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Tag: biochemistry

“Friggin’ awesome video” on the TCA cycle. h/t @DrKimlicka

By Wilson Lam, via Lynn Kimlicka.

First scientifically authentic (albeit fabricated) paper on #wookiee genetics. #chewbaccaFTW

In which we compare the common Wookiee with a newly discovered cave dwelling (pseudo albino) Wookiee species, and note a number of interesting gene expression differences.

APCMVol1pp7front

From the Journal of Praetachoral Mechanics/Science Creative Quarterly. Link to full text and full pdf article here.

Research paper on Hulk genetics. Need I say more?

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Briefly:

BACKGROUND
Superheroes possess exceptional characteristics that far exceed the scope of human capabilities, such as the tremendous strength and pigmentation observed in The Incredible Hulk following his exposure to γ-radiation. Here, we explore the underlying molecular mechanisms for the “superhuman” abilities seen in the Hulk, as compared to semi-superheroes Papa Smurf and Popeye the Sailor. In particular, we examine the role of epigenetic mechanisms, principally DNA methylation, in the genotypic expression of “super” genes and their phenotypic manifestation.

METHODS
Whole Transcriptome Shotgun Sequencing (WTSS) was conducted on The Incredible Hulk, Popeye the Sailor, and Papa Smurf to identify “super” genes. Whole Genome Shotgun Sequencing (WGSS) was subsequently performed on the Hulk, from which chromosome γ was assembled and Bacterial Artificial Chromosomes (BAC) were created. FISH-karyotyping was then employed for chromosome examination before and after treatment with γ-radiation. Methylation assays were conducted on CpG islands upstream of “super” genes to assess gene expression following treatment with activator substances spinach and smurf berries.

See the data and the full paper (pdf and full text copy) at the Science Creative Quarterly.

Keep Calm and Carry A Pipetteman: The T-shirt. #molecularbiology #geekwear

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T-shirt now available in honour of my lab’s Molecular Biology 5 day professional workshop (next one held in Vancouver from Feb 17th to 21st, 2014 – more details here). Note that all revenues go towards my lab’s outreach programming, which can be surveyed here.

Anyway, if you’re a scientist in need of a quick refresher in these techniques, or someone in a parallel field and want to learn more about the various methodologies that keep infiltrating your research discipline, then take a peek and consider signing up (or pass along to a colleague).

Also, if you’ve got a friendly neighbourhood bulletin board nearby, it would be AWESOME if you could put this poster (pdf) up somewhere.

T-shirt available for purchase here.

You know it’s all good, when you have to read Wookiee research papers. Wookienomics: it’s a thing… #starwars

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Note: eventually, some of these (I suspect) will be published in full at the Science Creative Quarterly.

Ridiculously detailed (but fake) research paper on the electrical abilities of #Pokemon #pikachu

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PLOS BIOLOGY (March 2013). Vol 11 Issue 3. e1001501 p1-6 

Click on the image to go to full text paper. Click here for pdf download.

ABSTRACT

Electrocytes contain membrane proteins that allow the polarization of the plasma membrane, thereby allowing the generation of electricity in animals. It has been long established how electricity is generated in the electric eel, but recent studies found similar electrocytes to be active in electric mice. We aimed to study the basis behind electric discharge in a land animal. We found that the voltage-gated sodium channel, Nav1.4a, was expressed in electric organs of the electric mouse, Pokemon pikachu and the electric eel, Electrophorus electricus. However, Nav1.4a was not expressed in the muscle cells of E. electricus while it was expressed in the muscle cells of P. pikachu and other rodents. We also found that P. pikachu and E. electricus shared similar amino acid substitutions at the nonconserved region of this protein. Voltage-clamp technique gave insight on the much greater potential differences generated by P. pikachu compared to electric eel and finally, microscopy analysis revealed greater Nav1.4a numbers in P. pikachu, potentially correlating with aforementioned greater electric potential generation, which perhaps lead to its capability to discharge electricity readily through air.

