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Screening a cDNA Library for Protein–Protein Interactions Directly in Planta

Screening a cDNA Library for Protein–Protein Interactions Directly in Planta | learning plant | Scoop.it

We used bimolecular fluorescence complementation technology to screen a plant cDNA library against a bait protein directly in plants. As proof of concept, we used the N-terminal fragment of yellow fluorescent protein– or nVenus-tagged Agrobacterium tumefaciens VirE2 and VirD2 proteins and the C-terminal extension (CTE) domain of Arabidopsis thaliana telomerase reverse transcriptase as baits to screen an Arabidopsis cDNA library encoding proteins tagged with the C-terminal fragment of yellow fluorescent protein. A library of colonies representing ∼2 × 105 cDNAs was arrayed in 384-well plates.

Sequential screening of subsets of cDNAs in Arabidopsis leaf or tobacco (Nicotiana tabacum) Bright Yellow-2 protoplasts identified single cDNA clones encoding proteins that interact with either, or both, of the Agrobacterium bait proteins, or with CTE. T-DNA insertions in the genes represented by some cDNAs revealed five novel Arabidopsis proteins important for Agrobacterium-mediated plant transformation. We also used this cDNA library to confirm VirE2-interacting proteins in orchid (Phalaenopsis amabilis) flowers. Thus, this technology can be applied to several plant species.


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Exclusive: TIME Talks to Google CEO Larry Page About Its New Venture to Extend Human Life | TIME.com

Exclusive: TIME Talks to Google CEO Larry Page About Its New Venture to Extend Human Life | TIME.com | learning plant | Scoop.it
Bold project, to be led by biotech pioneer Arthur Levinson, will tackle's some of health care's biggest problems
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A big player is coming!

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Science Magazine: Sign In

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Science 17 January 2014: 
Vol. 343 no. 6168 p. 262 
DOI: 10.1126/science.1249912PERSPECTIVE

RETROSPECTIVE

Frederick Sanger (1918–2013)Sydney Brenner

quote

"A Fred Sanger would not survive today's world of science. With continuous reporting and appraisals, some committee would note that he published little of import between insulin in 1952 and his first paper on RNA sequencing in 1967 with another long gap until DNA sequencing in 1977. He would be labeled as unproductive, and his modest personal support would be denied. We no longer have a culture that allows individuals to embark on long-term—and what would be considered today extremely risky—projects."

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The NODE: A day in the life of an Arabidopsis lab

The NODE: A day in the life of an Arabidopsis lab | learning plant | Scoop.it

The Node is running a series about model organisms, and here is their latest on .... Arabidopsis thaliana! Written by graduate student Narender Kumar from Louisiana State University.


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The familiar life style for most Arabidopsis growers!

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Mary Williams's curator insight, February 14, 1:41 AM

A nice introduction for students who haven't worked with one of plant science's favorite model organisms.

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Cell - Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

Cell - Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA | learning plant | Scoop.it
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The structure of Cas9 complex revealed!

 

Hot and fast!

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Voyager May Have Left Solar System—a Year Ago - Newser

Voyager May Have Left Solar System—a Year Ago - Newser | learning plant | Scoop.it
NPR
Voyager May Have Left Solar System—a Year Ago
Newser
"Basically it's just happily heading out towards... pretty much nowhere." How did scientists miss that little detail?
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Language of the Plant | Advancing Ag

Home » Language of the Plant

Language of the Plant

By Jerry Stoller

It may come as a shock to many people, but most vegetable crops have the same growth characteristics. Yes, there is a difference in degree between crops and even between varieties. The basic principles, however, are the same.
Objective of Crop Production:
• Maximize the production of carbon compounds (sugars) in the leaves.
• Move these compounds to the seeds, fruit, or storage tissue of the crop.
For many of our crops, we want strong cell wall tissue that will hold a lot of water. This adds low cost weight to the crop that we sell. As our crop grows, we see certain things; color, height, length of branches or vines, number of fruit, etc. If the crop gets under stress and losses color, we apply nitrogen. This may result in several days greener color; however, it does not solve our problem of yields and quality. It may even reduce quality. We need to have a better understanding of the language of the plants.

