This is a new pareto-front calculation for all hormone assays I performed for RSA. I started to plot all hormones into one plot but it was too noisy. So I decided to plot each hormone/experiment separately, for both control and salt stress, day 9 only.

This is a ICP-AES analysis for two tomato accessions grown in soil with and without salt stress, plus with different spraying regime for two hormones, ACC and IAA for almost 3 weeks.For each hormone, I harvested root and shoot after 10 d and 4 weeks of stress/spray.

This is a ICP-AES analysis for two tomato accessions grown in soil with and without salt stress, plus with different spraying regime for two hormones, ACC and IAA.For each hormone, we have two developmental stages, 10 d and 4 weeks, in which I have root vs shoot for 10d or root vs tip for 4weeks.

The purpose of this notebook was to extract list of genes for each time point.

The purpose of this notebook was to extract list of genes for each time point.

This experiment is done in September 2023 with 5 Arabidopsis genotypes for DUF247 project. In brief, seeds were germinate in 1/2 MS media for one week, and then trasplanted to the soil with 100% WHC for one more week until the soil reached 50% WHC, then salt stress was applied by soaking pots in 200 mM NaCl, resulting in final concentration of 100 mM NaCl. The shoot growth was measure over the period of 12 days, by measuring growth rate for 3 days before stress exposure and 9 days of stress exposure.

This is a ICP result for the 5 Arabidopsis genotypes grown in plates supplemented with 0, 75, and 125 mM NaCl for two weeks. due to lack of tubes, here you will see the result for the salt stress only.

the Cropreporter measurements were done in two time points, one week apart:early vs late measurements. The early measurements have between 5 to 10 replicates while the late one has 5 replicates only.

This is the shoot growth evaluation for ACC treatment in salty soil. seedlings were germinated in the 1/4 ms control plate for 4 days, at d5, they were transferred directly to the 100 mM soil for 4 weeks. the water maintained at 50 % WHC, and adjusted every other day. the plants were imaged by phenocage Raspi setup.

this is the RSA experiment for the 5 Arabidopsis genotypes.4 d germination in 1/2 ms, at d5, transferred to the +/- 0, 75, 125 salt, and scanned 5 times, for everyother day. root and shoots harvested after two weeks of stress. a.col, b.duf,c.wrky,d/e.2xko.

This is the photosynthetic parameters measurements obtained by CropReporter for my Arabidopsis 5 genotypes in soil experiment on Oct 2023. the same batch of seeds were used for RSA.

this is the shoot ion leakage experiment for the 5 Arabidopsis genotypes I did in soil.2 weeks old seedlings were subjected to 100 mM salt for 2 weeks. We measure Chl.Ind etc with CropReporter. Overall no difference in ion leakage between the genotypes as I expected based on my 2021 experiment. However, I did the RSA analysis for the same seedlings +/- in plate that I wait for those results to see whether I can replicate the duf story.I did average both trays.

this is the shoot ion leakage experiment for the 5 Arabidopsis genotypes I did in soil.2 weeks old seedlings were subjected to 100 mM salt for 2 weeks. We measure Chl.Ind etc with CropReporter. Overall no difference in ion leakage between the genotypes as I expected based on my 2021 experiment. However, I did the RSA analysis for the same seedlings +/- in plate that I wait for those results to see whether I can replicate the duf story.

Same as RSA for duf160-5 as Maryam did before.Seeds were sterilized with 50% bleach for 10 min, rinsed 5 times with MQ sterile water, and incubated at 4°C for 24 h. ½ ms media + sucrose (including vitamins) was made for both control and salt with 75 and 125 mM NaCl. Salt added after PH adjustment.The seeds were germinated for 4 complete days at control plate, and then at d5, they were transferred to +/- salt plates, and scanned for 5 times, every other day. and then the samples were harvested after 2 weeks on salt plate for root and shoot FW. The Arabidopsis growth chamber (#34 at BTI) had 21 °C and 16 h light/8 h dark cycle, with 60% humidity.

