Research Updates – Coronatine in nonhost disease resistance in plants

Pseudomonas syringae is the most widespread bacterial pathogen in plants. Several strains of P. syringae produce the phytotoxin coronatine, which inhibits plant defense responses and contributes to disease symptom development.

In a well-received PeerJ study  “Coronatine inhibits stomatal closure and delays hypersensitive response cell death induced by nonhost bacterial pathogens” published last year, Dr Seonghee Lee—Senior Research Associate at The Samuel Roberts Noble Foundation—found that coronatine inhibits stomatal closure in tomato epidermal peels and delays hypersensitive response cell death induced by nonhost bacterial pathogens, such as P. syringae pv. tabaci.



Dr Lee told us that his peers strongly supported this publication: “Since coronatine function is still not fully understood, my study was very helpful for researchers who work on plant-microbe interactions, and many of them have read the paper. This publication is now being cited and I can definitively say that it has influenced others“.

As can be seen, this article has already been cited 6 times, it has been viewed almost 2,000 times, and the PDF has been downloaded almost 1,400 times. A high ratio of downloads to views means that a large proportion of readers are choosing to save the article for future study, indicating that it continues to make a significant impact in the field.


Dr Lee is now working on the characterization of the metabolites produced by P. syringae pv. tabaci and P. syringae pv. tomato T1 that suppress early plant defense responses in their host plants, tobacco and tomato. To reach this goal, he is using analytical technologies such as high performance liquid chromatography (HPLC), mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy. The identification of a novel bacterial metabolite produced by P. syringae pv. tabaci and P. syringae pv. tomato T1 will be very useful to better understand the structure and function of metabolites similar to coronatine in plants.


Author Interview - Michael Proulx

The lighting of a scene is an important factor that the visual system considers to help it identify objects. As soon as you interpret a visual object as possibly being three-dimensional, your visual system immediately tries to determine where the light is coming from, and then uses this information to decode the object’s properties. Because the human visual system interprets lighting as coming from above, in the example below, we perceive the spheres whose upper part is brighter as emerging from this image, and the sphere whose upper part is darker as receding into it. It is called the ‘light from-above effect’.

Today we published “The perception of shape from shading in a new light” in which Dr Michael Proulx - Associate Professor of Psychology at the University of Bath - demonstrated that the light-from-above effect is permeable to outside influence.

Dr Proulx first became interested in how humans and non-human primates perceive three-dimensional shape-from-two-dimensional shading when reading a book by Donald Hoffman on “Visual Intelligence”. One of the ‘rules’ of vision (those efficient visual shortcuts revealed typically by illusions) that Hoffman describes is the ‘light from-above effect’.

It immediately occurred to me that an external light cue might overrule this light-from-above assumption, even if it was irrelevant and had no impact on the stimulus that was in fact two-dimensional”, Dr Proulx told us. “A candle was handy at the time I was reading this at home, so I placed it beneath a figure in the book (similar to the figure in my PeerJ study) and found that my perception of shape-from-shading reversed to match that of the candle below the page. This quick 18th-century-style experiment implied I was on to something! A review of the literature turned up some sophisticated computational evidence that an external light can indeed have this effect, but many researchers kept citing the light-from-above effect as if it was impermeable to outside influence. A couple of experiments later I had found a direct demonstration of this that can be experienced in a way foretold by the first-ever paper on this topic over 200 years ago by Rittenhouse!

Anyone can replicate the effect described in Proulx’s paper in a dark room with a single light placed below the image used in Figure 1A (see above). Individual differences in the perception of shape-from-shading exist, and Dr Proulx thinks that “this is a fascinating direction for future work in this area. The study of individual differences in perception and attention has made a number of exciting findings in the areas of neuroscience and psychology, and shape-from-shading is an excellent research area for the next big discovery.”

Dr Proulx used black-and-white stimuli in his study but it is also interesting to note that color perception would influence the three-dimensional shape perception. Indeed Fred Kingdom of McGill University has published a number of fascinating studies on the influence of color on perceiving shape-from-shading. “It makes an interesting link to my new work published in PeerJ in that it shows the importance of understanding how the visual system is able to use much more complex relationships when determining how we see the world”, Dr Proulx explained.

Dr. Proulx’s work in his Crossmodal Cognition Lab ranges from vision science to the study of vision impairment. He is currently working on a sensory substitution device, The vOICe, to translate images into sound such that participants can learn to see with their ears! “In this way we are investigating how well classical visual phenomena, such as shape-from-shading, can be perceived by the visually impaired with a vision restoration device”, he explained.