The key word for understanding the plant is STRESS. As with people and animals, STRESS is always present…sometimes great and sometimes small. Our objective is to minimize it. STRESS always starts in the roots. If they become flooded and lose oxygen, they cause plant STRESS. If the soil becomes too dry, the roots do not grow correctly and it causes plant STRESS. If the roots become“leaky” they attract diseases and it causes the plant STRESS. Roots try to grow continuously. They expand just behind the root cap. It is this area (about 10 mm) behind the root cap where most water and nutrients are absorbed for plant growth. The active roots remain active for about 7 to 14 days. The roots or rooting area older than 7 to 14 days are not functional. Therefore, actively growing new roots are essential for normal plant growth. If root growth is negatively affected, it
results in plant STRESS.It is important that the growing area just behind the root cap has adequate calcium for strong cell wall formation. If calcium is not sufficient in this critical zone, the root cells will be weak. This will result in “leaky” roots which will attract disease and cause plant STRESS. Roots not only supply the plant with water and nutrients, they supply necessary plant hormones such as Cytokinins. This hormone will help activate auxiliary bud activity and help suppress other hormones that may be “out of balance”. The balancing of Ethylene hormone may be Cytokinin’s most important function. Let’s now go above ground and learn about the plant. The plant is hormone driven. Most fertilizer nutrients affect hormones. The main nutrient to affect hormones is nitrogen…more importantly nitrate forms of nitrogen. It stimulates IAA and auxin that cause great terminal growth. The more nitrate you apply, the greater the vegetative growth will become.

Unfortunately, if the plant comes under STRESS, plants with higher nitrates will have more disease and lower quality of storage tissue (physiological disorders). In addition, more blooms will appear and more blooms and fruit will be aborted. We have all seen this. The hormones caused by nitrogen can increase yields and can also reduce yields and quality if the growing season causes STRESS. Why? When plants come under STRESS, protein hydrolyzes to ammonia. The ammonia becomes toxic and causes the plant to produce Ethylene (the aging hormone). In turn, Ethylene promotes enzymes that act like “PACK MAN” they eat up cell wall tissue that causes soft fruit, soft storage tissue, underdeveloped tissue, blossom-end-rot and other problems called physiological disorders.

The bad guy in the whole scenario is Ethylene…the aging hormone. It is stress related. It causes blooms. It causes blooms and fruit to abort. It causes maturity. If the plant is STRESSED early, it causes early dying. We have all seen plants forced in to early maturity (early dying) when crops are STRESSED by either abnormal weather or disease. If we have high levels of Ethylene in the plant creating a lot of “PAC MEN” who chew up cell walls, we have created a perfect situation for disease infection. If you have followed the above, let me now take you through the “plant talk”. We are trying to grow the most profitable crop, so we apply a liberal amount of nitrogen that primarily feed our plant in the form of nitrate. When the nitrate gets into the leaf, it produces protein and organic acids. The more nitrates that go into the leaves, the more organic acids will be produced in the leaves. The organic acids “demand” cations such as potassium, magnesium, and calcium to neutralize them. They prefer calcium. This increases the calcium gradient between the leaves and other plant parts…the “giant sucking sound”. This depletes other plant parts of needed calcium. This is what causes physiological disorders…bitter pit, hollow heart, blossom-end-rot, soft onion, cavity spot, tip burn, etc. Adequate boron in the plant will reduce the leaves “sucking ability”. This is why boron inhibits calcium problems.

The above problem is bad, but the worse is still to come. The calcium problem in the storage tissue usually happens when the plant is making vigorous growth. During this period, root growth slows down. The roots are not capable of supplying adequate calcium to alleviate this problem. In fact, calcium is drawn out of the root growing points and stolen growing points. Just as stolens abort their meristematic tissue during the rapid growth of potatoes, all plants abort meristematic root tissue. There simply is not enough calcium in the meristematic tissue for normal cell growth. The above cause “leaky roots” which attract disease. Worse yet, it causes STRESS.

This increases Ethylene in the plant which makes the plant susceptible to disease. The roots can no longer produce enough hormones to control the Ethylene build-up. It’s now fungicide time. If we could stop the buildup of Ethylene, I believe we could suppress disease development. So, high nitrogen use can cause physiological problems, quality problems, storage problems, and disease problems in our plants. Do we then greatly reduce the nitrogen that we use…even if it reduces the yield of our plants? NO!