AUTHOR SUMMARY

Many species of fish are able to generate weak or strong electric discharges, either for communication or for stunning predator or prey. The electric organ, made of electrocytes, is responsible for generating electric discharge. Electrocytes are thought to be derived from neuronal and muscle cells. The voltage-gated sodium channel, Nav1.4a, is found to be absent in the muscle cells, but is highly expressed in the electric organs of electric fishes. In our study, we looked at Nav1.4a in a species of mouse, P. pikachu, that also generates electricity, but through air instead of water. We compared this electric mouse with electric eel as well as nonelectric rodents. Here, we found that Nav1.4a is expressed in both the muscles and electric organs of P. pikachu. In terms of the amino acid sequence, the channel protein of P. pikachu was more similar to the electric eel rather than the rodents. We then observed that P. pikachu possessed much greater numbers of Nav1.4a and generated a much higher potential compared to the electric eel, which may explain its ability to discharge electricity through air.

Via the Science Creative Quarterly (with apologies to PLOS Biology)

Complex carbohydrates indeed

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By Gemma Correll.

Fake but very detailed scientific paper on the molecular mechanisms responsible for the Incredibles’ superpowers.

Superhero-Paper-Annika-and-Deb

(Click on the paper image to download full text pdf of the research paper).

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ABSTRACT
We demonstrated that the presence of superpower (SP) protein cleavage is responsible for the diversity of superpowers in a tissues-specific manner within The Incredibles family. This cleavage event produces two fragments, 135 kDa and 85 kDa, without a loss of peptide, as confirmed by Edman degradation. We speculate that the 85 kDa protein fragment is involved in the generation of superpower.

Annika Sun, Deborah Chen et al. “Cleavage of superpower protein determines the superpower phenotype in a tissue-dependent manner: How Incredible!” (2013) JOURNAL OF SUPERHERO RESEARCH. Vol 13 Vol 547. pp328-3332 doi:23.1724/SR20130328

Full text via the Science Creative Quarterly

Fake but very detailed scientific paper on why you can’t kill Wolverine. #nerdgasm

howlettpaper

(Click on the paper image to download full text pdf of the research paper).

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ABSTRACT:
Wolverine, a mutant from the X-men team, possesses super healing abilities. Wolverine’s healing abilities have striking similarities to that seen in axolotl, an amphibian with the capacity to regenerate amputated limbs. In this study we sought to determine the mechanisms by which Wolverine regenerates. We identified a novel protein, dubbed Howlett, that is nearly identical to the Amblox protein in axolotl which is known to be responsible for the amphibian’s limb regeneration. siRNA knockdown of the howlett and amblox genes demonstrated decreased replication in Wolverine and axolotl, respectively, and Howlett was found in all Wolverine tissues. Using mass spectrometry and x-ray crystallography, we identified an S2 pocket in the Howlett protein that we postulate contributes to the 5.66-fold increased specific activity observed over Amblox in cleaving a large substrate analogue. Our findings show that Howlett is a major contributor to Wolverine’s incredible regeneration capacity, and further investigation of the signaling and regulatory mechanisms associated with this novel protein could provide outstanding advances in the field of regenerative medicine.

Sigrid Alvarez, Emma Conway et al. (2013) “Howlett: Novel Wolverine Protein Contributes to Rapid Regeneration and Heightened Cellular Replication.”  JOURNAL OF SUPERHERO MUTATIONAL SCIENCE. Vol 13 Issue 2. pp297-302

Full text via the Science Creative Quarterly

The intracellular cell phone

cellphone

By Harantula, via IFLS

The Von Trapp Children Speak to a Geneticist

By DAVID NG

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LIESL: Why is it that we can all sing very well?

