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GRK 2039 Blog

* Annual GRK 2039 retreat 2019

written by Luisa Lübke 2019/07/03

From the 3rd to the 5th of June the annual GRK 2039 retreat took place in Lauterbad in the Black Forest. Like last year, the participating GRK members resided in the well- known Waldhotel Zollernblick, which is currently under construction and granted us not only a view of the Black Forest but also of a new pool.

The program for all three days mainly consisted of project presentations by the GRK members and three interesting tutorials, given by Prof. Roesky, Dr. Unterreiner and Dr. Ruben Ragg from Wiley. Dr. Ragg provided us with an astonishing insight into the job of a publisher.

After everybody enjoyed dinner at the hotel, the highlight of the first day was the poster session, in which each GRK member presented their project on a poster. Active discussions and newly formed co-operations were the result of this session. Afterwards a few members concluded the first evening in the newly built Bar area of the hotel.

As a team event all participants went on a four- hour hike in the afternoon of the second day. First the hike led us to a bird tower with the attempt of taking a new GRK 2039 group picture. The hike was then crowned by a dinner in the Friedrichs am Kienberg and a short 30 minute walk back to the hotel. Once more the evening was ended with a relaxing get together on the terrace of the hotel with a lovely view of the Black Forest. 

Thanks to Sahana for planning and organization of the schedule and to Franziska for organization of the trip.

* Berlin: 16. European Short Course on Time-resolved Fluorescence Spectroscopy

written by Julia Leier 2019/03/29

Vom 04. – 08. November fand in Berlin der jährliche Kurs zur zeitaufgelösten Fluoreszenzspektroskopie  von der Firma PicoQuant statt. Wir waren 40 Teilnehmer und rund 15 Sprecher und Trainer. Am ersten Tag wurde nach einer netten Begrüßung unter anderem von Joseph R. Lakowicz und Zygmunt „Karol“ Gryczynski eine allgemeine Einführung in das Thema der Fluoreszenz gegeben.

In den darauffolgenden Tagen wurden generelle und  instrumentelle Einweisungen zum Thema zeitaufgelöstes Einzelphotonenzählen (TCSPC), sowie der dazugehörigen Datenanalyse gegeben.

Die theoretischen Einheiten wurden von mehreren praktischen Sessions begleitet. Hier wurden wir in kleine Gruppen eingeteilt und konnten selbst Messungen durchführen. In den verschiedenen Stationen wurden an den jeweiligen Geräten zeitaufgelöste und stationäre Fluoreszenzspektren, TCSPC, Anisotropie und Mikroskopie gemessen. Eine weitere Station war die Datenanalyse, wobei hier die Analyse von den genannten Messungen erläutert und Hilfestellungen dazu gegeben wurden.

Joe und Karol beantworten allen Fragen der Teilnehmer, halfen bei instrumentellen Schwierigkeiten und gaben weitere Tipps für die jeweiligen Messungen.

Es war ein toller und vor allem lehrreicher Kurs. 

* What`s the trick behind effective visual communication?

written by Mikhail Khorenko 2019/01/10

On the 19th and 20th November the PhD members of the GRK-group had an opportunity to participate in a training course for efficient visual communication, given by Dr. Jernej Zupanc (Seyens Ltd.; www.seyens.com). The special focus of this course was on developing and structuring of scientific illustrations in order to make them more descriptive and appealing. The participants had to learn how to address different groups of interest, how complex graphic correlations can be simplified and which colour composition should be used in the illustrations to avoid disorientation and confusion of the observers. Moreover, typical examples of application were discussed in detail, based on self-made illustrations for journal publications as well as for poster or oral presentations of the participants.

A highlight of the training event and at the same time the biggest challenge for the PhD students was a task where everyone had to develop a drawing which would explain his or her research project without any oral comments. In a subsequent discussion in small groups the illustrator was first not allowed to comment his own drawing whilst the others had to interpret it. Thus, deficiencies of the individual graphic illustrations became obvious and were easily mended in teamwork. 

Besides the course itself, the participating GRK members spent a pleasant get-together evening enjoying cultural and culinary attractions of Schwetzingen, where this two-day event took place.

