FIRST GENOME SEQUENCED!!!!

Nucleotide sequence of bacteriophage phi X174 DNA. 
Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M.

Abstract

A DNA sequence for the genome of bacteriophage phi X174 of approximately 5,375 nucleotides has been determined using the rapid and simple 'plus and minus' method. The sequence identifies many of the features responsible for the production of the proteins of the nine known genes of the organism, including initiation and termination sites for the proteins and RNAs. Two pairs of genes are coded by the same region of DNA using different reading frames.

Nature. 1977 Feb 24;265(5596):687-95.

Why is this cool?

 Remember that revolution that I mentioned? Well, here is one of the big starting points. Fred Sanger and co-workers sequence the very first genome: Bacteriophage phi X174!! Just as a reminder, bacteriophages are viruses that kill bacteria and not so much anything else (I might be wrong about this last part). To put this in perspective, that first genome was published in 1977 years before home computing, AIDS (some debate here), the public use internet, and the Gulf War. To reveal more of the timeline, the first free living organism genome sequenced was 18 years later in 1995!! The size of the bacteriophage phi X174 genome is 5000 base pairs and only codes for 11 genes!! I'm not sure when the function for all those genes was determined, but that might be interesting. 
 Speaking of interesting viruses, one of the crazy ones has to be THE TRANSMODE VIRUS!!

Magus, Warlock's father and an old school Technarch.

The transmode (or techno-organic) virus seems to convert organic matter to techno-organic matter. The Technarchy are carriers of the virus and when organic matter is infected, the Technarchy can steal the life force of the infected. 

Cameron Hodge was a phalanx.

The infected organic matter becomes the phalanx, a hive mind geared towards creating more infection. After a certain amount of time, the phalanx can form a tower to call the Technarchy to have them steal the life force of the infected. The first Technarchy character to appear in a comic was Warlock!! He used to be my favorite character.

Warlock!!

 Cable was infected with a techno-organic virus, but I don't know if it was the Transmode virus.

ESSENTIAL GENES!!!!

Essential Bacillus subtilis genes.

Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauël C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JF, Sekiguchi J, Sekowska A, Séror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N. 

Abstract

To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximately 4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from bacteria with small genomes. Unexpectedly, most genes involved in the Embden-Meyerhof-Parnas pathway are essential. Identification of unknown and unexpected essential genes opens research avenues to better understanding of processes that sustain bacterial life.

Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4678-83. Epub 2003 Apr 7.

Why is this cool?

Leezle Pon is not a bacterium, but a small pox virus.

 The human genome is 3.3 billion base pairs and there are approximately 20,000 genes coded in it. Rats has a genome size of 2.75 billion base pairs that also code about 20,000 genes. This is amazing because it doesn't intuitively make sense about how an organism much smaller than humans can have a genome that codes for just about the same number of genes! Consider rice and corn. The rice genome has 340 million base pairs in it coding for about 30,000 genes. Corn has about 2.3 billion base pairs that code for about 30,000 genes. These are very different plants and their genome sizes reflect that, but the number of genes coded for does not reflect that. Both genomes code for close to the same number of genes! This inevitably leads to the question: HOW MANY GENES ARE NECESSARY FOR LIFE?!?
 That is exactly the question that these researchers set out to answer. There are some problems though. You can not mutate humans for research. You can do mice, but that is EXTREMELY EXPENSIVE. You could do plants, but that can take forever. Bacteria are inexpensive to use and easy to work with, so this research uses Bacillus subtilis to address the question. So, how did they do it?

 You would think that they would knockout one gene and tested if the organism still lived and if it did they would then knockout another and so on and so forth until they had the minimum number of genes required to maintain life in a nutrient rich environment. As it turns out, that approach is just not as easy as it sounds, so that went about a different way. They made a knockout for every gene in B. subtilis for a total of 4,100 different knockouts! Of those knockouts, only 192 genes were completely essential to maintain life.

BABY TEETH RADIATION!!!!

Strontium-90 absorption by deciduous teeth. 

REISS LZ.

Science. 1961 Nov 24;134:1669-73.

