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Biology 1B – Lecture 16: Population Genetics I


General Biology

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Biology 1B – Lecture 16: Population Genetics I

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The Promise of Personalized Medicine


The Promise of Personalized Medicine: we are on the threshold of a transformative new era in medical practice called personalize medicine. At the Medical College of Wisconsin, faculty members have been working at the forefront of research that is revealing the complex relationships between our genes, proteins and disease.

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The Promise of Personalized Medicine

Recommendation and review posted by sam

Spontaneously and rhythmically beating engineered human heart tissue from pluripotent stem cells


Spontaneously and rhythmically beating engineered human heart tissue from pluripotent stem cells The video has been provided and copyrighted by Malte Tiburcy and Wolfram-Hubertus Zimmermann

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Spontaneously and rhythmically beating engineered human heart tissue from pluripotent stem cells

Recommendation and review posted by Bethany Smith

Life sciences advance in gene therapy


Life sciences researchers have made a significant step towards curing cancer in mice through gene therapy.

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Life sciences advance in gene therapy

Recommendation and review posted by Bethany Smith

Spread of Plagues(Global Pandemic) part 1


Prayer: No pestilence shall come neigh my dwelling place for greater is he that is in he than he that is in this world. Live Avian Flu Virus Placed in Baxter Vaccine Materials Sent to 18 Countries socioecohistory.wordpress.com “But what remains unanswered are the circumstances surrounding the incident in the Baxter facility in Orth-Donau.” The contaminated product, a mix of H3N2 seasonal flu viruses and unlabelled H5N1 viruses, was supplied to an Austrian research company.

Link:
Spread of Plagues(Global Pandemic) part 1

Recommendation and review posted by Bethany Smith

Genetic Code: 28000 Victories


The very first sports car to bear the Porsche name won races. We treasure our heritage and never forget where we came from. In the field of motor sports we have achieved countless successes and written history.

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Genetic Code: 28000 Victories

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Wikipedia Accurate on Cancer Facts, But Hard to Read: Study

(HealthDay News) — The facts about cancer found on the website Wikipedia are about as accurate as the information on the disease found on the patient-oriented section of the U.S. National Cancer Institute’s Physician Data Query (PDQ), a comprehensive peer-reviewed cancer database, according to a new study.

Although experts from Thomas Jefferson University were hard-pressed to find errors on Wikipedia, they did find the content on the site was harder to read and included links to more dense information than the simplified, shorter explanations found on PDQ.

“There are a vast number of websites where patients can obtain cancer information,” study leader Dr. Yaacov Lawrence, adjunct assistant professor of radiation oncology at Jefferson Medical College of Thomas Jefferson University, and director of the Center for Translational Research in Radiation Oncology at the Sheba Medical Center in Israel, said in a university news release. Read more…

Ayurtox for Body Detoxification

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Recommendation and review posted by Bethany Smith

Clean Drinking Water Any Time, Anywhere

A large percentage of the world’s population does not have regular access to clean drinking water. Now there’s a possible solution; a personal water-filtering device called LifeStrawR. At about 12 inches in length. 1.2 inches in diameter and weighing less than two ounces, LifeStraw looks like a big fat drinking straw. But this “straw” removes nearly all bacteria, viruses, parasites, and even dirt from virtually any water supply. The device relies solely on the sucking action of the user to draw water through special filters. It’s effective for about 1,000 liters of water.

Currently, most LifeStraws are distributed through international aid agencies to people in poor countries who do not have access to clean water. There have been criticisms that the device is still a little too expensive for its intended market, but that may change over time, especially if similar devices eventually come on the market. In the U.S., LifeStraw is available only through several online sellers.

Disclaimer: I do not have a financial interest in LifeStraw. I just think it’s a clever solution to a worldwide public health problem.

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Recommendation and review posted by Bethany Smith

Further Adventures of a Chemist in Biology

Sincere apologies for not writing regularly on the blog. My chemical career trajectory has recently taken an unplanned turn and has required me to learn an other new skill set to succeed. I am now the CTO for my PI’s biotechnology company, which sounds cool to say, but isn’t as much fun as discussing science. My duties have now switched to making sales pitches, finding investors, writing SBIR grants, and making sure projects are progressing, I still found a little time to sneak in some science experiments last week. So lets get down to pretty pictures.

I xenografted some mice in the lab a few weeks ago for a collaborative project that didn’t go anywhere. Last week, the tumors grew past the point of no return, and at UCLA once they hit 1.5 cm we are mandated to euthanize the mice. Last week I also found myself with a little extra time and with the help of a fellow chemist we made some fluorescent molecules that “potentially” have interesting tumor targeting properties. As I had mice with tumors too big, and molecules that target tumor cells, I pretty much said what the hell and injected this molecule into the mice (Yes, I had ARC approval). A picture of the results is below with the control mouse on the left, injected mouse on the right. Areas colored red have the highest intensity, areas colored dark blue have the lowest intensity.

