Stuttering and Genetics

(by everydaybiology) Feb 24 2011

Ever since the release of the award-winning movie The King's Speech, there has been a lot of discussion about stuttering in the media.

The movie is the fictionalized story of the struggle of King George VI - "Bertie" to his family - to overcome his stuttering with speech therapy.  That summary doesn't make it sound particularly interesting, but I found the story to be quite engaging. By the end I was rooting for Bertie to make it through his big speech.

It's estimated that almost 1% of adults stutter, just like Bertie. After decades of research, the underlying causes are only beginning to be understood.

At this past week's annual meeting of the American Association for the Advancement of Science (AAAS) in Washington DC, there was a symposium that focused on recent developments in cross-disciplinary stuttering research.  The most interesting study discussed in that session looked at how genetics may contribute to the speech disorder.

NIH geneticist Dennis Drayna and his colleagues have been studying closely-related families in Pakistan. They discovered three mutations associated with stuttering in those families. The three affected genes - GNPTAB, GNPTG, and NAGPA - are involved in directing glycoproteins to the lysosomes. Lysosomes are tiny organelles inside the cell that break down waste material and cellular debris. If the proper glycoproteins don't end up in the lysosomes, carbohydrates and fatty materials can build up to toxic levels in the body's cells.

It was already known that some mutations in GNPTAB and GNPTG cause mucolipidosis, a disease that affects both neurological and physical development.  In its severest form, mucolipidosis causes mental retardation and skeletal deformities. The people who carry the mutations in GNPTAB and GNPTG associated with stuttering don't have the severe neurological and physical problems associated with mucolipidosis.

It's not entirely clear how the mutations in genes involved in cellular metabolism might affect the development of the brain and cause speech problems, so there's still a lot of research to be done. But no matter what the mechanism is, finding these mutations provides support to the idea that the cause of stuttering is primarily physiological rather than behavioral or psychological.

But these genes are only a small part of the story.  Only about 6% of stutterers carry a mutation in GNPTAB, GNPTG or NAGPA.  Drayna's team and other research labs are searching for  additional associated mutations.  The hope is that the ongoing research into the genetics of stuttering will ultimately lead to new effective therapies.

Listen to the  AAAS Podcast on "The Mysteries of Stuttering" for more about the research presented at the symposium.

Additional reading:
• Michael Palin: "Stuttering: It's on everyone's lips now" Los Angeles Times (2011)

• Howell P. "Listen to the lessons of The King's Speech" Nature 470 (7) (2011) doi:10.1038/470007a

* Schenkman L. "First Gene Mutations Linked to Stuttering"  (Science NOW 2010)

• Willyard C. "Ancient Mutation to Blame for Stuttering" (Science NOW 2011)

• You can find more information about current research and resources for stutterers on the Stuttering Foundation of America's web site.   The National Institutes of Health also provides information on stuttering.

• Read the original research article: Kang C. et al. "Mutations in the Lysosomal Enzyme-Targeting Pathway and Persistent Stuttering" N Engl J Med 362:677-685 (2010)  doi: 10.1056/NEJMoa0902630 (free full text)

• Learn more about the research presented at the 2011 AAAS Meeting.

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Cat Burglar Caught on Tape

(by everydaybiology) Feb 19 2011

GrrlScientist reports on her Punctuated Equilibrium blog over at the Guardian that a cat burglar has been stalking a San Mateo, California neighborhood. In this case the thief is 6-year-old Dusty, a mixed-breed housecat.  Dusty prowls the neighborhood at night and grabs gloves, shoes, toys and other items from his neighbors' yards and carries them home to share with his family.  His record is 11 items in a single night, and he seems to favor drying swimsuits.

Local station ABC 7 caught him in the act with their night vision camera. Watch their report:

Apparently Dusty's neighbors are understanding about his behavior, as they know where to go to find their missing items.

