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

3rd APPN meeting SAVE-THE-DATE!

by Jez,Jakub

Dear friends! We have just fixed the date and location for the 3rd Austrian Plant Phenotyping Network (APPN) meeting! Date: Thursday, 13th June 2019 Venue: BOKU Vienna, Festsaal, main building Please save the date! Last year we put emphasis on root phenotyping (https://www.appn.at/2ndappn_eppn2020-2/) this year the main focus will be (although not exclusively) on FIELD PHENOTYPING. Other plant phenotyping topics (controlled environments, root phenotyping and others) will be covered by the respective sessions and based on the received abstracts. Details, and the registration page will be open soon on www.appn.at<http://www.appn.at> Looking forward to receiving your abstracts and meeting you in June! Best regards, Gernot Bodner, Boris Rewald (local organizers) & APPN board [signature_1677033384]<http://www.appn.at/>

Feb. 27, 2019

Open position @VBCF Plants: Bioinformatician/Data Analyst (full-time)

by Jez,Jakub

Dear friends, We have opened a position for a Bioinformatician/Data Analyst to join our PlantS team and support the construction and validation of PHENOPlant and help us build our HT plant phenotyping data analysis pipelines. In between large-scale HT phenotyping projects, and within free capacities, the candidate is intended also to work on other projects for our users (non-strictly plant phenotyping related projects). Please help us (and maybe also yourself) to find an excellent candidate to support your research and spread the word: https://www.viennabiocenter.org/vbcf-jobs/ https://twitter.com/VBCF_PlantS/status/1098153265253023744 https://www.linkedin.com/feed/update/urn:li:activity:6504015287585771520 https://www.viennabiocenter.org/about/news/large-infrastructure-project-phe… Thank you very much. Best, Jakub [VBC Logo] Jakub Jeż Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77 090<tel:+43%20664%208084%2077%20090> 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>

Feb. 21, 2019

Re: [Plants-user] LED light survey results and planned measures

by Jez,Jakub

Dear Andreas, thanks you for your feedback. Nothing will be changed without informing you in advance and preliminary small-scale test! We will consider the smaller pots in our test, thanks. Best, Jakub On 21.02.19, 11:54, "plants-user on behalf of Andreas Bachmair" <plants-user-bounces(a)lists.vbcf.ac.at on behalf of andreas.bachmair(a)univie.ac.at> wrote: Dear Jakub, thanks for this informantive e-mail. We use higher light intensity (60% at MFPL toip floor), except for mutants in phototropic light receptors, where we have lower intensity. We did not observe more algal growth than before. Generally, I would prefer not to change the watering regime for this reason (we use chamber 21). A less frequent watering would practically prohibit use of smaller pots - it is already clear that pots smaller than the 7x7 cm size cause some water stress towards the end of the watering periods, as opposed to the larger pots that store more water which lasts till the next sub-irrigation. So I am asking not to change watering in chamber 21, or if this is necessary only to change one side (the internet will have the settings listed, so that every user can choose). Sincerely, Andreas > On 21.02.2019, at 11:33, Jez,Jakub <jakub.jez(a)vbcf.ac.at> wrote: > > Dear all, > > I would like to inform you about the results of the LED light survey and the planned measures. > > We got in total only 18 forms back (11 GMI, 7 MFPL) which corresponds to around 14% of total facility users. > However, negative and positive feedback was reported; let us focus on the negative topics. > > Two main issues have been identified in common: > • Too wet soil conditions and thus heavy algae growth on the soil surface > • Stressed plants (anthocyanins formation, early flowering, etc.) > > Add. 1: > The phytotrons and the light quality were designed and optimized towards providing best plant growth conditions; this applies unfortunately also to algae. > We assume that the lack of heat radiation, by using LED light, does not dry the soil surface in the same manner like fluorescent tubes did in the past. > In the next weeks we will test measures that could be applied towards optimal watering conditions. This will include an adjustment in the watering regime from twice a week to once in 5 days and adjustments in the watering holding time. It will be a challenge to find a compromise facilitating best watering conditions for young and older plants; Arabidopsis and e.g. N. benthamiana or others. > In parallel we will test different soil/sand/perlite ratios to optimize (lower) the water-holding abilities of the substrate. In case you have any suggestions/experience please do not hesitate to contact us. > We also suggest to not use the tray lids for young plants; or at least to reduce the time from one week to 2-3 days. > > Add. 2.: > Here we assume that the plant stress is caused by a too high light intensity; especially by the portion of the blue spectral range. (The wet soil (1.) might also contribute the total stress reaction). > In short, the new data and calculations indicates that the originally set values of 42% (GMI) and 46% (MFPL) were most probably too high for some of your accessions/mutants/lines. > At least they are too high to be considered as an overall standard setting. > The measured total intensity (µMol*m-2*-1) of the LED light is NOT equal to the same total intensity value of fluorescent tubes. This is mainly caused by the fact of the two different light qualities and the resulting different distribution of individual photons over the spectral range. > Our detailed spectral measurements suggest using a setting of 32% (GMI) and 38% (MFPL) as standard; especially in case of sensitive lines and/or experiments. > This settings will give you the same amount of photons belonging to the blue- and red spectral range as by using 4 fluorescent tubes. > All of you who are already happy with using higher values (60% and even 100%) can of course keep this settings. On the other hand, also lower settings might be meaningful in some cases. > We will also prepare a table/graph showing the relation of the set value to the total measured intensity. > > Please feel free to test the suggested settings in your phytotron/shelves. > How to: press both buttons at the same time until the value starts flashing, set then the desired value by pressing plus or minus button. Wait until the new setting stops flashing. > Alternatively you can also ask the facility staff to change the settings for you. > > We will ask you for your feedback on this new settings in the near future. > > In case of any comments or questions please do not hesitate to contact us. > > Best, Jakub > > P.S.: The different settings for GMI and MFPL phytotrons results from the different distance between your plants and the light source. > > > Jakub Jeż > Head, Plant Sciences Facility > T +43 1 7962324 7090 > M +43 664 8084 77 090 > jakub.jez(a)vbcf.ac.at > Vienna BioCenter Core Facilities GmbH > Dr. Bohr-Gasse 3 > 1030 Vienna > Austria > www.vbcf.ac.at > > > > > > > > > _______________________________________________ > plants-user mailing list > plants-user(a)lists.vbcf.ac.at > https://www.vbcf.ac.at/mailman/listinfo/plants-user _______________________________________________ plants-user mailing list plants-user(a)lists.vbcf.ac.at https://www.vbcf.ac.at/mailman/listinfo/plants-user

