An assembled flow cytometry chip with size comparable to a U.S. Quarter. Credit: Tony Huang
Inexpensive, portable devices that can rapidly screen cells for leukemia or HIV may soon be possible thanks to a chip that can produce three-dimensional focusing of a stream of cells, according to researchers.
“HIV is diagnosed based on counting CD4 cells,” said Tony Jun Huang, associate professor of engineering science and mechanics at Penn State. “Ninety percent of the diagnoses are done using flow cytometry.”
Huang and his colleagues designed a mass-producible device that can focus particles or cells in a single stream and performs three different optical assessments for each cell. They believe the device represents a major step toward low-cost flow cytometry chips for clinical diagnosis in hospitals, clinics and in the field.
“The full potential of flow cytometry as a clinical diagnostic tool has yet to be realized and is still in a process of continuous and rapid development,” the team said in a recent issue of Biomicrofluidics. “Its current high cost, bulky size, mechanical complexity and need for highly trained personnel have limited the utility of this technique.”
Flow cytometry typically looks at cells in three ways using optical sensors. Flow cytometers use a tightly focused laser light to illuminate focused cells and to produce three optical signals from each cell. These signals are fluorescence from antibodies bound to cells, which reveals the biochemical characteristics of cells; forward scattering, which provides the cell size and its refractive index; and side scattering, which provides cellular granularity. Processing these signals allows diagnosticians to identify individual cells in a mixed cell population, identify fluorescent markers and count cells and other analysis to diagnose and track the progression of HIV, cancer and other diseases.
“Current machines are very expensive, costing $100,000,” said Huang. “Using our innovations, we can develop a small one that could cost about $1,000.”
One reason the current machines are so large and expensive is the method used to channel cells into single file and the necessary alignment of lasers and multiple sensors with the single-file cell stream. Currently, cells are guided into single file using a delicate three-dimensional flow cell that is difficult to manufacture. More problematic is that these current machines need multiple lenses and mirrors for optical alignment.
“Our approach needs only a simple one-layer, two-dimensional flow cell and no optical alignment is required,” said Huang.
Huang and his team used a proprietary technology named microfluidic drifting to create a focused stream of particles. Using a curved microchannel, the researchers took advantage of the same forces that try to move passengers in a car to the outside of a curve when driving. The microfluidic chip’s channel begins as a main channel that contains the flow of carrier liquid and a second channel that comes in perpendicularly that carries the particles or cells. Immediately after these two channels join, the channel curves 90 degrees, which moves all the cells into a horizontal line. After the curve, liquid comes into the channel on both sides, forcing the horizontal line of cells into single file. The cells then pass through a microlaser beam.
An advantage of this microfluidic flow cytometry chip is that it can be mass-produced by molding and standard lithographic processes. The fibers for the optical-fiber delivered laser beams and optical signals already exist.
“The optical fibers are automatically aligned once inserted into the chip, therefore requiring no bulky lenses and mirrors for optical alignment,” said Huang. “Our machine is small enough it can be operated by battery, which makes it usable in Africa and other remote locations.”
The researchers tested the device using commercially available, cell-sized fluorescent beads. They are now testing the device with actual cells.
Working with Huang were Xiaole Mao, graduate student in bioengineering; Ahmad Ahsan Nawaz, Xz-Chin Steven Lin, Michael Ian Lapsley, Yanhui Zhao, graduate students in engineering science and mechanics, and Wafik S. el-Deiry, professor of medicine, Rose Dunlap Division Chair in Hematology/Oncology and associate director for translational research, Cancer Institute, all at Penn State, and J. Philip McCoy, National Heart, Lung, and Blood Institute at the National Institutes of Health.
Research into how carbohydrates are converted into energy has led to a surprising discovery with implications for the treatment of a perplexing and potentially fatal neuromuscular disorder and possibly even cancer and heart disease.
Until this study, the cause of this neuromuscular disorder was unknown. But after obtaining DNA from three families with members who have the disorder, a team led by University of Utah scientists Jared Rutter, Ph.D., associate professor of biochemistry and Carl Thummel, Ph.D., professor of human genetics, sequenced two genes and identified two mutations that cause this devastating disease.
“The ability to convert carbohydrates into energy is critical for people and other organisms to live. But when that process goes awry, potentially fatal health problems can occur,” Rutter says. “If we can figure out a way to correct the defects, we might be able to treat the disease.”
Rutter and Thummel are senior authors on a study published online in Science Express on Thursday, May 24, 2012.
The researchers studied two proteins, Mpc1 and Mpc2, which are among a dozen proteins they looked at in fruit flies, yeast, and then humans. They discovered that the two proteins play a pivotal role in the cellular process that produces the majority of ATP, a molecule that is the main source of energy for cells and is essential for people and other animals to live. Rutter and his colleagues also discovered that when Mpc1 and Mpc2 are impaired they cause the deadly and as of yet unnamed neuromuscular disorder. This disorder affects thousands of people worldwide.
