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Question of the Day: Physics or Genetics?

Some people love physics and math. With a few observations here and there, a physicist can infer the whole workings of the universe. "Oh, the moons of Jupiter seem to orbit around Jupiter at various speeds." Ahah! "The speed of light is finite!" He can do this because physics is so elegant and its rules are so universal. Even though it's all theoretical, there's a sort of inevitability to physics that makes it so appealing to me. Reading Eintein and Hawking, I've come to discover how the universe works in one way, and that is how it has to be. Let me put it this way: the same principles governing the way an apple falls from a tree is also the same principle underlying black holes forming from pulsars billions of light years away. It's so fascinating.

On the other hand, genetics and biology don't follow universal rules, and theories involving such a dynamic and living thing are never absolute or inevitable. Life is so dynamic; a biologist cannot make accurate inferences about life billions of years ago based on life today, and we may never know. An organism has a gene for lactose catabolism? So many different ways it could have acquires those genes. Independently, through lateral gene transfer, through a million simultaneous base substitutions, etc. Not to belabor the point, but it is inelegant in contrast to physics.

So which do you prefer, biology or physics? Do the isotopes in the stars interest you more, or do you prefer the study of animals and the causes of diseases?

I mentioned isotopes because I needed something to segue to what I did today; I cleaned up a super radioactive microfuge in the lab I work at today. The readings of tritium were off the charts, and so I did a pre-cleaning liquid scintillation count and two post-cleaning counts. Given the inherent danger of exposure to radioactivity, I still managed to have a blast.

No Science Sunday: Ambien Restores Speech For An Hour

A vibrant 24-year old man with cystic fibrosis suffers two massive strokes after headbutting a soccer ball. Doctors said the entire intellectual and visual area of his brain were essentially wiped out, and he would live his life as a vegetable. However, a medicine known as Ambien in the United States and Stilnox in Austrailia is able to restore his speech for an hour a day.

Their struggle, their remarkable spirit, and the bond Sally and Sam share is awesome. Awesome is definitely an overused word, but its use is appropriate here.

BRCA2 and Homologous Recombination

BRCA2, Breast Cancer 2 susceptibility protein, is encoded by BRCA2 gene mapped to 13q12.3. BRCA2 repairs DNA damage through homologous recombinbation, the exchange of identical or nearly identical sequences of DNA. Homologous recombination occurs mostly during sexual reproduction or repair of DNA damage. Unrepaired, DNA damage leads to mutations in the cell line, and eventually, cancer. Without BRCA2 protein, our body's ability to repair DNA damage and avoid cancer are seriously hindered. That is why people with defective BRCA2 are susceptible to breast cancer. DNA damage goes unrepaired, and cells  behave aberrantly.

An Overview of the Polymerase Chain Reaction

The polymerase chain reaction (PCR) is a method that selectively replicates desired DNA segments in vitro. It requires that we design two primers, each 20-30 base pairs long, that will hybridize to the 3’ ends flanking the desired DNA segment. The forward primer and reverse primer are anti-parallel and complementary to the nonsense and sense strand, respectively. For instance, if the nonsense strand of the DNA has the sequence 5’ TTG CCA GAT 3’, the forward primer is 5’ ATC TGG CAA 3’. Additionally, restriction enzyme recognition sites can be added onto the 5’ end of these primers to facilitate ligation of the target DNA into a cloning vector.

Flow Cytometry In A Nutshell

FACS was used in the trial treatments of leukemia last Saturday's post.

Fluorescence-activated cell sorting analysis, or FACS, uses a flow cytometer to separate individual cells in a heterogenous suspension based on epitope type. Fluorochrome-labeled antibodies are added to the cell sample. The antibodies bind to specific epitopes on or within the cell. The fluidics system delivers a stream of cells or particles one at a time through an interrogation point, where it passes through a laser. A cell traveling through the laser beam scatters the beam’s light forwards and sideways as a function of its size and granularity, respectively. When the laser beam strikes cells labeled with fluorescent-labeled antibodies, the fluorescent dye becomes excited and fluoresces at a unique wavelength. The intensity of the scattered and fluorescent light is collected and filtered by the optics system, recorded by the detector which translates the light into a quantifiable electrical impulse that can be represented graphically as a dot plot or a histogram.

We can use different fluorochromes at the same time, as long as their emission peaks are far enough apart for us to easily distinguish. A peripheral computer can instantaneously analyze the forward and side scatter light and fluorescence to identify the characteristics of individual cells and separate them into different subpopulations by charging each droplet with either a negative or positive charge, depending on the intensity and wavelength of fluorescence, as they leave the stream. The droplet is deflected either to the right or left by charged electrodes into one of three sample tubes. Intensity and wavelength of fluorescence and be plotted in a two dimensional box plot, where subpopulations in the sample can be distinguished by looking at two parameters. 