Feb. 21, 2019

Re: [Plants-user] LED light survey results and planned measures

by Andreas Bachmair

Dear Jakub, thanks for this informantive e-mail. We use higher light intensity (60% at MFPL toip floor), except for mutants in phototropic light receptors, where we have lower intensity. We did not observe more algal growth than before. Generally, I would prefer not to change the watering regime for this reason (we use chamber 21). A less frequent watering would practically prohibit use of smaller pots - it is already clear that pots smaller than the 7x7 cm size cause some water stress towards the end of the watering periods, as opposed to the larger pots that store more water which lasts till the next sub-irrigation. So I am asking not to change watering in chamber 21, or if this is necessary only to change one side (the internet will have the settings listed, so that every user can choose). Sincerely, Andreas > On 21.02.2019, at 11:33, Jez,Jakub <jakub.jez(a)vbcf.ac.at> wrote: > > Dear all, > > I would like to inform you about the results of the LED light survey and the planned measures. > > We got in total only 18 forms back (11 GMI, 7 MFPL) which corresponds to around 14% of total facility users. > However, negative and positive feedback was reported; let us focus on the negative topics. > > Two main issues have been identified in common: > • Too wet soil conditions and thus heavy algae growth on the soil surface > • Stressed plants (anthocyanins formation, early flowering, etc.) > > Add. 1: > The phytotrons and the light quality were designed and optimized towards providing best plant growth conditions; this applies unfortunately also to algae. > We assume that the lack of heat radiation, by using LED light, does not dry the soil surface in the same manner like fluorescent tubes did in the past. > In the next weeks we will test measures that could be applied towards optimal watering conditions. This will include an adjustment in the watering regime from twice a week to once in 5 days and adjustments in the watering holding time. It will be a challenge to find a compromise facilitating best watering conditions for young and older plants; Arabidopsis and e.g. N. benthamiana or others. > In parallel we will test different soil/sand/perlite ratios to optimize (lower) the water-holding abilities of the substrate. In case you have any suggestions/experience please do not hesitate to contact us. > We also suggest to not use the tray lids for young plants; or at least to reduce the time from one week to 2-3 days. > > Add. 2.: > Here we assume that the plant stress is caused by a too high light intensity; especially by the portion of the blue spectral range. (The wet soil (1.) might also contribute the total stress reaction). > In short, the new data and calculations indicates that the originally set values of 42% (GMI) and 46% (MFPL) were most probably too high for some of your accessions/mutants/lines. > At least they are too high to be considered as an overall standard setting. > The measured total intensity (µMol*m-2*-1) of the LED light is NOT equal to the same total intensity value of fluorescent tubes. This is mainly caused by the fact of the two different light qualities and the resulting different distribution of individual photons over the spectral range. > Our detailed spectral measurements suggest using a setting of 32% (GMI) and 38% (MFPL) as standard; especially in case of sensitive lines and/or experiments. > This settings will give you the same amount of photons belonging to the blue- and red spectral range as by using 4 fluorescent tubes. > All of you who are already happy with using higher values (60% and even 100%) can of course keep this settings. On the other hand, also lower settings might be meaningful in some cases. > We will also prepare a table/graph showing the relation of the set value to the total measured intensity. > > Please feel free to test the suggested settings in your phytotron/shelves. > How to: press both buttons at the same time until the value starts flashing, set then the desired value by pressing plus or minus button. Wait until the new setting stops flashing. > Alternatively you can also ask the facility staff to change the settings for you. > > We will ask you for your feedback on this new settings in the near future. > > In case of any comments or questions please do not hesitate to contact us. > > Best, Jakub > > P.S.: The different settings for GMI and MFPL phytotrons results from the different distance between your plants and the light source. > > > Jakub Jeż > Head, Plant Sciences Facility > T +43 1 7962324 7090 > M +43 664 8084 77 090 > jakub.jez(a)vbcf.ac.at > Vienna BioCenter Core Facilities GmbH > Dr. Bohr-Gasse 3 > 1030 Vienna > Austria > www.vbcf.ac.at > > > > > > > > > _______________________________________________ > plants-user mailing list > plants-user(a)lists.vbcf.ac.at > https://www.vbcf.ac.at/mailman/listinfo/plants-user

