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PBS NewsHour - Google+ - John B. Gurdon and Shinya Yamanaka share this year's Nobel…

PBS NewsHour - Google+ - John B. Gurdon and Shinya Yamanaka share this year's Nobel… | GenoCon 2 | Scoop.it
John B.Gurdon and Shinya Yamanaka share this year's Nobel Prize in Medicine and Physiology for their work in cellular reprogramming, 50 years after…...

How Yamanaka-san and Sir John Gurdon came to their idea! 

http://www.pbs.org/newshour/rundown/2012/10/-in-1962-john-b.html

 

Nobel Prize winner Sir John Gurdon talks to reporters on Oct. 8, 2012 in London. Gurdon and Shinya Yamanaka from Japan have both been awarded the Nobel prize for medicine or physiology for their work as pioneers of stem cell research. Photo by Peter Macdiarmid/Getty Images.

 

In 1962, John B. Gurdon of the United Kingdom discovered that a cell removed from the gut of a frog contained all the genetic information necessary to create the whole frog. More than 40 years later, Shinya Yamanaka of Japan found that by introducing a few genes to a mature mouse cell, he could reprogram it into a stem cell, capable of developing into any cell in the body.

 

Gurdon and Yamanaka share this year's Nobel Prize in Physiology or Medicine for their work in cellular reprogramming, 50 years after Gurdon's initial discovery. Their work in stem cells has led to a wave of advances, from cloning animals to allowing scientists to create embryonic cells without having to destroy embryos.

 

Gurdon was still a graduate student when he first transplanted genetic information from the nucleus of an intestinal cell of one frog into the fertilized egg cell of another whose own nucleus had been removed. That cell was able to reprogram and develop into a tadpole, proving that even mature, specialized cells have all the information needed to transform an embryo into an adult.

 

He relied on a technique called nuclear transfer to transplant the nuclei. The discovery flew in the face of established opinion, since other more established scientists hadn't been able to successfully make such a transfer, and it was thought then that a specialized cell is irreversibly tied to its fate.

 

"We had to go through a few years, in a sense, of letting the results sink in," Gurdon said in an early morning interview with the Nobel committee.

 

The same year that discovery was published, Yamanaka was born. And 40 years later, he took the science a big step farther. His research identified the four genes that made it possible to reverse mature stem cells into their embryonic state without using nuclear transfer. The "induced pluripotent embryonic stem cells" could then go on to become nerve cells, heart cells, gut cells.

That finding opened the possibility for skin cells to be reversed to embryonic cells and then reprogrammed into nerve, heart or other tissue cells for medical uses and disease treatment. Such reprogrammed cells have not yet been used to treat patients.

 

"They showed us that it is not a one-way street, that a cell retains the ability to go back to what it was in a primordial state, that it could rewind all its potential," said David Scadden of the Harvard Stem Cell Institute. "What that means is...what we think of as highly restricted has the capacity to become any other cell. If we can engineer that process, that opens up new possibilities for regenerative medicine."

 

And that's Yamanaka's goal.

"My goal all my life is to bring this stem cell technology to the bedside, to patients, to clinics," Yamanaka told Adam Smith, editorial director of Nobel Media early Monday morning.

In this interview with KQED's Quest, Yamanaka talks about his recent research using stem cell-derived nerve cells to treat animals with spinal cord injuries.

 

(the video in the link) http://youtu.be/rcFibJmKZrU

 

Gurdon told Nobel Media's Smith that the finding highlights the importance of basic science, even if there isn't an immediate benefit to health.

 

"So often it happens that the practical or theraupeutic benefits comes along quite a long time after the initial discovery," he said.

NewsHour correspondent Spencer Michels featured Yamanaka in this 2007 report on stem cell research.

http://www.pbs.org/newshour/bb/health/july-dec07/stemcell_10-08.html

 

Here's a story by KQED's Quest on the discovery. 

http://science.kqed.org/quest/2012/10/08/sf-scientist-wins-nobel-for-stem-cell-breakthrough/

 

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GenoCon2 | Open Genome Design Promoter Challenge 2 Concluded!

