Journal Club

Journal Club has returned for the Spring 2017 semester! We will meet every Monday at noon in Moore Hall room 473. Please bring your lunch and prepare for an excellent conversation. The PSGSC will also provide coffee and cookies!

This website will be used to post articles as well as facilitate discussion for Journal Club.

Questions? Comments? Suggestions? Please contact psgsc@rso.wisc.edu or Charlene Grahn at grahn2@wisc.edu.

 

Monday, March 13, 2017

What’s that noise? ‘Measurements and the replication crisis’

Hi Plant Scientists!

Please join us this Monday, March 13 at noon in Moore 473 , where Sarah Turner will lead a discussion on interpreting experimental data collected in noisy research settings.

Research questions and insights are driven by the ability to detect a signal in the presence of noise. As a result, it is tempting to assume that measurement error reduces effect sizes, i.e. a significant effect under noisy conditions would be all the more significant in the absence of random variation. In their recent article, Loken and Gelman describe this reasoning in the context of a relatable scenario: “if you learned that a friend had run a mile in 5 minutes, you would be respectful; if you learned she had done it while carrying a heavy backpack, you would be awed. The obvious inference is that she would have been even faster without the backpack.”

Although the above logic seems intuitive, Loken and Gelman advocate against this reasoning in scientific research, citing it as a contributing factor to the replication crisis in science. They explain how significance in noisy research settings can be overestimated, especially when sample sizes are small, leading to overstated effects that misinform future studies.

Why doesn’t the runner analogy translate to scientific research? What exactly is the replication crisis? How do error and sample sizes influence effect sizes? What cautionary steps can we take to reduce error and avoid logical fallacies in research?

Article by Loken and Gelman: http://science.sciencemag.org/content/355/6325/584?variant=full-text&sso=1&sso_redirect_count=1&oauth-code=780a25d8-ab19-4996-b5b2-60fb0eed5c93

 

Coffee and cookies will be provided to encourage a larger sample size at journal club!

If you would like to lead a Journal Club, please click here to sign up!

We hope to see you there!

Cheers,
PSGSC


Monday, February 27, 2017

Real bat pollinators manipulate artificial plant populations: Integrating in silico population genetics with animal behavior

Hi Plant Scientists!

Please join us this Monday, February 27 at noon in Moore 473 , where Andrew Maule will lead a discussion on studying the cognition-mediated evolution of floral nectar rewards driven by Commissari’s long-tongued bat.

It is an evolutionary paradox that flowers pollinated by birds and bats tend to have low-sugar nectar.  Behavioral studies show that bats preferentially favor nectar as sweet as 60% sugar content, however most plants produce nectar that is 18-23% sugar.  Given the tight coevolution of flowers and their pollinators, one would expect that pollinator preference would  drive plants to produce high-sugar nectar rewards.  Join us to discuss an intriguing experiment that uses radio-tagged bats, computer-controlled artificial ‘flowers’, and evolving in silico ‘genomes’ to explain this evolutionary phenomenon by observing floral evolution in real time.  Topics of discussion will include the theory of psychometrics and perception of rewards, and how proportional processing can explain this phenomenon of stabilizing selection.

Click here to access the popular press article by Ed Yong.

Click here to access the Science article by Nachev et. al.

 

Assuming Weber’s Law, coffee and cookies of a sufficient quality and quantity to attract plant science graduate students will be provided!

If you would like to lead a Journal Club, please click here to sign up!

We hope to see you there!

Cheers,
PSGSC


Monday, February 20, 2017

Toxic fruits: The role of plant scientists in addressing public health concerns

 

Hi Plant Scientists!

Please join us this Monday, February 20 at noon in Moore 473 , where Chris D’Angelo will lead a discussion on breeding for reduced toxicity and the plight of the Lychee fruit.

Every summer since the mid 1990s children in India have been dying from a brain disorder called hypoglycemic encephalopathy. What do all these deaths have in common? Lychee fruit. Unripe lychee fruits contain high levels of two compounds, hypoglycin A and MCPA, both of which can cause hypoglycemia in under-nourished individuals. The findings reported by Shrivastava et al. in the public health journal, The Lancet, garnered international attention as the story was picked up by mainstream media outlets two weeks ago. This week we will talk about the role that breeders can play in reducing toxicity in crop plants and the importance of interdisciplinary research in solving complex problems.