Dusty isn't the only feline thief roaming our cities and suburbs. Apparently this sort of "misdirected predation" behavior is not uncommon in urban cats. The UK cat site has a whole collection of cat thief stories - and those are just the ones who both got caught and had stories written about them.

Personally, if I had a cat I'd much prefer a "gift" of the neighbor's flip flops than a half-dead mouse.

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Do-it-yourself 3-D Bioscience Modelling

(by everydaybiology) Feb 17 2011

A picture's worth a thousand words.  Sometimes even more.  I think that's especially true when trying to imagine microscopic organisms and molecules, that simply can't be seen with the naked eye. And even better than a flat picture is a three-dimensional model that you can move and manipulate.

I have on good authority that it used to be that if you wanted to create a 3D image on your home computer you would have to invest in expensive software and wait seemingly forever for models to be processed or rendered.  But almost a decade ago, Blender - a free open source 3D modeling application - was released to the public. And over the years personal computers have gotten fast enough that it doesn't take days to render your images.

Blender has been used to make some pretty amazing animated shorts. But it's uses aren't limited to entertainment and commercials.

Blender Image Rendering

Blender rendering a microbe image.

Issue #31 (December 2010) of BlenderArt Magazine takes a look at how Blender can be used "Under the Microscope" to demonstrate scientific principles and visualize microrganisms and microscopic cellular components.

Biomolecular visualization specialists Raluca Mihaela Andrei, Mike Pan and Monica Zoppè, write about how to use BioBlender.  BioBlender is a Windows application used to view and manipulate 3D protein models using data from the  RCSB Protein Data Bank (pdb files).

An example of their work is  the video Protein Expressions (there is a stereo version on their web site):

In the same issue, physicist Enrique Sahagún describes how he animated a kinesin protein motor transporting a vesicle down a microtubule.  The result:

The magazine includes some full-page images that demonstrate  nicely that  biological visualizations on the microscopic level can be both powerful science and beautiful art.

You can download Issue 31 of BlenderArt Magazine- along with sample .blend files. - for free at The issue are also includes a couple of articles about creating physics visualizations, if bioscience isn't your thing.

If you are in the Boston area, you might want to consider attending the BioBlender workshop at the VizBi (Visualizing Biological Data) conference  on March 19th at the Broad Institute in Cambridge.

3D Models created with Blender:

Virtual worm @ WormBase

• IFC-CNR Scientific Visualization Unit videos and blender files

Firing Neurons, the Cell Dance 2010 Public Outreach Video Winner

•  XVIVO's Powering the Cell (I don't know that they used Blender, but it's fantastic animation)

Molecular Shots Portfolio

Online tutorials :

Jonathan Williams demonstrates how to use Blender to model a Microscopic Virus

Frederik Steinmetz shows how to construct a "Microcosm" using Blender 2.5


The image at the top is one of the Blender Magazine sample images in the process of rendering. I actually don't have any experience making 3D animations myself.  Thanks to Brian (who does use Blender) for pointing the magazine out to me!

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The Neurochemistry of Love

(by everydaybiology) Feb 14 2011

Hearts (Explored!)My love is as a fever, longing still
For that which longer nurseth the disease,
Feeding on that which doth preserve the ill,
The uncertain sickly appetite to please.
My reason, the physician to my love,
Angry that his prescriptions are not kept,
Hath left me, and I desperate now approve
Desire is death, which physic did except.
Past cure I am, now reason is past care,
And frantic-mad with evermore unrest;
My thoughts and my discourse as madmen's are,
At random from the truth vainly express'd;
For I have sworn thee fair and thought thee bright,
Who art as black as hell, as dark as night.
~ Sonnet 147, William Shakespeare

The pursuit of romantic love is a greater driving force than the sex drive, according to Rutgers University anthropologist Helen Fisher, who studies the neuroscience of love.  As she describes it, symptoms of love are indeed quite powerful:

Romantic love begins as an individual comes to regard another as special, even unique. The over then intensely focuses his or her attention on this preferred individual, aggrandizing the beloved's better traits and overlooking or minimizing his or her flaws. Lovers experience extreme energy, hyper activity, sleeplessness, impulsivity, euphoria, and mood swings. They are goal-oriented and strongly motivated to win the beloved. Adversity heightens their passion [ . . . ] They reorder their daily priorities to remain in contact with their sweetheart , and experience separation anxiety when apart. And most feel powerful empathy for their amour; many report they would die for their beloved.

