Thursday, June 12, 2008

The DNA Network

The DNA Network

I knew it could happen, I’ve seen it happen, I was watching out for it. [Synthesis]

Posted: 12 Jun 2008 07:05 PM CDT

DOH!
Despite all that, I just invited my entire addressbook to . After scowling at how everyone was selected by default and how there was no way to select only people who currently have accounts, I carefully went through the list and selected a small number of people. When I hit the send invitation button, the page re-loaded and told me I had to confirm my email address first, which I did, in a separate window. Then I hit the send button again, and IT SENT THE GODDAMN INVITE TO EVERYBODY IN THE WHOLE ADDRESS BOOK MAKING ME LOOK LIKE A GODDAMN N00B!

I knew something like this could happen, I was watching out for it, and they still got me! The bastards!

On a positive note, I did take the precaution of creating a special forwarding-only address just for them, so I could redirect the forward to the trash if that becomes necessary. Half the emails bounced anyways.

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Investing in Science Really Does Save Lives [adaptivecomplexity's column]

Posted: 12 Jun 2008 04:34 PM CDT

Pharyngula has an interesting graph showing the steady improvement in survival rates of childhood leukemia over the last 40 years. A disease that was essentially an automatic death sentence 40 years ago is now over 90% curable.

Passport to Paternity: One Man Receives DNA Test, Long-lost Daughter for Father’s Day [The DNA Testing Blog]

Posted: 12 Jun 2008 04:24 PM CDT

A Mountain View, Calif., man will finally be able to celebrate this Father’s Day after a 15-year-long battle to find and secure U.S. citizenship for his long-lost daughter from the Philippines. To celebrate Father’s Day, DNA Diagnostics Center paid off his DNA testing fees, just days before his daughter’s deadline for immigration was up. Michael Skipwith [...]

Career pathways in biotechnology [Discovering Biology in a Digital World]

Posted: 12 Jun 2008 02:52 PM CDT

Students in the United States take many convoluted and unnecessarily complicated paths when it comes to finding careers in biotechnology. If Universities and community colleges worked together, an alternative path could benefit all parties; students, schools, industry, and the community.

The image below illustrates the current paths and the approximate time that each one takes.

Read the rest of this post... | Read the comments on this post...

Human ovulation caught on tape [Bayblab]

Posted: 12 Jun 2008 01:26 PM CDT

Surgeons who were performing a partial hysterectomy witnessed a spontaneous ovulation and were lucky enough to have a camera to record the event. The pictures (I wish there was a video), will be published in the journal "Fertility and Sterility". Surprisingly, the ovulation was not an "explosive" event as it is assumed to be, but rather a 15 minute long and smooth release of the egg...

What’s on the web? (12 June 2008) [ScienceRoll]

Posted: 12 Jun 2008 01:12 PM CDT


  • SocialMatic: If you are tired of submitting to many social bookmarking sites, SocialMatic is for you because you can submit to 13 different sites automatically.

Jay Parkinson and Modern Healthcare [ScienceRoll]

Posted: 12 Jun 2008 12:30 PM CDT


You know well who Jay Parkinson is. I’ve written plenty of posts about him (see below). Now he launched something that really can shape the future of healthcare. See his slides presented at HIMSS Summit This is one of the most important medical slideshows published ever on the web.

jay-parkinson.jpg

WSJ Blog published an interview and Medgadet also covered the story.

Further reading:

This posting includes an audio/video/photo media file: Download Now

Info on iPSCs [Mary Meets Dolly]

Posted: 12 Jun 2008 12:30 PM CDT


I think I am finally rested enough from working and trying to raise a family that I can approach my computer to blog. (I just had to clean the house top to bottom first!)

A lot of people have been asking me about the ethics of induced pluripotent stem cells or iPSCs. These are cells that have been taken from an adult and reprogrammed into becoming more like an embryonic stem cell which are considered pluripotent. In case you forgot what pluripotent means, a pluripotent stem cell can become all of the tissue types in the body, EXCEPT placenta. (This is important as you will see later.)