Click here to access the article by Shrivastava et. al.

Click here to access the article by Das et. al.

Click here to access the article by Isenberg et. al.

Coffee and cookies will be ripe for the taking!

If you would like to lead a Journal Club, please click here to sign up!

We hope to see you there!

Cheers,
PSGSC


Monday, February 13, 2017- Miscanthus x giganteus as a potential bioenergy crop

Hi Plant Scientists!

Please join us this Monday, February 13 at noon in Moore 473 , where Kate Ivancic will lead a discussion on using perennial grasses to produce biofuel on marginal soils.

Miscanthus x giganteus has potential to be one of the great bioenergy grasses of our time. Changing soil salinity levels around the world propose a challenge to plant productivity and reduce arable acreage for commodity speciality crops. This paper explores the potential for M. giganteus production on marginal lands by quantifying the morphological, physiological, and biochemical responses of M. giganteus to different soil salinity levels over time. Join us for a thrilling discussion of  M. giganteus and the use of perennial grasses as bioenergy crops and phytoremediators as we venture into a future of uncertain soil conditions!

Click here to access the article by Stavridou et. al.

Coffee and cookies will be provided to fuel our discussion!

If you would like to lead a Journal Club, please click here to sign up!

We hope to see you there!

Cheers,
PSGSC


Monday, January 30, 2017- Contemporary Strategies for Crop Domestication

Hi Plant Scientists!

Please join us this Monday, January 30 at noon in Moore 473 , where Jamie Bugel will lead a discussion on strategies for contemporary domestication of new crops, including a pipeline strategy for identifying wild species that show potential for domestication and using genomic selection to increase domestication efficiency.

Over the past centuries traditional crop breeding and domestication methods have fed the world’s growing populations. As breeding techniques advance, breeders are able to use more varied tools to develop edible crops that can both feed our population and maintain the integrity of agricultural land. In journal club this week we will discuss one possible approach to developing new crops using domestication and touch on the domestication and breeding techniques of intermediate wheatgrass or Kernza™ and what has been accomplished thus far with this particular perennial crop.

Click here to access the article by DeHaan et. al.

Click here to access the article by Zhang et. al.

What advantages might domestication of novel crop species have over breeding to enhance performance of existing crops? How much can we expect molecular breeding techniques to shorten the timeline of crop domestication? What specific agricultural problems can we solve with novel crop domestication, and how can we identify the best plant to solve a particular problem?

Coffee and cookies will be provided to decrease the attrition rate of Journal Club through the Graduate Student Time Management Pipeline.

If you would like to lead a Journal Club, please click here to sign up!

We hope to see you there!

Cheers,
PSGSC


Monday, January 23, 2017

Hi Plant Scientists!

Please join us on Monday, January 23 at noon in Moore 473 for the first meeting of Journal Club in 2017, where Charlene Grahn will lead a discussion on the potential of extrafloral nectar and volatile organic compounds as breeding targets for enhancing the biological control of crop pests.

Biological pest control has proven successful in some perennial cropping systems and greenhouse environments by exploiting tri-trophic interactions between a host plant, an herbivorous pest, and the pest’s natural enemy (i.e. a predator, parasitoid, or insecticidal pathogen). Plant-produced volatile organic compounds and nectar rewards function in these interactions to increase the apparency and attractiveness of plant hosts to the pest’s natural enemy. Plant breeding and agricultural management practices have unintentionally decreased the ability of many crops to engage in tritrophic interactions, however the potential for enhancing these interactions through plant breeding by exploiting variability in plant-produced volatile organic compounds and nectar reward production has been explored only minimally. In this opinion article, the authors discuss potential breeding strategies for enhancing the efficacy and feasibility of biological control methods as well as some obstacles and risks that such breeding efforts might entail.

Please click here to access the article by Stenberg et. al.

How might the efficacy of biological control methods be precisely quantified? Can substantial enhancement of biological control methods realistically be achieved through plant breeding? How would a widespread adoption of biological control methods change the agricultural landscape nationally and internationally?

Coffee and cookies will be provided to enhance the apparency and attractiveness of Journal Club to plant science graduate students.