Why is this cool?

 So, in the 1950s and 1960s, the US was testing tons of nuclear weapons and people were getting nervous about mutually assured destruction and environmental consequences of nuclear fallout. A lone researcher took it upon himself to find out if nuclear weapon testing was leading to accumulation of radioactive material in humans. So, the researcher gathered baby teeth from around St. Louis and then tested then for radioactivity. What they found rocked many a parents' world: the teeth had RADIOACTIVE STRONTIUM-90 (kind of redundant because strontium-90 probably doesn't exist in a non-radioactive form)!!!!! They present data that the later a child was born, until 1954, the more radioactive strontium was found in his teeth!
 Was this radioactivity correlated with higher incidences of cancer later in life? I don't know, but I would bet so. It is very interesting, because both my parents were born in the early fifties and they probably still have strontium-90 in their teeth!! This paper was published in 1961 and that precedes an IMPORTANT MILESTONE IN AMERICAN HISTORY: STAN LEE'S RE-INVENTION OF MARVEL!!!

Made of Uranium-238

 Is it a coincidence that Stan Lee (born in 1922) had developed the greatest comics ever written shortly after widespread nuclear weapon testing? I think not. In fact, I believe Stan Lee to be made of radiation!!From 1961 to 1963, Stan created society defining characters such as:

THE AVENGERS!!

THE HULK!!

THE FANTASTIC FOUR!!

SPIDER-MAN!!

THE X-MEN!!!

Crow brains!!!

Tool-making new caledonian crows have large associative brain areas.

Mehlhorn J, Hunt GR, Gray RD, Rehkämper G, Güntürkün O.

Abstract

Animals with a high rate of innovative and associative-based behavior usually have large brains. New Caledonian (NC) crows stand out due to their tool manufacture, their generalized problem-solving abilities and an extremely high degree of encephalization. It is generally assumed that this increased brain size is due to the ability to process, associate and memorize diverse stimuli, thereby enhancing the propensity to invent new and complex behaviors in adaptive ways. However, this premise lacks firm empirical support since encephalization could also result from an increase of only perceptual and/or motor areas. Here, we compared the brain structures of NC crows with those of carrion crows, jays and sparrows. The brains of NC crows were characterized by a relatively large mesopallium, striatopallidal complex, septum and tegmentum. These structures mostly deal with association and motor-learning. This supports the hypothesis that the evolution of innovative or complex behavior requires a brain composition that increases the ability to associate and memorize diverse stimuli in order to execute complex motor output. Since apes show a similar correlation of cerebral growth and cognitive abilities, the evolution of advanced cognitive skills appears to have evolved independently in birds and mammals but with a similar neural orchestration.

Brain Behav Evol. 2010;75(1):63-70. Epub 2010 Mar 9.

Why is this cool?

 Crows and ravens are iconic animals. Seen everywhere from Nordic mythology where Odin has two ravens, Huginn and Muninn, to movies such as The Crow. Well, it turns out that those birds are extremely intelligent. 
 According to the abstract, the researchers took the brains of New Caledonian crows and compared them to other birds such as carrion crows, jays and sparrows. What they found was several areas in new caledonian crows are larger than in the other birds and that those areas are known for association and motor-learning. They note that in apes these areas are also large, leading one to think that these birds really are intelligent.

 Where does that leave us? Humans use to be the most intelligent animals on the planet, but now the pieces of behavior that distinguished us from other animals are being found everywhere. Is human intelligence astounding not for being completely different, but for being a higher degree? Ants form colonies, many animals hunt in packs, and there are many animals that live in herds. All of these can be considered proto-societies. Tool use has been seen in octopi, crows, and monkeys. Using tools is considered a big part of the human advances. Think about this: a tool is an inanimate object used to accomplish a task (my own definition, so it could be wrong). This includes guns, construction tools, clothes, cleaning implements, and hunting devices! The use of tools by animals suggests that the distinguishing feature of humans is not tool use. 
 What makes humans unique? Is it art or religion? I think the distinguishing feature is the ability of ideas to hijack our existence! Which encompasses both religion and art. When people are no longer starving or fighting for survival, they free their minds to explore thoughtspace! Maybe after thousands of years of exploring thoughtspace, they have made small adaptations that make entrance into thoughtspace easier. Eventually, they yearn for more thoughtspace, this manifests itself as art and religion and devotion to work. Why would thoughtspace become fixed in the human population? Because the byproducts of thoughtspace exploration have tremendous value in the real world? Byproducts? Not tool use, because any beast can use tools, but tool design and improvement. Anyway, it is flaky, but I think it might be something to consider.

