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Green Jobs Now Day of Action Recap

Yesterday was National Day of Action to demand a Better Economy, A Green Economy. I went to the Green Homes Renewable Energy Festival. Here is how I participated.
I'm ready!

















Go Green! Vote Green!

Visit Green for All for More information and to get involved. Sign the the I'm Ready Petition that will passed along to our Elected Officials.

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A Galaxy Cluster Makes Its Mark

A Galaxy Cluster Makes Its Mark
Abell 1689, shown in this composite image, is a massive cluster of galaxies located about 2.3 billion light years away that shows signs of merging activity. Hundred-million-degree gas detected by NASA's Chandra X-ray Observatory is shown as purple in this image, while galaxies from optical data from the Hubble Space Telescope are colored yellow. The X-ray emission has a smooth appearance, unlike other merging systems such as the Bullet Cluster or MACS J0025.4-1222. The temperature pattern across Abell 1689 is more complicated, however, possibly requiring multiple structures with different temperatures.

The long arcs in the optical image are caused by gravitational lensing of background galaxies by matter in the galaxy cluster, the largest system of such arcs ever found. Further studies of this cluster are needed to explain the lack of agreement between mass estimates based on the X-ray data and on the gravitational lensing. Previous work suggests that filament-like structures of galaxies are located near Abell 1689 along our line-of-sight to this cluster, which may bias mass estimates using gravitational lensing.



Abell 1689 – click for 864×897 image


More: here
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Green Jobs Now National Day of Action

Whew! This is one fabulous green-centered weekend. Today, Sept 27th is also a National Day of Action to Build a New Economy – a Green Economy.

So as you and your family are enjoying this day, celebrating Take a Child Outside Week or Public Lands Day, also think Celebrate the Developing a New Economy. In fact, some people are co-opting National Public Lands Day celebration as a Green Jobs Now Action Rallies. That’s great.
Learn more about Green for All and their great work here.

If you live in the St. Louis, Missouri Metro Area below is a list of Green Jobs Now Day of Action Events.
University City , MO
National Public Lands Day - 09/27
Other National Public Lands Events see my previous post.
St. Louis, MO
Green Jobs Now March and Rally- 09/27
St. Louis, MO
Green Homes & Renewable Energy Festival- 09/27
(I’m going to this one, so maybe I’ll see you out!)
Litchfield, IL
Green Jobs Now- 09/27

If you participate, let me know about it.
Have a great weekend.

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Go Outside! Take A Child Outside Week & National Public Lands Day

Go outside and enjoy this weekend! It's that perfect time of year when the height of the summer heat has passed, and the autumn breeze is taking over. The weather is perfect - not too hot, not cold. Plus, it is National Take a Child Outside Week! No kidding, September 24 - 30, 2008, is recommended as a time to take your family outdoors and share the love of nature and fresh air with your children, or the children in your life.

The Missouri Department of Conservation has a host of ideas for this week(end) to get you and yours out of doors.

And here's a recommendation from me - Celebrate National Public Lands Day, which is tomorrow, September 27, 2008.

National Public Lands Day is the nation’s largest hands-on volunteer effort to improve and enhance the public lands Americans enjoy.

In 2007, 110,000 volunteers built trails and bridges, planted trees and plants, and removed trash and invasive plants.

This annual event:

  • Educates Americans about critical environmental and natural resources issues and the need for shared stewardship of these valued, irreplaceable lands
  • Builds partnerships between the public sector and the local community based upon mutual interests in the enhancement and restoration of America's public lands; and
  • Improves public lands for outdoor recreation, with volunteers assisting land managers in hands-on work.
This year marks the 15th annual celebration of our nation's public lands such as city parks, state parks, national parks and forests, scenic drives and waterways, prairies and wildflower fields, evenmedians. These are all public lands. They belong to all of us. And since it's ours, shouldn't we pitch in?



If you live in the St. Louis, Missouri Metro Area there are several opportunities for you to get outside and participate. Several public lands in the area will be hosting hands-on workdays and exhibits this weekend.

Sat Sept 27 – Sun Sept 28

Visit one of these natural places.

National Park Service Jefferson National Expansion Memorial at the Gateway Arch

Columbia Bottom Conservation Area - Missouri Department of Conservation

Confluence Point State Park - Missouri Department of Natural Resources

Riverlands Migratory Bird Sanctuary - U.S. Army Corps of Engineers

Ruth Park Woods - The Green Center


Learn more about these events on The Confluence website

See you Outside!
DNLee
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International Polar Day! Celebrating the People of the Polar Regions

Today, September 24th, 2008 marks the sixth quarterly International Polar Day.


This is a special day within the bigger celebration of International Polar Year (IPY)- 2007-2009. IPY is a huge, multi-national research and educational awareness effort to bring attention to the importance of and the decline of precious Polar Ecosystems. This quarter’s International Polar day focuses on People – The People of the Polar Regions.