GenoCon2 | Open Genome Design Promoter Challenge 2 Concluded! | GenoCon 2 | Scoop.it
David Gifford's insight:

**Thank you for all your submissions!**

Stay tuned for further announcements...

*Deadline was Feb. 22 for Promoter Challenge A.

 

But please feel free to use all the applications and continue designing your own promoters!

 

We have updated PromoterCAD with a new UI, and added more explanatory tooltips. There are also new normalized data sources to help you find interesting genes, and the "Finish Now" command gives you the ability to fill in blank sequences with the natural promoter sequence from the last gene retrieved. Please give it a try!

 

Design synthetic DNA sequences on the computer as solutions to complex problem assignments. Use semantically linked data from scientific databases and literature to construct your solutions....

Tools used in this competition allow you to create solutions to problems easy and accessible, even to non-specialists and students like you. Challenge yourself today!

The reward for a good design: GenoCon pays for the synthesis of the DNA and its transformation into a real plant!

 

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Biology Hacklabs | The Scientist Magazine®

Biology Hacklabs | The Scientist Magazine® | GenoCon 2 | Scoop.it
Fueled by donations, sweat, and occasional dumpster diving, community laboratories for DIY biologists are cropping up around the country.
David Gifford's insight:

BioCurious is one of a dozen community DIY biology (DIYbio) hackerspaces in the United States that serve as havens for geeks, engineers, entrepreneurs, and anyone curious about biology. Today, through volunteered time, money, and equipment, and some creative funding schemes, these labs are popping up all over the country and around the world. According to DIYbio.org, a support organization for DIY biologists, there are currently 15 DIY groups in North America, 11 in Europe, two in Asia, and two in Australia/New Zealand. DIYbio community labs accept all manner of biocurious individuals. The labs require basic safety training for new members, then provide access to laboratory equipment and reagents, training in lab techniques and biotechnology, a supportive community, and, paramount to all, space to dabble.

“The goal is just to provide lab space for anyone to do whatever the hell they want,” says Cory Tobin, cofounder of a Los Angeles DIYbio lab called LA Biohackers. “It’s for people who want to learn biology for any reason.

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[GenoCon List] GenoCon2 Laptop Grand Prize / NEW Extended Feb 22 Deadline / GenoCon mailing list

[GenoCon List] GenoCon2 Laptop Grand Prize / NEW Extended Feb 22 Deadline / GenoCon mailing list | GenoCon 2 | Scoop.it
David Gifford's insight:

GenoCon participants, (日本語の案内は英語の後の説明をお読みください) We have extended the GenoCon2 deadline to February 22, 2013 for the Promoter Design Challenge! Design a plant promoter DNA sequence using the PromoterCAD software to search for functional regulatory DNA. Make a promoter which controls specific expression in a plant tissue such as leaf, stem, or root, or only at a particular time of day. Accepted DNA designs will be synthesized, transformed into real plants, and tested for gene expression! The grand prize award for Plant Promoter Design is a Dell XPS™ series 13 inch Ultrabook™ computer, courtesy of Dell Inc. We urge you to join our mailing list for important updates about entering GenoCon2.   If you would like to join the GenoCon mailing list just send an email togenocon-request@freelists.orgwith 'subscribe' in the Subject field OR by visiting the GenoCon list page at http://www.freelists.org/list/genocon All the Best, GenoCon Teamhttp://genocon.org -- Robert Sidney Cox IIIForeign Postdoctoral ResearcherRIKEN Yokohama David Gifford, Mailing List Administrator ===GenoCon参加者の皆様 この度、GenoCon2 課題A (植物プロモータデザイン)の締切を 2013年2月18日(ハワイ時間) まで延長しました。 課題Aでは、PromoterCAD(コンピュータ支援プロモータ設計)システムというサンプルプログラムを用意しました。このPromoterCADを使用すると、機能配列を探し出して、植物のプロモータDNA配列をデザインすることができます。 植物の組織(葉、茎、根など)や慨日リズムの特定の時間を制御して遺伝子発現するプロモータを作ってみましょう。GenoCon事務局で選んだ優秀なデザインは、実際にDNAを導入して、植物で実験を行います。 なお、第2回GenoConは以下のスポンサー企業にご協賛頂いております。http://genocon.org/ja/sponsor/ 受賞者の方には・Dell XPS™ series 13 inch Ultrabook™  (最優秀1名の方、スポンサーのDELLさんより)・トロフィーが贈呈される予定です。 GenoCon2に関する更新情報は、今後下記のメーリングリストを通じて行なう予定です。是非ともご登録ください。 登録方法(1)  genocon-request@freelists.org にタイトルを'subscribe'としてメールを送信してください(本文は空で大丈夫です)。(2)  http://www.freelists.org/list/genocon こちらのウェブサイトから登録してください。 ゲノコン事務局http://genocon.org Robert Sidney Cox IIIForeign Postdoctoral ResearcherRIKEN Yokohama David Gifford, Mailing List Administrator

