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From fundamental insights to better plants, sustainably grown, serving the world

Recent publications from the SIPS community – October 18, 2018

Co-regulation of ribosomal RNA with hundreds of genes contributes to phenotypic variations.

Li, B., Kremling, K., Wu, P., Bukowski, R., Romay, M., Xie, E., Buckler, E., and Chen, M. 2018. Genome Research.

The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development.

Wang, X., Bao, K., Reddy, U.K., Bai, Y., Hammar, S.A., Jiao, C., Wehner, T.C., Ramírez-Madera, A.O., Weng, Y., Grumet, R., and Fei, Z. 2018.  Horticulture Research 5:64.

Dynamic model-based recommendations increase the precision and sustainability of N fertilization in midwestern US maize production.

Sela, S., van Es, H.M., Moebius-Clune, B.N., Marjerison, R., and Kneubuhler, G. 2018.  Computers and Electronics in Agriculture 153:256-265.

SIPS takes on the active learning challenge

Cornell Chronicle [2018-10-03]

Dan Buckley works with Julia Smith and Chloe Carpenter, both ‘20

Hands-on “active learning” is an instructional method that is being increasingly adopted in classrooms across the College of Agriculture and Life Sciences (CALS). CALS is promoting this effort by supporting faculty with grant funding. This academic year, six proposals split $500,000 to help hundreds of students sharpen critical thinking skills, develop in-the-field experience, and become equipped with skills to tackle scientific problems rather than be passive learners.

Of the six courses funded to adopt active learning strategies, four are taught by SIPS faculty Taryn Bauerle, Chelsea Specht, Dan Buckley, and Kerik Cox.  Bauerle’s course, “The Nature of Plants” (PLHRT 1115) will be taught in  Springn 2019, as will Specht’s class on Evolutionary Plant Morphology.

However, active learning is already being implemented for the Fall 2018 courses supported by the grant funding. In Introductory Microbiology (BioMi 2900) taught by Esther Angert, professor in the Department of Microbiology, and Dan Buckley, professor in the Department of Microbiology and the School of Integrative Plant Science (SIPS), students were given reading assignments outside class to learn the flow of information in the cell. Classroom time was dedicated to learning the intricacies of DNA replication, transcription and translation in a more engaged way.

“This is complicated stuff; students often get confused and want to memorize a list of components,” said Buckley. “But it’s not something to be memorized: Cell function is a process, it’s a program.”

“We’ve been developing a lot of active-learning teaching strategies as we try to break students away from memorization,” said Angert.

Kerik Cox and students examine apples at Little Tree Orchards (photo: Edward Kitchen)

In Biology and Management of Plant Diseases (PLPPM 3010), active learning means getting students out of the lab and lecture hall to local farms. Rather than learn through lecture, students inspect squash, apples and other produce at an operating farm to see actual diseases, pests and problems and interact with growers.

“Our classes focus on plant disease, but what I wanted them to understand from their grower visit is the breadth of the integrated nature of the topic. For growers, diseases are a part of horticulture, plant breeding, entomology; it’s complex and multifaceted,” said Kerik Cox, associate professor in the Plant Pathology and Plant-Microbe Biology Section of SIPS, who co-teaches the course with support specialist Mary McKellar.

Plant science major Isabella Yannuzzi ’20 and others in the class visited the Silver Queen Farm in Trumansburg, New York. Ahead of the trip, students researched common local diseases. Face-to-face with the farmers, students asked about growing practices, the use of pesticides and crop rotation.

“I appreciate it when you get to go out and they let you apply your knowledge yourself; it’s different than reproducing knowledge on a test,” said Yannuzzi. “You get to see the information you’re learning and you actually get to use it.”

Cox said this semester the same amount of lecture material is being presented, but activities have been restructured. Cox and McKellar have strategized ways to get students thinking and applying their knowledge by posing scenarios and real-world examples during class time once dedicated to lecture.

Even small changes in the classroom can have a big impact, Merkel said. Having students talk among themselves, adding polls and questions during lectures, and flipping the classroom – a method for delivering instructional content before class, and using the class time for more active learning – are some strategies faculty have implemented.

