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Fangwei Gu

[Mary]
The US remains a major destination for plant scientists who wish to expand their horizons and improve their English language skills, but the path through the immigration system may seem daunting. Fangwei Gu is a PhD student at University of Michigan, Ann Arbor; I asked him to share his experiences of gaining admission to a US university. We are simultaneously publishing this article in Chinese (link).

[Fangwei]
How  many plant biologists that were not born in US do we have working in US labs? If you examine the list of speakers from the recent ASPB 2014 meeting you will see scientists originating from China, India, Japan, Korea, Germany and so on who are working in the US as PhD students and postdocs.

I am one of them. And while there are more opportunities for foreign scientists in the US compared to twenty years ago, one still needs to prepare for years in order to grab the opportunity. I started my plan in 2007 and got admitted as a graduate student in 2009. For an applicant whose native language is not English, a TOEFL (Test of English as a Foreign Language) test is required. Additionally, a GRE (Graduate Record Examinations) score is also necessary for the application. When I was applying, only two GRE test dates were available every year in China, as compared to thirty in 2014. Register early to be sure to get a place.Anonymous_globe_of_flags_1

While waiting for my test scores, I started my search online for programs. I knew I wanted to study plant development and I started with a ‘College Ranking’ list from US News. I checked the department of biology page from these universities and searched using ‘plant development’ as a key word. Then I wrote to the professors that I wanted to work with and asked whether they had any intention/funding to have a new graduate student. Finally I narrowed my list to seven US universities (although a list of ten to twenty is common).

After I had my list and scores I started the application procedure, which was partly done online. I submitted my CV, my personal statement to explain why I applied to this certain department, the contact info for three recommenders and my test scores. Then I sent my undergraduate transcripts, copy of my diploma and other required documents by mail.

These were merely the initial steps, the purpose of which was to win the opportunity to be considered for an interview. Unlike domestic students who can visit the campus for the interviews, most interviews for international applicants occur via Skype or telephone. I was fortunate to have my interview face to face with two professors in Beijing. They interviewed around 50 students from China, I and other five were admitted.

Admitted students can expect to receive the admission letter and I-20 (the immigration document for students) several weeks or months after the interview. Most foreign students need a F1 visa in order to enter the US. The immigration application process is less complicated than applying to a university, but it can still be painful. You can learn more about the immigration process here; SEVIS is the Student and Exchange Visitor Information System. One needs to fill in a DS-160 form online and contact the local US embassy or consulate to schedule an interview, during which the visa applicant will be asked the major and the future study plans. Since the F1 is a non-immigrant visa, the application could be denied if the applicant reveals any intention to stay in US after graduation. The length of the process to issue the visa varies; it took me 5 weeks to receive the visa.

The case for a post-doc is slightly different compared to a graduate student. They are recruited by PIs rather than departments. Therefore they don’t need to submit the application to the department (which means TOEFL and GRE tests are not required). In order to get the position, the applicant needs to directly contact the potential supervisor with the CV and research plan. A candidate will be interviewed through Skype or telephone (this is where the English ability being tested) before the supervisor sends out the offer letter. A post-doc needs a J1 VISA (see also http://en.wikipedia.org/wiki/J-1_visa) or a H1B VISA. More information about the two types of visa can be obtained from the National Postdocs Association.

And then congratulations! Welcome to America!

Other facts:

  1. The education/living fee for student is around $50,000 per year. If a student is coming to US without financial support from the university, he/she needs to provide the documents to prove he/she can afford the trip. A bank statement is typically required. (Meanwhile, the average family income in China in 2012 is $2,100).
  2. The fee for TOEFL, GRE, and visa application is about $100 – $150 for each.
  3. The application fee for international students can be higher compared to domestic students, at around $70 for each university. Also the application deadline may be earlier than for domestic students.

[Mary]
Fangwei Gu expects to complete his PhD studies in Erik Nielsen’s lab in 2015. In his spare time he writes for songshuhui.net, the most influential non-governmental organization for science communication to the public in China, and was recognized as one of the ‘Top 20 amazing writers’ from Guokr.com, which is a popular science site similar to Scientific American.

