Protocol: methodology for chromatin immunoprecipitation (ChIP) in Chlamydomonas reinhardtii.

Abstract:

: We report on a detailed chromatin immunoprecipitation (ChIP) protocol for the unicellular green alga Chlamydomonas reinhardtii. The protocol is suitable for the analysis of nucleosome occupancy, histone modifications and transcription factor binding sites at the level of mononucleosomes for targeted and genome-wide studies. We describe the optimization of conditions for crosslinking, chromatin fragmentation and antibody titer determination and provide recommendations and an example for the normalization of ChIP results as determined by real-time PCR.

journal_name

Plant Methods

journal_title

Plant methods

authors

Strenkert D,Schmollinger S,Schroda M

doi

10.1186/1746-4811-7-35

subject

Has Abstract

pub_date

2011-11-03 00:00:00

pages

35

issue

1

issn

1746-4811

pii

1746-4811-7-35

journal_volume

7

pub_type

杂志文章
  • Fluctuating light experiments and semi-automated plant phenotyping enabled by self-built growth racks and simple upgrades to the IMAGING-PAM.

    abstract:Background:Over the last years, several plant science labs have started to employ fluctuating growth light conditions to simulate natural light regimes more closely. Many plant mutants reveal quantifiable effects under fluctuating light despite being indistinguishable from wild-type plants under standard constant light...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-019-0546-1

    authors: Schneider D,Lopez LS,Li M,Crawford JD,Kirchhoff H,Kunz HH

    更新日期:2019-12-23 00:00:00

  • Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins.

    abstract:Background:Chloroplasts are critical organelles that perceive and convey metabolic and stress signals to different cellular components, while remaining the seat of photosynthesis and a metabolic factory. The proteomes of intact leaves, chloroplasts, and suborganellar fractions of plastids have been evaluated in the mod...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-020-00667-5

    authors: Bhattacharya O,Ortiz I,Walling LL

    更新日期:2020-09-24 00:00:00

  • Evaluation of quinclorac toxicity and alleviation by salicylic acid in rice seedlings using ground-based visible/near-infrared hyperspectral imaging.

    abstract:Background:To investigate potential effects of herbicide phytotoxic on crops, a major challenge is a lack of non-destructive and rapid methods to detect plant growth that could allow characterization of herbicide-resistant plants. In such a case, hyperspectral imaging can quickly obtain the spectrum for each pixel in t...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-020-00576-7

    authors: Wang J,Zhang C,Shi Y,Long M,Islam F,Yang C,Yang S,He Y,Zhou W

    更新日期:2020-03-05 00:00:00

  • Developing transgenic wheat to encounter rusts and powdery mildew by overexpressing barley chi26 gene for fungal resistance.

    abstract:BACKGROUND:The main aim of this study was to improve fungal resistance in bread wheat via transgenesis. Transgenic wheat plants harboring barley chitinase (chi26) gene, driven by maize ubi promoter, were obtained using biolistic bombardment, whereas the herbicide resistance gene, bar, driven by the CaMV 35S promoter wa...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-017-0191-5

    authors: Eissa HF,Hassanien SE,Ramadan AM,El-Shamy MM,Saleh OM,Shokry AM,Abdelsattar M,Morsy YB,El-Maghraby MA,Alameldin HF,Hassan SM,Osman GH,Mahfouz HT,Gad El-Karim GA,Madkour MA,Bahieldin A

    更新日期:2017-05-22 00:00:00

  • Machine learning driven non-invasive approach of water content estimation in living plant leaves using terahertz waves.

    abstract:Background:The demand for effective use of water resources has increased because of ongoing global climate transformations in the agriculture science sector. Cost-effective and timely distributions of the appropriate amount of water are vital not only to maintain a healthy status of plants leaves but to drive the produ...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-019-0522-9

    authors: Zahid A,Abbas HT,Ren A,Zoha A,Heidari H,Shah SA,Imran MA,Alomainy A,Abbasi QH

    更新日期:2019-11-18 00:00:00

  • Visualization of the impatiens downy mildew pathogen using fluorescence in situ hybridization (FISH).