FRED F**KIN' SANGER!!!!

The terminal peptides of insulin.

SANGER F.

Biochem J. 1949;45(5):563-74.

Determination of nucleotide sequences in DNA.

Sanger F.

Biosci Rep. 1981 Jan;1(1):3-18.

Why is this SUPER COOL?!

 Fred Sanger is the man who made a revolution possible. When you think REVOLUTION you think Che Guevara, Simon Bolivar, Confederates, Bastille Day, and piles of bodies. Sanger was the man who figured out how to sequence first proteins and then DNA!! He initiated a revolution that has washed over all of us!!

 His contributions led to discovering archaea! His contributions were modified to sequence our GENOME!!! He may have had a huge effect on diabetics...because he figured out the amino acid sequence of insulin and compared it to that of other animals and found them to be very similar...not sure on this one, but I THINK IT COULD HAVE HAPPENED!!

 Were scientists to immortalized like law-makers, Sanger would have to be given a monument that size of Atlanta, Georgia with DNA looking machines constantly whipping around a monolithic stature of a MAN CHOKING THE ENIGMAS OF NATURE!! It would be so gargantuan that it would be a city and every person would be a scientist with a Ph.D. and their research would be to OPTIMIZE THE HUMAN GENOME!! I don't know if Sanger was big into eugenics, so don't take that to heart.

XENOTRANSPLANTATION!!!

History of xenotransplantation.

Deschamps JY, Roux FA, Saï P, Gouin E.

Abstract

The present historical review reports the clinical experiences of transplantations from animal to human. The first transplantation attempts were made without any knowledge of the species barrier. The pioneers of xenotransplantation realized xenotransfusions as early as the 16th century, then cell and tissue xenotransplantations in the 19th century. At the beginning of the 20th century, xenotransplantation of testicles became the latest craze. At the same time, and later in the 1960s, organ xenotransplantations were attempted, with disappointing results. Mathieu Jaboulay, Serge Voronoff, Keith Reemtsma, James Hardy, Denton Cooley, Thomas Starzl, Christiaan Barnard and Leonard Bailey were among the pioneers of xenotransplantation. Recent trials concerned above all tissue and cell xenotransplantations. Nowadays, with encapsulation, transgenesis, and cloning, great advances have been made for controlling xenograft rejection, but ethical questions linked to the risk of infections have become a major pre-occupation within the scientific community and the general population.

Xenotransplantation. 2005 Mar;12(2):91-109.

Why is this cool?

 How can this not be cool!!? This is a brief article detailing the history of taking flesh and organs from other animals and just slapping into humans like some kid modding out his Xbox. I have not read the article, but the thing about xenotransplantation of testicles being the latest craze makes me cringe. 

 My fear of being forcibly modded out with xenotransplants reminds me of MULTI-FRACTOR (aka Jigsaw 2099)!!!!

 

 His story is that some ex-military guys captured him and used some gun to implant animal parts against his will. It sent chills down my spine and continues to do so to this day. It may be the source of my undying fear of Masque from the Morlocks.

 Other instances of transplantation, although less fear inducing, are the U-MEN!!!

The U-Men kill mutants and then take their mutations and implant them in one another!! The idea being that mutants are the next stage of evolution, but why should humans be left behind? Why must the humans be slaves to their genetic destiny?! AMERICA ISN'T ABOUT FATE!! IT IS ABOUT TAKING THE WORLD BY THE TAIL!!!

 It is also possible that the testicular xenografts from monkeys could have been a source of AIDS into humans. Sad face.

