Another way HIV is being cured…

This article identifies two membrane bound proteins and how they effect HIV. The proteins, SERINC5 and SERINC3 are transmembrane proteins that exist in the host cells that HIV likes to attack (usually the immune systems fighter T cells). The researchers showed how HIV-Nef, a protein associated with the development of AIDS seems to counteract SERINC3 and SERINC5 lowering their expression and allowing the infection rate of HIV in the body to soar. Researchers are very excited about drugs that could potentially target and inhibit this HIV-Nef protein to help lower the efficiency of all enveloped virus’s. In fact, using this method the researchers, using proteomics to find where the viral DNA was located, found that it reduced the infectivity of HIV 100 fold. This means that compared to a normal patient with HIV, a patient who has had these cell surface proteins inhibited has 100 times less HIV DNA in their fighter T cells.

Scientists have known for twenty years that Nef plays an important role in the development of AIDS and these studies seem to finally give a glimpse into how Nef does this. With the Nef protein silenced, or even greatly reduced we could potentially stop the development of AIDS in people who have already been infected with HIV. Interestingly, the HIV virus only contains nine genes in the form of single stranded RNA. To reproduce and continue to infect other cells, the DNA virus needs to actually invade the cell and take over some of it’s machinery. In turn, one virion of HIV can multiply exponentially inside an organism. Nef, one of the nine genes, is responsible for sequestering the SERINC3 and SERINC5 transmembrane proteins so that they cannot reach the surface of the cell. With the Nef protein inactivated, the SERINC3 and SERINC5 proteins are able to reach the surface of the cell membrane. Somehow these proteins prevent the HIV from injecting it’s genome, effectively stopping the virus from spreading. Researcher’s are hoping that this Nef-activated mechanism is not specific to HIV, or even enveloped virus’ but might be a universal tool in the fight against all viral infections.

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Gene Editing as a Potential Cure for HIV

dt_140710_hiv_virus_rna_800x600This article talks about how scientists are using new gene editing technology to disrupt and potentially destroy viral DNA. In this case scientists at Kyoto University used the CRISPR Cas-9 system to disrupt the DNA. The article first describes briefly what the CRISPR Cas-9 does. CRISPR stands for clustered regularly interspaced palindromic repetitions. Basically, it is a section of DNA, first discovered in bacteria, that can be utilized as a defense mechanism to protect a cell from viral infection. The CRISPR Cas-9 system is an RNA guided (or guide-RNA, aka gRNA) nuclease system. Let’s first take a look at what happens when a cell becomes infected by a virus. For example, we can look at the human immunodeficiency virus (HIV). HIV is a retrovirus meaning (among other things) it is a single-stranded RNA virus which incorporates itself into the host cells DNA through reverse transcriptase. HIV is interesting because of it’s ability to lie completely dormant for so many years. For simplicities sake lets say that the virus infects the cell and begins to attack immediately. In the large majority of these cases the host cell will die, however, if the host cell manages to survive it can do something very interesting and useful-assuming our cell has the CRISPR Cas-9 system. The CRISPR system will basically send out proteins that can read the amino acid sequence of the viral DNA. It then imbeds these copied sequences back into it’s own DNA code. Many short guide RNA strands can now be made. These strands will go off and associate with their matching sequence on the viral DNA. Lastly, an enzyme called Cas-9 will come and bind to these sites and make a double stranded cut in the viral DNA. After many of these double stranded cuts have been made in the viral DNA, the virus can no longer make many of it’s proteins and can no longer function correctly. What’s even more important is that this virus can not replicate itself so it cannot re-infect this cell, or any other cell in the organism. And, perhaps most importantly for our cell, because the viral DNA has been sequenced into this CRISPR region of it’s own DNA, all of this cells daughter cells will be immune to this virus. The CRISPR Cas-9 system then, is like a permanent vaccine that the cell gives to itself and all its descendants.

The researchers at Kyoto University attempted to edit and block the HIV virus that can lie dormant in the host cell sometimes referred to as a latent reservoir (LTR). Anti-retroviral therapy is able to keep active replication of HIV in check. The problem is that the LTR is always there and until now, has been resistant to therapy. The researchers report that when LTR-targeting CRISPR Cas-9 components were transfected into fighter T cells (the cells that HIV infects), the expression of LTR was significantly reduced. The researchers also report that the CRISPR Cas-9 may be a very useful tool in curing HIV.


