Author: Meg Byrne

Ecology Highlight: PLOS ONE at ESA 2013


climate change vulnerable species














Resisting Antibiotics: Some Bacteria Get By With a Little Help From Their Friends


Antibiotic resistance is often in the news, as it threatens the effectiveness of one of the foundations of modern medicine. Usually, the concern is about resistance that is inherent to the bacteria, or else develops in bacteria through genetic changes. A paper published today in PLOS ONE suggests another possibility.

In “Chemical communication of antibiotic resistance by a highly resistant subpopulation of bacterial cells,” authors Omar El-Halfawy and Miguel Valvano reveal that some species of bacteria may help others in surviving an antibiotic attack. In addition, they were able to provide insight into the mechanics of how the bacteria perform this action.

The study began with an observation of the bacterial species Burkholderia cenocepacia, which typically grows in the soil but can infect people who have cystic fibrosis and those with compromised immune systems. The authors noted that a subpopulation of the species was more resistant to the antibiotic polymyxin B than other bacteria of the species. In other words, these resistant bacteria were more likely to survive after treatment with polymyxin B, and levels of antibiotics that killed the less resistant bacteria did not harm this (more resistant) subpopulation.

When the authors grew the more-resistant B. cenocepacia with another strain of bacteria called Pseudomonas aeruginosa (a disease-causing bacterium that can co-exist with B. cenocepacia), the P. aeruginosa were much more resistant to the antibiotic than when they grew in isolation.

Why might the P. aeruginosa be more resistant when they were in the presence of B. cenocepacia?

The authors suspected that the B. cenocepacia were releasing something into their environment that interfered with the action of the antibiotic, making it less potent. Experiments revealed that the bacteria were indeed secreting two proteins molecules associated with increased antibiotic resistance: putrescine (named for its putrid odor!) and Ycel, a protein whose function was previously unknown.

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The large amounts of secreted putrescine blocked the antibiotics’ binding to the surface of the bacteria, and could make both B. cenocepacia and P.aeruginosa more resistant to polymyxin B when grown together.

Ycel, on the other hand, was able to bind to the antibiotic directly, presumably decreasing its potency. Ycel is predicted to bind amphiphilic molecules (such as detergents, which  are attracted to both water and oil). Consistent with this prediction, the authors showed that Ycel had a protective effect against amphiphilic antibiotics and less of an effect against others.

These results have implications for combating the growing problem of antibiotic resistance. If we could prevent bacteria from making putrescine or Ycel, antibiotic treatments might be more effective, helping us eventually outflank resistance.

Citations: El-Halfawy OM, Valvano MA (2013) Chemical Communication of Antibiotic Resistance by a Highly Resistant Subpopulation of Bacterial Cells. PLoSONE 8(7): e68874. doi:10.1371/journal.pone.0068874

Bragonzi A, Farulla I, Paroni M, Twomey KB, Pirone L, et al. (2012) Modelling Co-Infection of the Cystic Fibrosis Lung by Pseudomonas aeruginosa and Burkholderia cenocepacia Reveals Influences on Biofilm Formation and Host Response. PLoS ONE 7(12): e52330. doi:10.1371/journal.pone.0052330

Images: Pseudomonas aeruginosa doi:10.1371/journal.pone.0066257

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PLOS ONE Goes to the Mile-High City for ASM 2013

Bacillus anthracis - three color





















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How eels navigate to the Sargasso Sea

The migration of European eels (Anguilla anguilla) between freshwater habitats in Europe and North Africa and their spawning ground in the Sargasso Sea is one of the unsolved mysteries in animal navigation. Scientists have speculated that the eels may use the Earth’s magnetic field as a guide during their 6000 kilometer trip, and an article published today by Durif et al. strongly supports this idea.

To test the ability of eels to orient using a magnetic field, the authors used a carefully controlled laboratory setting, in which they eliminated other potential orientation cues, including odors, vibrations, light, and sounds.  They also created an artificial magnetic field, the same strength as the Earth’s magnetic field, which could be oriented in different directions.  Turning the artificial magnetic field between test runs helped rule out the possibility of the eels using other orientation cues.