Have you travelled to the US to work or study? Do you have any tips for those who want to follow in your footsteps? Please share any suggestions below!

 

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作者:玛丽·威廉姆斯 (Mary Williams)和 顾方为 (Fangwei Gu)

This article is also posted in English (link).

[玛丽]

       对于那些想要开拓眼界,并提高自己英语水平的植物学家来说,美国依然是他们的一个主要目的地。但通过移民系统前往美国的道路却注定不会轻松。顾方为是美国密歇根大学的一名博士生,他愿意向我们分享被美国大学录取的经验。本篇日志将以中英文双语的形式发布 (link)。

[方为]

有多少在美国实验室中工作的植物学家出生在美国之外?如果你翻阅美国植物生物学家协会2014年年会的名册,你会发现许多来自中国,印度,日本,韩国,德国等国家的研究生和博士后。

 

我是他们中的一员。诚然与20多年前相比,来自海外的科学家有更多的机会前往美国,但我们依然需要花上几年的努力来抓住这样的机会。我从2007年开始准备出国留学,并在2009年获得了博士的录取通知书。对于那些母语并非英语的学生来说,他们必须参加托福 (TOEFL )考试。此外,为了满足申请的条件,他们还需要提供 GRE 的成绩单。在我申请的时候,中国大陆每年只有两次参加GRE考试的机会。这个数字在2014年已经提高到了30次,但为了确保考位,学生们依旧需要提早注册。Anonymous_globe_of_flags_1

 

在等待托福和GRE考试成绩时,我开始在网上寻找想要申请的研究生项目。我想要从事植物发育方向的研究,所以我翻出了美国新闻网的《大学排名》(http://colleges.usnews.rankingsandreviews.com/best-colleges/rankings/national-universities),依次打开这些大学的生物系页面,并用“植物发育”作为关键词进行搜索。我列出了那些我想要加入的课题组的名字,并向相关教授询问,他们是否有招收研究生的意愿与资金。最终我定下了我想要申请的7所大学(一般候选大学名单会在10-20不等)。

 

当我有了选校名单和考试成绩后,我就开始了正式的申请。部分的申请工作是在网上进行的。我需要上传我的简历,我的个人陈述(回答为什么选择这所学校之类的问题),我的三名推荐人的联系方式,以及托福和GRE的成绩。之后我需要将我的本科成绩单,学位证书的复印件以及其他必须的材料一起寄往这些大学。

 

但这些只是个开头。这一切努力的目的仅仅在于让你在众多申请者中脱颖而出,并获得一个面试的机会。在美国本土的学生能够亲自访问学校并参加面试,但对我们这些国际学生来说,面试则一般用电话或者Skype进行。我很幸运地能够在北京与两名教授进行面对面的面试。他们在中国一共面试了将近50名学生,只有我和其他的5名学生最终被录取。

 

被录取的学生将在面试的几周或者几个月后收到录取通知和I-20(给学生的移民材料)。对许多国际学生来说,为了进入美国,他们需要有F1类型的签证。获得签证的过程比申请学校要来得简单,但依旧非常麻烦。你能从SEVIS的网站上(Student and Exchange Visitor Information System)得到更多相关的信息。F1签证的申请者需要在线填写一份DS-160表,并联系当地的美国大使馆或领事馆来预约面签。在面签的过程中,面试官会询问申请者一系列关于专业与未来学习计划的问题。由于F1是非移民签证的一种,如果申请者流露出任何毕业后想要留在美国的意图,那么他/她的申请就有可能被拒绝。通过面试后,签证签发的时间可长可短,我当时等了5周。

 

