Tag Archives: Stanford University

Protein levels determine whether you’re a blond or a brunette, study shows

A study from the Stanford University School of Medicine has found that certain protein levels determine whether you’re a blonde or a brunette.

For the first time, the molecular basis for one of the most important physical human traits was described, outlining that even the tiniest DNA changes could have a crucial impact on our genome, which has possibly affected the evolution, the migration and even the course of the history as we know it today. David Kingsley, PhD and expert in developmental biology, declared that:

‘We’ve been trying to track down the genetic and molecular basis of naturally occurring traits — such as hair and skin pigmentation — in fish and humans to get insight into the general principles by which traits evolve, and now we find that one of the most crucial signaling molecules in mammalian development also affects hair color.’

A protein called KITLG, commonly known as a stem cell factor, was found to be encoded in the genes whose expressions are regulated in the DNA. Turns out that a single change in the DNA according to this biological procedure is responsible for major physical traits, such as the predominantly blond hair of Northern Europeans.  This change was found to affect only the level of KITLG in hair follicles.

Another result of the study concerns the tissue-specific, small changes in the expression of genes, whose effect can be morphologically noticeable. Connecting specific DNA changes with specific clinical prototypic outcomes is clearly laborious, as the study conducted by David Kingsley and led by Cathrine Guenther (PhD) underlines. To be more specific, the change is called ‘subtle’ because it occurs over 350, 000 nucleotides away from the KITLG gene itself and its impact on the amount of gene expression is no bigger than 20 percent. The procedure involves replacing an adenine (a single nucleotide) by a guanine on human chromosome 12 and its impact is believed not to be significant, taking into consideration that, when it comes to gene expression, the scale is only referred to as ‘on’ or ‘off’.

Adaptive changes are often the result of variations in the level of regulatory regions controlling gene expression and not necessarily within the coding regions of the gene itself. His explanation of the result is that:

in this case, it controls hair color. In another situation, perhaps under the influence of a different regulatory region, it probably controls stem cell division. Dialing up and down the expression of an essential growth factor in this manner could be a common mechanism that underlies many different traits.

According to the researchers, there were a number of clues leading to the fact that the regulatory regions could be of increased importance in deciding the hair color, such as that (1) the adenine-to-guanine nucleotide change was already associated with blond hair color in Northern Europeans due to previous genome-wide studies and (2) the large mutation in lab mice (called inversion) usually affects multiple nucleotides near the KITLG gene, given the fact that the mice with two copies of the mutation, one for each chromosome, are white, while the ones with a single copy of the mutation are significantly lighter, as we previously explained.

Because this nucleotide switch only effects the KITLG expression by about 20 percent or so, it would have been difficult to believe it would have such an effect on hair color. For that we needed these very carefully constructed, well-controlled animal models. They clearly showed us that this small difference in expression is enough to switch hair color in these animals.It’s clear that this hair color change is occurring through a regulatory mechanism that operates only in the hair. This isn’t something that also affects other traits, like intelligence or personality. The change that causes blond hair is, literally, only skin deep.’


Scientists use embryonic stem cells to create bone, heart muscle in just 5 days

Researchers from Stanford University have quickly and efficiently created pure populations of 12 different cell types – including bone, heart muscle and cartilage – from ancestral embryonic stem cells.

Image credit Pixabay

Image credit Pixabay

Stem cells of these cell types have been created in the past, but the current study marks the first time that pure populations have been created in a matter of days as opposed to weeks or months. In addition, previous techniques typically led to impure mixtures that contained multiple cell types, limiting their practical use.

“Regenerative medicine relies on the ability to turn pluripotent human stem cells into specialized tissue stem cells that can engraft and function in patients,” said Irving Weissman, the director of Stanford’s Institute for Stem Cell Biology and Regenerative Medicine. “It took us years to be able to isolate blood-forming and brain-forming stem cells.”

“Here we used our knowledge of the developmental biology of many other animal models to provide the positive and negative signaling factors to guide the developmental choices of these tissue and organ stem cells,” he added. “Within five to nine days we can generate virtually all the pure cell populations that we need.”

Embryonic stem cells are pluripotent, meaning they have the ability to form into any cell type in the body. This process is guided by various time- and location-specific cues that occur within the embryo, ultimately pushing their development in the direction of a specific cell type. Scientists understand a lot about how this process is guided in animals such as fish, mice, and frogs, but due to the restrictions on human embryo cultivation, they know little about human embryonic development.

In the new study, the team learned that human stem cells move down a developmental path that is composed of a series of choices that present just two possible options. They found that the best way to guide these cells towards a particular fate was to encourage the differentiation into one lineage and at the same time block the other pathway. In other words, saying “yes” to one choice while simultaneously saying “no” to the other.