 I think the most successful xenotransplant was the installation of whisker pouches from newborn kittens into Julia Stiles' face.

REVIEW: Detection, isolation, and continuous production of cytopathic retroviruses (HTLV-III) from patients with AIDS and pre-AIDS.

So, today's paper deals with a game changer: AIDS!!! 

 The CDC first reported some disease spreading through the gay community in 1981 with case reports from five gay men. It wasn't until 1983 that AIDS was shown to be a virus and today's paper is a major point in that history.
 So what did the researcher's do? Well, they looked at the symptoms of AIDS and saw a connection with human T-cell lymphotrophic retroviruses (HTLV). The connections were:

1. Feline leukemia virus causes immune deficiency in cats. This virus is similar to HTLVs known at the time.

2. Known HTLVs preferentially infect and kill helper T-cells.

3. HTLVs may be transmitted by intimate contact and blood products.

Well, what are the symptoms of AIDS that suggest HTLVs?

1. AIDS stands for ACQUIRED IMMUNODEFICIENCY SYNDROME!!! (see previous point 1)
2. AIDS patients have extremely reduced helper T-cell counts!! (see previous point 2)
3. People with multiple sex partners, people who share needles for intravenous drug use, and people who have received blood transfusions were among the infected!!! (see previous point 3)

 A continuous production was set up to isolate large amounts of virus particles and, ultimately, to characterize by reverse transcriptase!! What is reverse transcriptase? It turns out that HTLVs are retroviruses meaning that their genomes are RNA based instead of DNA based! Reverse transcriptase is an enzyme that can convert an RNA sequence into a DNA sequence.

 How did they set up a continuous production of the virus? Doesn't a virus infect, exploit, and then DESTROY?! How can you get continuous production? Well, it turns out that sometimes a virus can infect and instead of killing without reason the virus can integrate its DNA (after the action of reverse transcriptase) into the host (helper T-cell) genome. This integration allows the cell to live at least until the viral genome becomes activated and kills everything. Those living cells were co-cultured with cells that were killed by the virus. So, in summary, a cell line that can live with the virus is grown with cells that are killed by the virus and the death of the latter leads to large amounts of viral particles, allowing for characterization!! Characterization means that they:

1. Determined how quickly cells died after being infected, 6 days.

2. Tested antibody reactivity of AIDS positive patient serum to the virus, yes.

3. Compared of reverse transcriptase results with previous HTLV data, it matched.

4. Determined how novel the new HTLV (at the time dubbed HTLV-III) was when compared to HTLV-I and HTLV-II, somewhat.

 And that was how the causative agent of AIDS was uncovered. Sadly, we lost one of our greatest to AIDS: KLAUS NOMI!!!

 I'm sure that he is wondering where this crazy disease came from and a lot of other people have also wondered. Some explanations from the internet are:

Humans eating monkey meat! Humans kill the monkey and get monkey blood on themselves. Eventually, a human gets infected with a monkey virus and BAM AIDS!!

The CIA engineered a supervirus to kill blacks and gays to clean AMERICA!! I have no idea why an intelligence gathering agency would want to kill blacks or gays. That is weird.

Side effects include: permanent loss of immune system.

A drug company developing a vaccine to polio using monkeys to produce the virus. The vaccine may have worked, but when injected into humans, HTLV-III tagged along!

Genome battle: Humans vs. Chimpanzees!!!

Initial sequence of the chimpanzee genome and comparison with the human genome.

Chimpanzee Sequencing and Analysis Consortium.

Abstract

Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.

Nature. 2005 Sep 1;437(7055):69-87.

Why is this cool?

 What does it mean when people say that humans and chimpanzees are 98% genetically similar? That is the question for this paper. Well, not that question exactly, but close enough. So, the researchers sequenced the chimpanzee genome and compared it to the human genome. 

Just to make it known:

Base pairs in the human genome: 3,200,000,000

Base pairs in the chimpanzee genome: 2,900,000,000

Single base pair changes: 35,000,000

Insertion or deletions: 5,000,000

Chromosomal rearrangements: A handful.

