Journal: Methods in enzymology

Article Title: Characterization of the tumor immune infiltrate by multiparametric flow cytometry and unbiased high-dimensional data analysis

doi: 10.1016/bs.mie.2019.11.012

Figure Lengend Snippet: Visualization methods.

Article Snippet: Some of the algorithms used for this purpose are briefly described below (see also ). table ft1 table-wrap mode="anchored" t5 caption a7 Method Environment Description Limitations PhenoGraph R (included in Cytofkit), Phyton, MATLAB ™ , FlowJo Exchange plug-in Based on nearest-neighbor graph, followed by definition of communities as interconnected events Number of clusters not customizable Not so fast ClusterX R (defined in Cytofkit) Based on densities in the tSNE projection map Fast Limited to tSNE ability to define clusters Number of clusters not customizable FlowSOM R package (included in Cytofkit), FlowJo Exchange plug-in Based in Self-Organization Maps (SOM) follow by hierarchical clustering Very fast Number of clusters customizable For exploratory analysis, hard to determine the number of clusters Open in a separate window Clustering methods.

Techniques:

Journal: Methods in enzymology

Article Title: Characterization of the tumor immune infiltrate by multiparametric flow cytometry and unbiased high-dimensional data analysis

doi: 10.1016/bs.mie.2019.11.012

Figure Lengend Snippet: Clustering methods.

Article Snippet: Some of the algorithms used for this purpose are briefly described below (see also ). table ft1 table-wrap mode="anchored" t5 caption a7 Method Environment Description Limitations PhenoGraph R (included in Cytofkit), Phyton, MATLAB ™ , FlowJo Exchange plug-in Based on nearest-neighbor graph, followed by definition of communities as interconnected events Number of clusters not customizable Not so fast ClusterX R (defined in Cytofkit) Based on densities in the tSNE projection map Fast Limited to tSNE ability to define clusters Number of clusters not customizable FlowSOM R package (included in Cytofkit), FlowJo Exchange plug-in Based in Self-Organization Maps (SOM) follow by hierarchical clustering Very fast Number of clusters customizable For exploratory analysis, hard to determine the number of clusters Open in a separate window Clustering methods.

Techniques:

Journal: Plant Methods

Article Title: Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants

doi: 10.1186/1746-4811-9-4

Figure Lengend Snippet: Advantages and disadvantages between geoponics, agar plates and three distinct aggregate hydroponics methods for cultivating arabidopsis plants

Article Snippet: Gas exchange measurements were adjusted on the basis of the leaf area contained within: i) the extended reach chamber (LiCOR) estimated by taking a scaled photograph and analysis of the percentage of the leaf within the chamber window using ImageJ (National Institute of Health, NIH) as detailed in [ ] or, ii) the whole Arabidopsis plant chamber (LiCOR) by estimating the rosette size using a customised code developed in MATLAB® 2010b (Mathworks Inc., Natick, MA, USA) and the Image Analysis Toolbox® to process scaled photographs semi-automatically.

Techniques:

Journal: Plant Methods

Article Title: Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants

doi: 10.1186/1746-4811-9-4

Figure Lengend Snippet: Simplified Arabidopsis hydroponics growth method. Flow chart outlining the timeline and key steps in the process. Timing (in bold) on right of arrows indicate time between steps (d: days). Images on right-hand panel showing setup of seed germination and representative images of seedlings and mature plants, including view of roots contained within centrifuge tubes of 5-week old plant. Also refer to protocol, and Additional file and online tutorial video ( http://www.youtube.com/watch?v=c9neVLaS63c ) for more detailed descriptions of the equipment set-up.

Article Snippet: Gas exchange measurements were adjusted on the basis of the leaf area contained within: i) the extended reach chamber (LiCOR) estimated by taking a scaled photograph and analysis of the percentage of the leaf within the chamber window using ImageJ (National Institute of Health, NIH) as detailed in [ ] or, ii) the whole Arabidopsis plant chamber (LiCOR) by estimating the rosette size using a customised code developed in MATLAB® 2010b (Mathworks Inc., Natick, MA, USA) and the Image Analysis Toolbox® to process scaled photographs semi-automatically.