博士后赴美的过程与研究生有着些许不同。他们直接受雇于实验室的负责人,而并非被院系录取。因此他们并不需要准备院系的申请材料,也无需参加托福和GRE考试。为了得到博士后的职位,申请者往往需要直接与潜在的导师联系,并附上自己的简历和研究计划。导师会通过电话或Skype与候选人们进行面试,而这也是测试申请者英语能力的场合。通过面试的申请者会收到聘书。为了进入并合法地留在美国工作,博士后需要J1(http://j1visa.state.gov/,或参阅 http://en.wikipedia.org/wiki/J-1_visa)或H1B类(http://en.wikipedia.org/wiki/H-1B_visa)签证。大家可以从全美博士后协会的网站上(http://www.nationalpostdoc.org/publications-5/toolkits/quick-guide-to-visas)得到更多关于这两种签证的信息。

 

如果你经历了以上的这些步骤,那么恭喜了,欢迎来到美国!

 

其他的事实:

  1. 一名学生每年的学费和生活费大约在5万美元左右。如果一名学生没有从大学处得到资助,那么他/她需要提供财产证明(一般是银行对帐单)来证实他/她能够承担这些费用。但我们也要知道,2012年中国家庭的平均年收入是2100美元(http://www.nytimes.com/2013/07/20/world/asia/survey-in-china-shows-wide-income-gap.html?_r=0)。

 

  1. 托福考试,GRE考试和签证申请的费用都在100-150美元不等。

 

  1. 国际学生的申请费(平均在70美金)往往比美国本土学生的申请费要贵,而申请的截止日期也更早。

 

[玛丽]

顾方为 目前在埃里克·尼尔森(Erik Nielsen)的课题组,预期在2015年获得博士学位。在工作之余,他也是中国最大的科学传播类非政府组织——科学松鼠会(http://songshuhui.net/)的成员,以作者的身份为之供稿。此外,他入选了果壳网(http://www.guokr.com/,一家类似于科学美国人的网站)的20名神奇作者名单,获得了“最玲珑剔透多面手奖”。

 

你也是从海外来到美国工作或者学习的吗?你对那些想要跟随你的脚步的晚辈们有着什么有用的建议?欢迎在本文下分享你的经历!

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NRC Publishes Review of AFRI Program

Dear US ASPB members:

A very important report, “Spurring Innovation in Food and Agriculture: A review of the USDA Agriculture and Food Research Initiative (AFRI) Program,” was recently published by the National Research Council (NRC) of the National Academy of Sciences. A large portion of the researchers in our community are, have been, or will be funded through AFRI. Because it is the principal funding agency supporting plant science research and training in the agricultural space, we have a vested interest in its continued growth and success.

NAS

 

 

In an effort to facilitate the improvement of AFRI and its ability to leverage cutting edge science to address societal needs with regard to the provision of food, fuel, and fiber, ASPB actively supported the NRC review of AFRI. Some of you may recall that we circulated a survey via the monthly Member Chatter to solicit your views and perspectives on the issues being considered by the NRC committee. The results of your feedback were then used to craft a presentation delivered by Peggy Lemaux, then serving as ASPB President, to the NRC committee. All of ASPB’s top concerns were addressed by this NRC report.

Briefly, some of the major issues articulated in ASPB’s comments that were addressed in the NRC review of the AFRI program were as follows:

  • Front and center in our remarks to the committee was the issue of the general lack of funding for research, especially plant research. In response, the NRC called for the increased “public investment in competitive agricultural R&D to ensure [the United States] continues its role of a global leader in the innovations and technologies that are needed to promote health and well-being and to feed growing worldwide populations sustainably.”
  • Second, we shared the ASPB community’s concern about the current generation of young scientists, especially assistant professors, who are in their first positions and need to launch their research programs in order secure tenure. The NRC concluded that “AFRI should carefully examine the causes of the decline in the numbers of applicants, awardees, and trainees and adjust its grant programs to ensure that future generations of young scientists are not lost inadvertently from food and agriculture R&D because of funding policies.”
  • A third area of concern was the unpredictable cycling of grant priorities. In response, the NRC report urges AFRI to 1) “develop a strategic plan that identifies priorities for its overall program goals…” and 2) “have a more consistent and predictable program portfolio and funding strategy to enable better planning by the food and agricultural research community.”