I’ll admit my own shortcomings. I don’t know much about the people of the Polar regions. So, I really appreciate the educational materials provided by the website. I read them and now I know that people of Arctic regions face many of the same challenges that we do – public health, raising families, maintaining communities, and adapting in the natural world. Please check out the materials. If you are an educator please conduct these activities with your students. Or if you are a parent or after-school youth leader, please consider these activities to keep your children busy and mentally active. They are a great resource.
Discussion Activity
People Summary

Finally, check out my other posts about International Polar Year.

I even launced a Virtual Balloon to mark my participation in this event. Will you launch yours, too.

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Wordless Wednesday: Summer Says Goodbye

Cone Flowers losing their petals and turning brown at an urban prairie garden at Chicago's Lurie Garden in Millenium Park.

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NPR stories about Urban Science

It is the start of autumn and along with crisp air and changing leaf colors, millions of birds are migrating south now. Along the river ways and waterways of this nation, several thousand species of birds will use these waterways, even man-made ponds and farm fields are rest stops on the long flight. Some will stay, many more will only pass through -- stopping over for the night, resting, eating and continuing south.
I was listening to NPR (National Public Radio) on the way home yesterday and I heard this wonderful commentary about helping migrating birds that get disoriented in big cities: The Magic Hedge: Haven For A Lost Bird In Chicago by Julie Zickefoose. Please check it out.

And All Things Considered did a piece about how Hurricane Ike has also impacted pets: Hurricane-Hit Pets Seek New Homes by Noah Adams. They so, stole my story. I presented this to you a week ago. But, please check out, too.
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mTOR, MAPK, and cancer

Recent studies are making it increasingly apparent that cancer is really many different diseases – hundreds actually – in the sense that there are hundreds of distinct problems at a molecular level that can result in the symptoms of cancer in a large variety of tissue types. It is necessary to regard all these problems as distinct diseases, because different techniques will be necessary to deal effectively with each one.

One of the things we are now understanding is that it is not simply mutations in a few specific genes that account for most different cancers. Instead, each different type of cancer can be attributed to mutations in one or several genes randomly chosen from a larger set that collectively defines some specific signaling "pathway" in a cell. Or perhaps even several interrelated pathways.

See here for one account of some of the latest research on this. I'd like to discuss the papers that cover this research, but first I'd like to discuss some slightly earlier research that provides a simpler look at the issue.

I've already written about one particular pathway of special importance, the one associated with mTOR. That discussion, from last April, is here.

As you recall, mTOR is a serine/threonine kinase. The pathway in which it plays a prominent part regulates the growth, proliferation, motility, and survival of cells. And also angiogenesis. From that list it should be obvious why malfunctions in the pathway can give rise to cancer. The pathway, in turn, integrates input from a number of upstream pathways, such as those involving intercellular signaling molecules like insulin, IGF-1, and mitogens.

The name mTOR is short for mammalian target of rapamycin. Rapamycin, also known as sirolimus, is a bacterial product that was originally of interest for its antifungal properties. It was subsequently found to have immunosuppressive and antiproliferative properties. These properties, in turn, are a consequence of the fact that rapamycin binds to a protein complex called mTOR complex 1 (mTORC1). The antiproliferative properties, of course, are due to the importance of mTOR in regulating cell proliferation and motility.

All this stuff is well known to cancer biologists and not new. In particular, much research has been devoted to finding useful inhibitors of mTOR. Unfortunately, however, the research hasn't been as successful at actually treating cancer as might have been hoped:

A Role For MAPK Inhibitors Combined With MTORC1 Inhibitors (8/21/08)
Nearly a decade ago, while it was being tested as an immunosuppressive agent to prevent organ rejection in transplant patients, the drug rapamycin was also discovered to have anti-tumor properties. Since then, several rapamycin analogs known as mTOR (mammalian target of rapamycin) inhibitors have been tested in clinical trials for the treatment of various types of cancer.

But despite promising early results, mTOR inhibitors have proven less successful than originally expected.


The problem is that the mTOR inhibitors that have been tried as anti-cancer drugs also seem to stimulate another pathway that promotes cell growth and proliferation:
Now research led by scientists at Beth Israel Deaconess Medical Center (BIDMC) identifies a previously unrecognized problem faced by these agents when it comes to attacking cancers. ... [T]he new findings show that at the same time that rapamycin analogs are halting tumor growth by inhibiting the mTOR protein complex 1 (mTORC1), they are activating the MAPK (mitogen-activated protein kinase) pathway -- thereby encouraging cancer cell survival.


The MAPK pathway has also been under intensive investigation in connection with cancer. As the name implies, kinases in this pathway are activated by mitogens – external signals that promote mitosis. These kinases also affect cell survival and apoptosis. So it's reasonable to guess that adding a MAPK inhibitor to an mTOR inihibitor might counteract the MAPK-stimulating effect of the mTOR inhibitors.