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New GenoCon 2 Entry: Promoter Design to Maintain Fertility of Transgenic Plant by New MotifRanking Plugin | Mash up the Linked Open Data in the GenoCon2 Genomic Design Contest!

New GenoCon 2 Entry: Promoter Design to Maintain Fertility of Transgenic Plant by New MotifRanking Plugin  | Mash up the Linked Open Data in the GenoCon2 Genomic Design Contest! | GenoCon 2 | Scoop.it
Overexpression of heterogeneous genes can have unfavorable effects on plants. Especially, sterility is a serious risk because it makes it difficult to generate and maintain the transgenic plants .
David Gifford's insight:

We are pleased to announce a new entry to GenoCon2 Promoter Design Challenge A, and Special Programming Challenge!

According to the entrant, Mochizuki-san "In order to overcome the problem, I designed a site-specific promoter. It is expected that the promoter will induce a gene expression in root but suppress that in pollens, which involve in fertility directly.

I used newly-developed plugin MotifRanking on the official CAD system to build up the promoter. Whereas conventional plugins provide only 1 gene locus giving the highest or lowest gene expression, the new plugin allows users to select from top or bottom 10 locus. Thus this plugin broadens the options, and thereby more suitable motifs can be embeded in promoter sequence.

There is still time to enter - Deadline is January 31!

http://genocon.org 

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Genomics 101 | The Scientist Magazine®

Genomics 101 | The Scientist Magazine® | GenoCon 2 | Scoop.it
Undergraduate students delve into genomics and synthetic biology thanks to a new breed of technologically advanced courses.

Thanks to Omri Amirav-Drory at

 http://www.genomecompiler.com/news/2012/12/5/build-a-genome.html

Omri reports: "Check out this interesting article from The-Scientists

http://www.the-scientist.com/?articles.view/articleNo/33358/title/Genomics-101/ 

A new class at John Hopkins University: Biology 420, aka Build-a-Genome. The future is here!

 

The class description is interesting: "In this combination lecture/laboratory “Synthetic Biology” course, students will learn how to make DNA building blocks used in an international project to build the world’s first synthetic eukaryotic genome, Saccharomyces cerevisiae v. 2.0. Please study the wikiwww.syntheticyeast.org for more details about the project. Following a biotechnology boot-camp, students will have 24/7 access to computational and wet-lab resources and will be expected to spend 15-20 hours per week on this course. Advanced students will be expected to contribute to the computational and biotech infrastructure."

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GenoCon 2 Genomic Design Contest -- Challenge A 10 days left! Go Compete!

GenoCon 2 Genomic Design Contest -- Challenge A 10 days left! Go Compete! | GenoCon 2 | Scoop.it

*EXTENDED to Feb. 22 for Promoter Challenge A!

*Final Submission before midnight Hawaii time ! *

http://GenoCon.org

 

We have decided to extend the promoter design challenge by two weeks, so you can have more time to refine your designs and create new ones.

We have updated PromoterCAD with a new UI, and added more explanatory tooltips. There are also new normalized data sources to help you find interesting genes, and the "Finish Now" command gives you the ability to fill in blank sequences with the natural promoter sequence from the last gene retrieved. Please give it a try!