This is root system architecture analysis and ICP-MS results for root of LA1511 treated on plate with or without salt. at d5 the seedlings were transferred to +/- salt, while their shoot that are exposed to outside of plates being sprayed +/- IAA for 5 days. after 10 days at salt, seedlings were harvested for ICPMS.and we only analyzed /traced RSA for d9. 3 replicates for each condition.

Experimental description: The seeds were sterilized in 50% bleach for 30 min with gentel shaking, then rinsed 5 times with dionized water, and incubated at 4 °C overnight. Then seeds were germinated in ¼ MS control with vitamins plate for 4 days in growth chamber. At d5, the seedlings were transferred to either 100 mM salt or control plates, and started being scanned for 5 total consecutive days (starting from d5 to d9). The growth chamber condition was 26 °C and 12 h light (7 am to 7 pm)/12 h dark cycle, with 60% humidity (Chamber #35).The root tracing was done using ImageJ SamrtRoot plugin. Shoot and root fresh weight were measured after 10 d at salt. Genotype definition code: M248=a, M058=b, LA1511=c.

These are ICP-MS analysis of the root and shoot samples of the IAA shoot application for LA1511 performed on the plate. LA1511 treated on plate with or without salt. at d5 the seedlings were transferred to +/- salt, while their shoot that are exposed to outside of plates being sprayed +/- IAA for 5 days. after 10 days at salt, seedlings were harvested for ICPMS.

This is RSA analysis of F2 population created from the cross between LA1511 and M248.The seeds for each parents and F2 individuals were germinated on 1/4 ms plates for 4 complete days. At d5, germinated seedlings were transferred to 1/4 ms plates containing 100 mM salt. The plates were scanned from d5 to d9, and seedlings were harvested after 10 days in salt condition. The root tracing of d9 was done by undergraduate Trent Donaldson “20230227_RSA_M248LA1511_F2_100mM_Salt_d9_only_traced”.

This is RSA analysis of F2 population created from the cross between LA1511 and M248.The seeds for each parents and F2 individuals were germinated on 1/4 ms plates for 4 complete days. At d5, germinated seedlings were transferred to 1/4 ms plates containing 100 mM salt. The plates were scanned from d5 to d9, and seedlings were harvested after 10 days in salt condition. The root tracing of d9 was done by undergraduate Trent Donaldson “20230227_RSA_M248LA1511_F2_100mM_Salt_d9_only_traced”.

The seeds were sterilized in 50% bleach for 10 min, then rinsed 5 times with dionized water, and incubated at 4 °C overnight. Then seeds were germinated in ¼ MS control with vitamins plate for 4 days in growth chamber. At d5, the seedlings were transferred to either 100 mM salt or control plates, and started being scanned for 5 total consecutive days (starting from d5 to d9). The growth chamber condition was 26 °C and 19 h light /5 h dark cycle, with 60% humidity (Chamber #35).The root tracing was done using ImageJ SamrtRoot plugin by Trent Donaldson. Shoot and root fresh weight were measured after 10 d at salt and then dried and sent for ICP-MS analysis.This F1 created by crossing LA1511 to M248.

I followed the code at https://rpubs.com/mjulkowska/Cowpea06SideView2022 for this 7-side view image analysis. This is a continuous salt stress from plate to soil.

This is a pareto-front components calculation for 3 tomatoes experienced ACC and salt treatments on plate. Alpha and distance components data calculated by Arjun from 20220620_RSA_M248M058LA1511_ACC_100mM_Salt. The root tracing was done by Stacey Na in April 2023.

This is a pareto-front components calculation for 3 tomatoes experienced cytokinin and salt treatments on plate. Alpha and distance components data calculated by Arjun from 20221118_RSA_M248M058LA1511_cyto_100mM_Salt_2days. The root tracing was done by Trent Donaldson in March 2023.

This is a pareto-front components calculation for 3 tomatoes experienced GA3 and salt treatments on plate. Alpha and distance components data calculated by Arjun from 20220315_RSA_M248M058LA1511_GA_100mM_Salt-selected. The root tracing was done by Stacey Na in March 2023.