Are you with me? Anyhow, what the new research does is show how there's a feedback loop that connects mTOR inhibition with MAPK activation.

Inhibition of mTORC1 leads to MAPK pathway activation through a PI3K-dependent feedback loop in human cancer
Numerous studies have established a causal link between aberrant mammalian target of rapamycin (mTOR) activation and tumorigenesis, indicating that mTOR inhibition may have therapeutic potential. In this study, we show that rapamycin and its analogs activate the MAPK pathway in human cancer, in what represents a novel mTORC1-MAPK feedback loop. ... We further show that rapamycin-induced MAPK activation occurs in both normal cells and cancer cells lines and that this feedback loop depends on an S6K-PI3K-Ras pathway.

PI3K is another important signaling kinase about which there is a lot of other interesting current research – which we'll get around to discussing at some point. Ras is a G protein known to be very important in cancer because it activates MAPK pathways.

Are you beginning to get the picture of how complicated cancer can be, due to the interaction of pathways?

Fortunately, the research also shows that MAPK inhibition can offset problems due to mTOR inhibition:
[P]harmacological inhibition of the MAPK pathway enhanced the antitumoral effect of mTORC1 inhibition by rapamycin in cancer cells in vitro and in a xenograft mouse model. Taken together, our findings identify MAPK activation as a consequence of mTORC1 inhibition and underscore the potential of a combined therapeutic approach with mTORC1 and MAPK inhibitors.

Another research group has already confirmed the same thing, using the same MAPK inhibitor (PD0325901):

Anti-tumor Effects Are Enhanced By Inhibiting Two Pathways Rather Than One (8/21/08)
In the second study, Cory Abate-Shen and colleagues, at Columbia University College of Physicians and Surgeons, New York, and the University of Medicine & Dentistry of New Jersey, Piscataway, show that simultaneous inhibition of the mTOR and MAPK signaling pathways inhibited the in vitro growth of prostate cancer cell lines and the in vivo growth of prostate tumors in a mouse model of prostate cancer.

Here's their research paper:

Targeting AKT/mTOR and ERK MAPK signaling inhibits hormone-refractory prostate cancer in a preclinical mouse model
The AKT/mammalian target of rapamycin (AKT/mTOR) and ERK MAPK signaling pathways have been shown to cooperate in prostate cancer progression and the transition to androgen-independent disease. We have now tested the effects of combinatorial inhibition of these pathways on prostate tumorigenicity by performing preclinical studies using a genetically engineered mouse model of prostate cancer. We report here that combination therapy using rapamycin, an inhibitor of mTOR, and PD0325901, an inhibitor of MAPK kinase 1 (MEK; the kinase directly upstream of ERK), inhibited cell growth in cultured prostate cancer cell lines and tumor growth particularly for androgen-independent prostate tumors in the mouse model.

AKT is yet another family of serine/threonine kinases, often associated with mTOR, that is deeply involved in tumorigenicity. There's a lot of recent research on it that should also be discussed... some other time.

Further reading:

From Metabolism to Oncogenes and Back - Part II – 3/21/08 blog post that discusses many cancer-related signaling pathways, including mTOR, AKT, PI3K, Ras, and their connection with metabolism



ResearchBlogging.org
Arkaitz Carracedo, Li Ma, Julie Teruya-Feldstein, Federico Rojo, Leonardo Salmena, Andrea Alimonti, Ainara Egia, Atsuo T. Sasaki, George Thomas, Sara C. Kozma, Antonella Papa, Caterina Nardella, Lewis C. Cantley, Jose Baselga, Pier Paolo Pandolfi (2008). Inhibition of mTORC1 leads to MAPK pathway activation through a PI3K-dependent feedback loop in human cancer Journal of Clinical Investigation DOI: 10.1172/JCI34739


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Announcing 2 Important Dates in Science Awareness


September 24th is International Polar Day

I posted about International Polar Year several times. 2007-2008 were designated as International Polar Years. It is a huge, multi-national research and educational awareness effort to bring attention to the importance of and the decline of precious Polar Ecosystems.

September 27th is National Public Lands Day
This is a day to foster awareness and appreciation of publicly owned natural spaces. It is also a grand-scale Service project. Volunteers are asked to help preserve and sometimes re-store these areas for future enjoyment by the public.

If you were unaware of these two special projects, this is a perfect time to learn more about them. And I love thematic teaching and learning – that’s why I like blogging about special days or call to actions. It’s a perfect way to connect people (and students) to current and relevant events and teach basic ecological concepts.

I’ll be posting special blog submissions for these days. So please participate!
You can :
1) Check out my posts and do some of your research into these projects
2) Join me in blogging about these topics on these days to help raise awareness
and/or
3) Tell me about how you celebrated these special days
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Producing PRODUCE from Waste water - I told you so

Back in April there was alot stink raised about a science study that spread sewage on the lawns of Baltimore residents. That study, conducted by scientists from John Hopkins University, and funded by federal research grants, was designed to lower the lead levels in the soil in order to prevent lead poisoning in children.