Now, comes the commercial!! We reduce the nitrate nitrogen that our plant feeds on. This reduces organic acids in the leaves and reduces the “giant sucking sound” of calcium.
• We use Nitro-Plus which is liquid amine nitrogen and calcium solution, instead of the common forms of nitrogen. We supply a larger quantity of calcium in the feeding zone of the roots and stolens.
• We inject Nitro-Plus into the bed or seeding areas before transplanting or seeding.
• We use Nitro-Plus (soil applications), and (foliar applications) integrated into our total nitrogen program.. We recommend that this unique nitrogen supplies at least 1/3 of total nitrogen applied. Where STRESS is greater, higher rates are beneficial. The other method which is used in conjunction with the Nitro-Plus program is a foliar treatment which will suppress Ethylene build-up in the plant.
• We spray with Harvest Plus GA, SET, Desert Mix, Calcium 5 S, Calcium 5 X and Nitrate Balancer every 7 to 14 days according to the plant needs.
What should we see, if we follow this program?
1. A larger diameter stem.
2. A larger and whiter root growth.
3. More branches and fruiting points.
4. A more even set of fruit.
5. Wider leaves.
6. Stronger cell walls:
a) Less drooping of the plants.
b) Stronger stems.
c) Heavier tissue.
7. More storage tissue.
8. Less early dying.
9. Better storage and/or shelf life.

“WE CAN ONLY LEARN BY UNDERSTANDING THE LANGUAGE OF THE PLAN


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OA book: Abiotic Stress - Plant Responses and Applications in Agriculture

OA book: Abiotic Stress - Plant Responses and Applications in Agriculture | learning plant | Scoop.it

This recently published Open Access book includes up-to-date, well-written chapters on many aspects of plant responses to abiotic stress. Good resource for students and researchers!

 


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Albert Einstein Quotes - 147 Science Quotes - Dictionary of Science Quotations and Scientist Quotes

Albert Einstein Quotes - 147 Science Quotes - Dictionary of Science Quotations and Scientist Quotes | learning plant | Scoop.it
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Reading Assignments for "Environment and Human History"

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very interesting topic, and excellent readings

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Phytopathogen type III effectors as probes of biological systems - Microbial Biotechnology

Phytopathogen type III effectors as probes of biological systems - Microbial Biotechnology | learning plant | Scoop.it

Amy Huei-Yi Lee; Maggie A. Middleton; David S. Guttman; Darrell Desveaux

 

Summary:

Bacterial phytopathogens utilize a myriad of virulence factors to modulate their plant hosts in order to promote successful pathogenesis. One potent virulence strategy is to inject these virulence proteins into plant cells via the type III secretion system. Characterizing the host targets and the molecular mechanisms of type III secreted proteins, known as effectors, has illuminated our understanding of eukaryotic cell biology. As a result, these effectors can serve as molecular probes to aid in our understanding of plant cellular processes, such as immune signalling, vesicle trafficking, cytoskeleton stability and transcriptional regulation. Furthermore, given that effectors directly and specifically interact with their targets within plant cells, these virulence proteins have enormous biotechnological potential for manipulating eukaryotic systems.


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Freddy Monteiro's curator insight, February 27, 2013 12:34 AM

For quite some time effector proteins started to be regarded as potential molecular tools to investigate cellular processes. This is an expanding field and I hope effector biology may help on our understanding of plant biology and molecular evolution dynamics.

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Fluorescent fusion protein knockout mediated by anti-GFP nanobody - Nature Struct. Mol. Biology

Fluorescent fusion protein knockout mediated by anti-GFP nanobody - Nature Struct. Mol. Biology | learning plant | Scoop.it

http://www.nature.com/nsmb/journal/v19/n1/full/nsmb.2180.html

Caussinus et al (2012)

The use of genetic mutations to study protein functions in vivo is a central paradigm of modern biology. Recent advances in reverse genetics such as RNA interference and morpholinos are widely used to further apply this paradigm. Nevertheless, such systems act upstream of the proteic level, and protein depletion depends on the turnover rate of the existing target proteins. Here we present deGradFP, a genetically encoded method for direct and fast depletion of target green fluorescent protein (GFP) fusions in any eukaryotic genetic system. This method is universal because it relies on an evolutionarily highly conserved eukaryotic function, the ubiquitin pathway. It is traceable, because the GFP tag can be used to monitor the protein knockout. In many cases, it is a ready-to-use solution, as GFP protein-trap stock collections are being generated in Drosophila melanogaster and in Danio rerio.