 

Design synthetic DNA sequences on the computer as solutions to complex problem assignments. Use semantically linked data from scientific databases and literature to construct your solutions....

Tools used in this competition allows you to create solutions to problems easy and accessible, even to non-specialists and students like you. Challenge yourself today!

The reward for a good design: GenoCon pays for the synthesis of the DNA and its transformation into a real plant!

 

*deadlines are 23:59:59 Hawaii-Aleutian Standard Time (HAST)

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Community links for the GenoCon2 Synthetic Biology Genomic Design Contest | Facebook

Community links for the GenoCon2 Synthetic Biology Genomic Design Contest | Facebook | GenoCon 2 | Scoop.it

1. The http://GenoCon.org website containing

- GenoCon2 Challenges with backgrounds,measurement concept, basic science, and manuals

- GenoCon2 Timelines Contest Procedure Overview  GenoCon News About Us

  

2. The http://LinkData.org database  Using LinkData.org you can make an account, find useful data for GenoCon2 and upload your own data.

Using the LinkDataApp programing space http://app.linkdata.org/

you can: 

a) Find useful programs to analyze and process GenoCon2 data,

b) Make your own forked program copy to customize and design your own programs from scratch to enter to GenoCon2

c) Enter The GenoCon2 Contest

d) Write your reports explaining how your programs and designs work 

e) Share and Collaborate using your programs with other GenoCon2 community members

 

3.The GenoCon.org facebook page

 http://www.facebook.com/GenoCon.org/

and GenoCon2 facebook group 

http://www.facebook.com/groups/genocon

 

The GenoCon.org facebook page provides news and interesting links and a place to post community information The GenoCon facebook group provides a forum for questions and answers with the organizers and participants in the GenoCon Community

The LinkData App page http://on.fb.me/VehmUw

in the GenoCon.org facebook page provides links to and descriptions of design tools and entries to the GenoCon contest Challenges shared openly with the the GenoCon 2 Community. 

 

4. GenoCon2 on Scoop.it provides additional news and interesting links.

 http://www.scoop.it/t/genocon-2

 

5. @GenoCcon2 on Twitter for the latest headlines and links.

https://twitter.com/GenoCon2

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Gen9 - 2012 G-Prize Contest Winners Announced

Gen9 - 2012 G-Prize Contest Winners Announced | GenoCon 2 | Scoop.it

2012 Gen9 G-Prize
Rewarding innovators and disruptors who can transform an industry using synthesized DNA constructs.

The inaugural G-Prize contest, conceived and exclusively sponsored by Gen9, was launched to foster creative and innovative approaches for using synthetic DNA libraries to advance research in the production of pharmaceuticals, chemicals, biofuels and food.

The winners of the 2012 G-Prize are:

1st place (500 GeneBits, up to 500kb):
Tanja Kortemme, University of California, San Francisco
Computer-Aided Design of Sensor/Actuators

2nd place (300 GeneBits, up to 300kb):
Sarel Fleishman, Weizmann Institute (Rehovot, Israel)
Computational Design of Novel Binding Antibodies: Designing High-Specificity and High-Affinity Insulin Binders

3rd place (100 GeneBits, up to 100kb, two winners):
Alfonso Jaramillo, Institute of Systems & Synthetic Biology (Evry, France)
Combinatorial Synthesis of RNA Integrated Circuits to Program Living Cells

Xavier Duportet, Massachusetts Institute of Technology
Towards the Manipulation of Genomes On-Demand: High Throughput Discovery of New Recombination Sites

CEO’s Award (100 GeneBits, up to 100kb):
Lynn Rothschild, NASA
DNA Toolkit for Space Exploration


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薬学部3年生の江藤諒さんが第1回GenoCon(国際合理的ゲノム設計コンテスト)で優秀プログラム賞を受賞

薬学部3年生の江藤諒さんが第1回GenoCon(国際合理的ゲノム設計コンテスト)で優秀プログラム賞を受賞 | GenoCon 2 | Scoop.it
長崎大学、ニュース&トピックス...