Do No Harm has a great Fact Sheet on iPSCs and how they compare to their more hyped embryonic brothers. It is a good read to keep you up to date.

I think an important addition is the claim that inducing an adult cell to become pluripotent may create an embryo and therefore defeats the purpose of the procedure. THis is not the case. A zygote, (a single celled embryo) is totipotent which means it can become all of the tissue types of the body AND also placenta. It is a complete organism. Which means that if impanted in a uterus, it has the chance to grow into an infant. Therapeutic cloning by SCNT creates a totipotent cell, or a zygote which is allowed to grow to the 200 cell stage where pluripotent stem cells are available. This organism would then destroyed for its inner stem cell mass.

Any induced pluripotent cell is NOT totipotent. It is not a complete organism. It is just a cell. This is an important distinction to make and keep clear.

Doc makes ESC movie called "Hope" [Mary Meets Dolly]

Posted: 12 Jun 2008 12:21 PM CDT

The hype just never ends.  A doctor has written a movie called "Hope" that is about embryonic stem cell research, specifically.  Here is the plot:

"Hope" centers on a conservative U.S. senator who opposes embryonic
stem cell research. That belief is tested when his son is left a
quadriplegic after an ugly crime, and the senator faces intense
pressure from his family to take him to India, where stem cell research
offers hope. But the senator knows that course would likely cost him
his constituents' support.

"The point of the movie is to put the whole issue in a personal
perspective," Chawla said. "All of these people saying no (to the
research), what would they say if they need it some day?"

Honestly.  This is ridiculous.  Besides the name of the movie, the article states:

Supporters contend that embryonic stem cell research has shown the most
promise for growing replacements for damaged tissue, which could lead
to treatments for myriad diseases including diabetes, Parkinson's,
Alzheimer's and spinal cord injuries.

Once again, I ask "WHAT HOPE?"  Where are the clinical trials that show embryonic stem cells curing humans?  Instead of saying , "Where's the beef?"  I am asking "Where's the data?"  Where is the data, people?



Treating people like spare parts [Mary Meets Dolly]

Posted: 12 Jun 2008 11:57 AM CDT



What strikes me more than anything about out Brave New World, is our willingness to disregard the well-being of the very children we are trying to create. It is the height to egotism to purposefully create children either in the image we desire or to be used as "spare parts" for research or another child. I find it extremely disturbing. A symptom of a time when we want what we want, when we want it and who cares about how it affects anyone else.

Awhile back Fr. Raymond J. De Souza commented on Britian's House of Commons acceptance of "Human Fertilisation and Embryology Bill that would allow the creation
of animal-human hybrid embryos; would permit genetic screening of
embryos to select so-called "saviour siblings"; and would remove the
obligation to consider the role of fathers in artificial reproduction."

Fr. Souza rightly points out that this Bill makes a sharp departure from traditional Western Civilization values that see children as a good in their own right:

It is a hallmark of Western civilization that children are to be seen
as good in their own right, persons with rights and dignity entrusted
to the care of their parents. This is such a commonplace idea that we
do not stop to consider it a great civilizational achievement, but it
is.... It was the long painstaking work of centuries --drawing upon both
religious and civil resources -- to arrive at the cultural and legal
consensus that the child does not exist as an object for the benefit of
others, but that the child must be treated as a subject for his own
sake.

This seems like such a no brainer. Fr. Souza is right. Most people probably are unaware of this ethic and therefore cannot see how it has been abandoned. Screening a bunch of sibling embryos for genetic compatibility with a sick older child and tossing the rest, is clearly saying that it is acceptable for one child to be created for the benefit of another and not for his own benefit. Fr. Souza goes on:

The animating spirit behind the West-minster votes this week was quite
different -- that new life can be created for the purposes of others,
independent of its own interests. The Frankenstein-esque practice of
manufacturing animal-human hybrids is solely for the purpose of
destroying such embryos for medical research purposes. The desire to
create "saviour siblings" is flatly utilitarian -- the new child is
conceived for the explicit purpose of providing tissues and organs for
his siblings. The decision to no longer require fertility clinics to
consider who might be the father of the child is being hailed as a
great advance for lesbian couples and single women, but does anyone
pretend that fathers are irrelevant to the best interests of the child?