This is a ICP-MS analysis result, DW and FW for the same batch of samples we performed RSA + pareto-front components calculation for 3 the tomatoes experienced cyto and salt treatments on plate. Original data can be found in 20221118_RSA_M248M058LA1511_cyto_100mM_Salt_selected. The root tracing was done by undergraduate Trent Donaldson in Feb2023.

This is a RSA analysis for 3 tomatoes experienced ACC and salt treatments on plate. The seeds were germinated on 1/4 ms plate for 4 complete days, and then transferred to treatment plates at d5, and being scanned for 5 consecutive days. The root tracing was done by undergraduate student Stacey Na in April 2023.

The seeds were sterilized in 50% bleach for 10 min, then rinsed 5 times with dionized water, and incubated at 4 °C overnight. Then seeds were germinated in ¼ MS control with vitamins plate for 4 days in growth chamber. At d5, the seedlings were transferred to either 100 mM salt or control plates, and started being scanned for 5 total consecutive days (starting from d5 to d9). The growth chamber condition was 26 °C and 19 h light /5 h dark cycle, with 60% humidity (Chamber #35).The root tracing was done using ImageJ SamrtRoot plugin by Trent Donaldson. Shoot and root fresh weight were measured after 10 d at salt.

This is RSA analysis of F2 population created from the cross between LA1511 and M248.The seeds for each parents and F2 individuals were germinated on 1/4 ms plates for 4 complete days. At d5, germinated seedlings were transferred to 1/4 ms plates containing 100 mM salt. The plates were scanned from d5 to d9, and seedlings were harvested after 10 days in salt condition. The root tracing of d9 was done by undergraduate Trent Donaldson “20230227_RSA_M248LA1511_F2_100mM_Salt_d9_only_traced”.

This is a RSA analysis for 3 tomatoes experienced cytokinin and salt treatments on plate. The seeds were germinated on 1/4 ms plate for 4 complete days, and then transferred to treatment plates at d5, and being scanned for 5 consecutive days. The root tracing was done by undergraduate student Trent Donalson in Dec.2022-January2023.

The seeds were sterilized in 50% bleach for 10 min with gentle shaking, then rinsed 5 times with deionized water, and incubated at 4 °C overnight. Then seeds were germinated in ¼ MS + sucrose (with vitamins) control plate for 4 complete days in growth chamber #35. At d5, the seedlings were transferred to either 100 mM salt or control plates, and started being scanned for 5 total consecutive days (starting from d5 to d9). The growth chamber condition was 26 °C and 20 h light /4 h dark cycle, with 60% humidity (Chamber #35).The root tracing was done using ImageJ SamrtRoot plugin. Shoot and root fresh weight were measured after 10 d in treatment plates.

This is a RSA analysis for 3 tomatoes experienced GA and salt treatments on plate. The seeds were germinated on 1/4 ms plate for 4 complete days, and then transferred to treatment plates at d5, and being scanned for 5 consecutive days. The root tracing was done by undergraduate student Stacey Na in Dec.2022-January2023.

This is a RSA calculation for 3 tomatoes experienced ABA and salt treatments on plate. The seeds were germinated on 1/4 ms plate for 4 complete days, and then transferred to treatment plates at d5, and being scanned for 5 consecutive days. The root tracing was done by REU student YALMARIE NUMAN-VAZQUEZ in summer 2022.

This is a ICP-MS analysis result, DW and FW for the same batch of samples we performed RSA analysis for 3 the tomatoes experienced ACC and salt treatments on plate. Original data can be found in Julkowska LabArchitecture Labplate images\20220620_RSA_M248M058LA1511_ACC_100mM_Salts. The root tracing was partially done by REU student YALMARIE NUMAN-VAZQUEZ in summer 2022.The samples were also weighed and sent for ICP-MS by her. Thank you.

The growth condition was exactly similar to the plants used for FY staining, seeds germinated for 4 complete days on control condition, and at d5 the seedlings were transferred to +/- 75 mM NaCl for two complete days. Then the roots were harvested and used to measure the suberin monomers using the GC-MS.