In fact, love can affect your brain like an addiction.  When love is reciprocated it's a constructive addiction, while rejection of love is a destructive addiction.  It's powerful effects have shaped and been shaped by evolution, and - Fisher argues - have even helped drive the development of human culture.

Here's an interesting lecture at UC San Diego where Fisher talks about the evolution and neuroscience of romantic love and the development of poetry and art (20 minutes):

If you are interested in more, also check out Fisher's 2008 TED talk about the brains in love (16 min.):

Happy Valentine's Day!

Technical reading:

Fisher HE et al. "Reward, Addiction and Emotion Regulation Systems Associated With Rejection in Love" J. Neurophysiol 104: 51-60 (2010)  (free pdf)

Fisher H "The Drive to Love: The Neural Mechanism for Mate Selection" in The New Psychology of Love, 2nd Edition. RJ Sternberg and K Weis (Eds.) New Haven: Yale University Press (2006) (free pdf)

Fisher HE et al. "Romantic love: a mammalian brain system for mate choice"  Phil Trans R Soc B 360: 2173-2186. (2006) (free pdf)

More of Fisher's publications.

Image: Hearts (Explored!) by qthomasbower, on Flickr

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Happy Darwin Day!

(by everydaybiology) Feb 12 2011

Sorry for the long posting hiatus.  The past couple of months seem to have flown by unexpectedly quickly. I thought a post celebrating Darwin Day would be an ideal way to get back into the swing of things.

Today, February 12th, is the 202nd anniversary of the birth of Charles Darwin. The day is celebrated by biology-loving folk all over the world as International Darwin Day.

So far there hasn't been any official recognition of Darwin's birthday here in the U.S. (at least that I know of).  But I'm proud to say that a few days ago Representative Pete Stark (D-CA)* submitted  House Resolution 81 in support of officially designating February 12th, 2011 as Darwin Day.

I quite like that the resolution was framed as support of science in general. As Stark said in his introduction to the Resolution:

Charles Darwin was born on February 12, 1809 and his life has had a profound impact on the course of human history.  Darwin’s theory of evolution by natural selection has not only provided a compelling explanation for the diversity of life, it is also the foundation of modern biology and genetics.  Darwin exemplified the scientific curiosity that has led to new scientific breakthroughs that have helped humanity solve numerous problems and improve our quality of life.

Charles Darwin is worthy of recognition and honor.  His birthday should be a time for us to celebrate the advancement of human knowledge and the achievements of reason and science.  It should also be a time for Congress and other elected officials to ensure that children are being taught scientific facts and not religious dogma in our public schools.

The mention of "religious dogma" is sure to antagonize those Representatives who think their religious beliefs can take the place of science (or at least think their constituents want them to believe that). And Stark  threw in  in a bit about climate change, which seems  like a poke at Republican climate change deniers. But even so, I'm hoping the bill at least garners enough support to pass out of committee.

But even if it passes, it will be too late to celebrate Darwin's birthday this year.

So to celebrate  Charles Darwin's birthday right now, I give you Australian poet Emily Ballou, reading from her collection The Darwin Poems:

As you read this Darwin Day may be over, at least for this year. But you can still celebrate:

• Read Darwin's original notebooks, diaries, and publications at Darwin Online. Not only can you read Darwin's works on evolution, but the notes on the development and growth of his children and his best selling book The Formation of Vegetable Mould through the Action of Worms, with Observations on their Habits (all about earthworm behavior and ecology)

• Ask your US Representative to support House Resolution 81 in Recognition of Darwin Day

• Listen to the 2008 Humanist Hour podcast interviewing P. Thomas Carroll, who transcribed thousands of Darwin's letters and personal correspondence.

