The Hub - Boyce Thompson Institute · Mech Shop Staff Kudos 2 Departures 3 Safety Updates 3 Booking BTI Rooms & Calendar Info 3 PGS Updates 4 Employee Anniver-saries 4 BTI Paybands,

State of the Institute by David Stern

March 2013 Volume 15, Issue 1 The Hub

1

I want to start by giving a warm wel‐come to Michelle Cilia’s laboratory, now opera ng on the first floor. BTI’s mission is, above all, discovery, and when by bringing a new scien st on board, we generate new research opportuni es and integrate new perspec ves. Michelle’s BTI appointment would not have been possible without close collabora on between USDA‐ARS, Cornell, and BTI, underscoring the im‐portance of our affilia ons and rela on‐ships with our neighbors.

2013, so far, has brought a mixed bag of economic news of direct relevance to BTI. On the one hand, the stock market has reached new highs, which is likely correlat‐ed with healthy increases in BTI’s endow‐ment – although we must await quarterly reports before being certain. Be er eco‐nomic health in the U.S. is also good for BTI in the sense that it should generally create more and be er career opportuni es, which will help those transi oning out of the ins tute. On the other hand, the aus‐terity mindset in Washington DC, most re‐cently exhibited as “sequestra on,” has put a new and unwelcome squeeze on research funding. While the short‐term impact on BTI funding is likely to be rela vely small, reduced funding to the agencies can only mean lower success rates in the future. But with Washington lurching from one crisis to another, we should not be surprised if se‐questra on is superseded by another budg‐et deal or deals, that paint a different fate for research funding. In a posi ve sense, research and development, along with workforce training, tend to play well in both Republican and Democra c circles.

Early in 2013, I convened a Plant Sci‐ence Research Summit at the Howard Hughes Medical Ins tute in Bethesda, MD, on behalf of ASPB. Along with co‐organizers Sally Mackenzie (Univ. Nebraska) and Kathy Munkvold (ASPB Public Affairs Manager and former BTI postdoc), and facilitator Sue

New Arrivals 2

Grants & Awards 2

Business Office Reno-vations

2

Mech Shop Staff Kudos 2

Departures 3

Safety Updates 3

Booking BTI Rooms & Calendar Info

3

PGS Updates 4

Employee Anniver-saries

4

BTI Paybands, Com-pensation Philosophy

5

Greenhouse Update 5

Building Info 4

Education & Outreach 6

IT Support Updates 6

PCIC Update 7

Congrats Josh Judkins 7

Japanese Food Innova-tion Workshop 2012

8

BTI Mission: To advance and com-municate scientific knowledge in plant bi-ology to improve agri-culture, protect the en-vironment and enhance human health.

In This Issue... Hartman (who helped with BTI’s strategic plan‐ning), 15 scien sts represen ng academia, in‐dustry and private founda ons spent a day and a half discussing the most promising future direc ons for plant science research. A sum‐mary of the proceedings, a list of par cipants and a photo can be found here.

While the Summit report is s ll being final‐ized, my preliminary discussions with officials from NSF, DOE and USDA show considerable enthusiasm for the ini a ves represen ng the group’s consensus. The report envisions a data‐rich era that will enormously deepen our knowledge of how plants func on, and how they interact with their bio c and abio c envi‐ronments. We also believe that researchers will increasingly tap into the spectacular array of plant diversity, to iden fy what we are calling “adaptomes” – gene c packets that underpin the unique biology and chemistry of plants with a wide array of lifestyles. Combining knowledge of plant func on – from genome to organ – with iden fica on of unique adap ve features, promises to make possible previously unimagi‐nable plant modifica ons through breeding or even synthe c biology. The Summit report also discusses career paths, and proposes profound changes in how we approach graduate student training.

One of the overarching themes of the Sum‐mit report is interdisciplinarity. Just within BTI, we have experts in proteomics, synthe c chem‐istry, plant gene cs and epigene cs, cell and organellar biology, computa onal biology, and bio c interac ons. It is at the interfaces of these areas that many novel scien fic advances are achieved. Just as one example, my own laboratory is collabora ng with engineers that create microfluidic devices, in order to speed up screening for algae that produce unique hydrocarbons. Indeed, while the computa onal‐experimental interface is familiar to many of us, joining with engineers, physicists, and struc‐tural biologists, are just a few of the other op‐portuni es for plant biologists to broaden their horizons.