The authors found that the eels consistently oriented in a particular direction with respect to magnetic north and that the eel’s particular orientation varied with water temperature.  Below 12 oC, which is the temperature range associated with eel migration, the eels oriented in the direction they had been transported from the holding tank to the testing tank.  This also corresponded with the direction of increasing water temperature.  Above 12 oC, the eels oriented at right angles to the direction they had been transported, which the authors speculate might reflect foraging behavior during times of the year the eels are not migrating.

Thus, eels seem capable of using the Earth’s magnetic field as a navigational guide.  They also seem to integrate this information with other cues, such as water temperature, to determine their direction of movement.

While these results provide some insight into how eels navigate to their spawning ground, other mysteries about eel migration remain, including where the spawning ground in the Sargasso Sea is precisely located.  For further reading about eel migration, see another paper published in PLOS ONE in October, in which Béguer-Pon et al. tagged adult American eels (Anguilla rostrata) to map their migration to the Sargasso Sea but instead learned something about porbeagle shark predation.

Image credit: Steffen Zienert (

Citations: Durif CMF, Browman HI, Phillips JB, Skiftesvik AB, Vøllestad LA, et al. (2013) Magnetic Compass Orientation in the European Eel. PLoS ONE 8(3): e59212. doi:10.1371/journal.pone.0059212

Béguer-Pon M, Benchetrit J, Castonguay M, Aarestrup K, Campana SE, et al. (2012) Shark Predation on Migrating Adult American Eels (Anguilla rostrata) in the Gulf of St. Lawrence. PLoS ONE 7(10): e46830. doi:10.1371/journal.pone.0046830

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No sense of direction? Consider consulting some carp

The ability to navigate using the earth’s magnetic field is a skill that is not unique to humans.  Over the last few decades, scientists have discovered that numerous organisms have an ability to tell which way is north.  And the list is growing.

In one study, “Magnetic Alignment in Carps: Evidence from the Czech Christmas Fish Market,” Hart et al. reported that carp tend to align themselves along a north-south axis.  The authors photographed over 14,000 carp swimming in plastic tubs at pre-Christmas fish markets and found that, on average, the fish positioned themselves facing either the North Pole or the South Pole.

While the authors have not yet proven that carp can sense the geomagnetic field, they did rule out other possible orientation cues, including light, wind, temperature, and water flow. What benefit a common orientation may provide the fish remains unknown.  One possible explanation the authors present is that it may help the fish coordinate their movement when they swim in a school.

Some other organisms also have an ability to detect localized magnetic fields.  In a paper titled “Desert Ants Learn Vibration and Magnetic Landmarks,” Buehlmann et al. demonstrated that ants can sense a strong magnetic field created by two small magnets and use this as a landmark to find their nest.

In the absence of any other landmark (such as a vibrational, visual, or olfactory cue), ants who had been trained to associate the magnetic field with the nest entrance spent a lot more time near the magnetic field than ants who were naive to this landmark.  It is unclear how relevant this experiment is to ants in their natural environment, but the study nevertheless highlights the ants’ ability to sense a magnetic field.

While little is known about how carp align with the earth’s magnetic field or how ants sense a localized magnetic field, more is known about how some tiny organisms, aptly named magnetotactic bacteria, orient with a magnetic field.  These bacteria form straight chains of nano-size magnetic particles within the cells. The magnetic chains are attached to intracellular structures, thus allowing the bacteria to align passively with the earth’s magnetic field, like compass needles.

In a paper published earlier this month, Kalirai et al. showed that some magnetotactic bacteria form anomalous magnetic chains, with some sections of the chain oriented north and others south.  This finding contradicts scientists’ previous understanding that all the magnetic particles in a single chain would have the same alignment.  The study raises many questions: Would bacteria with anomalous magnetic chains have a competitive disadvantage in their natural environment?  Is there a single genetic mutation that leads to the anomalous magnetic chains?

All three of these studies raise intriguing questions, and we look forward to future discoveries from these scientists.

Image: Arrows indicate the orientation of carp swimming in a plastic tub (Hart et al. PLOS ONE 2012)



Buehlmann C, Hansson BS, Knaden M (2012) Desert Ants Learn Vibration and Magnetic Landmarks. PLoS ONE 7(3): e33117. doi:10.1371/journal.pone.0033117

Kalirai SS, Bazylinski DA, Hitchcock AP (2013) Anomalous Magnetic Orientations of Magnetosome Chains in a Magnetotactic Bacterium: Magnetovibrio blakemorei Strain MV-1. PLoS ONE 8(1): e53368. doi:10.1371/journal.pone.0053368

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Great Genetics: PLOS ONE at ASHG

For the 2012 American Society for Human Genetics conference in San Francisco, we are highlighting a selection of recently published articles in the area.  In the last two years, PLOS ONE has published over 700 articles on human genetics; the eight summarized below are among the top 5% with regard to post-publication citations, HTML views, PDF downloads, and bookmarking.