 What do these numbers mean? Well, that is an amazing question and it has not been answered yet. But, we can some what answer from our basic knowledge of chimps and humans. The list of differences:

1. Chimps don't have the same language abilities as human.

2. Chimps are super hairy, humans not so much.

3. Arm and leg lengths in humans are different than in chimps.

4. Chimps have a bone in their penis, humans don't.

5. Humans are the only animals with psychic powers.

 Just so you know, Mandrill doesn't count for chimps because he is a human who looks like a mandrill. Mandrill's may look like all he does is look freaky, but he can secretly control women with his PHEROMONES!! Although, as far as pheromone-using-mind-controllers go, none can ever beat PURPLE MAN!!!

To villainy!

 He fell into a vat of mystery chemical and was given pheromone-based, mind-control powers and the best skin color ever: PURPLE! He has never bested anyone with the exception of Jessica Jones and that didn't even go far enough. He captured her and made her watch his debauchery? Lame. His supervillainy knows no bounds and he doesn't ever touch Jewel? Whatever. Although, outside of that one thing, Bendis made Purple Man a serious villain.

 Ok, so those two have hormone based powers, not psychic powers, but I have never heard of a psychic animals. The closest to a psychic animal was Bunicula.

TOOL USE IN OCTOPI!!!

Defensive tool use in a coconut-carrying octopus.

Finn JK, Tregenza T, Norman MD.

Curr Biol. 2009 Dec 15;19(23):R1069-70.

Why is this cool?

 This is not a paper, but a correspondence, but it is still absurdly amazing! The researchers observed octopi carrying around coconut half shelfs!
"So what?"
 You may not have realized this, but tool use is an indicator of cognition 2.0 and has never, NEVER, been observed in cephalopods! Those dang octopi are up to serious mental boosting, because they have utilized a coconut for survival! Octopi in Northern Sulawesi and Gilimanuk, Bali were observed carrying the shells and using them for shelter. They were even able to observe an octopus finding coconut half shells and use them as shelter and then carry them off!
 Those octopi are pretty smart, but can they do MAGIC? I didn't think so. That is why octopi have to worship their EVIL GOD: SHUMA-GORATH!!!

 As far as bad-ass characters go, Shuma-Gorath tops the list and then writes a new one where it is still on top! It can do pretty much anything, except best Dr. Strange in any kind of battle. That ol' former Sorcerer Supreme is a wily one with all sorts of tricks up his sleeve.
 Ok, so you know how Dr. Strange is no longer the Sorcerer Supreme? And then Agamotto came and reclaimed his eye only to be defeated by the New Avengers? Well, did you notice that he was really worried about something coming. Something so powerful that even Agamotto needed more power! I think that it is SHUMA-GORATH!!! In case, you are not aware how powerful Agamotto is, know that he fought Galactus and held his own. So, you know something awesome is coming.

MALARIA ANNIHILIATION ATTACK!!!

Development of transgenic fungi that kill human malaria parasites in mosquitoes. 

Fang W, Vega-Rodríguez J, Ghosh AK, Jacobs-Lorena M, Kang A, St Leger RJ.

Abstract

Metarhizium anisopliae infects mosquitoes through the cuticle and proliferates in the hemolymph. To allow M. anisopliae to combat malaria in mosquitoes with advanced malaria infections, we produced recombinant strains expressing molecules that target sporozoites as they travel through the hemolymph to the salivary glands. Eleven days after a Plasmodium-infected blood meal, mosquitoes were treated with M. anisopliae expressing salivary gland and midgut peptide 1 (SM1), which blocks attachment of sporozoites to salivary glands; a single-chain antibody that agglutinates sporozoites; or scorpine, which is an antimicrobial toxin. These reduced sporozoite counts by 71%, 85%, and 90%, respectively. M. anisopliae expressing scorpine and an [SM1](8):scorpine fusion protein reduced sporozoite counts by 98%, suggesting that Metarhizium-mediated inhibition of Plasmodium development could be a powerful weapon for combating malaria.

Science. 2011 Feb 25;331(6020):1074-7.

Why is this cool?

