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jamimmunology: Good pipetting rules of thumb

jamimmunology: Good pipetting rules of thumb | plant resistance | Scoop.it
A few tips to minimise risk to yourself when using micropipettes

Via Chris Upton + helpers
Kangquan Yin's insight:

"but hurrying usually means you do things the wrong way (both in terms of your data’s and your own safety"---real word!

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Ed Rybicki's comment, October 19, 2013 4:59 AM
How about all those injuries people got using the Pipetman glass pipette holders? There was a slicing injury from a broken pipette glancing along the ball of the the thumb; there was a "core sample" injury from sticking a broken pipette INTO the ball - and so on. Terrible things!
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Genome-Wide Characterization of miRNAs Involved in N Gene-Mediated Immunity in Response to Tobacco Mosaic Virus in Nicotiana benthamiana

Genome-Wide Characterization of miRNAs Involved in N Gene-Mediated Immunity in Response to Tobacco Mosaic Virus in Nicotiana benthamiana | plant resistance | Scoop.it
Genome-Wide Characterization of miRNAs Involved in N Gene-Mediated Immunity in Response to Tobacco Mosaic Virus in Nicotiana benthamiana
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Position statement on new crop breeding tools published by UK’s major plant science funder - BBSRC

The Biotechnology and Biological Sciences Research Council (BBSRC) has published a position statement on new and emerging techniques for crop improvement. These novel techniques, which can introduce precise genetic changes into plants, are currently being used in research labs as a tool to help understand the function of genes. Commercial applications are likely to follow: new and improved crop varieties produced with these methods could be available world-wide over the coming years.

 

 


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future is not very far

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Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants

Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants | plant resistance | Scoop.it
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Agrobacterium Strains | DNA Cloning Service

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useful~

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BioTechniques - Top Ten BioTechniques News Stories

BioTechniques - Top Ten BioTechniques News Stories | plant resistance | Scoop.it
We present the Top Ten news articles published in BioTechniques, as calculated by number of downloads over the past 30 days. Learn more...
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PLOS ONE: Humans Have Antibodies against a Plant Virus: Evidence from Tobacco Mosaic Virus

PLOS ONE: Humans Have Antibodies against a Plant Virus: Evidence from Tobacco Mosaic Virus | plant resistance | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Trends in Plant Science - Plastid non-coding RNAs: emerging candidates for gene regulation

Trends in Plant Science - Plastid non-coding RNAs: emerging candidates for gene regulation | plant resistance | Scoop.it

Recent advances in transcriptomics and bioinformatics, specifically strand-specific RNA sequencing, have allowed high-throughput, comprehensive detection of low-abundance transcripts typical of the non-coding RNAs studied in bacteria and eukaryotes. Before this, few plastid non-coding RNAs (pncRNAs) had been identified, and even fewer had been investigated for any functional role in gene regulation. Relaxed plastid transcription initiation and termination result in full transcription of both chloroplast DNA strands. Following this, post-transcriptional processing produces a pool of metastable RNA species, including distinct pncRNAs. Here we review pncRNA biogenesis and possible functionality, and speculate that this RNA class may have an underappreciated role in plastid gene regulation.


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BioTechniques - Top Ten BioTechniques Cloning Articles

BioTechniques - Top Ten BioTechniques Cloning Articles | plant resistance | Scoop.it
We present the Top Ten molecular biology cloning articles published in BioTechniques, as calculated by number of downloads over the past 30 days. Learn more...
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American chemical giant out of NZ court case - New Zealand Herald

American chemical giant out of NZ court case - New Zealand Herald | plant resistance | Scoop.it
American chemical giant out of NZ court case New Zealand Herald Crown forestry research institute Scion made the initial application to have the technique, known as zinc finger nuclease or ZNF-1, exempted from New Zealand laws governing genetic...
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TALEN-engineered AR gene rearrangements reveal endocrine uncoupling of androgen receptor in prostate cancer - PNAS

(via T. Lahaye, thx)

Nyquist et al. (2013)