    abstract:Background:Plasmopara obducens is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of Impatiens that causes high crop loss. Currently, there are no available methods for the microscopic detection of P. obducens from leaves of impatiens, which may be contributing to the spread of the...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-018-0362-z

    authors: Salgado-Salazar C,Bauchan GR,Wallace EC,Crouch JA

    更新日期:2018-10-24 00:00:00

  • A new approach to varietal identification in plants by microsatellite high resolution melting analysis: application to the verification of grapevine and olive cultivars.

    abstract:BACKGROUND:Microsatellites are popular molecular markers in many plant species due to their stable and highly polymorphic nature. A number of analysis methods have been described but analyses of these markers are typically performed on cumbersome polyacrylamide gels or more conveniently by capillary electrophoresis on ...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/1746-4811-4-8

    authors: Mackay JF,Wright CD,Bonfiglioli RG

    更新日期:2008-05-19 00:00:00

  • Correction to: Soybean iron deficiency chlorosis high throughput phenotyping using an unmanned aircraft system.

    abstract::[This corrects the article DOI: 10.1186/s13007-019-0478-9.]. ...

    journal_title:Plant methods

    pub_type: 已发布勘误

    doi:10.1186/s13007-019-0495-8

    authors: Dobbels AA,Lorenz AJ

    更新日期:2019-10-10 00:00:00

  • Testing deep placement of an 15N tracer as a method for in situ deep root phenotyping of wheat, barley and ryegrass.

    abstract:Background:Deep rooting is one of the most promising plant traits for improving crop yield under water-limited conditions. Most root phenotyping methods are designed for laboratory-grown plants, typically measuring very young plants not grown in soil and not allowing full development of the root system. Results:This s...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-019-0533-6

    authors: Chen S,Svane SF,Thorup-Kristensen K

    更新日期:2019-12-09 00:00:00

  • Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays.

    abstract:: Microarrays are routine tools for transcript profiling, and genomic tiling arrays such as the Arabidopsis AGRONOMICS1 arrays have been found to be highly suitable for such experiments because changes in genome annotation can be easily integrated at the data analysis level. In a transcript profiling experiment, RNA la...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/1746-4811-8-18

    authors: Müller M,Patrignani A,Rehrauer H,Gruissem W,Hennig L

    更新日期:2012-06-13 00:00:00

  • Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana.

    abstract:BACKGROUND:Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulat...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-015-0087-1

    authors: Cumbie JS,Filichkin SA,Megraw M

    更新日期:2015-09-04 00:00:00

  • Deep learning-based detection of seedling development.

    abstract:Background:Monitoring the timing of seedling emergence and early development via high-throughput phenotyping with computer vision is a challenging topic of high interest in plant science. While most studies focus on the measurements of leaf area index or detection of specific events such as emergence, little attention ...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-020-00647-9

    authors: Samiei S,Rasti P,Ly Vu J,Buitink J,Rousseau D

    更新日期:2020-07-30 00:00:00

  • Rapid fluorescent reporter quantification by leaf disc analysis and its application in plant-virus studies.

    abstract:BACKGROUND:Fluorescent proteins are extraordinary tools for biology studies due to their versatility; they are used extensively to improve comprehension of plant-microbe interactions. The viral infection process can easily be tracked and imaged in a plant with fluorescent protein-tagged viruses. In plants, fluorescent ...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/1746-4811-10-22

    authors: Pasin F,Kulasekaran S,Natale P,Simón-Mateo C,García JA

    更新日期:2014-07-05 00:00:00

  • SpikeSegNet-a deep learning approach utilizing encoder-decoder network with hourglass for spike segmentation and counting in wheat plant from visual imaging.

    abstract:Background:High throughput non-destructive phenotyping is emerging as a significant approach for phenotyping germplasm and breeding populations for the identification of superior donors, elite lines, and QTLs. Detection and counting of spikes, the grain bearing organs of wheat, is critical for phenomics of a large set ...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-020-00582-9

    authors: Misra T,Arora A,Marwaha S,Chinnusamy V,Rao AR,Jain R,Sahoo RN,Ray M,Kumar S,Raju D,Jha RR,Nigam A,Goel S

