A TEXT POST

Nest-building behavior of Monk Parakeets - Author Interview

Today we published a new study describing the nest-building behavior of Monk Parakeets. This work suggests that intervention during the earlier stages of nest building, by excluding Monk Parakeets from electric lines adjacent to poles, may be an effective, non-lethal method of reducing or eliminating parakeets nesting on, and damaging, utility poles.
We invited the first author, Kevin Burgio, to comment on his research and his experience publishing with us.

PJ: Can you tell us a bit about yourself?

KRB: I am a Ph.D. student at the University of Connecticut where I study the distributions and biology of parrots found in North America (historically and presently). In my spare time, when I’m not hanging out with my daughter, I also research parasite diversity and distributions, and the macroecology of birds and mammals.
imagePrior to college, I spent six years in the US Air Force working as a combat medic and dental hygienist, and also worked for three years in a public health dental facility. I originally planned on becoming a dentist, given my background; however, I developed a neurological disorder which causes my hands to shake uncontrollably. Given limited options, I decided to forego treatment and change career paths in the middle of my undergraduate degree. After taking an ornithology class with my coauthor and current PhD advisor, Dr. Margaret Rubega, I decided to study birds and we’ve been working together ever since! 

Credit: Chris Field

PJ: Can you briefly explain the research you published in PeerJ ?

KRB: Monk Parakeets, and their nests, have created quite a controversy in the US and other places they have naturalized in the past 50 years. Just the other day, I read in The Guardian that the United Kingdom has spent about £260,000 over the past few years to capture just 60 Monk Parakeets and collect a bunch of their eggs in efforts to get rid of their relatively small population.
Monk Parakeets are the only parrot species that builds their own nests out of sticks, and for reasons we do not yet fully understand, have been building these nests on electric poles. These nests can cause fires and power outages, and managing this problem is costly for electric companies. Past aggressive management (trapping and euthanasia), has led to protests and lawsuits aimed at protecting these birds despite the fact they aren’t native.  As an undergrad, I read about this controversy in newspaper articles here in Connecticut, and figured that if we just knew enough about their behavior, we could find a way to prevent the nesting on these poles, which would mitigate the conflict between the electric companies, their customers, and those concerned with the welfare of these birds.  This research is an important step in reaching this goal, since it identifies a behavior that may be key to preventing the parakeets from nesting on the poles.

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Credit: Kevin Burgio

PJ: Do you have any anecdotes about this research?

KRB: Watching and recording bird behavior is harder than it sounds. During my first “field season”, I went out to collect data for this project in the middle of a very cold November. I spent a few weeks sitting in my car, watching for nest building in these residential neighborhoods while trying to stay warm. At one promising pole, I parked my car and waited for 4 or 5 hours for birds to start renesting, but they never came. Apparently, I had left my lights on, and my car battery died. I had to call a tow truck to jump my battery, and imagine how nervous I was, sitting outside someone’s house with a car full of binoculars, scopes, notebooks, and cameras. The mechanic jumped my car and I went on my merry way. A few weeks later, the same exact thing happened pretty close to where the original incident happened. The same mechanic came to jump me again. I was mortified! I am surprised he didn’t call the police. To make a long story short, I did not record a single observation in three weeks. That was my first real taste of science.

PJ: What surprised you the most with these results?

KRB: Other researchers have done great research exploring how to deal with the problem posed by Monk Parakeet nests; however, what surprised me the most is that no one had thought to just watch the parakeets build their nests on utility poles before! It was clear after watching them building their nests for a short period of time what seemed important to them. Our results confirmed our initial hypothesis, which we formed only after an hour or two of observation.

PJ: What kinds of lessons do you hope the public takes away from the research?

KRB: I think it is important to highlight the role of basic scientific research, and how it can have direct real-world applications. For such a costly and problematic conflict between birds and people, that has been a problem for more than a decade now, it seems a win-win solution came down to a couple of biologists, sitting in a car, watching and recording these parakeets do what they do.