To produce ATP, the body metabolizes carbohydrates and converts them into pyruvate, which then typically enters into the mitochondria in cells. Once inside the mitochondria—a self-contained unit often referred to as a cellular power plant—pyruvate is consumed in the production of ATP. Rutter and his fellow researchers discovered that Mpc1 and Mpc2 are critical for pyruvate entry into mitochondria. When Mpc1 and Mpc2 are eliminated or mutated, pyruvate cannot enter into mitochondria and ATP is not efficiently produced – and that’s when serious health problems can arise, including the neuromuscular disorder that in its most severe forms is deadly.
The ramifications of this study go beyond the production of ATP and birth defects seen in the neuromuscular disorder. The findings may be useful in understanding some of the metabolic defects associated with cancer and heart disease, according to Rutter. Cancer cells typically don’t consume their pyruvate in the production of ATP at the same rate as normal cells. Instead, they convert the pyruvate to lactate. This property of cancer cells is called the Warburg Effect and is named after Nobel laureate and cancer researcher Otto Heinrich Warburg. Some forms of heart disease have a similar problem.
Further study based on the current research may provide important information regarding those diseases, according to Rutter. “That might be the most important outcome of our studies in the long run,” he says.
The study’s first author is Daniel K. Bricker, a doctoral student in human genetics at the University of Utah. Researchers from Harvard University, and the Laboratoire de Biochimie and the Institut de Genetique et de Biologie Moleculaire et Cellulaire, both in France, also contributed to the study.
Antimicrobial peptides (AMPs) are molecules produced in the skin to fend off infection-causing microbes. Vitamin D has been credited with a role in their production and in the body’s overall immune response, but scientists at the University of California, San Diego School of Medicine say a hormone previously associated only with maintaining calcium homeostasis and bone health is also critical, boosting AMP expression when dietary vitamin D levels are inadequate.
The finding, published in the May 23, 2012 online issue of Science Translational Medicine, more fully explains how the immune system functions in different situations and presents a new avenue for treating infections, perhaps as an alternative to current antibiotic therapies.
The immunological benefits of vitamin D are controversial. In cultured cell studies, the fat-soluble vitamin provides strong immunological benefits, but in repeated studies with humans and animal models, results have been inconsistent: People with low levels of dietary vitamin D do not suffer more infections. For reasons unknown, their immune response generally remains strong, undermining the touted immunological strength of vitamin D.
Working with a mouse model and cultured human cells, Gallo and colleagues discovered why: When levels of dietary vitamin D are low (it’s naturally present in very few foods), production of parathyroid hormone (PTH), which normally helps modulate calcium levels in blood, is ramped up. More PTH or a related peptide called PHTrP spurs increased expression of AMPs, such as cathelicidin, which kill a broad spectrum of harmful bacteria, fungi and viruses.
“No one suspected a role for PTH or the PTH-related peptide in immunity,” said Richard L. Gallo, MD, PhD, professor of medicine and chief of UCSD’s Division of Dermatology and the Dermatology section of the Veterans Affairs San Diego Healthcare System. “This may help resolve some of the controversy surrounding vitamin D. It fills in the blanks.”
For example, the findings relate to the on-going debate over sun exposure. Sunlight triggers the production of vitamin D. Low levels of vitamin D have been claimed in some studies to increase the risk of cardiovascular disease and cancer, but other studies have failed to confirm this. On the other hand, high levels of solar exposure that could increase vitamin D have been shown to increase the risk of skin cancer.
“Since sunlight is a carcinogen, it’s a bad idea to get too much of it,” said Gallo. “PTH goes up when levels of vitamin D from diet and sun exposure are low. PTH may be what permits us to have low D in the diet and not kill ourselves with too much UV radiation.”
Gallo said PTH’s newly revealed immunological role provides a new connection between the body’s endocrine system (a system of glands secreting different regulatory hormones into the bloodstream) and its ability to fight invasive, health-harming pathogens.
While much more work remains to be done, including human studies, it’s possible that PTH or PTHrP might eventually become an effective antibiotic treatment without the risk of antibiotic resistance in targeted microbes. One challenge would be how to specifically limit treatment to the targeted infection. “Maybe that could be done by developing the therapy as a cream,” Gallo said.
Co-authors of the study are Beda Muehleisen, Carolos Aguilera and George Sen, Division of Dermatology, UC San Diego; Daniel D. Bikle, Department of Medicine and Dermatology, UC San Francisco; Douglas W. Burton, Veterans Administration San Diego Healthcare System; Leonard J. Deftos, Veterans Administration San Diego Healthcare System and Department of Medicine, UC San Diego.
This research has been funded in whole or in part by the National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), under contract number HHSN272201000020C to the Atopic Dermatitis Research Network and grant numbers R01 AI052453 and R01 AI0833358; the National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, under grant numbers R01 AR052728; and the Veterans Administration Merit Award (ID:1145995). Additional funding was received from the State of California Tobacco-Related Disease Research Program (#18XT-0182) and the Swiss National Science Foundation (PBZHP3-125571 and PASMP3_140073).