Overall, the time in Schwetzingen was very exciting and informative for everyone. Follow our research and you will probably notice soon how the graphics and illustrations get better and better – thanks to Dr. Jernej Zupanc!

* Merry Christmas and a Happy New Year!

written by Franziska Rönicke 2018/12/22

Thank you Tim for organizing our GRK christmas party! It was a very nice to meet before the holidays. 

I wish you all a Merry Christmas and a good start into the year 2019!

 

* Besser argumentieren für Frauen

written by Sophina Christ 2018/12/21

Das Argumentieren, die Kunst der Überzeugung, muss gelernt sein. Aus diesem Grund haben die weiblichen Mitglieder unseres Graduiertenkollegs (GRK) 2039, an einem Argumentationskurs für Frauen teilgenommen. Ihr fragt euch jetzt sicher warum dieser Kurs speziell nur für uns Frauen angeboten wurde. Das liegt nicht daran, dass wir Frauen schlechter argumentieren. „Sogar das Gegenteil ist der Fall. Frauen kommunizieren sehr gut!“ sagt unsere Dozentin Kristin Raabe. Im Laufe des Workshops kristallisiert sich heraus, dass Männer und Frauen allerdings auf unterschiedliche Art und Weise kommunizieren. Frauen sind Expertinnen in der Beziehungssprache. Sie wollen Gemeinsamkeiten zwischen sich und ihren Gesprächspartnern herstellen und haben ein Bedürfnis gemocht zu werden. Männer sehen die Kommunikation im beruflichen Umfeld oft als Wettbewerb, den es zu gewinnen gilt. Es gibt viele Studien, die belegen, dass Männer und Frauen in unterschiedlichen Sprachwelten leben. Aber Vorsicht: Schwarzweißmalerei ist bei diesem Thema nicht angebracht, denn die Grenzen zwischen den Geschlechtern sind fließend.  Manche Männer kommunizieren eben sehr emphatisch und manche Frauen, können mit ihrer geschliffenen Rhetorik jeden „Gegner“ verbal ausschalten. Wichtig ist es, die eigenen Stärken in der Kommunikation geschickt einzusetzen und wenn einem mal eine dominierende „männliche“ Rhetorik begegnet, die richtige Abwehrstrategie parat zu haben. Ziel des Workshops war es unter anderem uns für diese Kommunikationsunterschiede zu sensibilisieren. Im beruflichen Umfeld soll natürlich auch über die eigene Arbeit geredet werden und dabei ist es hilfreich dies knapp und verständlich zu tun. Viele Hilfsmittel wurden uns in dem Kurs zur Hand gegeben, auch die Technik des sogenannten Küchenzurufs. Dabei arbeitet eine Person in der Küche, während jemand anders im Nebenraum dieser Person eine Botschaft zuruft – beispielsweise über den Inhalt eines gerade gelesenen Artikels. Fast jedem Menschen fällt es in so einer akustisch schwierigen Situation leicht, sich auf das Wesentliche zu beschränken. Der Küchenzuruf beinhaltet also die Kernbotschaft eines Themas. Wenn es uns auch gelingt, in Meetings oder bei Vorträgen klare Kernbotschaften zu transportieren, lassen sich viele Missverständnisse vermeiden. Schließlich ist es auch im beruflichen Umfeld essenziell seine Argumente so vorzubringen, dass die Gesprächspartner überzeugt werden. Dabei kann auch die klassische Rhetorik helfen, die schon auf Aristoteles zurückgeht. Auch Schlagfertigkeit und eine gelungene Körpersprache lassen sich trainieren und können dann effizient eingesetzt werden.  Im Argumentations-Seminar haben wir das anhand von Spielen und Übungen trainiert, um anschließend das frisch Gelernte aktiv vor laufender Kamera auszuprobieren. Die darauffolgende Analyse des Filmmaterials gab Aufschluss über Ticks, Körpersprache und vieles mehr. Insgesamt fand ich den Argumentationskurs für Frauen interessant, locker und spannend, was vor allem an unserer kompetenten Dozentin Kristin Raabe lag. Vielen Dank! I