Techniques:

Journal: Plant Methods

Article Title: Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants

doi: 10.1186/1746-4811-9-4

Figure Lengend Snippet: Comparisons of Arabidopsis shoot growth kinetics and protoplast transformation efficiency between soil and hydroponics system. A ) Shoot biomass during vegetative growth phase of Arabidopsis Col-0 is equivalent between soil-grown and hydroponically-grown plants under short-day photoperiod (8 h:16 h) until seven weeks post-germination. Mean ± SD (n = 6 plants per timepoint, per condition). No significant differences were found between growth conditions at each timepoint using a t -test (P < 0.01). B ) Transfection efficiency of Arabidopsis mesophyll protoplasts were determined by fluorescence microscopy comparing two quantities (5 μg and 10 μg) of two sGFP-expressing plasmids under a single CaMV 35S promoter, pHBT-sGFP(S65T)-NOS (GenBank accession number: EF090408) and pGWB406 (GenBank accession number: AB294430) of 4.2 kb and 12.4 kb, respectively as per Conn et al. . For each condition n = 5 independent transformations, each with cell counts > 100 protoplasts. Data presented as the proportion of GFP-expressing cells; Mean + SEM. Asterisks indicate significant difference between soil and hydroponics derived protoplasts within each condition (P < 0.01).

Article Snippet: Gas exchange measurements were adjusted on the basis of the leaf area contained within: i) the extended reach chamber (LiCOR) estimated by taking a scaled photograph and analysis of the percentage of the leaf within the chamber window using ImageJ (National Institute of Health, NIH) as detailed in [ ] or, ii) the whole Arabidopsis plant chamber (LiCOR) by estimating the rosette size using a customised code developed in MATLAB® 2010b (Mathworks Inc., Natick, MA, USA) and the Image Analysis Toolbox® to process scaled photographs semi-automatically.

Techniques: Transformation Assay, Transfection, Fluorescence, Microscopy, Expressing, Derivative Assay

Journal: Plant Methods

Article Title: Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants

doi: 10.1186/1746-4811-9-4

Figure Lengend Snippet: Calcium-dependent transcriptional responses of Arabidopsis leaves and roots of hydroponically-grown plants. qPCR performed on RNA isolated from the ( A ) shoots and ( B ) roots (above and below the hypocotyls, respectively) of 5-week old Arabidopsis KC464 plants grown under three different Ca activities (a Ca LCS = 0.025mM; a Ca BNS = 1 mM; a Ca HCS = 5 mM) for seven days. n = 9, from three biological replicates per tissue. Mean + SD. Asterisk indicates significant expression difference from BNS (P < 0.01). qPCR performed as described in Conn et al. [ , ] with primers listed in Additional file .

Article Snippet: Gas exchange measurements were adjusted on the basis of the leaf area contained within: i) the extended reach chamber (LiCOR) estimated by taking a scaled photograph and analysis of the percentage of the leaf within the chamber window using ImageJ (National Institute of Health, NIH) as detailed in [ ] or, ii) the whole Arabidopsis plant chamber (LiCOR) by estimating the rosette size using a customised code developed in MATLAB® 2010b (Mathworks Inc., Natick, MA, USA) and the Image Analysis Toolbox® to process scaled photographs semi-automatically.

Techniques: Isolation, Expressing

Journal: Plant Methods

Article Title: Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants

doi: 10.1186/1746-4811-9-4

Figure Lengend Snippet: Gas exchange measurements for Arabidopsis Col-0 measured using the LiCOR extended reach chamber or whole plant chamber whilst growing in hydroponics. A Transpiration or B Net CO 2 assimilation/photosynthesis measured using 6-week old plants growing the basal nutrient solution. Individual plants were exposed to light intensity of ~350 μmol m -2 s -1 at least 30 min prior to the start of measurement. The rosette was allowed to acclimatise inside the Arabidopsis whole rosette or extended reach chamber for at least 10 min before gas exchange data were recorded with reference CO 2 concentration set at 500 μmol mol -1 , flow rate at 500 μmol s -1 (for the whole plant chamber) or 100 μmol s -1 (for the extended reach chamber) light intensity at 350 μmol photons m -2 s -1 and relative humidity at 56%. Data shown as Mean + SEM of fifteen biological replicates. No significant differences were found between each dataset using a t -test (P < 0.01).

Article Snippet: Gas exchange measurements were adjusted on the basis of the leaf area contained within: i) the extended reach chamber (LiCOR) estimated by taking a scaled photograph and analysis of the percentage of the leaf within the chamber window using ImageJ (National Institute of Health, NIH) as detailed in [ ] or, ii) the whole Arabidopsis plant chamber (LiCOR) by estimating the rosette size using a customised code developed in MATLAB® 2010b (Mathworks Inc., Natick, MA, USA) and the Image Analysis Toolbox® to process scaled photographs semi-automatically.

Techniques: Concentration Assay