenovirus is a captured terrorist that squealed information on how to identify our HIV terrorists. They tell your cells to look for the “tattoos” of HIV so that they can be dealt with swiftly and severely.

This is the wanted list for the 9/11 bombing. The immune system does an analogous job of cataloging “terrorists” too

Further Studies Needed

Aside from your usual gang of anti-vaxxers who outrightly abhor the very notion of a new vaccine, there are many other hurdles to be overcome before this vaccine ends up in your local clinic. For one thing, there hasn’t been any human clinical trials yet. The scientists also have assess the effect of the fusion protein constantly getting produced in your body. Moreover, they need to extend the period of protection from HIV to work as a viable vaccine.

However, the Science behind their technique is incredible. It truly reflects decades of work probing the biochemistry of the HIV. This paper shows how the research effort to create an anti-HIV vaccine is taking the right steps in the right direction.

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.

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

A post shared by Jonathan (@chancharan_) on

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.

Screen Shot 2015-02-14 at 7.49.48 AM

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).

http://upload.wikimedia.org/wikipedia/commons/thumb/8/8f/H2O_Polarization_V.1.svg/2000px-H2O_Polarization_V.1.svg.png

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.

20150214_071714

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 cellsAnd 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 😀


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.

Screen Shot 2015-02-14 at 7.09.25 AM

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

n00b guide to microRNAs

Cells can be seen as chemical machines composed of various interacting parts. These parts work in a very precise manner and are highly regulated. As such, cells are quite similar to the modern day computer that processes a lot of information. While you’re reading this article, many other process are happening in the background. You could be playing music or “legally” downloading a movie while your internet browser is open.

Ahoy there matey come on aboard me ship!

However, you don’t have all programs running simultaneously or else you’ll end up frying your computer. In the same way, the cell does not run all of the programs it has simultaneously. Genes are only opened (or “expressed” in biology nerd speak) when they are needed by the cell. Recent studies have shown that genes are regulated by a special class of RNA called microRNAs or miRNAs. But before we tackle what miRNAs are let’s first have a review of the central dogma.

Modifying the Central Dogma

You’ve probably first heard of RNA in a basic biology class. It’s usually taught in tandem with the concept of the central dogma in molecular biology. In case you forgot what it is or you were asleep when it was taught, the easiest way to remember it is: DNA->RNA->Protein. A gene composed of DNA is transcribed into messenger RNA (mRNA) and mRNA is translated to protein. That is its most basic form still taught in elementary or high school classes. [pro tip: don’t confuse miRNAs w/ mRNAs they’re two entirely different things]

https://i1.wp.com/biowiki.ucdavis.edu/@api/deki/files/225/03genessimplecomplex.gifTHIS ISN’T EVEN MY FINAL FORM

But we’ve moved on from that simple model. We now know that RNA is not just a transient intermediate of DNA. RNA is a dynamic player involved in the regulation of gene expression. One of the relatively new forms of RNA discovered is miRNA. It is a short sequence composed of 21-23 base pairs (A,C,U,G combinations) that can bind to numerous mRNA transcripts. When it binds to a particular mRNA, it signals the cell to degrade that mRNA or prevent translation into protein.

Mechanism of miRNA action

In English pls?

An easier way to understand how miRNAs work is to go back to our computer analogy. We can think of mRNA transcripts as running programs and miRNAs as task managers. Following our analogy, miRNAs can control whether individual transcripts are shut off. This control is exercised through the amount of miRNAs present in one cell. The more miRNAs there are, the more mRNAs are degraded. Hence, the effect of miRNAs on mRNA is similar to a task manager closing programs in a computer. But instead of clicking to end a program, more miRNAs are produced to silence mRNA expression.

Another difference is that there is no universal miRNA that can shut off all mRNAs. There are many miRNAs out there that exercise control over mRNAs. That’s like saying a task manager can control only a specific set of programs. But this lack of miRNA universality is actually useful for medical diagnostics. Scientists can track the expression miRNAs that regulate a set of important genes implicated in a given disease.

miRNAs in diagnostics

For instance, a miRNA that controls a set of genes related to tumor suppression can be tracked to diagnose if a patient has cancer. The expression profile of a dozen miRNAs is sufficient to say if one has this disease even before the deleterious effects manifest. This is particularly important in breast cancers or pancreatic cancers that are typically diagnosed only in their late stages. Early detection can lead to better treatment options for a patient and increase the likelihood of survival.

Harvesting miRNAs for diagnostics can potentially be done using nothing more than urine samples. In my next entry, I’ll talk about how this is made possible by newly discovered extracellular structures called exosomes or you can check this link to have a bird’s eye view of how they can be used in diagnostics.

n00b guide to Molecular Biology

A primer on the blog series

When I tell relatives what major I’m taking up, I often get puzzled stares and the same confused questions. They immediately assume that I’m a masochistic pre-med major or that I work with some crazy stem cell shit. Of course, I laugh with them and play along with their silly jokes but I often get the urge to tell them all about the interesting things we study.

However, the difficult part in getting people to understand what we do is the large information gap that exists. I can’t explain how the dynamics of gene regulation work when they don’t even know what a gene actually is. But even if the concepts we study might seem completely foreign, I still want people to appreciate how amazing our cellular machinery is. I want people to know more about why disease progress the way they do or why cancer is such a difficult disease to treat. I want people to understand why I’m excited about my major even when the workload is insane at best.

