Author Archives: Catherine Zandonella

How do bacteria clog medical devices? Very quickly. (PNAS)

stone-figure-2D_540 A new study has examined how bacteria clog medical devices, and the result isn’t pretty. The microbes join to create slimy ribbons that tangle and trap other passing bacteria, creating a full blockage in a startlingly short period of time.

The finding could help shape strategies for preventing clogging of devices such as stents — which are implanted in the body to keep open blood vessels and passages — as well as water filters and other items that are susceptible to contamination. The research was published in Proceedings of the National Academy of Sciences.

Click on the image to view movie. Over a period of about 40 hours, bacterial cells (green) flowed through a channel, forming a green biofilm on the walls. Over the next ten hours, researchers sent red bacterial cells through the channel. The red cells became stuck in the sticky biofilm and began to form thin red streamers. Once stuck, these streamers in turn trapped additional cells, leading to rapid clogging. (Image source: Knut Drescher)

Using time-lapse imaging, researchers at Princeton University monitored fluid flow in narrow tubes or pores similar to those used in water filters and medical devices. Unlike previous studies, the Princeton experiment more closely mimicked the natural features of the devices, using rough rather than smooth surfaces and pressure-driven fluid instead of non-moving fluid.

The team of biologists and engineers introduced a small number of bacteria known to be common contaminants of medical devices. Over a period of about 40 hours, the researchers observed that some of the microbes — dyed green for visibility — attached to the inner wall of the tube and began to multiply, eventually forming a slimy coating called a biofilm. These films consist of thousands of individual cells held together by a sort of biological glue.

Over the next several hours, the researchers sent additional microbes, dyed red, into the tube. These red cells became stuck to the biofilm-coated walls, where the force of the flowing liquid shaped the trapped cells into streamers that rippled in the liquid like flags rippling in a breeze. During this time, the fluid flow slowed only slightly.

At about 55 hours into the experiment, the biofilm streamers tangled with each other, forming a net-like barrier that trapped additional bacterial cells, creating a larger barrier which in turn ensnared more cells. Within an hour, the entire tube became blocked and the fluid flow stopped.

The study was conducted by lead author Knut Drescher with assistance from technician Yi Shen. Drescher is a postdoctoral research associate working with Bonnie Bassler, Princeton’s Squibb Professor in Molecular Biology and a Howard Hughes Medical Institute Investigator, and Howard Stone, Princeton’s Donald R. Dixon ’69 and Elizabeth W. Dixon Professor of Mechanical and Aerospace Engineering.

“For me the surprise was how quickly the biofilm streamers caused complete clogging,” said Stone. “There was no warning that something bad was about to happen.”

By constructing their own controlled environment, the researchers demonstrated that rough surfaces and pressure driven flow are characteristics of nature and need to be taken into account experimentally. The researchers used stents, soil-based filters and water filters to prove that the biofilm streams indeed form in real scenarios and likely explain why devices fail.

The work also allowed the researchers to explore which bacterial genes contribute to biofilm streamer formation. Previous studies, conducted under non-realistic conditions, identified several genes involved in formation of the biofilm streamers. The Princeton researchers found that some of those previously identified genes were not needed for biofilm streamer formation in the more realistic habitat.

Read the abstract.

Drescher, Knut, Yi Shen, Bonnie L. Bassler, and Howard A. Stone. 2013. Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems. Proceedings of the National Academy of Sciences. Published online February 11.

This work was supported by the Howard Hughes Medical
Institute, National Institutes of Health grant 5R01GM065859, National Science Foundation (NSF) grant MCB-0343821, NSF grant MCB-1119232, and the Human Frontier Science Program.

Where the wild things go (Folia Primatologica)

A lack of fresh water makes swamp life hard for animals such as the endangered Zanzibar red colobus monkey, pictured here drinking from a container of fresh water provided by locals. (Photo by Katarzyna Nowak)

by Morgan Kelly, Office of Communications

Ecologists have evidence that some endangered primates and large cats faced with relentless human encroachment will seek sanctuary in the sultry thickets of mangrove and peat swamp forests. These harsh coastal biomes are characterized by thick vegetation — particularly clusters of salt-loving mangrove trees — and poor soil in the form of highly acidic peat, which is the waterlogged remains of partially decomposed leaves and wood. As such, swamp forests are among the few areas in many African and Asian countries that humans are relatively less interested in exploiting (though that is changing).