If you would like to lead a Journal Club, please click here to sign up!

We hope to see you there!

Cheers,

PSGSC


Monday, December 12, 2016 – Darwin + Mendel <3

Hi Plant Scientists!

Please join us this Monday, December 12 at noon in Moore 473 for the 2016 finale of Journal Club, where Irwin Goldman will lead a discussion on new evidence regarding the highly speculated and intriguing relationship between Darwin and Mendel.

In a perspective piece that celebrates the sesquicentennial anniversary of Mendel’s classic paper, Experiments on Plant Hybrids, Fairbanks and Abbott propose evidence of Darwin’s influence on Mendel’s interpretations and theory. They describe the history of translation and controversy surrounding Mendel’s work, including R.A. Fisher’s “abominable discovery” that Mendel may have falsified his results. To address shortcomings in previous translations of Mendel’s paper, they propose a new translation that (1) improves the accuracy and accessibility of Mendel’s original work and (2) employs Darwin’s phraseology from the Origin of Species, providing a 19th century Darwinian tone that is consistent with the timing of the original publication. This translation, coupled with marginalia from Mendel’s copy of Origin of Species, suggests that Darwin influenced Mendel’s writing in the final sections of his paper, supporting Fisher’s previous observation that “the reflection of Darwin’s thought is unmistakable.”

Click here to access the paper by Fairbanks and Abbott.

How might an exchange between Darwin and Mendel have reshaped the course of modern biology? What is the impact of phraseology on how we discuss and interpret scientific literature? Is there compelling evidence of a bromance between Darwin and Mendel?

Coffee, chocolate, and peers are the Elements which go forth to promote the Lebensbedingungen and Variabilität of Journal Club.

We hope to see you there!

Cheers,
PSGSC


Monday, November 28, 2016
Back to the Bayesics

Hi Plant Scientists!

Please join us on Monday, November 29 at noon in Moore 473 to discuss the basics of Bayesian statistical inference and potential applications in genetics. We encourage participation regardless of familiarity with the topic, as the goal is to focus on big picture concepts in Bayesian statistics.

The advent of high-power computing has ushered in a revolution in statistics, specifically regarding Bayesian frameworks. As we continue to generate large data, there is an increasing need for more robust, efficient, and flexible statistical methods that provide biological insight. In their 2004 review, Beaumont and Rannala compare the use of Bayesian approaches to other statistical methods, explain why the use of Bayesian reasoning has increased in genetics, and highlight the shortcomings and future potential of these methods.

As an example, we will walk through the Monty Hall problem: Your PI gives you a choice of three doors. There is a degree behind one door, and five more years of grad school behind the other two. You pick door #2, and your PI, who knows what is behind the doors, opens door #3, which shows five more years of grad school. Your PI then asks if you’d like to switch your choice to door #1 – is it to your advantage to switch? Hint: You should always switch your answer!

What are the principles of Bayesian inference? When are Bayesian methods worth the high computational and interpretive investments? Are you currently using or is there an opportunity to integrate Bayesian frameworks in your research?

Click here to access the article by Beaumont and Rannala.

Please click here to access an additional resource by Shoemaker, Painter, and Weir.

Prior information suggests a high probability of coffee and chocolate at Journal Club.

We hope to see you there!

Cheers,

PSGSC


Monday, November 21, 2016
Agricultural journals in the Victorian era

Hi Plant Scientists!

Please join us Monday, November 21st at noon in Moore 473, where Charlene Grahn will discuss the development and influence of agricultural journals in the Victorian era.

Public dissemination of science was instrumental in advancing the farming practices of Victorian England during a period of unprecedented population growth. Early 19th century agricultural scholars lamented that farmers were ‘not a reading class,’ however by the end of the century over half of all English farmers subscribed to at least one agricultural periodical or newspaper. The Journal of the Royal Society of Agricultural Science is one such publication that shaped agriculture during the Victorian era by fostering communication between scientists and farmers.

How does modern agricultural science compare to its nascent form? What insights can we gain from the successes and failures of past scientific journals? How have technological advancements changed science communication in the past and how might it continue to do so in the future?