Mary McKellar assists with sample analysis (photo: Matt Hayes)

McKellar said incorporating more active learning in the classroom is helping students see the bigger picture and the “Why” of what they are learning.

“I think a lot of times students get hung up on the details and forget why they are learning the material,” she said. “It’s not just to memorize. Instead, students are learning the biology of these pathogens to better understand how to manage disease.”

The proposal submitted by Cox and McKellar emphasized that student evaluations had motivated the move toward more active learning.  Specifically, students expressed a desire for authentic fieldwork in observing and collecting plant diseases and more opportunities to understand how to apply disease management strategies using approaches that considered growers, crop production, pathogen biology, and the environment.

The complete list of SIPS courses receiving funding:

  • Integrating Active Learning to Promote Critical Thinking in the Nature of Plants (PLHRT 1115)
    • Instructor: Taryn Bauerle, associate professor in the Horticulture Section of SIPS
  • Engaged Teaching in Organismal Biology in Insect Biology (ENTOM 2120), Herpetology (BioEE4700) and Evolutionary Plant Morphology
    • Chelsea Specht, professor, Section of Plant Biology in SIPS
    • Patrick O’Grady, professor, Department of Entomology
    • Kelly Zamudio, professor, Department of Ecology and Evolutionary Biology.
  • Development and Implementation of a Problem Based Learning Project for Biology and Management of Plant Diseases (PLPPM 3010) (full proposal)
    • Kerik Cox, associate professor, Section of Plant Pathology and Plant-Microbe Biology in SIPS
    • Mary McKellar, teaching support specialist, SIPS
  • Introductory Microbiology Lecture (BioMi 2900)
    • Esther R. Angert, professor, Department of Microbiology
    • Daniel H. Buckley, professor, SIPS and Department of Microbiology
PLPPM 3010 students visiting Hosmer Vineyards (photo: Mary McKellar)

Recent publications from the SIPS community – October 11, 2018

Global Data Analysis Shows That Soil Nutrient Levels Dominate Foliar Nutrient Resorption Efficiency in Herbaceous Species.

Wang, Z., Fan, Z., Zhao, Q., Wang, M., Ran, J., Huang, H., and Niklas, K.J. 2018.  Frontiers in Plant Science 9.

Downy Mildew: A Serious Disease Threat to Rose Health Worldwide.

Salgado-Salazar, C., Shiskoff, N., Daughtrey, M., Palmer, C.L., and Crouch, J.A. 2018. Plant Disease 102:1873-1882.

First Report of Sudden Death Syndrome of Soybean Caused by Fusarium virguliforme in New York.

Cummings, J.A., Myers, K.L., and Bergstrom, G.C. 2018. Plant Disease 102:2036-2036.

Poor Control of Cucurbit Powdery Mildew Associated with First Detection of Resistance to Cyflufenamid in the Causal Agent, Podosphaera xanthii, in the United States.

McGrath, M.T., and Sexton, Z.F. 2018 Plant Health Progress:222-223.

Biomass production of herbaceous energy crops in the United States: field trial results and yield potential maps from the multiyear regional feedstock partnership.

Lee, D.K., Aberle, E., Anderson, E.K., Anderson, W., Baldwin, B.S., Baltensperger, D., Barrett, M., Blumenthal, J., Bonos, S., Bouton, J., Bransby, D.I., Brummer, C., Burks, P.S., Chen, C., Daly, C., Egenolf, J., Farris, R.L., Fike, J.H., Gaussoin, R., Gill, J.R., Gravois, K., Halbleib, M.D., Hale, A., Hanna, W., Harmoney, K., Heaton, E.A., Heiniger, R.W., Hoffman, L., Hong, C.O., Kakani, G., Kallenbach, R., Macoon, B., Medley, J.C., Missaoui, A., Mitchell, R., Moore, K.J., Morrison, J.I., Odvody, G.N., Richwine, J.D., Ogoshi, R., Parrish, J.R., Quinn, L., Richard, E., Rooney, W.L., Rushing, J.B., Schnell, R., Sousek, M., Staggenborg, S.A., Tew, T., Uehara, G., Viands, D.R., Voigt, T., Williams, D., Williams, L., Wilson, L.T., Wycislo, A., Yang, Y., and Owens, V. 2018. GCB Bioenergy 10:698-716.