GENETICIST: Liesl, that is an excellent question! And essentially one that boils down to the classic debate of nature versus nurture. Are your genes responsible for this particular talent, or has it more to do with your upbringing? Looking at this scenario objectively, I would have to say that it is both. There have been reports that the ability to have perfect pitch—that is the ability to distinguish musical notes without points of reference—is a hereditary phenomenon, thereby strongly suggesting a genetic basis. This would seem to be supported by your father’s musical talent as well. Of course, you’ve also had the benefit of being tutored by your wayward novice governess with all-world pipes, Maria.

In conclusion, like most things pertaining to our individuality, we are influenced by both our biology and our surroundings.

GRETL: I think Liesl is very beautiful. Why am I not as pretty?

GENETICIST: Assuming no mutational errors occur during the production of sperm and egg cells, there was approximately a 1-in-70,000,000,000,000 chance that you would have been an identical clone of your sister. If you included the multitude of mutational and regulatory events that ensue during this process, that statistic would escalate to an even smaller chance that is, quite frankly, unfathomable to calculate. How did I get to this absurd number? Well, one must realize that your genetic instructions are housed as a collection of 23 pairs of chromosomes (i.e., 46 in all). In other words, it is correct to say that each human has two sets of instructions—one given to you by your father, and one by your mother. If you keep in mind that your parents themselves also have 23 pairs of chromosomes, and you realize that the child may receive only one from each pair, the likelihood of siblings having the same 46 chromosomes is the fantastic number mentioned above.

However, Gretl, do not fret. You are the youngest of the lot and still have a good chance to blossom into a stunning flower like your sister Liesel. Furthermore, cosmetic surgery these days I hear is quite impressive. And then there is always the chance of Liesl having a disfiguring accident—I hear she may be a Nazi sympathizer, which is never a good thing.

FRIEDRICH: Yes, Liesl is hot. Sometimes, even I have feelings for her. Why is it bad for me to feel that way?

GENETICIST: Incestuous relationships, as well as being frowned upon by most of society, are also disadvantageous from a biological point of view. In the genetic world, diversity breeds fitness. One example is to imagine the following. You have a set of genes that determine the ability of your immune system to recognize and combat various pathogens. Your sister Liesl also has a set of genes that do the same thing. And because you and your sister come from the same genetic pool (you have the same parents), Liesl’s immunity is quite likely to be similar to yours. Do you not see that the net effect of this is that you would create offspring with a limited repertoire of immune-system genes? Compare that to your having a child with, say, Marcia from The Brady Bunch, and you will note that this union will create offspring that have the benefit of a wider genetic pool (your parents and Marcia’s parents), thereby allowing your children to acquire a more diverse and fitter immune system.

Also, dude, she’s your sister.

BRIGITTA: Why do all of our siblings have blondish hair and blue eyes, whereas Marta and I have dark hair and dark eyes?

GENETICIST: You are thinking, perhaps, that your mother was a whore? It is true that the disparity in your outward appearances is a mite unusual. However, there is no reason to believe that any adultery has occurred. Here is the reason why. Although it is generally thought—though not confirmed—that extreme blondness (as in the case of Louisa and Friedrich) has a recessive distribution, there are numerous factors that can account for your instances of dark hair and dark eyes. First, hair and eye color are very subjective terms. Is Greta or Kurt blond, dirty blond, or strawberry blond? Genetic characterization is very difficult when the observational characterization is less than strict. Second, the pigmentation of hair is normally attributed to melanin levels, which have been shown to vary greatly during different stages of a person’s life. You may have noticed, for example, that a person’s childhood hair color tends to be lighter than their adult hair color. Third, the amount of melanin that an individual produces is influenced in part by their environment. For instance, melanin acts to protect the person from the damaging effects of the sun’s radiation. In conclusion, I do not feel that there is anything to worry about. Besides, you did not mention Liesl, who herself has dark hair. Did you omit her because you are secretly jealous of her hotness?

KURT: I think I might want to be with another boy. Is this to do with my DNA?