Yet conservationists have been slow to consider these tropical hideaways when keeping tabs on the distribution of threatened animals such as Sumatran orangutans and Javan leopards, according to a recent Princeton University study in the journal Folia Primatologica. To draw attention to peat and mangrove swamps as current — and possibly future — wildlife refuges, Katarzyna Nowak, a former postdoctoral researcher of ecology and evolutionary biology at Princeton, compiled a list of 60 primates and 20 felids (the large-cat family that includes tigers and leopards) known to divide their time between their natural forest habitats and some 47 swamp forests in Africa and Asia.

Because swamp forests often lack food sources, fresh water and easy mobility, few mammals are exclusive to these areas, Nowak reported. Consequently, conservation groups have not intensely monitored the animals’ swamp use.

But the presence of endangered cats and primates in swamp forests might be seriously overlooked, Nowak found. About 55 percent of Old World monkeys — primates such as baboons and macaques that are native to Africa and Asia — take to the swamps either regularly, seasonally or as needed. In 2008, the Wildlife Conservation Society reported that the inaccessible Lake Télé swamp forest in the Republic of the Congo was home to 125,000 lowland gorillas — more than were thought to exist in the wild. Among big cats, the Bengal tiger, for instance, holds its sole ground in Bangladesh in the Sundarbans, the world’s largest mangrove forest.

Princeton University research compiled 21 swamp forests in Africa (left) and 26 in Asia where primates and felids (a large cat family that includes tigers and leopards) are known to seek refuge from human encroachment. The colored dots indicate the overall “threat score,” or vulnerability, of species living in a particular site. Purple denotes a site with high species diversity, and where some resident primates and felids are likely listed as a conservation concern on the Red List of the International Union for Conservation of Nature. (Image by Katarzyna Nowak)

Life in the swamps can still be harsh for some animals. Species such as the crab-eating macaque and fishing cat can adapt somewhat readily to a life of swimming and foraging for crustaceans. Meanwhile, Zanzibar’s red colobus monkey — driven to coastal mangroves by deforestation — can struggle to find the freshwater it needs, as Nowak reported in the American Journal of Primatology in 2008. Such a trend could result in local extinction of the red colobus nonetheless, she said.

Nowak concludes that swamp forests beg further exploration as places where endangered species such as lowland gorillas and flat-headed cats have preserved their numbers — and where humans could potentially preserve them into the future.

Read the abstract.

Citation: Nowak, Katarzyna. 2013. Mangrove and Peat Swamp Forests: Refuge Habitats for Primates and Felids. Folia Primatologica. Vol. 83, no. 3–6, pp. 361–76.

Forecast is for more snow in polar regions, less for the rest of us (Journal of Climate)

A new climate model predicts declines in snowfall in the U.S. over the next 70 years. Source: GFDL
Click on image to enlarge.

By Catherine Zandonella, Office of the Dean for Research

A new climate model predicts an increase in snowfall for the Earth’s polar regions and highest altitudes, but an overall drop in snowfall for the globe, as carbon dioxide levels rise over the next century.

The decline in snowfall could spell trouble for regions such as the western United States that rely on snowmelt as a source of fresh water.

The projections are the result of a new climate model developed at the National Oceanic and Atmospheric Administration (NOAA) Geophysical Fluid Dynamics Laboratory (GFDL) and analyzed by scientists at GFDL and Princeton University. The study was published in the Journal of Climate.

The model indicates that the majority of the planet would experience less snowfall as a result of warming due to a doubling of atmospheric carbon dioxide. Observations show that atmospheric carbon dioxide has already increased by 40 percent from values in the mid-19th century, and, given projected trends, could exceed twice those values later this century. In North America, the greatest reductions in snowfall will occur along the northeast coast, in the mountainous west, and in the Pacific Northwest. Coastal regions from Virginia to Maine, as well as coastal Oregon and Washington, will get less than half the amount of snow currently received.