    更新日期:2020-03-18 00:00:00

  • Hyperspectral band selection using genetic algorithm and support vector machines for early identification of charcoal rot disease in soybean stems.

    abstract:Background:Charcoal rot is a fungal disease that thrives in warm dry conditions and affects the yield of soybeans and other important agronomic crops worldwide. There is a need for robust, automatic and consistent early detection and quantification of disease symptoms which are important in breeding programs for the de...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-018-0349-9

    authors: Nagasubramanian K,Jones S,Sarkar S,Singh AK,Singh A,Ganapathysubramanian B

    更新日期:2018-10-03 00:00:00

  • Computer aided data acquisition tool for high-throughput phenotyping of plant populations.

    abstract:BACKGROUND:The data generated during a course of a biological experiment/study can be sometimes be massive and its management becomes quite critical for the success of the investigation undertaken. The accumulation and analysis of such large datasets often becomes tedious for biologists and lab technicians. Most of the...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/1746-4811-5-18

    authors: Vankadavath RN,Hussain AJ,Bodanapu R,Kharshiing E,Basha PO,Gupta S,Sreelakshmi Y,Sharma R

    更新日期:2009-12-10 00:00:00

  • Correction to: The Tree Drought Emission MONitor (Tree DEMON), an innovative system for assessing biogenic volatile organic compounds emission from plants.

    abstract::[This corrects the article DOI: 10.1186/s13007-017-0166-6.]. ...

    journal_title:Plant methods

    pub_type: 杂志文章,已发布勘误

    doi:10.1186/s13007-017-0249-4

    authors: Lüpke M,Steinbrecher R,Leuchner M,Menzel A

    更新日期:2017-11-16 00:00:00

  • Protocol: a rapid and economical procedure for purification of plasmid or plant DNA with diverse applications in plant biology.

    abstract:: Research in plant molecular biology involves DNA purification on a daily basis. Although different commercial kits enable convenient extraction of high-quality DNA from E. coli cells, PCR and agarose gel samples as well as plant tissues, each kit is designed for a particular type of DNA extraction work, and the cost ...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/1746-4811-6-1

    authors: Li JF,Li L,Sheen J

    更新日期:2010-01-14 00:00:00

  • An in vitro protocol for rapidly assessing the effects of antimicrobial compounds on the unculturable bacterial plant pathogen, Candidatus Liberibacter asiaticus.

    abstract:Background:Most bacteria are not culturable, but can be identified through molecular methods such as metagenomics studies. Due to specific metabolic requirements and symbiotic relationships, these bacteria cannot survive on typical laboratory media. Many economically and medically important bacteria are unculturable; i...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-019-0465-1

    authors: Krystel J,Shi Q,Shaw J,Gupta G,Hall D,Stover E

    更新日期:2019-07-31 00:00:00

  • Real-time, non-destructive and in-field foliage yield and growth rate measurement in perennial ryegrass (Lolium perenne L.).

    abstract:Background:In-field measurement of yield and growth rate in pasture species is imprecise and costly, limiting scientific and commercial application. Our study proposed a LiDAR-based mobile platform for non-invasive vegetative biomass and growth rate estimation in perennial ryegrass (Lolium perenne L.). This included de...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-019-0456-2

    authors: Ghamkhar K,Irie K,Hagedorn M,Hsiao J,Fourie J,Gebbie S,Hoyos-Villegas V,George R,Stewart A,Inch C,Werner A,Barrett B

    更新日期:2019-07-10 00:00:00

  • Poinsettia protoplasts - a simple, robust and efficient system for transient gene expression studies.

    abstract:BACKGROUND:Transient gene expression systems are indispensable tools in molecular biology. Yet, their routine application is limited to few plant species often requiring substantial equipment and facilities. High chloroplast and chlorophyll content may further impede downstream applications of transformed cells from gr...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/1746-4811-8-14

    authors: Pitzschke A,Persak H

    更新日期:2012-05-04 00:00:00

  • Protocol: genetic transformation of the fern Ceratopteris richardii through microparticle bombardment.