Emerging Pleiotropic Mechanisms Underlying Aluminum Resistance and Phosphorus Acquisition on Acidic Soils.

Magalhaes, J.V., Piñeros, M.A., Maciel, L.S., and Kochian, L.V. 2018. Frontiers in Plant Science 9.

Land restoration in food security programmes: synergies with climate change mitigation.

Woolf, D., Solomon, D., and Lehmann, J. 2018. Climate Policy 18:1260-1270.

Cornell-TUAT Workshop focuses on Science and Sustainability Communication

-Magdalen Lindeberg

Graduate students and postdocs from Cornell University and Tokyo University of Agriculture and Technology (TUAT) participated in a joint workshop October 5 – 9, directed at broadening understanding of sustainability related initiatives in Ithaca and Japan. Jointly coordinated by graduate students from Cornell and TUAT, ten participants from TUAT and seven Cornell grad students and postdocs toured the Ithaca and Agritech campuses, visited alternative energy facilities, and attended talks on science communication by SIPS Communications Director Magdalen Lindeberg and Bruce Lewenstein, Professor of Science Communication in the Department of Science & Technology Studies.  The workshop culminated with participants giving fun and engaging presentations on solutions to climate change and other environmental challenges at a special Science Cabaret event. The 2018 workshop was coordinated by three graduate students from TUAT and and four from Cornell including SIPS grad students Penelope Lindsay and Hannah Thomas and postdoc Phil Conklin. Conklin is supported by NSF Postdoctoral Fellowship #1612235, for which public outreach is a important component. Cornell participants were drawn from SIPS, Computer Science, Engineering, and Materials Science.

Cornell has been hosting workshops in collaboration with Tokyo University of Agriculture and Technology since 2013 with the goal of broadening students’ cultural and academic horizons and with a particular focus on the intersection of the environment and technology. Cornell workshop participants have the opportunity to visit Tokyo as part of the exchange.  Gillian Turgeon, professor in the Plant Pathology and Plant-Microbe Biology Section, Professor and Vice Dean Tsutomu Arie from TUAT, and Associate Professor Yoko Ichijo have been instrumental in the creation and continued funding of the TUAT-Cornell exchange.

Cornell and TUAT workshop participants
Workshop participants making presentations at Ithaca’s Science Cabaret

Zaitlin honored in “Advanced in Virus Research”

-Magdalen Lindeberg

Zaitlin at the CSIRO lab in Australia in 1956

A special volume of Advances in Virus Research is dedicated to the memory of Milton Zaitlin (1927–2016), professor and virologist in Plant Pathology and Plant-Microbe Biology.  Zaitlin worked in plant virology for 50 years, was one of the founding members of the American Society for Virology (ASV), and organized the 1st meeting of the ASV at Cornell in 1982. His achievements were recognized by AAAS to which he was elected as a Fellow in 1969. He was made a Fellow of APS in 1978 and received the APS Award of Distinction in 2006.

The special volume includes a retrospective on his career, achievements, and legacy written by Peter Palukaitis of Seoul Women’s University and former faculty member in Plant Pathology and Plant Microbe Biology, and Marilyn Roosinck of Penn State University.

Seven chapters in the special volume are written by students, post-docs, and visiting scientists who worked with Zaitlin and went on to manage research programs focused on a variety of plant viruses. Among those still actively conducting research are Ervin Balázs, John Carr, Ralf Dietzgen, Fernando García-Arenal, George Lomonossoff, and Bill Wintermantel, in addition to Andy Jackson who has recently retired.

Zaitlin playing poker in 2016

Read more:

Chapter One – In Memoriam: The Career, Achievements, and Legacy of Milton Zaitlin.

Palukaitis, P., and Roossinck, M.J. 2018. Pages 1-21 in: Advances in Virus Research, P. Palukaitis and M.J. Roossinck, eds. Academic Press.