GENETICIST: Unfortunately, the answer is currently unknown. There have been numerous reports that have tried to implicate specific genetic regions to homosexual behavior, but presently those studies, although titillating, are at best only an indication that there is a hereditary factor for this type of sexual orientation. However, there is an abundance of ongoing research in this area, particularly with homosexual men. If you are interested, perhaps you could participate in the scientific process. Of course, it is important to remember that the Nazis do not dig gay people.

LOUISA: Why doesn’t anybody remember who I am?

GENETICIST: Alas, it appears that this is because you are the second child. I would not be surprised if there are very few pictures of you. It is not, I assume, because your parents did not love you, but simply a facet of being born after the initial excitement and newness of parenthood has passed. This, of course, has nothing to do with genetics. In order to be taken more notice of, you could try different fashions, or perhaps a new haircut. In truth, Liesl could probably give you better advice, as I am, sadly, only a geneticist.

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Originally published at McSweeney’s

In which Minecraft is used to create a working neuron. #whoa

neuronminecraft

Here is a close-up of the voltage-gated Sodium Channel…

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By AllUpInHyuh. See details here (click – this is very cool).

This is what photographic film looks like, when it passes through your digestive system.

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filminbody02

Kingston University photography students Luke Evans and Josh Lake decided to turn themselves into human cameras by eating 35mm film squares and letting their bodies do the rest. The single film segments were first ingested, excreted (in a dark room) then washed.

Via Fresh Photons.

Looks like we can’t run the ethanol precipitation today. #funny

lookslikewecantruntheethanolppttoday

From Saturday Morning Breakfast Cereal.

Sciencegeek Advent Calendar Extravaganza! – Day 20

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PRETTIEST CHRISTMAS LIGHTS EVER
Animated gifs of epithelial cells doing the mitosis

                    mit04 mit03

                    mit02 mit01

From Infinity Imagined, via Fresh Photons. (Source:MICROSCOPYU.COM)

Just staring at this makes me think about the brilliance of nature. Just consider the complexity of what’s going on during mitosis – you have a genome, compartmentalized with chromosomes, doubling. Then, you have a perfect splitting of the two copies into two separate cells!

That’s like having a group of people in a room, then somehow making copies of all of them, and then getting them to split perfectly into two groups, so that one set of them can move (in an orderly fashion) to another room entirely. But now imagine doing that blindfolded, and without being able to utter a sound to each other, and essentially getting this done solely on the basis of touch. Wondrous…

(see more of Popperfont’s Sciencegeek Advent Calendar Extravanganza here)

What are the general features of photosynthesis? #funny

By mirko92.

Angry Words From a Gnome Who to This Day Continues to Think The Human Genome Project was Actually The Human Gnome Project

By DAVID NG

It’s hard to believe that the Human Gnome Project formally began in 1990s. It was quite frankly a great time for all of us gnomes as we thought we had finally gained the attention and respect we deserved as a community. But decades later, we as a community are disappointed, angry, full of resentment, and still addicted to nicotine.

To our knowledge, of the billions of research funds given to human gnome initiatives, none of it ever actually went to fund “gnome” research. Instead, a sizable portion went to human human research, and in an apparent slap in the face to my kindred, significant amounts also went towards research looking at bacterial, yeast, worm, fugu, fly, and mouse genetics. Suffice to say, that with the exception of humans, these are all organisms that do not smoke pipes. To say that this has been hard on my community is an understatement of vast proportions. Apart from the soaring lung-cancer rates, I find I am continually aware of other lost opportunities the money could have been used towards.

For instance, for whatever reason, we as a race are forever doomed by our incessant need to wear pointy hats. I hate my stupid hat—loath it with a passion. And yet I have to wear it. We all do. Why this is so has been mystery for many an age. Maybe that’s why I go through 70 grams of tobacco each day. And whilst pointy hats are fine for garden work (one of our main sources of economic recovery), they are hardly advantageous in the current global market—especially when first impressions play a key role. Surely, there is an underlying neurological basis for this behavior—a basis that science could have elucidated.