It’s an arduous task but I do not believe it is impossible. So in my next few blog entries, I’ll *attempt* to give the uninitiated a taste of some molecular biology concepts that might appeal to the general public. For my first entry, I’ll introduce microRNAs and explain how they are important in the study of gene expression regulation and cancer diagnosis.

A CRISPR Way of Looking at DNA

Capture

[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.

Life in the Context of Thermodynamics

I remember now that I made a wordpress account for voicing out my philosophical inquiries regarding the nature of God. It was an emotionally stressful night that finally led me to write a blog entry. However, I let this account gather dust because I was afraid that the people who raised me as a conservative Catholic would happen upon this page and be extremely disappointed. Perhaps my high school self would be disappointed as well. But in time, I have learned to accept that I am an agnostic. I’ve heard most of the arguments for the existence of a God and I’ve pondered on them (mostly before exams because my brain loves to distract itself with philosophical musings when it’s working on full blast).

One of the arguments I used to hear often was that life is too complex to have arisen on its own. There must be an intelligent designer that engineered the mechanisms of life processes. I found this reasoning disconcerting because it assumes a being that we can neither prove or disprove to exist. We just need to accept the limitations of Science in answering this fundamental question regarding life.Even if I try forgetting this question, it always comes back to haunt me.

How do you reconcile the complexity of life with the Physical laws that govern the universe?

I recall even asking this question when I had the dengue fever. In Chem 16, we were taught the basics of thermochemistry and it was then that I wondered how the 2nd law of thermodynamics seem to contradict life itself. The entropy of the universe is always increasing but why is life incredibly complex? In retrospect, I think this question stems from my failure to completely understand the second law. Organisms are open systems where energy and matter can flow freely; the net entropy of the universe still increases despite a local decrease in entropy.

This is where non-equilibrium thermodynamics come into play. I was introduced partly to this concept while reading Biochemistry by Mary Campbell and was completely enamored by it when I read quanta magazine’s article about Jeremy England’s take on this issue (https://www.quantamagazine.org/20140122-a-new-physics-theory-of-life/). According to him, life is not just consistent with the laws of thermodynamics; they DEMAND life to exist.

In my capacity as a biology student to understand what was going on, I think that when a system is pushed very far away from equilibrium through an input of energy, it can organize itself into something more complex so as to dissipate excess energy more efficiently. To illustrate, think of a mixture of biooligomers in solution. The number of favorable reactions in that system is dwarfed by millions of reactions that happen within a bacteria of comparable mass. Hence, the net entropy in living organisms is far greater than that of biooligomers in solution.

I think it’s humbling to think of life simply as efficient machines to increase the entropy of the universe. A lot of people would not probably agree with me when I say I find this extremely satisfying to think about. Here is a set of fundamental laws that can explain the dynamic complexity of life in a few set of equations. While it doesn’t answer the very important question of why the universe had such low entropy during its inception (was it because of God? :O), it does put life in a different context–an important framework that facilitates scientific inquiry.

Refolding of Proteins to their Native State

So I spent a solid two hours just trying to get reliable sources on this article I saw on the internet where researchers supposedly “unboiled” an egg (http://www.cnbc.com/id/102364302). I happened upon that article a few days ago when my Orgo chem classmate shared it on Facebook. My initial reaction was that of amazement. One of the first things you learn in basic biochemistry is that it’s extremely difficult to renature a protein once it has denatured. The free energy landscape consists of numerous energy minimas where a protein can get trapped in when it attempts to refold properly. Armed with this knowledge, my excitement slowly died down to skepticism. CNBC is a reliable news network but it often happens that journalists misrepresent recent discoveries in Science. I had to understand what was going on.

This article gnawed at me ever since I read it because the headline sounds too good to be true. So I tried reading on the vortex fluidic device (VFD), the machine that was used in the experiment. However, it’s an extremely difficult read unless you’re a Chemist or an Engineer. One of my frustrations as a biology major is that I’m not equipped with the technical knowledge to understand complex machines. I supposedly have “biotechnology” in my degree as well but I think I only have superficial knowledge to actually merit that title in my diploma when I graduate. I once attempted to read a paper on a continuous process for producing biofuels from algae a few years ago and I can’t even say I understood 25% of what the authors wrote. There was simply too many references to unit operations and chromatography techniques that I have no prior knowledge on. I downloaded that paper and hoped that someday I will be able to understand what the researchers did.

Going back to the article I read, the VFD is essentially a machine that spins liquid into a very thin film in order to speed up a chemical reaction. You get a similar vortex when you mix powdered drinks like Tang in a glass of water. It’s just that this process is more controlled. I eventually found a freely available preview page from the original paper published. It included Weiss, who co-authored the first Chemical Biology textbook as my batchmate, Mao, pointed out (I won’t digress again from the discussion. I’ll probably just make another entry about my fascination with Chemical Biology in the future)  Being a preview page I only got a glimpse of the paper but I think this summarizes what they did:

“We imagined applying the VFD with a similar range of input energies to the refolding of proteins…”

Since the folding of a protein to its native state is just a thermodynamic process, I think they just made the the folding more favorable. However, I’m really disappointed because I can’t get into the details because the paper is behind a paywall. While I understand that publishers need to get money from papers, I hope that my university can provide us with subscriptions to these publications. We are a state university after all