薬学部3年生の江藤 諒さん(薬科学科)が,理化学研究所が主催する、第1回GenoCon(国際合理的ゲノム設計コンテスト)で優秀プログラム賞を受賞しました。GenoConは、理研サイネスに統合されているゲノムデータやタンパク質データなどの公開データベース群を活用して、植物の生理機能を高めるためのDNA配列を参加者に合理的に設計してもらうコンテストです。

選考委員会からの受賞理由として、
「コドンの最適化方法を確率的なアルゴリズムで具体的に実装した江藤氏に決定した。アルゴリズムの説明も分かりやすく説明されており、他の人がこのプログラムを読んで理解できるため、さらなる改良を誘導する効果がある点が高く評価された。また、実際にこのアルゴリズムで最適化されたDNA配列が十分機能することも実験審査で確認された。」
との通知を受けています。

また、その栄誉をたたえるための記念のトロフィーには、江藤さんがデザインしたDNA配列を持つ植物体がアクリル封入されています。

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課題A スペシャルプログラミングチャレンジの応募マニュアルが公開されました!応募締め切りは2月22日です。 | GenoCon2

課題A スペシャルプログラミングチャレンジの応募マニュアルが公開されました!応募締め切りは2月22日です。 | GenoCon2 | GenoCon 2 | Scoop.it

GenoCon2 課題Aのスペシャルプログラミングチャレンジの応募マニュアルが公開されました。
募集期間は10月10日から2月22までです。
プログラミングが得意な学生さんや一般の方の
ご参加をお待ちしております!

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GenoCon2 課題Bの応募マニュアルが公開されました! 応募締切は11月21日です。 | GenoCon2

GenoCon2 課題Bの応募マニュアルが公開されました! 応募締切は11月21日です。 | GenoCon2 | GenoCon 2 | Scoop.it

GenoCon2 課題Bの応募マニュアルが公開されました。
募集期間は10月10日から11月21までです。
大学生・大学院生・研究者・一般の方だけでなく、
高校生の方からのご参加もお待ちしております!

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Plant power - The ultimate way to go green: Birger Lindberg Møller at TEDxCopenhagen 2012

Synthetic biology is a new movement setting the hearts and minds of scientists across the world on fire. But really plants, and not scientists, are at the center of this movement: They can help us think completely out-of-the-box for solutions to the challenges we as a global community are facing in the move to a biobased society. Plants are world champions in driving complex chemistry with sunlight as the sole energy input and using carbon dioxide from the atmosphere as carbon source. Let's collaborate!


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Life is Suite: A group of software apps helps synthetic biologists work faster and better » Systems Engineering | Blog Archive | Boston University

Life is Suite: A group of software apps helps synthetic biologists work faster and better » Systems Engineering | Blog Archive | Boston University | GenoCon 2 | Scoop.it

by

Art Jahnke

"As biologists continue the decades-long race to map the genomes of living things, a group of forward-thinking BU engineers is asking the kind of questions that engineers can’t help but ask: what if we built a different genome?

Known as synthetic biologists, they believe that with some skillful genomic tweaks, living organisms, such as cells and microbes, can be put to work doing things that are too dangerous or not even possible for higher life-forms like ourselves.

 

.....Traditionally, as much as anything can be traditional in a field that is just a few years old, finding the correct DNA sequences would be a painstakingly slow and error-prone process, but Densmore has some help in the form of a software tool suite called Clotho. He describes Clotho, named for the youngest of the Three Fates in Greek mythology and the one who spins the thread of life, as an app environment, similar to the iPhone software platform, where a variety of tools can perform specific yet interconnected tasks. In this case, however, the tools connect to repositories of biological “parts” organized in such a way that they can be used to transform descriptions readable by humans into gene networks, designing DNA assembly commands for liquid-handling robots or archiving designs to share with other labs. Densmore admits that he’s a big fan of Clotho—and he should be. He built it.

