Second Round for POLARBEAR: Improving Measurements of CMB Polarization

Cosmology (the study of the origin and evolution of our universe) may seem to be one of the most daunting subfields of physics. We can’t travel back in time to see the Big Bang for ourselves or even any light that has escaped from its very beginning. Fortunately, the universe did leave us a trace of its childhood through the Cosmic Microwave Background (CMB). The CMB is made up of the oldest photons we will ever be able to detect.

Just after the Big Bang, our universe existed in a very hot and dense state. Atoms were not able to exist until the universe was about 300,000 years old and had expanded enough so that the temperature fell to about 3000 K (5000°F). After the formation of neutral atoms, photons were able to travel freely without scattering and their orientations or polarization changed.

Here at Cal, Prof. Adrian Lee’s experimental cosmology group is looking at the polarization of the CMB. In an interview in 2014, Adrian used a romantic metaphor to describe this polarization, “Think of it like this: the photons are bouncing off the electrons, and there is basically a last kiss, they touch the last electron and then they go for 14 billion years until they get to telescopes on the ground. That last kiss is polarizing.” He describes the stage in our universe’s history where photons can finally travel freely. More specifically, the POLARBEAR experiment looks at B-modes of the CMB. These B-mode polarization patterns formed at the photons’ last point of scattering, if the matter nearby was unevenly distributed. B-mode polarization also occurs after the photons have begun travelling freely when passing through large gravitational fields. Photons can be both B-mode and E-mode polarized, and these patterns differ geometrically as seen in the image below.

SabrinaBerger1

The current experiment POLARBEAR 1 (PB1) employs microwave detectors on the Huan Truan Telescope in a Chilean desert. POLARBEAR is a collaboration of over 70 researchers around the world and was first used for observations in 2012. PB1 was the first experiment to be successful in detecting pure B-modes that form through gravitational lensing. This experiment enabled the group to determine the total mass along the path of each photon, and their main focus so far has been to map the matter distribution of the universe back to the “inflationary” period of the universe. Inflation is a term used to describe the exponential expansion of the universe in extraordinarily little time very shortly after the Big Bang. POLARBEAR measurements have very wide astrophysical applications, including providing evidence for inflation, constraining the mass of the neutrino, and dark energy’s evolution.

SabrinaBerger2

POLARBEAR 2 (PB2), the newest addition to the POLARBEAR experiment, will include three different experiments and new telescopes with higher sensitivity. Its first update to PB1 will be released for observing sometime late next year. The three telescopes will be built to eventually completely replace PB1 in the next three years. “The biggest deal is that PB2 is much more sensitive than PB1. Our ability to measure the actual signal of the CMB is limited by our number of detectors. PB1 has only a small set of detectors, with only one detector attached to each antenna. Whereas on PB2, we’re making our focal plane, where all of our detectors sit, a lot larger. This enables us to more than double the amount of our detectors,” said Charles Hill, a third year graduate student working on the PB2 experiment.

This international team is working tirelessly to produce the second round of experiments for POLARBEAR.

 

If you would like to read more about the POLARBEAR telescope and see who makes up the team of collaborators from UC Berkeley and beyond, see the experiment’s website below:

http://bolo.berkeley.edu/polarbear/

 

You can read the 2014 UC Berkeley news article about POLARBEAR here:

http://news.berkeley.edu/2014/10/21/polarbear-seeks-cosmic-answers-in-microwave-polarization/

 

You can read more about E-mode and B-mode polarization here:

http://background.uchicago.edu/~whu/intermediate/Polarization/polar5.html

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Activity-Based Protein Profiling: Discovering Novel Therapeutic Strategies for Disease

In the post-genomic era, we are faced with the daunting challenge of translating all of this genomic information into cures for human diseases. One of the major bottlenecks for drug discovery is that much of the genome remains uncharacterized, hampering our efforts to uncover their biological or therapeutic functions. Another challenge is that many of the protein targets that we know to be drivers of human diseases belong to a category known as “undruggable,” meaning that we have no means of developing pharmacological or biologic tools against the target for developing a therapeutic.

