Transcriptional and proteomic responses towards early nitrogen depletion in Arabidopsis thaliana

Plant roots acquire nitrogen predominantly as ammonium and nitrate, which besides serving as nutrients, also have signaling roles. Re-addition of nitrate to starved plants rapidly and di-rectly transcriptionally re-programs the metabolism and induces root architectural changes, but the earliest responses to nitrogen deprivation are unknown. In this thesis, the early transcriptional response of developed roots to nitrate or ammonium deprivation were analyzed in two Arabidopsis ecotypes contrasting in their nitrogen use efficiency: the inefficient genotype Col-0 and the efficient Tsu-0. The rapid transcriptional repression of known nitrate-induced genes proceeded the tissue NO3- concentration drop, with the transcription factor genes LBD37/38 and HRS1/HHO1 among those with earliest significant change. Some transcripts were stabilized by nitrate, but similar rapid transcriptional repression occurred in loss-of-function mutants of the nitrate response factor NLP7. In contrast, an early transcriptional response to ammonium deprivation was almost completely absent. In Col-0, the analysis was extended with the proteome and phospho-proteome resulting in a rapid and transient perturbation of the proteome induced by ammonium deprivation and a differential phosphorylation pattern in proteins involved in adjusting the pH and cation homeostasis, plasma membrane H+, NH4+, K+ and water fluxes. Fewer differential phosphorylation patterns in transporters, kinases and other proteins occurred with nitrate deprivation. The deprivation responses are not just opposite to the resupply responses, identify NO3--deprivation induced mRNA decay and signaling candidates potentially reporting the external nitrate status to the cell. Transcrip-tome comparison revealed only few N-nutrition related genes between both ecotypes contributing the increased NUE of Tsu-0, which probably relies on higher biomass accumulation. Besides, Tsu-0 confirmed the transcriptional depletion response of Col-0.Pflanzen nehmen Stickstoff vorwiegend in Form von Ammonium und Nitrat auf. Neben Nährstoffen fungieren diese auch als Signalstoffe. Wenn nach Mangel Pflanzen wieder mit Nitrat versorgt werden, wird der Stoffwechsel direkt und innerhalb kürzester Zeit umprogrammiert und die Wurzelarchitektur verändert. Die frühesten Reaktionen einer Pflanze auf Stickstoffmangel sind jedoch unbekannt. In dieser Arbeit wurden die frühesten transkriptionellen Reaktionen von voll entwickelten Wurzeln gegenüber Ammonium und Nitratmangel in zwei Arabidopsis-Ökotypen untersucht, die sich in ihrer Stickstoffnutzungseffizienz unterscheiden: dem ineffizienten Genotyp Col-0 und dem effizienten Tsu-0. Die schnelle transkriptionelle Repression bekannter nitratinduzierter Gene, darunter die Transkriptionsfaktoren LBD37/38 und HRS1/HHO1 mit den frühesten signifikanten Veränderungen, gingen mit dem Absinken des Nitratgehalts im Gewebe einher. Manche Transkripte wurden durch Nitrat stabilisiert, aber eine ähnlich schnelle Repression trat in auch Funktionsverlustmutanten des bekannten Tran-skriptionsfaktors NLP7 der Nitrat-Antwort auf. Gegenüber Ammoniumentzug fehlte eine frühe Mangelantwort hingegen nahezu vollständig. In Col-0 wurde die Analyse um das Proteom und Phosphoproteom erweitert. Eine schnelle, jedoch transiente Veränderung des Proteoms wurde durch Ammoniummangel ausgelöst. Zudem wurden differentielle Phosphorylierungen in Proteinen festgestellt, die an der Regulation des pH- und des Kationengleichgewichts, sowie dem Austausch von H+, NH4+, K+ und Wasser durch die Plasmamembran beteiligt sind. Mit Nitratmangel traten weniger differentielle Phosphorylierungen auf, hauptsächlich in Transportern, Kinasen und anderen Proteinen. Die Nitratmangelantwort entspricht nicht einfach der gegenteiligen Nitratantwort. Möglicherweise übertragen mangelinduzierter mRNA-Abbau und potenzielle Signalproteine den externen Stickstoffstatus in die Zelle weiter. Der Vergleich der Transkriptome zwischen Col-0 und Tsu-0 ergab nur wenige differentiell exprimierte stickstoff-relevante Gene, welche zur höheren Stickstoffnutzungseffizienz von Tsu-0 beitragen könnten. Diese ist vermutlich auf höhere Biomassebildung zurückzuführen. Anhand der von Tsu-0 gewonnenen Transkriptomdaten wurden zudem die Stickstoffmangelantworten von Col-0 bestätigt

