Plant Genetics, N...
Follow
Find
4.9K views | +0 today
Plant Genetics, NGS and Bioinformatics
Papers and topics in plant genetics, NGS and bioinformatics
Curated by Ali Taheri
Your new post is loading...
Your new post is loading...
Scooped by Ali Taheri
Scoop.it!

A Collection of new RNA-Seq Videos from The Broad Institute

A Collection of new RNA-Seq Videos from The Broad Institute | Plant Genetics, NGS and Bioinformatics | Scoop.it
  7:30 BroadE: Trinity – How it works   5:20 BroadE: The General Approach to De novo RNA-Seq Assembly Using De Bruijn Graphs   5:38 BroadE: Introduction to De Novo RNA-Seq Assembly using Trinity   3:00 BroadE: Strand-specific RNA-Seq is Preferred ...
more...
No comment yet.
Rescooped by Ali Taheri from rosescackle
Scoop.it!

Upcoming Webinar - Part One of Field Phenomics: Developing and Using a Sensor Array - eXtension

Upcoming Webinar - Part One of Field Phenomics: Developing and Using a Sensor Array - eXtension | Plant Genetics, NGS and Bioinformatics | Scoop.it

Thursday, October 24, 2013, 1:00 PM EDT

This webinar is the first in a two part series on high throughput field phenotyping. This presentation describes the development and use of a field-based sensor array.

 

http://www1.gotomeeting.com/register/782515976


Via Plant Breeding and Genomics News, rosescackle
more...
No comment yet.
Rescooped by Ali Taheri from cereal bioinformatics
Scoop.it!

UNIX tips: Learn 10 good UNIX usage habits

UNIX tips: Learn 10 good UNIX usage habits | Plant Genetics, NGS and Bioinformatics | Scoop.it
Adopt 10 good habits that improve your UNIX(R) command line productivity -- and break away from bad usage patterns in the process.

Via Nathan Watson-Haigh
more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

Geminiviruses: masters at redirecting and reprogramming plant processes

Geminiviruses: masters at redirecting and reprogramming plant processes | Plant Genetics, NGS and Bioinformatics | Scoop.it

The family Geminiviridae is one of the largest and most important families of plant viruses. The small, single-stranded DNA genomes of geminiviruses encode 5–7 proteins that redirect host machineries and processes to establish a productive infection. These interactions reprogramme plant cell cycle and transcriptional controls, inhibit cell death pathways, interfere with cell signalling and protein turnover, and suppress defence pathways. This Review describes our current knowledge of how geminiviruses interact with their plant hosts and the functional consequences of these interactions.

more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

Great potential for faster diagnoses with new nanotechnology method

Great potential for faster diagnoses with new nanotechnology method | Plant Genetics, NGS and Bioinformatics | Scoop.it
Great potential for faster diagnoses with new nanotechnology method

The more accurately we can diagnose a disease, the greater the chance that the patient will survive. That is why many researchers are working to improve the quality of the diagnostic process. Researchers at the Nano-Science Center, University of Copenhagen have discovered a method that will make the process faster, cheaper and more accurate. This is possible, because they are combining advanced tools used in physics for research in biology at nanoscale, two scientific disciplines usually very distant from each other.

Read more: http://www.nanowerk.com/news2/newsid=32590.php#ixzz2ggDtTnSH

more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

South Korean Scientists Use E. Coli to Make Gasoline

South Korean Scientists Use E. Coli to Make Gasoline | Plant Genetics, NGS and Bioinformatics | Scoop.it
Escherichia coli can cause serious food poisoning but Korean scientists have come up with a more helpful use for the sometimes-deadly bacteria: producing gasoline.
more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

RNA-Seq Reveals New Control Genes for qRT-PCR Analysis of Human Cancer Cells

RNA-Seq Reveals New Control Genes for qRT-PCR Analysis of Human Cancer Cells | Plant Genetics, NGS and Bioinformatics | Scoop.it
Accurate quantification of gene expression by qRT-PCR relies on normalization against a consistently expressed control gene. However, control genes in common use often vary greatly between samples, especially in cancer.
more...
No comment yet.
Rescooped by Ali Taheri from Plants and Microbes
Scoop.it!