Activity-based protein profiling (ABPP) is an exciting technology that is enabling researchers to identify new therapeutic targets and even develop new and safer pharmacological agents for therapeutic discovery. ABPP uses active-site directed chemical probes to directly assess the functional states of large numbers of proteins directly in complex biological systems. These activity-based probes consist of a chemical warhead that binds to functional sites within proteins and a handle which can be used for visualization of these targets by fluorescence or identification of these targets by mass spectrometry-based proteomics. When applied to various disease settings, ABPP has been successfully used to discover many promising therapeutic targets for diseases such as cancer, inflammation, depression and anxiety, obesity, and neurodegenerative diseases. An additional unique feature of this ABPP technology is that it also enables the development of inhibitors against protein targets that are targeted by activity-based probes, even those that are uncharacterized and considered to be undruggable. Because the activity-based probes are binding to functional sites within proteins, small-molecule inhibitors can be competed against the probe binding, enabling inhibitor discovery and accelerating the process of drug discovery. In addition, because the probes themselves are binding across many proteins in-parallel, the selectivity of these inhibitors can be assessed on a proteome-wide level. Developing selective inhibitors that specifically inhibit the therapeutic target but not unrelated off-targets help in mitigating toxicities and side-effects, thus contributing to new and safer drugs.

ABPP, started in Benjamin Cravatt’s laboratory at The Scripps Research Institute, has contributed to several interesting discoveries. For example, Cravatt and Daniel Nomura, now an Associate Professor at UC Berkeley, demonstrated that the enzyme monoacylglycerol lipase (MAGL) controls a fatty acid network that contributes to tumor growth (6). Their study showed that MAGL could be a target for cancer treatment and, curiously, suggested that there is a link between a high-fat diet and cancer progression. Nomura and Cravatt also showed that MAGL inhibition in the brain leads to elevations in endogenous cannabinoid lipid levels that act on the cannabinoid receptors (the same receptor that THC from marijuana binds) and also lowers pro-inflammatory eicosanoids lipid levels to inhibit inflammation and protect and neurodegeneration in the brain. Very potent and selective MAGL inhibitors have been developed using the ABPP technology and have recently entered Phase I clinical trials in humans through Abide Therapeutics in La Jolla, CA. Nomura’s lab at Berkeley has continued to identify novel therapeutic targets and potential therapeutic leads for treating cancer using the ABPP technology.

Hopefully, in the near future, drugs created thanks to ABPP will be successful in clinical trials.

Acknowledgments

Daniel Nomura has critically read and edited the blog post, sharing his valuable insights into ABPP technology.

References

1. National Cancer Institute. SEER Stat Fact Sheets: All Cancer Sites. http://seer.cancer.gov/statfacts/html/all.html (accessed Nov 22, 2015).

2. The Scripps Research Institute. The Cravatt Lab Research. http://www.scripps.edu/cravatt/research.html (accessed Nov 22, 2015).

3. Medina-Cleghorn, D.; Nomura, D. K. Exploring Metabolic Pathways and Regulation through Functional Chemoproteomic and Metabolomic Platforms. Chemistry & Biology. 2014, 21, 1171-1184. http://www.sciencedirect.com/science/article/pii/S1074552114002361 (accessed Nov 22, 2015).

4. Cravatt, B. F.; Wright, A. T.; Kozarich, J. W. Activity-Based Protein Profiling: From Enzyme Chemistry to Proteomic Chemistry. Annu. Rev. Biochem. 2008, 77, 383-414. http://www.annualreviews.org/doi/pdf/10.1146/annurev.biochem.75.101304.124125 (accessed Nov 22, 2015).

5. Bogyo, M. Finding enzymes that are actively involved in cancer. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 2379-2380. http://www.pnas.org/content/107/6/2379.full (accessed Nov 22, 2015).

6. Nomura, D. K.; Long, J. Z.; Niessen, S.; Hoover, H. S.; Ng, S. W.; Cravatt, B. F. Monoacylglycerol lipase regulates a fatty acid network that promotes cancer pathogenesis. Cell, 2010, 140, 49-61. http://www.sciencedirect.com/science/article/pii/S0092867409014391 (accessed Nov 22, 2015).