DNA-Free Genome Editing: Past, Present and Future

Genome Editing using engineered endonuclease (GEEN) systems rapidly took over the field of plant science and plant breeding. So far, Genome Editing techniques have been applied in more than fifty different plants; including model species like Arabidopsis; main crops like rice, maize or wheat as well as economically less important crops like strawberry, peanut and cucumber. These techniques have been used for basic research as proof-of-concept or to investigate gene functions in most of its applications. However, several market-oriented traits have been addressed including enhanced agronomic characteristics, improved food and feed quality, increased tolerance to abiotic and biotic stress and herbicide tolerance. These technologies are evolving at a tearing pace and especially the field of CRISPR based Genome Editing is advancing incredibly fast. CRISPR-Systems derived from a multitude of bacterial species are being used for targeted Gene Editing and many modifications have already been applied to the existing CRISPR-Systems such as (i) alter their protospacer adjacent motif (ii) increase their specificity (iii) alter their ability to cut DNA and (iv) fuse them with additional proteins. Besides, the classical transformation system using Agrobacteria tumefaciens or Rhizobium rhizogenes, other transformation technologies have become available and additional methods are on its way to the plant sector. Some of them are utilizing solely proteins or protein-RNA complexes for transformation, making it possible to alter the genome without the use of recombinant DNA. Due to this, it is impossible that foreign DNA is being incorporated into the host genome. In this review we will present the recent developments and techniques in the field of DNA-free Genome Editing, its advantages and pitfalls and give a perspective on technologies which might be available in the future for targeted Genome Editing in plants. Furthermore, we will discuss these techniques in the light of existing– and potential future regulations

Instrumented gait analysis: a measure of gait improvement by a wheeled walker in hospitalized geriatric patients

Background In an increasing aging society, reduced mobility is one of the most important factors limiting activities of daily living and overall quality of life. The ability to walk independently contributes to the mobility, but is increasingly restricted by numerous diseases that impair gait and balance. The aim of this cross-sectional observation study was to examine whether spatio-temporal gait parameters derived from mobile instrumented gait analysis can be used to measure the gait stabilizing effects of a wheeled walker (WW) and whether these gait parameters may serve as surrogate marker in hospitalized patients with multifactorial gait and balance impairment. Methods One hundred six patients (ages 68–95) wearing inertial sensor equipped shoes passed an instrumented walkway with and without gait support from a WW. The walkway assessed the risk of falling associated gait parameters velocity, swing time, stride length, stride time- and double support time variability. Inertial sensor-equipped shoes measured heel strike and toe off angles, and foot clearance. Results The use of a WW improved the risk of spatio-temporal parameters velocity, swing time, stride length and the sagittal plane associated parameters heel strike and toe off angles in all patients. First-time users (FTUs) showed similar gait parameter improvement patterns as frequent WW users (FUs). However, FUs with higher levels of gait impairment improved more in velocity, stride length and toe off angle compared to the FTUs. Conclusion The impact of a WW can be quantified objectively by instrumented gait assessment. Thus, objective gait parameters may serve as surrogate markers for the use of walking aids in patients with gait and balance impairments

Scenario set-up and forcing data for impact model evaluation and impact attribution within the third round of the Inter-Sectoral Model Intercomparison Project (ISIMIP3a)

This paper describes the rationale and the protocol of the first component of the third simulation round of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP3a, www.isimip.org) and the associated set of climate-related and direct human forcing data (CRF and DHF, respectively). The observation-based climate-related forcings for the first time include high-resolution observational climate forcings derived by orographic downscaling, monthly to hourly coastal water levels, and wind fields associated with historical tropical cyclones. The DHFs include land use patterns, population densities, information about water and agricultural management, and fishing intensities. The ISIMIP3a impact model simulations driven by these observation-based climate-related and direct human forcings are designed to test to what degree the impact models can explain observed changes in natural and human systems. In a second set of ISIMIP3a experiments the participating impact models are forced by the same DHFs but a counterfactual set of atmospheric forcings and coastal water levels where observed trends have been removed. These experiments are designed to allow for the attribution of observed changes in natural, human and managed systems to climate change, rising CH4 and CO2 concentrations, and sea level rise according to the definition of the Working Group II contribution to the IPCC AR6