2

Kyeiwaa Amofa-Boachi, Intern, Mueller Lab

Mariam Betsiashvili, Visit-ing Scholar, Jander Lab

Melike Bor, Fullbright Scholar, Jander Lab

Qinghe Cao, Visiting Scholar, Fei Lab

Cynthia Du, Research As-sistant, Van Eck Lab

Chen Jiao, Visiting Scholar, Fei Lab

Jeong Seob Kim, Visiting Scholar, Fei Lab

Jin Seon Kim, Research Support Worker, Catala Lab

Radmila Kovac, Waterloo Intern, Stern Lab

Jie Yuen Ong, Intern, Mueller Lab

Michelle Sweeney, Re-search Specialist, Cilia Lab

Weihua Wang, Research Assistant, Van Eck Lab

Jay Worley, Postdoc, Mar-tin Lab

Yi Zheng, Postdoctoral Associate, Fei Lab

Coupling live cell imaging and mass spec‐trometry technologies to probe the dy‐namic virus‐plant host interface Michelle Cilia AIPI/BTI 1/1/13‐12/31/13 $35,175

Expanding the Medicago truncatula hap‐map as a platform for exploring the genet‐ics of legume symbioses Maria Harrison NSF $516,103

New Arrivals

Grants and Awards

New G

rants

Business Office Relocations and Renovations

The grants and accounts payable staff in the business office have temporarily relocated to the 4th floor due to renova ons taking place over the next few months. You will find: Mary Westlake and Shirley Geddes in Room 405. Contact both at 254‐1317. Sara Courson and Amy Yanosh in Room 413. Contact both at 254‐1212. All other business office and HR staff will remain in their current offices for the me being. For HR‐related business, please enter via the door off the main lobby. Jane, Pa and Sophia’s offices can be accessed via the 1st floor hallway door.

Mechanical Shop Staff Can Do It All

Amidst the many daily tasks performed by our Mechanical Shop staff, they were instrumental in moving the four Business Office staff to the 4th floor, making sure they had what they need‐ed to do their jobs during their temporary reloca on, AND dismantling the exis ng space in less than a day and a half! Many thanks to Dave and Charlie! They take care of so much that we take for granted.


Safety Updates

3

Muhammad Asif, Visiting Scholar, Klessig Lab

Ry Forseth, Graduate Stu-dent, Schroeder Lab

Ted Rozelsky, IT Support

Roshni Samarth, Visiting Scholar, Mueller Lab

Di Shen, Visiting Scholar , Fei Lab

Departures

Each day, every person going to work does not think "Today is the day I am going to have a big accident". It happens; 13 people die every day while at work. When people die in work‐related accidents, organiza ons will a empt to ins ll preventa ve programs to deter a future accident. If fatal accidents occur frequently, our government intervenes with laws and regula ons. Regu‐la ons surround seat belts, motorcycle helmets, car airbags, safety glasses and more recently, assault rifles. One may argue the pros and cons of regula ons, however, they exist because of the increased occurrences of accidents and fatali es. And, with government laws come s ff penal es (has anyone paid a speeding cket lately!). Laws and regula ons are designed to protect us, and the people around us. The government requires training for hazard communica on, laboratory safety, chemical waste disposal, etc. to help everyone understand the dangers they face at work. It is impera ve that chemicals are labeled properly. If you have not done so yet, please take the hazard communica on training. No one wants to be the subject to a he y fine. More importantly, we must prevent an accident from happening.

Please use your Cornell exchange account to book BTI mee ng rooms and equip-ment. Instruc ons for using the web‐based version “OWA” are available at: h p://b .cornell.edu/instruc ons: scroll down to “How to reserve mee ng space and public equip‐ment at BTI”. You can also use the Outlook applica on that is included in MS Office for mac or pc. For assistance, contact b [email protected].

Adding mee ng to your calendar from a received email message: MAC Office 2011: With the message open, select the “Mee ng” bu on in the Outlook toolbar. A new mee ng window should pop up with the details from the email (including the email’s addressees listed as the mee ng invitees) PC Office 2010: View messages in your Inbox, right click on the desired mee ng, select Move To —‐ Calendar. Enter date, me, etc. Save. A link to the email message will appear in the main windows. PC

Sending mee ng invita on as an email a achment: MAC Office 2011: From the calendar, File Menu, Create new email. Click and drag the event from the calendar into a achment sec on of message and it will ap‐pear as an .ics a achment. OR From the calendar item, drag the event to your desktop and it will create a .ics file Create a new email message and a ach the file. PC Office 2010: With the mee ng open, choose File — Save As. Choose the loca on to save the mee ng file (.i.e., Desktop). Mee ng is saved as an .ics file. Create the email message and a ach this .ics file to the email message and send. OR From the calendar item, drag the event to your desktop and it will create a .ics file