“We learned during this process that it is equally important to understand how unwanted cell types develop and find a way to block that process while encouraging the developmental path we do want,” said Kyle Loh, co-lead author of the study, which was published July 14 in the journal Cell.

Through careful guidance of the developmental pathway, Loh and the team were able to push stem cell differentiation in the direction that they wanted, leading to the creation of 12 different cell lineages in a quick and effective manner.

“Next, we’d like to show that these different human progenitor cells can regenerate their respective tissues and perhaps even ameliorate disease in animal models,” he said.

NASA officially starts program to look for alien life

Just after NASA researchers made the bold claim that they will find alien life in less than 20 years, the space agency has officially launched a project to look for it. The Nexus for Exoplanet System Science, or “NExSS” will be a project integrating several fields of science, aiming to better understand exoplanets with the potential to host life, as well as planet-life interactions.

An image charge with symbolism: the search for life beyond our solar system requires unprecedented cooperation across scientific disciplines. NASA’s NExSS collaboration includes those who study Earth as a life-bearing planet (lower right), those researching the diversity of solar system planets (left), and those on the new frontier, discovering worlds orbiting other stars in the galaxy (upper right).
Credits: NASA

“This interdisciplinary endeavor connects top research teams and provides a synthesized approach in the search for planets with the greatest potential for signs of life,” says Jim Green, NASA’s Director of Planetary Science. “The hunt for exoplanets is not only a priority for astronomers, it’s of keen interest to planetary and climate scientists as well.”

The study of exoplanets is a relatively new field, but has blossomed incredibly in recent years. The first exoplanet was discovered only in 1995, but in the last six years alone, we’ve managed to find over 1,000 exoplanets with thousands of additional candidates waiting to be found. Scientists are working on establishing not only the ‘Goldilocks area‘, in which planets might hold liquid water, but also the search for biosignatures, or signs of life.

Of course, in order to do this, astronomy is simply not enough – you need to understand how the chemistry and geology of an exoplanet might interact with biology, and what visible signals they give out. James Graham, a UC Berkeley professor of astronomy, and leader of the Berkeley/Stanford team explains that the project will bring together researchers from several fields.

“We’re combining techniques to discover new information about how planets form, their range of properties and what sorts of planets are most common, with the eventual goal of finding terrestrial planets and venues for life in the universe,” Graham said.

NExSS will tap into the collective expertise from each of the science communities supported by NASA’s Science Mission Directorate:

  • Earth scientists develop a systems science approach by studying our home planet.
  • Planetary scientists apply systems science to a wide variety of worlds within our solar system.
  • Heliophysicists add another layer to this systems science approach, looking in detail at how the Sun interacts with orbiting planets.
  • Astrophysicists provide data on the exoplanets and host stars for the application of this systems science framework.

The Yale University team, headed by Debra Fischer, will design new spectrometers with the stability to reach Earth-detecting precision for nearby stars. The team will also make improvements to Planet Hunters, www.planethunters.org, a web interface that allows citizen scientists to search for transiting planets in the NASA Kepler public archive data. Meanwhile, a group led by Neal Turner at NASA’s Jet Propulsion Laboratory, California Institute of Technology, will work to understand why so many exoplanets orbit close to their stars. A team at the University of Wyoming, headed by Hannah Jang-Condell, will explore the evolution of planet formation while a Penn State University team, led by Eric Ford, will strive to further understand planetary formation by investigating the bulk properties of small transiting planets and implications for their formation.

The entire thing will be coordinated by Natalie Batalha of NASA’s Ames Research Center, Dawn Gelino with NExScI, the NASA Exoplanet Science Institute, and Anthony del Genio of NASA’s Goddard Institute for Space Studies. All in all, researchers from ten universities will participate.

All in all, it’s a huge thing, with huge potential implications; it may finally help us understand whether or not we are alone in the galaxy.

Source: NASA.

Abandoned wells can be ‘super-emitters’ of greenhouse gas

Princeton University researchers have uncovered a previously unknown and potentially substantial source of methane emissions: abandoned oil and gas wells. After analyzing wells from Pennsylvania, they found that a worrying amount of them leaked significant quantities of the greenhouse gas.

Alana Miller (left), a Princeton senior majoring in civil and environmental engineering, and Mary Kang, then a doctoral researcher in civil and environmental engineering at Princeton, conduct research that found abandoned oil and gas wells emit methane, a powerful greenhouse gas. (Photo courtesy of Robert Jackson, Stanford University)

A previous Stanford study estimated about 3 million abandoned wells in the United States alone, so if these wells are indeed leaking big quantities of methane, then there’s serious reason to worry about this. For this study Princeton researchers chose very diverse wells,from fields in Pennsylvania but these measurements need to also be taken in other states with a long history of oil and gas development such as California and Texas.