Video: UK Fungus Day: When Fungi Attack Trees (2013)

In this video Bristol woodsman Steve England explains the different ways fungi can digest wood. The first UK Fungus Day is taking place on 12th -- 13th October 2013, giving visitors the chance to explore the amazing world of fungi. Find out more about events here: http://ukfungusday.co.uk and follow #ukfungusday on Twitter: https://twitter.com/ukfungusday2013 ;

The video is produced by the British Society for Plant Pathology (http://www.bspp.org.uk) and is presented by Steve England (http://steveengland.co.uk).


Via Mary Williams, Kamoun Lab @ TSL
more...
Mary Williams's curator insight, September 30, 2013 1:57 PM

Fascinating!  The only part I didn't like is the set of related videos about toenail fungus that youtube is pushing to accompany this - yuck! I think I prefer to learn about plant fungi....

Jennifer Mach's comment, October 1, 2013 11:45 AM
That orange tree fungus looks like a Chicken of the Woods (Laetiporus sulphureus). Yummy!
Rescooped by Ali Taheri from Plants and Microbes
Scoop.it!

Annual Review Microbiology: A Paradigm for Endosymbiotic Life: Cell Differentiation of Rhizobium Bacteria Provoked by Host Plant Factors (2013)

Annual Review Microbiology: A Paradigm for Endosymbiotic Life: Cell Differentiation of Rhizobium Bacteria Provoked by Host Plant Factors (2013) | Plant Genetics, NGS and Bioinformatics | Scoop.it

Symbiosis between Rhizobium bacteria and legumes leads to the formation of the root nodule. The endosymbiotic bacteria reside in polyploid host cells as membrane-surrounded vesicles where they reduce atmospheric nitrogen to support plant growth by supplying ammonia in exchange for carbon sources and energy. The morphology and physiology of endosymbionts, despite their common function, are highly divergent in different hosts. In galegoid plants, the endosymbionts are terminally differentiated, uncultivable polyploid cells, with remarkably elongated and even branched Y-shaped cells. Bacteroid differentiation is controlled by host peptides, many of which have antibacterial activity and require the bacterial function of BacA. Although the precise and combined action of several hundred host peptides and BacA has yet to be discovered, similarities, especially to certain insect-bacterium symbioses involving likewise host peptides for manipulation of endosymbionts, suggest convergent evolution. Rhizobium-legume symbiosis provides a rich source of information for understanding host-controlled endosymbiotic life in eukaryotic cells.


Via IvanOresnik, Jean-Michel Ané, Kamoun Lab @ TSL
more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

Points of Significance: Error bars

Points of Significance: Error bars | Plant Genetics, NGS and Bioinformatics | Scoop.it
Nature Methods 10, 921 (2013).
doi:10.1038/nmeth.2659
Authors: Martin Krzywinski & Naomi Altman
The meaning of error bars is often misinterpreted, as is the statistical significance of their overlap.
more...
No comment yet.
Rescooped by Ali Taheri from Plants and Microbes
Scoop.it!

Video: Big Question: Feast or famine?

How are we going to feed a growing world without destroying the planet? Great video via The University of Minnesota's Institute on the Environment.


Via Kamoun Lab @ TSL
more...
Jean-Michel Ané's curator insight, September 28, 2013 12:27 PM

Really good video from colleagues in Minnesota highlighting the BIG problem that we are facing right now. How are we going to feed our growing human population in the next decades without destroying our planet and us ultimately? It is an exciting time to do research in plant sciences, microbiology, and agriculture to addess this issue but this is just one tool. We will need to have a serious collaborations, innovation and political courage at the international level to solve this issue.

Rescooped by Ali Taheri from Emerging Research in Plant Cell Biology
Scoop.it!