PJ: Where do you hope to go from here?

KRB: Taking this research to the next step, Dr. Rubega and I are currently working with a Connecticut utility equipment manufacturer, MidSun Group Inc., to create prototypes of a device that block Monk Parakeet access to the electric lines near the poles. We plan to experimentally test the efficacy of these devices in partnership with a local electrical company.

PJ: Why did you choose to reproduce the complete peer-review history of your article?

KRB: I believe that peer-review is an under-appreciated, yet critical, part of science. I haven’t published many papers yet in my short career (this is my third!), yet each time, the reviewers and editors had a huge impact on the finished product and their hard work made each paper stronger. Allowing anyone to see how this manuscript benefited by the peer-review process gives the reviewers and editor credit for the job they did, which would be otherwise hidden behind the scenes. 

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

KRB: One of the faculty in my department is an Academic Editor over there (Dr. Chris Elphick) and he and I have talked off and on about open access publishing over the past year or two. His enthusiasm for PeerJ, coupled with a great paper you recently published by one of my fellow UConn PhD students (Lily Lewis), were key in the decision to submit this paper to you.

PJ: Do you have any anecdotes about your overall experience with us? Anything surprising?

KRB: The most surprising thing that happened in my experience was that the Academic Editor actually apologized for taking about a week to give us a decision about our first revision! A week! I have another paper in review right now that took almost six months just to get our first decision. All said and told, our paper went through two revisions and will still be published just a little more than two months from the initial submission date. I find that amazing.

PJ: Would you submit again, and would you recommend that your colleagues submit?

KRB: Most definitely. The ease and speed of the process really allowed me to spend more time doing research, rather than fussing around with format changes and etc. Also, the research money I would have spent on publishing fees elsewhere will now be used for actual research. From my experience, publishing with PeerJ has been more efficient, more cost-effective, and just as thorough.

PJ: Many thanks for your time!

Join Kevin Burgio and thousands of other satisfied authors, and submit your next article to PeerJ.

A TEXT POST

Research Update - Bacterial curli protein and amyloid sequences

Last year, PeerJ published “Bacterial curli protein promotes the conversion of PAP248-286 into the amyloid SEVI: cross-seeding of dissimilar amyloid sequences”. Over a year has passed since that publication, and the article has already been cited several times, so we felt it would be informative to ask Ayyalusamy Ramamoorthy—lead author on this publication—to comment on the impact of his work.

PJ: Can you tell us a bit about yourself

imageAR: I am Robert W. Parry collegiate professor of Chemistry and Biophysics at the University of Michigan, Ann Arbor, USA. My research focuses on biophysical and biochemical studies of amyloid proteins and membrane proteins, and also on the development of high-resolution solid-state NMR spectroscopy to study biomacromolecules.

PJ: Can you briefly explain the research you published in PeerJ?

AR: Amyloid aggregates of the fragments of prostatic acid phosphatase (PAP248-286) (called SEVI (Semen Enhancer of Viral Infection)) have been shown to significantly enhance HIV infection. In the study published in PeerJ, we investigated the influence of exogenous factors that could promote SEVI fiber formation in-vivo, since the aggregates of SEVI are formed very slowly in in vitro conditions.  We have shown that a bacterially-produced extracellular amyloid (curli or Csg) acts as a catalytic agent for SEVI formation from PAP248-286 at low concentrations in vitro, producing fibers that retain the ability to enhance HIV infection. Cross-seeding PAP248-286 with curli only moderately affects the nucleation rate while significantly enhancing the growth of fibers from existing nuclei. This pattern is in contrast to most previous observations of cross-seeding, which show cross-seeding partially bypasses the nucleation step but has little effect on fiber elongation. Seeding other amyloidogenic proteins (IAPP(islet amyloid polypeptide) and Aβ1−40) with curli showed varied results. The ability of curli fibers to interact with proteins of dissimilar sequences suggests cross seeding may be a more general phenomenon than previously supposed.

PJ: What was the reception of your peers to this publication, and would you say that this publication has influenced others?

