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Open position @VBCF Plants: Bioinformatician/Data Analyst (full-time)
by Jez,Jakub Feb. 21, 2019

Feb. 21, 2019

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>

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LED light survey results and planned measures
by Jez,Jakub Feb. 21, 2019

Feb. 21, 2019

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>

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New LED light for plant growth feedback survey!
by Jez,Jakub Feb. 1, 2019

Feb. 1, 2019

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>

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VBCF PlantS new office: PG12
by Jez,Jakub Dec. 10, 2018

Dec. 10, 2018

Dear all, PlantS moved today to a new office: PG12 You can find us right next to the GMI IT service desk/net4biz. Best, Anna, Steffi and Jakub -- Jakub Jeż Head, Plant Sciences Facility [cid:image001.png@01D33C34.13393AC0] VIENNA BIOCENTER CORE FACILITIES GmbH Dr. Bohr-Gasse 3 | 1030 Vienna | Austria VBC 2 | Plaza Floor | room PG-12 phone: +43 1 796 2324 7090 mobile: +43 664 8084 7 7090 e-mail: jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@csf.ac.at> web: www.vbcf.ac.at<http://www.csf.ac.at/> www.vbcf.ac.at/plants<http://www.csf.ac.at/plants> Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> Austrian Plant Phenotyping Network – APPN www.appn.at<http://www.appn.at>

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Paternity leave 2nd and last part: October - December 2018
by Jez,Jakub Oct. 3, 2018

Oct. 3, 2018

Dear all, Due to some important deadlines at work I had to split my paternity leave into two parts. The second (and last) part will start on the 11th October and run till the 11th January 2019. During this time, I will be again remotely available to coordinate the Facility – but please consider that I will be travelling with very limited internet access and a time shift. Stefanie’s working hours will be increased during this time period. I am also very happy to announce that Anna Smolka has very recently started at the PlantS Facility on a part-time basis (0.2FTEs). She will mainly be involved in our HT plant phenotyping and image analysis service. For urgent issues (technical problems, pest infestations, etc.) please write to: plants(a)vbcf.ac.at<mailto:plants@vbcf.ac.at> For daily facility issues like e.g. consumables, standard phytotron programming, booking system, please contact: anneliese.auer(a)gmi.oeaw.ac.at<mailto:anneliese.auer@gmi.oeaw.ac.at> For programming of complex environments, the HT plant phenotyping service and the image analysis service please contact: stefanie.koemeda(a)vbcf.ac.at<mailto:stefanie.koemeda@vbcf.ac.at> For APPN.at related issues: appn(a)vbcf.ac.at<mailto:appn@vbcf.ac.at> In doubt, please write to plants(a)vbcf.ac.at<mailto:plants@vbcf.ac.at> I am looking forward to seeing you again! Kind regards, Jakub -- Jakub Jeż Head, Plant Sciences Facility [cid:image001.png@01D33C34.13393AC0] VIENNA BIOCENTER CORE FACILITIES GmbH Dr. Bohr-Gasse 3 | 1030 Vienna | Austria VBC 2 | Plaza Floor | room PG-3 phone: +43 1 796 2324 7090 mobile: +43 664 8084 7 7090 e-mail: jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@csf.ac.at> web: www.vbcf.ac.at<http://www.csf.ac.at/> www.vbcf.ac.at/plants<http://www.csf.ac.at/plants> Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> Austrian Plant Phenotyping Network – APPN www.appn.at<http://www.appn.at>

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NEW SOIL for testing: Gramoflor Topf Nr. 2006
by Jez,Jakub Sept. 20, 2018