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aamoros2's curator insight, June 24, 9:39 AM

Proteínas fluorescentes.

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How Lytro’s Weird Design Tells A Story About Revolutionary Tech

How Lytro’s Weird Design Tells A Story About Revolutionary Tech | learning plant | Scoop.it
If you had to give an award for the year’s most breakthrough piece of consumer tech, there’s a good chance it would go to Lytro, a camera company which recently unveiled its first product. Unlike other cameras, you never need to focus it.

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Receptor Kinase Signaling Pathways in Plant-Microbe Interactions - Annual Review of Phytopathology, 50(1):451

Receptor Kinase Signaling Pathways in Plant-Microbe Interactions - Annual Review of Phytopathology, 50(1):451 | learning plant | Scoop.it

A very enjoyable review: Although the FLS2 CLV3 debate is not raised, the wide overview of structural studies and pathogenic and symboitic RLKS is nice.

 

Meritxell Antolín-Llovera, Martina K. Ried, Andreas Binder, and Martin Parniske

 

ABSTRACT

Plant receptor-like kinases (RLKs) function in diverse signaling pathways, including the responses to microbial signals in symbiosis and defense. This versatility is achieved with a common overall structure: an extracytoplasmic domain (ectodomain) and an intracellular protein kinase domain involved in downstream signal transduction. Various surfaces of the leucine-rich repeat (LRR) ectodomain superstructure are utilized for interaction with the cognate ligand in both plant and animal receptors. RLKs with lysin-motif (LysM) ectodomains confer recognitional specificity toward N-acetylglucosamine-containing signaling molecules, such as chitin, peptidoglycan (PGN), and rhizobial nodulation factor (NF), that induce immune or symbiotic responses. Signaling downstream of RLKs does not follow a single pattern; instead, the detailed analysis of brassinosteroid (BR) signaling, innate immunity, and symbiosis revealed at least three largely nonoverlapping pathways. In this review, we focus on RLKs involved in plant-microbe interactions and contrast the signaling pathways leading to symbiosis and defense.


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「Bioinformatics」生物信息新手入门+编程语言选择

「Bioinformatics」生物信息新手入门+编程语言选择 | learning plant | Scoop.it
从今天开始在这里开始分享生物信息的知识和学习心得。…
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学习生物信息学的感受,PERL和PYTHON

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LabWrite for Students

LabWrite for Students | learning plant | Scoop.it
LabWrite Overall Help1. What is LabWrite?

LabWrite is a web-based tutorial to help you with your labs. It provides guidance you need before--during, and after lab--to make the most of your lab experience. The core of LabWrite is the lab report, helping you write your lab report step-by-step. Although with some exploration you may easily learn how to use LabWrite, your instructor should provide the initial overview and training for using LabWrite. Go to How to Use LabWrite on the main homepage for more information on using the LabWrite site.

2. Why use LabWrite?

LabWrite materials are intended to help you improve your lab report writing skills as well as help you learn science. Whether you've written lab reports before or not, you'll find materials in LabWrite to assist you with all aspects of writing a lab report. LabWrite focuses on the process of writing lab reports. It provides a structure for your thinking so that you do not feel lost in the lab experience. From the moment you read the lab unit in your lab manual to the moment you actually sit down to write your lab report, LabWrite offers materials to help you with each step. Even when you get your graded lab report back from your instructor, LabWrite can help you interpret and improve your grade.

By helping you understand the process involved in writing good lab reports, LabWrite helps you become better writers of science. Its goal is that you begin to see writing lab reports as an opportunity to really understand the science you are covering in lab and not just as busy work. No matter what scientific field you're in, LabWrite helps you with organization, thinking, and technical skills you may find useful later on.

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I think this site will be helpful for students to better their experiment records!