Plant Cell: An Arabidopsis Soil-Salinity–Tolerance Mutation Confers Ethylene-Mediated Enhancement of Sodium/Potassium Homeostasis

Plant Cell: An Arabidopsis Soil-Salinity–Tolerance Mutation Confers Ethylene-Mediated Enhancement of Sodium/Potassium Homeostasis | Plant Genetics, NGS and Bioinformatics | Scoop.it

The soil salinity tolerance of an Arabidopsis mutant is shown to be caused by a mutation in the ETO1 gene that results in ethylene overproduction. Increased ethylene causes root stele reactive oxygen species (ROS)–dependent reductions in root Na influx and xylem loading and stelar ROS-independent enhancement of root K status, thus improving plant Na/K homeostasis and salinity tolerance.

 

See also the In Brief about this article: www.plantcell.org/content/early/2013/09/22/tpc.113.250911.full.pdf


Via Mary Williams, Jennifer Mach
more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

'Highly programmable' DNA cubes could be used for drug delivery (Wired UK)

'Highly programmable' DNA cubes could be used for drug delivery (Wired UK) | Plant Genetics, NGS and Bioinformatics | Scoop.it
In research carried out at McGill University in Canada, lipid-tipped DNA chains attached to DNA cubes folded back inside, creating places for hydrophobic molecules to be carried
more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

Outside influence: Genes outside nucleus have disproportionate effect

Outside influence: Genes outside nucleus have disproportionate effect | Plant Genetics, NGS and Bioinformatics | Scoop.it

http://elife.elifesciences.org/content/2/e00776

New research from the University of California, Davis, shows that the tiny proportion of a cell's DNA that is located outside the cell nucleus has a disproportionately large effect on a cell's metabolism.

more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

Advanced genetic tools for plant biotechnology

Advanced genetic tools for plant biotechnology | Plant Genetics, NGS and Bioinformatics | Scoop.it
Nature Reviews Genetics.
doi:10.1038/nrg3583
Authors: Wusheng Liu, Joshua S. Yuan & C. Neal Stewart Jr

Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.

more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

On the front line: structural insights into plant–pathogen interactions

On the front line: structural insights into plant–pathogen interactions | Plant Genetics, NGS and Bioinformatics | Scoop.it
Ali Taheri's insight:

Over the past decade, considerable advances have been made in understanding the molecular mechanisms that underpin the arms race between plant pathogens and their hosts. Alongside genomic, bioinformatic, proteomic, biochemical and cell biological analyses of plant–pathogen interactions, three-dimensional structural studies of virulence proteins deployed by pathogens to promote infection, in some cases complexed with their plant cell targets, have uncovered key insights into the functions of these molecules. Structural information on plant immune receptors, which regulate the response to pathogen attack, is also starting to emerge. Structural studies of bacterial plant pathogen–host systems have been leading the way, but studies of filamentous plant pathogens are gathering pace. In this Review, we summarize the key developments in the structural biology of plant pathogen–host interactions.

more...
No comment yet.
Rescooped by Ali Taheri from Plant Biology Teaching Resources (Higher Education)
Scoop.it!

Plant Physiol. Focus Issue: Calcium signaling

Plant Physiol. Focus Issue: Calcium signaling | Plant Genetics, NGS and Bioinformatics | Scoop.it

Want to talk about calcium signaling? Of course you do! It's important in the regulation of stomatal aperture, stress response, interactions with microbes etc.

Check out the focus issue of Plant Physiology on calcium signalling - lots of uptakes, reviews and new research, with an overview by Alex Webb here: www.plantphysiol.org/content/163/2/457.full.html


Via Mary Williams
more...
Andres Zurita's curator insight, October 9, 2013 10:33 AM

Great Issue with several interesting topics, and free acce$$

Scooped by Ali Taheri
Scoop.it!

