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Rescooped by chein cherry from Plant Biology Teaching Resources (Higher Education)
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An Optical Clearing Technique for Plant Tissues Allowing Deep Imaging and Compatible with Fluorescence Microscopy

An Optical Clearing Technique for Plant Tissues Allowing Deep Imaging and Compatible with Fluorescence Microscopy | to step further on my research | Scoop.it

In this new article in Plant Physiology, an effective new tissue clearing method is used in plants with impressive results. I think this could be easily incorporated for use by undergraduate students. Previously developed as "Scale" method for use in animal tissues, the results were similarly effective (http://www.nature.com/neuro/journal/v14/n11/full/nn.2928.html). See a stunning image of a cleared mouse embryo here: http://www.riken.jp/en/pr/press/2011/20110830_3/.


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Scientists Find Area Of The Brain That Motivates Us To Exercise | IFLScience

Scientists Find Area Of The Brain That Motivates Us To Exercise | IFLScience | to step further on my research | Scoop.it
Scientists have discovered a tiny region of the brain that controls a mouse’s desire to run and join in on other rewarding activities. Called the dorsal medial habenula, the structure is similar in mice and men, and its ability to regulate mood and motivation should be the same across the two species. 

Via Luisa Meira
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gracefull

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Advances and Computational Tools towards Predictable Design in Biological Engineering

Advances and Computational Tools towards Predictable Design in Biological Engineering | to step further on my research | Scoop.it

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Via Gerd Moe-Behrens
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wish it is dazzling enough

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Gerd Moe-Behrens's curator insight, August 28, 2014 5:40 PM

by
Pasotti L, Zucca S.

"The design process of complex systems in all the fields of engineering requires a set of quantitatively characterized components and a method to predict the output of systems composed by such elements. This strategy relies on the modularity of the used components or the prediction of their context-dependent behaviour, when parts functioning depends on the specific context. Mathematical models usually support the whole process by guiding the selection of parts and by predicting the output of interconnected systems. Such bottom-up design process cannot be trivially adopted for biological systems engineering, since parts function is hard to predict when components are reused in different contexts. This issue and the intrinsic complexity of living systems limit the capability of synthetic biologists to predict the quantitative behaviour of biological systems. The high potential of synthetic biology strongly depends on the capability of mastering this issue. This review discusses the predictability issues of basic biological parts (promoters, ribosome binding sites, coding sequences, transcriptional terminators, and plasmids) when used to engineer simple and complex gene expression systems in Escherichia coli. A comparison between bottom-up and trial-and-error approaches is performed for all the discussed elements and mathematical models supporting the prediction of parts behaviour are illustrated."

 http://bit.ly/1tHXAFj

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Origin of plant auxin biosynthesis: Trends in Plant Science

Origin of plant auxin biosynthesis: Trends in Plant Science | to step further on my research | Scoop.it
•Current phylogenetic data do not support the existence of IAA biosynthesis in algae.•Plant Trp-dependent IAA biosynthesis has been shaped by gene transfer.•IAA biosynthesis in plants evolved in response to microbe–plant interactions.

 

The recent finding of the tryptophan aminotransferase (TAA)/flavin monooxygenase (YUC) pathway as the principal route of auxin production in plants provides an opportunity to revisit the origin of plant auxin biosynthesis. Phylogenetic analyses of the TAA and YUC gene families provide very little evidence for the production of indole-3-acetic acid (IAA) in algae. Instead, horizontal gene transfer of YUCs from bacteria to the ancestral land plant suggests that the TAA/YUC pathway is a land plant innovation. In this Opinion article we postulate that the origin of tryptophan-dependent IAA biosynthesis in land plants might have evolved in response to interactions with microbes, particularly bacteria, allowing plants to counteract bacterial activities and control their own auxin signaling.

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China pulls plug on genetically modified rice and corn

Reasons behind move not clear
chein cherry's insight:

anyway, interest balance. 

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A Set of Versatile Brick Vectors and Promoters for the Assembly, Expression, and Integration of Synthetic Operons in Methylobacterium extorquens AM1 and Other Alphaproteobacteria

A Set of Versatile Brick Vectors and Promoters for the Assembly, Expression, and Integration of Synthetic Operons in Methylobacterium extorquens AM1 and Other Alphaproteobacteria | to step further on my research | Scoop.it

Via Gerd Moe-Behrens
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Gerd Moe-Behrens's curator insight, August 12, 2014 2:51 PM

by
Schada Borzyskowski, Remus-Emsermann M, Weishaupt R, Vorholt JA, Erb TJ.