Eva Agnes Csato Festschrift

ürkoloji ve Genel Dilbilim alanlarının önemli isimlerinden Eva Â. Csatö Johanson, 11 Haziran 1948'de Macaristan'ın Szombathely şehrinde doğmuştur. Bizler, Türkoloji ve Dilbilim alanlarından meslektaşlarının kalemlerinden çıkmış otuz beş makaleyi içine alan bu kitabı, Eva'ya 65. doğum günü armağanı olarak sunmaktan büyük bir mutluluk duyuyoruz. Eva, Budapeşte'de, Eötvös Lorând Üniversitesinde, Tarih ve İngiliz Dili bölümlerini bitirdikten sonra, 1976'da Norveç/Oslo'ya yerleşmiştir. Öğrenimine Oslo Üniversitesinde Genel Dilbilim ve Türkoloji, Uppsala Üniversitesinde ise Macar Dili Araştırmaları okuyarak devam etmiştir. Some aspects ofthe syntax ofHungarian and Turkish. A study in syntactic typology adlı doktora tezini 1985 yılında Oslo Üniversitesinde tamamlamıştır. Bizlerin Eva ile tanışıklığı ve dostluğu, onun 1986'da Johannes Gutenberg Üniversitesi (Mainz/Almanya), Doğu Bilimleri Enstitüsü, Türkoloji Bölümüne araştırmacı olarak gelmesini takip eden yıllara kadar uzanır. O yıllardan itibaren bu kitaba makaleleriyle katkıda bulunmuş olan bilim insanları gibi bizler de Eva ile çok sayıda projede birlikte çalıştık, birlikte sayısız konferansa katıldık, ortak kurslarda dersler verdik ve dilbilimsel Türkoloji ile Genel Dilbilimin farklı konuları üzerine tartışmalarda bulunduk. Eva, her zaman kararlı, konusuna hakim ve ikna edici argümanları olan tartışmacılardan biri olmuş, ayrıca üzerinde çalıştığımız bütün konulara ve dillere büyük bir ilgiyle yaklaşmıştır. Onun bilgisinden ve desteğinden, pek çok meslektaşı ve öğrencisi gibi bizler de gerek öğrencilik yıllarımızda gerekse sonrasında her zaman yararlandık. Tanıyan bütün meslektaşları ve öğrencileri bilirler ki Eva, öğrencilerini her zaman destekleyen, öğrenci tezlerini teslim tarihinden bir iki gün önce kendi bilgisayarından basma inceliğini gösterecek kadar duyarlı bir akademisyendir. Eva'nın, ileri seviyede yok olma tehlikesiyle karşı karşıya olan Karayca hakkında yürüttüğü kapsamlı saha çalışmaları ve araştırmaları hepimiz için bir örnek teşkil eder. O, Türkoloji alanında sadece teorik araştırma yapmakla kalmayan, aynı zamanda, üzerinde çalıştığı yok olmak üzere olan dilin korunması, hatta tekrar canlandırılması için kendisini o dil topluluğuna adayan az sayıda bilim insanından biridir. Editörler olarak her birimiz bu adanmışlığa yakından şahit olma şansını bulduğumuz için mutluyuz. Yazılarıyla bu armağan projesinin gerçekleşmesini sağlayan meslektaşlarımıza, hazırlık aşamasındaki desteği için Prof. Dr. Emine Yılmaz'a ve kitabı yayımlamayı kabul eden Hacettepe Üniversitesine teşekkürlerimizi sunmayı bir borç biliriz. Eva'ya meslektaşları ve dostları olarak daha nice verimli, sağlıklı, mutlu yıllar diliyoruz

Scenario setup and forcing data for impact model evaluation and impact attribution within the third round of the Inter-Sectoral Model Intercomparison Project (ISIMIP3a)

This paper describes the rationale and the protocol of the first component of the third simulation round of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP3a, http://www.isimip.org, last access: 2 November 2023) and the associated set of climate-related and direct human forcing data (CRF and DHF, respectively). The observation-based climate-related forcings for the first time include high-resolution observational climate forcings derived by orographic downscaling, monthly to hourly coastal water levels, and wind fields associated with historical tropical cyclones. The DHFs include land use patterns, population densities, information about water and agricultural management, and fishing intensities. The ISIMIP3a impact model simulations driven by these observation-based climate-related and direct human forcings are designed to test to what degree the impact models can explain observed changes in natural and human systems. In a second set of ISIMIP3a experiments the participating impact models are forced by the same DHFs but a counterfactual set of atmospheric forcings and coastal water levels where observed trends have been removed. These experiments are designed to allow for the attribution of observed changes in natural, human, and managed systems to climate change, rising CH4 and CO2 concentrations, and sea level rise according to the definition of the Working Group II contribution to the IPCC AR6