“The research indicates that this is a source of methane that should not be ignored,” said Michael Celia, the Theodore Shelton Pitney Professor of Environmental Studies and professor of civil and environmental engineering at Princeton. “We need to determine how significant it is on a wider basis.”

Pound for pound, methane (CH4) is 20 times more potent as a greenhouse gas than carbon dioxide, but it is emitted in much lower quantities; still, it’s considered to be the second most important contributor to the greenhouse effect. Methane is produced naturally through decomposition but also by humans, most notably through the oil and gas industry. While oil and gas companies have worked to reduce emissions for their newer wells, very little attention has been paid to older wells and in most parts of the world (US included), they have been virtually ignored. Many wells that date back to the 19th century and early 20th century are abandoned and not recorded anywhere officially.

Mary Kang, a former doctoral candidate in civil and environmental engineering at Princeton was studying carbon sequestration through burial. She found that quite often, the carbon manages to escape underground storage, and this led her to wonder if something similar is happening with old wells. But she first ran into a big problem.

“I was looking for data, but it didn’t exist,” said Kang, now a postdoctoral researcher at Stanford.

In a new paper, Mary worked with colleagues to get new data and fill in the gaps. Initially, she focused on 19 wells in Pennsylvania. While all the wells had some level of methane emission, about 15 percent emitted much more than the others – over a thousand times more. Denise Mauzerall, a Princeton professor and a member of the research team said it was critical to understand what makes these wells different from the others.

A well pipe emerges from the ground in the Allegheny National Forest in northwestern Pennsylvania. Researchers covered pipes from 19 wells with instruments to measuring gases emitted by the well. (Photo courtesy of Mary Kang, Department of Civil and Environmental Engineering)

This makes a lot of sense, because unfortunately, putting a plug on every single abandoned well is not realilstic. But putting a plug on these high emitters is much more doable.

“The fact that most of the methane is coming out of a small number of wells should make it easier to address if we can identify the high-emitting wells,” said Mauzerall, who has a joint appointment as a professor of civil and environmental engineering and as a professor of public and international affairs at the Woodrow Wilson School.

Judging by their sample size, they extrapolated the results to see how much of the total human-emitted greenhouse gases come from abandoned wells. The result was shocking: 10%. Of course, the sample size is very small and the results are still preliminary, but the figure is shocking – it’s as big as current oil and gas production; and unlike active oil and gas wells, which will emit for 10-15-20 years, abandoned wells will emit for centuries to come.

“This may be a significant source,” Mauzerall said. “There is no single silver bullet but if it turns out that we can cap or capture the methane coming off these really big emitters, that would make a substantial difference.”

Journal Reference: Mary Kanga, Cynthia M. Kannoa, Matthew C. Reida, Xin Zhangb, Denise L. Mauzeralla, Michael A. Celiaa, Yuheng Chenc and Tullis C. Onstottc. Direct measurements of methane emissions from abandoned oil and gas wells in Pennsylvania.


Iranian is the first woman to win prestigious math award

Maryam Mirzakhani, who was born and raised in Iran, has been awarded the highest honour a mathematician can attain: the Fields Medal.

It’s one of those moments which will go down in history – for the first time in almos 80 years, a woman has won the Fields Medal (officially known as the International Medal for Outstanding Discoveries in Mathematics). Maryam Mirzakhani, an Iranian maths professor at Stanford University in California was rumoured to be among the favorites for quite a while, due to her groundbreaking studies, which seem downright esoterical to less mathematical minds.

Born and raised in Iran, Mirzakhani completed a PhD at Harvard in 2004, even though her childhood passion was literature.

“I dreamed of becoming a writer,” she said in an interview for the Clay Mathematics Institute (CMI) in 2008. “I never thought I would pursue mathematics before my last year in high school.”

Nowadays, she works on geometric structures on surfaces and their deformations. She has a particular interest in hyperbolic planes, which can look like the edges of curly kale leaves. As a matter of fact, hyperbolic planes are so strange that they may be easier to crochet than explain. Mirzakhani says that while advanced math is not for everybody, most students don’t give math enough chances. Frances Kirwan at Oxford University, one of Britain’s leading mathematicians, said:

“Maths is a hugely rewarding subject, but sadly many children lose confidence very early and never reap those rewards. It has traditionally been regarded as a male preserve, though women are known to have contributed to its development for centuries – more than 16 centuries if we go back to Hypatia of Alexandria.

This may also motivate more female students to dive even deeper into research and academic careers.

“In recent years around 40% of UK undergraduates studying maths have been women, but that proportion declines very rapidly when we look at the numbers progressing to PhDs and beyond. I hope that this award will inspire lots more girls and young women, in this country and around the world, to believe in their own abilities and aim to be the Fields medallists of the future.”