Dr Proulx chose PeerJ to publish his fascinating work and he is very happy about it! “The review process at PeerJ was incredibly helpful yet critical. The efficiency of producing the proof was astonishing, and well done.” We hope to read more on Dr Proulx’s research soon!

Join Dr Proulx and thousands of other satisfied PeerJ authors and submit your next manuscript to PeerJ!


Author Interview - Abel Valdivia and the invasive lionfish

Take a look at this awesome image featured on our homepage. It illustrates the article “Re-examining the relationship between invasive lionfish and native grouper in the Caribbean” which we published today.


This study re-evaluated the potential ecological relationship between the invasive Indo-Pacific lionfish and native predators such as groupers, in the Caribbean. The authors tested the hypothesis of biotic resistance - the idea that native species could negatively affect the invasion success of introduced species. While there are several examples of biotic resistance across different systems, in particular examples of native species controlling the distribution of invasive plants, there is little to no evidence that native predators can control the distribution and expansion of invasive predators at a large geographical spatial scale.

This group of researchers re-evaluated whether native large-bodied grouper and other predators are controlling the abundance of exotic lionfish (Pterois volitans/miles) on Caribbean coral reefs. They assessed the relationship between the biomass of lionfish and native predators at 71 coral reefs in three biogeographic regions while taking into consideration several cofactors which may affect fish abundance including among others, wind exposure, time since invasion, proxies for fishing pressure, and habitat structural complexity. Their results indicate that the abundance of lionfish was not negatively related to the abundance of large-bodied groupers and other predators. Lionfish abundance was instead controlled by several physical site characteristics, and possibly by culling. Taken together, their results suggest that managers cannot rely on current native grouper populations to control the lionfish invasion.

This was a fascinating study, and so we invited Abel Valdivia, corresponding author on this article, to answer a few questions.

PJ: What were your motivations for undertaking this research?

AV: The invasion of lionfish into the Caribbean basin over the past ten years provides a unique possibility to study marine species invasion at a large geographical scale. Species invasion is one of the major threats the oceans face today, and can be closely related to issues such as fishing and climate change. With rising temperatures due to global warming, several marine species are shifting their geographical range; occupying new environments; establishing new ecological interactions with established residents, and therefore changing the community structure and composition of the invaded systems. Marine invasions due to human introductions or ocean warming are important to understand at a large spatial scale since it will be a very common phenomenon in the near future.

Lionfish have spread to every shallow and deep habitat of the Western Atlantic and the Caribbean, including coral reefs environments, seagrass meadows, mangrove root systems, estuarine habitats, and even depths over 90 meters. Lionfish have even been reported in the colder waters near Boston, Massachusetts. We are still investigating the negative impacts of this invader on all of these already disturbed ecosystems, but one thing is clear - their voracious appetite threatens small fish and juveniles of depleted fish populations including commercially and ecologically important species such as groupers, snappers, and herbivores.  The failure of the Caribbean region to constrain invasion success may be partially associated with the lack of native predatory capacity due to overfishing, or simply to weak biotic resistance by native predators and competitors to a novel predator.

PJ: How would you say your study is controversial?

AV: Over the past few years some studies have hinted that native groupers could potentially prey on invasive lionfish and therefore act as natural bio-control of the invader. There is one study that reported lionfish in the stomachs of at least two species of large groupers. However, it was not clear if the lionfishes were already dead when the groupers ate them. Another study found a negative relationship between the biomass of native Nassau grouper and lionfish at a relative small spatial scale in the Exuma Cays Land and Sea Park in the Bahamas. In fact, we were excited to test the generality of this negative relationship in a paper published last year. Unfortunately, we did not find any evidence that grouper or any other predators (including sharks) or competitors (same size native predators) were negatively related to lionfish and concluded that other physical environmental variables and culling were the main drivers of lionfish distribution and abundance.

Our current study expands on those findings by adding new factors that are known to affect fish abundance (e.g., fishing and reef structural complexity). We also tested whether lack of native predatory capacity was an issue across the Caribbean. While some reefs actually had a low abundance of native predators due to overfishing, other well-protected reefs with high abundances of sharks, groupers and snappers exhibited a high abundance of lionfish. Therefore, the lack of predatory capacity does not limit the control of the invader. In general there is actually little to no evidence that abundant native predators can constrain the distribution and abundance of invasive predators. For example, the expansion and proliferation of the invasive Burmese python in the Florida Everglades was never constrained by the abundant native American alligator.