"The discipline of synthetic biology requires standardized tools and genetic elements to construct novel functionalities in microorganisms; yet, many model systems still lack such tools. Here, we describe a novel set of vectors that allows the convenient construction of synthetic operons in Methylobacterium extorquens AM1, an important alphaproteobacterial model organism for methylotrophy and a promising platform organism for methanol-based biotechnology. In addition, we provide a set of constitutive alphaproteobacterial promoters of different strengths that were characterized in detail by two approaches: on the single-cell scale and on the cell population level. Finally, we describe a straightforward strategy to deliver synthetic constructs to the genome of M. extorquens AM1 and other Alphaproteobacteria. This study defines a new standard to systematically characterize genetic parts for their use in M. extorquens AM1 by using single-cell fluorescence microscopy and opens the toolbox for synthetic biological applications in M. extorquens AM1 and other alphaproteobacterial model systems."

 http://bit.ly/1Bc1F8e

Rescooped by chein cherry from Global Aquaculture News & Events
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Watch: Very Rare Calico Lobster Caught in Maine

Watch: Very Rare Calico Lobster Caught in Maine | to step further on my research | Scoop.it
You could call it a lucky catch: A fisher recently captured an extremely rare "calico" lobster in Maine.

Via Perendale Publishers (Tuti Tan)
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amazing

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Rescooped by chein cherry from Plant and Seed Biology
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[Arabidopsis] GABI-Kat will most probably terminate by the end of 2014! :-(


Via Loïc Lepiniec
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Synthetic biology: Rewriting the code of life


Via Gerd Moe-Behrens, Loïc Lepiniec
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Gerd Moe-Behrens's curator insight, May 28, 2014 5:09 PM

by
Andrea Du Toit

"The genetic code of all living organisms is based on the sequence of the four nucleobases adenine, thymine, cytosine and guanine, which form paired bonds (G·C and A·T) in the DNA double helix. Now, Malyshev et al. report the generation of the first semi-synthetic microorganism that stably replicates an unnatural…"

 http://bit.ly/SfWOAo

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Science: Control of cell division in the quiescent center by ERF115

Science: Control of cell division in the quiescent center by ERF115 | to step further on my research | Scoop.it
Stem cells are crucial for the continuous generation of new cells. Although the importance of stem cells in fuelling plant growth and development still many questions on their tight molecular control remain unanswered.

The link above goes to Science Daily summary, and here is a link to the article out now in Science Express http://www.sciencemag.org/content/early/2013/10/23/science.1240667.abstract


Via Mary Williams, ROOTSPROUT
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Biologists develop transparent soil that reveals hidden world of plant roots

Biologists develop transparent soil that reveals hidden world of plant roots | to step further on my research | Scoop.it

Newly developed transparent soil could help shed light on the secret world of plant roots. The new material, developed by biologists, chemists and physicists, could improve crops and identify new ways of preventing outbreaks of food poisoning.

 

Plants absorb water and minerals with root systems that can encompass a volume larger than the above-ground parts of plants. Scientists would love to learn more about roots, but much about them remains hidden underground.

 

"There are so many things to discover in soil, and we don't know yet what they are," said theoretical biologist Lionel Dupuy at the James Hutton Institute in Dundee, Scotland.

 

Now, after two years of trial and error involving painstaking tinkering with the acidity, grain size and nutrient content of a variety of artificial soil-like materials, watered in a customized liquid solution, Dupuy and his colleagues managed to develop a transparent soil in which they could grow plants. The material allows 3-D imaging of the rhizosphere -- the realm of soil involving plant roots and the organisms associated with them.

 

The soil is made of 350-to-1,600-micron-wide pellets of a synthetic material known as Nafion. This compound often finds use in power-generating fuel cells because of how it can help control the flow of current-carrying ions. Past research revealed that the material had another talent: films of bacteria could grow on Nafion membranes. Also, the scientists could modify the Nafion grains to bind to ions dissolved in the surrounding liquid solution, mimicking natural soil chemistry.

 

This artificial soil is not especially transparent on its own. However, when saturated with a specially designed water-based solution, the way the soil and the solution each bend or "refract" light renders the combination transparent. A similar effect can be seen if you place one clear glass jar in another clear glass jar and fill the smaller jar and the space between jars with paint thinner — the smaller jar will seem to disappear.

 

Although this material does not perfectly mimic real soil, its physical and chemical qualities are close.


Via Dr. Stefan Gruenwald
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Your Blood Type Could Affect Your Memory | IFLScience

Your Blood Type Could Affect Your Memory | IFLScience | to step further on my research | Scoop.it
Individuals with a rare blood type may have an increased risk of developing memory problems later in life, new research has found. According to the study, which has been published in Neurology, people with AB blood were almost twice as likely to develop cognitive impairment as individuals with other blood types.  