ASPB will continue to engage USDA around the concerns of our community and the recommended remedies proposed by the NRC. Further, we will use the report as an opportunity to advance the goals set forth by the “Plant Science Decadal Vision.” To learn more about the NRC review of the AFRI program, please click here to view the report prepared by Lewis-Burke Associates, ASPB’s government relations consultants, and click here to view the full report. As always, please feel free to share your comments and questions with ASPB’s director of legislative and public affairs, Tyrone Spady.

Sincerely,
Alan M. Jones, Ph.D.
President, American Society of Plant Biologists

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Charging ahead with plant nutrition

Teaching Tools in Plant Biology has released the first of a three-part series on the topic of Plant Nutrition, “Plant Nutrition 1: Membrane Transport and Energetics, K Nutrition and Na Toxicity”,  co-authored by Michael Blatt.

This lesson starts by describing the central role of membrane transport and energetics in plant nutrition. The proton-motive force needed for ions to be transported across membranes is generated by membrane-localized H+-ATPases and PPases, which can consume as much as a third of a cell’s metabolic energy.TTPB29Graphicsmall

The interplay between two similar but very different ions, K+ and Na+, is described to illustrate the connection between energetics and nutrition. Potassium is an essential nutrient and one of the elements most widely used in synthetic fertilizers to enhance yields, sodium is one of the elements that most limits plant growth, yet several transporters only poorly discriminate between them. Thus, in K-poor soils, plants are can be more susceptible to Na toxicity, whereas augmenting soils with K-containing soils can increase their tolerance. The genetics behind salinity tolerance has been studied intensively in close relatives of crop plants but also in extremely salt-tolerant halophytes, and the results of these studies are contributing to the development improved crop varieties.

In this lesson, the connection between ionic charge distribution across membranes and real-world food production challenges is made explicit; we hope you find it electrifying.

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Outreach is a Hybrid

What Transpires When Scientists Reach Out?

Broader Impacts and Community Service – compatible outreach options

Outreach matters. Good outreach advances science. Some folks conduct outreach through broader impact goals. Others get involved at the community level. What’s the difference? Where do you fit in?

Outreach-is-Hybrid

Broader Impacts Action Items:
1. Learn more about Broader Impacts from a recent summit here.
2. Share examples of successful plant biology broader impacts statements and reports. Send them to Katie@aspb.org to help populate an archive of quality sample statements and outcomes.

Community Service Action Items:
1. Nominate a US-based high school teacher or public librarian with whom you collaborate for free online access to ASPB’s journals.
2. Serve as a Science Fair judge or Career Day speaker.  Search here for a Career Day PPT & other resources to share.
3. Invite a local high school student into your lab for a month/semester/summer of hands-on experience and mentoring.

 

  Excellent input from Sarah Wyatt (Ohio University) aided in the creation of this post.

 

 

 


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Last but not least, as a very active member of the iConnect team, I went to the workshop regarding the funding opportunities available from three of the most important federal agencies in the United States: USDA (United States Department of Agriculture), DOE (Department of Energy) and NSF (National Science Foundation). It was very popular, as I could not find a place to sit at all. Well over 70 people attended! I am including a picture inside the room taken in a hurry, as the questions and answers were all so interesting I did not want to get distracted!

2014funders

As a Mexican early career faculty, currently sending proposals to different federal agencies in my country, I know how it feels to be in the ballgame. As my colleagues and collaborators in the U.S. have told me before, it was important to update my information on the state of funding in the United States, to know how I can help them, if it is the case. When I was a postdoc at Texas A & M University, economic crisis hit hard on our University system. It was difficult to see new and seasoned professors suffer a good deal of stress due to the lack of funding. Unfortunately the economy has improved but the amount of money destined to research has not increased. It is a bit depressing due to the great effort we invest preparing our proposals. It was the general feeling of many of the attendees to this workshop, I believe.