......."
http://bit.ly/WqKa13


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23andMe: This is Me TV Ad

23andMe's first TV ad shows people exploring their own DNA, to take charge of their health and learn more about themselves.
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GenoCon2 Special Programming Challenge Winner – MotifRanking Plugin by Masahiro Mochizuki

GenoCon2 Special Programming Challenge Winner – MotifRanking Plugin by Masahiro Mochizuki | GenoCon 2 | Scoop.it
David Gifford's insight:

Based on his excellent Plugin design, we selected Masahiro Mochizuki as the GenoCon2 2013 Special Programming Challenge Winner for his original geen expression mining plugin MotifRanking.
We strongly encourage the current participants to try out Mochizuki san’s tool MotifRanking in the last few days of the contest. Click here to view the App and Plugin: http://app.linkdata.org/run/app1s264i


"PromoterCAD with New Plugin MotifRanking" 

Masahiro Mochizuki explains, “Overexpression of heterogeneous genes can have unfavorable effects on plants. Especially, sterility is a serious risk because it makes it difficult to generate and maintain the transgenic plants. In order to overcome the problem, I designed a site-specific promoter. It is expected that the promoter will induce a gene expression in root but suppress that in pollens, which involve in fertility directly.

I used newly-developed plugin MotifRanking on the official CAD system to build up the promoter. Whereas conventional plugins provide only 1 gene locus giving the highest or lowest gene expression, the new plugin allows users to select from top or bottom 10 loci. Thus this plugin broadens the options, and thereby more suitable motifs can be embedded in promoter sequence.”

 

IFor more information on the GenoCon2 Synthetic Biology Genomic Design Contest held October 8, 2012 – February 22, 2013 please visit the GenoCon2 Website. http://GenoCon.org

 

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New Extended Feb. 22 Submission Date! Challenge A - Promoter Design Launches | GenoCon2

New Extended Feb. 22 Submission Date! Challenge A - Promoter Design Launches | GenoCon2 | GenoCon 2 | Scoop.it

New Extended Submission Date Friday February 22, 2013

GenoCon2 Design Challenge A is officially launched! The challenge is to design a synthetic Arabidopsis promoter system of 500 base-pairs (or less) for selectively controlling the expression of a gene. These 500 base-pairs must be consecutive, and within the region prescribed by the GenoCon genetic vector and measurement assay system.

Solutions may (1) localize gene expression to specific plant tissues such as the leaves, shoots, or wounds, (2) control the time of gene expression such as in plant senescence and circadian regulation, or may use a combination of both approaches.

http://genocon.org/assignment-2012/assignment-a/background-2012/

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New Jan. 18 Round 2 deadline! Challenge B – Formaldehyde Detoxification | GenoCon2

New Jan. 18 Round 2 deadline! Challenge B – Formaldehyde Detoxification  | GenoCon2 | GenoCon 2 | Scoop.it

New Round 2 Deadline Friday January 18, 2013

The GenoCon2 Challenge B assignment: design a DNA sequence conferring to the model organism Arabidopsis thaliana the functionality to eliminate and detoxify airborne formaldehyde.

Successfully engineered in previous work, your task is to increase the performance of formaldehyde absorption. DNA sequences which improve upon previous designs or which use completely new methods to add this function to the plant to absorb and remove formaldehyde effectively are both accepted

http://genocon.org/assignment-2012/assignment-b/measurement-2012-challenge-b/

 

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GenoCon2 課題Bの応募締切が2013年1月18日まで延長されました

GenoCon2 課題Bの応募締切が2013年1月18日まで延長されました | GenoCon 2 | Scoop.it

GenoCon2 課題Bの応募締切が2013年1月18日まで延長されました。
課題B - ホルムアルデヒド無毒化

GenoCon2 課題Bは「空気中からホルムアルデヒドを除去して効果的に無毒化する機能を、実験植物のシロイヌナズナに付与するための塩基配列をデザインせよ!」です。