It is a result like this that makes me happy for working at the crossroads of Chemistry and Biology. I love being able to make a chemical at the bench and walking downstairs to tail-inject my mice and see the results immediately. The molecule obviously has strong uptake into tumors. The question everyone naturally will ask next is, “how does this happen? What is the uptake mechanism?” Those are questions I’m not sure how to answer, if anyone has suggestions let me know.

Mitch


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Blog Carnival: The Diels-Alder Reaction!

No reaction is more elegant, more heartwarmingly satisfying than the Diels-Alder reaction.  No reaction is also more nuanced.  It appears deceptively simple and yet has the ability to create immense structural complexity often without additional reagents and sometimes solvent-free.  Straightforward enough for an undergraduate organic chemistry class, yet intricate enough to spend several days in a graduate organic chemistry class reading into the engrossing story that is the Diels-Alder reaction.  It is by far my favorite reaction and the subject of my Blog Carnival Post.  And I am grateful to BRSM for deciding not to blog about the Diels-Alder Reaction. :)

First reported in 1928 by Otto Diels (1876-1952) and his graduate student Kurt Alder (1902-1958), the chemists at once saw the importance of their work and wanted the exclusive rights to utilize their reaction.  They write in their 1928 paper: “[T]he possibility of synthesis of complex compounds related to or identical with natural products such as terpenes, sesquiterpenes, perhaps even alkaloids, has been moved to the near prospect … We explicitly reserve for ourselves the application of the reaction developed by us to the solution of such problems.”  Fortunately for us, this exclusivity no longer applies.  Oh, by the way, the pair won the 1950 Nobel Prize in Chemistry for the reaction.

Striped away from all its layers of complexity, at its core, the Diels-Alder reaction (here’s a 3-D animation of the Diels-Alder Reaction) is a reaction of a conjugated diene (4? electrons, in the s-cis conformation) and an alkene (2? electrons, called the dienophile) to form a cyclohexene ring – the reaction is classified as a [4? + 2?] cycloaddition.  This is the bare-bones Diels-Alder reaction we all remember from undergraduate organic chemistry classes.  Straightforward, right?  The Diels-Alder is usually the only cycloaddition reaction to make it into undergraduate organic textbooks.  And that may be as deep as most undergraduate texts delve into the Diels-Alder reaction. (Click images for larger throughout.  And, like CJ, I also went with the hand-drawn structures.)

The Diels-Alder Reaction

The Diels-Alder Reaction

But the story is so much more interesting and rich.  Note that the electrons don’t really start and end anywhere in particular.  Like Kekulé’s apocryphal tail-eating snake, the electrons travel around in a ring in this mechanism; the Diels-Alder reaction joins other privileged mechanisms – electrocyclizations (Nazarov) and sigmatropic rearrangements (Cope, Claisen) – in the tribe known as pericyclic reactions.  Pericyclic reactions are an immensely rewarding cadre of reactions to study.  This is one of the few times where thoroughly wading through the theory behind the reactions pays great dividends in clarifying the reactions and predicting their products.

Pericyclic Examples

Examples of Other Pericyclic Reactions

Let’s look at application.  Your prototypical, run-of-the-mill Diels-Alder reaction yields a cyclohexene.  For most undergraduate courses, the regiochemical implications of this are enough.  An ambitious professor will make the diene a cyclic diene, which yields a bridged bicyclic system.  Those are always fun to draw.  A tethered diene and dienophile will form a fused bicycle (and tether a dienophile to a cyclic diene to make a sweet looking tricycle).  And for bonus fun, positioning a diene and a dienophile at opposite ends of a macrocycle leads to a transannular Diels-Alder, which has the awesome acronym TADA!

Diels-Alder Reaction Examples

Examples of the Diels-Alder Reaction

One of my favorite applications of the Diels-Alder exploits the fact that this reaction can run in reverse if the conditions are right (we call this a retro Diels-Alder) to turn a cyclohexene into a diene and a dienophile.  Reacting an unsaturated lactone as the diene with an alkyne as the dienophile produces an intermediate bridged bicyclic lactone.  A retro-Diels-Alder follows to liberate gaseous carbon dioxide, which bubbles out of solution, to yield a substituted benzene ring.  Very slick reaction.

Diels-Alder/Retro Diels-Alder Sequence

Diels-Alder/Retro Diels-Alder Sequence

Vollhardt’s 1980 synthesis of estrone showcases a beautiful example of an intramolecular Diels-Alder reaction.  Under thermal conditions, the benzocyclobutene (prepared in remarkably short order through alkyne trimerization methodology) undergoes a 4?-electrocyclic ring opening (another pericyclic reaction) to give an intermediate ortho-quinodimethane – a perfectly situated and highly reactive diene.  The pendant dienophile readily reacts with this diene to close the last two rings of the cholesterol framework.