Sept. 20, 2018

Dear all, There is a new soil substrate available for testing at both PlantS locations: Gramoflor Profi-Substrat Topf Nr. 2006 Why? As you might know, we regularly had inconsistent and low product quality of our standard substrate ED63, in the past. Sometimes the soil is too dry and can’t take water, another time too wet and full of fungi; perhaps you also remember the “country smell” in the Facility. . . On the other hand, the rough structure makes it necessary to sieve the soil for sensitive experiments including HT plant phenotyping. Therefore, we have started looking for a similar but more professional and homogenous substrate to (depending on your feedback, fully or partially) replace the ED63 in future. How? We have propagated Arabidopsis and N. benthamiana on seven new soil types and compared them to the two standard substrates under standard conditions in two independent experiments. Parameters that were scored include all Lemnatec features (size, shape, color etc. over time), flowering time, plant height, dry weight and seed weight and a thorough visual examination by Anneliese. Based on these results we have decided to give the Gramoflor Profi-Substart Topf Nr. 2006 a chance. Overall, the performance of Gramoflor 2006 is highly comparable to ED63 while providing a highly homogeneous structure and batch quality. Please drop us a mail for detailed results. What do we know about the winner: Gramoflor Profi-Substart Topf Nr. 2006 All-purpose potting-soil for professional use, moderately fertilized (1.2 kg/m3), mixture of slightly decomposed bog peat with organic and/or mineral and/or synthetic additives; pH=5.8 (5.4-6.2) same as ED63, medium rough structure, includes clay, mineral fertilizers, slow-release fertilizers. https://www.gramoflor.com/files/profiflyer_de_130115_ansicht.pdf (Line: Topf+TonXL GF-Topf) What will happen to ED63: We will, of course, keep providing the ED63 in parallel and order upon actual usage. In case of questions please contact us. We are very happy to receive your valuable feedback on the new substrate! Kind regards, the VBCF PlantS Team supported by the FFG FEMTech grant (Klara Wuketich)

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Plant Phenotyping Forum Invitation - 13 September, 1-5pm, Vienna BioCenter Campus
by Jez,Jakub Sept. 5, 2018