PJ: What challenges did you face while doing this research underwater?

AV: Doing this research underwater is full of challenges, from adverse weather; strong currents; often poor visibility; underwater time constraints due to excess nitrogen diving at 45-50 feet, and boats sinking through to recreational divers picking up our tape transects because they thought we were “polluting” the reef.

We usually dived in a team of at least 4 to 8 divers at the same time. A couple of divers usually do one belt transect set at a time. However, due to the length of transects your dive buddy is not with you all the time, since she/he might be looking for lionfish. Thus keeping track of everyone while doing fish surveys is almost impossible because you could lose track of the fish you are counting. We came up with a simple underwater safety sound system when we could not see each other. This system consisted on two bangs on the SCUBA tanks to check that you dive buddy was ok and nearby, followed by a similar response of your dive buddy. Repeated banging on the tank was a sign of emergency, but fortunately we never used that code.

PJ: What is next in your research?

AV: Currently, we are working to understand the impact of the lionfish invasion on the entire fish community structure, composition and functional diversity in the Belizean Mesoamerican barrier. We have been monitoring the Belizean reef since 2009 and visited the same 16-18 sites every summer since then. The first records of lionfish in Belize were reported in 2010. Thus we know the fish community structure and composition before the invasion. By comparing fish communities without lionfish and the progression after the invasion we will be able to determine the impact of lionfish at a relative large and continuous spatial scale.

My own dissertation research focuses on the role of predatory reef fish in Caribbean coral reefs when human impacts like fishing are eliminated. The inability of the system in controlling species invasion might be due in part to lack of native predators. Although, we proved that this is not the case in our study (at least for some reefs), we actually lack information of natural baselines for predator abundance across the region. Therefore we do not know for sure how much natural predatory capacity these reef had. In fact, our models of expected predator biomass in the absence of human impacts (like fishing, pollution, habitat modification) and taking into account several physical, biotic, and management related variables, predict that we have lost between 80-95% of large fish predators like reef sharks, groupers, snappers, jacks and barracudas across the entire Caribbean.

PJ: Anything else you would like to mention?

AV: Lionfish in the Caribbean are here to stay. Unfortunately we cannot rely on native predators to control their abundance and distribution. Although there are a few claims that native predators could learn to hunt and to naturally eat lionfish without human aid (few dive sites feed local predators with dead lionfish), there is no evidence that this could be feasible at the scale necessary for conservation. Currently, fishing lionfish for consumption is the best, direct, and most effective way to decrease local abundance at least temporarily. 



Author Interview With Dr. Carolyn McKune

"No animal should ever have to ‘qualify’ for pain medication”


Today, we publish a very interesting article dealing with the evaluation of pain in animals undergoing surgical procedures, by Dr Carolyn McKune and her group. Dr McKune has had the opportunity to work and teach at veterinary schools in the US, Canada, and the Caribbean, as well as work with pharmaceutical companies and private referral practices. She is the owner of Mythos Veterinary L.L.C.

Dr Philip Jones (@pmgjones), the Academic Editor on the paper was very enthusiastic about Dr McKune’s research: “Nobody would ever want an animal to suffer in pain after having undergone a surgical procedure. However, compared to humans, very little research has been done on how best to measure pain in animals, and, similarly, very little is know about how best to treat pain in animals. Since I am an anesthesiologist, frequently dealing with pain issues (in humans — who can tell me when something hurts!), I was fascinated by Dr McKune’s novel research on pain after ovariohysterectomy in dogs. She and her team performed a three-arm clinical trial hoping to find a method of reducing pain after this procedure. Important insights into the measurement and treatment of pain in dogs were obtained from this clinical trial. I hope that more and more academic veterinarians will undertake similar research with the goal of perioperative pain reduction in animals.”

We were very interested in this work and felt it would be informative to have Dr McKune answer a few questions.

PJ: What is the take-home message of your article?

CMM: The take home message of our manuscript, “Challenges in evaluation of pain and a pre-incisional line block”, is simple: pain in animals is difficult to successfully detect. Those of us privileged enough to work with animals are obligated to understand this fact when managing their pain, and provide analgesia when we anticipate pain is present.

PJ: What challenges did you face while doing this research?