Diels-Alder Example in Estrone Synthesis

Estrone Synthesis: Diels-Alder Example

Similarly, Corey’s 1969 prostaglandin F2? synthesis is a retrosynthetic masterpiece which every aspiring organic chemist needs to study.  Only a five-membered ring exists in the product, yet Corey had the vision to see that carbon atoms 6-11 (prostaglandin numbering) could form the 6 carbon atoms of the cyclohexene Diels-Alder product.  Diels-Alder reaction of the cyclopentadiene derivative and a ketene equivalent yielded a bridged bicyclic product.  Conversion to the ketone, followed by Baeyer-Villiger oxidation, gave the bridged bicyclic lactone.  A few steps later, the bridged lactone had been converted into the fused lactone which we now call the Corey lactone in homage to the organic chemistry giant.

Diels-Alder Example in Prostaglandin Synthesis

Prostaglandin Synthesis: Diels-Alder Example

The Diels-Alder reaction is not merely restricted to the synthetic lab; nature also enjoys a good Diels-Alder reaction from time to time.  And who can forget the endiandric acids from the pericyclic chemistry unit in their graduate organic chemistry class?  The unsaturated acid with seven double bonds is a naturally occurring polyene.  Once formed, the molecule spontaneously undertakes three separate pericyclic reactions to form an incredible amount of molecular complexity as a single pair of enantiomers.  Initial 8? conrotatory electrocyclization yields a cyclooctatriene.  A 6? disrotatory electrocyclization forms a fused bicycle.  Depending on which diastereomer is formed in this electrocyclization, the bicycle is in perfect orientation to perform one of two Diels-Alder reactions to form either endiandric acid B or endiandric acid C.    All this occurs non-enzymatically in nature.

Endiendric Acid: Diels-Alder Example

Endiendric Acid Synthesis: Diels-Alder Example

Where would we be without the Diels-Alder reaction?  Two ?-bonds, a ring, and up to four new contiguous stereocenters prepared in one elegant reaction.  Through judicious choice of starting materials, an enormous amount of molecular complexity can be formed.  My students always laugh at me for having a favorite reaction.  I don’t care.  The Diels-Alder reaction will always be my very favorite reaction.

 

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I almost cut this last part out of the final draft.  It’s a lot of the theory behind the Diels-Alder reaction.  But it’s just so cool to see it all come together I had to include it:

Like all pericyclic reactions, the Diels-Alder reaction is governed by what we now call the Woodward-Hoffman(-Corey???) rules.  For a pericyclic reaction to proceed, the p-orbitals of the reactants must overlap.  And the sign of the overlapping p-orbitals must be the same: the sign of the terminal orbitals in the HOMO of the diene and the LUMO of the dienophile must match.  This happens naturally with the HOMO/LUMO overlap in the [4? + 2?] Diels-Alder cycloaddition, though this analysis fails with the HOMO/LUMO overlap in the analogous [2? + 2?] cycloaddition (but if you photochemically excite one electron up one orbital level, this changes which orbital is the HOMO and the corresponding orbital signs.  Thus [2? + 2?] cycloadditions are said to be thermally disallowed, but photochemically allowed).

Molecular Orbital Picture for the Diels-Alder Reaction

Molecular Orbital Analysis for the Diels-Alder Reaction

The reaction works best when the HOMO and LUMO are close in energy.  Since the antibonding LUMO is always higher in energy than the bonding HOMO, anything to raise the energy of the HOMO and/or lower the energy of the LUMO makes Diels-Alder reactions more facile.  Chemists have long known that adding Electron Donating Groups (EDGs) to the diene and Electron Withdrawing Groups (EWGs) to the dienophile make for a smoother Diels-Alder reaction (although Inverse-Demand Diels-Alder reactions are known).  Adding a Lewis acid to further stabilize the LUMO helps, too.  But once you start tinkering with the electronic distribution of the ?-system, you have to deal with the unintended consequence of altering the regioselectivity of the reaction.  If this is accounted for when planning the Diels-Alder reaction, however, this regioselectivity can be strategically used to the chemist’s advantage by plotting the partial charges and reacting the partial positive charges with the partial negative charges.

Regiochemical Analysis of the Diels-Alder Reaction

Regiochemical Analysis of the Diels-Alder Reaction

While regiochemistry is relatively easy to predict and control for simple systems, the stereochemical outcome of the reaction can be harder to grasp.  A Diels-Alder reaction has the ability to produce as many as four new contiguous stereocenters in a single reaction.  That’s a possibility of as many as 2^4 = 16 different stereoisomeric products that could form.  Since the reaction is concerted (and suprafacial), however, eight of these stereochemical outcomes are impossible to access.