Via Luisa Meira
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From Apathy to Apogee

From Apathy to Apogee | to step further on my research | Scoop.it
Hardly anyone believed George Rédei’s research mattered — until it changed everything.

Via Mary Williams
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PLETHORA gradient formation mechanism separates auxin responses

PLETHORA gradient formation mechanism separates auxin responses | to step further on my research | Scoop.it

During plant growth, dividing cells in meristems must coordinate transitions from division to expansion and differentiation, thus generating three distinct developmental zones: the meristem, elongation zone and differentiation zone1. Simultaneously, plants display tropisms, rapid adjustments of their direction of growth to adapt to environmental conditions. It is unclear how stable zonation is maintained during transient adjustments in growth direction. In Arabidopsis roots, many aspects of zonation are controlled by the phytohormone auxin and auxin-induced PLETHORA (PLT) transcription factors, both of which display a graded distribution with a maximum near the root tip2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12. In addition, auxin is also pivotal for tropic responses13, 14. Here, using an iterative experimental and computational approach, we show how an interplay between auxin and PLTs controls zonation and gravitropism. We find that the PLT gradient is not a direct, proportionate readout of the auxin gradient. Rather, prolonged high auxin levels generate a narrow PLT transcription domain from which a gradient of PLT protein is subsequently generated through slow growth dilution and cell-to-cell movement. The resulting PLT levels define the location of developmental zones. In addition to slowly promoting PLT transcription, auxin also rapidly influences division, expansion and differentiation rates. We demonstrate how this specific regulatory design in which auxin cooperates with PLTs through different mechanisms and on different timescales enables both the fast tropic environmental responses and stable zonation dynamics necessary for coordinated cell differentiation.

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Branching patterns of root systems: quantitative analysis of the diversity among dicotyledonous species

Branching patterns of root systems: quantitative analysis of the diversity among dicotyledonous species | to step further on my research | Scoop.it

Background and Aims Root branching, and in particular acropetal branching, is a common and important developmental process for increasing the number of growing tips and defining the distribution of their meristem size. This study presents a new method for characterizing the results of this process in natura from scanned images of young, branched parts of excavated roots. The method involves the direct measurement or calculation of seven different traits.

Methods Young plants of 45 species of dicots were sampled from fields and gardens with uniform soils. Roots were separated, scanned and then measured using ImageJ software to determine seven traits related to root diameter and interbranch distance.

Results The traits exhibited large interspecific variations, and covariations reflecting trade-offs. For example, at the interspecies level, the spacing of lateral roots (interbranch distance along the parent root) was strongly correlated to the diameter of the finest roots found in the species, and showed a continuum between two opposite strategies: making dense and fine lateral roots, or thick and well-spaced laterals.

Conclusions A simple method is presented for classification of branching patterns in roots that allows relatively quick sampling and measurements to be undertaken. The feasibilty of the method is demonstrated for dicotyledonous species and it has the potential to be developed more broadly for other species and a wider range of enivironmental conditions.

 

 

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A comparison study of Agrobacterium-mediated transformation methods for root-specific promoter analysis in soybean - Springer

A comparison study of Agrobacterium-mediated transformation methods for root-specific promoter analysis in soybean - Springer | to step further on my research | Scoop.it

Key message

Both in vitro and in vivo hairy root transformation systems could not replace whole plant transformation for promoter analysis of root-specific and low-P induced genes in soybean.

Abstract

An efficient genetic transformation system is crucial for promoter analysis in plants. Agrobacterium-mediated transformation is the most popular method to produce transgenic hairy roots or plants. In the present study, first, we compared the two different Agrobacterium rhizogenes-mediated hairy root transformation methods using either constitutive CaMV35S or the promoters of root-preferential genes, GmEXPB2 and GmPAP21, in soybean, and found the efficiency of in vitro hairy root transformation was significantly higher than that of in vivo transformation. We compared Agrobacterium rhizogenes-mediated hairy root and Agrobacterium tumefaciens-mediated whole plant transformation systems. The results showed that low-phosphorous (P) inducible GmEXPB2 and GmPAP21 promoters could not induce the increased expression of the GUS reporter gene under low P stress in both in vivo and in vitro transgenic hairy roots. Conversely, GUS activity of GmPAP21 promoter was significantly higher at low P than high P in whole plant transformation. Therefore, both in vitro and in vivo hairy root transformation systems could not replace whole plant transformation for promoter analysis of root-specific and low-P induced genes in soybean.