Booking BTI Rooms and Various Calendar Information

PGS Updates


4

January:

Joan Curtiss, Chief Operat-ing Officer ................ 15 Yrs

Dierdra Daniels, Research Assistant Harrison Lab

..................................... 2 Yrs

Paul Debbie, Intellectual Property Manager ....13 Yrs

Lesa Gold, Payroll & Bene-fits Specialist, Human Re-sources ........................ 5 Yrs

Sergey Ivanov, Postdoctoral Associate, Harrison Lab

....................................... 1 Yr

Shalina Labarr, Greenhouse Helper ......................... 3 Yrs

Lyza Maron, Research Asso-ciate, Kochian Lab ..... 6 Yrs

Katherine Parks, Research Support Worker, Martin Lab ................................. 1 Yr

Charlie Paucke, Building Mechanic .................... 7 Yrs

Marina Pombo, Postdoctoral Associate, Martin Lab

....................................... 1 Yr

David Stern, President ..........

................................ 24 Years

Xia Xu, Research Specialist, Apel Lab ..................... 2 Yrs

Yimin Xu, Research Special-ist, Giovannoni Lab ..... 1 Yr

2013 Dis nguished Lecturer: Dr. Michael Gray from Dalhousie University in Halifax, Nova Sco a, will be visi ng BTI April 2‐3, 2013. He will give two seminars, the first en tled “Mitochondrial Evolu on: Genome vs. Prote-ome” on April 2nd at 4 pm in the BTI auditorium, and the second en tled “Spectacular and Bi-zarre: RNA Edi ng and Its Evolu on” on April 3rd at 10 am in the BTI auditorium. Dr. Gray’s research is focused around the structure, func on and evolu on of mitochondria and ribo‐somes in pro sts. Currently, he is also involved in the analysis and annota on of genome data from several pro sts. To learn more about Dr. Gray’s research, please visit his website: h p://www.biochem.dal.ca/faculty/facultypages/gray/. Also, if you are interested in mee ng with Dr. Gray during his visit, please contact Benoit Castandet ([email protected]). PGS Fest Seminars: Dr. Susan Brown will be the next PGS Fest speaker on Thursday April 18th at 4 pm in the BTI auditorium, followed by a happy hour in the atrium. Dr. Brown is a professor in Cornell’s De‐partment of Agriculture and Life Sciences and Department of Plant Breeding and Gene cs. Her research is focused on the use both tradi onal breeding and transgene technology to develop new apple varie es, furthering our knowledge of the gene cs of key traits in apples and iden ‐fying molecular markers for important characteris cs for use in marker‐assisted breeding (MAB). For more informa on about Dr. Brown’s research, please visit her website: h p://hort.cals.cornell.edu/cals/hort/people/faculty.cfm?netId=skb3, and for any ques ons regarding her seminar contact Nigel Gapper ([email protected]). PGS Bioinforma cs Course: This course will meet every Tuesday from March 19th to May 7th from 1-2 pm in the BTI atri-um. Topics covered include: web tools and introduc on to linux, RNA‐seq analysis (running assembly programs and analysis), R‐programming with a focus on RNA‐seq analysis and basic graphing, and basic scrip ng in linux and understanding exis ng Perl scripts. Pre‐registra on is required, and registra on is now full. If you have any ques ons please contact Noe Fernandez ([email protected]). Journal Club: The next journal club will be presented by Natalie Henkhaus on April 11th at 4 pm in room 215. The PGS journal club con nues approximately once per month throughout the year. If you would like to present a recent or historical ar cle, please contact Vered Tzin ([email protected]) or Benoit Castandet ([email protected]).

Employee Anniversaries ...

Building Information:

A er hours access: Remember, you need your CU ID card to access BTI during non‐business hours. If you experi‐ence problems with a door a er hours, please no fy b [email protected] so any problems can be addressed. Tape on walls and doors: Please use the special “WallSaver” tape when pos ng flyers or no ces on any BTI wall or door. Order from Staples on a purchase order: h p://www.staples.com/3M‐Wallsaver‐Removable‐Poster‐Tape/product_916223


Greenhouse and Growth Chamber News

5


Did you know:

The greenhouse staff water over 14,500 square feet of greenhouses and chambers up to four mes a day?