And what about our facial hair? Believe me, it is not because we are particularly fond of our beards. It’s not even because tobacco pipes look cooler in this context. Our beards just happen to grow at amazingly fast rates! This is not such a huge issue with me and the other male gnomes, but my poor wife actually has to shave every 45 minutes or else deal with social harassment. This is also compounded by the fact that services, like laser hair removal or electrolysis, are just too expensive, especially on a gardener’s income. Ironically, the only gnomes who could possibly afford these high tech solutions are the few who have made it into Hollywood where maintaining the typecast “bearded” look is required anyway. Furthermore, even when a hairless gnome is needed on a movie set (e.g., Mini Me in the Austin Powers franchise), we still get passed over because of our goddamn pointy hats! I bet billions could have sorted this problem out a long time ago.

But if there was ever a strong case for gnome research, you only need to look at my poor Uncle Bill. This unlucky bastard of a gnome must have some bladder problem or something, since he is (no exaggeration) urinating constantly. Seriously, I don’t think he’s even had a chance to put his penis away since he started 14 years ago! And the truth of the matter is that this particular problem is relatively rampant in my circles. Most start off fishing, and then they feel the urge and then whammo! It’s like a disease. I don’t think it’s too difficult to appreciate the magnitude of this medical condition. Aside from the psychological pain endured, imagine how uncomfortable it must be to leave it “out” constantly in all manner of weather conditions. I don’t care if you are the gardener type— when it’s cold, it’s cold! Plus, it makes smoking a pipe tricky.

Anyway, I’m not here to preach endlessly about our problems. I just here to say I want a fair piece of the action. If the project is called the Human Gnome Project, then it only makes sense that at least some of the money should go towards gnome research—right?

O.K., I’ve said my piece. I really have to go outside now to smoke my pipe—stupid human nicotine patch, piece-of-crap waste of money …

(This is very old and originally published at Yankee Pot Roast, inspired by this)

Genes to Cells cover has cats doing the mitotic spindle on it!

Via Fresh Photons.

Cellular Generation and Intracellular Diversion: the paintings

By Regina Valluzzi. Available for purchase here and here (via Fresh Photons)

Keep Calm and Carry a Pipetteman. Molecular Biology Workshop Game On! Please RT

As usual, my lab will be hosting a professional workshop for those in need of a molecular biology updating; or for those who are new to the area and need a quick (and intensive) course on the subject. The 5 days do include both hands on and lecture style elements, and it’s also an excuse to come to beautiful Vancouver.

Also, don’t forget that all revenue from this workshop goes towards our public science outreach programs (like our fieldtrips, science writing, phylomon, etc – see bioteach.ubc.ca).

I’d thought I’d include the notice in my blog, because I had a bit of graphic design fun with our poster. Maybe this is even geeky enough to consider turning into a tshirt?

Anyway, if you’re a scientist (or not – we’ve had some lawyers and an economist attend before), and you need some highly recommended molecular biology training, please do follow the link at the bottom, and maybe I’ll see you in July!

(Click here to download pdf poster)

To inquire about registration, please contact Dr. David Ng at db@interchange.ubc.ca

(1) ONE WEEK VERSION
Dates: July 23rd to July 27th, 2012 (5 days: Monday to Friday)
Price: CAN$1400 (does not include room or board)

Reviews and Testimonies can be found here.

INSTRUCTOR: Dr. David Ng

DESCRIPTION: Updated for 2012: This intense 5 day workshop will focus on a myriad of different techniques used in the molecular manipulation of DNA (general cloning, transformation, silica kits, pI kits, PCR, qPCR), RNA (isolation, reverse transcription) and protein (SDS-PAGE, 2D gels), as well as inclusion of exercises in some basic bioinformatics tools. Primarily aimed at researchers who are new to the area, familiar but require a quick updating, or would like more practical bench training.

For full details, please see here.

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