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BIOGLOW | Glowing Plant

BIOGLOW | Glowing Plant | learning plant | Scoop.it
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Bioglow’s Starlight Avatar™ Variety - the world’s first autoluminescent glowing plant.
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Crystal structures of the phosphorylated BRI1 kinase domain and implications for brassinosteroid signal initiation - Bojar - The Plant Journal - Wiley Online Library

Crystal structures of the phosphorylated BRI1 kinase domain and implications for brassinosteroid signal initiation - Bojar - The Plant Journal - Wiley Online Library | learning plant | Scoop.it

Brassinosteroids, which control plant growth and development, are sensed by the membrane receptor kinase BRASSINOSTEROID INSENSITIVE 1 (BRI1). Brassinosteroid binding to the BRI1 leucine-rich repeat (LRR) domain induces heteromerisation with a SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK)-family co-receptor. This allows the cytoplasmic kinase domains of BRI1 and SERK to interact, transphosphorylate and activate each other. Here we report crystal structures of the BRI1 kinase domain in its activated form and in complex with nucleotides. BRI1 has structural features reminiscent of both serine/threonine and tyrosine kinases, providing insight into the evolution of dual-specificity kinases in plants. Phosphorylation of Thr1039, Ser1042 and Ser1044 causes formation of a catalytically competent activation loop. Mapping previously identified serine/threonine and tyrosine phosphorylation sites onto the structure, we analyse their contribution to brassinosteroid signalling. The location of known genetic missense alleles provide detailed insight into the BRI1 kinase mechanism, while our analyses are inconsistent with a previously reported guanylate cyclase activity. We identify a protein interaction surface on the C-terminal lobe of the kinase and demonstrate that the isolated BRI1, SERK2 and SERK3 cytoplasmic segments form homodimers in solution and have a weak tendency to heteromerise. We propose a model in which heterodimerisation of the BRI1 and SERK ectodomains brings their cytoplasmic kinase domains in a catalytically competent arrangement, an interaction that can be modulated by the BRI1 inhibitor protein BKI1.


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Nature Biotech: Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease (2013)

Nature Biotech: Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease (2013) | learning plant | Scoop.it

http://www.nature.com/nbt/journal/v31/n8/full/nbt.2655.html

 

Sustainable intensification of crop production is essential to ensure food demand is matched by supply as the human population continues to increase. This will require high-yielding crop varieties that can be grown sustainably with fewer inputs on less land. Both plant breeding and genetic modification (GM) methods make valuable contributions to varietal improvement, but targeted genome engineering promises to be critical to elevating future yields. Most such methods require targeting DNA breaks to defined locations followed by either nonhomologous end joining (NHEJ) or homologous recombination. Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) can be engineered to create such breaks, but these systems require two different DNA binding proteins flanking a sequence of interest, each with a C-terminal FokI nuclease module. We report here that the bacterial clustered, regularly interspaced, short palindromic repeats (CRISPR) system, comprising a CRISPR-associated (Cas)9 protein and an engineered single guide RNA (sgRNA) that specifies a targeted nucleic acid sequence, is applicable to plants to induce mutations at defined loci.


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Elizabeth Jones's curator insight, October 2, 2013 1:25 PM

CRISPR-Cas9 is hot right now, and it's being used in several different ways: for genome-editing in cells of various species (here they're showing it works in plants),  or to create heritable changes (i.e. new transgenic animal lines), and also as a transcription factor to regulate gene expression without altering the nuclear DNA. 

 

Constructs that use Cas9 and synthetic guide RNA (sgRNA) can be customized to target any gene of interest, and can produce insertions, deletions, or incorportation of variant sequences into genomic DNA. Customized constructs can be ordered from gene synthesis suppliers such as GenScript, and delivered much more quickly and cheaply than they can be produced in a typical lab using traditional molecular cloning techniques. 

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Metabolo-proteomics to discover plant biotic stress resistance genes.

Plants continuously encounter various environmental stresses and use qualitative and quantitative measures to resist pathogen attack. Qualitative stress responses, based on monogenic inheritance, have been elucidated and successfully used in plant improvement. By contrast, quantitative stress responses remain largely unexplored in plant breeding, due to complex polygenic inheritance, although hundreds of quantitative trait loci for resistance have been identified. Recent advances in metabolomic and proteomic technologies now offer opportunities to overcome the hurdle of polygenic inheritance and identify candidate genes for use in plant breeding, thus improving the global food security. In this review, we describe a conceptual background to the plant-pathogen relationship and propose ten heuristic steps streamlining the application of metabolo-proteomics to improve plant resistance to biotic stress.