* Prof. Dr. Jacqueline K. Barton

written by Fabian Lang 2018/12/10
On October 23rd we had the pleasure to welcome Prof. Jaqueline K. Barton from the California Institute of Technology (Caltech), USA as the guestspeaker for the 15th Criegee-Lecture “DNA Signaling”. Prof. Barton is one of the world’s leading nucleic acid chemists, awarded e.g. with the National Medal of Science (2011) and the Prestley Medal (2015).
In her talk Prof. Barton presented her research which focuses on the development and use of electrochemical methods which take advantage of DNA charge transfer chemistry. Her research group is using this characteristic of DNA to answer fundamental questions about the charge transfer process and to develop a highly sensitive platform for the detection of DNA-binding proteins and mRNAs. Other DNA charge transfer studies in her research group focus on investigating the mechanistic and kinetic properties of electron and hole propagation along DNA. The DNA base pair stack enables charge transfer over long distances but is sensitive to disorders in base-base interactions, which occur at single base mismatches. 
The GRK members Franziska, Larissa, Samantha and Fabian had the possibility to have a talk with Prof. Barton during lunch in the Gastdozentenhaus. Prof. Barton told us about the American education system and gave a deep insight in the way to become a PhD and a Professor in the USA. We learned a lot about the differences to the German education system and that in the USA the academic way after the PhD is more popular than in Germany.

* Nacht der Wissenschaften am KIT –Jagd auf die schnellsten chemischen Reaktionen

written by Philipp Jöckle 2018/11/26
Am 16.11.2018 führte Priv.-Doz. Dr. Andreas-Neil Unterreiner bei der Nacht der Wissenschaften des KITs mit seinem Vortrag „Ultraschnell – Jagd auf die schnellsten chemischen Reaktionen“ in die Welt ultraschneller Bewegungen und Reaktionen von Molekülen ein. Er begeisterte die zahlreichen Besucher von jung bis alt im voll besetzten Tulla-Hörsaal mit vielen spannenden Fragen, welchen er in interessanten Beispielen und sportlichen Einlagen auf den Grund ging: Was ist überhaupt schnell, oder gar ultraschnell? Ist die menschliche Reaktionszeit bereits schnell? Zum Beispiel beim Versuch den Klaviertastenanschlag-Rekord zu brechen (13,73 Hz). In Relation zu den vorausgehenden Prozess-Kaskaden, die zu einer menschlichen Reaktion führen, ist die Antwort nein. Zum Beispiel spielt sich die cis-/trans-Isomerisierung von Retinal als Startschuss des Sehprozesses auf einer (ultra-)kurzen Zeitskala von einigen hundert Femtosekunden (1 fs = 10-15 s) ab. Durch die induktive Herangehensweise von Priv.-Doz. Dr. Unterreiner war es dem Publikum möglich, auch komplexen Zusammenhängen einfach zu folgen und einen Eindruck für Zeitskalen von Translations-, Rotations- und Schwingungsbewegungen von Molekülen und deren Reaktionen zu gewinnen. Daran anschließend stellte Priv.-Doz. Dr. Unterreiner einen Bezug zu aktuellen Themen der Grundlagenforschung her. Zum Beispiel werden photophysikalische Fragestellungen im Rahmen des Projektbereichs M2 im GRK 2039 zu Molekülen für die fluoreszente Bildgebung von Zellen mittels zeitaufgelöster fs-Spektroskopie untersucht. Zusammengefasst gab Priv.-Doz. Dr. Unterreiner einen sehr spannenden und informativen Vortrag, der Wissenschaftlern wie Nicht-Wissenschaftlern einen Einblick in die schnellsten Molekülbewegungen, die das Schicksal einer jeden chemischen Reaktion bestimmen, ermöglichte.