Physicists have trapped and cooled exotic particles called excitons so effectively that they condensed and cohered to form a giant matter wave.
This feat will allow scientists to better study the physical properties of excitons, which exist only fleetingly yet offer promising applications as diverse as efficient harvesting of solar energy and ultrafast computing.
“The realization of the exciton condensate in a trap opens the opportunity to study this interesting state. Traps allow control of the condensate, providing a new way to study fundamental properties of light and matter,” said Leonid Butov, professor of physics at the University of California, San Diego. A paper reporting his team’s success was recently published in the scientific journal Nano Letters.
Excitons are composite particles made up of an electron and a “hole” left by a missing electron in a semiconductor. Created by light, these coupled pairs exist in nature. The formation and dynamics of excitons play a critical role in photosynthesis, for example.
Like other matter, excitons have a dual nature of both particle and wave, in a quantum mechanical view. The waves are usually unsynchronized, but when particles are cooled enough to condense, their waves synchronize and combine to form a giant matter wave, a state that others have observed for atoms.
Scientists can easily create excitons by shining light on a semiconductor, but in order for the excitons to condense they must be chilled before they recombine.
The key to the team’s success was to separate the electrons far enough from their holes so that excitons could last long enough for the scientists to cool them into a condensate. They accomplished this by creating structures called “coupled quantum wells” that separate electrons from holes in different layers of alloys made of gallium, arsenic and aluminum.
Then they set an electrostatic trap made by a diamond-shaped electrode and chilled their special semiconducting material in an optical dilution refrigerator to as cold as 50 milli-Kelvin, just a fraction of a degree above absolute zero.
A laser focused on the surface of the material created excitons, which began to accumulate at the bottom of the trap as they cooled. Below 1 Kelvin, the entire cloud of excitons cohered to form a single matter wave, a signature of a state called a Bose-Einstein condensate.
Other scientists have seen whole atoms do this when confined in a trap and cooled, but this is the first time that scientists have seen subatomic particles form coherent matter waves in a trap.
Varying the size and depth of the trap will alter the coherent exciton state, providing this team, and others, the opportunity to study the properties of light and mater in a new way.
This most recent discovery stems from an ongoing collaboration between Leonid Butov’s research group in UC San Diego’s Division of Physical Sciences, including Alexander High, Jason Leonard and Mikas Remeika, and Micah Hanson and Arthur Gossard in UC Santa Barbara’s Materials Department. The Army Research Office and the National Science Foundation funded the experiments, and the Department of Energy supported the development of spectroscopy in the optical dilution refrigerator, the technique used to observe the exciton condensate in a trap.
A new UCLA rat study is the first to show how a diet steadily high in fructose slows the brain, hampering memory and learning — and how omega-3 fatty acids can counteract the disruption. The peer-reviewed Journal of Physiology publishes the findings in its May 15 edition.
“Our findings illustrate that what you eat affects how you think,” said Fernando Gomez-Pinilla, a professor of neurosurgery at the David Geffen School of Medicine at UCLA and a professor of integrative biology and physiology in the UCLA College of Letters and Science. “Eating a high-fructose diet over the long term alters your brain’s ability to learn and remember information. But adding omega-3 fatty acids to your meals can help minimize the damage.”
While earlier research has revealed how fructose harms the body through its role in diabetes, obesity and fatty liver, this study is the first to uncover how the sweetener influences the brain.
Sources of fructose in the Western diet include cane sugar (sucrose) and high-fructose corn syrup, an inexpensive liquid sweetener. The syrup is widely added to processed foods, including soft drinks, condiments, applesauce and baby food. The average American consumes roughly 47 pounds of cane sugar and 35 pounds of high-fructose corn syrup per year, according to the U.S. Department of Agriculture.
“We’re less concerned about naturally occurring fructose in fruits, which also contain important antioxidants,” explained Gomez-Pinilla, who is also a member of UCLA’s Brain Research Institute and Brain Injury Research Center. “We’re more concerned about the fructose in high-fructose corn syrup, which is added to manufactured food products as a sweetener and preservative.”
Gomez-Pinilla and study co-author Rahul Agrawal, a UCLA visiting postdoctoral fellow from India, studied two groups of rats that each consumed a fructose solution as drinking water for six weeks. The second group also received omega-3 fatty acids in the form of flaxseed oil and docosahexaenoic acid (DHA), which protects against damage to the synapses — the chemical connections between brain cells that enable memory and learning.
“DHA is essential for synaptic function — brain cells’ ability to transmit signals to one another,” Gomez-Pinilla said. “This is the mechanism that makes learning and memory possible. Our bodies can’t produce enough DHA, so it must be supplemented through our diet.”
The animals were fed standard rat chow and trained on a maze twice daily for five days before starting the experimental diet. The UCLA team tested how well the rats were able to navigate the maze, which contained numerous holes but only one exit. The scientists placed visual landmarks in the maze to help the rats learn and remember the way.
Six weeks later, the researchers tested the rats’ ability to recall the route and escape the maze. What they saw surprised them.