 Malaria is a major issue outside of the States, so a lot of research is geared towards finding a way to prevent it. You may remember that one way was to kill the mosquitoes, but today's paper does so by killing the bacterium in mosquitoes that causes malaria.
 From the abstract, it seems that the researchers took the fungal strain (M. anisopliae) and engineered it to express one of three different peptides/toxins:
1. Salivary gland and midgut peptide 1 (SM1)
2. A single chain antibody that binds (agglutinates) sporozites (Plasmodium spores).
3. Scorpine, a toxin which kills bacteria.
 When the mosquitoes were infected with one of the three engineered fungal strains and the bacteria that causes malaria (Plasmodium) and then they measured the presence of sporozites, they found amazing decreases in sporozite amounts! The best for killing the sporozites was the fungal strain expressing scorpine.

  A question is: how do they expect to use this technology to fight malaria? For some reason, some people think that all trangenic organisms have no place in nature and should be highly regulated or never used. It is a heated debate that keeps going on because the people opposed to transgenic organisms believe in doomsday scenarios where corn or rice or fish that have been genetically altered grow into super beings and devastate everything about our world. These megacorns would boils the seas! The ultrarice would cut down the rainforest! Hyperfish would take our jobs and ruin the economy!!

  The only real threat that transgenic organisms have to anything is hunger. What if there is a vast plot to keep one part of the world hunger and poor forever to maintain cheap labor!? Other uses for transgenic organisms are: producing medicines, producing industrial catalysts, and chemical detoxification!

Tuskegee experiment!!

Untreated Syphilis in the Male Negro: A Comparative Study of Treated and Untreated Cases

R.A. Vonderlehr, T. Clark, O.C. Wenger, and J.R. Heller Jr.

Ven Dis Inform 17: 260-265, 1936 

Why is this cool?

 In 1932, the Public Health Service began a study to observe the long term effects of untreated syphilis. They noticed that a large number of black men (male negros for those not familiar with oldspeak) in the rural South had syphilis. Would these men have sought treatment if they knew they had syphilis? Maybe. Could they have afforded treatment if it were available? Maybe. Did the researchers deny the infected men treatment? I don't know. Were these men made aware of their syphilitic condition? I don't know. Did the researchers have a duty to treat the infected and cure them? Maybe. Were all of the infected treatable? I don't know. Was the research necessary? I don't know.

Ok, she is not black,but you needed to see what syphilis can do.

 As you can see, there are a lot of questions that get lost in the emotions of the Tuskegee experiment. Too quickly, people condemn the U.S. government for allowing such a thing to happen without considering the reasons for the study. That is why it is so important to read the original work instead of depending on secondary, tertiary, or even quaternary sources on the research.

 So, let's begin. The experiment started with 399 syphilitic black men, 201 non-syphilitic, and 275 who had syphilis, but were treated in the first two years of infection. A detailed history for each patient was taken and then they just watched them waste away. What were the results? I don't know, because I haven't read it just yet. I do know that the group in charge of the experiment published at least 10 papers about what they saw!

REVIEW: An Ancient Divergence among Bacteria

When you learned about life in school, you most likely learned the FIVE KINGDOM system, shown below:

 In this system,

Animalia are the various self propelled animals of the world including humans, elephants, platypi, and octopi.

Plantae are are the green things out there.

Fungi are just things to put on pizza.

Protista are eukaryotic single celled organisms, such as yeast for making bread.

Finally, monera are prokaryotic organisms, like E. coli the workhorse of most scientific work!

 This classification system was fine and good, because it made sense with the current state of science. Things that looked alike belonged together. Well, with the discovery of DNA as our genetic material and the improvement in techniques to sequence DNA, people got to wondering if the genetic code also reflected the system that was previously devised. Today's paper that establishes that the five kingdom system is flawed and (through later work) that there are THREE DOMAINS OF LIFE!!!!

Spider-man was drawn by Skottie Young, Bat-mite by Ryan Sook, and I don't know for Mr. Mxyzptlk.