* Efficiently Photocontrollable or not? Biological Activity of Photoisomerizable Diarylethenes

written by Tim Schober 2018/11/21

I. V. Komarov, S. Afonin, O. Babii, T. Schober, A. S. Ulrich, Chem. Eur. J. 2018, 24, 1–11.

For the fundamental understanding of biological processes and systems, experimental scientists utilize various controlling tools – to perturb biological systems and generate reciprocal knowledge by analyzing biological response. Such knowledge is useful, for example, for comprehending mechanisms of human diseases. At the same time, practicing the biosystem perturbation allows developing effective modulators that serve as treatments or diagnostic tools. Recently non-ionizing light has emerged as an exciting way of imposing biocontrol, non-invasively and orthogonally to most bioprocesses.  Medical utility of light as the controlling principle is explored in the fields of optogenetics and photopharmacology. Both disciplines make use of molecular photoswitches to transmit the light signal. Their use also permits an unprecedented spatiotemporal control through the external light application with modern miniature light sources and light guides, resulting in activation/deactivation of such photoswitchable modulators at will only where their action is required. In our recent concept paper, we discuss the use of so-called diarylethenes – a novel class of molecular photoswitches broadly applied in technical applications, but underexplored for in vivo biocontrol. Unlike commonly known and vastly applied azobenzenes, diarylethenes upon photoswitching do not undergo dramatic conformational changes. Instead, they switch between rigid and very flexible photophorms, therefore their structure-function relationships are more complex. Notably, the rigid form can be switched to the flexible form with red light, which makes diarylethene-based photoswitches attractive for applications in living organisms. We analyze current scarce in number examples of diarylethene-mediated biocontrol and define types of processes or biosystems where this rigidity/flexibility interplay can lead to beneficial usages.

* Frontiers in Delivery of Therapeutics

written by Tim Schober 2018/10/15
Tartu (Estonia), 21.-24.08.2018
This proceeding conference series is organized by Prof. Ülo Langel, who is the world key opinion leader in the field of cell-penetrating peptides for many years now. In this year edition, for the first time, the “peptides for intracellular delivery” topic has been expanded to all kinds of carriers, including liposomes, nanoparticles, exosomes, viral particles. The talks and posters presented current pharmacologically relevant examples of delivering medically relevant proteins, small molecules, SSO, siRMAs and plasmids. Combining the expertise from other-than peptides-only fields and strong focus on therapeuticall cargoes leads to a better understanding of fundamental delivery mechanisms and enables generation of new practically useful ideas.
Our member Tim Schober gave an oral presentation about his results on developing photocontrollable cell-penetrating peptides.
 
Abstract:
Towards photocontrol of the cell entry of cell-penetrating peptides
Tim Schober, Oleg Babii, Sergii Afonin, Igor V. Komarov and Anne S. Ulrich
 
Photoswitchable drugs can be delivered to their in vivo targets via illumination with non-invasive red light with unprecedented spatiotemporal resolution. Herein we expand this delivery concept to in-cell transport, by enabling photocontrol of peptide cell-penetrating ability. We designed several oligo-arginine-based cyclic cell-penetrating peptides, each of having a diarylethene-based photoswitch (DAE) in the backbone. For some amphipathic 10-mer peptides, we observed well-pronounced differences in uptake between the two photoforms. We explain the differences by the changes in rigidity/flexibility and in backbone exposure upon photoswitching, which differentially affect both, the entry-enabling preorganized charge display and peptide CPP-activity deteriorating intramolecular aggregation.

* Impressions about the microfluidics conference in Heidelberg

written by Sahana Sheshachala 2018/09/04

I recently participated in a three-day microfluidics conference at Heidelberg, Germany. The conference titled “Microfluidics 2018: New Technologies and Applications in Biology, Biochemistry and Single-Cell Analysis” is one of the biggest conferences in Europe organized by EMBL (European Molecular Biology Laboratory) focusing on current state-of-the art in the field of microfluidics and its applications in Molecular Biology. This was my first conference as a PhD student and I could not have asked for more. It was a great opportunity for an early researcher like me to get insights into the current trends and directions in the field of microfluidics, given that my doctoral studies involves microfluidic applications in the field of chemical biology.

Prior to the conference, I kept myself informed with the general information on the relevant lectures and keynote speakers. I was very impressed with the structuring and contents of the topics covered in the conference. The gathering was an amalgamation of some of the pioneer research groups in the field of microfluidics.