After listening the alarming numbers regarding population growth without control, I was wondering if a positive effect could be the increasing number of people dedicated to science. This is good news, right? But, what about lab space and funds? Well, I am an optimist and, as with many of my colleagues, a fighter. I think that these federal agencies are trying to help us but they have to support the best of the best, therefore the only thing we have to do is prepare our proposals until we reach excellence and keep trying until we get funded or drop dead!

The workshop was very complete as USDA‐NIFA, USDA‐ARS, DOE and NSF program staff discussed current research and education opportunities available in their agencies for Plant Biologists. Please visit each agency website to find which program fits better your interests and needs.

In addition, the speakers gave us useful advice on how to navigate the process. One key clue is to contact directly the program director and ask as many questions as might be needed. The process is very transparent as it is peer reviewed. However, the proposal to be successful has to pass several reviewing filters and be at the very top of the proposals to be recommended for funding. Nowadays we all are doing outstanding science and preparing our proposals as excellent as we can. As I said before, to be successful we will have to be the best of the best.

Below is the list of the staff members of each agency who presented a very complete view of the programs that they currently support.

Liang‐Shiou Lin, Shing Kwok and Pushpa Kathir, NIFA
Sharlene Weatherwax and Gail Mclean, DOE
Karen Cone and Diane Okumura, NSF

It was a useful workshop, but there were too many people interested that the time was not enough. I hope this kind of workshop continues during Plant Biology meetings as many more people will be looking for a place to obtain this kind of information.

Thanks to the organizers and the agencies staff members who were helping us with our questions and concerns.

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During the recent Plant Biology conference, editors from the ASPB journals The Plant Cell and Plant Physiology shared insights and fielded questions about how to publish in top journals, to an audience of about 100 early career researchers.

Mike Blatt (Editor-in-Chief of Plant Physiology) recognized the important contributions of the journals’ geographically diverse academic editorial boards (see http://www.plantphysiol.org/site/misc/edboard.xhtml and http://www.plantcell.org/site/misc/edboard.xhtml). He noted that both journals have very high impact and h-factors, and publish research of broad fundamental importance.

CoversMuch of what he and the next speaker, Leon Kochian (Editorial Board Plant Physiology, & Cornell University) spoke about can be found in the journal’s Instructions for Authors page, which is mandatory reading for anyone seeking to publish. In particular, they highlighted the importance of making sure that the article you submit fits the mandate of the journal, which is summarized:

“Research Articles must either present original findings that offer substantially new and fundamental insights into the biological processes of plants and/or set out novel and useful approaches, tools and resources that will enable scientific progress.”

They encouraged prospective authors to examine carefully the research areas covered by the journal, as well as the different types of article published, both of which are indicated in the Instructions for Authors. Mike urged authors to read the ASPB’s Ethics in Publishing statement and specific guidelines about how to manage image data.

Leon provided suggestions for good writing practices, including the importance of asking the right question, mastering the relevant literature, having a good story, and telling it in a clear, logical and interesting way (described later as “the 3 Cs: clear, concise and captivating”). He summarized by reminding us that “Writing a good paper is one of the hardest things you’ll ever do.”

The second half of the workshop was devoted to a question and answer session, led by two members of The Plant Cell’s editorial board, Blake Meyers (University of Delaware) and Bill Lucas (University of California, Davis). Several questions centered on how the review process works. Blake and Bill pointed out that top journals like The Plant Cell and Plant Physiology use a peer-review system that gets anonymous insights from top scientists (in contrast to some other journals that use professional editors for much of the decision making). Reviewer’s anonymity was discussed, with the majority sentiment being that anonymity can ensure the most useful reviews as well as protect reviewers from repercussion.

The question of having one’s work scooped by another group was raised repeatedly. Two points were made by the panellists: first, that it is extremely unlikely that identical experiments were done, and so your work still has value in its different approach, and second, that the journal editors and reviewers can often coordinate publication of two related papers as back-to-back articles, ensuring that both research groups get credit for their findings.