Many people think these measures are compassionate. I suppose if you only consider researchers, and the parents and siblings it could be seen that way. WHere is the compassion for the human embryo being experimented on? Where is the compassion for the embryos that don't make the genetic cut? Where is the compassion for the young adult who knows he was created in a dish to satisfy his mother's "need"? Where is the compassion for the child who is confused about Father's Day?

I would venture that many people think this has nothing to do with them or their families. They would be wrong. Once one class of humans are seen as desirable biologival material, theh we all do. Fr. Souza says it best:

The conception of a human person principally as an instrument for the
satisfaction of others' needs or desires is a radically different way
of looking at children. It has been oft-noted that we live in a
therapeutic society; the U. K. has now arrived at the point where new
life itself is looked at as a therapy for others.

Now that we see "new life as a therapy for others" when does "older life" become the same?

Invitrogen to Acquire Applied Biosystems for $6.7B [SEQanswers.com]

Posted: 12 Jun 2008 11:48 AM CDT

+ Big news today. Invitrogen acquires ABI. From :

Read more and join the community...

Ask a Librarian: Online [ScienceRoll]

Posted: 12 Jun 2008 11:38 AM CDT


Yale University Science Libraries came up with a great idea. From now, you can contact one of their librarians through Meebo, GTalk, AIM, MSN, etc. Here is a screenshot of the widget:

Reference service is intended to assist the academic research of students, faculty, and staff of Yale University. If you are not affiliated with Yale, we can reply to your question only if it concerns the University or some unique resource of the University Library: Please send an email to science dot reference at yale dot edu.

The Science Libraries Reference staff will attempt to respond to questions by the end of the following business day. A Reference Librarian is available at the Kline Science Library during regular business hours (Monday - Friday, 9:00 a.m. - 5:00 p.m.).

I wish the library of my university did the same…

Sherpa Hits San Francisco [The Gene Sherpa: Personalized Medicine and You]

Posted: 12 Jun 2008 10:43 AM CDT

Imagine rounding up everyone that is influential in the Genome Sequencing world on the science side, then add a healthy set of journalists, mix in a group of Venture Capitalists and put the leaders...

[[ This is a content summary only. Visit my website for full links, other content, and more! ]]

Invitrogen buys into next generation sequencing, and a lot more…… [Next Generation Sequencing]

Posted: 12 Jun 2008 09:08 AM CDT

Invitrogen Corporation and Applera Corporation today announced that their Boards of Directors have approved a definitive merger agreement, under which Invitrogen will acquire all of the outstanding shares of Applera's Applied [...]

Where Do Genes Come From? [adaptivecomplexity's column]

Posted: 12 Jun 2008 07:57 AM CDT

In biology, everything has a history. Creationists love to try to calculate the probability of a new gene spontaneously coming into existence, but that's not how genes are born. New genes most often come from other genes: one gene gets duplicated by a freak accident (like the accidental duplication of a chunk of chromosome, a whole chromosome, or even an entire genome), so that you suddenly have a cell with two working copies of the same gene. As time goes on (that is, time on an evolutionary scale), those two duplicate genes start to divide up the work that was originally done by just one gene. One copy might end up specializing in one particular task, picking up mutations along the way that gradually transform this copy into an independent gene in its own right, with its own specialized function. From one gene, you get two, each with a distinct role in the cell.