The conference hall at the EMBL center Heidelberg, the ARC Auditorium was fascinating in terms of its construction, perfectly designed for the scientific conferences. Particularly astonishing was the architecture of the hall way inspired by DNA double helix, through which the posters were aligned. The educational and product based stalls present there were from various companies, institutions and start up’s. The conference was attended by close to 200 people and one could say the gathering was quite international. The topics covered during conference were categorized into several segments covering sub topics. The poster sessions were distributed between two days and the large student gathering created a very vibrant atmosphere. The first lecture was delivered by Prof. Stephen Quake from Stanford, who provided a solid start to the conference through his engaging presentation about single cell genomics. The lectures throughout the day were very informative and inspiring at the same time, although I struggled a bit to process all the information that was coming through the fast moving slides. The next segment had some flash talk sessions from a set of students and I felt the flash talks were a great way to attract the audience to one’s poster. Imagining myself delivering one of these flash talks in the next conference, I eagerly waited for the poster sessions and took a note of the posters that were interesting to me.

Poster sessions turned out to be more enjoyable and resourceful than I imagined and I was able to have some very insightful interactions with many graduate students from various institutions around the globe. We did exchange a lot of information and discussed scientific problems concerning our research. Personally, for me, the interaction was very beneficial as I got answers and insights into new approaches for a few of the practical problems that I was facing in the lab. This to me was the best part of the conference as I found out how one approaches a particular scientific problem with a creative mind.

On the other hand, I was still trying to gather my courage to talk to the Professor I wanted to talk to, and saved it for the next day. Thanks to the organizers, in the evening everyone enjoyed the live telecast of the football world cup and then dispersed for the dinner.

The second and third day lectures were more relevant to my line of research about droplet-based microfluidics and its implications in the field of single cell analysis, antibody discovery and other related fields.I thoroughly enjoyed the talk by Prof. David A. Weitz from Harvard University on single cell analysis using droplet microfluidics and was fascinated to know how the microfluidic droplets can be manipulated for a particular application using simple chip designs. An interesting segment of the conference that intrigued me as a chemist was the topics on new microfluidic modules and designs which largely implied the exponential growth of new microfluidic modules and their ability to cross the scientific barrier in solving more complex phenomena in biomedical field. And I finally managed to have short interaction with one of the professors in the tea session and the interaction boosted my confidence for further networking and social interaction.

At the end, I would like to express my sincere gratitude to the GRK 2039 for providing funding for my very first conference and EMBL for structuring the conference so well.

„Was genau passiert in Lebewesen und wie können wir es sichtbar machen?“

written by Larissa Doll and Samatha Wörner 2018/08/28

Am Girls´ Day 2018 hatte das „GRK 2039 - Molekulare Architekturen für die fluoreszente Bildgebung von Zellen“ die Chance, Schülerinnen einen Einblick in unser Forschungsprogramm zu ermöglichen. Um ihnen die Themengebiete Chemie, Biologie und Physik näher zu bringen, wurden verschiedene Stationen durchlaufen. Dabei konnten sie auch einen Einblick in die Quervernetzung dieser Themen und somit auch in das GRK 2039 bekommen und es wurde deutlich, wie wichtig das Zusammenarbeiten im Rahmen eines Graduiertenkollegs ist. An der ersten Station wurde den Schülerinnen die Eigenschaften von Photoschaltern durch Bestrahlung mit Licht bildlich vorgeführt. Auch die Theorie dahinter wurde mit Anwendungsbeispielen aus der Photopharmakologie erklärt. Um einen Einblick in den Laboralltag zu bekommen, konnten die Mädchen anschließend ausprobieren, wie beispielsweise das Arbeiten an einer Glove-Box oder HPLC funktioniert. Noch mehr praktische Erfahrung wurde an der dritten Station durch die Isolierung von DNA aus Zwiebeln gewonnen. Diese wurde durch Anfärben sichtbar gemacht. Zur weiteren Veranschaulichung für die zuvor erklärten und gezeigten Systeme von organischen und bioorganischen Molekülen, wurden abschließend angefärbte Zellen im Fluoreszenzmikroskop betrachtet. Dabei konnten die verschiedenen Zellorganellen farblich unterschieden werden. Final konnte sogar ein lebender Zebrafischembryo im Mikroskop untersucht werden.

Zusammenfassend war es eine gelungene Möglichkeit, schon jungen Menschen die Wichtigkeit des naturwissenschaftlichen Zusammenarbeitens zu vermitteln. Wir hatten viel Spaß dabei und freuen uns auf weiteres Interesse am GRK 2039.