Sept. 5, 2018

The registration for the Plant Phenotyping Forum closes soon, do not miss to register and to join the meeting. - 13 September, 1-5pm, Vienna Biocenter Campus - Registration: https://www.appn.at/plant-phenotyping-forum/ In case you can’t join in person you can follow and participate in the LIVE BROADCAST of the penal discussion: https://join.me/plant-phenotyping Looking very much forward to meeting you, Jakub Jez and Roland Pieruschka [/Users/jakub.jez/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_397492860]<http://www.appn.at/> Von: Pieruschka, Roland Gesendet: Freitag, 10. August 2018 16:07 An: FM-emphasis <emphasis(a)fz-juelich.de> Betreff: Plant Phenotyping Forum Invitation - 13 September, 1-5pm, Vienna BioCenter Campus Dear all, It is our pleasure to invite you to the Plant Phenotyping Forum discussing the role of Austria and Eastern Europe in plant phenotyping for sustainable agriculture. The Forum will address the plant phenotyping landscape and role of Austria, Czech Republic and Slovakia within the context of European plant phenotyping initiatives such as EMPHASIS and EPPN2020 with the goal to advance basic plant research, plant breeding and foster sustainable agriculture. The meeting will take place on September 13, 2018 , 1-5pm at the Vienna BioCenter Campus, Research Institute of Molecular Pathology, IMP Lecture Hall. (Free) registration: https://www.appn.at/plant-phenotyping-forum/ Confirmed participants and speakers (in alphabetical order): Marian Brestic, Prof., Slovak Agricultural University in Nitra, Department of Plant Physiology (SUA) Hermann Bürstmayr, Head, Division of Plant Breeding and Head, Institute for Biotechnology in Plant Production (BOKU) Pavel Hauptvogel, Director, Research Institute of Plant Production (NPPC) Ivan Ingelbrecht, Head, Plant Breeding and Genetics Laboratory, (IAEA) Jakub Jez, Head, VBCF Plant Sciences Facility & coordinator Austrian Plant Phenotyping Network (APPN) Gabriela Pastori, Chair, ESFRI Strategy Working Group on Health and Food Uli Schurr, Head, IBG-2: Plant Sciences, FZ Jülich & Coordinator ESFRI EMPHASIS project Lukas Spichal, Palacky University Olomouc, coordinator of the Czech Plant Phenotyping Network (CZPPN) Andreas Walter, Operating Director BioImaging Austria (CMI) A panel discussion, moderated by Uli Schurr, will follow the presentations. For those interested, we will tour the VBCF Plant Sciences Facility incl. the HT phenotyping platform. The full program is attached to this mail. Please feel free to share & spread the word! Looking very much forward to meeting you, Jakub Jez and Roland Pieruschka [Das Bild wurde vom Absender entfernt. https://www.appn.at/wp-content/uploads/2017/03/Logo-full.png] https://www.appn.at/ Welcome [www.appn.at]<https://www.appn.at/> www.appn.at<http://www.appn.at> Welcome to the Austrian Plant Phenotyping Network (APPN) - "Enhancing the Austrian Plant Phenotyping Community!" Summary: Within this Plant Phenotyping Forum, we will discuss the role of Austria and Eastern Europe in agricultural production, as regions with huge potential and long-term traditions in the agricultural sector. Specifically, breeding and the consideration of environmental effects for continental climatic environments may require new breeding efforts in this region, including new strategies to develop new germplasm in pre-breeding programs and the application of modern breeding technologies, specifically to improve stress resistance to close the yield gap in times of a changing climate. In this context, the need to characterize the phenotype is essential to understand fundamental processes, which determine the structure and function of plants in particular. While significant progress has been made in molecular methods in recent years and the genomes of several plants have been sequenced this knowledge is not sufficient to simulate the phenotype of a plant without knowing the history and the dynamic interaction of the plant with its environment. Plant phenotyping - quantitative analysis of structure and function of plants - has become the major bottleneck and, quantitative information on genotype-environment relations is the key to address future challenges. Increasing the plant biomass production quantitatively and qualitatively can provide major contributions to grand challenges like food security on a global level, at the same time reducing a major driver for migration movements. Beyond fostering scientific progress, plant phenotyping requires a community effort. In this context EPPN2020, a EU funded I3 project provides access to key plant phenotyping facilities in Europe while EMPHASIS, a ESFRI listed project aims at the development of a long term sustainable pan European plant phenotyping infrastructure that addresses the needs of the diverse users from academia and industry including the operation and development of a pan-European e-infrastructure to effectively collect, process and provide data for the community. ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -- Tato sprava bola prehladana na vyskyt virusov a nebezpecneho obsahu antivirovym systemom MailScanner<http://www.mailscanner.info/>, a zda sa byt cista.

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SD phytotrons: sensitive experiments ongoing
by Jez,Jakub Aug. 30, 2018

Aug. 30, 2018

Dear all, Please note that there are sensitive experiments ongoing in the SD phytotrons. Please do not enter the SD phytotrons (#10, #13 and #18/19) during the dark period! The light period is indicated by the blue light above every single phytotron (ON = ON), so there is no need to open neither the door nor the small window. Thank you for your cooperation. Best regards, Jakub -- Jakub Jeż Head, Plant Sciences Facility [cid:image001.png@01D33C34.13393AC0] VIENNA BIOCENTER CORE FACILITIES GmbH Dr. Bohr-Gasse 3 | 1030 Vienna | Austria VBC 2 | Plaza Floor | room PG-3 phone: +43 1 796 2324 7090 mobile: +43 664 8084 7 7090 e-mail: jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@csf.ac.at> web: www.vbcf.ac.at<http://www.csf.ac.at/> www.vbcf.ac.at/plants<http://www.csf.ac.at/plants> Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> Austrian Plant Phenotyping Network – APPN www.appn.at<http://www.appn.at>

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Plant Phenotyping Forum Invitation - 13 September, 1-5pm, Vienna BioCenter Campus
by Jez,Jakub Aug. 10, 2018