It sounds like a nice evolutionary story, but do scientists have any real examples of duplicate genes evolving new functions?

read more

My visit to the University of Toronto [The Daily Transcript]

Posted: 12 Jun 2008 07:17 AM CDT

Yesterday I had a great time visiting the biochemistry department at the University of Toronto. I met up with Lary Moran of Sandwalk who gave me a tour of the place. (We also got caught up in a huge discussion that culminated in a bet ... I will disclose the details at a future date.)

Later that night I met up with some local bloggers, Philip of Biocurious, Eva of Easternblot and John of Confession of a Science Librarian. Eva should be posting some pictures at some point.

I'm going to start preparing for today's talk. Wish me luck.

Read the comments on this post...

Odd Google hits [Genetic Future]

Posted: 12 Jun 2008 06:59 AM CDT

Every now and then I randomly sample the searches visitors have used to stumble across this site. Although most are disappointingly predictable, every now and then there's one that makes me smile: something cute, like "identical twin butterflies"; slightly sad, like "one leg longer than the other is it genetic?" (I imagine a lop-sided Googler deciding whether or not to reproduce); or downright incomprehensible, like "what genetic gene is stronger?"

As of today I have a new favourite:
why cant science answer what will i do with my genetic power
This makes me imagine Wolverine or Hiro, rather plaintively searching the internet for answers. Sorry, guys - this site won't help you, at least until someone does a genome-wide association study for time distortion abilities...


Subscribe to Genetic Future.

Genome Viewers/Editors - Three of the Best [Bitesize Bio]

Posted: 12 Jun 2008 06:25 AM CDT

When you need to see the “big picture” in molecular biology then you need to take a look at the whole genome of the organism that are interested in.

From what I’ve seen, most people don’t do this; the general workplan that I’ve seen is that researchers only ever delve into the genome to look for a specific gene/protein sequence (unless of course their work involves genome analysis, phylogeny etc).

That’s a shame becuase not only does taking in the whole genome view help you keep a perspective on the system you are working on, it can also be extremely useful for with strategies such as knock-ins and homologous recombination where having a rough idea of what surrounds your sequence of interest can be invaluable. So maintaining a good understanding of how to use them is a valuable tool.

A number of online and offline genome are viewers available, each with it’s own set of pros and cons. Here is an overview three that I have tried.

Artemis

Artemis is a genome viewer available from Sanger Institute. Its a java based tool with a 3-paned interface window that depicts the genome at various resolutions. Alternating between the different resolutions is a bit tricky but once you get a hold of it shouldn't be difficult. There is a also search tool that allows your to track down the particular feature that you're looking for.

A great feature of Artemis is that it allows you to edit the sequence annotations and features. Although the tool isn't perfect and is a bit finicky at times, it gets the job done.

Artemis supports the most common filetypes -EMBL, GENBANK, FASTA or raw format. Extra sequence features can be added in in EMBL, GENBANK or GFF format.

The best thing I like about Artemis is that there is a web version as well as an offline version, which means once you get used to it you can run it on or offline on any computer anywhere that has java.

Apollo

Apollo genome viewer is another java based genome viewer and annotation tool. It is a part of the Gmod project which runs most of the online genome viewers. The tool came out of a collaboration between the Berkeley Drosophila Genome Project and The Sanger Institute.

Apollo has a similar set of features to Artemis provides, but I found the interface to be less user-friendly. But that's just a personal opinion so you would be best to have a go at using both Artemis and Apollo and decide for yourself which is best. Again, the user guide will help you make best use of Apollo.

The NCBI Genome Workbench

The NCBI Genome Workbench is far more than just a genome viewer. As the name suggests, it is a complete and customizable workbench of tools that allow you to organize sequence data, which you can retrieve from NCBI databases or from your own files, for a project then view and manipulate them in a variety of ways. There is no online version available but downloading and installing NCBI genome workbench is quite simple.

The software allows you to view sequences as flat sequence files, phylogenetic trees, alignments and more.

