November 2019 - plants-user - lists.vbcf.ac.at

Construction works @PlantS Facility GMI and MFPL

by Jez,Jakub

Dear all, Next week small construction works are planned that might slightly affect the daily operation (mostly accessibility/corridor) of the Facility. In the next weeks we will also need to shut down phytotron #22 and #23 (one by the other) for a significant amount of time. No other phytotrons will be affected! GMI -1: Tuesday 3rd Dec and Wednesday 4th Dec Replacement of a pipe in the corridor (this particular pipe is not at all related to the operation of our Facility). MFPL 8th floor: 2.5 weeks from the 2nd December on CO2 System installation in #22 and #23 In case of any questions please do not hesitate to contact me. Best, Jakub [VBC Logo] Jakub Jez Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77090<tel:+43%20664%208084%2077090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at> Chair, Austrian Plant Phenotyping Network (APPN<https://www.appn.at/>) and Support Group Member of ESFRI EMPHASIS<https://emphasis.plant-phenotyping.eu/> project Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> LinkedIn: www.linkedin.com/in/jezjakub<http://www.linkedin.com/in/jezjakub> [signature_589218479] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

Nov. 29, 2019

Re: [Plants-user] PLANT STRESS NEWS! Please read!

by Jez,Jakub

Dear Peter, Thank you for your prompt feedback! Well, this is certainly not all, but a (if not the) crucial factor. We will also of course continue with LED spectra experiment and share with you the results. There are so many factors to be considered! We will also investigate the fluorescent tube chamber at the GMI. Issues to consider here are: the type of fluorescent tubes (T8 GMI vs. T5 MFPL), 4 tubes or 6 tubes, watering (some users water from the top!), pot size (height, washing out of nutrients) and soil sieving. Regarding the surrounding LED light I just want to clarify that the LEDs are giving a down pointed light with way less cross-lighting than fluorescent tubes. The experiments are also (if possible) done I the most upper shelf unit to avoid cross-light as good as possible. As discussed, we also could not measure any significant difference in the spectrum irrespective of the position and direction of our spectrometer. But, yes, we will also investigate this! Thanks. ! Attached please find the image of the tray exposed to the full standard LED light spectrum; left side fertilized, right side no treatment. Systematic information will follow. This was just an update and quick fix mail in order to help you as soon as possible (image was taken today, same as the fluo tube image shared in the last mail!). No stress symptoms so far; but a significant difference between treatment and control. Best, Jakub From: Peter Schloegelhofer <peter.schloegelhofer(a)univie.ac.at> Date: Thursday, 28. November 2019 at 11:34 To: VBCF Pant Sciences Facility user mailing list <plants-user(a)lists.vbcf.ac.at> Cc: GMI All <gmi.all.intern(a)gmi.oeaw.ac.at>, "VBCFplants.GRP" <plants(a)vbcf.ac.at> Subject: Re: [Plants-user] PLANT STRESS NEWS! Please read! Dear Jakub, dear all, many thanks for the info and I am sure that sub-optimally fertilised soil contributes to the stress. I am not convinced though that this is all. I would like to hear more about the GMI chamber that has exclusively fluorescent lamps installed but apparently houses plants without stress symptoms. What soil was used there? As I mentioned to Jakub in an earlier email the plants in chamber #21 (relating to the picture) are still exposed to the light from the LEDs, though not directly. They are grown under fluorescent tubes, but are surrounded by LEDs. Can I/we get some more systematic information on this please. Many thanks and best regards, Peter On 28 Nov 2019, at 11:03, Jez,Jakub <jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at>> wrote: Dear friends, In the last weeks/months we have been investigating the plant stress issue, mainly focusing on the LED light spectrum. Always comparing to the fluorescent tube standard. Surprisingly, also the fluorescent tube setup shows same plant stress issues! Which was not the case in the very beginning when we have tested and decided for the new type of soil. See picture attached to this mail: Phytotron: #21 Soil: Gramoflor2006; not sieved; with perlite Light: Fluorescent tubes; LD Watering: Flooding twice a week Left side of the tray: WUXAL treated plants (once, after 1 month, 2ml/L) Right side of the tray: untreated plants Our new hypothesis focuses on the soil. In particular, on the soil composition and the available nutrients. From today’s point of view, it looks like the composition of the soil might have changed over the last months (without informing us); but this needs further investigation. The automated watering system (flooding) also eventually contributes negatively to the problem by washing out nutrients; twice a week. Also sieving might be suboptimal. Red leaves are known to be a symptom for Phosphor/Phosphate deficiency. We are in touch with the soil supplier and with APPN soil scientist from the BOKU to find a long-term solution. As a quick fix * you can fertilize your plants with WUXAL fertilizer which is available in the Facility (once after ~1month; 2ml/L; watering from the top). * Use a long-term fertilizer (OSMOCOTE) * Use the old type of soil ED63 Please contact Anneliese in case of questions for the quick fix. We will keep you posted on further steps and present you soon our final results and the long-term solution. Looking forward to your valuable feedback on your quick-fix results. Best wishes, yours PlantS Team <image001.png> Jakub Jez Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77090<tel:+43%20664%208084%2077090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at/> Chair, Austrian Plant Phenotyping Network (APPN<https://www.appn.at/>) and Support Group Member of ESFRI EMPHASIS<https://emphasis.plant-phenotyping.eu/> project Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> LinkedIn: www.linkedin.com/in/jezjakub<http://www.linkedin.com/in/jezjakub> <image002.png> FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021! <IMG_20191127_150054_resized_20191127_043144973[2].jpg>_______________________________________________ plants-user mailing list plants-user(a)lists.vbcf.ac.at<mailto:plants-user@lists.vbcf.ac.at> https://www.vbcf.ac.at/mailman/listinfo/plants-user Dr. Peter Schlögelhofer Department of Chromosome Biology Max Perutz Labs University of Vienna Dr. Bohr-Gasse 9 1030 Vienna Austria Phone: +43 1 4277 56240 Email: peter.schloegelhofer(a)univie.ac.at<mailto:peter.schloegelhofer@univie.ac.at>