* Welcome Julia Leier!

written by Julia Leier 2018/08/21

We also want to welcome Julia Leier!

She just started  her PhD in the group of PD Andreas Unterreiner:

 

Hi,

I’m Julia, a new member of the GRK 2039.

 

This is how I got here: After finishing school I moved to Gießen to study ecotrophology (nutritional science) at the Justus-Liebig-University with the focus on biochemistry. There I got very interested in chemistry, which initiated my decision to study chemistry and mathematics for a teaching profession at the Karlsruhe Institute of Technology after finishing my bachelor degree. Here I specialised in physical chemistry, where I wrote my scientific work in the research group of PD Dr. A.-N. Unterreiner.

 

For my PhD I joined this research group within the GRK in June 2018. My aim is to analyse the photophysical and -chemical properties of various molecules on an ultrashort time scale. Therefore I’m using a femtosecond broadband transient absorption spectrometer as well as steady-state methods like absorption spectroscopy in the UV and visible spectra region and fluorescence spectroscopy. After photo-excitation there is typically a manifold of possible relaxation pathways. Whereby the fluorescence and its competing pathways are of special interest. In order to additionally enable the investigation of fluorescence lifetimes of up to a few picoseconds, I’m building an experimental setup called fluorescence up-conversion.

 

Currently I collaborate with two GRK members to analyse the properties of flavine derivatives for electron transfer in the DNA and the environmental influence of photoswitchable peptides.

* Welcome Monja Kunkel!

written by Monja Kunkel 2018/07/19

We are happy to welcome Monja as a new member in our research training group!

I asked her to introduce herself so that we all know a little bit more about her background and her new doctoral project:

 

Hi all,

my name is Monja and I‘m from Lahr, a small town only about 100 km to the south of Karlsruhe. For my bachelor‘s degree in chemistry I went to the Albert-Ludwigs-Universität Freiburg. Afterwards, I decided to move to Karlsruhe because of the great offering of physical and theoretical chemistry lectures at the Karlsruhe Institute of Technology. During my Master‘s at the KIT I also learned much about chemical biology, which was very interesting to me.

In the group of Prof. M. Elstner, chemical and biological problems are studied at various levels of theory, which perfectly fits to my interests. Hence, I chose this group for writing my master thesis. Finally, in May I joined the group starting my PhD.

My new project in the GRK deals with the development of a blood glucose sensor working by means of fluorescence. The basic idea is to link a fluorescent dye molecule to a natural glucose binding system, in this case the glucose binding protein (GBP). The conformation of the protein changes by binding a glucose molecule, so that also the fluorescent dye is moved. Due to the various environment of the dye, its optical properties change, too.

My part in this collaborative project is to find a good position for the dye in the protein by means of molecular dynamics simulations and quantum chemical calculations of the fluorescence.

I‘m happy to be a member of the GRK due to the close collaboration between the research groups.

* Paper Update: Photoaktivierbare Nanopartikel lösen gezielt den programmierten Zelltod aus!

written by Anna Meschov 2018/07/04
In der vorliegenden Publikation handelt es sich um photoaktivierbare, anorganisch-organische Gd43+[AlPCS4]34− Hybridnanopartikel. Diese Nanopartikel sind ohne Lichteinwirkung nicht toxisch, lösen jedoch nach einer Behandlung mit nahinfrarotem Licht eine Bildung von reaktiven Sauerstoffspezies (ROS) in der Zelle aus, was zum programmierten Zelltod (Apoptose) führt. Solche Nanopartikel könnten unter anderem bei der Krebsbehandlung im Rahmen der photodynamischen Therapie Einsatz finden. In der Publikation sind die analytische Charakterisierung der Nanopartikel sowie in vitro und in vivo Experimente dargestellt, die deren Wirkung sowohl in den Zellen, als auch in einem lebenden Organismus (Zebrafisch) bestätigen.
 

Original Publikation: Gd43+[AlPCS4]34− Nanoagent Generating 1O2 for Photodynamic Therapy

Authoren: Marieke Poß, Eva Zittel, Carmen Seidl, Anna Meschkov, Leonel Muñoz, Ute Schepers and Claus Feldmann