We can rationalize the following eight possibilities with the following analysis.  When the dienophile approaches the diene in a Diels-Alder reaction, the diene can be oriented any one of eight ways with respect to the dienophile.  Four of these orientations will be disfavored due to regiochemical arguments outlined above.  Two of the remaining orientations will have the dienophile substituent tucked under the diene (endo transition state), and the other two will have the dienophile substituent pointing away from the diene (exo transition state).  While pointing the large substituent away from the diene might seem like the best orientation for steric reasons, the Diels-Alder reaction prefers the endo transition state, eliminating two other orientations.  The remaining two orientations will react without preference to give a racemic mixture of enantiomers… unless some external stereocontrol is imparted on the system (chiral Lewis acid, chiral auxiliary, etc).  From 16 possible outcomes to two (and maybe even one!) by reasoning through the theoretical underpinnings.  That’s so cool.

Stereochemical Analysis of the Diels-Alder Reaction

Stereochemical Analysis of the Diels-Alder Reaction

But enough theory.  If I want theory, I can go back to grad school (and I don’t see anyone running back to take a graduate level organic chemistry course at their local university…)

Thanks for listening.


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‘Artificial leaf’ makes fuel from sunlight

Researchers led by MIT professor Daniel Nocera have produced something they’re calling an “artificial leaf”: Like living leaves, the device can turn the energy of sunlight directly into a chemical…

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‘Alarm clock’ gene explains wake-up function of biological clock

Ever wondered why you wake up in the morning —- even when the alarm clock isn’t making jarring noises? Wonder no more. Researchers at the Salk Institute for Biological Studies […]

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Mercury not like other planets

Only six months into its Mercury orbit, the tiny MESSENGER spacecraft has shown scientists that Mercury doesn’t conform to theory. Its surface material composition differs in important ways…

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‘Micro’-chemo and Cancer Pill Combo Tested in Liver Cancer Patients

A combination of an oral drug, called sorafenib, and a method for injecting microbeads of chemotherapy directly into tumors has been proven safe for liver cancer patients and may improve […]

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Sexting driven by peer pressure

Both young men and women experience peer pressure to share sexual images via the new phenomenon of ‘sexting’, preliminary findings from a University of Melbourne study has found ‘Sexting’ is […]

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Red wine ingredient resveratrol stops breast cancer growth

Cheers! A new research report appearing in the October 2011 issue of The FASEB Journal (https://www.fasebj.org) shows that resveratrol, the “healthy” ingredient in red wine, stops breast…

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Everyone’s a Little Bit Racist, but It May Not Be Your Fault

Everyone’s a little bit racist, posits the song from the musical Avenue Q. But it may not be your fault, according to research in the latest edition of the British […]

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Knockout of protein prevents colon tumor formation in mice

A protein that regulates cell differentiation in normal tissue may play a different role in colon and breast cancer, activating proliferation of damaged cells, according to researchers at the…

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Lift weights, eat mustard, build muscles?

New research in The FASEB Journal suggests that rats fed homobrassinolide, found in the mustard plant, produced an anabolic effect, and increased appetite and muscle mass, as well as the […]

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Hepatitis C patients likely to falter in adherence to treatment regimen over time

Patients being treated for chronic hepatitis C become less likely to take their medications over time, according to a new study from the Perelman School of Medicine at the University […]

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Doctors To Use ‘Trained’ Stem Cells To Heal Heart


Scientists at Ohio State University Medical Center are using specially treated stem cells in an effort to limit the damage of a heart attack.

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Doctors To Use ‘Trained’ Stem Cells To Heal Heart

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Multiple Sclerosis Stem Cell Therapy News Coverage


see http://www.cellmedicine.com

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Multiple Sclerosis Stem Cell Therapy News Coverage

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Genetic Bucket Chain, Part 1


This is the story of how you and Inuk are almost certainly both direct descendants of Confucius. NOTE: Yes, Julius Caesar was a poor choice, and Cleopatra is not much better.

More here:
Genetic Bucket Chain, Part 1

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Cells of the Immune System


http://www.handwrittentutorials.com – This tutorial looks at the differentiation of the cells of the immune system. Beginning with the stem cell, the tutorials maps the differentiation of the cells to their functional state.

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Cells of the Immune System

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Stem Cells-Iran-08-28-2011


http://www.presstv.com In this episode of Iran, Mahsa Mortazavi reports on the Stem Cell cord bank which is a modern method of curing diseases among the family members through stem cells.

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Stem Cells-Iran-08-28-2011

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