Complete volume

Milton Zaitlin, pioneer of plant virology, dies at 89 (Cornell Chronicle, March 2017)

Plant Sciences Majors showcase ePortfolios

-Magdalen Lindeberg

Students majoring in Plant Sciences and enrolled in PLSCI 1110 presented their ePortfolios on October 4 at an afternoon open house in 404 Plant Science. PLSCI 1110 “Collaboration, Leadership, and Career Skills in the Plant Sciences”, taught by Marvin Pritts and Leah Cook, provides students with opportunities to meet other students and faculty associated with the Plant Sciences Major; develop collaboration, leadership, and career skills in the discipline; and make connections with the world beyond the campus.  Thirty-eight students are currently enrolled in the class.

Plant Sciences Majors Mable Orhiekhoe, Ally Hermanson, and Ileana Katzman

Students at the Thursday event come to the Plant Sciences Major from diverse backgrounds and shared their excitement at being in a place where people are so passionate about plants. Alice Gevorgyan was one of many students interested in plant breeding and plant genetic modification. A native of San Carlos CA, Gevorgyan learned about Cornell after hearing an interview with Susan McCouch on the “Talking Biotech” podcast. Several also expressed interest in plants and human health including Josh Rauch, a sophomore who recently changed his major to Plant Sciences. Other transfers include Ally Hermanson, a San Diego native who transferred to Cornell from Virginia Tech, and James Cagle, a transfer student from Finger Lakes Community College. Cagle decided to pursue college after several years of farming where he was inspired by his interactions with extension educators.  He is interested in plant pathology, breeding, and physiology. Many of the students expressed enthusiasm about the research opportunities available to them at Cornell. Cagle is working in the programs of Matt Ryan and Rebecca Nelson. Danielle Sonnenleiter, a freshman interested in plant genetic modification, is working in the Plant Transformation Facility.

ePortfolios function as an online curriculum vitae, capturing student training, experiences and interests using a variety of media. Students in the Plant Science Major are required to add to their ePortfolios throughout their course of study, including information on courses, papers, and projects, a reflection on an out-of-class experience, seminar summaries, and research experience where relevant. Each student’s final portfolio is presented to their faculty advisor to show that learning objectives have been achieved.

According to Cook, one of the main goals of PPLSCI 1110 is to build a sense of community among the students before they move through the core curriculum together. Students reflected that the process of creating ePortfolios was useful for reflecting on what they had done and identifying areas in need of attention.

James Cagle talks with SIPS faculty member Kathie Hodge
Alice Gevorgyan and Sonia Lulla share their ePortfolios with SIPS faculty member Klaas van Wijk

Recent publications from the SIPS community – October 4, 2018

Towards integrative taxonomy in Neotropical botany: disentangling the Pagamea guianensis species complex (Rubiaceae).

Prata, E.M.B., Sass, C., Rodrigues, D.P., Domingos, F.M.C.B., Specht, C.D., Damasco, G., Ribas, C.C., Fine, P.V.A., and Vicentini, A. 2018. Botanical Journal of the Linnean Society 188:213-231.

Eighty years of maize breeding alters plant nitrogen acquisition but not rhizosphere bacterial community composition.

Emmett, B.D., Buckley, D.H., Smith, M.E., and Drinkwater, L.E. 2018.  Plant and Soil 431:53-69.

Flurprimidol and Paclobutrazol Substrate Drenches on Potted Pineapple Lily.

Lyons, S.D., Miller, W.B., Wien, H.C., and Mattson, N.S. 2018.  HortTechnology 28:445-449.

Bulb Circumference Influences Growth and Crop Quality in Pineapple Lily

Lyons, S.D., Miller, W.B., Wien, H.C., and Mattson, N.S. 2018. HortTechnology 28:450-452.

Assessment and Valuation of the Northern Grapes Project Webinar Series.

Particka, C.A., Stafne, E.T., and Martinson, T.E. 2018. HortTechnology 28:524-528.

Characterisation and mefenoxam sensitivity of Phytophthora spp. from ornamental plants in Italian nurseries.