Towards establishing broad-spectrum disease resistance in plants: silicon leads the way

Towards establishing broad-spectrum disease resistance in plants: silicon leads the way | Plant Genetics, NGS and Bioinformatics | Scoop.it

Plants are constantly threatened by a wide array of microbial pathogens. Pathogen invasion can lead to vast yield losses and the demand for sustainable plant-protection strategies has never been greater. Chemical plant activators and selected strains of rhizobacteria can increase resistance against specific types of pathogens but these treatments are often ineffective or even cause susceptibility against others. Silicon application is one of the scarce examples of a treatment that effectively induces broad-spectrum disease resistance. The prophylactic effect of silicon is considered to be the result of both passive and active defences. Although the phenomenon has been known for decades, very little is known about the molecular basis of silicon-afforded disease control. By combining knowledge on how silicon interacts with cell metabolism in diatoms and plants, this review describes silicon-induced regulatory mechanisms that might account for broad-spectrum plant disease resistance. Priming of plant immune responses, alterations in phytohormone homeostasis, regulation of iron homeostasis, silicon-driven photorespiration and interaction with defence signalling components all are potential mechanisms involved in regulating silicon-triggered resistance responses. Further elucidating how silicon exerts its beneficial properties may create new avenues for developing plants that are better able to withstand multiple attackers.

more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

Absolutely everything you need to know about how the government shutdown will work

Absolutely everything you need to know about how the government shutdown will work | Plant Genetics, NGS and Bioinformatics | Scoop.it
The government is likely to shut down on Tuesday. Here's our comprehensive explainer on what will happen next.
more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

New metabolic pathway to more efficiently convert sugars into biofuels

New metabolic pathway to more efficiently convert sugars into biofuels | Plant Genetics, NGS and Bioinformatics | Scoop.it
UCLA chemical engineering researchers have created a new synthetic metabolic pathway for breaking down glucose that could lead to a 50 percent increase in the production of biofuels.
more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

'Dont perish: a step-by-step approach to writing and publishing a scientific paper'

more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

The way you say it

Nature Methods 10, 917 (2013).
doi:10.1038/nmeth.2686
Wording criticism constructively is important before and after publication.
more...
No comment yet.
Rescooped by Ali Taheri from The science toolbox
Scoop.it!

Points of significance: Importance of being uncertain : Nature Methods : Nature Publishing Group

Points of significance: Importance of being uncertain : Nature Methods : Nature Publishing Group | Plant Genetics, NGS and Bioinformatics | Scoop.it
Statistics does not tell us whether we are right. It tells us the chances of being wrong.

Via Niklaus Grunwald
more...
No comment yet.
Scooped by Ali Taheri
Scoop.it!

Association Mapping Using TASSEL Software - eXtension

Association Mapping Using TASSEL Software - eXtension | Plant Genetics, NGS and Bioinformatics | Scoop.it
Author: M. Awais Khan, University of Illinois, Urbana-Champaign This article introduces the concept of association mapping and the related...
more...
No comment yet.
Rescooped by Ali Taheri from Tracking the Future
Scoop.it!

3D Printing Aims to Deliver Organs on Demand

3D Printing Aims to Deliver Organs on Demand | Plant Genetics, NGS and Bioinformatics | Scoop.it

Dying patients could someday receive a 3D-printed organ made from their own cells rather than wait on long lists for the short supply of organ transplants. Such a futuristic dream remains far from reality, but university labs and private companies have already taken the first careful steps by using 3D-printing technology to build tiny chunks of organs.


Via Szabolcs Kósa
more...
Kristy Schofield's curator insight, September 28, 2013 6:31 PM

so strange!

Joshua Zemanek's curator insight, October 2, 2013 12:07 PM

After reading this article, I thought that creating organs instead of taking them from donors would be so much more efficient in the world today. The only problem is that we are very far from doing so. However, we already have people creating the first steps to creating functioning artificial organs. This would very efficient and helpful for people with major health problems. The furthest they've made it was by building tiny chunks of organs, but that's still revolutionary. My connection to the U.S. is that with the number of accidents in our country, this could help with a ton of medical problems people experience.

Saghit Rethmeier's comment, October 4, 2013 9:29 AM
This is amazing, Its crazy that out techonology is advanced enough to be able to do this. Im interested to see how far it will be taken and what possibilitites there are in the future.