The excellent zoomable graphics mode is the real strength of this package. It allows you to easily explore your sequence data at different levels of detail - individual genes can be viewed alone or in their genomic context and can be BLASTed straight from the graphical view. A nice set of alignment analysis tools is also available and BLAST and analysis results can be saved to your project making this a great way to keep track of your sequence data and analyses.

The tool supports quite a number of file formats, and I had no problems working with FASTA and most other file formats however when I tried to import the complete 1st chromosome of Dicyostelium which is in a GFF3 format the program kept crashing repeatedly, so clearly some bugs still need to be ironed out.

The NCBI genome workbench is a great idea, and provides a number of useful tools that make the program a must-have but the interface is a bit clunky and takes some getting used to. However, the site has a comprehensive set of instructions/tutorials to help you get up the learning curve quickly.

What’s your tool of choice?, drop us a line in the comments.

Photo: Semi-detached

CLC Genomics Workbench [Mailund on the Internet]

Posted: 12 Jun 2008 03:37 AM CDT

My friends at CLC Bio has just released their Genomics Workbench.  When I talked to them last Friday, I couldn’t quite figure out what the marked for this software is, but Next Generation Sequencing is a hot topic right now, so there probably is one.

Anyway, I wish them luck with it!

Researchers reveal insights into hidden world of protein folding [Think Gene]

Posted: 11 Jun 2008 10:46 PM CDT

The proteins upon which life depends share an attribute with paper airplanes: Unless folded properly, they just won’t fly.

But researchers have been puzzled by how the long, linear proteins cranked out by the ribosome factories in a cell are folded into the shapes they must assume to perform their function. They only have known that for many of the most complex and essential proteins, the folding takes place out of sight, hidden in the inner cavity of a type of molecule called a chaperonin.

Now Stanford researchers have begun prying open the lid, literally, on the inner workings of chaperonin molecules by deducing the mechanism by which the lid operates on a barrel-shaped chaperonin called TRiC.

“Understanding how the lid opens and closes really helps us understand how everything moves inside the chaperonin,” said Judith Frydman, associate professor of biology and one of two senior authors of a paper published online this week in Nature Structural & Molecular Biology.

“This is just the beginning, but now we can start to understand how the protein is pushed inside the cavity of the chaperonin and what this folding chamber looks like,” Frydman said. Learning how a protein is manipulated inside TRiC while it is being folded is a crucial step in Frydman’s larger plan.

“Our goal is to eventually exert control,” she said. “If we could re-engineer the chaperonin to either fold better misfolded proteins or alternatively to remove them from circulation, then we could prevent those proteins from being harmful to cells.”

Misfolded proteins have been implicated in a number of diseases, including some cancers, as well as ailments related to aging, such as Alzheimer’s and Parkinson’s diseases.

“Folding is one of the key steps for the health of the cell,” Frydman said.

Virtually all proteins have to be folded-some in complex configurations-in order to function properly, and many are known to require a molecule called a chaperone to fold them. Frydman estimates that perhaps 10 percent of the proteins needing chaperones must have one that, like TRiC, is part of the subset called chaperonins. Other work done in Frydman’s lab has shown that proteins that have very complex folds seem to require chaperonins.

“Many of the proteins that have these complex folds are the most important ones for life,” Frydman said. “The proteins that control the cell cycle, tumor suppressers and the proteins that control the shape of the cell are dependent on chaperonins to get to the folded state.

“If the chaperones don’t work well, then all these proteins that have been made become toxic,” she said.

TRiC, like all chaperonins, consists of a double-ringed structure that gives it a barrel shape. One ring opens to admit the raw protein into the inner recesses of the folding machine, then closes tightly while, inside the chaperonin “black box,” the mysteries of molecular origami unfold-or, more correctly, fold. Upon completion of the folding, the ring at the other end opens up to push out the finished product.

“It is really like a nanomachine. It closes off, the protein is trapped inside and something-we don’t understand what-happens inside this chamber, and the protein comes out folded,” Frydman said. “It is a very complex mechanism.”

The rings at each end of the barrel have to synchronize their actions for the sequence of events to happen correctly.