“The second group of rats navigated the maze much faster than the rats that did not receive omega-3 fatty acids,” Gomez-Pinilla said. “The DHA-deprived animals were slower, and their brains showed a decline in synaptic activity. Their brain cells had trouble signaling each other, disrupting the rats’ ability to think clearly and recall the route they’d learned six weeks earlier.”
The DHA-deprived rats also developed signs of resistance to insulin, a hormone that controls blood sugar and regulates synaptic function in the brain. A closer look at the rats’ brain tissue suggested that insulin had lost much of its power to influence the brain cells.
“Because insulin can penetrate the blood–brain barrier, the hormone may signal neurons to trigger reactions that disrupt learning and cause memory loss,” Gomez-Pinilla said.
He suspects that fructose is the culprit behind the DHA-deficient rats’ brain dysfunction. Eating too much fructose could block insulin’s ability to regulate how cells use and store sugar for the energy required for processing thoughts and emotions.
“Insulin is important in the body for controlling blood sugar, but it may play a different role in the brain, where insulin appears to disturb memory and learning,” he said. “Our study shows that a high-fructose diet harms the brain as well as the body. This is something new.”
Gomez-Pinilla, a native of Chile and an exercise enthusiast who practices what he preaches, advises people to keep fructose intake to a minimum and swap sugary desserts for fresh berries and Greek yogurt, which he keeps within arm’s reach in a small refrigerator in his office. An occasional bar of dark chocolate that hasn’t been processed with a lot of extra sweetener is fine too, he said.
Still planning to throw caution to the wind and indulge in a hot-fudge sundae? Then also eat foods rich in omega-3 fatty acids, like salmon, walnuts and flaxseeds, or take a daily DHA capsule. Gomez-Pinilla recommends one gram of DHA per day.
“Our findings suggest that consuming DHA regularly protects the brain against fructose’s harmful effects,” said Gomez-Pinilla. “It’s like saving money in the bank. You want to build a reserve for your brain to tap when it requires extra fuel to fight off future diseases.”
The left photo shows destructive proteins (green) lining blood vessels in living brain tissue of mice with the human ApoE4 gene; after the drug cyclosporine A is added, the harmful proteins are nearly gone (right). (Credit: Image Courtesy of University of Rochester medical Center)
A well-known genetic risk factor for Alzheimer’s disease triggers a cascade of signaling that ultimately results in leaky blood vessels in the brain, allowing toxic substances to pour into brain tissue in large amounts, scientists report May 16 in the journal Nature.
The results come from a team of scientists investigating why a gene called ApoE4 makes people more prone to developing Alzheimer’s. People who carry two copies of the gene have roughly eight to 10 times the risk of getting Alzheimer’s disease than people who do not.
A team of scientists from the University of Rochester, the University of Southern California, and other institutions found that ApoE4 works through cyclophilin A, a well-known bad actor in the cardiovascular system, causing inflammation in atherosclerosis and other conditions. The team found that cyclophilin A opens the gates to the brain assault seen in Alzheimer’s.
“We are beginning to understand much more about how ApoE4 may be contributing to Alzheimer’s disease,” said Robert Bell, Ph.D., the post-doctoral associate at Rochester who is first author of the paper. “In the presence of ApoE4, increased cyclophilin A causes a breakdown of the cells lining the blood vessels in Alzheimer’s disease in the same way it does in cardiovascular disease or abdominal aneurysm. This establishes a new vascular target to fight Alzheimer’s disease.”
The team found that ApoE4 makes it more likely that cyclophilin A will accumulate in large amounts in cells that help maintain the blood-brain barrier, a network of tightly bound cells that line the insides of blood vessels in the brain and carefully regulates what substances are allowed to enter and exit brain tissue.
ApoE4 creates a cascade of molecular signaling that weakens the barrier, causing blood vessels to become leaky. This makes it more likely that toxic substances will leak from the vessels into the brain, damaging cells like neurons and reducing blood flow dramatically by choking off blood vessels.
Doctors have long known that the changes in the brain seen in Alzheimer’s patients – the death of crucial brain cells called neurons – begins happening years or even decades before symptoms appear. The steps described in Nature discuss events much earlier in the disease process.
The idea that vascular problems are at the heart of Alzheimer’s disease is one championed for more than two decades by Berislav Zlokovic, M.D., Ph.D., the leader of the team and a neuroscientist formerly with the University of Rochester Medical Center and now at USC. For 20 years, Zlokovic has investigated how blood flow in the brain is affected in people with the disease, and how the blood-brain barrier allows nutrients to pass into the brain, and harmful substances to exit the brain.
At Rochester, Zlokovic struck up a collaboration with Bradford Berk, M.D., Ph.D.,a cardiologist and CEO of the Medical Center. For more than two decades Berk has studied cyclophilin A, showing how it promotes destructive forces in blood vessels and how it’s central to the forces that contribute to cardiovascular diseases like atherosclerosis and heart attack.