7. Long et al. Selective Blockade of 2-Arachidonoylglycerol Hydrolysis Produces Cannabinoid Behavioral Effects. Nat. Chem. Biology. 2009, 5, 37-44. http://www.nature.com/nchembio/journal/v5/n1/full/nchembio.129.html (accessed Nov 22, 2015).

8. Special Feature. Greatest Hits. Nat. Chem. Biology. 2015, 11, 364-367. http://www.nature.com/nchembio/journal/v11/n6/full/nchembio.1815.html (accessed Nov 22, 2015).

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Analysing the Link between Global Warming, Hurricane Patricia, and Future Tropical Storms

PallaPic1

For a brief time, Hurricane Patricia had taken America by storm (pun definitely intended). On the night of Wednesday October 21st, Patricia was an under-the-radar tropical depression that drew little attention. Then, due to a combination of high ocean temperatures, low pressures, and low wind currents, Patricia began to grow at a rate that astounded and terrified not only scientists, but much of America as well (1). By the morning of Friday October 23rd, Patricia was “the most powerful storm ever measured by the U.S. Hurricane Center” (2).

Patricia’s rapid growth and destructive power has largely been attributed to the weather phenomenon known as El Nino, when the temperature of the Pacific Ocean near the equator rises and the air pressure in the eastern Pacific Ocean drops. But as Patricia was dominating headlines across the country, many media outlets also chose to focus on the effect climate change, more specifically global warming, has had on the destructive potential of hurricanes. Many of these articles argued that as global warming continues, tropical storms will increase in strength and danger, and cite Patricia as an example. Furthermore, many of these pieces called for steps to counter global warming to mitigate the future danger of hurricanes, as well as advocated for stronger hurricane defenses to prepare for more powerful storms. However, a number of articles also proposed the opposite argument – Patricia’s record-breaking strength is not the result of global warming.

But looking outside of the realm of popular science, is Patricia evidence that global warming is causing more dangerous hurricanes?

The link between global warming and Patricia is tenuous at best; it is difficult to divorce the amplification of Patricia due to El Nino from the amplification due to climate change. Moreover, no single weather phenomenon can be solely attributed to a large-scale trend like global warming, nor should a single event or storm be held as indicative of a trend as widespread as climate change. While no scientific literature exists on the subject (Patricia is too recent a phenomenon), climate experts like Kerry Emanuel, who was among the first to predict that global warming would increase the strength of hurricanes, have declined to state that Patricia specifically is evidence of the link between climate change and hurricane intensity (3).

However, looking beyond Patricia, does science indicate that global warming has led or will lead to more destructive hurricanes?

Well, kind of, but not really. Recently, scientific literature has increasingly found links between climate change and more destructive hurricanes. However, many of these articles stop short of explicitly stating a causal link between global warming and more powerful hurricanes. A 1987 article in Nature by Kerry Emanuel predicted a significant increase in the destructive potential of hurricanes due to greenhouse gas-induced climate change, but the increase of the magnitude of Emanuel’s predictions has not been seen (4).

Emanuel returned to the subject in 2005 and demonstrated an increase in the destructiveness of hurricanes that correlates strongly to increased ocean temperatures (5). Webster, et al. also found an increase in the number of category 4 and 5 hurricanes, between 1970 and 2005, which was, in their words, “not inconsistent” with models that correlated increased hurricane intensity with global warming (6). However, both these studies conceded that the measured increases could be within normal variance of hurricane intensity.

Two recent studies in Nature Geoscience tied increased hurricane intensity to greater economic losses on the United States, but both qualified their results with the statement that increased hurricane intensity cannot clearly be tied back to climate change (7,8).

The end result: scientists have not disproven the notion that global warming will lead to more powerful hurricanes, but they haven’t definitively proven it either. The reality may be that scientists will not be able to definitively state this link exists until these stronger storms are actually upon us. However, even without definitive proof, the evidence in favor of the notion continues to grow.