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ABA signal transduction at the crossroad of biotic and abiotic stress responses

ABA signal transduction at the crossroad of biotic and abiotic stress responses | learning plant | Scoop.it

Abscisic acid (ABA) regulates key processes relevant to seed germination, plant development, and biotic and abiotic stress responses. Abiotic stress conditions such as drought induce ABA biosynthesis initiating the signalling pathways that lead to a number of molecular and cellular responses, among which the best known are the expression of stress-related genes and stomatal closure. Stomatal closure also serves as a mechanism for pathogen defence, thereby acting as a platform for crosstalk between biotic and abiotic stress responses involving ABA action. We will describe a pathway model that starts with ABA binding to the PYR/PYL/RCAR family of receptors, followed by inactivation of 2C-type protein phosphatases and activation of SnRK2-type kinases, and eventually lead to activation of ion channels in guard cells and stomatal closure.

 


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Transcriptional regulation by miRNA mimics that target sequences downstream of gene termini - Molecular BioSystems (RSC Publishing)

PaperPrevious Article|Next ArticleTranscriptional regulation by miRNA mimics that target sequencesdownstream of gene termini
Scott T. Younger and David R. CoreyMol. BioSyst., 2011,7, 2383-2388
DOI: 10.1039/C1MB05090G
Received 02 Mar 2011, Accepted 03 May 2011
First published on the web 18 May 2011

Transcriptome studies have revealed that protein-coding loci within the humangenome are overlapped at their 3′-termini by noncoding RNA (ncRNA) transcripts. Small duplex RNAs designed to be fully complementary to these 3′ ncRNAs can modulate transcription of the upstream gene. Robust regulation by designed RNAssuggests that endogenous small RNAs might also recognize 3′ ncRNAs and regulategene expression. A genome-wide evaluation revealed that sequences immediatelydownstream of protein-coding genes are enriched with miRNA target sites. We experimentally tested miRNA mimics complementary to the well-characterized 3′-terminus of the human progesterone receptor (PR) gene and observed inhibition of PR transcription. These results suggest that recognition of ncRNA transcripts that overlap gene termini may be a natural function of endogenous small RNAs.



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Phytopathogen type III effectors as probes of biological systems - Microbial Biotechnology

Phytopathogen type III effectors as probes of biological systems - Microbial Biotechnology | learning plant | Scoop.it

Amy Huei-Yi Lee; Maggie A. Middleton; David S. Guttman; Darrell Desveaux

 

Summary:

Bacterial phytopathogens utilize a myriad of virulence factors to modulate their plant hosts in order to promote successful pathogenesis. One potent virulence strategy is to inject these virulence proteins into plant cells via the type III secretion system. Characterizing the host targets and the molecular mechanisms of type III secreted proteins, known as effectors, has illuminated our understanding of eukaryotic cell biology. As a result, these effectors can serve as molecular probes to aid in our understanding of plant cellular processes, such as immune signalling, vesicle trafficking, cytoskeleton stability and transcriptional regulation. Furthermore, given that effectors directly and specifically interact with their targets within plant cells, these virulence proteins have enormous biotechnological potential for manipulating eukaryotic systems.


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Freddy Monteiro's curator insight, February 27, 2013 12:34 AM

For quite some time effector proteins started to be regarded as potential molecular tools to investigate cellular processes. This is an expanding field and I hope effector biology may help on our understanding of plant biology and molecular evolution dynamics.

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Screening a cDNA Library for Protein–Protein Interactions Directly in Planta

Screening a cDNA Library for Protein–Protein Interactions Directly in Planta | learning plant | Scoop.it

We used bimolecular fluorescence complementation technology to screen a plant cDNA library against a bait protein directly in plants. As proof of concept, we used the N-terminal fragment of yellow fluorescent protein– or nVenus-tagged Agrobacterium tumefaciens VirE2 and VirD2 proteins and the C-terminal extension (CTE) domain of Arabidopsis thaliana telomerase reverse transcriptase as baits to screen an Arabidopsis cDNA library encoding proteins tagged with the C-terminal fragment of yellow fluorescent protein. A library of colonies representing ∼2 × 105 cDNAs was arrayed in 384-well plates.