Please visit https://archive.org/details/journalofroyalag1518roya to access a digitized volume of The Journal of the Royal Agricultural Society of England. Original copies of the journal will be available for browsing during journal club!

Gather with your fellow Men of Science for an afternoonified discussion over coffee and chocolate!

If you would like to lead a Journal Club, please click here to sign up!

We hope to see you there!

Cheers,

PSGSC


Monday, November 14, 2016
Global adaptation of populations

Hi Plant Scientists!

Note: Due to a scheduling conflict, journal club will be held from 11:30-12:30 pm in Moore 473.

Please join us Monday, November 14th at 11:30am in Moore 473, where Shelby Ellison will discuss how genetic adaptation to local environments has helped modern humans spread across the globe.

Akin to artificial selection within plants, selective pressures in response to regional conditions have influenced global human genomic diversity. Identification of genetic variation associated with adaptation is in part due to improved genomic technologies, statistical analyses, and larger sample sizes. In this review, Fan et al. illustrate the use of emerging data sets and tools to better understand recent human evolution.

What are the current population genomic tools to detect selection/adaptation within populations? Is the plant community better or worse equipped to use these tools? Are there untapped resources that we can use to better sample global plant populations?

Click here to access the article by Fan et al.

Does coffee and chocolate tolerance increase your journal club fitness?

Are you interested in leading a Journal Club? Please click here to sign up!

We hope to see you there!

Cheers,

PSGSC


Monday, November 7, 2016
BLAST to the past

Hi Plant Scientists!

Please join us Monday, November 7, at noon in Moore 473, where Guillaume Ramstein will discuss the use of genetics in paleoanthropology.

There is more to statistical genetics than just association studies… Analyses typical of this field can yield conclusions like “this gene is positively associated to [some trait of interest]”. But interestingly, it can also yield conclusions like “the first farmers of the southern Levant and the Zagros Mountains were strongly genetically differentiated, and each descended from local hunter–gatherers”!… The study of Lazaridis et al. is remarkable not only because it exemplifies the power of DNA information and sequencing technologies, but also because it provides new insight about ancient human demography.

How can DNA information be so useful as to help elucidate the multiplicity of origins in prehistoric farming? How familiar are we already to the methods that the authors used to reach such fascinating conclusions?

Please click here to access the article by Lazaridis et al.

Do coffee and cookies influence the population structure of journal club?

Are you interested in leading a Journal Club? Please click here to sign up!

We hope to see you there!

Cheers,
PSGSC


Monday, October 31, 2016
Halloween special- reanimating zombie data!

Hi Plant Scientists!

Please join us on Monday, October 31 at noon in Moore 473 for a special Halloween edition of Journal Club. Joe Gage will lead a discussion on a topic that terrifies all scientists: best practices in scientific computing.

Reanimating old data or scripts is the scientific equivalent of a zombie apocalypse – you dig into the depths of an archived folder, only to find the poorly annotated remains of a previously robust analysis. What was that variable again? Is that script written in an ancient alien language? How long will you be bunkered up to troubleshoot? In this guide, Wilson et al. use their combined expertise to outline “good enough” practices for scientific computing, providing the armaments needed to combat challenges in data management and organization for researchers with all levels of technical skill.

Which practices do you currently implement in your research? What resources exist to facilitate use of these guidelines? How can you best arm yourself to fight zombie analyses?

Please click here to access the article by Wilson et al.

Journal club provides the resources needed to reanimate your Monday: coffee, chocolate, and invigorating scientific discussion!

Are you interested in leading a Journal Club? Please click here to sign up!

We hope to see you there!

Cheers,
PSGSC


Monday, October 24, 2016
Symposium Highlight: Dr. John Kress

Hi Plant Scientists!

Please join us Monday, October 24 at noon in Moore 473, where Lynn Maher will highlight research on DNA barcoding by Dr. John Kress, who will be speaking at the Annual DuPont Plant Sciences Symposium on Nov 4!

We will look at the use of DNA barcodes to understand complex plant-herbivore interactions in an effort to create and maintain biodiversity. Discussion will include an overview of the methodology, broader uses of DNA barcodes and how Dr. Kress has used this method in his work.

What are DNA barcodes and why should we care? Can this type of network construction be applicable in our own research? Join us to find out!