In very cold regions of the globe, however, snowfall will rise because as air warms it can hold more moisture, leading to increased precipitation in the form of snow. The researchers found that regions in and around the Arctic and Antarctica will get more snow than they now receive.

The highest mountain peaks in the northwestern Himalayas, the Andes and the Yukon region will also receive greater amounts of snowfall after carbon dioxide doubles. This finding clashes with other models which predicted declines in snowfall for these high-altitude regions. However, the new model’s prediction is consistent with current snowfall observations in these regions.

The model is an improvement over previous models in that it utilizes greater detail about the world’s topography – the mountains, valleys and other features. This new “high-resolution” model is analogous to having a high-definition model of the planet’s climate instead of a blurred picture.

The study was conducted by Sarah Kapnick, a postdoctoral research scientist in the Program in Atmospheric and Oceanic Sciences at Princeton University and jointly affiliated with NOAA’s Geophysical Fluid Dynamics Laboratory in Princeton, and Thomas Delworth, senior physical scientist at GFDL.

Read a plain-language summary of the article on GFDL’s web site.

Read the abstract.

Citation: Kapnick, Sarah B. and Thomas L. Delworth, 2013. Controls of Global Snow Under a Changed Climate. Journal of Climate. Early online release published Feb. 6. http://dx.doi.org/10.1175/JCLI-D-12–00528.1

This work was supported by the Cooperative Institute for Climate Science, a collaborative institute between Princeton University and GFDL.

New light shed on pesky “snakes” that cool fusion reactions (Physical Review Letters)

By John Greenwald, Princeton Plasma Physics Laboratory

Corkscrew-shaped instabilities called “snakes” have long been a common feature of the hot, electrically charged plasma gas that fuels fusion reactions, which could provide a future source of clean and abundant energy for generating electricity. Such snakes trap impurities released from the plasma-facing walls of experimental fusion vessels called tokamaks, and these impurities radiate away copious amounts of energy, cooling the plasma to temperatures below those required to create fusion reactions. Understanding the formation and survival of snakes can thus be essential to eliminating the problem so that fusion can take place.

New experimental data reported today in Physical Review Letters sheds light on how snakes form and survive in fusion plasmas. The paper, whose lead author is Luis Delgado-Aparicio of the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL), cites recent experiments on the Alcator C-Mod tokamak at the Massachusetts Institute of Technology Plasma Science and Fusion Center (MIT-PSFC). The findings compiled by a multidisciplinary team show that the formation of snakes cannot be explained, as previously thought, by plasma pressure alone. Instead, the formation reflects complex interactions among phenomena that include the separately evolving plasma density and temperature conditions that produce the plasma pressure. This separate evolution of density and temperature also enables the snakes to survive periodic relaxations of plasma pressure known as sawtooth instabilities.

Left: Time sequence of a snake, in red, depicted by x-ray detectors. The sawtooth crash occurs halfway through the sequence and barely perturbs the snake.
Right: X-ray reconstruction of cross-section of crescent snake inside Alcator C-Mod.
Credit: Luis Delgado-Aparicio

Read the abstract.

Citation:
Delgado-Aparicio, Luis; Linda Sugiyama, MIT; Robert Granetz, MIT; David Gates, PPPL; John Rice, MIT; Matthew Reinke, MIT; Manfred Bitter, PPPL; Eric Fredrickson, PPPL; Chi Gao, MIT; Martin Greenwald, MIT; Kenneth Hill, PPPL; Amanda Hubbard, MIT; Jerry Hughes, MIT; Earl Marmar, MIT; Novimir Pablant, PPPL; Yuri Podpaly, MIT; Steven Scott, PPPL; Randy Wilson, PPPL; Steve Wolfe, MIT; and Steve Wukitch, MIT. 2013. Formation and stability of impurity “snakes” in tokamak plasmas. Physical Review Letters 110, 065006.