Feb. 21, 2019

LED light survey results and planned measures

by Jez,Jakub

Dear all, I would like to inform you about the results of the LED light survey and the planned measures. We got in total only 18 forms back (11 GMI, 7 MFPL) which corresponds to around 14% of total facility users. However, negative and positive feedback was reported; let us focus on the negative topics. Two main issues have been identified in common: 1. Too wet soil conditions and thus heavy algae growth on the soil surface 2. Stressed plants (anthocyanins formation, early flowering, etc.) Add. 1: The phytotrons and the light quality were designed and optimized towards providing best plant growth conditions; this applies unfortunately also to algae. We assume that the lack of heat radiation, by using LED light, does not dry the soil surface in the same manner like fluorescent tubes did in the past. In the next weeks we will test measures that could be applied towards optimal watering conditions. This will include an adjustment in the watering regime from twice a week to once in 5 days and adjustments in the watering holding time. It will be a challenge to find a compromise facilitating best watering conditions for young and older plants; Arabidopsis and e.g. N. benthamiana or others. In parallel we will test different soil/sand/perlite ratios to optimize (lower) the water-holding abilities of the substrate. In case you have any suggestions/experience please do not hesitate to contact us. We also suggest to not use the tray lids for young plants; or at least to reduce the time from one week to 2-3 days. Add. 2.: Here we assume that the plant stress is caused by a too high light intensity; especially by the portion of the blue spectral range. (The wet soil (1.) might also contribute the total stress reaction). In short, the new data and calculations indicates that the originally set values of 42% (GMI) and 46% (MFPL) were most probably too high for some of your accessions/mutants/lines. At least they are too high to be considered as an overall standard setting. The measured total intensity (µMol*m-2*-1) of the LED light is NOT equal to the same total intensity value of fluorescent tubes. This is mainly caused by the fact of the two different light qualities and the resulting different distribution of individual photons over the spectral range. Our detailed spectral measurements suggest using a setting of 32% (GMI) and 38% (MFPL) as standard; especially in case of sensitive lines and/or experiments. This settings will give you the same amount of photons belonging to the blue- and red spectral range as by using 4 fluorescent tubes. All of you who are already happy with using higher values (60% and even 100%) can of course keep this settings. On the other hand, also lower settings might be meaningful in some cases. We will also prepare a table/graph showing the relation of the set value to the total measured intensity. Please feel free to test the suggested settings in your phytotron/shelves. How to: press both buttons at the same time until the value starts flashing, set then the desired value by pressing plus or minus button. Wait until the new setting stops flashing. Alternatively you can also ask the facility staff to change the settings for you. We will ask you for your feedback on this new settings in the near future. In case of any comments or questions please do not hesitate to contact us. Best, Jakub P.S.: The different settings for GMI and MFPL phytotrons results from the different distance between your plants and the light source. [VBC Logo] Jakub Jeż Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77 090<tel:+43%20664%208084%2077%20090> 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>

Feb. 21, 2019

Re: [Plants-user] New LED light for plant growth feedback survey!

by Jez,Jakub

Dear all, This is a friendly reminder on the deadline for submitting your LED light feedback. Until now we have received 7 feedbacks only! We urgently need especially your negative feedback to be able to improve; if you do not respond I must assume you are satisfied with the LED light and the settings. Best, Jakub From: Jakub Jez <jakub.jez(a)vbcf.ac.at> Date: Friday, 25. January 2019 at 16:03 To: gmi <gmi.all.intern(a)gmi.oeaw.ac.at>, "plants-user(a)lists.vbcf.ac.at" <plants-user(a)lists.vbcf.ac.at> Cc: "VBCFplants.GRP" <plants(a)vbcf.ac.at> Subject: New LED light for plant growth feedback survey! Dear all, We have been running the new LED light systems for about one year now (depending on the type and the location). Now it is time to ask you for your feedback! Please fill out the short survey (link below) till the end of January. Negative feedback is very important to improve – positive feedback is also welcomed. Link: https://www.appn.at/quiz/led-light-feedback/ Deadline: 1st February 2019 From mid of February on we will approach you individually and/or in a form of a user meeting to discuss in detail. The results will also be discussed in the GMI GL meeting and VBCF PlantS UC meeting. Many thanks for your cooperation and your time. Have a nice weekend. Best, Jakub [VBC Logo] Jakub Jeż Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77 090<tel:+43%20664%208084%2077%20090> 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>

Feb. 1, 2019