Understand the complexity of your dietary network with free coffee and cookies!

Please click here to access the article, Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes

Are you interested in leading a Journal Club? Please click here to sign up!
We hope to see you there!

Cheers,

PSGSC


Monday, October 17, 2016
Symposium Highlight: Dr. Jessie Alt

Hi Plant Scientists!

Please join us next Monday, October 17 at noon in Moore 473, where Kevin Cope will discuss the discovery of a new soybean aphid biotype. This discovery was made in part by Dr. Jessie Alt, a research scientist at DuPont Pioneer and a speaker at this year’s annual Plant Sciences Symposium.

The soybean aphid (Aphis glycines) was first reported in the United States in 2000 as an invasive pest of soybean (Glycine max).  It is now one of the most damaging pests in soybean production, causing upwards of 50% yield loss during heavy infestation. Previously, there were three soybean aphid biotypes that had been identified, but a new biotype, collected near Lomira, WI, was reported by Jessie Alt and Molly Ryan-Mahmutagic in 2013. We will discuss how they confirmed the isolate was a distinct biotype, as well as the various sources of resistance to aphid biotypes 1, 2, and 3 via antibiosis or antixenosis.

Why is it important to understand the precise mechanisms of resistance? How can these resistance traits be incorporated into commercial lines of soybean? How would you identify resistance to Biotype 4 in soybean breeding lines?

Coffee and cookies will be provided to break down resistance to attending journal club.

Click here to access the article by Alt and Ryan-Mahmutagic.

Are you interested in leading a Journal Club? Please click here to sign up!

We hope to see you there!

-PSGSC


Monday, October 10, 2016
Symposium Highlight: Dr. Dan Chitwood

Revealing the plant cryptotype

Hi Plant Scientists!

Please join us Monday, October 10 at noon in Moore 473, where Adam Bolton will lead a special edition discussion on an article by Dr. Dan Chitwood, who will be presenting at the DuPont Plant Sciences Symposium on Nov 4! Dan will be sharing developments from his research on the morphometric analysis of leaves.

Phenotyping is a critical, and often difficult, component to any genetics or breeding program. The last few years has seen an shift in focus from genomics to phenomics, which attempts to measure multiple scalar traits to capture the phenome of an organism. An article by Daniel Chitwood and Christopher Topp proposes the terms holophenotype, to mean the totality of and organism’s phenotype, and cryptotype, which is the combination of individual traits that maximizes the separation of types. How close do you think we can get to capturing the holophenotype of a single organism? Even if we could measure the entirety of a phenotype, how would we even begin to interpret  it? Would the effect size of existing QTL decrease? How can we best quantify a phenotype over developmental time?

Coffee and cookies will be provided to positively influence the phenome of journal club.

Please click here to access the paper by Chitwood and Topp (2015) – Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits

Are you interested in leading a Journal Club? Please click here to sign up!
Cheers,
PSGSC

Monday, October 3, 2016

Hi Plant Scientists!

Please join us Monday, October 3 at noon in Moore 473, where Madeline Wimmer will help welcome the cold weather with a discussion on breeding cold hardy perennial fruit crops.

There are many breeding efforts for perennial fruit crops in Minnesota and Wisconsin, including dramatic fluctuations in temperature. This discussion will focus specifically on cold climate wine grapes, but a reference article on perennial fruit crop breeding by J.J. Luby is referenced for background on breeding perennial crops for cold hardiness. Madeline will walk us through this exciting topic using wine grapes as a case study! How do perennial crops differ from annual and biennial crops? What traits are most important for cold hardiness? Which crops are adaptable?

Adaptation to journal club conditions will be encouraged with coffee and cookies.

Click here to access the article by J.J. Luby

Are you interested in leading a Journal Club? Please click here to sign up!
We hope to see you there!

Cheers,
PSGSC


Monday, September 26, 2016

From region to reason

Hi Plant Scientists!

Please join us Monday, September 26, at noon in Moore 473, where Chris D’Angelo will discuss the use of CRISPR-directed mitotic recombination to identify causal variants.