この機能は過去の遺伝子工学研究で成功例が報告されていますが、今回の課題は、ホルムアルデヒドを無毒化させる能力をさらに改良することです。
過去のDNAデザインを改良するアイディアも、全く新しい手法を用いて、植物体にホルムアルデヒドを効果的に吸収し除去する機能を付与して頂いても、いずれのデザインも受け付けます。

 

http://genocon.org/ja/challenges/assignment-b/

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2013年2月22日よりGenoCon2 課題Aの応募が開始されました

2013年2月22日よりGenoCon2 課題Aの応募が開始されました | GenoCon 2 | Scoop.it

2013年2月22日よりGenoCon2 課題Aの応募が開始されました。

 

GenoCon2 課題Aは「組織/時期特異的な遺伝子発現をコントロールする人工植物プロモータをデザイン

せよ!」です。

 

課題Aでは、シロイヌナズナの遺伝子発現をコントロールするプロモータ配列を、500塩基以内でデザインして頂きます。この500塩基以内の配列は、一続きの配列で、ゲノコンであらかじめ用意したベクターと測定方法に合うように設計してください。

課題の取り組み方としては、(1) 葉、茎、あるいは植物の損傷部といった特定の組織でのみ遺伝子を発現させるプロモータのデザインや、(2) 植物の老化や慨日リズムの調節に関わる遺伝子発現のタイミングを制御するプロモータのデザイン、またはそれらを組み合わせたものなど、さまざまなアイディアが出てくることを期待しています。

 

http://genocon.org/ja/challenges/assignment-a/

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Design for Formaldehyde-detoxifying Plant by Expression of a Cell wall-anchored Enzyme. | Mash up the Linked Open Data | GenoCon 2

Design for Formaldehyde-detoxifying Plant by Expression of a Cell wall-anchored Enzyme. | Mash up the Linked Open Data | GenoCon 2 | GenoCon 2 | Scoop.it
The design is intended for giving plants to the ability to detoxify formaldehyde by expression of cell wall-anchored formaldehyde dehydrogenase. The enzyme is based on formaldehyde dehydrogenase from Pseudomonas putida.

 

In this design, a signal peptide is added to its N-terminus whereas a cellulose-binding protein from Heterodera schachtii is fused to the C-terminus. This enzyme catalyze a dismutation in the cell wall, so that it efficiently protects plant body from extracellular formaldehyde. Furthermore, the transgenic plants have potential as a material for formaldehyde-detoxifying fiber.

 

This is one of the first submissions underway for Genocon2 Challenge B, by a veteran of the first Genocon 2010! Join GenoCon 2 and mash up the linked open data!

http://genocon.org

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GenoCon 2 Synthetic Biology Design Contest Starts! Challenge B Entry Handbook released

GenoCon 2 Synthetic Biology Design Contest Starts! Challenge B Entry Handbook released | GenoCon 2 | Scoop.it

The Official contest period has begun! Please go ahead and enter the GenoCon2 Synthetic Biology Design Contest! Polish your bioinformatics skills for biotech. Design DNA sequences to transfer formaldehyde resistance, and GenoCon will synthesise a real transgenic arabidopsis plant with your design if you are a finalist. A prize is awarded for the best performing genomics design. And that is just Challenge B; there is also Challenge A...

 

Please refer to the GenoCon2 Entry Handbook for Challenge B PDF that you can download here http://genocon.org/assignment-2012/assignment-b/how-to-enter-challengeb/

We look forward to your entry!

          

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Fork Your Own GenoCon2 Data Mining Plug-in to Compete or Share to find useful Gene Expression Patterns

Fork Your Own GenoCon2 Data Mining Plug-in to Compete or Share to find useful Gene Expression Patterns | GenoCon 2 | Scoop.it

The creative activity of the GenoCon2 Special programming challenge is to “mine” GenoCon2 data mashups by looking for new associations and genes with interesting or useful expression patterns.

 

Examples can include sets of genes that are all expressed in the same growth condition, at the same time of day, and/or in the same part of the plant. We provide basic functions and example workflows which show how to look for a gene expression property (e.g. highly expressed in leaf tissue in young plants) and retrieve the functional DNA sequences to add to a synthetic promoter design.