This work was performed under U.S. DOE contracts including DE-FC02-99ER54512 and others at MIT and DE-AC02-09CH11466 at PPPL. Computational support was provided by the National Energy Research Scientific Computing Center under DE-AC02-05CH11231.

Organizations shape pharmacists’ work as gatekeepers (Social Science and Medicine)

By Michael Hotchkiss, Office of Communications

Pharmacists regularly face a range of ethical dilemmas, from deciding whether to dispense emergency contraception to managing requests for narcotics, and must navigate a range of relationships with other health-care professionals.

Using 95 interviews with pharmacists working in retail and hospital settings, Princeton researcher Elizabeth Chiarello shows how organizations shape the way pharmacists exercise their roles as medical, legal, fiscal and moral gatekeepers. An article by Chiarello based on the research was published online by the journal Social Science and Medicine.

According to the paper by Chiarello, a sociologist working as a postdoctoral research associate at the Office of Population Research within the Woodrow Wilson School of International and Public Affairs, the findings suggest new directions for theorizing about ethical decision-making in medical contexts.

Read the abstract.

Chiarello, Elizabeth. 2013. How Organizational Context Affects Bioethical Decision-Making: Pharmacists’ Management of Gatekeeping Processes in Retail and Hospital Settings. Social Science and Medicine. doi: 10.1016/j.socscimed.2012.11.041

Funding for this research was provided by the Andrew W. Mellon Foundation, the American Council of Learned Societies, the U.S. Department and Health and Human Services Agency for Healthcare Research and Quality, the Princeton University Office of Population Research, the Princeton University Center for Health and Wellbeing, and a grant from the University of California, Irvine Center for Organizational Research.

The effective collective: Grouping could ensure animals find their way in a changing environment (Science)

Golden shiners were used to study collective behavior (Image courtesy of Sean Fogarty)

By Morgan Kelly, Office of Communications

For social animals such as schooling fish, the loss of their numbers to human activity could eventually threaten entire populations, according to a finding that such animals rely heavily on grouping to effectively navigate their environment.

Princeton University researchers report in the journal Science that collective intelligence is vital to certain animals’ ability to evaluate and respond to their environment. Conducted on fish, the research demonstrated that small groups and individuals become disoriented in complex, changing environments. However, as group size is increased, the fish suddenly became highly responsive to their surroundings.

These results should prompt a close examination of how endangered group or herd animals are preserved and managed, said senior researcher Iain Couzin, a Princeton professor of ecology and evolutionary biology. If wild animals depend on collective intelligence for migration, breeding and locating essential resources, they could be imperiled by any activity that diminishes or divides the group, such as overhunting and habitat loss, he explained.

“Processes that increase group fragmentation or reduce population density may initially appear to have little influence, yet a further reduction in group size may suddenly and dramatically impact the capacity of a species to respond effectively to their environment,” Couzin said. “If the mechanism we observed is found to be widespread, then we need to be aware of tipping points that could result in the sudden collapse of migratory species.”

The work is among the first to experimentally explain the extent to which collective intelligence improves awareness of complex environments, the researchers write. Collective intelligence is an established advantage of groups, including humans. As it’s understood, a group of individuals gain an advantage by pooling imperfect estimates with those around them, which more or less “averages” single experiences into surprisingly accurate common knowledge. For instance, the paper in Science cites a 1907 study that predicted with near precision the weight of an ox based on the estimates of 787 people.

With their work, Couzin and his coauthors uncovered an additional layer to understanding collective intelligence. The conventional view assumes that individual group members have some level of knowledge albeit incomplete. Yet the Princeton researchers found that in some cases individuals have no ability to estimate how a problem needs to be solved, while the group as a whole can find a solution through their social interactions. Moreover, they found that the more numerous the neighbors, the richer the individual — and thus group — knowledge is.

These findings correlate with recent research showing that collective intelligence — even in humans — can rely less on the intelligence of each group member than on the effectiveness of their communal interaction, Couzin said. In humans, research suggests that such cooperation would take the form of open and equal communication among individuals regardless of their respective smarts, he said.