The advent of linkage and association studies has identified thousands of genomic regions contributing to phenotypic variation. However, fine mapping and causal variant analysis is often not pursued due to limitations with recombination rate. In a recent Science publication, Sadhu et al. outline a method for CRISPR-directed mitotic recombination, which will allow researchers to rapidly identify casual variants for phenotypic variation by inducing “loss of heterozygosity” (LOH). What avenues does this technology open for scientific discovery? What are the possible trade-offs and/or bottlenecks of this technology? How accessible is this approach to the general research community?

Free coffee and cookies has been identified as a causal variant for journal club attendance.

Click here to access the article by Sadhu et al.

Are you interested in leading a Journal Club? Please click here to sign up!

We hope to see you there!

Cheers,
PSGSC


Monday, September 19, 2016

Is sharing caring?

Hi Plant Scientists!

Please join us this Monday, September 19 at noon in Moore 473 for a discussion on the ethics and logistics of data sharing.

The sciences are facing many new challenges in the information age, especially how to manage large data sets and making them accessible to other researchers. Data sharing has many advantages, including increasing transparency and repeatability in research. However, widespread access to data often overlooks the context of the data collection, such as why certain parameters were chosen and experimental constraints. A recent editorial by Longo and Drazen in the New England Journal of Medicine discusses these issues in the context of clinical trials and provide insight into possible alternatives to promote data sharing and synergistic collaborations.

What resources exist to facilitate data sharing? How can these resources be improved? What are the ethical concerns? Is there a way to capture the advantages of data mining while still involving the original researchers?

Click here to access the article (only 1.5 pages!) by Longo and Drazen

Journal club is dedicated to the sharing of coffee, cookies, and scientific discussion in a synergistic environment.

Are you interested in leading a Journal Club? Please click here to sign up!

We hope to see you there!

Cheers,
PSGSC


Monday, September 12, 2016

The Spandrels of San Marco

Welcome back, Plant Scientists! The PSGSC is excited to kick off another semester of informal and intellectual discussion!

What do spandrels, diminutive tyrannosaurus arms, and evolution have in common?

To find out, please join us Monday, September 12 at noon in Moore 473 to discuss “The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme” by S.J. Gould and R.C. Lewontin.

The most compelling stories of evolution often involve a competitive adaptation that arises via natural selection. We can become so fascinated by the origin of a single trait that we lose sight of the big picture, perhaps overlooking indirect explanations resulting from developmental constraints or population structure. In their classic 1979 article, Gould & Lewontin provide the famous analogy to spandrels, which they define as triangular spaces formed by the intersection of two rounded arches in domed churches. Spandrels are an architectural constraint, but also provide a convenient, seemingly intentional, space for mosaics. With captivating rhetoric, Gould & Lewontin argue that  biologists often ascribe trait origins to an adaptive advantage without due consideration for alternatives, although in the case of architecture it is clear that “spandrels do not exist to house evangelists”.

Gould & Lewontin 1979

Does this article provide a convincing critique of adaptationist thinking? How are the topics presented relevant in modern science? What parallels can we draw to our own research? How can we broaden our perspective to avoid “just-so” storytelling?

For those interested, click here for an eloquent criticism of this article by Jeremy Fox

Did coffee and cookies originate with Journal Club or arise as an adaptation to encourage participation?

Are you interested in leading a Journal Club? Please sign up here!

We hope to see you there!


Monday, May 2, 2016

Reviving the pulse of pulses

Happy International Year of the Pulses! To celebrate these delicious legumes, please join us Monday, May 2 at noon in Moore 473, where Carlos Arbizu will lead a discussion on Andean bean diversity.

The United Nations, in collaboration with the FAO, declared 2016 the International Year of Pulses (IYP) to improve public awareness, encourage production, and increase dietary use of pulses. Pulses, which include beans, chickpeas, and lentils, are cultivated in many countries and are valued for their high amounts of protein, fiber, and micronutrients. Large-seeded dry beans (kidney and cranberry beans), also known as “Andean beans,” are an important source of food in the Americas and Africa. Despite their dietary importance, research on these crops is lagging behind their Mesoamerican counterparts. A study conducted by Cichy and collaborators (2015) genotyped and phenotyped a diversity panel, aiming to improve use of Andean bean germplasm in breeding efforts. What are the major challenges influencing pulse production and how are they being addressed? What efforts can we make to improve the utilization of pulses in the diet and in land management?