AR: Cross seeding of amyloid formation is an important aspect to be investigated for a variety of amyloid proteins and the implications in amyloid diseases. Under in vivo conditions, interactions between different types of amyloid proteins could influence the properties of an amyloid protein which could play important roles in amyloid diseases.  Our study has changed the way researchers think about amyloid aggregation and the interpretation of in vitro results to better understand amyloid diseases like Alzheimer’s disease and type-2 diabetes. Now, many research groups are investigating synergistic aspects of different types of amyloids like amyloid-beta and amylin (or also known as islet amyloid polypeptide protein), and in some cases to search for amyloid inhibitors for the potential development of drugs to treat amyloid diseases.

PJ: Why do you think it has been highly cited and downloaded?

AR: Investigation of misfolding of amyloid proteins is a very hot area of research and it is also multidisciplinary. Researchers from physics, biophysics, engineering, chemistry, and medicine are engaged in this area of research to address questions related to different aspects of amyloid proteins. Any new findings related to protein misfolding will have a high impact  in these areas. So, our publication has been found to be highly significant and is therefore having an excellent impact in these areas.

Our study has reported a highly significant significant phenomenon and it has a broader impact on other areas of amyloid diseases as well. For example, research focused on the biophysical aspects of protein misfolding and aggregation, development of amyloid inhibitors, biochemical or chemical biology studies of amyloid-induced cell toxicity and other areas in aging related diseases significantly benefit from the findings reported in our publication reported in PeerJ.

PJ: How has your research progressed since the publication?

AR: We are investigating many different aspects of amyloid proteins: high-resolution structural studies of amyloid oligomers, development of amyloid inhibitors, amyloid-membrane interactions, factors influencing cell toxicity, etc. We have also made excellent contributions in the areas of type-2 diabetes and Alzheimer’s disease related amyloid proteins. We have reported high-resolution structures of amyloid-beta and amylin proteins.

We are also investigating synergistic interactions between other amyloid proteins that include amylin (or IAPP) and insulin, amylin and amyloid-beta, and the role of cell membrane. Investigation of the mechanisms of amyloid-induced cell toxicity and the role of molecular crowding are also in progress in my laboratory.

We hope to read more about Prof Ramamoorthy’s research soon, and we encourage any others working in related fields to submit their work to PeerJ.

A TEXT POST

PeerJ responds to request from US Federal Government on challenge of reproducibility in science

This week, as part of the request from The Office of Science and Technology Policy and the National Economic Council for public comments to provide input into an upcoming update of the Strategy for American Innovation, PeerJ offered a response in answer to the following question:

Given recent evidence of the irreproducibility of a surprising number of published scientific findings, how can the Federal Government leverage its role as a significant funder of scientific research to most effectively address the problem?”

Reproducibility is critical in science. Without it science is unable to flourish, and scientists are unable to build on the work of others.  Aristotle’s dictum that there is ‘no scientific knowledge of the individual’ seemingly holds true today, as much of the research published in the 21st Century is the result of building on, or testing the findings of others.

The term reproducible research refers to the idea that the ultimate product of academic research is the paper, along with the full computational environment used to produce the results in the paper such as the code and data (1). The full academic output can then be used to reproduce the results and create new work based on the research. Alongside reproducibility lies repeatability – the idea that anyone in the same lab can repeat the same experiment using the same methods and specimens. For science to flourish it is imperative that reproducibility and repeatability become the cornerstones.

Science can only advance on the foundation of the trusted discoveries of others.  But like any good building project there is a financial cost to laying these foundations. Scientific research is often funded by governments, and other associated funding bodies, all looking to ensure their money is spent optimally. For instance, some recent research published on reproducibility in the field of cancer studies at the MD Anderson Cancer Center (2) points to the statistic that only 41.5% - 45.4% of scientific outputs were actually reproducible by those surveyed. Other research in this area suggests alarmingly lower figures still of 11% (3).