“As a cardiologist, I’ve been interested in understanding the role of cyclophilin A in patients who suffer from cardiovascular illness,” said Berk, a professor at the Aab Cardiovascular Research Institute. “Now our collaboration in Rochester has resulted in the discovery that it also has an important role in Alzheimer’s disease. The finding reinforces the basic research enterprise – you never know when knowledge gained in one area will turn out to be crucial in another.”
In studies of mice, the team found that mice carrying the ApoE4 gene had five times as much cyclophilin A compared to other mice in cells known as pericytes, which are crucial to maintaining the integrity of the blood-brain barrier. Blood vessels died, blood did not flow as completely through the brain as it did in other mice, and harmful substances like thrombin, fibrin, and hemosiderin, entered the brain tissue.
When the team blocked the action of cyclophilin A, either by knocking out its gene or by using the drug cyclosporine A to inhibit it, the damage in the mice was reversed. Blood flow resumed to normal, and unhealthy leakage of toxic substances from the blood vessels into the brain was slashed by 80 percent.
The team outlined the chain of events involved. Briefly:
When ApoE4 is present, cyclophilin A is much more plentiful;
Cyclophilin A causes an increase in a the inflammatory molecule NF Kappa B;
NF Kappa B boosts levels of certain types of molecules known as MMPs or matrix metalloproteinases that are known to damage blood vessels, reducing blood flow.
Altogether, the activity results in a dramatic boost in the amount of toxic substances in brain tissue. And when the cascade is interrupted at any of several points – when ApoE4 is not present, when cyclophilin A is blocked or shut off, or when NF Kappa B or the MMPs are inhibited – the blood-brain barrier is restored, blood flow returns to normal, and toxic substances do not leak into brain tissue.
For many years, researchers studying Alzheimer’s disease have been focused largely on amyloid beta, a protein structure that accumulates in the brains of patients with Alzheimer’s disease. The latest works points up the importance of other approaches, said Zlokovic, an adjunct professor at Rochester. At USC, Zlokovic is also deputy director of the Zilkha Neurogenetic Institute, director of the Center for Neurodegeneration and Regeneration, and professor and chair of the Department of Physiology and Biophysics.
“Our study has shown major neuronal injury resulting from vascular defects that are not related to amyloid beta,” said Zlokovic. “This damage results from a breakdown of the blood-brain barrier and a reduction in blood flow.
“Amyloid beta definitely has an important role in Alzheimer’s disease,” added Zlokovic. “But it’s very important to investigate other leads, perhaps where amyloid beta isn’t as centrally involved.”
In addition to Bell, Berk and Zlokovic, authors include, from Rochester, Ethan Winkler, Itender Singh, Abhay Sagare, Rashid Deane, Zhenhua Wu, and Jan Sallstrom. Additional authors include David Holtzman from Washington University School of Medicine, and Christopher Betsholtz and Annika Armulik of the Karolinska Institutet in Sweden.
At Rochester, Zlokovic’s team was anchored in the Center for Neurodegenerative and Brain Vascular Disorders, which was directed by Zlokovic, and in the Department of Neurosurgery. Bell was a graduate student with Zlokovic and now does research in the laboratory of Joseph Miano, Ph.D., at the Aab Cardiovascular Research Institute.
The work was funded by the National Institute of Neurological Disorders and Stroke and the National Institute on Aging.
A 100-fold upsurge in human-produced plastic garbage in the ocean is altering habitats in the marine environment, according to a new study led by a graduate student researcher at Scripps Institution of Oceanography at UC San Diego.
In 2009 an ambitious group of graduate students led the Scripps Environmental Accumulation of Plastic Expedition (SEAPLEX) to the North Pacific Ocean Subtropical Gyre aboard the Scripps research vessel New Horizon. During the voyage the researchers, who concentrated their studies a thousand miles west of California, documented an alarming amount of human-generated trash, mostly broken down bits of plastic the size of a fingernail floating across thousands of miles of open ocean.
At the time the researchers didn’t have a clear idea of how such trash might be impacting the ocean environment, but a new study published in the May 9 online issue of the journal Biology Letters reveals that plastic debris in the area popularly known as the “Great Pacific Garbage Patch” has increased by 100 times over in the past 40 years, leading to changes in the natural habitat of animals such as the marine insect Halobates sericeus. These “sea skaters” or “water striders”—relatives of pond water skaters—inhabit water surfaces and lay their eggs on flotsam (floating objects). Naturally existing surfaces for their eggs include, for example: seashells, seabird feathers, tar lumps and pumice. In the new study researchers found that sea skaters have exploited the influx of plastic garbage as new surfaces for their eggs. This has led to a rise in the insect’s egg densities in the North Pacific Subtropical Gyre.
Such an increase, documented for the first time in a marine invertebrate (animal without a backbone) in the open ocean, may have consequences for animals across the marine food web, such as crabs that prey on sea skaters and their eggs.