Androgen receptor (AR) target genes direct development and survival of the prostate epithelial lineage, including prostate cancer (PCa). Thus, endocrine therapies that inhibit the AR ligand-binding domain (LBD) are effective in treating PCa. AR transcriptional reactivation is central to resistance, as evidenced by the efficacy of AR retargeting in castration-resistant PCa (CRPC) with next-generation endocrine therapies abiraterone and enzalutamide. However, resistance to abiraterone and enzalutamide limits this efficacy in most men, and PCa remains the second-leading cause of male cancer deaths. Here we show that AR gene rearrangements in CRPC tissues underlie a completely androgen-independent, yet AR-dependent, resistance mechanism. We discovered intragenic AR gene rearrangements in CRPC tissues, which we modeled using transcription activator-like effector nuclease (TALEN)-mediated genome engineering. This modeling revealed that these AR gene rearrangements blocked full-length AR synthesis, but promoted expression of truncated AR variant proteins lacking the AR ligand-binding domain. Furthermore, these AR variant proteins maintained the constitutive activity of the AR transcriptional program and a CRPC growth phenotype independent of full-length AR or androgens. These findings demonstrate that AR gene rearrangements are a unique resistance mechanism by which AR transcriptional activity can be uncoupled from endocrine regulation in CRPC.

 


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Pine Wilt Disease

Pine Wilt Disease | plant resistance | Scoop.it

Reasearchers, Donald,P.A., Stamps, W.T. and Linit, M.J. tell us the more about pinewood nematode causing pine wilt disease.

 

"Pine wilt is a dramatic disease because it usually kills affected trees within a few weeks to a few months. The pine wood nematode (Bursaphelenchus xylophilus) that causes death of the trees is microscopic. Most plant-parasitic nematodes are associated with plant roots, but the pine wood nematode is found in aboveground parts of the tree. Nematodes kill the tree by feeding on the cells surrounding the resin ducts. This causes resin to leak into the tracheids, resulting in "tracheid cavitation" or air pockets in the water transport system. Just as a person cannot drink through a straw with holes in it, the tree cannot move water upward and consequently wilts and dies. Pine sawyer beetles (Monochamus spp.) vector the nematodes. The nematodes hitch a ride with the beetles and thus move from tree to tree as the beetles feed on the young shoots of pine."


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OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in...

OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in... | plant resistance | Scoop.it

Oaks (Quercus spp.), which are major forest trees in the northern hemisphere, host many biotic interactions, but molecular investigation of these interactions is limited by fragmentary genome data. To date, only 75 oak expressed sequence tags (ESTs) have been characterized in ectomycorrhizal (EM) symbioses. We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone (DF159) of Quercus robur. Sixteen 454 and eight Illumina cDNA libraries from leaves and roots were prepared and merged to establish a reference for RNA-Seq transcriptomic analysis of oak EMs with Piloderma croceum. Using the Mimicking Intelligent Read Assembly (MIRA) and Trinity assembler, the OakContigDF159.1 hybrid assembly, containing 65 712 contigs with a mean length of 1003 bp, was constructed, giving broad coverage of metabolic pathways. This allowed us to identify 3018 oak contigs that were differentially expressed in EMs, with genes encoding proline-rich cell wall proteins and ethylene signalling-related transcription factors showing up-regulation while auxin and defence-related genes were down-regulated. In addition to the first report of remorin expression in EMs, the extensive coverage provided by the study permitted detection of differential regulation within large gene families (nitrogen, phosphorus and sugar transporters, aquaporins). This might indicate specific mechanisms of genome regulation in oak EMs compared with other trees.


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Amercian Academy of Microbiology: How Microbes Can Help Feed the World (2013)

Amercian Academy of Microbiology: How Microbes Can Help Feed the World (2013) | plant resistance | Scoop.it

Executive Summary

A greater focus on the role of microbiology in agriculture combined with new technologies can help mitigate potential food shortages associated with world population increases according to a new report from the American Academy of Microbiology.

“Microbes are essential partners in all aspects of plant physiology, but human efforts to improve plant productivity have focused mostly on the plant,” says Ian Sanders of University of Lausanne, chair of the colloquium that produced the report. “Optimizing the microbial communities that live in, on and around plants, can substantially reduce the need for chemical fertilizers, pesticides and herbicides.”

The report, "How Microbes can Help Feed the World," is based on the deliberation of a group of scientific experts who gathered for two days in Washington DC in December 2012 to consider a series of questions regarding how plant-microbe interactions could be employed to boost agricultural productivity in an environmentally and economically responsible way.

It starts with a startling statistic: In order to feed the estimated global population of 9 billion in the year 2050, agricultural yields will have to increase by 70-100%.

Improved understanding of plant-microbe interactions has the potential to increase crop productivity by 20% while reducing fertilizer and pesticide requirements by 20%, within 20 years, according to the report. These estimates rest on the recognition that all plants rely on microbial partners to secure nutrients, deter pathogens and resist environmental stress.