Finally, the issue of rejection was raised; Plant Physiology initially rejects 70% of its submissions. Learning to cope with rejection is one of the most important and challenging skills you need to acquire. Mike shared a useful guide to responding to rejection that includes the humorous retort “Your rejection was carefully reviewed by three experts in our laboratory, and based on their opinions, we find that it is not possible for us to accept your rejection.If you want to write an angry letter after reading your reviews, feel free to do so (it can be cathartic), but whatever you do, DON’T SEND IT! Deep breaths, discussion and sleep will help you respond more rationally. All of the panellists wanted to impart the message that the objective of the reviewers and editors is to support the scientist, to ensure that they get useful feedback, and ultimately to publish the best quality research.

And that’s really what makes science work, isn’t it?

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Next Generation Sequencing: Opportunities and Resources

As part of the iConnect team, I had the good fortune to go to several workshops during the conference Plant Biology 2014 organized by the American Society of Plant Biologists.

 

ASPB offers a diverse set of venues to acquire new skills and improve our careers by encouraging networking and initiation of collaborations. This year, for the Next Generation Sequencing workshop, ASPB organizers invited seven (the magic number?) experts with different levels of experience on bioinformatics. The event was sponsored by the ASPB Membership Committee and the speakers were Jason Williams and Christos Noutsos  from Cold Spring Harbor Laboratory, Nicole Hopkins from University of Arizona who is also working on iPlant Collaborative initiative (support@iplantcollaborative.org), Todd Mockler from Donald Danforth Plant Science Center, Kranthi Mandadi from Texas A&M University, Pankaj Jaiswal from Oregon State University and David Horvath from ARS-USDA. I have included a picture of them. They all are very photogenic!

Next Generation Sequencing Workshop Speakers

Next Generation Sequencing Workshop Speakers. (from left) Kranthi Mandadi, Pankaj Jaiswal, Christos Noutsos, Nicole Hopkins, Jason Williams, Todd Mockler, and David Horvath.

David Horvath, the workshop organizer, welcomed us, introduced all the speakers, mentioned each one’s expertise, and talked about iPlant Collaborative initiative, a National Science Foundation supported project aiming to provide “a place at the cyberspace where the power of high performance computing and data resources are available for life scientists”, therefore deep analysis of large sets of bioinformatics data is now possible in one place that is constantly curated and improved.

 

The common feeling among my colleagues and I was that due to the increasing availability of platforms, software and tools for bioinformatics analysis, it can be very confusing and challenging if you do not have a place where to start and have advice. iPlant Collaborative initiative offers several means of support to the very beginner and the more advanced user. It contains contact information of experts and places to put your questions and obtain answers from a community willing to help. Also, it contains confidentiality and security settings and links to other databases as GenBank and European Nucleotide Archive, in addition to the most trusted tools and software that are currently validated for use and publication.

 

The objective of the workshop was basically to know where the resources were and how to start and continue learning. We were around 50 people attending the workshop, with broad interests and projects but with the common goal to apply bioinformatics to the analysis of our data. We sat in groups of around six people, to allow a very dynamic round table discussion driven by one of the speakers, who changed table every 15 minutes. Each one of the speakers provided a unique perspective about the use of different tools and their own experiences. At the end, we concluded that we should not be overwhelmed for the large set of data to analyze, because there are places where to look and ask for help. iPlant Collaborative initiative is a very good place to go as it contains a complete set of settings to help us.

 

At the end I would like to thank the organizers and the speakers for a very helpful workshop. I hope to see you again in the near future.

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Thank You WORLD!

Looking back, we can all agree that it was a fantastic conference in Portland, full of exciting talks, eye-catching posters, motivated scientists, stimulating workshops, committee meetings, etc.

So foremost, Thank You to the organizers, to all who came out to Portland, a special Thank You to the iConnect Team, and of course to the sponsors, for making this meeting possible.