Especially among members of the Black-blog-o-sphere, this was a big shock and there was outrage. But what surprised me more, was how unfamiliar most people were to the routine re-use of sewer water and sewer waste in commercial farming and landscape practices. This practice really disgusted people. I guess I really took this information for granted because I've known since I was child that manure made good fertilizer. Farmers and landscapers use animal manure all the time to get pasture, crops, and lawns to grow tall and beautiful.



I addressed this topic, a little, but I mainly focused on educating people on how common it is to re-use waste water and sewage. I'm scanning my feed aggregator and low! Look what was announced: A new report by an international research organization finds that urban farmers in developing countries overwhelmingly rely on waste water for irrigation.

A shot of a Mexican farmer washes his spring onion crop in a river containing sewage.

Fresh produce from wastewater is a summary or web release (written in real people language) produced by the Environmental, Science & Technology Journal.

In urban areas were people depend on food being produced and transported from elsewhere, the cost to eat can get prohibitive. Even here in the US, we're beginning to feel the pressure. So, urban farming is an ideal (cost-effective) way for people to feed themselves and make some extra money selling extras to others. Water is still an important and often limiting factor. And in poorer nations, mass amounts of "clean water" just isn't necessarily available. You use what you've got. Industriousness is the provider of many. You see, waste water is filled with nutrients. Plants can take in alot of those chemicals and use them to grow strong and tall. Plus, waste water is free. I mean, it hasn't been treated with chemicals to make it potable or worth drinking. So it doesn't cost anything to use it.

I hope this gives you another reason to remember to wash your fruits and veggies off before eating them

DNLee

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Wordless Wednesday: Taken Down by Ike

A Black Locust Tree (Robina pseudoacacia) that was felled in the wake of the Ike Storm that blew threw the Mid-west.
The tree seemed quite healthy, I suspect it fell because of the very wet soil. When soil becomes too wet and becomes the consistency of pudding, the roots just can't hold on and the weight of the tree brings it right down.




Location: The Principia (campus grounds), St. Louis, MO.

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Pets and Wildlife also hit hard by Hurricane Ike

Hurricane Ike has been devastating. Even as far away as the Midwest, we had some 'residual' damage, flooding, power outages, and deaths.

But natural disasters like this storm also separate families from the their pets, not to mention the lives of many companion and homeless animals. The Houston SPCA and other area animal agencies are hard-at-work with animal rescues.

The Houston SPCA has activated its Animal Response Hotline. Operators will be accepting lost and found animal reports, rescue reports and offering other animal related information. The hotline will be staffed from 10 a.m. to 6 p.m. Call notes are available so those who call in after hours may leave a message which will be returned first thing in the morning.
The number is 713-435-2990.

We don't think about how wildlife fares during storms. But think about it. Many trees are taken down or damaged during storms and this forever changes the urban forestry landscape in an area. It is often the old trees that fall and do the most damage - the same trees that serve as historical and important shelter sites, food resources, territory boundaries, and ecological landmarks for urban wildlife. With flooding, animals retreat to trees or little pockets of dry land or rooftops. These dry places are little islands, often providing no shelter or food, forces animals to huddle in close proximity that they are not accustomed to. Fighting and predation often result. And the food is gone, drowned in water, and starvation becomes a reality.

For the most part wildlife tends to be okay after such disasters. But I'm speaking in overall terms. In other words, the population should bounce back and everything will be fine after a while. But on an individual scale, there is always lost: shelters, refuges or hiding places, and scarcity of food. And it's usually the most vulnerable that don't fair so well - the sick and ailing, old, and the young.

Ike's Smallest Victims - This is a video of the urban wildlife that were also victims of Hurricane Ike. Wildlife Rehab and Rescue are sheltering over 200 baby squirrels and a flying squirrel who were injured in Hurricane Ike at the Houston SPCA. Video by Meg Loucks. September 14, 2008.

(A baby squirrel being hand-fed milk formula by a volunteer.)


Houston SPCA publishes Updates from the frontline that can be accessed here.
Or you may want to donate to their efforts.
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Urban Wildlife Watch: House Sparrows

The House Sparrow is perhaps the most common bird in the world. This little brown bird is everywhere – no kidding. The bird was actually brought to the United States from Europe in the 1840’s. Originally released in Central Park New York , these little birds are spread all over the U.S. map. And they seem to thrive in cities!

I met Dr. Peter Pap at the 12th Annual ISBE conference at Cornell University and found his research about the House Sparrow so great. He looked at the size and colors of the feathers on the chest, called a bib, and at the feathers on the underside of the wing. The bib of the male House Sparrow is actually very distinct and stands out like a big black patch. If you were to pluck one of these feathers you’d find that it is actually both black and white, with black being the dominant color. Also, not all bibs are the same size. Some bibs are larger than others. Why is that? That’s what Dr. Peter Pap set out to discover.