Stanford stops investing in coal companies

Following a recommendation of Stanford’s Advisory Panel on Investment Responsibility and Licensing, the Board of Trustees announced that Stanford will not make direct investments in companies which have coal mining as their principal activity.

Put your money where your research is

Stanford will stop investing in coal companies. Image via David J. Philip/AP

Major Universities are very active in terms of investments – which makes a lot of sense. If you have some of the world’s best economists, you’d want to somehow capitalize on that, right? But the thing is, if you’re a leading university, then you also want to act ethically and morally, and I’m glad to see that Stanford is doing just that.

“Stanford has a responsibility as a global citizen to promote sustainability for our planet, and we work intensively to do so through our research, our educational programs and our campus operations,” said Stanford President John Hennessy. “The university’s review has concluded that coal is one of the most carbon-intensive methods of energy generation and that other sources can be readily substituted for it. Moving away from coal in the investment context is a small, but constructive, step while work continues, at Stanford and elsewhere, to develop broadly viable sustainable energy solutions for the future.”

This means that Stanford will divest their investments in coal companies and will refrain, in the future, to invest in approximately 100 publicly traded companies for which coal extraction is the primary business. This initiative was started (or at least accelerated) by a student-led organization known as Fossil Free Stanford, who petitioned the University to stop these investments. It took a while, but Stanford finally acted.

“Fossil Free Stanford catalyzed an important discussion, and the university has pursued a careful, research-based evaluation of the issues,” said Steven A. Denning, chairman of the Stanford Board of Trustees. “We believe this action provides leadership on a critical matter facing our world and is an appropriate application of the university’s investment responsibility policy.”

The next step, and also an important goal, is replacing other fossil fuels with renewable energy sources, but the infrastructure and current alternatives don’t allow them to do this efficiently, without wasting a lot of resources. Hopefully, in the future, things will change for this too. 

Big University, big money

Stanford does not disclose specific investments in its portfolio nor their individual value, though it provides information on endowment holdings and performance by broad asset category. Last year for example, they had a whopping endowment of $18.7 billion.

In recent years, they became much more active in fighting climate change and promoting alternatives to fossil fuels. They conduct an extensive array of research in this area, are actively working on reducing campus emissions and employee drive-alone rates. I’m glad to see them also putting their money to more sustainable uses.

Tiny neuromicroscope can see inside a moving animal’s brain

A team of neuroscientists from Stanford University have managed to create a remarkably tiny device capable of monitoring brain activity in a rodent or other small animals. The device can be manufactured extremely cost-effective and might prove to be an invaluable tool for researchers of the new decade.

A fluorescence microscope of tiny proportions - it weights only 2 grams! Credit: Dan Stober, Stanford News Service

A fluorescence microscope of tiny proportions - it weights only 2 grams! Credit: Dan Stober, Stanford News Service

Mice have always been the lab subjects of choice, and besides running around mazes for cheesy treats, rodents have now a new reason to rejoice. I mean, what mouse wouldn’t love one of these beauts wrapped around its head? The tiny microscope, weighing only 2 grams, is capable of monitoring up to 200 individual brain cells as the subjects moves around its environment. That’s actually more than a very expensive lab-sized equipment can rend, which requires the subject not to move.

The device, in principle, works by detecting fluorescent light, often used in biological research to mark different cells. Due to its tiny size and weight it can be easily strapped on a mouse’s head and used to accurately determine its brain pattern. Mice could be drugged and thus researchers will be able to see at a cerebral level how it interacts with the subject, or better understand what regions of the brain are more active when a subject is performing a particular task. Applications are numerous.

The cost? Well, the development cost for the prototype is figured at $50,000, however future models could drop in price extremely. First of all, all its components are already mass-produced everywhere on the mobile market, especially its core component, a complementary metal-oxide-semiconductor (CMOS) sensor, which can be found in most modern cell phone’s camera.

“The massive volume of the cell-phone market is driving costs down while not sacrificing performance,” says Aydogan Ozcan, professor of electrical and biomedical engineering at the University of California, Los Angeles. “Scientists are realizing that with cost-effective compact architecture, they can have components that a decade ago would cost thousands of dollars, if you could find them.”

The team of researchers, lead by Mark Schnitzer, a neuroscientist at Stanford University, got the idea to create this device after they understood they need to manufacture their own microscope to study how the brain directs movement. In the process, they managed to create a highly feasible and lucrative device, which quite possible might become highly commercial appealling in the future. Schnitzer and colleagues have already established a small start-up with this in mind.

“The advancement in being able to make a fluorescent scope this compact is really significant,” says Daniel Fletcher, a bioengineer at the University of California, Berkeley, who was not involved in the research. “For the animal to be able to carry the whole microscope along with it opens a lot more possibilities in studying behavior.

The study was published in this week’s issue of Nature Methods.