Unfortunately, we are left with some mind boggling stats. For example, there is the fact that the human population is increasing exponentially, whereas the food we produce grows merely arithmetically.

And so as the conference progressed, a defining question was posed: How can we achieve a reliable, sustainable, equitably-produced supply of nutritious food for a growing and increasingly urbanized world population within the context of climate change?

We are now most certainly aware that a sustainable agricultural intensification will be inevitable because maintaining current per capita food consumption with no increase in yield and no decrease in post-harvest and food waste will require almost doubling of the world’s cropland area within 40 years. This is not a viable approach to food security.

The present technologies in research are no doubt improving rapidly. We can all agree on that, but while, for example, next generation sequencing-based approaches are helping to improve the efficiency of breeding crops adapted to specific environments, we simultaneously need to provide farmers with information about the newest cultivars, technologies, etc.

As a result, immerging translational research and reduction in losses due to pests, pathogens, and environmental stresses could, and likely will, be equivalent to creating more land and more water! And that is purely thanks to the plant research being carried out globally.

The critically important basic discoveries being made in plant epigenetics, immunity, pathogen genomics, plant-environment interactions, structural biology, and metabolic engineering; discoveries will remain a driving force in agricultural innovation.

Ultimately, the continued translation of basic research into tangible agricultural and crop improvements will rely not only on the research itself but also on communicating the vital role that agriculture and plant genetics plays in all of our lives.

We were exposed to the social, economic, biological, environmental, and ethical aspects of food production.

We have been taking notes, growing our To Do lists. So if at least of few of those aims are realized before the next meeting, we will be in great shape.

Such a stance along with the growing population of plant scientists should no doubt translate into beneficial yields. I feel it’s time to move on beyond the GM debate, beyond the natural/unnatural argument, beyond the dualism of good versus bad and move toward adopting a continuum perspective that will allow for useful policies to be implemented.

I will be looking forward to seeing everyone in Minneapolis.

And for Goodbye a reminder

Ode to a Cluster of Violets
Pablo Neruda

Crisp cluster
plunged in shadow.
Drops of violet water
and raw sunlight
floated up with your scent.
A fresh
subterranean beauty
climbed up from your buds
thrilling my eyes and my life…

Read on

For more information and inspiration about worldwide impacts of plant biology, see the Decadal Vision report and related blog posts.

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I was eagerly waiting to write a post on this topic. This workshop attracted a lot of conference attendees, since current day plant biology research cannot move forward without these resources. Unfortunately it was kind of an effort to pack too many eggs in one basket within a limited time which could not meet expectations of many attendees. However a short note on the tools and resources described might be helpful for our readers.

Tanya Beraradini introduced the audience with the past and future of The Arabidopsis Information Resource (TAIR) which collects information and maintains the genetics and molecular biology data for the model plant Arabidopsis thaliana. It is managed by Phoenix Bioinformatics Corporation and is supported through institutional, lab and personal subscriptions. You can search and view the data using Gbrowse or interactive sequence viewer and they also have some tools like Mapviewer, AraCyc pathway, Patmatch, Motif search etc. for different analysis. The datasets can be downloaded as bulk.

Next, Chris Town from J. Craig Venter Institute (JCVI) talked about the first release of the Arabidopsis Information portal (AIP). This is an NSF and BBSRC-funded collaborative project between the JCVI, the Texas Advanced Computing Center (TACC) at the University of Texas at Austin and the University of Cambridge, with technical assistance from TAIR. The aim was to make a flexible community – extensible portal to enhance the next generation of Arabidopsis research. It has the enhanced search retrieval and display capabilities. It also enable community participation in functional annotation and own a language- and region-specific presentation of scientific content.