    abstract:BACKGROUND:The inability to genetically transform any fern species has been a major technical barrier to unlocking fern biology. Initial attempts to overcome this limitation were based on transient transformation approaches or achieved very low efficiencies. A highly efficient method of stable transformation was recent...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-015-0080-8

    authors: Plackett AR,Rabbinowitsch EH,Langdale JA

    更新日期:2015-07-03 00:00:00

  • Rapid quantification of plant-powdery mildew interactions by qPCR and conidiospore counts.

    abstract:UNLABELLED: BACKGROUND:The powdery mildew disease represents a valuable patho-system to study the interaction between plant hosts and obligate biotrophic fungal pathogens. Numerous discoveries have been made on the basis of the quantitative evaluation of plant-powdery mildew interactions, especially in the context of ...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/1746-4811-8-35

    authors: Weßling R,Panstruga R

    更新日期:2012-08-31 00:00:00

  • The Rg1 allele as a valuable tool for genetic transformation of the tomato 'Micro-Tom' model system.

    abstract:BACKGROUND:The cultivar Micro-Tom (MT) is regarded as a model system for tomato genetics due to its short life cycle and miniature size. However, efforts to improve tomato genetic transformation have led to protocols dependent on the costly hormone zeatin, combined with an excessive number of steps. RESULTS:Here we re...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/1746-4811-6-23

    authors: Pino LE,Lombardi-Crestana S,Azevedo MS,Scotton DC,Borgo L,Quecini V,Figueira A,Peres LE

    更新日期:2010-10-07 00:00:00

  • An improved procedure for isolation of high-quality RNA from nematode-infected Arabidopsis roots through laser capture microdissection.

    abstract:BACKGROUND:Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene express...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-016-0123-9

    authors: Anjam MS,Ludwig Y,Hochholdinger F,Miyaura C,Inada M,Siddique S,Grundler FM

    更新日期:2016-04-26 00:00:00

  • A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing.

    abstract:Background:Woody tropical plants contain high levels of complex organic compounds that inhibit the chemical procedures needed to extract RNA or DNA, thus compromising downstream applications such as RNA sequencing and analysis of gene expression. To overcome this issue, researchers must use extraction protocols using C...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-019-0447-3

    authors: Barbier FF,Chabikwa TG,Ahsan MU,Cook SE,Powell R,Tanurdzic M,Beveridge CA

    更新日期:2019-06-05 00:00:00

  • A convenient method for simultaneous quantification of multiple phytohormones and metabolites: application in study of rice-bacterium interaction.

    abstract:BACKGROUND:Simultaneous analysis of multiple functional-related phytohormones and their metabolites will improve our understanding of interactions among different hormones in the same biologic process. RESULTS:A method was developed for simultaneous quantification of multiple phytohormones, abscisic acid, indole-3-ace...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/1746-4811-8-2

    authors: Liu H,Li X,Xiao J,Wang S

    更新日期:2012-01-15 00:00:00

  • DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R.

    abstract:Background:Progress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of the specifical biological system are responding in particular perturbation, integrative approach in which experimental ...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-018-0345-0

    authors: Zagorščak M,Blejec A,Ramšak Ž,Petek M,Stare T,Gruden K

    更新日期:2018-08-30 00:00:00

  • Automatic segmentation and measurement methods of living stomata of plants based on the CV model.

    abstract:Background:The stomata of plants mainly regulate gas exchange and water dispersion between the interior and external environments of plants and play a major role in the plants' health. The existing methods of stomata segmentation and measurement are mostly for specialized plants. The purpose of this research is to deve...

    journal_title:Plant methods

    pub_type: 杂志文章

    doi:10.1186/s13007-019-0453-5

    authors: Li K,Huang J,Song W,Wang J,Lv S,Wang X

    更新日期:2019-07-03 00:00:00

  • Recent achievements obtained by chloroplast transformation.

    abstract::Chloroplasts play a great role for sustained wellbeing of life on the planet. They have the power and raw materials that can be used as sophisticated biological factories. They are rich in energy as they have lots of pigment-protein complexes capable of collecting sunlight, in sugar produced by photosynthesis and in m...

    journal_title:Plant methods

    pub_type: 杂志文章,评审

    doi:10.1186/s13007-017-0179-1

    authors: Adem M,Beyene D,Feyissa T

    更新日期:2017-04-19 00:00:00