The US government gives around $30 billion every year in science funding through the NIH (4) which is mainly distributed in research grants to academic scientists. If you were to take the lowest reproducibility rate of 11% that potentially could mean up to 89% of this money (over $26 billion) is wasted. As a tax paying member of the general public you would want to ensure that the government is able to plough your hard earned capital into funds that yield results over and above those figures. It is therefore commendable that the Federal Government is looking to address this issue and leverage it’s role as a significant funder of scientific research.

Beyond the practicalities of finance, there is also an interesting dilemma. Since the middle of the 20th century, life science research concepts and technologies have rapidly grown from the discovery that DNA is the blueprint for life to sequencing and synthesizing new life altogether. Technologies like microarrays, mass spectrometry, high-throughput assays and imaging have been developed, making biology a data-rich science. With all these new tools you could reasonably expect that science would become more rigorous and precise, but with the reproducibility crisis it appears that something entirely opposite could be happening.

So how do we ensure that scientists are provided with the right conditions for their work to be reproducible?

The current state of affairs results from a combination of the complex nature of modern scientific research, a lack of accountability for researchers, and the incentives created by a publish-or-perish culture in academia.

For a scientific researcher to disseminate their work they are hugely reliant on scientific publishers. The publishing of scientific research has always had a large part to play in the visibility of research, and ultimately the reproducibility of science.  At PeerJ we believe that the more scientific outputs are made available to all, the better it is for science. We would therefore encourage the Federal Government to put more resource into enforcing open access mandates, to ensure scientific research is opened up to all.  

PeerJ publishes articles using a Creative Commons CC-BY licence, which means that authors retain their own copyright, while at the same time others can freely copy and reuse the articles without needing to ask for further permission. If a publisher asks an author to sign over copyright then it becomes difficult, expensive, or impossible for others to access the research. Just as we don’t believe in paywalls blocking access to research, nor do we believe in authors being unable to retain full ownership of their work. By being fully CC-BY, authors and readers don’t need to worry about sharing or reusing articles, so everyone benefits and ultimately science flourishes. The challenge facing those authors who do wish to publish through open access licensing is the proliferation of choice. Choice of licence can be a good thing, but only if there is interoperability in these licences. For instance there is not one common standard among OA licences, and the recently released STM OA licences don’t necessarily operate alongside Creative Commons licences (5). We recommend the move towards everyone using one specific interoperable OA licence.

Scientific journals have a significant role to play in encouraging reproducibility in the first place. They can require more descriptive materials and methods sections and provide unlimited space for them, so that other scientists will know exactly how an experiment was conducted and how they can replicate it. At PeerJ we encourage authors to submit relevant data during the review process, and we would encourage the Federal Government to ensure that more scientific publishers are asking their authors to do so when they submit their work to journals. The current incentive structure for authors does not reward the publication of replication studies. At PeerJ we not only encourage this for our authors, but most importantly our publishing platform enables authors to do just that. We recommend that the Federal Government, and all funders, set aside financial commitment for the replication and publication of the work they fund. We also suggest that the Federal Government looks to set up a specific program incentivising authors to make their data, trackable identifiers, and materials available with publication.

We believe in an open and transparent peer review process. Journals need specialized reviewers to ensure that manuscripts for technically or statistically advanced experiments are vetted thoroughly prior to publication. PeerJ harnesses the talent of thousands of reviewers able to bring their scientific expertise to bear on assessing the science behind the article. But unique to other scientific publishers we encourage our peer reviewers to provide their name as part of their review; and we also give our authors the option to publish the full peer review history of their article alongside the published version. We are hopeful that as more and more journals allow this, and as more and more authors and reviewers experience it, it will become a standard feature of all journals. Ultimately, the reason for doing this is to improve the process of review and publication and to provide fresh new insights for readers. We would ask that the Federal Government consider encouraging and rewarding those publishers which practice some form of open peer-review.