“We don’t know how the rings coordinate,” Frydman said. “What we have is evidence that this machine works like a two-stroke motor, so that opening one ring closes the other, and when that other ring opens, the first one is closed.”

Timing is critical because if a protein does not stay in the chaperonin long enough, it may not have time to fold properly. Conversely, if it lingers too long, it may also fold incorrectly. And sometimes proteins are not made correctly by the ribosome, so they simply do not bind well to their chaperone, making proper folding impossible.

Frydman discovered TRiC in 1992. She determined that it was important for folding some of the essential proteins and had a complex structure, but was stymied in her efforts to unravel its workings because the technology needed to peer into TRiC’s inner sanctum did not yet exist.

Recently, she began an interdisciplinary collaboration with Wah Chiu, a professor at Baylor College of Medicine in Houston, Texas, who is also director of the National Center for Macromolecular Imaging, located at Baylor.

Through combining biological experimentation with high-resolution imaging and computational modeling, Frydman and Chiu (the other senior author of the paper in Nature Structural & Molecular Biology) succeeded in uncovering how the lids at either end of the TRiC chaperonin open and close.

“What we found is that this lid opens like the iris of a camera,” Frydman said. “Previously, it was thought that the TRiC opens its lid like the flaps on a cardboard box and that the molecular machine didn’t really change shape.”

The motion of the lids has major implications for what happens inside the molecule.

“What has been so intriguing is that everything is connected,” she said. “This is a very large machine and every part of the machine is communicating with the other parts.”

Being so interconnected means that when the lids on the TRiC are twisting open and shut like the aperture on a camera, that rotation is transferred into the interior of the chaperonin. That has provided Frydman with important information on how a protein might line up inside the folding apparatus and how it begins to fold up once the lid is shut.

What they are learning has immense promise from the point of view of protein engineering and production, as well as potential for novel therapeutics, Frydman said.

“If one could understand what the environment in there looks like, what this machine does, what the cell does to fold its proteins, then we could begin to design ways to fold proteins for therapeutic purposes,” she said.

Source: Stanford University

Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Christopher R Booth, Anne S Meyer, Yao Cong, Maya Topf, Andrej Sali, Steven J Ludtke, Wah Chiu & Judith Frydman. Nature Structural & Molecular Biology. Published online: 08 June 2008; | doi:10.1038/nsmb.1436

Josh says:

I thought the crystal structure of chaperones was solved, and that it showed the chaperone open and closed, and this definitely suggested that it had a lid on either end that opened on a hinge. This new research is certainly interesting though, and could help explain how chaperones help proteins fold; perhaps the closing process is what helps to fold the protein. This is, however, just my own speculation.

Need microRNA processing? Get Smad [Think Gene]

Posted: 11 Jun 2008 10:33 PM CDT

Researchers at Tufts University School of Medicine and Tufts Medical Center have found that Smad proteins regulate microRNA (miRNA) processing. Understanding the role of Smad proteins enables researchers to investigate abnormal miRNA processing which is a contributing factor in development of cardiovascular disorders and cancer. The study was published online today in Nature.

“We found that Smad proteins, the signal carriers of a group of proteins that help regulate cells, promote the processing of a subset of microRNA, including miR-21. Smad proteins control the processing of miRNA from a primary copy of RNA (pri-miRNA) to precursor miRNA (pre-miRNA),” explains corresponding and senior author Akiko Hata, PhD, assistant professor at Tufts University School of Medicine and a member of the biochemistry program faculty at the Sackler School of Graduate Biomedical Sciences. “Smad proteins move to the nucleus of the cell and interact with a specific complex, called the Drosha microprocessor complex, to promote the processing of pri-miR-21 to pre-miR-21, eventually leading to an increase in mature miR-21 levels.”