On a weekend or holiday, this takes one person a full 8 hours?

The greenhouse staff rou nely care for thousands of plants per day?

There is a greenhouse staff member here 365 days a year, including holidays, to make sure plants are cared for?

We have very well trained staff? The greenhouse staff are all trained in Integrated Pest Management and Best Management Prac ces for Greenhouses?

This includes areas such as pest and pathogen ID, pes cide and fer lizer storage and use, nutrient management, pest control, weed control, and new greenhouse construc‐on.

The use of integrated pest management reduces the need for the applica on of hazard‐ous pes cides and allows for healthier plants for research use?

The next time you log in to mypaychex, be sure to take a look at the 2013 paybands, compen-sation philosophy and postdoc salary scale documents. After logging in, select Human Re-sources On-Line and Company Documents.

BTI Paybands and Compensation Philosophy

February:

Patti FitzPatrick, Controller .................................. 2 Yrs

Jerrie Haines, Greenhouse Assistant .................... 1 Yr

Maria Harrison, Professor

................................ 10 Yrs

George Hoffman, Stockroom Clerk ...................... 13 Yrs

Veronique Levesque-Tremblay, Research Assis-tant, Harrison Lab .... 1 Yr

Angella Macias, Research Support Worker, Martin Lab ............................. 1 Yr

Patricia Manosalva, Research Associate, Klessig Lab ....

.................................. 6 Yrs

Linyong Mao, Postdoctoral Associate, Fei Lab

.................................. 2 Yrs

December 2012 Volume 15, Issue 1 The Hub

6

March:

Hyong Woo Choi, Postdoc-toral Associate, Klessig Lab ......................... 2 Yrs

Fabiana Csukasi Cabrera, Postdoctoral Associate, Catala Lab ............. 2 Yrs

Jeremy Edwards, Research Associate, Mueller Lab

.................................. 1 Yr

Dezi Elzinga, Graduate Student, Jander Lab ......

.................................. 4 Yr

Daniela Floss, Postdoctoral Associate, Harrison Lab .................................. 2 Yr

Shih-Chi Hsu, Postdoctor-al Associate, Stern Lab .

.................................. 2 Yr

Kate Krupnik, Lab Services Assistant ................ 9 Yrs

Jianyong Li, Postdoctoral Associate, Kochian Lab

................................ 2 Yrs

Bridget Rigas Garzon, Di-rector of Development and External Relations .

.................................. 1 Yr

Miaoying Tian, Senior Research Associate, Klessig Lab ......................... 8 Years

Education and Outreach News

Each summer the BTI Educa on Outreach Program offers professional development opportu‐ni es for teachers. One goal of the program is to provide plant science lab ac vi es that link to BTI research topics and connect students to real world research applica ons. Each lab ac‐vity goes through a series of test runs and reviews by teachers and outreach educators to

ensure that it will work well within the constraints of a classroom. Imagine the stock room is replaced with a grocery store, beakers turn into plas c cups, and there is no fume hood! When the ac vity is ready, it is introduced to summer professional development par cipants. Once put in the hands of the teachers, it has the poten al to reach an exponen al number of students. A key element to the success of the program is maintaining a strong rela onship with the teacher par cipants by offering them opportuni es to bring their students to BTI and bringing guest speakers to their classrooms throughout the year. So far in 2013, we are very thankful for the help from our volunteers who assisted in a school visit and field trips to BTI! Thank you to those who have volunteered with outreach this winter!

Amber Ho o, TC3 Bio Class

Natalie Henkhaus, Expand Your Horizons

Coralie Salesse-Smith, Erika Hughes and Tom Fisher-York, Cascadilla School Science Fair

Joshua Judkins, Gary Horvath, Fillmore Central School field trip to BTI

Joyce Van Eck, Cascadilla School Field trip to BTI


IT Support Updates

Internet Connec ons at BTI Network connec ons within BTI are available via Ethernet (cable from a wall port) or Wireless (RedRover). BTI’s IT Department manages Ethernet access and must assign a proper IP ad‐dress and verify that your computer meets basic security criteria. No device should join the BTI network without appropriate review. Confiden al Informa on on Public Computers When using the public scanners in the Resource Center, please be sure to remove any image files created. Personal, confiden al informa on is frequently found when regular mainte‐nance is performed. Scanning Images and Documents Several scanners are available for public use at BTI, including the Epson Perfec on V750 (higher end scanner), Epson Perfec on 2480 Photo flatbed and the Snap Scan device; all in the Resource Center. You can also scan documents at the 1st floor copier. Scans can be emailed to you or scanned to a usb s ck.