Works Cited:

  1.       Vance, E. (2015, October 23). How Hurricane Patricia Quickly Became a Monster Storm. Retrieved from http://www.scientificamerican.com/.
  2.       Chandler, A. (2015, October 23). Bracing for Patricia. Retrieved from http://www.theatlantic.com/.
  3.       Mooney, C. (2015, October 23). Why record-breaking hurricanes like Patricia are expected on a warmer planet. Retrieved from https://www.washingtonpost.com/.
  4.       Emanuel, KA. (1987). The dependence of hurricane intensity on climate. Nature, 326, 483–485.
  5.       Emanuel K. (2005). Increasing destructiveness of tropical cyclones over the past 30 years. Nature, 436, 686-688.
  6.    Webster, PJ, et al. (2005). Changes in Tropical Cyclone Number, Duration, and Intensity in a Warming Environment. Science, 309 (5742), 1844-1846.
  7.       Hallegatte S. (2015). Climate change: Unattributed hurricane damage. Nature Geoscience, 8, 819–820.

8.       Estrada, F, et al. (2015). Economic losses from US hurricanes consistent with an influence from climate change. Nature Geoscience, 8, 880–884.

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The Human Microbiome: Slowly Getting There

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At this point in time, the study of the human microbiome is not a novelty. Quite a lot of time and money has gone into pursuing the promising field, hoping that collecting data from the trillions of microorganisms in and on our bodies will offer insights into how they affect health and diseases. While the microbiome has bene shown to heavily affect us—the food we eat, our immune system and infections, organ developments, even behavioral traits—our knowledge regarding the microbiome is still extremely limited. The goal of predicting an individual’s propensity for certain diseases (and ultimately preventing them) using the human microbiome seems more distant than not.

Part of the reason of why this research seems to be progressing slowly is the vast amount of data that needs to be processed and the time required to amass it. Specifically, months are required for bacteria collection (mainly from feces—relatively unappealing to the masses and probably another reason the field is not popular) and for gene sequencing. Biotech companies such as Biomiic have started working on how to process and present collected data at a much faster rate (as reported in the following article http://bostinno.streetwise.co/2015/10/05/havard-ilab-startup-microbiome-data-from-poop/)

Once data can be processed more powerfully, perhaps the field will advance rapidly. After all, even the world’s largest collaborative biological project—The Human Genome Project—was only possible because of remarkable progress in sequencing and computing technology.Reynaldi1Pic1

Another reason that often comes up is practicality. To what extent can we utilize microorganisms for therapeutics purposes? A lot of the bacteria seems impossible to be cultured, and even then, we don’t know how effective treatments with microbes are (though in certain cases they have been proven to be very succesful, as in the famous case of C. diff infections: http://www.medicalnewstoday.com/articles/291532.php ).

In any case, the study of the human microbiome is extremely valuable as our microbiome is an integral part of our lives. Perhaps once it gains more popularity and funding, more will be discovered regarding these organisms that call us their home.

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The Enigma of the Brain

SarahRockwood

The 1,200 cm^3 mass of neurons inside our heads, more commonly known as the brain, has been frustratingly elusive in its nature for as long as we’ve known of its existence. How does it work? What does ours, as humans, do so differently from everyone else’s? What is it about the brain that even makes us “human”? These questions have long been tantalizing scientists, take philosophical dead ends, and leave us with more questions than when we started. But now, a ground-breaking project is bringing us one step closer to answering those questions.

The Human Connectome project is split between two consortia; Washington University, University of Minnesota, and Oxford University launched the first project while Harvard, MIT, and UCLA followed close behind. Over five years, the macro-cortices of 1,200 patients (twins and their siblings) will be analyzed and the data will be used to map the neural connections that create the massive network within our brains. By using resting-state functional MRI and diffusion imaging, the scientists will slowly be able to uncover the details of brain connectivity. With structural and functional MRI, they can also determine the shape of the cortex and the network’s relationship to behavior.

With an estimated 100 billion neurons comprising the average adult brain, there are over 100 trillion possible neuronal connections, or synapses, within every single person in a unique configuration. Taking on the challenge of mapping every single one of those is no small task, but the insights gained from it could revolutionize our understanding of the brain and facilitate research in many brain disorders such as autism, Alzheimer’s, and schizophrenia.