Via Francis Martin
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WOX5 Suppresses Activity to Establish Quiescence at the Center of the Root Stem Cell Niche

WOX5 Suppresses  Activity to Establish Quiescence at the Center of the Root Stem Cell Niche | to step further on my research | Scoop.it

In Arabidopsis, stem cells maintain the provision of new cells for root growth. They surround a group of slowly dividing cells named the quiescent center (QC), and, together, they form the stem cell niche (SCN). The QC acts as the signaling center of the SCN, repressing differentiation of the surrounding stem cells [ 1 ] and providing a pool of cells able to replace damaged stem cells [ 2, 3 ]. Maintenance of the stem cells depends on the transcription factor WUSCHEL-RELATED HOMEOBOX 5 (WOX5), which is specifically expressed in the QC [ 4 ]. However, the molecular mechanisms by which WOX5 promotes stem cell fate and whether WOX5 regulates proliferation of the QC are unknown. Here, we reveal a new role for WOX5 in restraining cell division in the cells of the QC, thereby establishing quiescence. In contrast, WOX5 and CYCD3;3/CYCD1;1 both promote cell proliferation in the nascent columella. The additional QC divisions occurring in wox5 mutants are suppressed in mutant combinations with the D type cyclins CYCD3;3 and CYCD1;1. Moreover, ectopic expression of CYCD3;3 in the QC is sufficient to induce cell division in the QC. WOX5 thus suppresses QC divisions that are otherwise promoted by CYCD3;3 and CYCD1;1, in part by interacting with the CYCD3;3 promoter to repress CYCD3;3 expression in the QC. Therefore, we propose a specific role for WOX5 in initiating and maintaining quiescence of the QC by excluding CYCD activity from the QC.

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Lectin domains at the frontiers of plant defense

Lectin domains at the frontiers of plant defense | to step further on my research | Scoop.it

The whole group of plant lectins comprises an elaborate collection of proteins capable of recognizing and interacting with specific carbohydrate structures, either originating from the invading organisms or from damaged plant cell wall structures. Due to the vast diversity in protein structures, carbohydrate recognition domains and glycan binding specificities, plant lectins constitute a very diverse protein superfamily. In the last decade, new types of nucleocytoplasmic plant lectins have been identified and characterized, in particular lectins expressed inside the nucleus and the cytoplasm of plant cells often as part of a specific plant response upon exposure to different stress factors or changing environmental conditions. In this review, we provide an overview on plant lectin motifs used in the constant battle against pathogens and predators during plant defenses.


Via Elsa Ballini
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Nature Plants, new journal

We welcome our new sister journal Nature Plants and the increased commitment to the plant science community that it represents. This is an opportunity for Nature Genetics to emphasize the use of genetic and genomic tools and resources in discovering new plant biology and solving major agricultural challenges.

Via Loïc Lepiniec
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Identification of genes preventing transgenerational transmission of stress-induced epigenetic states


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Biologists develop transparent soil that reveals hidden world of plant roots

Biologists develop transparent soil that reveals hidden world of plant roots | to step further on my research | Scoop.it

Newly developed transparent soil could help shed light on the secret world of plant roots. The new material, developed by biologists, chemists and physicists, could improve crops and identify new ways of preventing outbreaks of food poisoning.

 

Plants absorb water and minerals with root systems that can encompass a volume larger than the above-ground parts of plants. Scientists would love to learn more about roots, but much about them remains hidden underground.

 

"There are so many things to discover in soil, and we don't know yet what they are," said theoretical biologist Lionel Dupuy at the James Hutton Institute in Dundee, Scotland.

 

Now, after two years of trial and error involving painstaking tinkering with the acidity, grain size and nutrient content of a variety of artificial soil-like materials, watered in a customized liquid solution, Dupuy and his colleagues managed to develop a transparent soil in which they could grow plants. The material allows 3-D imaging of the rhizosphere -- the realm of soil involving plant roots and the organisms associated with them.

 

The soil is made of 350-to-1,600-micron-wide pellets of a synthetic material known as Nafion. This compound often finds use in power-generating fuel cells because of how it can help control the flow of current-carrying ions. Past research revealed that the material had another talent: films of bacteria could grow on Nafion membranes. Also, the scientists could modify the Nafion grains to bind to ions dissolved in the surrounding liquid solution, mimicking natural soil chemistry.

 

This artificial soil is not especially transparent on its own. However, when saturated with a specially designed water-based solution, the way the soil and the solution each bend or "refract" light renders the combination transparent. A similar effect can be seen if you place one clear glass jar in another clear glass jar and fill the smaller jar and the space between jars with paint thinner — the smaller jar will seem to disappear.

 

Although this material does not perfectly mimic real soil, its physical and chemical qualities are close.


Via Dr. Stefan Gruenwald, chein cherry
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