“This paper shows a dramatic increase in plastic over a relatively short time period and the effect it’s having on a common North Pacific Gyre invertebrate,” said Scripps graduate student Miriam Goldstein, lead author of the study and chief scientist of SEAPLEX, a UC Ship Funds-supported voyage. “We’re seeing changes in this marine insect that can be directly attributed to the plastic.”
The new study follows a report published last year by Scripps researchers in the journal Marine Ecology Progress Series showing that nine percent of the fish collected during SEAPLEX contained plastic waste in their stomachs. That study estimated that fish in the intermediate ocean depths of the North Pacific Ocean ingest plastic at a rate of roughly 12,000 to 24,000 tons per year.
The Goldstein et al. study compared changes in small plastic abundance between 1972-1987 and 1999-2010 by using historical samples from the Scripps Pelagic Invertebrate Collection and data from SEAPLEX, a NOAA Ship Okeanos Explorer cruise in 2010, information from the Algalita Marine Research Foundation as well as various published papers.
In April, researchers with the Instituto Oceanográfico in Brazil published a report that eggs of Halobates micans, another species of sea skater, were found on many plastic bits in the South Atlantic off Brazil.
“Plastic only became widespread in late ’40s and early ’50s, but now everyone uses it and over a 40-year range we’ve seen a dramatic increase in ocean plastic,” said Goldstein. “Historically we have not been very good at stopping plastic from getting into the ocean so hopefully in the future we can do better.”
Coauthors of the study include Marci Rosenberg, a student at UCLA, and Scripps Research Biologist Emeritus Lanna Cheng.
Funding for SEAPLEX was provided by the University of California Ship Funds, an innovative program that allows a new generation of scientists to gain valuable scientific training at sea, Project Kaisei/Ocean Voyages Institute, the Association for Women in Science-San Diego and the National Science Foundation’s (NSF) Integrative Graduate Education and Research Traineeship program. The NOAA Okeanos Explorer Program (2010 Always Exploring expedition) and National Marine Fisheries Service provided support for the 2010 samples. Other study support was provided by Jim and Kris McMillan, Jeffrey and Marcy Krinsk, Lyn and Norman Lear, Ellis Wyer and an anonymous donor. Other support was provided by the California Current Ecosystem (CCE) program, part of NSF’s Long-Term Ecological Research (LTER) program.
Colored patches represent parallelogram outlines around pairs of triangles that have formed chiral super-structures. Parallelograms having different “handedness” and orientations are color-coded and superimposed over each other.(Credit: Thomas G. Mason and Kun Zhao)
The overwhelming majority of proteins and other functional molecules in our bodies display a striking molecular characteristic: They can exist in two distinct forms that are mirror images of each other, like your right hand and left hand. Surprisingly, each of our bodies prefers only one of these molecular forms.
This mirror-image phenomenon — known as chirality or “handedness” — has captured the imagination of a UCLA research group led by Thomas G. Mason, a professor of chemistry and physics and a member of the California NanoSystems Institute at UCLA.
Mason has been exploring how and why chirality arises, and his newest findings on the physical origins of the phenomenon were published May 1 in the journal Nature Communications.
“Objects like our hands are chiral, while objects like regular triangles are achiral, meaning they don’t have a handedness to them,” said Mason, the senior author of the study. “Achiral objects can be easily superimposed on top of one another.”
Why many of the important functional molecules in our bodies almost always occur in just one chiral form when they could potentially exist in either is a mystery that has confounded researchers for years.
“Our bodies contain important molecules like proteins that overwhelmingly have one type of chirality,” Mason said. “The other chiral form is essentially not found. I find that fascinating. We asked, ‘Could this biological preference of a particular chirality possibly have a physical origin?'”
In addressing this question, Mason and his team sought to discover how chirality occurs in the first place. Their findings offer new insights into how the phenomenon can arise spontaneously, even with achiral building-blocks.
Mason and his colleagues used a manufacturing technique called lithography, which is the basis for making computer chips, to make millions of microscale particles in the shape of achiral triangles. In the past, Mason has used this technique to “print” particles in a wide variety of shapes, and even in the form of letters of the alphabet.
Using optical microscopy, the researchers then studied very dense systems of these lithographic triangular particles. To their surprise, they discovered that the achiral triangles spontaneously arranged themselves to form two-triangle “super-structures,” with each super-structure exhibiting a particular chirality.
In the image that accompanies this article, the colored outlines in the field of triangles indicate chiral super-structures having particular orientations.
So what is causing this phenomenon to occur? Entropy, says Mason. His group has shown for the first time that chiral structures can originate from physical entropic forces acting on uniform achiral particles.
“It’s quite bizarre,” Mason said. “You’re starting with achiral components — triangles — which undergo Brownian motion and you end up with the spontaneous formation of super-structures that have a handedness or chirality. I would never have anticipated that in a million years.”
Entropy is usually thought of as a disordering force, but that doesn’t capture its subtler aspects. In this case, when the triangular particles are diffusing and interacting at very high densities on a flat surface, each particle can actually maximize its “wiggle room” by becoming partially ordered into a liquid crystal (a phase of matter between a liquid and a solid) made out of chiral super-structures of triangles.