Aug. 10, 2018

Dear all, It is our pleasure to invite you to the Plant Phenotyping Forum discussing the role of Austria and Eastern Europe in plant phenotyping for sustainable agriculture. The Forum will address the plant phenotyping landscape and role of Austria, Czech Republic and Slovakia within the context of European plant phenotyping initiatives such as EMPHASIS and EPPN2020 with the goal to advance basic plant research, plant breeding and foster sustainable agriculture. The meeting will take place on September 13, 2018 , 1-5pm at the Vienna BioCenter Campus, Research Institute of Molecular Pathology, IMP Lecture Hall. (Free) registration: https://www.appn.at/plant-phenotyping-forum/ Confirmed participants and speakers (in alphabetical order): Marian Brestic, Slovak Agricultural University in Nitra, vice-rector for research and science Hermann Bürstmayr, Head, Division of Plant Breeding and Head, Institute for Biotechnology in Plant Production (BOKU) Pavel Hauptvogel, Director, Research Institute of Plant Production (NPPC) Ivan Ingelbrecht, Head, Plant Breeding and Genetics Laboratory, (IAEA) Jakub Jez, Head, VBCF Plant Sciences Facility & coordinator Austrian Plant Phenotyping Network (APPN) Gabriela Pastori, Chair, ESFRI Strategy Working Group on Health and Food Uli Schurr, Head, IBG-2: Plant Sciences, FZ Jülich & Coordinator ESFRI EMPHASIS project Lukas Spichal, Palacky University Olomouc, coordinator of the Czech Plant Phenotyping Network (CZPPN) Andreas Walter, Operating Director BioImaging Austria (CMI) A panel discussion, moderated by Uli Schurr, will follow the presentations. For those interested, we will tour the VBCF Plant Sciences Facility incl. the HT phenotyping platform. The full program is attached to this mail. Please feel free to share & spread the word! Looking very much forward to meeting you, Jakub Jez and Roland Pieruschka [https://www.appn.at/wp-content/uploads/2017/03/Logo-full.png] https://www.appn.at/ Welcome [www.appn.at]<https://www.appn.at/> www.appn.at Welcome to the Austrian Plant Phenotyping Network (APPN) - "Enhancing the Austrian Plant Phenotyping Community!" Summary: Within this Plant Phenotyping Forum, we will discuss the role of Austria and Eastern Europe in agricultural production, as regions with huge potential and long-term traditions in the agricultural sector. Specifically, breeding and the consideration of environmental effects for continental climatic environments may require new breeding efforts in this region, including new strategies to develop new germplasm in pre-breeding programs and the application of modern breeding technologies, specifically to improve stress resistance to close the yield gap in times of a changing climate. In this context, the need to characterize the phenotype is essential to understand fundamental processes, which determine the structure and function of plants in particular. While significant progress has been made in molecular methods in recent years and the genomes of several plants have been sequenced this knowledge is not sufficient to simulate the phenotype of a plant without knowing the history and the dynamic interaction of the plant with its environment. Plant phenotyping - quantitative analysis of structure and function of plants - has become the major bottleneck and, quantitative information on genotype-environment relations is the key to address future challenges. Increasing the plant biomass production quantitatively and qualitatively can provide major contributions to grand challenges like food security on a global level, at the same time reducing a major driver for migration movements. Beyond fostering scientific progress, plant phenotyping requires a community effort. In this context EPPN2020, a EU funded I3 project provides access to key plant phenotyping facilities in Europe while EMPHASIS, a ESFRI listed project aims at the development of a long term sustainable pan European plant phenotyping infrastructure that addresses the needs of the diverse users from academia and industry including the operation and development of a pan-European e-infrastructure to effectively collect, process and provide data for the community.

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TODAY: VBCF PlantS beer hour and 5years party!
by Jez,Jakub Aug. 2, 2018

Aug. 2, 2018

Dear friends, Don’t miss our beer hour / 5 years party! TODAY, 5pm @IMBA Atrium There will be LIVE Music by Dave McKendry typical “Heurigen” food honored Austrian wine (white, red and the best rosé I have ever had!) Draft beer: Weitra Bräu Hadmar Bio Sacher Cake! Looking forward to meeting you! Your VBCF PlantS Team, Klara, Stefanie, Jola, Anneliese & Jakub [cid:image001.png@01D42A50.797D44B0]

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