He hypothesized that birds with larger black bibs were in better condition and better fed than birds with smaller black bibs. He fed birds different types of diets – high and low quality diets – and later measured the size of their bibs. Better fed birds, the ones in better condition did have larger black bibs.
In nature this can be a very important difference. Birds in better condition are able to secure better territories and mates so that they can have more babies. Considering how much some people like to feed birds and put out bird feeders, we may actually be contributing to the overall better quality of birds in our neighborhoods.

Look out for House Sparrows and take a closer look at that black bib on its chest.
Are the bibs of different birds the same size or do they differ?
Are the bibs of birds who frequently visit bird feeders nearly all the same or do you see of differences?
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Community Organizing in Action - School Supply Drive for KidSmart (St. Louis)


The new school year has begun and the public education issues in St. Louis and throughout our nation are major issues that need to be addressed. Last week, my friends and I hosted a School Supply Drive.

We collected over $400 worth of much needed school supplies for needy St. Louis area classrooms for KidSmart. This organization allows teachers from needy public schools to shop for school and class room supplies for free. Needy is defined as a school that has 70% or more of its students receiving free lunch. So this means there are quite a few inner-city/urban schools that greatly benefit from this organization and contributors' philanthropy.

I'm no community organizer in the most romantic sense, but I beleive in doing what I can to help others. And I am especially interested in giving under-resourced urban children every leg-up possible. Plus, I dedicated to Service to All Mankind. Assisting those whose life is dedicated to service - e.g. teachers makes me feel good. Did you know most teachers spend $400 or more of their own money to purchase school and classroom supplies? They are neither reimbursed by their school districts nor receive tax credits beyond a $250 cap. And the poorer the school or district, the more the teacher tends to spend.

I encourage those of you who care about education and equalizing life's opportunities for all people to find a way to help others. Volunteer your time or use your talents to benefit a worthy cause to help others.

I challenge other Bloggers who work with young people to host a Community Event to benefit youth and education issues in your areas. Please let me know about it.

DNLee
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Messier 83 - The "Thousand-Ruby Galaxy"

The Thousand-Ruby Galaxy (9/2/08)
This dramatic image of the galaxy Messier 83 was captured by the Wide Field Imager at ESO's La Silla Observatory, located high in the dry desert mountains of the Chilean Atacama Desert. Messier 83 lies roughly 15 million light-years away towards the huge southern constellation of Hydra (the sea serpent). It stretches over 40 000 light-years, making it roughly 2.5 times smaller than our own Milky Way. However, in some respects, Messier 83 is quite similar to our own galaxy. Both the Milky Way and Messier 83 possess a bar across their galactic nucleus, the dense spherical conglomeration of stars seen at the centre of the galaxies.

This very detailed image shows the spiral arms of Messier 83 adorned by countless bright flourishes of ruby red light. These are in fact huge clouds of glowing hydrogen gas. Ultraviolet radiation from newly born, massive stars is ionising the gas in these clouds, causing the great regions of hydrogen to glow red. These star forming regions are contrasted dramatically in this image against the ethereal glow of older yellow stars near the galaxy's central hub. The image also shows the delicate tracery of dark and winding dust streams weaving throughout the arms of the galaxy.




Messier 83 – click for 1280×1280 image
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Wordless Wednesday: Bunny Rabbit


On the Campus of Cornell University, Ithaca, NY. Let me get very close.
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The first stars

Once upon a time when the universe was very young, before there were even galaxies that could be "far, far away", the first stars were born.

The story of how this probably happened, which astrophysicists have been trying to figure out for decades, is rather interesting. Only with results announced at the end of July has the story begun to come into good focus.

The main reason is has taken so long to understand how the first stars formed is that it is quite impossible to see individual stars from the earliest era. Indeed, some of the earliest galaxies we can see (consisting of billions of stars), even with our best telescopes, are about 13 billion light-years away, as they looked about 700 million years after the big bang. This corresponds to a redshift of about 7.5. (See here.)

It follows that the first stars had to have formed some time before that, but as of now we have no way to observationally verify an approximate date. Since it takes time for a galaxy to form out of individual stars, the first star probably formed within the first 500 million years or so after the big bang.

The only way, currently, we can even guess when the first star formed is by starting from what we know – the laws of physics and information we have about the composition of the universe in that time period – in order to do computer calculations (simulations) of the process that should have led to formation of the first stars. Results from the best simulation yet performed have recently been announced.