“Mature miR-21 targets a tumor suppressor gene important for programmed cell death in both cancer cells and in smooth muscle cells, the cells that help our veins and arteries contract and relax,” contextualizes Brandi Davis, first author, and PhD candidate in the department of biochemistry at Tufts University School of Medicine. “Abnormal miRNA processing is a contributing factor in cardiovascular disorders and cancer, yet little is known about its regulation.”

Hata, Davis and colleagues designed a series of experiments to determine how members of a super-family of growth factors, called the transforming growth factor β (TGFβ) family, which is a group of proteins that help regulate cellular functions, can cause miRNA levels to increase. By exposing cells to members of the TGFβ family, the researchers were able to observe that, over time, levels of pre-miR-21 and mature miR-21 increased, while levels of pri-miR-21 did not change. “Since pri-miR-21 levels did not change, we concluded that the TGFβ family of growth factors doesn’t begin to play a role in miRNA processing until the pri-miRNA to pre-miRNA step,” explains Hata, who is also an investigator in the Molecular Cardiology Research Institute (MCRI) at Tufts Medical Center.

“Smad proteins were thought to act exclusively by regulating the transcription of DNA into messenger RNA (mRNA) in response to TGFβ signaling. This finding reveals a new role of Smad proteins as regulators of miRNA processing,” comments Giorgio Lagna, PhD, co-author, investigator in the MCRI at Tufts Medical Center and also an assistant professor at Tufts University School of Medicine. “If we want to generate a drug that regulates signaling by TGFβ, we now have the option to target different pathways downstream of TGFβ and achieve much more specific outcomes.”

MiRNAs are small gene products that regulate gene expression by interaction with mRNA. The role of mRNA in a cell is to carry the instructions for making proteins from the DNA in the nucleus to another part of the cell where the instructions are carried out and the proteins are made. “Thus, cells with abnormal miRNA levels may have abnormal protein levels, putting the organism at risk for many diseases including cancer and cardiovascular disorders. More research needs to be done to elucidate further the roles of miR-21 and other miRNA molecules,” explains Hata “because better understanding of how miRNAs effect disease may lead to a clearer understanding of disease initiation and progression.”

Source: Tufts University, Health Sciences

Davis BN, Hilyard AC, Lagna G, Hata A. Nature. 2008 “SMAD proteins control DROSHA-mediated microRNA maturation.” Advance Online Publication, June 11, 2008, doi 10.1038/nature07086

Josh says:

It does make sense for transcription factors to also affect miRNAs. If a protein is already used for controlling the expression of certain genes required for a specific function, it seems logical to use the same protein to regulate miRNA processing for that same function. While evolution does not always make the logical choice, things like this are becoming increasingly more common.

Vitamin D: New way to treat heart failure? [Think Gene]

Posted: 11 Jun 2008 10:27 PM CDT

Strong bones, a healthy immune system, protection against some types of cancer: Recent studies suggest there’s yet another item for the expanding list of vitamin D benefits. Vitamin D, “the sunshine vitamin,” keeps the heart, the body’s long-distance runner, fit for life’s demands.

University of Michigan pharmacologist Robert U. Simpson, Ph.D., thinks it’s apt to call vitamin D “the heart tranquilizer.”

In studies in rats, Simpson and his team report the first concrete evidence that treatment with activated vitamin D can protect against heart failure. Their results appear online ahead of print in the Journal of Cardiovascular Pharmacology.

In the study, treatments with activated vitamin D prevented heart muscle cells from growing bigger – the condition, called hypertrophy, in which the heart becomes enlarged and overworked in people with heart failure. The treatments prevented heart muscle cells from the over-stimulation and increased contractions associated with the progression of heart failure.

About 5.3 million Americans have heart failure, a progressive, disabling condition in which the heart becomes enlarged as it is forced to work harder and harder, making it a challenge even to perform normal daily activities. Many people with heart disease or poorly controlled high blood pressure go on to experience a form of heart failure called congestive heart failure, in which the heart’s inability to pump blood around the body causes weakness and fluid build-up in lungs and limbs. Many people with heart failure, who tend to be older, have been found to be deficient in vitamin D.