“We discovered that just two physical ingredients — entropy and particle shape — are enough to cause chirality to appear spontaneously in dense systems,” Mason said. “In my 25 years of doing research, I never thought that I would see chirality occur in a system of achiral objects driven by entropic forces.”
As for the future of this research, “We are very interested to see what happens with other shapes and if we can eventually control the chiral formations that we see occurring here spontaneously,” he said.
“To me, it’s intriguing, because I think about the chiral preference in biology,” Mason added. “How did this chiral preference happen? What are the minimum ingredients for that to occur? We’re learning some new physical rules, but the story in biology is far from complete. We have added another chapter to the story, and I’m amazed by these findings.”
To learn more, a message board accompanies the publication in Nature Communications, an online journal, as a forum for interactive discussion.
This research was funded by the University of California. Kun Zhao, a postdoctoral researcher in Mason’s laboratory, made many key contributions, including fabricating the triangle particles, creating the two-dimensional system of particles, performing the optical microscopy experiments, carrying out extensive particle-tracking analysis and interpreting the results.
Along with Mason, co-author Robijn Bruinsma, a UCLA professor of theoretical physics and a member of the California NanoSystems Institute at UCLA, contributed to the understanding of the chiral symmetry breaking and the liquid crystal phases.
As people pump groundwater for irrigation, drinking water, and industrial uses, the water doesn’t just seep back into the ground — it also evaporates into the atmosphere, or runs off into rivers and canals, eventually emptying into the world’s oceans. This water adds up, and a new study calculates that by 2050, groundwater pumping will cause a global sea level rise of about 0.8 millimeters per year.
“Other than ice on land, the excessive groundwater extractions are fast becoming the most important terrestrial water contribution to sea level rise,” said Yoshihide Wada, with Utrecht University in the Netherlands and lead author of the study. In the coming decades, he noted, groundwater contributions to sea level rise are expected to become as significant as those of melting glaciers and ice caps outside of Greenland and the Antarctic.
Between around 1970 and 1990, sea level rise caused by groundwater pumping was cancelled out as people built dams, trapping water in reservoirs so the water wouldn’t empty into the sea, Wada said. His research shows that starting in the 1990s, that changed as populations started pumping more groundwater and building fewer dams.
The researchers looked not only at the contribution of groundwater pumping, which they had investigated before, but also at other factors that influence the amount of terrestrial water entering the oceans, including marsh drainage, forest clearing, and new reservoirs. Wada and his colleagues calculate that by mid-century, the net effect of these additional factors is an additional 0.05 mm per year of annual sea level rise, on top of the contribution from groundwater pumping alone.
The research team’s article is being published today in Geophysical Research Letters, a journal of the American Geophysical Union.
The last report of the United Nations Intergovernmental Panel on Climate Change in 2007 addressed the effect on sea level rise of melting ice on land, including glaciers and ice caps, Wada said. But it didn’t quantify the future contribution from other terrestrial water sources, such as groundwater, reservoirs, wetlands and more, he said, because the report’s authors thought the estimates for those sources were too uncertain.
“They assumed that the positive and negative contribution from the groundwater and the reservoirs would cancel out,” Wada said. “We found that wasn’t the case. The contribution from the groundwater is going to increase further, and outweigh the negative contribution from reservoirs.”
In the current study, the researchers estimated the impact of groundwater depletion since 1900 using data from individual countries on groundwater pumping, model simulations of groundwater recharge, and reconstructions of how water demand has changed over the years. They also compared and corrected those estimates with observations from sources such as the GRACE satellite, which uses gravity measurements to determine variations in groundwater storage.
With these groundwater depletion rates, Wada and his colleagues estimate that in 2000, people pumped about 204 cubic kilometers (49 cubic miles) of groundwater, most of which was used for irrigation. Most of this, in turn, evaporates from plants, enters the atmosphere and rains back down. Taking into account the seepage of groundwater back into the aquifers, as well as evaporation and runoff, the researchers estimated that groundwater pumping resulted in sea level rise of about 0.57 mm in 2000 — much greater than the 1900 annual sea level rise of 0.035 mm.
The researchers also projected groundwater depletion, reservoir storage, and other impacts for the rest of the century, using climate models and projected population growth and land use changes. The increase in groundwater depletion between 1900 and 2000 is due mostly to increased water demands, the researchers find. But the increase projected between 2000 and 2050 is mostly due to climate-related factors like decreased surface water availability and irrigated agricultural fields that dry out faster in a warmer climate.
If things continue as projected, Wada estimates that by 2050, the net, cumulative effect of these non-ice, land-based water sources and reservoirs — including groundwater pumping, marsh drainage, dams, and more — will have added 31 mm to sea level rise since 1900.
The new study assumes that, where there is groundwater, people will find a way to extract it, Wada said, but some of his colleagues are investigating the limits of groundwater extraction. One way to decrease groundwater’s contribution to sea level rise, he noted, is to improve water efficiency in agriculture — to grow more with less groundwater.