Kyoto Study:


Brief Introduction into CRISPR Cas-9

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Resistance to Cancer in Elephants

The paper I chose to summarize involves a study done on elephants to determine why they rarely get cancer. For decades elephants have been known to be super resistant to cancer and until recently no one knew why. Researchers from University of Utah and Arizona State University in collaboration with Ringling Bros. Center for Elephant Conservation believe they have found the answer. The secret seems to lie in the DNA code of elephants. The DNA of the largest land animal on Earth contains 38 copies of a certain gene that codes for p53, which is a tumor suppressor. Thirty-eight that is, compared with just two copies in humans. Furthermore, the researchers believe that elephants may have a more aggressive way to target and destroy pre-cancerous cells. Joshua Schiffman, a co-senior author, says, “Nature has already figured out how to prevent cancer. It’s up to us to learn how different animals tackle the problem”. For many years elephant health has been a real mystery. Because elephants have about 100 times more cells overall compared to humans, they should be 100 times more susceptible to a cell malfunctioning and becoming cancerous. This study also confirmed, by looking at a large database of elephant deaths, that elephants die of cancer between two and five times less often than humans. That is, elephants have a 5% cancer mortality rate compared to between 11% and 25% in humans. The researchers analyzed the genome of the African elephant and discovered at least 40 variations of the cancer suppressing gene p53, 38 of which are retrogenes meaning they are variations of the same basic gene. The researchers also drew blood from many of the elephants and performed some interesting experiments. One experiment they did was subjecting the DNA of the elephants to damage which can be a facilitator of cancer. The elephant cells reacted by committing apoptosis. The researchers mentioned that because elephants are so massive and have so many cells they should be extinct by now due to the increase in risk of cancer. They believe that the elevated levels of the p53 gene is natures way (through evolution) of preventing cancer. Humans with Li-Fraumeni disease contain only one active p53 gene (as apposed to the normal two), and the researchers compared the blood tests from the elephants with humans who suffer from the disease. They found that after subjecting the DNA of both groups to damage the elephant cells committed programmed death five times more often than human cells from people with Li-Fraumeni disease. The researchers concluded that more p53 expression may lead to a much stronger resistance to cancer. As usual more research is needed to fully understand exactly how this gene could be used or studied to help better resist cancer in humans I just hope elephant blood doesn’t become as valued as their ivory.


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Interpreting Data and The Rosenhan Experiment

The lens in which we interpret data and experiments is crucial and can often become a hindrance, a blind spot on our lens if you will. For example, if we are evaluating a patients neurological condition and we have a doctrine in mind, say phrenology, we are more likely than not to find  something that we are looking for (a false positive). If we have instead, a doctrine of localization when we are examining the patient we will more likely than not find evidence for localization. The same holds true for a theory of neuroplasticity and each separate type of plasticity.What can be alarming is when we are presented with identical data, yet come up with two entirely different theories of explanation. This kind of subjective theory is dangerous in science and needs to be considered when we are conducting experiments and interpreting data and as we are reading over results of experiments and studies alike. This is exactly what double-blind studies attempt to guard for by taking away any preconceived notion of what a patient is (or is not) receiving. Double blind studies essentially strip away the subjective thoughts and opinions and leave us with objective data. I do not know if there is a science that isn’t vulnerable to this type of mistake. Certainly, the softer fields of philosophy and psychology are the most vulnerable with chemistry and physics being the least. Although, I would say that theoretical physics is very susceptible to this subjective error. Not only because theoretical physics necessarily involves making difficult predictions but additionally because the field is just so incredibly complicated.

Speaking of theEinstein famously disliked the implications of quantum mechanics that revolutionized physics in the first three decades of the 20th century. During international physics conferences Einstein would routinely pester Niels Bohr and the rest of the quantum mechanics founders, conjuring up thought experiments that seemed to contradict quantum theory.  After much dismay and some clever thinking Bohr would come up with an answer, usually by the end of the conference. The point I would like to make here is that even two of the smartest people who ever lived disagreed fundamentally about the same sets of rules and equations. Science, and especially in complex fields like theoretical physics, how you interpret data can be a very tricky business indeed. In fact, there were many new and often radical theories being proposed to explain the experimental results of quantum mechanics. This lead to something called The Copenhagen Interpretation which lead by Bohr, attempted to lay down a clear concise interpretation of the very odd world we were just beginning to discover. So, more objectivity leads to less room for interpretation but at some point complexity makes simple interpretation all but impossible.