Seeds were sterilized with 50% bleach for 10 min, rinsed 5 times with MQ sterile water, and incubated at 4°C for 24 h. ½ ms media + sucrose (including vitamins) was made for both control and salt with 75 and 125 mM NaCl. Salt added after PH adjustment.The seeds were germinated for 4 complete days at control plate, and then at d5, they were transferred to +/- salt plates, and scanned for 5 times, every other day. and then the samples were harvested after 2 weeks on salt plate for root and shoot FW. The Arabidopsis growth chamber (#29 at BTI) had 21 °C and 16 h light/8 h dark cycle, with 60% humidity.

20220818_Suberin_quantification_duf-5_col_roots this is the suberin quantification based on Fluorol yellow staining of the roots of duf-5 and col under control and 75 mM salt stress for two days.The seedlings were grown together for a total 4 days, and then 2 days at 75 mM salt. They were fixed and stained 24 hr prior to imaging (no anillin blue counter staining). Before analyzing the images, we need the following steps: 1.First start convert image to HSB using Image> Type>HSB…and then quantify the Brightness signals. 2.Quantification of suberin seedlings were done by using one rectangular per each root section in FIJI, and then extract data points by ANALYZE>PLOT PROFILE>LIST to get the distance and gray value intensity for each section or ctrl+K to copy and past all data corresponding to each replicate in one excel sheet. With this method, we get gray value and distance in pixel however, we do not need distance here.we only need gray value. 3.Use same zoom-in option when analyzing the images, (30% magnification)no change in zoom setting in this case, just opened the image in Fiji and quantified it with one rectangular section. in total, I have 3 replicates for col-control, 4 R for duf-control, 5 R for col-salt, and 5 for duf-salt.

This is the ICP-MS data, DW, and FW for RSA for GA+ salt samples for 3 tomatoes accessions done on March 2022. Two GA concentrations included 1 and 5 UM. original data “20220315_RSA_M248M058LA1511_GA_100mM_Salt-selected”.

This is a ICP-MS analysis result, DW and FW for the same batch of samples we performed pareto-front components calculation for 3 the tomatoes experienced ABA and salt treatments on plate. Original data can be found in 20220606_RSA_M248M058LA1511_ABA_100mM_Salt_2days. The root tracing was done by REU student YALMARIE NUMAN-VAZQUEZ in summer 2022.

This is a ICP-MS analysis result, DW and FW for the same batch of samples we performed pareto-front components calculation for 3 the tomatoes experienced IAA and salt treatments on plate. Original data can be found in 20220406_RSA_M248M058LA1511_IAA_100mM_Salt experiment done on December 2021.Because Low and High IAA had similar effect on root system architecture, I only traced and sent high IAA for ICP-MS analysis.

20220623_Gus-staining- quantification-GG013-14-_all_replicates_root_only this is the gus quantification signal for roots of transgenic lines expressing DUF247 promoter under control and 75 mM salt stress for three days.Before analyzing the images, we need the following steps: 1.First start convert image to HSB using Image> Type>HSB…and then quantify the signals. 2.Quantification of gus seedlings were done by using the rectangular option in FIJI, and then trace the root, and extract data points by ANALYZE>PLOT PROFILE>LIST to get the distance and gray value or ctrl+K to copy and past all data in excel sheet. With this method, we get gray value and distance in pixel. 3.Use same zoom-in option when analyzing the images, i.e. 200% magnification 4.then sum all gray values for each sample, and then divide each gray value by sum of all gray values to obtain real intensity. We also need to calculate the distance from 100% of main root length in each case to graph in order to have equal size of length for root under control and salt.I have 15 and 18 replicates for control and salt, respectively.

This is a pareto-front components calculation for 3 tomatoes experienced IAA and salt treatments on plate. Alpha and distance components data calculated by Arjun from 20220406_RSA_M248M058LA1511_IAA_100mM_Salt experiment done on December 2021.Because Low and High IAA had similar effect on root system architecture, I only traced and included high IAA here for this dataset. Also for d5, there is no LR so this date was omitted from pareto calculation.