Infectious diseases—both old and new—continue to exact a devastating toll, causing some 13 million fatalities per year around the world.
Vaccines remain the best line of defense against deadly pathogens and now Kathryn Sykes and Stephen Johnston, researchers at Arizona State University’s Biodesign Institute, along with co-author Michael McGuire from the University of Texas Southwestern Medical Center are using clever functional screening methods to attempt to speed new vaccines into production that are both safer and more potent.
In a recent study appearing in the journal Proteome Science, the group used high-throughput methods to identify a modulator of immune activity that exists naturally in an unusual pathogen belonging to the Poxviridae family of viruses.
Parapoxvirus infection causes immune cell accumulation at the site of infection; direct screening in the host for this biological activity enabled the isolation of an immunomodulator—labeled B2. Indeed, B2 by itself causes immune cell accumulation at the site of skin injection. When added to a traditional influenza vaccine, B2 improves the vaccine’s protective capacity. Furthermore, the immunomodulator also demonstrated the ability to shrink the size of cancerous tumors, even in the absence of any accompanying specific antigen.
In the past, the process of vaccine discovery involved the random selection of naturally attenuated strains of viruses and bacteria, which were found to provide protection in humans. Examples of this approach include the use of vaccinia to protect against smallpox and attenuated mycobacterium bovis (BCG) to protect against tuberculosis.
In recent years, many vaccines have been developed using only selected portions of a given pathogen to confer immunity. These so-called subunit vaccines have several advantages over whole pathogen vaccines. Genetic components that allow a given pathogen to elude immune detection for example may be screened out, as well as any factors causing unwanted vaccine side effects. Through careful screening, just those elements responsible for eliciting protective immune responses in the host can be extracted from the pathogen and reassembled into an effective, safer subunit vaccine.
In practice, the process of narrowing the field of promising subunit candidates from the whole genome of a pathogen has often been time consuming, laborious and perplexing. In the current study, their earlier-developed strategy, known as expression library immunization, is extended to develop a scheme to find the protein-encoding segments—known as open reading frames (ORFs)—from a pathogenic genome that have any biological function of interest.
This simple, yet powerful technique uses the host’s immune system itself to rapidly reduce any pathogenic genome (viral, fungal, bacterial or parasitic) to a handful of antigens capable of conferring protection in the host.
The advantage of this in vivo technique is that it offers a means of rapidly screening entire genomes, with the results of the search displaying desired immunogenic traits. The mode of entry of vaccines designed in this way closely resembles the natural infection process of host cells—an improvement over live attenuated vaccines.
This promising approach has been used effectively to engineer a vaccine against hepatitis and may provide a new avenue for the development of protective agents against pathogens that have thus far eluded traditional vaccine efforts, including HIV and ebola.
“We had developed a method for screening for protective subunits against a specific disease,” Sykes says. “However this type of safer vaccine design is notoriously less potent than the whole pathogen designs. What we needed was a method to find generally useful vaccine components that would serve to enhance and control immunity.”
The group chose the pathogen parapoxvirus ovis (known as the Orf virus) for the current set of experiments, in which expression library immunization techniques were used to screen for an immunogenic factor buried in the pathogen’s genome.
Parapoxvirus ovis causes a highly infectious disease known as Orf, which is prevalent in sheep and goats and may be transmitted cutaneously to humans handling these animals, causing pustular lesions and scabs.
Once the group had sequenced the full genome of parapoxvirus, PCR was used to amplify all the viral open reading frames, which code for all of the viruse’s proteins. Each ORF, comprising a library of genomic components, was compiled into a unique high throughput expression construct, and these were randomly distributed into sub-library pools. These pools were directly delivered into sets of mice for in vivo expression. Functional testing for the activity desired identified B2 as the immune cell accumulator.
In further experiments, the team co-delivered B2L as an additive or adjuvant for an influenza gene vaccine, to see if it could improve survival rates in mice challenged with the influenza virus. The co-immunized mice indeed displayed full protection against influenza compared with 50 percent protection of the control group, immunized with influenza vaccine alone.
In addition to infectious agents like Orf, non-infectious diseases including cancer may be amenable to vaccine defense. Thus far however, the discovery of tumor-specific antigens has been frustrating. One approach may lie in using non-specific immunogenic factors like B2.
In the current study, two forms of cancer were investigated in a mouse model, following the administering of B2 alone, in the absence of a disease antigen. The experiments evaluated B2’s ability to enhance survival and shrink tumor size. In the case of an aggressive melanoma, tumor size was significantly reduced and survival rate improved. Administration of B2 to an infection induced by a breast cancer cell line also showed a modest but measureable reduction in tumor size.
With the growing popularity of sub-unit vaccines, the need arises for more effective adjuvants, which may be used to compensate for the reduced immunogenicity of such vaccines compared with their whole-pathogen counterparts. Techniques similar to those applied here to isolate and evaluate B2 could potentially permit the screening of virtually any genome for any gene-encoded activity testable in an organism.