Another great example of how we can misread and misinterpretation is The Rosenhan Experiment. This was a famous experiment conducted by a Stanford psychologist and professor who wanted to investigate the validity of psychiatric diagnoses. He and his colleagues (12 in total) attempted to get admitted into various mental hospitals across the U.S. The pseudo-pataients, as they were dubbed, confessed that they were experiencing tried auditory hallucinations. All twelve of them were admitted and diagnosed with psychiatric disorders. Following admission the pseudo-patients acted normally and after some time (I am not sure exactly how long) they told the staff that their auditory hallucinations had resided. All were forced to admit to having mental disorders and had to agree to take anti-psychotic drugs. The average time spent in the mental hospitals by the pseudo-patients was 19 days and upon release all but one patient was diagnosed with schizophrenia in remission. The second part of the experiment was not planned by Rosenhan but occurred when an offended psychiatric hospital administration challenged Rosenhan to send pseudo-patients to their facilities claiming they could spot the fakes. After a few weeks the psychiatric hospital released their results. Out of 193 new patients the hospital had seen 41 were labelled as potential pseudo-patients, in effect, patients who were lying and faking their symptoms. In reality however, Rosenhan had sent exactly zero pseudo-patients to the hospital. How could this hospital think that more than a fifth of patients they saw were faking it?

In science and medicine mistaking a false positive as a true positive is at best embarrassing and at worst deadly. Interestingly, evolution has programmed organisms to detect false positives and to react to them if they were true positives. This makes sense if we consider how animals interact in the wild. Consider a rabbit getting scared by a rustling in the bushes. Even if the rustling is nothing but the wind it is always optimal for the rabbit to respond as if the rustling was a lion. In other words it is much more favorable, evolutionarily, to be mistaken about a false positive than it is to be eaten.

Further Reading on The Rosenhan Experiment:

Further Reading on The Copenhagen Interpretation:

Further Reading on Data Analysis:

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The True Value of A Neuroscience Degree

The long term effect of my neuroscience degree is not about the extremely complex and detailed knowledge I have memorized to pass exams. It is the fact that I have a very solid foundation of neuroscience on which to build upon. In most areas I will have a basic understanding, in some areas I will have a very proficient understanding and in a few areas that I was (and still am) most interested in I will have an advanced understanding in. But, the real value of my degree is that I now have, at the very least, a basic understanding of just about any given field of neuroscience (behavioral, cognitive, immunology, endocrinology, virology, etc.) or any field related to neuroscience (genetics, epigenetics, optogenetics, stem cell therapy, etc.). The true value of studying neuroscience the past few years is not specifically what i’ve learned, but what I am now capable of learning. You can not just jump into a field like neuroscience, or chemistry, or physics and have any kind of comprehensive understanding of the science after a few months or perhaps even a year, no matter how hard you study. No matter how hard you work it takes a certain amount of time and a certain amount of exposure to the hundreds, thousands of concepts and ideas and theories and historical breakthrough’s to achieve any sort of grasp on your field as a whole. You need to hear things and read things over and over again if they are going to stick with you long term. It is like joining a new culture and learning a new language, quite literally in many aspects. You must get a feel for the science you’re studying, an understanding of it’s past and knowledge of it’s present state. Anyone can memorize brain related words and pathways but without context they are close to meaningless. I once heard that  becoming an expert in a field of science takes a decade and I think this probably true.  Three years ago I would not have been able to read a scientific article and come away with any real understanding. Now I feel confident that I can read almost any scientific article and come away with, at the very least, a proficient understanding of what I read, and that is what I am most proud of.
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What do you think?

“From a long view of the history of mankind, seen from, say, ten thousand years from now, there can be little doubt that the most significant event of the 19th century will be judged as Maxwell’s discovery of the laws of electrodynamics. The American Civil War will pale into provincial insignificance in comparison with this important scientific event of the same decade.”

-Richard P. Feynman

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How Come Some People Believe In the Paranormal?