Nov. 28, 2019

Re: [Plants-user] PLANT STRESS NEWS! Please read!

by Peter Schlögelhofer

Dear Jakub, dear all, many thanks for the info and I am sure that sub-optimally fertilised soil contributes to the stress. I am not convinced though that this is all. I would like to hear more about the GMI chamber that has exclusively fluorescent lamps installed but apparently houses plants without stress symptoms. What soil was used there? As I mentioned to Jakub in an earlier email the plants in chamber #21 (relating to the picture) are still exposed to the light from the LEDs, though not directly. They are grown under fluorescent tubes, but are surrounded by LEDs. Can I/we get some more systematic information on this please. Many thanks and best regards, Peter > On 28 Nov 2019, at 11:03, Jez,Jakub <jakub.jez(a)vbcf.ac.at> wrote: > > Dear friends, > > In the last weeks/months we have been investigating the plant stress issue, mainly focusing on the LED light spectrum. > Always comparing to the fluorescent tube standard. > Surprisingly, also the fluorescent tube setup shows same plant stress issues! > Which was not the case in the very beginning when we have tested and decided for the new type of soil. > > See picture attached to this mail: > Phytotron: #21 > Soil: Gramoflor2006; not sieved; with perlite > Light: Fluorescent tubes; LD > Watering: Flooding twice a week > Left side of the tray: WUXAL treated plants (once, after 1 month, 2ml/L) > Right side of the tray: untreated plants > > Our new hypothesis focuses on the soil. > In particular, on the soil composition and the available nutrients. > From today’s point of view, it looks like the composition of the soil might have changed over the last months (without informing us); but this needs further investigation. > The automated watering system (flooding) also eventually contributes negatively to the problem by washing out nutrients; twice a week. > Also sieving might be suboptimal. > > Red leaves are known to be a symptom for Phosphor/Phosphate deficiency. > > We are in touch with the soil supplier and with APPN soil scientist from the BOKU to find a long-term solution. > > As a quick fix > you can fertilize your plants with WUXAL fertilizer which is available in the Facility (once after ~1month; 2ml/L; watering from the top). > Use a long-term fertilizer (OSMOCOTE) > Use the old type of soil ED63 > > Please contact Anneliese in case of questions for the quick fix. > > We will keep you posted on further steps and present you soon our final results and the long-term solution. > > Looking forward to your valuable feedback on your quick-fix results. > > Best wishes, yours PlantS Team > > <image001.png> > Jakub Jez > Head, Plant Sciences Facility > T +43 1 7962324 7090 <tel:+43179623247090> > M +43 664 8084 77090 <tel:+43%20664%208084%2077090> > jakub.jez(a)vbcf.ac.at <mailto:jakub.jez@vbcf.ac.at> > Vienna BioCenter Core Facilities GmbH > Dr. Bohr-Gasse 3 > 1030 Vienna > Austria > www.vbcf.ac.at <https://www.vbcf.ac.at/> > > Chair, Austrian Plant Phenotyping Network (APPN <https://www.appn.at/>) and Support Group Member of ESFRI EMPHASIS <https://emphasis.plant-phenotyping.eu/> project > > Twitter: @VBCF_PlantS <https://twitter.com/VBCF_PlantS> > LinkedIn: www.linkedin.com/in/jezjakub <http://www.linkedin.com/in/jezjakub> > <image002.png> > > FFG PHENOPlant <https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021! > > > > > > > > > > > > > <IMG_20191127_150054_resized_20191127_043144973[2].jpg>_______________________________________________ > plants-user mailing list > plants-user(a)lists.vbcf.ac.at <mailto:plants-user@lists.vbcf.ac.at> > https://www.vbcf.ac.at/mailman/listinfo/plants-user <https://www.vbcf.ac.at/mailman/listinfo/plants-user> Dr. Peter Schlögelhofer Department of Chromosome Biology Max Perutz Labs University of Vienna Dr. Bohr-Gasse 9 1030 Vienna Austria Phone: +43 1 4277 56240 Email: peter.schloegelhofer(a)univie.ac.at