Although we cannot (yet) directly observe conditions or objects existing within the time period in question, we can infer a variety of facts about them. Some of the direct data we have is based on observations of the cosmic microwave background (CMB). This is radiation that is now observed in the microwave part of the spectrum, although it was much more energetic when it originated approximately 380,000 years after the big bang. Additional data came from observations by the Spitzer Space Telescope, announced in 2005, involving diffuse infrared light that began as ultraviolet light emitted by the first stars. (See here.)

What we know of that period is encompassed in what is called the cold dark matter model (CDM) of the universe. Very good evidence from a variety of sources exists for the overall parameters of this model. The parameters include an overall density of matter (both ordinary and dark matter) that is – at the present time – 30% of the total energy density (with the balance being dark energy). Of that 30%, 26% is dark matter and the remaining 4% is ordinary baryonic matter.

These fractions vary with time, because the density of matter is always decreasing as the universe expands. However, since dark energy (in the form of a cosmological constant) is proportional to volume, the amount of dark energy is always increasing, while its density (per unit volume) remains constant. What this means is that in the early universe during the time we're concerned with, the energy density due to matter was a much larger percentage. However, the ratio of dark matter to baryonic matter remained constant, at 6.5 to 1.

In the big bang model, the earliest chemical elements formed, just a few minutes after the big bang, were hydrogen, helium, and a little bit of lithium. (See here.) By mass, about 75% of this matter was hydrogen, and most of the rest was helium. Since these elements are stable, these proportions did not change for hundreds of millions of years – until the first stars formed.

Another thing we know from the CMB is that there were slight variations from place to place in the average density of matter. Over time, the regions which were slightly more dense than average tended to contract under the force of gravity, and these regions continued to grow denser, relative to everything else.

Eventually there were distinct, though rather diffuse, clouds consisting of dark matter, hydrogen atoms, hydrogen molecules (H2), and a little helium. The rate of collapse at this point is very much driven by the dark matter, since there's 6 times as much of it as of ordinary matter. In these low-density clouds, the pressure due to kinetic energy of gas particles was low compared to the force of gravitation.

You may be wondering why star formation at this early time is such a mystery. After all, stars are forming all the time in the present day. The process is more complex than might at first be supposed, but we have reasonable, albeit incomplete, models of how it happens, and there isn't any great mystery. We can, for example, predict that unless a gas cloud is sufficiently massive, it won't collapse to form a star at all. That is, the gas cloud will never become hot enough and dense enough for thermonuclear reactions to start, so that there is a sustainable source of energy (other than gravitational) to enable the star to shine. Instead, what you get from a cloud that's too small is a brown dwarf, essentially just a ball of gas where there is equilibrium between gravitational force and gas pressure.

But what stellar models show is that even if you start with a sufficiently large cloud of gas, in order that it can collapse far enough to begin thermonuclear reactions it is necessary, paradoxically, that at some point along the way the cloud can dispose of some of its internal kinetic energy. Unless this happens, the cloud has too much internal energy, so its pressure is too high, and equilibrium is reached before the cloud is dense enough to go thermonuclear.

The models further show that the factor which allows energy to be radiated away at the right time is the presence of enough heavy elements. But the kicker is that there were no heavy elements in the early universe – only hydrogen and helium. All other elements up to iron in atomic weight were formed in the first stars from internal thermonuclear reactions. And these elements were only distributed into the interstellar medium when stars of the first generation that were sufficiently large exploded as supernovae, and in the process created all other, heavier chemical elements as well.

But what hasn't been clear, until now, is whether stars could form at all without elements heavier than helium. Perhaps the most that could happen, unless individual clouds were extremely massive, is that contraction would stall, as it does in brown dwarfs. On the other hand, if a gas cloud is too massive, it might be unstable and explode before entering a star-like state that is stable for some significant length of time. In the present universe, the largest known stars have masses around 100 times the mass of our sun, and such stars live only a million years or so before going supernova.

Fortunately, the new simulations now show how stars could form from sufficiently large clouds, even in the absence of heavy elements.

The set of simulations reported on here starts with conditions as they were about 300 million years after the big bang (corresponding to a redshift of 14). One example starts with a gravitationally bound gas cloud of 500,000 solar masses (M), mostly dark matter. This cloud had a temperature of 1000 K, hydrogen and helium atoms, and a small fraction of molecular hydrogen, which enabled efficient radiative cooling to begin with.

The simulation proceeded through a range of 20 orders of magnitude in density, covering about 100,000 years. In the process, the gas became mostly opaque to radiation, so radiative cooling ceased. This means that from then on, the process was "adiabatic", unable to dissipate internal kinetic energy, so that temperature rose quickly. At a certain point in the simulation, a flattened disk-like structure of .1 M formed. Because the disk was thin, radiation could escape in a perpendicular direction, allowing further cooling. The final outcome, after several other stages, was a .01 M protostar – defined as a pressure-supported, constant-density atomic gas core.