2D results with two different parameters makes visualizing cell populations so easy!

A histogram measuring the frequency of celled labeled with antibody A is plotted on the y-axis of the two-parameter box plot, and another histogram measuring the frequency of cells labeled with antibody B is plotted on the x-axis. The box plot in this example shows two subpopulations, distinguished by the intensity of fluorescence f protein expression.

New Cure for Leukemia?

Leukemia is the cancer of white blood cells.

The Penn scientists targeted chroniclymphocytic leukemia (CLL) by hacking a harmless version of the HIV virus to hack T cells in order to kill cancer cells. In previous studies, the cancer-killing cells died out quickly after infusion, but in this study, the genetically engineered cells multiplied a thousand-fold and were sustained for over 4 months. 

Let's go over the study first.  Three patients with chemotherapy resistant tumors had their blood drawn, separated, modified, and cultured. These patients underwent lymphodepleting chemotherapy, and their blood was reinjected. Endpoint assays were conducted a month after reinjection.

They did the same thing in mice, and the cells of interest were sustained for over six months, although I'm not sure whether the same monthly cycle was repeated. It doesn't say. But the cells of interest reached levels of up to 95% of white blood cells, up from 2.3-4.46% (figure 2). After an initial decay with first-order kinetics, the CART19 cell numbers stabilized between three to six months after reinjection. The fact that the cell levels were sustained after four months is at least some evidence the body can remanufacture the CART19 cells on their own.

No Science Sunday: GMSoccerPicks

Best Soccer News and Write Ups. Ever.

GMSoccerPicks is a must-read blog for you soccer fans out there. He's got some real insight as an avid soccer fan, and his commentaries should not be missed. The blog is updated daily, so if you're into soccer, bookmark it!


You can also join the hundreds of people following @gmsoccerpicks on Twitter and get soccer news as it happens, or like GMSoccerPicks on Facebook to get soccer write-ups in your newsfeed.

Enumerating Bacteria In Lab

Serial dilutions allow us to do viable cell counts or total cell counts.

Serial dilution and plating can determine the amount of viable cells in a culture. Serial dilutions allow a discrete number of colonies of bacteria to grow, whereas concentrated cultures may contain billions of bacteria per milliliter. In serial dilutions, smaller dilutions are repeated in succession, and the dilutions can be multiplied to obtain the total dilution. Thus, serial dilutions are more practical than doing the total dilution in a single time. For example, if I have a 100 ml bacterial culture, I can add 1 ml of it to 99 ml of water, add 1 ml of the first dilution to 99 ml of water, and then add 1 ml of the second dilution to another 99 ml of water. I end up with a 10-2 X 10-2 X 10-2 = 10-6 dilution of the original bacteria culture. I can then plate .1 ml of the final dilution on growth medium. The goal is to dilute the culture so that, when plated, the number of bacterial colonies is discrete and each colony arises from one viable bacterial cell. We can use the number of viable cells in the undiluted culture by dividing apparent colony-forming units with the product of milliliters used and the dilution factor. For example, if 150 colony-forming units were counted on the plate that was streaked with .1 ml of the 10-6 dilution, there is about 150 / (.1 ml X 10-6) = 1.5 x 109 bacteria/ml in the original culture. This method is useful because I am using only a small portion of the original culture, and large volumes of solution are not required for many-fold dilutions.

Evolution and G6PD Deficiency

Evolution takes place over thousands of years, when I asked about evolution, I was looking for an answer that had the same scope. I wasn't not talking about the past few decades, but the past few thousand years. So while some made very valid comments on botox and the nebulous cultural standards of beauty, the answer I liked best looked at the bigger picture and had some specific examples to support his thoughts.

Question of the Day

Why hasn't evolution gotten rid of the ugly and genetically dysfunctional individuals? It's survival of the fittest, right? For the past hundred thousands of years, wouldn't ugliness and genetic diseases be slowly weeded out?

M Fawlful won the 8 GB SD card. Congratulations!

Huntington's Disease Explained Simply

Cells in our body (except sperm cells and eggs) have two copies of every gene, one copy from your father, and the other from your mother. Genes are like blueprints or instruction manuals that tell the cell how to make proteins, the building blocks of the cell. Thus, genes and the proteins they encode for determine everything about the cell: how it grows, what it looks like, how it will respond to signals from its environment. Changes, or mutations, to these genes will cause changes to the proteins and affect the cell, much like a word-change in a sentence will change its meaning.

No Science Sunday: Wine Edition

It's Sunday, the day of rest! I like to relax on Sundays and read books with big bag of Flaming Hot Cheetos and a few glasses of good wine.