But most of all, this research could reveal a little more to the secret of what makes us human, and what makes every one of us a unique addition to this world.

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Scientists Selling Genetically-Engineered Micro-Pigs

 

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Who doesn’t love things that are fun-sized? While most pet owners would gladly keep their furry friends baby sized forever, a group of scientists in China has taken things a step further. Geneticists from leading genomics research institute BGI in Shenzhen, China have begun selling genetically engineered micro-pigs as pets starting at US$1600.

By deactivating a growth hormone receptor or GHR gene, scientists have effectively stunted the growth of Bama pigs. Normally mature pigs weigh up to 100 pounds, but mature micro-pigs grow to only about 30 pounds, or the size of an average dog. By introducing an enzyme called transcription activator-like effector nucleases, or TALENs, to the cloning process, scientists were able to disable one of two growth hormone genes that cause Bama pigs to mature to their full size.

Of course, cloning Bama fetuses comes with adverse health effects and shortened lifespan, as evidenced by other cloned mammals, such as Dolly the sheep. However, by breeding the genetically engineered male micro-pigs with normal female pigs, half of the offspring are born as micro-pigs without the adverse health effects of being born as clones.

Having more similar genetic and physiological makeup to humans than the typical lab rat, but often rejected for lab work for their large size, micro-pigs were originally intended to serve as subjects for human disease in genetic research. However, a fringe pet market for unusually small animals has given their products new purpose. As of now, BGI states that profit is currently their main objective with their new micro-pigs.

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Recent Breakthroughs in the World of 2D Materials

Author: Kevin P. Nuckolls

In the past few years, the search for new and exciting two-dimensional materials has taken over both the field of material science and nanotechnology. These materials have displayed previously unimaginable characteristics, including their novel electronic properties or extraordinary mechanical characteristics, making them some of the best candidates for solving some of the world’s toughest problems in numerous of scientific disciplines. One of the most promising candidates in field of research is graphene, a single-atom thick layer of carbon atoms arranged in a hexagonally tiled formation.

Researchers at Cornell University have become interested in some of the mechanical properties of graphene. Some of the most significant findings have been discovered by a man named Paul L. McEuen, who is the corresponding author on the newly published Nature paper entitled “Graphene kirigami”. McEuen realized that a sheet of graphene, given its strength and resilience, could be used to build complex three-dimensional structures by playing an analogous role to paper in the art of kirigami. The word “kirigami” is derived from the Japanese words “kiru”, meaning “to cut”, and “kami”, meaning “paper”. The ability to fold and cut sheets of graphene into a seemingly infinite number of nanoscale, durable structures could revolutionize the role graphene plays in a number of research fields.

kevinpic1                            Simple kirigami spring made of (a) paper and (b, c) graphene

McEuen’s group first sought to identify whether or not graphene has the correct physical characteristics to be used for kirigami. One of the most important material parameters for kirigami is a material’s Föppl-von Kármán number, which is a ratio of the material’s in-plane stiffness to out-of-plane bending stiffness. Using several different nanoscale material testing methods, his group found that the number associated with graphene was very similar to that of paper, making it an excellent medium for kirigami. With these promising results, his group proceeded to successfully cut and fold sheets of graphene into simple, nanoscale mechanical systems, such as springs and hinges. These devices can be manipulated using not only physical means, but also magnetic means by attaching the ends of the springs or hinges to small blocks of magnetic material. This feature would allow for remote control over such systems, thus allowing for a myriad of new applications in nanotechnology.

Kevinpic2Various forms of graphene kirigami

Researchers at Shanghai Jiao Tong University have explored the possibility of creating new two-dimensional materials out of other group-IV elements, following the precedent set by carbon in forming sheets of graphene. Previously, two-dimensional, silicon-based silicene and germanium-based germanene had been synthesized and examined. The experimentally unprecedented synthesis and characterization of a material called stanene was achieved by a team lead by Jin-feng Jia, who is the corresponding author on the recently published Nature Materials paper entitled “Epitaxial growth of two-dimensional stanene”. Stanene is a 2D allotrope, or atomic configuration, of tin atoms that form a buckled honeycomb lattice, comprised of two triangular, offset sublattices of tin atoms. The thickness of this system is about 0.1nm, which fluctuates slightly depending on the material’s surroundings.