The temperature of this protostar was 10,000 K, far short of what is needed for thermonuclear reactions. And the protostar was not especially dense – about the same as ordinary water. At this point, however, the simulation exhibited strong shock waves in the hot gas. The simulation stopped here because of the complexity of the protostar. So there is definitely further work to be done. The simulation did not reach the point where thermonuclear reactions would start, but it's a big step anyway, roughly halfway to the final goal.

At the point where the simulation ended, gas was accreting from the surrounding cloud rapidly enough to allow growth to 10 M in just 1000 years. This could continue to 100 M or more, which is the expected size of the largest initial stars. However, growth might stop short of that figure, if radiation pressure from thermonuclear reactions rises too fast. On the other hand, if the star grows to much more than 100 M, it could collapse into a black hole, taking the heavy elements with it. Only further simulations can clarify what might happen.

Several lines of evidence show that extremely massive (~100 M) stars existed in the first generation. For instance, there were stars large enough and hot enough to emit photons with enough energy to ionize hydrogen atoms. We know that before stars existed, all hydrogen must have been in the form of an unionized gas – yet before a billion years after the big bang, most of the hydrogen was ionized again. In addition, studies of the CMB indicate a large contribution of light from very bright stars and galaxies in that early time.

There are several other important results from these simulations. One is that it is actually much easier to simulate in detail the formation of the earliest stars than of later generations. This is because in the present universe there are a number of complicating factors, such as relatively abundant heavy elements, strong magnetic fields, and significant turbulence, that raise large obstacles to simulation. Being able to simulate star formation under simpler conditions is an important step to making good simulations under present conditions.

Another valuable result of full simulation of the earliest stars is the ability to predict what galaxies composed of such stars will look like (in terms of color, size, and luminosity) when we are eventually able to detect them with the upcoming James Webb Space Telescope after its projected launch in 2013. Having the predictions available beforehand will help increase confidence in the validity of the whole model.

Further reading:

Protostar Formation in the Early Universe – research article published 8/1/08 in Science

The Cosmic Rosetta Stone – commentary on the research, published 8/1/08 in Science

New simulation accurately tracks seeds of first stars – 7/31/08 news article in Science News

Filling the Gap in Stellar History – 7/31/08 news article in ScienceNOW

Universe's first stars bulk up in new simulation – 7/31/08 New Scientist news article

The first stars – 7/31/08 press release

Additional news reports:




ResearchBlogging.org
N. Yoshida, K. Omukai, L. Hernquist (2008). Protostar Formation in the Early Universe Science, 321 (5889), 669-671 DOI: 10.1126/science.1160259


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Urban Wildlife Watch: Voles

Voles are also called field mice, but there are several different types of field mice; it is a catch all phrase for mice that live out in nature. Voles are most common in undisturbed or not-so-much disturbed land areas - like field, woods, overgrown lots, and especially rural areas. But they can do okay in urban areas as long as there is some great lawns for them to occupy. A great sign of a vole in your yard is if you have sunken trails, usually along the fence line. Voles use tunnels or runways and they love tall grass. For those of you have have cats that do some hunting, you may have seen an unlucky vole in your pet cat's mouth. Unlike house mice, they have stouter bodies, are more uniformly brown and are distinct because of their small ears and short tail.

NPR has been busy lately - sharing many interesting stories about animal behavior. And of course my great (and nerdy) friends call me up and say "Oooh, did you hear that story on NPR about X animal? Do you know about that? Do you know the researcher?" Earlier this week NPR did a feature on faithfulness and genes that looks at the Mighty, Mighty Microtus ochrogaster - the Prairie vole: Marriage Woes? Husband's Genes May Be At Fault

Aren't they just cute and adorable? [photo credit: flynnroad.net/pix/vole/images/babies%207.JPG] And they are also monogamous, So researcher Dr. Larry Young from Emory (and yes, I do know of him. I haven't met him personally, but I gave him -his lab) many of my prairie voles last year when my studies were complete --- so there's a fewer than 6 degrees of separation, here....just go with me). Back to the Story. Dr. Young studies psychology and using animal models to duplicate some aspects of human behavior. This research looks at the biological underpinnings of monogamy and perhaps fidelity. Read the story, it's quick and easy so interesting.

My research with voles looks at how the family dynamics of this species influence how the young ones grow up and behave later in life. I am analyzing the results as at this moment (literally, no kidding), so I'll be quite happy to share it with you all in a few short weeks when I defend. Yeah!

In the meantime here are some pictures of me at work with the voles. Though I catch wild voles in the field, I raise them in lab and study them there.

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Wordless Wednesday: Snug as a Bug


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Induced pluripotent stem cells III

There is still some news from here that we need to look at. It has to do with reducing the risk of tumorigenicity by using a signaling protein Wnt3a – a member of the Wnt family of proteins – in place of the c-Myc transcription factor for inducing pluripotency in differentiated adult cells.