Authors should also be in a position to publish more negative results – those in which an experiment had no effect or clear outcome – because the lack of a finding can sometimes be as important as a finding itself. As technology enables cloud-based storage of all data and file types we encourage authors to openly share their negative results through open data platforms in order that others may learn from the outcomes of their experiments.  We would ask that the Federal Government supports those researchers in making their negative data openly available to the world, perhaps by making the reporting of negative (as well as positive) results a requirement of funding.

Scientists are in the privileged position of being able to shape the world for the benefit of mankind, nature and our planet’s future. As outlined, reproducibility and repeatability are the cornerstones for building on scientific discovery and making breakthroughs that help make the world a better place. Without it scientists can’t learn from the work of others, or indeed ensure their own work leaves a legacy to others. It is up to the publishers of scientific research to ensure we do everything we can to provide the best ecosystem for this. It is up to our governments to foster the right environment for that to happen, and reward those who contribute to engendering this.

A TEXT POST

Guest post - Sequence the sputum: using metagenomics to diagnose tuberculosis

Today, PeerJ is pleased to publish the work of Prof. Mark Pallen and his group, in which they describe a new DNA sequencing method to diagnose tuberculosis. Mark Pallen, Professor of Microbial Genomics and Head of the Microbiology and Infection Unit at the Warwick Medical School, wrote the following guest post, giving us some details concerning the study.

image“Laboratory diagnosis of tuberculosis (TB) using conventional approaches is a long drawn-out process, which takes weeks or months—plus, relying on laboratory culture means using techniques that date back to the 1880s!

In a report published today in the peer-reviewed journal PeerJ, we describe a new approach to the diagnosis of TB that relies on metagenomics—that is direct sequencing of DNA extracted from sputum—to detect and characterize the bacteria that cause TB without the need for time-consuming culture in the laboratory. Using the latest high-throughput sequencing technologies and some smart bioinformatics, we can now obtain sequences from the bacteria that cause TB in just a few days straight from clinical samples and gain insights into their genome sequences and the lineages they belong to, all without having to culture cells or capture or amplify DNA.

In this study, first-year PhD student Emma Doughty (https://twitter.com/EmmaDoughty6) and bioinformatician Dr Martin Sergeant, both working at Warwick Medical School, have worked with African scientists Dr Martin Antonio and Dr Ifedayo Adetifaworking at the MRC Unit in The Gambia to develop and exploit novel sequencing and analytic approaches. They detected sequences from the TB bacteria in all eight sputum samples they investigated and were able to assign the bacteria to a known lineage in seven of the samples. Two samples were found to contain sequences from Mycobacterium africanum, a variety of the TB bacterium that is particular to West Africa.

This is part of a connected program of research in the Pallen group, where we have been using metagenomics to detect bacterial pathogens in contemporary and historical human material. Last year, we used metagenomics to obtain an outbreak strain genome from stool samples from an E. coli outbreak and to recover TB genomes from ~200-year-old Hungarian mummies. Earlier this year, we recovered the genome of Brucella melitensis, which causes an infection called brucellosis in livestock and humans, from a 700-year-old skeleton from Sardinia, Italy.

We now aim to work on a larger number of sputum samples, perhaps looking at a hundred consecutive samples in the fullness of time. But, before then, we need to spend a bit more time optimising our DNA extraction protocols. We were pleasantly surprised that the protocol we used worked “out of the box”, but we are confident that we can improve things so we get fewer human DNA sequences and more mycobacterial sequences from each sample. If we can increase coverage of the TB genomes, we may soon be able to detect mutations associated with drug-resistance directly from the sputum.

The final goal, shimmering on the horizon, is that we might one day be able to extract information from all the macromolecules in a sample (DNA, RNA, proteins) so that we get a read-out of what pathogens are there, what virulence or resistance genes are being expressed, what host responses are switched on and also maybe detect cancerous or pre-cancerous changes in the patient’s genome. This is probably going to rely on a new kind of approach: nanopore sequencing—to learn more about this, watch the recent Bioinformatics and Balti session on YouTube. The future is looking very exciting!