The researchers placed fish known as golden shiners in experimental tanks in groups as low as one and as high as 256. The tanks featured a moving light field that was bright on the outer edges and tapered into a dark center. To reflect the changing nature of natural environments, they also incorporated small patches of darkness that moved around randomly. Prolific schoolers and enthusiasts of darkness, the golden shiners would pursue the shaded areas as the researchers recorded their movement using computer vision software. Although the fish sought the shade regardless of group size, their capability to do so increased dramatically once groups spanned a large enough area.

The researchers then tracked the motion of individual fish to gauge the role of social influence on their movement. They found that individuals adjusted their speed according to local light level by moving faster in more brightly lit areas, but without social influence the fish did not necessarily turn toward the darker regions. Groups, however, readily swam to dark areas and were able to track those preferred regions as they moved.

This collective sensing emerged due to the coherent nature of social interactions, the authors report. As one side of the group slowed and turned toward the shaded area, the other members did as well. Also, slowing down increased density and resulted in darker regions becoming more attractive to these social animals.

Couzin worked with lead authors Andrew Berdahl, a Princeton graduate student, and postdoctoral fellow Colin Torney, both currently in Couzin’s lab, as well as with former lab members Christos Ioannou and Jolyon Faria, who are now at the University of Bristol and the University of Oxford, respectively.

Read the abstract.

Citation: Berdahl, Andrew, Colin J. Torney, Christos C. Ioannou, Jolyon J. Faria, and Iain D. Couzin. 2013. Emergent sensing of complex environments by mobile animal groups. Science. Article first published online: Jan. 31, 2013. DOI: 10.1126/science.1225883

This work was supported in part by grants from the National Science Foundation, the U.S. Office of Naval Research, the U.S. Army Research Office and the Natural Sciences and Engineering Research Council of Canada.

Researchers harness nature to produce the fuel of the future (PNAS)

By Catherine Zandonella, Office of the Dean for Research

Hydrogen has tremendous potential as an eco-friendly fuel, but it is expensive to produce. Now researchers at Princeton University and Rutgers University have moved a step closer to harnessing nature to produce hydrogen for us.

The team, led by Princeton chemistry professor Annabella Selloni, takes inspiration from bacteria that make hydrogen from water using enzymes called di-iron hydrogenases. Selloni’s team uses computer models to figure out how to incorporate the magic of these enzymes into the design of practical synthetic catalysts that humans can use to produce hydrogen from water.

In this latest paper, Selloni and co-authors present a solution to an issue that has dogged the field: the catalysts designed so far are susceptible to poisoning by the oxygen present during the reaction. By making changes to the catalyst to improve the stability of the structure in water, the researchers found that they had also created a catalyst that is tolerant to oxygen without sacrificing efficiency. What is more, their artificial catalyst could be made from abundant and cheap components, such as iron, indicating that the catalyst could be a cost-effective way of producing hydrogen.

Selloni and her team conducted their research in silico — that is, using computer modeling. The goal is to learn enough about how these catalysts work to someday create working catalysts that can make vast quantities of inexpensive hydrogen for use in vehicles and electricity production.

The team included Patrick Hoi-Land Sit, an associate research scholar in chemistry at Princeton; Roberto Car, Princeton’s Ralph W. *31 Dornte Professor in Chemistry, and Morrel H. Cohen, a Senior Chemist at Princeton and Member of the Graduate Faculty of Rutgers University. Selloni is Princeton’s David B. Jones Professor of Chemistry.

Read the abstract.

Citation: Sit, Patrick H.-L., Roberto Car, Morrel H. Cohen, and Annabella Selloni. Oxygen tolerance of an in silico-designed bioinspired hydrogen-evolving catalyst in water. PNAS 2013; published ahead of print January 22, 2013, doi:10.1073/pnas.1215149110

This work was supported by the Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-FG02-06ER-46344. We also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US Department of Energy under Contract DE-AC02-05CH11231. The team also used computational resources from the Princeton Institute for Computational Science and Engineering (PICSciE) and the Office of Information Technology (OIT) High Performance Computing Center and Visualization Laboratory at Princeton University.

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