• Learn more about evolutionary biology at the University of California Museum of Paleontology's Understanding Evolution site

• Buy some Darwin-related gear to support The Beagle Project. The project aims to build a working replica of the HMS Beagle, the ship that "carried Charles Darwin around the world"

• The bill was co-sponsored by fellow Democrat  Massachusetts Representative Edward Markey

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Green Christmas Trees

(by everydaybiology) Dec 13 2010

This weekend was the annual Christmas tree lighting in the small  park in front my local City Hall.  As you can see from the picture, the decorations aren't the most inspired - nothing but white lights, large ornaments (which you can't see after dusk) and a broad white garland that unfortunately looks a bit toilet paper-like when viewed from a distance.

I personally prefer more brightly colored holiday decor. But one of the nice things is that no tree was killed to decorate our civic center. It grows there year round, providing greenery even in the hottest part of summer. Very ecologically sound, that.

Of course a living tree isn't a usually a practical option when you put up a Christmas tree in your living room. It's not just that a tall potted fir is difficult to move. You also need someplace to put the tree when Christmas is over and the decorations have been removed – planting it in your yard requires a lot of space, considering that firs and spruces and pines can grow as tall as 100 feet.

But I was interested to read about another option in the LA Times this weekend.  The Living Christmas Co. rents potted Christmas trees for the season. You just pick out your tree, and it will be delivered to your home - assuming you live in western LA County, then picked up again after Christmas.  You can even adopt a special tree of your own to be delivered year after year. It's both easy and "green".

The company's owner,  Scott "Scotty Claus" Martin explains his philosophy:

"How, on one hand can something mean new hope, new joy, new love, and on the other hand be so easily discarded? And is that really Christmas?" he said.

The company's mission is not just to be sustainable but "regenerative," he said. Beyond saving trees, that means using all recyclable materials, running delivery trucks on biodiesel and employing adults with disabilities to maintain the trees around the year.

There are similar companies in San Diego, San Francisco, Portland and many other cities.

The down side is that it seems a bit pricey. A 6 foot tree costs $80 to rent, plus another $40  for delivery and pickup.   Adopting a specific tree costs another $50 per year, only offset a bit by a $20 credit towards the next year's rental. And of course a living tree requires more TLC than one that's going to end up on the curb come January.

Despite the cost and extra care required, I find the idea pretty appealing. It just seems so wasteful to cut down a tree, only to toss it out after a couple of weeks. We usually don't spend Christmas at home, so the past few years we've only put up a token little artificial tree.  But if tree rental becomes popular enough to spread way out the the 'burbs where we live, maybe we'll give it a try.

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There's an App for that! Free Biology Mobile Applications

(by everydaybiology) Dec 10 2010

I was surfing around for sciency holiday e-cards, when I came across this cute albino alligator looking for a kiss from the California Academy of Sciences.  You can choose one of several e-gifts, including polar bear wallpaper, a catchy tune,  or a Golden Gate Park field guide mobile application .

If you download the Golden Gate Park Field Guide iPhone app this month, you can just show it at the ticket window for $5 off admission through December 24th. That's a great deal if you happen to be in the San Francisco area.

That inspired me to see what other biology-related free iPhone/iPod Touch applications I could find.  I haven't had a chance to try them out yet, but the ones below looked the most interesting. I've noted which ones are available for Android devices as well.

Wildlife and Nature

While the Audubon and Petersons field guides will cost you, there are several apps that allow you to find, record and share wildlife sightings for free.

Golden Gate Park Field Guide (iPhone App store): Field guide, park map, self-guided activities, share your wildlife sightings.