AIELLO, D., HANSEN, Z.R., SMART, C.D., POLIZZI, G., and GUARNACCIA, V. 2018. Phytopathologia Mediterranea 57:2(245-256)

Free amino acid composition of apple juices with potential for cider making as determined by UPLC-PDA

Ma, S., Neilson, A.P., Lahne, J., Peck, G.M., O’Keefe, S.F., and Stewart, A.C. Journal of the Institute of Brewing 0.

High levels of abiotic noise in volatile organic compounds released by a desert perennial: implications for the evolution and ecology of airborne chemical communication.

Wilson, J.K., Woods, H.A., and Kessler, A. 2018. Oecologia 188:367-379.

Disruption of Chloroplast Function Through Downregulation of Phytoene Desaturase Enhances the Systemic Accumulation of an Aphid-Borne, Phloem-Restricted Virus.

DeBlasio, S.L., Rebelo, A.R., Parks, K., Gray, S.M., and Heck, M.C. 2018.  Molecular Plant-Microbe Interactions 31:1095-1110.

Blumenols as shoot markers of root symbiosis with arbuscular mycorrhizal fungi.

Wang, M., Schäfer, M., Li, D., Halitschke, R., Dong, C., McGale, E., Paetz, C., Song, Y., Li, S., Dong, J., Heiling, S., Groten, K., Franken, P., Bitterlich, M., Harrison, M.J., Paszkowski, U., and Baldwin, I.T. 2018. eLife 7:e37093.

Maintenance of grafting-induced epigenetic variations in the asexual progeny of Brassica oleracea and B. juncea chimera.

Yu, N., Cao, L., Yuan, L., Zhi, X., Chen, Y., Gan, S., and Chen, L. 2018.  The Plant Journal 96:22-38.

Acetaldehyde and Ethanol Metabolism during Conditioning and Air Storage of ‘Honeycrisp’ Apples.

Al Shoffe, Y., Shah, A.S., Nock, J.F., and Watkins, C.B. 2018.  HortScience 53:1347-1351.

Rapid improvement of domestication traits in an orphan crop by genome editing.

Lemmon, Z.H., Reem, N.T., Dalrymple, J., Soyk, S., Swartwood, K.E., Rodriguez-Leal, D., Van Eck, J., and Lippman, Z.B. 2018. Nature Plants 4:766-770.

Order-level fern plastome phylogenomics: new insights from Hymenophyllales

Kuo, L.-Y., Qi, X., Ma, H., and Li, F.-W. 2018. American Journal of Botany 105:1545-1555.

Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes

Zhou, C., Duarte, T., Silvestre, R., Rossel, G., Mwanga, R., Khan, A., George, A., Fei, Z., Yencho, G., Ellis, D., and Coin, L. 2018.  [version 1; referees: 1 approved with reservations]. Gates Open Research 2.

October update from SIPS director Chris Smart

Dear SIPS Community

I hope you are all healthy and happy! Unfortunately it seems that a rather severe cold has hit many folks at Cornell.

SIPS External Review April 7-10, 2019 will be the dates for our first ever SIPS external review. A committee of five faculty from across the country will visit SIPS and will meet with many members of our community. The goal is to get feedback on how we are coming together as a school, and identify areas where we can make improvements. The committee will visit both the Ithaca and Geneva campuses, and we will have opportunities for folks at LIHREC, HVRL, and CLEREL to join in via zoom. I am working with the executive committee on a self-study that will be distributed to the external review committee before they arrive.

Faculty search updates:

  • Assistant Professor: Grape Disease Ecology & Epidemiology (Geneva Campus). The position announcement is below, and review of applications will begin October 15, 2018. Please do forward this link to everyone that might be interested.
  • Assistant/Associate Professor: Breeding for Sustainable Forage Cropping Systems. The search committee has been formed and the position description is being finalized.
  • Assistant/Associate Professor: Digital Agriculture: Agronomy. The search committee has been formed and the position description is being finalized.
  • Assistant/Associate Professor: Specialty Crop Systems. The search committee has been formed and the position description is being finalized.
  • NEW NEWS! Assistant/Associate Professor of Plant-Microbe Biology (from the last academic year). Negotiations with Clare Casteel are extremely close to being complete, and I am quite certain that Clare will join SIPS in July 2019