This press release gives the executive summary:

Embryonic-like Stem Cells Can Be Created Without Cancer-causing Gene (8/6/08)
Currently, IPS cells can be created by reprogramming adult cells through the use of viruses to transfer four genes (Oct4, Sox2, c-Myc and Klf4) into the cells' DNA. The activated genes then override the adult state and convert the cells to embryonic-like IPS cells.

However, this method poses significant risks for potential use in humans.

First, the viruses employed in the process, called retroviruses, are associated with cancer because they insert DNA anywhere in a cell's genome, thereby potentially triggering the expression of cancer-causing genes, or oncogenes. Second, c-Myc is a known oncogene whose overexpression can also cause cancer. For IPS cells to be employed to treat human diseases such as Parkinson's, researchers must find safe alternatives to reprogramming with retroviruses and oncogenes.

Earlier research has shown that c-Myc is not strictly required for the generation of IPS cells. However, its absence makes the reprogramming process time-consuming and highly inefficient.

To bypass these obstacles, the Whitehead researchers replaced c-Myc and its retrovirus with a naturally occurring signaling molecule called Wnt3a. When added to the fluid surrounding the cells being reprogrammed, Wnt3a promotes the conversion of adult cells into IPS cells.

What amounts to a crude form of gene therapy has been used to make IPS cells. The idea is to insert extra copies of genes for 4 different transcription factors into a cell's DNA in order to raise the expression level of those factors. The problem is that every insertion of a gene into a cell's DNA risks damage to some other random gene in the DNA. Wnt3a, on the other hand, is a signaling protein that normally affects cells only by attaching to receptors on the cell surface.

So what has been accomplished here is that the number of transcription factor genes that need to be inserted into the DNA is reduced from 4 to 3. In addition, the factor that is eliminated, c-Myc, has tumorigenicity risks of its own. Therefore, this research represents a small but useful improvement. However, it is probably only a first step.

More about the present research: here

We discussed earlier research aimed at eliminating use of c-Myc in making IPS cells here.

In fact, just a little bit earlier than the research discussed above, a team from Germany reported, on July 31 in Nature, making IPS cells by adding just two transcription factors. However, they didn't start with adult somatic cells, but with neural stem cells that already had higher expression levels of Sox2 and c-Myc. Given that, they needed to add only Oct4 and either Klf4 or more c-Myc. Here's the abstract:

Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors
Here we show that adult mouse neural stem cells express higher endogenous levels of Sox2 and c-Myc than embryonic stem cells, and that exogenous Oct4 together with either Klf4 or c-Myc is sufficient to generate iPS cells from neural stem cells. These two-factor iPS cells are similar to embryonic stem cells at the molecular level, contribute to development of the germ line, and form chimaeras. We propose that, in inducing pluripotency, the number of reprogramming factors can be reduced when using somatic cells that endogenously express appropriate levels of complementing factors.

Keep in mind that there's a further variable that's important here: the efficiency of the process, i. e. the yield of IPS cells obtained as a percentage of original cells at the beginning. It should be obvious that a fair amount of work still needs to be done to find a method of making IPS cells that's both efficient and produces cells that are potentially safe to use in therapeutic applications (as opposed to pure research).

OK, enough of that. Let's move on to something new.

One of the interesting questions about IPS cells is about exactly how close they are to actual embryonic stem cells, which are pluripotent by definition. The best way to measure the degree of closeness is by comparing gene expression levels between embryonic stem cells and IPS cells.

The next research has done exactly that. In fact, it studies gene expression levels for stem-like cells obtained from a wide variety of sources:

A new test distinguishes embryonic stem cells and those with equal therapeutic potential (8/24/08)
To distinguish adult stem cells from pluripotent cells, Loring’s team compared the gene activity of about 150 stem cell samples of various types, including reprogrammed cells, embryonic stem cells and neural stem cells. Out of this comparison popped 299 interacting genes that form what the researchers call a pluripotency network, or PluriNet. Measuring the activity of these genes could reliably distinguish the different kinds of stem cells, the team reports.

Here's the abstract for this research:

Regulatory networks define phenotypic classes of human stem cell lines
We report here the creation and analysis of a database of global gene expression profiles (which we call the 'stem cell matrix') that enables the classification of cultured human stem cells in the context of a wide variety of pluripotent, multipotent and differentiated cell types. Using an unsupervised clustering method to categorize a collection of ∼150 cell samples, we discovered that pluripotent stem cell lines group together, whereas other cell types, including brain-derived neural stem cell lines, are very diverse. Using further bioinformatic analysis we uncovered a protein–protein network (PluriNet) that is shared by the pluripotent cells (embryonic stem cells, embryonal carcinomas and induced pluripotent cells). Analysis of published data showed that the PluriNet seems to be a common characteristic of pluripotent cells, including mouse embryonic stem and induced pluripotent cells and human oocytes. Our results offer a new strategy for classifying stem cells and support the idea that pluripotency and self-renewal are under tight control by specific molecular networks.


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