Project Noah (iPhone App store):  Field guide, share wildlife sightings. They have a special project to document the impact of the Gulf oil spill on wildlife.  You can your Google account to sign in and share your sightings and photos.

WildObs Observer (iPhone App store; Android Market): Record  and share wildlife encounters. Has companion apps: WildObs Lookup (iPhone App store) field guide;  WildObs Lookout (iPhone App st0re) to find out what others have observed around your location;  and WildObs Naturalist (iPhone App store) to "keep your encounters and re-use them". WildObs is a partner of the National Wildlife Federation's Wildlife Watch. A free WildObs account is required.

NatureFind (iPhone App store):  This app allows you to search for nature spots and events near your ZIP code.

Science News

Get science-related news.

Scientific American Advances (iPhone App Store): Scientific American news and in-depth reporting. Requires registration at to view content. (iPhone App Store): Science news stories and the latest published research in Nature and the other journals from the Nature Publishing Group. News articles, abstracts and some research articles are free.

Science Mobile (iPhone App Store, Android): news from ScienceNOW, abstracts from the journal Science. This doesn't look as useful as Nature's app.

Molecules and Anatomy

For exploring the bits that organisms are made of.

Molecules (iPhone App store): 3-dimensional rendering of molecules that you can manipulate.  You can download molecules from the RCSB Protein Data Bank or elsewhere online.

BioCourseWare: Apps developed by the University of Nottingham, aimed at students in the biological sciences. Their free offerings include a Biology Dictionary, History of Genetics, and  Genetic Decoder.

Nature Human Genome Special Edition (iPad App): Nature's Human Genome at 10, repackaged into an interactive app for the iPad.  It looks pretty neat, but it's not available for the iPhone.

BrainTutor 3D (iPhone App store) : Explore a three-dimensional model of the  human brain.

Paleontology Apps

For learning about animals that no longer walk the Earth.

Dinosaurs (iPhone App Store): This app from the American Museum of Natural History allows you to explore their amazing dinosaur fossil collection.

MEanderthal Mobile App (iPhone App Store, Android):  This app from the Smithsonian Museum of Natural History allows you to morph yourself into a Neanderthal.  I suspect the novelty of this wears off pretty quickly.


If any of you use one of the wildlife spotting apps,  how well does it work for you? Is there a better free option?

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The Christmas Bird Count

(by everydaybiology) Dec 07 2010

For over a century the Audubon Society has organized a massive citizen science undertaking: The Christmas Bird Count. Tens of thousands of volunteers help take a census of the bird populations of Canada, the United States, Mexico and Central and South America.

Data from the annual surveys has provided biologists and conservationists a picture of long term changes in the distribution of North American bird populations.

For example, analysis of data collected over the past 40 years shows that the the winter range of many bird populations - 177 of the 305 species examined -  has shifted north, in some cases hundreds of miles. The shift correlates with an increase in mean January temperatures of almost 5 degrees during that period, and it's likely that climate change is at least partially responsible. Based on that data, the Audubon Society's report on birds and climate change (pdf) concludes that "ecological disruptions that threaten birds, other wildlife and human communities [due to climate change] are likely already in motion".

The Christmas Bird Count has also helped identify common bird species - from  meadowlarks to hummingbirds -  that "have taken a nosedive" over the past 40 years.

On the other hand, doves and pigeons have expanded their ranges along with growing urban and suburban development.

It's data that would be difficult to collect without an army of volunteers.

If you'd like to participate, this year's Christmas Bird Count begins on December 14th and runs through January 5th.  You'll need to register for a count:

There is a specific methodology to the CBC, but everyone can participate. The count takes place within "Count Circles," which focus on specific geographical areas. Each circle is led by a Count Compiler. Therefore, if you are a beginning birder, you will be able to join a group that includes at least one experienced birdwatcher. In addition, if your home is within the boundaries of a Count Circle, then you can stay home and report the birds that visit your feeder once you have arranged to do so with the Count Compiler. There is a $5 fee to participate in the CBC for all field participants aged 19 or older.