The report looks in depth at the intimate relationship between microbes and agriculture including why plants need microbes, what types of microbes they need, how they interact and the scientific challenges posed by the current state of knowledge. It then makes a series of recommendations, including greater investment in research, the taking on of one or more grand challenges such as characterization of the complete microbiome of one important crop plant, and the establishment of a formal process for moving scientific discoveries from the lab to the field.

“New technologies are making plant-microbe ecosystems easier to study and investment in this area of research could have dramatic benefits,” says Marilynn Roossinck, Pennsylvania State University, who helped organize the colloquium.


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The Scale of the Universe 2

Zoom from the edge of the universe to the quantum foam of spacetime and learn about everything in between.
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amazing~
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Lack of detectable oral bioavailability of plant microRNAs after feeding in mice

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Which one is right?
Cell Res. 2012 Jan;22(1):107-26. doi: 10.1038/cr.2011.158. Epub 2011 Sep 20.

 

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA.

 

Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K, Zhang CY.Source

Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.

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A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves - Hickman - 2013 - The Plant Journal - Wiley Online Library

A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves - Hickman - 2013 - The Plant Journal - Wiley Online Library | plant resistance | Scoop.it
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why the picture is so vague?

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jamimmunology: Good pipetting rules of thumb

jamimmunology: Good pipetting rules of thumb | plant resistance | Scoop.it
A few tips to minimise risk to yourself when using micropipettes

Via Chris Upton + helpers
Kangquan Yin's insight:

"but hurrying usually means you do things the wrong way (both in terms of your data’s and your own safety"---real word!

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Ed Rybicki's comment, October 19, 2013 4:59 AM
How about all those injuries people got using the Pipetman glass pipette holders? There was a slicing injury from a broken pipette glancing along the ball of the the thumb; there was a "core sample" injury from sticking a broken pipette INTO the ball - and so on. Terrible things!
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转基因水稻权威专家高引用《科学》论文遭撤销 引发相关论文质疑 --快讯--新闻 --生物360 --生命科学界资讯站

这篇论文是 2009 年,由转基因水稻领域的权威、加州大学戴维斯分校植物遗传学家 Pamela Ronald 领导完成,研究报道称他们发现了水稻免疫系统识别的一个细菌分子,这项研究是这一实验室长期研究的成果,有助于解析这种重要的农作物如何抵抗感染。目前论文已经被引用 131 次。
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Biotechnology: Rewriting a genome

Biotechnology: Rewriting a genome | plant resistance | Scoop.it

A bacterial enzyme that uses guide RNA molecules to target DNA for cleavage has been adopted as a programmable tool to site-specifically modify genomes of cells and organisms, from bacteria and human cells to whole zebrafish.

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Trends in Plant Science - A survey of dominant mutations in Arabidopsis thaliana

Following the recent publication of a comprehensive dataset of 2400 genes with a loss-of-function mutant phenotype in Arabidopsis (Arabidopsis thaliana), questions remain concerning the diversity of dominant mutations in Arabidopsis. Most of these dominant phenotypes are expected to result from inappropriate gene expression, novel protein function, or disrupted protein complexes. This review highlights the major classes of dominant mutations observed in model organisms and presents a collection of 200 Arabidopsis genes associated with a dominant or semidominant phenotype. Emphasis is placed on mutants identified through forward genetic screens of mutagenized or activation-tagged populations. These datasets illustrate the variety of genetic changes and protein functions that underlie dominance in Arabidopsis and may ultimately contribute to phenotypic variation in flowering plants.


Via GMI Vienna
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could this result be transferred to other model plants?

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Visualizing virus assembly intermediates inside marine cyanobacteria

Abstract - "Cyanobacteria are photosynthetic organisms responsible for ~25% of organic carbon fixation on the Earth. These bacteria began to convert solar energy and carbon dioxide into bioenergy and oxygen more than two billion years ago. Cyanophages, which infect these bacteria, have an important role in regulating the marine ecosystem by controlling cyanobacteria community organization and mediating lateral gene transfer. Here we visualize the maturation process of cyanophage Syn5 inside its host cell, Synechococcus, using Zernike phase contrast electron cryo-tomography (cryoET)1, 2. This imaging modality yields dramatic enhancement of image contrast over conventional cryoET and thus facilitates the direct identification of subcellular components, including thylakoid membranes, carboxysomes and polyribosomes, as well as phages, inside the congested cytosol of the infected cell. By correlating the structural features and relative abundance of viral progeny within cells at different stages of infection, we identify distinct Syn5 assembly intermediates. Our results indicate that the procapsid releases scaffolding proteins and expands its volume at an early stage of genome packaging. Later in the assembly process, we detected full particles with a tail either with or without an additional horn. The morphogenetic pathway we describe here is highly conserved and was probably established long before that of double-stranded DNA viruses infecting more complex organisms."