Sequential screening of subsets of cDNAs in Arabidopsis leaf or tobacco (Nicotiana tabacum) Bright Yellow-2 protoplasts identified single cDNA clones encoding proteins that interact with either, or both, of the Agrobacterium bait proteins, or with CTE. T-DNA insertions in the genes represented by some cDNAs revealed five novel Arabidopsis proteins important for Agrobacterium-mediated plant transformation. We also used this cDNA library to confirm VirE2-interacting proteins in orchid (Phalaenopsis amabilis) flowers. Thus, this technology can be applied to several plant species.


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MIT: How human language could have evolved from birdsongs

MIT: How human language could have evolved from birdsongs | learning plant | Scoop.it

Linguistics and biology researchers propose a new theory on the deep roots of human speech. “The sounds uttered by birds offer in several respects the nearest analogy to language,” Charles Darwin wrote in “The Descent of Man” (1871), while contemplating how humans learned to speak. Language, he speculated, might have had its origins in singing, which “might have given rise to words expressive of various complex emotions.” 

Now researchers from MIT, along with a scholar from the University of Tokyo, say that Darwin was on the right path. The balance of evidence, they believe, suggests that human language is a grafting of two communication forms found elsewhere in the animal kingdom: first, the elaborate songs of birds, and second, the more utilitarian, information-bearing types of expression seen in a diversity of other animals.

 

The idea builds upon Miyagawa’s conclusion, detailed in his previous work, that there are two “layers” in all human languages: an “expression” layer, which involves the changeable organization of sentences, and a “lexical” layer, which relates to the core content of a sentence. His conclusion is based on earlier work by linguists including Noam Chomsky, Kenneth Hale and Samuel Jay Keyser.

Based on an analysis of animal communication, and using Miyagawa’s framework, the authors say that birdsong closely resembles the expression layer of human sentences — whereas the communicative waggles of bees, or the short, audible messages of primates, are more like the lexical layer. At some point, between 50,000 and 80,000 years ago, humans may have merged these two types of expression into a uniquely sophisticated form of language.

To consider the difference between the expression layer and the lexical layer, take a simple sentence: “Todd saw a condor.” We can easily create variations of this, such as, “When did Todd see a condor?” This rearranging of elements takes place in the expression layer and allows us to add complexity and ask questions. But the lexical layer remains the same, since it involves the same core elements: the subject, “Todd,” the verb, “to see,” and the object, “condor.” 

Birdsong lacks a lexical structure. Instead, birds sing learned melodies with what Berwick calls a “holistic” structure; the entire song has one meaning, whether about mating, territory or other things. The Bengalese finch, as the authors note, can loop back to parts of previous melodies, allowing for greater variation and communication of more things; a nightingale may be able to recite from 100 to 200 different melodies. 

By contrast, other types of animals have bare-bones modes of expression without the same melodic capacity. Bees communicate visually, using precise waggles to indicate sources of foods to their peers; other primates can make a range of sounds, comprising warnings about predators and other messages.

Humans, according to Miyagawa, Berwick and Okanoya, fruitfully combined these systems. We can communicate essential information, like bees or primates — but like birds, we also have a melodic capacity and an ability to recombine parts of our uttered language. For this reason, our finite vocabularies can generate a seemingly infinite string of words. Indeed, the researchers suggest that humans first had the ability to sing, as Darwin conjectured, and then managed to integrate specific lexical elements into those songs.


Via Dr. Stefan Gruenwald
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Thriving since 1960, my garden in a bottle: Seedling sealed in its own ecosystem and watered just once in 53 years

Thriving since 1960, my garden in a bottle: Seedling sealed in its own ecosystem and watered just once in 53 years | learning plant | Scoop.it
Gardener David Latimer, from Cranleigh, Surrey, first planted his bottle garden in 1960 and finally sealed it tightly shut 12 years later as an experiment - and it's still going strong.

Via The BioSync Team
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is that a possible way to set up closed ecosystems for journey to Mars?

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SIN JONES's comment, February 15, 2013 9:39 AM
amazing!