Find a count circle near you (unfortunately only searchable by state or province).

Even if you can't participate in the Christmas Count, you might be interested in similar bird observation projects:

Images from  from Our Winter Birds: How to Know and How to Attract Them by Frank M. Chapman (1918).  Chapman, an ornithologist with the American museum of Natural History and officer in the Audubon Society, proposed the first Christmas Bird Count in 1900. Top image: Tree Sparrow. Bottom Image: Northern Shrike.

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A virus walks into a bar . . .

(by everydaybiology) Dec 03 2010

A little geeky humor for Friday night: science comedian Brian Malow at the 2009 WonderFest at UC Berkeley.

Go to ForaTV for a larger video or to download the audio track.

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Sudoku-solving bacteria

(by everydaybiology) Dec 01 2010

One of the goals of synthetic biology is to engineer bacteria into biological "machines" that can be used to produce energy, deliver drugs, or synthesize materials. If the engineered bacteria could selectively communicate with each other, would expand their possible uses.

A team of students from the University of Tokyo decided to create E. coli bacteria that could selectively communicate with each other for this year's Internationally Genetically Engineered Machine (iGEM) competition, held last November 6-8 at MIT.

Sudoku Puzzle

Sudoku Puzzle

As a proof-of-principal for their bacterial communication system, the Japanese team created microbes that could solve a Sudoku puzzle.

Sudoku puzzles are usually made from a 9x9 grid made up of nine 3x3 squares. The numerals 1 through 9 can only be used once in each row, once in each column, and once in each 3x3 square. The puzzles start out with some of the numbers already filled in, and the goal is to fill in the blanks. You can see an example of a starting grid over on the right -->

Even though a Sudoku puzzle uses numbers, it's not a math puzzle - no adding, subtracting or other number manipulation is required. It's a logic puzzle. It could work just as well with nine different pictures or nine different letters or nine different colors.

The simple logic rules of the game were an ideal way to demonstrate the ability of the modified bacteria to communicate.

The Japanese team's modified bacteria were designed to solve a 4x4 Sudoku grid.  They engineered 16 genetically different bacteria, one for each spot on the grid. Each of those strains of bacteria has the ability differentiate into one of 4 types. Each of those types can then direct "detection bacteria" to produce a corresponding fluorescent color.

Just like any Sudoku puzzle, the grid begins with some of the squares already solved, like this:

E.Coli Sudoku Puzzle

The differentiated bacteria produce signals that tell the other bacteria their type. The undifferentiated bacteria are able to detect which of the 4 types are already present in the same "row",  "column" and "block", while ignoring information from irrelevant "squares". For example, undifferentiated bacteria representing square 4 would need to detect which differentiated types were already present in squares 1-3 (the same row), squares 8, 12, and 16 (the same column), and squares 3, 7 and 8 (the same block).  They would have to ignore the bacteria in irrelevant squares 11 and 13.

Here is their video of how the system works, which is a bit clearer than my explanation:

The students already have figured out - at least theoretically - how to modify their system so that bacteria would be able to solve a 9 x 9 Sudoku grid.

But that isn't the only use of such engineered microbes. Bacteria that can differentiate between relevant and irrelevant communications could ultimately be used to design bacterial logic circuits for parallel calculation devices. Maybe someday we'll be able to use bacteria to plug away at difficult computing problems.

You  can read the technical details to learn more about the biochemistry of the system.

And if you want to test your own Sudoku skills, I recommend the daily puzzle here.

(Project via New Scientist)


Top image: A Sudoku layout generated by the GNU programSu Doku Solver and contributed in the public domain by Lawrence Leonard Gilbert. From Wikipedia.
Bottom Image: "16 kinds of E. coli corresponding to each cell" by the UT Tokyo iGEM team, shared under a Creative Commons Attribution-ShareAlike license.

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