 

We will judge submitted functions based on their novelty, usefulness, and implementation. With social networking participants can discuss programming functions, find out which functions the DNA designers with more biological experience would like to have, and even share code under development. We encourage group participation, and our system automatically tracks the history of code forking so credit can be given to all contributors.

 

If you want to learn more about making your own biological design program, how our data is structured, how to submit and test your program, or anything else about the programming challenge please head over to our manuals section for more details!

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GenoCon2 課題A スペシャルプログラミングチャレンジの募集中です(応募締切: 2月22日) | GenoCon2

GenoCon2 課題A スペシャルプログラミングチャレンジの募集中です(応募締切: 2月22日) | GenoCon2 | GenoCon 2 | Scoop.it

課題Aのスペシャルプログラミングチャレンジでは、遺伝子に関連する興味深い、有用な発現パターンの新たな組合わせを見つけ出すアプリケーションを募集します。 

サンプルの遺伝子のデータセットは、同一の発生条件、日周振動の同じ時刻、植物の同じ部位において発現する、全ての遺伝子を含みます。 私達の方では、遺伝子発現の性質(例. 若い植物の葉の組織で高い発現量を示す)を見つけて、機能DNA配列を探し出して、人工プロモータデザインへ付け加える、JavaScript関数やCADワークフローの基本的なセットを提供します。 


私達は、応募されたプラグイン関数を、新規性、使い易さ、実装方法に基づいて評価します。ソーシャルネットワークを利用する事で、参加者同士で関数のプログラミングについて議論し、生物学実験の経験の豊富なDNA設計者が使用したいと思える関数を探し出し、開発中のコードをシェアします。 私達はグループでの参加をお勧めします。システムでは、ソースコードをforkした履歴を自動的に記録しますので、開発に貢献した全ての人が評価されます。

自分のデザインプログラムをつくる方法、自分のデータをつくる方法、自分のプログラムを応募提出・検証する方法、その他プログラミングチャレンジに関してもっと知りたい方は、課題Aのマニュアルページをご覧下さい!

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Craig Venter: Health, Genomics, Research and Power

Biologist and entrepreneur Craig Venter discusses the intersection between health, genomics, research and power.

 

For the full 46 minute interview go to 

http://fora.tv/2012/10/16/Craig_Venter_Health_Genomics_Research_and_Power

 

More previews of Many other interviews from the October 15-16 Living by Numbers Health Conference by WIRED and the Robert Wood Johnson Foundation

http://fora.tv/conference/wired_health_conference_living_by_numbers

 

"a new conversation on the future of healthcare with 200 expert leaders from the worlds of medicine, science, technology, and business.

....a clear, compelling argument that today there is a new opportunity to bring data into real-time decision-making for doctors, researchers, hospitals, and individuals. This combination has the potential to transform people's lives.

.....spanning the gap between healthcare and technology, connecting pioneering researchers with ambitious entrepreneurs. First and foremost, .... a forum for ideas. Expect new connections, new opportunities, and new insights in how better data is driving us all toward better health."

 

The full interviews are here:

http://fora.tv/conference/wired_health_conference_living_by_numbers/buy_programs


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Coders Of The Future Will Not Be Engineers

Coders Of The Future Will Not Be Engineers | GenoCon 2 | Scoop.it

http://bit.ly/RfoamH

 

Biologists who code with genes will be the new cool kids on the block. Web-2.0 startups will be a thing of the past. Whereas there will be some innovation in the Web-3.0 and Web-4.0 space, the true revolutions will be occurring in the hard sciences.

Startup successes will shift from coding in binary to coding in quaternary — the base-4 system of the genes. Other revolutions will occur in the nanotech space, coding products from the atom up using the periodic table of elements as ingredients.

 

Hacking will not mean coding in binary on a computer to create a new app, Web-2.0 service, or SaaS product. Instead, biohacking will be the hot pursuit. This I call CaaS — Cells as a service. Cells will be our manufaturing plants. Cells will be our computers. Cells will be our platform on which we innovate. CaaS will be the new open source mantra.


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