Nov. 28, 2019

PLANT STRESS NEWS! Please read!

by Jez,Jakub

Dear friends, In the last weeks/months we have been investigating the plant stress issue, mainly focusing on the LED light spectrum. Always comparing to the fluorescent tube standard. Surprisingly, also the fluorescent tube setup shows same plant stress issues! Which was not the case in the very beginning when we have tested and decided for the new type of soil. See picture attached to this mail: Phytotron: #21 Soil: Gramoflor2006; not sieved; with perlite Light: Fluorescent tubes; LD Watering: Flooding twice a week Left side of the tray: WUXAL treated plants (once, after 1 month, 2ml/L) Right side of the tray: untreated plants Our new hypothesis focuses on the soil. In particular, on the soil composition and the available nutrients. From today’s point of view, it looks like the composition of the soil might have changed over the last months (without informing us); but this needs further investigation. The automated watering system (flooding) also eventually contributes negatively to the problem by washing out nutrients; twice a week. Also sieving might be suboptimal. Red leaves are known to be a symptom for Phosphor/Phosphate deficiency. We are in touch with the soil supplier and with APPN soil scientist from the BOKU to find a long-term solution. As a quick fix * you can fertilize your plants with WUXAL fertilizer which is available in the Facility (once after ~1month; 2ml/L; watering from the top). * Use a long-term fertilizer (OSMOCOTE) * Use the old type of soil ED63 Please contact Anneliese in case of questions for the quick fix. We will keep you posted on further steps and present you soon our final results and the long-term solution. Looking forward to your valuable feedback on your quick-fix results. Best wishes, yours PlantS Team [VBC Logo] Jakub Jez Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77090<tel:+43%20664%208084%2077090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at> Chair, Austrian Plant Phenotyping Network (APPN<https://www.appn.at/>) and Support Group Member of ESFRI EMPHASIS<https://emphasis.plant-phenotyping.eu/> project Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> LinkedIn: www.linkedin.com/in/jezjakub<http://www.linkedin.com/in/jezjakub> [signature_949803173] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

Nov. 28, 2019

NEW EXPERTISE @PlantS: Machine Learning, Data Analysis, Basic Statistics, Data Visualization and Scripting

by Jez,Jakub

Dear all, In the light of the upcoming high-throughput plant phenotyping infrastructure (PHENOPlant) and also the closure of the BioComp facility, we have extended and strengthened our service portfolio by providing expertise in: * Machine Learning (e.g. image segmentation & classification) * Data analysis and basic statistics (not strictly phenotyping data related) * Data Visualization * Tools/scripting (e.g. script-based workflow automation: experiment design, sample randomization, sample identification (QR codes), etc.) * Small, in-house hardware programming and electronics projects (see PHENOBox) in collaboration with the workshop powered by @Stewart,Ethan<mailto:ethan.stewart@vbcf.ac.at> (Staff Scientist) & @Seitner,Sebastian<mailto:sebastian.seitner@vbcf.ac.at> (Software Engineer; programmer of the PHENOBox). Supported languages: Python, C, R, Java, JavaSript and TypeScript. Please do not hesitate to contact me for further information and requests. Best, Jakub.

Nov. 21, 2019