Got a date or going to a fancy dinner? Looking to spend 9 or 10 bucks on the best bottle of wine to enjoy with your company? Go for a wine made in Portugal as a general rule of thumb. Given Portugal has the lowest wages in EU, they're pump out good wines at a comparatively low price.

25 bucks? No thanks.

Yesterday, I was at a wine shop looking for a good bottle of wine for a professor of mine, and I overheard a lady smugly complaining about how she is so sensitive to sulfites in "lesser wines" and it gives her headaches. I could tell she had no idea what she was talking about. Sulfite allergies manifest in asthmatic or anaphylactic reactions, never headaches. I guess some people like throwing around buzzwords they hear once at a wine tasting at a bar or read about Consumer Reports. Anyways, the salesman offered her a Conundrum, which she happily got.

Conundrum is definitely expensive, and I am not sure if they're worth the money, given that there any many superior wines priced a little less.  I got an Evolution from Oregon for myself. It's as good for only 15 dollars. I certainly can't tell the difference. YMMV.

Unrelated note: saved 70 bucks today by changing my own engine and cabin air filters myself.

Regulation of Morphology of Corn Smut, Ustilago maydis

Basidiomycota, in contrast to other fungi such as Ascomycota, produce basidia that yield four sexual spores called basidiospores. U. maydis is part of this phylum. Its mating-type is determined by a tetrapolar system with two unrelated loci, a and b. There are two idiomorphs for the a locus, a1 and a2. Haploid U. maydis cells have either the 4.5kb a1 locus with genes mfa1, pra1, and rfa2, or the 8kb a2 locus with genes mfa2, pra2, lga2, and rga2. mfa1 and mfa2 encode pheromone precursors, pra1 and pra2 genes encode pheromone receptors for the a2 and a1 pheromone, respectively. rfa2, lga2, and rga2 are thought to function within mitochondria. The pheromone encoded by one idiomorph will bind to the receptor of the opposite cell type, activating a signaling cascade that induces G2 arrest and the formation of conjugation hyphae. The b locus contains two genes, bE and bW, and regulates the switch to the pathogenic filamentous stage, as well as tumor induction and the formation of teliospores. The complex mating-type regulation is not specific to U. maydis, and other Basidiomycetes such as Schizophyllum commune and Coprinus cinereus.

Ethics

I designed two new banners. Let me know which one you prefer. Click to enlarge both of them.

Yesterday, I asked whether you would kill an innocent girl to cure the world of HIV/AIDS, ultimately saving millions of lives. Given that HIV and AIDS kills 6,500 people every day, leaving millions of children as orphans in Africa alone, is the killing of one innocent person justified?

I couldn't kill one person to save millions of lives because doing so means I have to ask myself, "How far would I go? How many people would I kill to save millions?" Let's ask the question again, except this time, you have to kill ten innocent people to cure the world of HIV/AIDS. Would you still do it? What about killing a hundred? A thousand? Many of you justified killing one person to save millions, but would you kill thousands of people? At what point would you stop and say, "Alright, this isn't ethical anymore."

To the people who said they would kill the girl yesterday, how many people would you kill to cure the world of AIDS?

Question of the Day: Anti-HIV Antibody Edition

CN3D 4.3. Click to enlarge.

Jmol. Click to enlarge.

The first is modeled by the researchers, using the CN3 program. There's more colors available and the graphics look better. The one on the bottom is the same anti-HIV antibody in the Jmol program that I meddled with a little bit (ID: 3RPI).

This antibody mimics CD4 binding, locking onto to the spikes of HIV-1 so HIV-1 can't bind to (CD4) white blood cells. By characterizing its unique structure, researchers can design many novel antibodies that could efficiently inhibit the virus' entry into host white blood cells. 

 Random ethical hypothetical question here: You are granted the ability to cure HIV and AIDS and save millions of lives, but in order to use this ability, you must kill an innocent girl. You must choose between curing HIV and killing someone. What would you do? Explain your reasoning. I'll post my answer tomorrow.

Mesothelioma and Asbestos

First, the mesothelium. It's a frictionless monolayer lining that covers the internal organs. The luminal side has lots of microvilli that told fluids and proteins to allow intracoeolmic movement. It also helps leukocytes and other cells of the immune system to travel about in the fluid.

Mesothelium cells, with connective tissues.