Kevinpic3

Molecular structure of stanene, top and side views

Jia’s group was able to grow these single layers of stanene upon a substrate of Bi2Te3 using a technique called molecular beam epitaxy (MBE). Through MBE, a substrate is placed in a chamber at extremely high vacuum pressures. The material one wishes to deposit is then heated until it becomes gaseous, which condense upon the surface of the substrate. Reflection high energy electron diffraction (RHEED) is many times used to monitor the progress of this process. Jia’s group then analyzed the atomic and electronic structures of the stanene and Bi2Te3 system and found that experimental data they obtained agreed quite well with their theoretical predictions and calculations.

Kevinpic4Image of 2D stanene on Bi2Te3 using scanning tunneling microscopy, top view

 

If you’d like to read more about the developments in graphene kirigami, check out the full paper at the following link:

http://www.nature.com/nature/journal/v524/n7564/full/nature14588.html

If you’d like to read more about the developments of stanene, check out the full paper at the following link:

http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat4384.html

 

 

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Earth Week 2015: How you can help

Every year, we celebrate Earth Day on April 22 to mark the anniversary of a movement that started in 1970. The founder, Gaylord Nelson, then a US Senator of Wisconsin, thought of the idea after the 1969 massive oil spills in Santa Barbara, California. Inspired by the student anti-war movement (much of which started here at Berkeley), he realized that by introducing sustainability into the public conscience, he would be able to force politicians to pay attention to environment protection. As a result, on the 22nd of April, thousands across the nation took to the streets to raise awareness about sustainability, and hundreds of protests were organized. The movement lives on today as Earth Day, and, more recently, has been extended to Earth Week.

You don’t have to plant a forest, or save the whales, to make a difference this Earth Week. Starting small can make a tremendous difference if everyone pitches in. Here are some ways you can help:

1. Cancel your paper bills and switch to online bills. This can save 23 pounds of wood and 29 pounds of greenhouse gas emissions every year.

2. Rather than visiting a large grocery store chain, buy locally produced sustainable food.

3. Get into the habit of carrying around a reusable mug for coffee or tea. This way you’ll always have it handy whenever you need a pick-me-up.

4. Go vegetarian once a week. Did you know that it requires around 2,500 gallons of water to produce one pound of beef? Considering that California is in a drought, you can really help out by going meat-less as often as possible.

5. Take shorter showers, and skip baths entirely.

6. Open your windows and turn off the lights! You’ve probably heard this one before, but it can’t be said enough. Since the days are getting longer now, there’s no reason your lights should be on between the hours of 9 in the morning and 6 in the evening.

7. Start actively recycling and composting. It can be confusing knowing exactly what to put in each different trash bin, but this post from the Daily Clog can help you out with that.

8. Reevaluate your shopping choices: there are so many brands available to us, and as students, we generally pick the cheapest one. However, there’s always a way to find a balance between price and sustainability, so do some research to find the products that are the least damaging to the environment.

9. Take reusable bags when you go grocery shopping. Grocery shopping for students is a whole process, so plan it out so that you have reusable bags with you when you go.

10. Share and discuss! Share these ideas with others, and raise awareness about the environment, sustainability, and helping out in your community.

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Editor’s Picks

Light’s dual nature as both a particle and a wave has confused us all since the theory was proposed. For the first time, scientists have captured a photograph of light behaving as both a particle and a wave, using electrons to image the light.

Ever wonder why you really can’t eat just one potato chip? In this investigative journalism piece, Michael Moss explores the science behind addictive junk food, gathering research from multiple interviews, observations, and scientific studies.

If you’ve ever heard an a cappella performance (Pitch Perfect, anyone?) you’ve heard someone beatboxing. The range of sounds that the human voice can produce is truly amazing. This article explores some of the mechanisms behind the phenomenon, and how this may elucidate the processes in human communication.

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