CMM: There are numerous challenges when one is performing a research project in clinical subjects. Personally, the hardest part of this project was that, in order to study their pain, I had to knowingly allow an animal to become painful. While mentally I anticipated this would be challenging, this was compounded by the fact that many of the shelter dogs were a variety of a very stoic dog breed—the pit bull. It was heart breaking to see these dogs which were so submissive to their human (hence, why people have tragically used these guys for dog fighting) that they would not show me ANY behavioral signs of pain. It was very distressing to know some of these animals had no analgesia present, and yet they calmly let me handle them, palpate near their wounds, etc. It was if they were saying “I have a human being to touch me; what more could I need?” It was just heart breaking.  This really drove home for me the take home message of this article—no animal should ever have to ‘qualify’ for pain medication. They should receive analgesia because we know logically they are in discomfort. We should also treat them with great respect and kindness, so we are worthy of the trust they place in us.

PJ: What kind of lessons do you hope the audience takes away from your research?

CMM: It is tempting to say, based on this research, that something like an ovariohysterectomy (commonly known as a “spay”), is not painful. However, this is highly unlikely to be the case—what human being, with the ability to verbally communicate, would consider a major abdominal procedure not painful? It is much more likely that pain is subtle in nature, animals are stoic, and even when using multiple assessment tools, we (who are not experiencing the procedure ourselves) are unlikely to accurately quantify pain in each and every patient. The inability to verbally communicate is an obstacle that we simply cannot over come, and therefore the onus is on us to provide adequate analgesia to any patient undergoing a procedure that is painful for a verbal responder.

PJ: How did you first hear about PeerJ, and what persuaded you to submit to us?

CMM: It was actually my husband (Michael J. Dark), who has published with PeerJ that suggested submitting to PeerJ. I’m very glad he did.

PJ: What was your experience of the review process?

CMM: I had an excellent editor and reviewers, who definitely enhanced the quality of the submission through their thorough review.

PJ: Anything else you would like to highlight?

CMM: PeerJ has an excellent staff. Because of the degree of automation used by PeerJ in the submission process, I assumed the responses to submitting authors would be robotic. Nothing could be further from the truth. I actually feel like I know some of the PeerJ staff personally now, and am very impressed with their efficiency and dedication.

PJ: In conclusion, how would you describe PeerJ in three words?

CMM: Worthy of Opus One (www.opusonewinery.com) :)

PJ: Many thanks!

Join Dr McKune, and thousands of other satisfied PeerJ authors - send your next article to PeerJ!


Research Updates - Assessing insect responses to climate change

In a well-received and cited PeerJ article “Assessing insect responses to climate change: What are we testing for? Where should we be heading?” published last year, Dr Nigel Andrew et al. examined how research on climate change affecting insects was being assessed, what factors were being tested, and where the studies were performed, from over 1700 papers published between 1985 and 2012.

Over a year has passed since that publication, and the article has already been cited several times, so we wanted to check in with Dr Andrew to see where is research was now headed.

Dr. Andrew, who is Associate Professor of Entomology and Zoology Museum Curator at the University of New England, told us that “this PeerJ publication has helped researchers think about research directions and future needs for spending tight research budgets and time frames.

He continues: “The reception of my peers to this publication has been very positive in the sense that it has given data to some of the assumptions that we have been making about the type of questions researchers have been asking and the type of data that has been produced. One of the key aspects of the paper that has been well received is the need to biologists to still go out and collect data from the field. A lot of great information can be gleaned from the current literature, but we are still very much at the tip of the iceberg in terms of understanding biotic responses to climate change. Understanding ecological, physiological and behavioural responses of individuals and populations to a changing climate is still a key research priority.

There has been a huge increase in the number of papers assessing insect responses to climate change in the last 18 months. Really interesting is the shift for researchers to assess microclimate influences and temperature fluctuations in a much more sophisticated manner. It is becoming clearer that it’s the extreme that play a key role particularly in having sub-lethal effects in individuals, and these effects can influence longevity and fecundity.

Dr Andrew, who is also President of the Ecological Society of Australia, is now assessing the influence of temperature variation, nutrition, and competition on different life-stages, populations and species of ants and dung beetles along environmental gradients. His group is also using citizen science to assist in collecting data and get the wider public interested in biology.

We hope to read more about this important research in future papers!


Image of Iridomyrmex purpureus an ant species being studied by this group. Photo by Yinika Perston.