 Why does sequencing DNA matter so much? Can't we just look at the bacterium and compare create a more refined tree for the five kingdom system? The problem with that is that bacteria look pretty much the same. There are some that are really different, but most of them look like a squiggling speck. The DNA sequences though are passed down through time and when comparing to other sequences they can reveal a great many details! This was back when comparing DNA sequences didn't make you a molecular biologist, it made you a MOLECULAR PALEONTOLOGIST!!!

 There is a problem though. At this time (1977), DNA sequencing "technology" consisted of some GUNG-HO graduate student, an organism, and an arduously long procedure to get the DNA sequences by hand. Nowadays, there are machines that determine the DNA sequence and can do so in an afternoon. Since it takes forever and a day to get a DNA sequence, you cannot just sequence an entire genome. To really hammer the point home, it took 13 years to sequence the human genome and that was with significant help from the US government. The first bacterial genome was not completed until 1995, eight years before the human genome was completed. So, what gene or region of the DNA do you sequence? Obviously, the one that changes the least. This gene turned out to be the 16S ribosomal RNA sequence. 

 The ribosome is a large structure of RNAs (ribonucleic acids) and some proteins that are responsible for taking your messenger RNA and translating it into proteins. All Earth bound organisms have a ribosome and they are all very similar. Since there are several RNAs that make up the ribosome, they choose the the 16S ribosomal RNA to sequence. Why the 16S? Previous research pointed towards it being the best.

 The researchers took two bacteria-like organisms (Methanobacterium ruminantium and Methanobacterium thermoautotrophicum) and sequenced the 16S ribosomal RNA and then compared it to the other 16S ribosomal RNAs and they found a surprise. When compared to the sequences of the other bacteria, the two that they sequenced were extremely different and points to a divergence from bacteria that antedates the previously oldest division of bacteria!!!

Origin of plague!!!

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.

Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, Achtman M.

Abstract

Plague is a pandemic human invasive disease caused by the bacterial agent Yersinia pestis. We here report a comparison of 17 whole genomes of Y. pestis isolates from global sources. We also screened a global collection of 286 Y. pestis isolates for 933 SNPs using Sequenom MassArray SNP typing. We conducted phylogenetic analyses on this sequence variation dataset, assigned isolates to populations based on maximum parsimony and, from these results, made inferences regarding historical transmission routes. Our phylogenetic analysis suggests that Y. pestis evolved in or near China and spread through multiple radiations to Europe, South America, Africa and Southeast Asia, leading to country-specific lineages that can be traced by lineage-specific SNPs. All 626 current isolates from the United States reflect one radiation, and 82 isolates from Madagascar represent a second radiation. Subsequent local microevolution of Y. pestis is marked by sequential, geographically specific SNPs.


Nat Genet. 2010 Dec;42(12):1140-3. Epub 2010 Oct 31.

Why is this cool?

 Imagine everyone around you dying. WOW on all levels. It is even some next level WOW. Every child should already know the many symptoms of plague infection and its effect on the world, but does everyone know the origin of where Yersinia pestis came from? I didn't and that is why today's paper was really cool.
 The researchers gathered many different strains of Y. pestis from around the world and then they compared the genetic sequences at different areas of the genome looking for single nucleotide polymorphisms (SNP). A SNP is where one letter of the genetic sequence has been changed to another. By comparing the presence or absence of SNPs the researchers were able to put together a tree that shows which strain of Y. pestis is the oldest. Once they knew that, they looked at where that strain from, in this case it was China. Using the locations of isolation of each strain and the sequence comparison tree, the researchers put together a map of Y. pestis movement. The plague started in China and then moved everywhere else, presumably along trade lines! Global transportation is again the culprit!
 When I think of Y. pestis, I unavoidably think of the Morlocks! Probably because one of them was named Plague!

 

 The coolest Morlock? It has to be Masque!! 

 His power is to shape your skin and organs into anything he likes..BAM! From ages 18-26, I had a serious fear of someone changing my appearance into something disgusting and crazy. Masque was my worst fear. This character is seriously underutilized! Too many people focus on crazy cosmic level badasses like Magneto, Galactus, or Mephisto, but what about the day to day madness of some loon coming in and changing my face into a big elbow!? True terror.