Two of these papers address the genetic underpinnings of Alzheimer disease.  By mining genetic data, Jones et al. linked two physiological processes, cholesterol metabolism and the innate immune response, to late-onset Alzheimer disease development.  In a paper published in September of this year, Jun et al. discovered a correlation between the presence of cataracts and Alzheimer disease, and identified genetic variations in the gene encoding for the δ-catenin protein that may be the link between these two conditions.

Looking at another eye disorder, Nakano et al. investigated the genetic component of glaucoma.  Their research identified genetic variations among people of Japanese ancestry that are associated with certain types of glaucoma.

Another paper looked at the potential role of epigenetic modification in type 2 diabetes. Specifically, Bell et al. compared DNA from healthy women and women with type 2 diabetes and examined variations in DNA methylation, a chemical modification to the DNA that affects gene expression.  The analysis revealed significant methylation differences in regions of DNA previously associated with type 2 diabetes, suggesting that variations in DNA methylation may play a role in the disease.

Two studies considered variations in the number of repeats of specific DNA sequences, which can affect disease pathology and even drive evolution.  Valsesia et al. investigated DNA copy number variations and their effect on gene expression in seven different melanoma cell lines.  Their research identified candidate genes and molecular pathways involved in metastatic melanoma.  Zhang et al. compared the performance of four software programs in detecting copy number variations in DNA sequences longer than 1,000 bases.  The authors found inconsistency even among the most established programs, emphasizing the work that still needs to be done in this area.

Another paper addressed the issue of chromosome translocation, or the abnormal rearrangement of parts of chromosomes.  In a collaboration between biologists and physicists, Engreitz et al. showed that the three-dimensional organization of DNA in the cell nucleus may help explain certain chromosomal translocations linked to human disease.

Finally, using data from the Human Genome Diversity Project, Kirin et al. profiled the lengths and frequencies of DNA sequences that are identical on maternal and paternal chromosomes.  This large-scale analysis allowed the authors to make conclusions about historic and contemporary patterns of intra-communal parentage in different human populations.

If you are at the ASHG, we hope that you stop by the PLOS booth and meet some of the PLOS staff.  We will be at booth # 1606.  Also, if you have published in PLOS ONE, we have a stylish PLOS ONE author t-shirt to give you.  We look forward to seeing you there.

Acknowledgments:  Thank you to Martin Fenner for helping us with the article-level metrics analysis.  Thank you to Eric Martens and Matt Hodgkinson for designing the literature search and helping analyze the final results.  Finally, thank you to Camron Assadi for coordinating our efforts.

Image:  Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, et al. (2011) Network-Guided Analysis of Genes with Altered Somatic Copy Number and Gene Expression Reveals Pathways Commonly Perturbed in Metastatic Melanoma. PLoS ONE 6(4): e18369. doi:10.1371/journal.pone.0018369


Bell CG, Finer S, Lindgren CM, Wilson GA, Rakyan VK, et al. (2010) Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus. PLoS ONE 5(11): e14040. doi:10.1371/journal.pone.0014040

Engreitz JM, Agarwala V, Mirny LA (2012) Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease. PLoS ONE 7(9): e44196. doi:10.1371/journal.pone.0044196

Jones L, Holmans PA, Hamshere ML, Harold D, Moskvina V, et al. (2010) Genetic Evidence Implicates the Immune System and Cholesterol Metabolism in the Aetiology of Alzheimer’s Disease. PLoS ONE 5(11): e13950. doi:10.1371/journal.pone.0013950

Jun G, Moncaster JA, Koutras C, Seshadri S, Buros J, et al. (2012) δ-Catenin Is Genetically and Biologically Associated with Cortical Cataract and Future Alzheimer-Related Structural and Functional Brain Changes. PLoS ONE 7(9): e43728. doi:10.1371/journal.pone.0043728

Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, et al. (2010) Genomic Runs of Homozygosity Record Population History and Consanguinity. PLoS ONE 5(11): e13996. doi:10.1371/journal.pone.0013996

Nakano M, Ikeda Y, Tokuda Y, Fuwa M, Omi N, et al. (2012) Common Variants in CDKN2B-AS1 Associated with Optic-Nerve Vulnerability of Glaucoma Identified by Genome-Wide Association Studies in Japanese. PLoS ONE 7(3): e33389. doi:10.1371/journal.pone.0033389


Zhang D, Qian Y, Akula N, Alliey-Rodriguez N, Tang J, et al. (2011) Accuracy of CNV Detection from GWAS Data. PLoS ONE 6(1): e14511. doi:10.1371/journal.pone.0014511

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A selection of influential PLOS ONE papers on tropical medicine and malaria

For the XVIII International Congress for Tropical Medicine and Malaria Conference in Rio de Janeiro, PLOS ONE is highlighting eight recent articles.  Since January 2011, PLOS ONE has published almost 700 articles in the areas of tropical neglected diseases, tropical medicine, and malaria.  We’re sharing with you some of the papers that have received the most attention.  The authors on these papers come from across the globe, representing Brazil, Colombia, Ethiopia, France, the Netherlands, Papua New Guinea, Spain, Sri Lanka, Switzerland, the United Kingdom, and the United States.

One paper in particular has stood out.  Researchers found a novel therapy that could revolutionize the treatment of viral infections from the common cold to Ebola.  The therapy eliminates cells that contain viral RNA while leaving uninfected cells unharmed.  In the study, the therapy was effective against 15 different viruses, including dengue flavivirus, rhinoviruses, and H1N1 influenza virus.

An article published last month reported that malaria incidence in Sri Lanka has declined by 99.9% since 1999, despite ongoing conflict in the country.  The success of the malaria program could be explained in part by effective prevention measures, early detection, and maintaining the program in conflict zones.  In less than a month, the paper has received over 1,000 views.

Bacteria on people’s skin can affect how attractive they seem to malaria-transmitting mosquitoes.  Research published last December found that malaria mosquitoes preferred people whose skin had an increased number of bacteria but fewer overall types.  The article received significant press coverage and has been viewed almost 10,000 times.

Although a vaccine that blocks malaria transmission is theoretically possible, several obstacles have prevented its development, including producing Plasmodium parasite antigens in a cost-effective manner.  A paper published in May 2012 showed algae can make Plasmodium proteins that can elicit an antibody response.  This approach could bring down overall costs of a vaccine.  Since publication this paper has been viewed over 3,500 times.

A different approach to combatting malaria is to increase the mosquito’s defenses against the parasite.  A paper published in January 2011 showed that it is possible to insert an anti-malarial gene into a specific location in the Anopheles gambiae genome.  This technique decreased infections of Plasmodium yoelii nigeriensis and could be effective against other Plasmodium parasites.  Since publication this paper has received over 2,000 views.

The results from a World Health Organization-led effort to estimate the global incidence of leishmaniasis, a parasitic disease spread by sandflies, published in May 2012.  To obtain an accurate estimate of the disease burden, the authors collected data from 98 countries and 3 territories.  The authors stressed the importance of this in-depth assessment in helping policy makers and aid organizations determine funding priorities for this underreported disease.  The paper has been viewed over 5,000 times.

One strategy parasites use to evade the host’s immune system, initiate infection, and even manipulate host behavior is to imitate the host’s proteins.  A study published in March 2011 presented a method for scanning entire parasite genomes to identify proteins that are mimicking host proteins.  The paper received over 4,000 views and was featured on the This Week in Parasitism podcast.

Finally, a new method for diagnosing infection by Schistosoma mansoni, the parasite that causes schistosomiasis, was published in June 2012.  This method, which is based on detecting the parasite’s DNA, provides greater sensitivity than the most routinely used diagnostic approach, requires only a urine sample, and has a relatively low cost.

If you are at the ICTMM, we hope that you have had a chance to stop by the PLOS booth, pick up one of the PLOS ONE postcards, and meet staff from PLOS Pathogens and PLOS Neglected Tropical Diseases.

Acknowledgment:  Thank you to Martin Fenner for helping us use the PLOS Article Level Metrics to identify influential PLOS ONE papers in the areas of tropical neglected diseases, tropical medicine, and malaria.