This article described the science of belief. Belief in the super natural such as ghosts, belief that the government is hiding aliens from the public, belief that bigfoot is real are some of the things that researchers were interested in. While being in a STEM field I consider myself to be some what of a skeptic and I take pride in not believing in everything I read and watch. For me, personally, there needs to be a certain amount of scientific professionalism at the very least and I usually look for peer reviewed articles or double blind studies as the best proof of truth. With that said, I think there is always an amount of trust we must give to what we are reading no matter the subject matter. For example, we of course cannot hear and see directly all the information we take in so we have to trust what we are reading is true. It is up to each person individually to set there own standard of truth, although I think many people may not have a standard at all. Things get even more complicated when we move away from the objective sciences into the world of opinionated politics. In summary, the research team gave people a test to measure what kind of thinkers they were. The test differentiated between intuitive thinkers and reflective thinkers. I don’t think the test is a very good parameter for someone’s belief in a certain phenomena as belief is something that develops over a lifetime and takes into account family and social environment, cultural norms, personal life events, as well as intelligence and curiosity. Nonetheless, researchers reported that the reflective thinkers, who were supposed to be more cautious and perhaps skeptical than their intuitive counterparts, were less likely to believe things like their astrological sign and phenomena like UFO’s or bigfoot. I think this article is very interesting and gets to the heart of belief and truth in science, a topic that cannot be under valued, especially in today’s world.


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evolution analysis

-there is an equation that can predict evolutionary-survival of the fittest type change. If you take a mouse that has pressure from the environment to get bigger you can calculate, using the amount of pressure, to estimate how long(in generations of the animal) it would take for that mouse to grow to the size of an elephant. The calculation Richard was talking about actually involved pressure from the environment on the mouse to get bigger, but the pressure was very small, basically undetectable to field work, experiment, etc. The time it would take a mouse to grow to the size of an elephant is so fast, takes so few generations, maybe tens of thousands, maybe less, that the fossil records would be undetectable. In other words this animal evolved so incredibly fast that you wouldn’t be able to find fossils of intermediate species, instead you would find two animals that seem to be completely different, or at least not closely related. This phenomena explains why there are such gaps in the evolutionary fossil records, which may in fact never be filled.

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Culture, not Education.

physics at harvard is no different than physics at the local community college. An apple will fall to the earth at the same rate whether you are in CT or an inner city. True, there may be more skilled and knowledgable professors at a prestigious university, but we can simplify the situation by saying we are attending the same basic class, let it be Intro to classical physics, at both Harvard, or Yale, or Berkeley, etc.) and our small, quaint inner city community college. Let’s simplify the situation even further, so there are no discrepancies in my arguement. For the sake of my persuasion let’s say that both courses have been standarized by Professor X and they contain the exact same textbook, powerpoint slides, student tutors, etc. Therefore, our two classes are nearly identical and there are no significant differences that would lead you to a better education at one school versus the other. I think it is also safe to generalize this idea of ubiquity to the other hard sciences as well, whether it be chemistry, biology, neuroscience, engineering, etc. Science, especially as you work your way up to the harder, more objective science fields, cannot be taught so differently from university to university. I realize the degrees such as the humanities and the arts and business and economics and even the social sciences may allow a little bit more leeway in how they are approached and understood, but not enough to justify the dfference in tuition between the most and least expensive colleges. Now, if physics is physics no matter your environment (excluding a blackhole) and business management is business management no matter the name of your business school why are the costs of attending college so incredibly different? It’s because we, as students, and especially undergraduates, are not paying for an education, rather we are paying for a culture in which to be educated in. A professor or faculty member, a graduate student or even one of your fellow students are most likely to be the best and brightest if you attend a place like harvard or princeton. These people are only as valuable to you insofar as you take advantage of them, and they of you. These colleagues and mentors are really the main difference between schools. Associating with them, building relationships and networking in this environment is just as valuable and in many cases more valuable than the actual education you recieve. In this sense you are paying to be accepted into a group of intellectuals who can provide invaluable advice, opportunities and connections you would otherwise miss out on at a cheaper community college.

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Scientific Discover & Age

Why do academic students/post-docs make their major discoveries or contributions to their field between the ages of 23-33 so often? It is the peak of your bodies lifetime and may also be the peak of the brains performance. Also, this is the time frame when students are at the peak of their career academically, when they are introduced to the deepest most complex problems of their field for the first time. The novel approach may be the key here. Additionally, these people are post-adolescent and usually pre-family/marriage (maybe not marriage in the past)……

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