Next talk was on the iPlant Collaborative. Jason Williams from CSHL talked about the initiative in a title “Scalable Cyberinfrastructure for life science.” CI or CyberInfrastructure provides technological and sociological solution for the high throughput computational biology which consists of the hardware, software and people. The iPlant Collaborative is a dynamic virtual organization. The project is led by scientists at the University of Arizona (UA), the Texas Advanced Computing Center (TACC), Cold Spring Harbor Laboratory (CSHL) and University of North Carolina at Wilmington (UNCW). It includes a data storage facility, interactive web based analytical platform, cloud infrastructure for storage, computational data analysis. They provide support for scaling computational algorithms to run on large, high speed computers. They also have programs for education and training on how to use the CI for scientist at all levels.

Pankaj Jaiswal from Oregon State University delivered the next talk entitled “Gramene: A resource for comparative plant Genomics.” Gramene mainly deals with the grass genomes. As an information resource Gramene facilitates researchers by providing added value to the existing data of grass genomes. It takes advantage of genomic sequence known in one species to identify and understand the corresponding genes, pathways and phenotypes in the other related species. It contains information on Taxonomy ontology, Gene ontology, plant ontology, trait ontology and environment ontology. The genome module used here is adopted from Ensembl. It has cMAP and BLAST options. Literature supporting all data provided are also organized in the Literature database. It has a completely new look from the earlier version which is user friendly. And informative.

Peifen Zhang, from Carnegie Institution for Science talked about “PMN: metabolic pathway databases of 17 viridiplantae species, an introduction and demo of use cases.” PMN (Plant Metabolic Network) focuses on bringing the biochemical pathway databases focuses on plant metabolism. There is a growing need to place the sequenced and annotated genomes in a biochemical context in order to facilitate discovery of enzymes and engineering of metabolism. PMN, first made public in June 2008, generates an infrastructure for drawing together diverse sources of plant metabolism information.

The next talk was on Medicago truncatula genome resources at JCVI, Chris Town talked about the project which was initiated with a generous grant from Samuel Roberts Noble Foundation to the University of Oklahoma. Beginning in 2003 (and renewed in 2006), the National Science Foundation and the European Union’s Sixth Framework Programme provided funding to complete sequencing of the euchromatic genespace.

Asher Pasha, from University of Toronto, delivered a talk on the title “Data Sets, Web services and Visualization Apps from the Bio-Analytic Resource for use in the Arabidopsis Information Portal and other Cyberinfrastructure Assets.” As part of a Genome Canada grant, the Bio-Analytic Resource for Plant Biology (BAR) is providing seven modules to the Arabidopsis Information Portal: two modules for gene expression (transcript abundance and transcript structure) based on publish microarray and RNA-seq data sets, a module covering 90,000 conserved sequences in the Brassicaceae from Mathieu Blanchette and collaborators via the VEGI Project in a novel sequence conservation viewer (GeneSlider), a module for a database of almost 100k protein-protein interactions plus a viewer app, a module for viewing protein structures for ca. 500 experimentally-determined protein structures and predicted structures covering ~70% of the Arabidopsis proteome, an Expressolog/Synteny module and a zoomable user interface app to navigate between the biological organizations by the Arabidopsis Information Portal (AIP). Progress on these and other potential modules were discussed.

Doreen Ware and Sunita Kumari, from CSHL talked about “The DOE Systems Biology Knowledgebase: An integrated knowledgebase for biofuel research.” In 2011, DOE Office of Biological and Environmental Research (BER) launched KBase (KBase.us), an open-source, open-architecture software and data environment for systems biology research. It provides a computational framework for integrating and analyzing large datasets. High-level data types currently supported by KBase include genomes (of bacteria, archea, and eukaryotes), metagenomes, transcriptomes, proteomes (mapped to genomes), interactomes, phenotypes, 16s amplicons, expression data, enzymes, ontologies, pathway data, protein annotations, protein-protein interactions, regulons, and ribosomes. KBase pulls these data types from existing international repositories. So in future, data submitted to these standard resources wil be automatically integrated into the Kbase system. Because KBase pulls these data types from existing international repositories, future data submitted to these standard resources ultimately will be integrated into the KBase system. Powerful tools in Kbase allow users to analyze an simulate data for generating and testing hypotheses, designing biological functions or proposing new experiments.

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