“Heart failure will progress despite the best medications,” says Simpson, a professor of pharmacology at the U-M Medical School. “We think vitamin D retards that progression and protects the heart.”

The U-M researchers wanted to show whether a form of vitamin D could have beneficial effects on hearts that have developed or are at risk of developing heart failure. They used a breed of laboratory rats predisposed to develop human-like heart failure.

The researchers measured the effects of activated vitamin D (1,25 dihydroxyvitamin D3, a form called calcitriol) in rats given a normal diet or a high-salt diet, compared to control group rats given either of the same two diets, but no vitamin D treatment. The rats on the high-salt diet were likely to develop heart failure within months.

The rats on the high-salt diet, comparable to the fast food that many humans feast on, quickly revealed the difference vitamin D could make.

“From these animals, we have obtained exciting and very important results,” Simpson says.

After 13 weeks, the researchers found that the heart failure-prone rats on the high-salt diet that were given the calcitriol treatment had significantly lower levels of several key indicators of heart failure than the untreated high-salt diet rats in the study. The treated rats had lower heart weight. Also, the left ventricles of the treated rats’ hearts were smaller and their hearts worked less for each beat while blood pressure was maintained, indicating that their heart function did not deteriorate as it did in the untreated rats. Decreased heart weight, meaning that enlargement was not occurring, also showed up in the treated rats fed a normal diet, compared to their untreated counterparts.

Simpson and his colleagues have explored vitamin D’s effects on heart muscle and the cardiovascular system for more than 20 years. In 1987, when Simpson showed the link between vitamin D and heart health, the idea seemed far-fetched and research funding was scarce. Now, a number of studies worldwide attest to the vitamin D-heart health link.

The new heart insights add to the growing awareness that widespread vitamin D deficiency—thought to affect one-third to one-half of U.S. adults middle-aged and older—may be putting people at greater risk of many common diseases. Pharmaceutical companies are developing anti-cancer drugs using vitamin D analogs, which are synthetic compounds that produce vitamin D’s effects. There’s also increasing interest in using vitamin D or its analogs to treat autoimmune disorders.

In more than a dozen types of tissues and cells in the body, activated vitamin D acts as a powerful hormone, regulating expression of essential genes and rapidly activating already expressed enzymes and proteins. In the heart, Simpson’s team has revealed precisely how activated vitamin D connects with specific vitamin D receptors and produces its calming, protective effects. Those results appeared in the February issue of Endocrinology.

Sunlight causes the skin to make activated vitamin D. People also get vitamin D from certain foods and vitamin D supplements. Taking vitamin D supplements and for many people, getting sun exposure in safe ways, are certainly good options for people who want to keep their hearts healthy. But people with heart failure or at risk of heart failure will likely need a drug made of a compound or analog of vitamin D that will more powerfully produce vitamin D’s effects in the heart if they are to see improvement in their symptoms, Simpson says.

Vitamin D analogs already are on the market for some conditions. One present drawback of these compounds is that they tend to increase blood calcium to undesirable levels. Simpson’s lab is conducting studies of a specific analog which may be less toxic, so efforts to develop a vitamin D-based drug to treat heart failure are moving a step closer to initial trials in people.

Source: University of Michigan Health System

1,25-Dihydroxyvitamin-D3 Treatment Reduces Cardiac Hypertrophy and Left Ventricular Diameter in Spontaneously Hypertensive Heart Failure-Prone (cp/+) Rats Independent of Changes in Serum Leptin. Peter Mancuso, PhD; Ayesha Rahman, PhD; Stephen D Hershey, MD; Loredana Dandu, BS; Karl A Nibbelink, MD; Robert U Simpson, PhD. Journal of Cardiovascular Pharmacology. POST COPYEDIT, 15 May 2008. 10.1097/FJC.0b013e3181761906

Josh says:

I’ve always said that taking a multivitamin everyday has to increase your lifespan.

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