PS: We have been very impressed with the service offered by PeerJ, with just two weeks from submission to acceptance!”

Prof. Mark Pallen

A TEXT POST

Atypical early histories on pet or performer chimpanzees – Author Interview

Today, we published the result of a multi-institutional research showing that chimpanzees raised primarily around humans with less experience around their own species during the first four years of life, tend to show reduced social competencies as adults than those with more natural early histories. This project was led by Steve Ross, Director of the Lester E. Fisher Center for the Study and Conservation of Apes at Lincoln Park Zoo in Chicago, IL, USA. We were very interested in hearing more about this research so we invited him to answer a few questions.

PJ: Can you tell us a bit about yourself?

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I’m the Director of the Lester E. Fisher Center for the Study and Conservation of Apes at Lincoln Park Zoo and for about twenty years I have primarily studied the behavior and psychology of chimpanzees. I am primarily interested in measuring, assessing and then ultimately improving the welfare of chimpanzees, and as such, I’ve been fortunate to work in a wide range of settings from laboratories to zoos to sanctuaries. In 2009 I started Project ChimpCARE, which is a non-partisan initiative that aims to use science, and education to understand and address issues surrounding privately-owned chimpanzees such as pets and performers.

PJ: Can you briefly explain the research you published in PeerJ?

This was the first study to come out of a multi-year, multi-disciplinary and multi-institutional initiative in which my post-doc, Dr. Hani Freeman and I, aimed to assess the long-term developmental outcomes on chimpanzees that had been previously housed as pets and performers. These chimpanzees typically have very unusual social histories and many have virtually no experience with their own species until they are fortunate enough to find new homes in accredited zoos or sanctuaries. We used a variety of methods to measure how these atypical early histories affected chimpanzees long after those periods of human influence were over and in this paper, we describe what we found from our behavioral data.

PJ: Do you have any anecdotes about this research?

The research was really motivated by what we had heard from zoos and sanctuaries that were managing these ex-pet and ex-performing chimpanzees. These chimpanzees were often very slow to integrate with other chimpanzees despite the best efforts of the staff. I’ve often heard it described as them “not being able to speak chimpanzee” or not being able to relate to others of their kind. We wanted to take an objective and scientific assessment of this phenomenon, which would not only be useful in characterizing the long-term outcomes of the controversial practices of private ownership of apes, but also give us a more complete academic perspective on the importance of early rearing environments.

PJ: What kinds of lessons do you hope the public takes away from the research?

There is growing discontent with the fact that, in the United States, you can own a pet chimpanzee: a highly complex, intelligent and dangerous wild animal that is endangered in its native habitat. But even today, people point to the fact that these animals seem loved and well cared for by their owners. Having worked with many chimpanzee owners, I know they care for their chimpanzees, but they don’t have the skills or resources to provide the physical and more importantly, the appropriate social environments they require. The data in this paper shows there are very likely long-term consequences to private ownership (high human influence) for chimpanzees.

PJ: Where do you hope to go from here?

We have a lot of data yet to be published including interesting comparisons across personality traits, physiological measures and some cognitive testing. We’ll be utilizing the Chimpanzee-Human Interaction (CHI) Index that we introduced in this paper, to understand the degree to which human influences affect chimpanzees across a broad spectrum of outcomes.

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Kathy is a female chimpanzee at Lincoln Park Zoo who was raised around other chimpanzees in her natal group - Photo credit ©Lincoln Park Zoo


PJ: How would you describe your experience of our submission/review process?

The speed of the process, which was nice, did not lead me to believe that the process was any less rigorous that other journals in which I’ve published - just more efficient. It helped also that the staff has been friendly and helpful too.
I own an electric car and the feeling of being an “early-adopter” on a fresh, new and exciting endeavor that seems destined to be the new normal is fun. Publishing with PeerJ feels a little like that too.

PJ: Many thanks for your time!

Join Steve Ross and thousands of other satisfied PeerJ authors - send your next article to PeerJ and put the fun back into publishing!