Plant Cell Imaging Center Update by Mamta Srivastava

7

Josh Judkins, Schroeder Lab, who recently accepted a chemical biology summer internship at Pfizer Neuro-science in Cambridge, Mass.

A er the first successful year of using the Hybrid Detector (HyD) for SP5 confocal, we have installed another HyD replacing PMT4. Old PMT2 and PMT4 are now HyD detectors. Now Confocal SP5 can be used to perform 2 color simultaneous or sequen al data acquisi on in HyD mode. Some Tips in Confocal Imaging: Motorized Stage Applica ons in Confocal

BTI Core Values

Integrity

Mutual Respect

Excellence

Collaboration

Innovation

Congrats to...

Tile Scan Applica on: Proper set up of the Tile func on enables you to scan mul ple par al images from a speci‐men and s tch them together to form a com‐plete image. By extension, this feature makes possible to scan a much larger field of view than a high magnifica on objec ve alone would be able to give you, and s ll keeps the high resolu on of the objec ve. Tile scan calibra on is required in order to have all the images aligned in x and y. To avoid any gap and/or misalignment of the resul ng le, you must precisely adjust the le scan.

Mark & Find Applica on: This feature enables you to define mul ‐posi on experiments to observe a large number of cells within one experiment, saving valuable me. You can define the cur‐rent posi on of your sample and recall it later from a list, which also includes other previous‐ly stored posi ons. This enables you to quickly step through several posi ons to compare them, or to record mul ple me series in a pseudo parallel manner.

To schedule an appointment for training, or for ques ons about any applica on, please con‐tact Mamta Srivastava at [email protected] or call (607)254‐4436 between 9:00 AM and 1:00PM.


8

While touring the Instant Ramen Noodle Museum in Tokyo I learned the story of ‘Mr. Noodle.’ The instant ramen noodle was invented in 1958 by Momofuku An-do, a 48-year-old bankrupt businessman. Ando was inspired by the post-war food shortage in Japan and wanted to make a product that was tasty, inexpensive and non-perishable. After a year of experiment-ing with various noodle preservation methods, he discovered that deep-frying the noodles preserved them perfectly. He started the Nissin Com-pany to sell his ramen noo-dle soup which became a hit in Japan. The company went on to successfully market the Cup Noodle worldwide in 1971.

Reflections on the Japanese Food Innovation Workshop, 2012 ……………..Liz Brauer

This past summer was a memorable one for me. Not only did I a end a very interes ng MPMI conference in Kyoto, Japan, but prior to the conference I had the privilege of being invited to spend two weeks at the Tokyo University of Agriculture and Technology (TUAT). While I met many wonderful people and learned a lot about TUAT research, the highlight of my me there was when I had the opportunity to lead a workshop for Japanese high school students.

The workshop was hosted by TUAT’s Innova on Advancement Organiza on, that runs a workshop each year on different topics. The program is designed to engage high school stu‐dents in cri cal thinking and serve as a forum for the students to prac ce their leadership and presenta on skills. As the workshops are conducted in English, students have the added challenge of prac cing their English.

Together with TUAT staff and students, we decided this year’s topic should be “Japanese food innova on”. I was given a lot of autonomy in how to run the workshop and I led sever‐al discussions with 10 graduate students to design it. We decided to structure the workshop around challenging students to develop a Japanese food product that could be marketed to the rest of the world. This idea was par ally inspired by Japan’s famous export, Mr. Noodle. The product came to mind partly because it is a graduate student staple, and partly because we had recently toured the Instant Raman Noodle Museum (see sidebar).

Following two introductory seminars by Dr. Gillian Turgeon (Cornell Departments of Plant Pathology and Plant‐Microbe Biology) and Dr. Takao Nitani from TUAT, workshop par ci‐pants were divided into groups of five to brainstorm ideas. The students had to iden fy po‐ten al markets and come up with a final product proposal under the guidance of the TUAT graduate students. Each high school student had a role to play; two students presented their group’s idea, while three others gave feedback to other groups. All of the groups did a great job of developing both feasible and interes ng ideas. The organizers voted on their favorite product and the top group won a prize for their product, Daigakuimo, a Japanese snack made from sweet potato.

It was a successful workshop thanks to the hard work of the organizers, the graduate stu‐dents and the high school students themselves. Down the road, this approach could be an effec ve way for us to engage with poten al future graduate students.

The Story of Mr. Noodle