 

 


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UC researchers seeking link between a virus & breast cancer - Scoop.co.nz (press release)

UC researchers seeking link between a virus & breast cancer - Scoop.co.nz (press release) | plant resistance | Scoop.it
CBSSports.com UC researchers seeking link between a virus & breast cancer Scoop.co.nz (press release) A University of Canterbury (UC) led research team is studying to see if there is a strong link between breast cancer and a virus, to help reduce...
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Pine Wilt Disease: A threat to European forestry

Pine Wilt Disease: A threat to European forestry | plant resistance | Scoop.it

Researchers Claudia Vicente , Margarida Espada, Paulo Vieira, and Manuel Mota, discuss the risks from pinewood nematode to European forestry.

 

"Bursaphelenchus xylophilus, the pinewood nematode (PWN) and causal agent of Pine Wilt Disease (PWD), was detected for the first time, in 1999, in Portugal, and in Europe. Despite the efforts of the Portuguese National Forestry and Quarantine Authorities, the disease has spread to new forest areas in the centre of mainland Portugal, in 2008, and to the island of Madeira, in 2009. More recently, two foci of PWD were reported from Spain. The free circulation of non-treated wood and wood products, as part of global trade, may explain this phenomenon, which constitutes a threat to other European forestlands. This review gathers the most recent up-to-date information about PWD in Europe, as well as in other countries, presenting integrative management procedures for detection and control, and the scientific knowledge generated over the last decade, to understand the complex biological system behind the disease."


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Molecular Plant Pathology: Top 10 plant-parasitic nematodes in molecular plant pathology (2013)

Molecular Plant Pathology: Top 10 plant-parasitic nematodes in molecular plant pathology (2013) | plant resistance | Scoop.it

The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a ‘top 10’ list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematodeRotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10)Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly.


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Petter Françoise's curator insight, October 10, 2013 2:48 AM

many are recommended for regulation by EPPO

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Top5 Research Articles of 2012

Top5 Research Articles of 2012 | plant resistance | Scoop.it

2012 is almost over now and I would like to highlight my Top 5 research articles of 2012, which were really inspiring for our own research:

 

 

 

 

 

"Tomato TFT1 Is Required for PAMP-Triggered Immunity and Mutations that Prevent T3S Effector XopN from Binding to TFT1 Attenuate Xanthomonas Virulence"

 

by Kyle W. Taylor , Jung-Gun Kim , Xue B. Su, Chris D. Aakre, Julie A. Roden, Christopher M. Adams, Mary Beth Mudgett

 

http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002768

 

 

"RPN1a, a 26S proteasome subunit, is required for innate immunity in Arabidopsis"

 

by Chunpeng Yao,Yingying Wu,Haozhen Nie, Dingzhong Tang

 

http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2012.05048.x/abstract;jsessionid=F9F0853B8F1EF05907031DFED65A88B2.d03t03

 

 

"NPR3 and NPR4 are receptors for the immune signal salicylic acid in plants"

 

by Zheng Qing Fu, Shunping Yan, Abdelaty Saleh, Wei Wang, James Ruble,      Nodoka Oka, Rajinikanth Mohan, Steven H. Spoel, Yasuomi Tada, Ning Zheng   & Xinnian Dong

 

http://www.nature.com/nature/journal/v486/n7402/full/nature11162.html

 

 

"A Xanthomonas uridine 5′-monophosphate transferase inhibits plant immune kinases"

 

by Feng Feng, Fan Yang, Wei Rong, Xiaogang Wu, Jie Zhang, She Chen, Chaozu He & Jian-Min Zhou

 

http://www.nature.com/nature/journal/v485/n7396/abs/nature10962.html

 

 

"A Bacterial Acetyltransferase Destroys Plant Microtubule Networks and Blocks Secretion"

 

by Amy Huei-Yi Lee, Brenden Hurley, Corinna Felsensteiner, Carmen Yea, Wenzislava Ckurshumova, Verena Bartetzko, Pauline W. Wang, Van Quach, Jennifer D. Lewis, Yulu C. Liu, Frederik Börnke, Stephane Angers, Andrew Wilde, David S. Guttman, Darrell Desveaux

 

http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1002523

 

 


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