How exactly does asbestos cause cancer? Well, it's made up of little tiny fibers that people inhale it. These fibers travel into the lungs and stick to its linings, damaging the membrane.  Intra-pleural inoculation of asbestos in rats have demonstrated that asbestos cause lesions within the lining, recruiting phagocytes and macrophages to the site of the lesion. The macrophages are part of the immune response, and they eat up cells which have asbestos in them. This in turn damages the macrophages and cause oxidative stress. Additionally, it is thought that smaller asbestos fibers can sometimes become entangled within the chromatin itself in the cell, and disrupt with the process of cellular division by interfering the packing and segregation of chromosomes. After many cycles of cellular division, the DNA damage accumulates. The subsequent damage induces the cell to undergo DNA repair, which is often error-prone. This is how asbestos damages the tissues, ultimately causing lesions to develop into a malignant tumor in the mesothelium.

Genetic Engineering and Gene Therapy

Our genes play a role in a lot of things: our chances of getting cancer or diabetes, about how tall we will get, our looks, how long we live, whether or not we get genetic disorders like Huntington's Disease, how fat we get. Gene therapy and genetic engineering has the potential to change all of that. In the movie Gattaca, people are genetically engineered to be physically perfect, with great stamina, perfect vision, the whole shebang. People who haven't undergone genetic engineering are called invalids and are forced to take on menial jobs like janitorial work, for instance, because of their predisposition to diseases and physical abnormalities.
Mesothelioma symptoms 
The question of the day is... If you are expecting a baby with a genetic disorder like diabetes or Huntington's Disease, would you have your baby's genetic makeup altered to prevent said genetic disorder? If you could choose whether your children were predisposed to cancer or not, would you make that choice, or leave it to nature? What about more trivial things that can improve your child's quality of life and give him more opportunities, like height, longevity, or eye color? Should people be allowed to make these choices, if science ever makes these choices viable? More importantly, if these choices ever become available, is it okay for society to discriminate based on our genotype? Mesothelioma structured settlement

The Wiedemann-Franz Law and Electron's Independent Spin and Charge

In 1853, Wiedermann and Franz found that elemental metals conducted electricity and heat at roughly the same ratios at the same temperature. This is because electricity moves through electrons, and heat uses electron's charge and spin to move through a metal. "For the past 150-plus years, the Wiedemann-Franz law has proved to be remarkably robust, the ratio varying at most by around 50 per cent amongst the thousands of metallic systems studied."

In 1996, American physicists C. L. Kane and Matthew Fisher predicted that the Wiedemann-Franz Law could be violated if electrons were confined to a single dimension. Electrons in 1D would have independent charge and spin excitation. Well, scientists have found a metal that could prove this, 15 years later.

Perianal Sweat... Why You Should Use Deodorant

She looks hot! Very warm, indeed!

Eccrine sweat glands are found only in primates and reach their greatest development in humans. They are distributed all over the body, producing sweat for cooling. When we are warm, the hypothalamus tells the eccrine glands to start cooling us off as the sweat evaporates.

Apocrine sweat glands are larger and are limited to axilla (armpits) and perianal areas in humans. Because of the substances that are contained within apocrine sweat (e.g. protein, ammonia, lipids, chromogranins) it has a more thick and milky consistency than eccrine sweat. The healthy bacteria covering your body loves to munch away on apocrine sweat, and they multiply and divide when there is apocrine sweat. As the grow, they produce a lot of waste, which is what causes body odor.

Do you wear deodorant, or antiperspirant? There are some whisper going around about cancer and aluminum in many antiperspirants. The next post may be about a connection between the two!

TTAG In-Depth Article on Extremophilic Bacteria

Extremophilic bacteria thrive in extreme conditions. Bacteria in deep sea vents have to withstand high heat and/or high pressure conditions. They must have adapted to their extreme environment by having specific genes that encode more resilient proteins or have special metabolic pathways. What many researchers have done is analyze the genome of extremophilic bacteria, then compare their unique proteins with proteins from microbes that live in more ordinary environments.

A deep sea vent, known as a black smoker, where diverse extremophilic microbes thrive.

Bacteria from the deep sea were compared with shallow water counterparts by Dr. Lauro, such as Enterococcus faecalis with Carnobacterium. Dr. Reytor compared protein synthesis between extremophilic bacteria and temperate mesophiles such as common pathogens. Protein synthesis at these extreme conditions is made possible by deep sea extremophiles and other bacteria in extreme environments survive because their genome has additional genetic clusters, though their function is unknown. Dr. Costa, meanwhile, spent most of his time overviewing the metabolic pathways of these extremophiles, indirectly by measuring the concentrations of nitrite, nitrate, ammonia, and sulfide, as well as other organic and inorganic compounds within the native waters of the bacterium species. Costa's emphasis on the geochemistry and the setting of the bacteria will show where some thermophilic and extremophilic bacteria grow best. 

Question of the Day: Do you believe in evolution?

Tell me if you believe in evolution, and why or why not! If not, what do you believe in?