This is a pareto-front components calculation for 3 tomatoes experienced ABA and salt treatments on plate. Alpha and distance components data calculated by Arjun from 20220606_RSA_M248M058LA1511_ABA_100mM_Salt_2days. The root tracing was done by REU student YALMARIE NUMAN-VAZQUEZ in summer 2022.

This is ICP-MS data, DW, and FW for RSA for GA+ salt samples for 3 tomatoes accessions done on March 2022. Two GA concentrations included 1 and 5 UM. original data “20220315_RSA_M248M058LA1511_GA_100mM_Salt-selected”

this experiment was performed on January 2022 in order to address whether there is a difference in tissue accumulation of the 3 tomato accessions, M248, M058, LA1511. These samples were grown similar to RSA set-up , 4 d on germination/control plates, d5 to +/- 100 mM salt, and then tissues including stem, leaves, and roots were harvested after 10 d on salt.

this is the duf-5 soil salt phenotyping experiment. 1 week on control plate, 1 week on soil at 100% WHC, and then a two weeks old seedlings or three weeks old seedlings were treated with 200 mM salt. the water holding capacity were at 50% throughout experiment. weight loss in water compensated with water only. and then at week 5 samples collected for ICP-MS of rosette leaves.

this is the ion leakage analysis for the duf160-5 and col plants grown on soil for salt experiment. 2 weeks old seedlings were treated with either water or 200 mM salt (known as 2wk here), and the other tray treated with 200 mM salt at week 3 after germination( known as 3wk here).the experiment period was almost 4 weeks: 2wk ctrl+ 2wk salt, then harvested AND 3 wk ctrl + 1 wk salt, then harvested.so the ion leakage performed by time of harvesting ~ 4 weeks old plants by collecting 3 equal sizes leaf disc into 2 ml deionized water, incubate at RT overnight, followed by measuring initial conductivity. then samples were boiled at 80 centigrade degrees for 2 hr in water batch, followed by overnight cooling at RT with gentle shaking. final conductivity was measured following day. to calculate the conductivity, initial conductivity/final conductivity*100.

ICP-MS on root and shoot of Arabidopsis duf247-5 and col-0 grown on plate containing varoius concentrations of NaCl including 0, 75, and 125 mM NaCl. However, the 125 mM samples were not sent for the analysis because we have not seen any phenotype in RSA of col-0 and duf mutant grown at this concentration.So this is the ICP-MS result for col and duf160-5 root and shoot grown on the 1/2 MS plate +/-75 mM salt. After two weeks salt stress, shoot and root were weighted and harvested for ICP-MS. this is the same batch as RSA analysis for this allele on January 2021.

Seeds were sterilized with 50% bleach for 10 min, rinsed 5 times with MQ sterile water, and incubated at 4°C for 24 h. ½ ms media + sucrose (including vitamins) was made for both control and salt with 75 and 125 mM NaCl. Salt added after PH adjustment.The seeds were germinated for 4 complete days at control plate, and then at d5, they were transferred to +/- salt plates, and scanned for 5 times, every other day. and then the samples were harvested after 2 weeks on salt plate for root and shoot FW. The Arabidopsis growth chamber (#34 at BTI) had 21 °C and 16 h light/8 h dark cycle, with 60% humidity.

Seeds were sterilized with 50% bleach for 10 min, rinsed 5 times with MQ sterile water, and incubated at 4°C for 24 h. ½ ms media + sucrose (including vitamins) was made for both control and salt with 75 and 125 mM NaCl. Salt added after PH adjustment.The seeds were germinated for 4 complete days at control plate, and then at d5, they were transferred to +/- salt plates, and scanned for 5 times, every other day. and then the samples were harvested after 2 weeks on salt plate for root and shoot FW. The Arabidopsis growth chamber (#34 at BTI) had 21 °C and 16 h light/8 h dark cycle, with 60% humidity.