Cichy et al 2015

More information about the International Year of Pulses

In solidarity with the UN and FAO, JC will be provide pulse-inspired treats and a beverage made from coffee beans.

We hope to see you there!

Monday, April 25, 2016

To regulate or not to regulate, that is the question…

Please join us Monday, April 25 at noon in Moore 473, where Lynn Maher will discuss the regulation of organisms edited with CRISPR-Cas9.

The advent of novel DNA-editing technologies, such as zinc finger nucleases, TALENs, and CRISPR-Cas9, has raised questions regarding the existing regulatory framework for genetically modified organisms. Last week, USDA-APHIS informed Yinong Yang, a plant pathologist at Penn State, that a mushroom he developed using CRISPR-Cas9 would not be regulated, making it the first organism edited with CRISPR-Cas9 system to escape USDA oversight. The mushroom in question was engineered to resist browning by knocking out a polyphenol oxidase (PPO) gene, the same mechanism used to reduce browning in Arctic apples and Innate potatoes, which were subject to USDA scrutiny.

Is this a new era for GMOs? As scientists, how can we reframe the public discourse and stigmas surrounding gene-editing technology? What opportunities does this precedent offer, at the industry and academic level, for other products developed using CRISPR-Cas9?

Scientific American article: Gene-Edited CRISPR Mushroom Escapes U.S. Regulation

Webber 2014 – “Does CRISPR-Cas open new possibilities for patents or present a moral maze?”

“Whether ’tis nobler in the mind to deliberate
The intricacies and bureaucracy of regulation
Or to eat cookies and drink a sea of coffee,
And by listening gain knowledge.”

There is still one opening to present a topic of your choice at journal club! The sign-up sheet and previous topics can be accessed here.

We hope to see you there!

Monday, April 18, 2016

Please join us Monday, April 18 at noon in Moore 473, where Guillaume Ramstein will lead a discussion on the business models of scientific publishing.  

The industry of publishing is going through an interesting era! The “publishing giants” have typically applied a model based on subscriptions or one-article fees and, as the recent merger between Nature Publishing Group and major publisher Springer illustrates, they tend to get bigger! On the other hand, open-access journals (like PLoS ONE) and repositories (like arXiv) distribute articles for free, and are gaining importance in the game. Remarkably, strong and unlawful reactions to the traditional subscription model are also arising, through a science-paper equivalent of Napster: Sci-Hub. As a (future) scientist, what do you condone or condemn in these models? What evolution would like to see in the diffusion of (your) scientific knowledge? Come and share your opinion next Monday! 

Two articles about the changing landscape in the publishing industry can be accessed at:

van Noorden 2016 (open access vs. subscription, in Nature News)

Article about Sci-Hub in the New York Times: Should all research papers be free?

Attend Journal Club to enjoy open access to coffee, cookies, and scientific dialogue.

For those interested in leading a discussion this semester, there is still one opening! The sign-up sheet, including previous topics, can be found here: Journal Club Sign Up Sheet

We hope to see you there!

Monday, April 11, 2016

Please join us Monday, April 11 at noon in Moore 473 for a discussion about germplasm conservation and seed industry consolidation.

Crop wild relatives are widely lauded as a valuable source of genetic diversity, but how well do conservation efforts truly capture ecological diversity? A recent study by Alvarez et al. quantified the global conservation and availability of wild accessions for 81 crops, highlighting collection gaps and the corresponding lack of diversity. The authors stress the need for a concerted effort to develop more comprehensive gene banks, which are constrained by lack of funding, political challenges, and biological limitations. The availability of genetic resources also stands to be impacted by recent consolidation within the seed industry (e.g. Dow & Dupont, Syngenta & Chem China). What are options for improving existing gene banks? Is there a trade-off between industry consolidation and conservation priorities (e.g. access to genetic resources and utilization of crop diversity)?

Alvarez et al 2016

NPR article regarding seed industry consolidation

Does coffee and cookie consumption increase the diversity of scientific discourse? Find out by enjoying complementary coffee and cookies at journal club.

Interested in sharing a topic with your plant sciences peers? The sign-up sheet, including previous topics, can be found here: Journal Club Sign Up Sheet

We hope to see you there!

-PSGSC