Congratulations to the following people who were recognized with a SIPS Kudos in the last month! Thanks for your effort and passion in support of SIPS

  • Bridget Cristelli
  • Brian Flannigan

PLEASE remember to recognize people in our SIPS community that have gone above and beyond. All you have to do is complete the brief form here:

All the best,



Recent publications from the SIPS community – September 27, 2018

Derivation of regional risk screening values and intervention values for cadmium-contaminated agricultural land in the Guizhou Plateau.

Zhang, S., Song, J., Cheng, Y., and McBride, M.B. 2018.  Land Degradation & Development 29:2366-2377.

Carbon Footprint of a University Compost Facility: Case Study of Cornell Farm Services.

Schwarz, M., and Bonhotal, J. 2018. Compost Science & Utilization 26:128-143.

Weed Seedbank and Weed Biomass Dynamics in a Long-Term Organic Vegetable Cropping Systems Experiment.

Mohler, C.L., Caldwell, B.A., Marschner, C.A., Cordeau, S., Maqsood, Q., Ryan, M.R., and DiTommaso, A. 2018.  Weed Science 66:611-626.

Climate Change and Its Consequences for Cultural and Language Endangerment

Rehg, K.L., Campbell, L., and Dunn, C.P. (2018). In The Oxford Handbook of Endangered Languages. : Oxford University Press, 2018-08-21.

Preharvest aminoethoxyvinylglycine (AVG) and 1-methylcyclopropene (1-MCP) effects on ethylene and starch concentrations of ‘Empire’ and ‘McIntosh’ apples.

Doerflinger, F.C., Nock, J.F., Miller, W.B., and Watkins, C.B. 2019.  Scientia Horticulturae 244:134-140.

In Memoriam: The Career, Achievements, and Legacy of Milton Zaitlin

Palukaitis, P., and Roossinck, M.J. 2018. Chapter One. Pages 1-21 in: Advances in Virus Research, P. Palukaitis and M.J. Roossinck, eds. Academic Press.

Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening

Lü, P., Yu, S., Zhu, N., Chen, Y.-R., Zhou, B., Pan, Y., Tzeng, D., Fabi, J.P., Argyris, J., Garcia-Mas, J., Ye, N., Zhang, J., Grierson, D., Xiang, J., Fei, Z., Giovannoni, J., and Zhong, S. 2018. Nature Plants.

DiTommaso speaks on weeds and climate to the Australasian Weed Congress

-Magdalen Lindeberg

How is climate change affecting agriculture? How can we prepare ourselves for expected challenges in weed management?  These are some of the questions addressed by Toni DiTommaso, in his keynote address to the 2018 Australasian Weed Congress, “Climate Change and Weed Migration: What do we know and what next?”
DiTommaso provided additional comments in an interview with WeedSmart, an Australian podcast fosusing on weed control and emerging weed issues. Australia has experienced steady reductions in rainfall over the past 20 years while growers in New York are seeing an increase in extreme climate events such as flooding and unexpected freezes.  Given that these trends are predicted to continue, together with warming temperatures, DiTommaso emphasized the importance of diversifying cropping systems and developing more climate resilient varieties. New weed challenges are also expected to emerge, and growers are urged to follow updated management recommendations and report changes they observe in weed species.  Some research also suggests that changing CO2 levels may impact herbicide efficacy.

DiTommaso, professor and chair of the SIPS Soil and Crop Sciences Section, researches environmental effects on weed species and strategies for weed control through manipulation of biotic and abiotic factors.

The Australasian Weed Congress is a biennial conference and carries on a long tradition of bringing the weed management community together to discuss new developments and share information about cutting-edge and best weed management practices. The conference attracts more than 250 delegates from across Australasia and globally. Other speakers discussed topics including research priorities for weed suppression in Australia and developments in robotic weed sensing.

The complete WeedSmart podcast can be found at: The interview with DiTommaso begins at the 5 minutes mark.

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