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iamartinoESR 10
Luca Iamartino
Institute of Molecular Biology and Biotechnology – FORTH, Greece

Seconded to: Institute of Molecular Biology and Biotechnology – FORTH, Greece

For the Period: 27 June 2016 to 30 June 2016

As part of my PhD project, I spent four days in the lab of Prof. Nektarios Tavernarakis, in the FORTH Institute in Heraklion, Greece from 27th to the 30th of June, 2016.
Joining this laboratory allowed me to gain some experience in the biology of the C. elegans: worm’s husbandry and care. Moreover, I got some experience in specific molecular biology techniques, related to this animal platform, as RNAi through worm feeding and UV DNA damage induction.
Finally the great environment of the lab with kind and talented researchers deeply contributed to my training.

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SR ESR 10
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Date 2016-11-25 File Size 259.52 KB Download 0
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uwakahESR 13
Eberechi Innocentia Uwakah
ATLAS Biolabs GmbH, Germany

Seconded to:Prof. Dr. Peter Nürnberg ;Cologne Center of Genomics (CCG),Cologne,Germany.
Prof. Dr. Björn Schumacher, CECAD, Cologne,Germany

For the Period: 1 April 2016 to 16 May 2016

The aim of my visit was to work on a collaborative project with a PhD student of my Supervisor at CCG. I analysed the alternative splicing data generated by Cuffdiff using SpliceR, the sample data were from Dupuytren Disease patients.
The CCG is a inter-faculty center for large scale technologies in genomics, supporting both groups from the medical and natural science faculties of the University of Cologne.The working environment is superb, I totally enjoyed everything the work,the people and the city. My colleagues were friendly, willing, inspiring and supportive. I had the privilege of attending the weekly seminar series at the group to listen to interesting research work done in the group.
While doing my secondment, I also attended the 2nd Cologne Ageing conference in April. 

The whole experience was a rewarding one. Sharing my research topic with few colleagues helped and improved my work. I also established contact with them, eventually I am back here to complete my PhD work.

Finally, I am very grateful to my supervisor, all the staffs and my colleagues at the CCG, and Marie Curie for making such opportunity possible for me and providing all the support and comfort for my PhD work.

Finally, I am very grateful to my supervisor, all the staffs and my colleagues at the CCG, and Marie Curie for making such opportunity possible for me and providing all the support and comfort for my research and well-being.

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SR ESR 13
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Date 2016-11-25 File Size 96.02 KB Download 0
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Prof. Dr. Peter Nürnberg ;Cologne Center of Genomics (CCG),Cologne,Germany.
Prof. Dr. Björn Schumacher, CECAD, Cologne,Germany      

perezESR 7
Julio Aguado Pérez
IFOM - The FIRC Institute of Molecular Oncology Foundation, Italy

Seconded to: Joachim Lingner, École polytechnique fédérale de Lausanne, Lausanne, Switzerland

For the Period: 12 Dec 2015 to 20 Dec 2015

Within my PhD project, I have completed a secondment in Lausanne (Switzerland) in the laboratory of Joachim Lingner at EPFL SV ISREC UPLIN. The purpose of my week stay at EPFL was to understand and improve my knowledge in the detection of non-coding RNAs by the use of the Northern Blot technique. In particular, I have implemented a protocol that allows the detection of rare RNA species.
To briefly set up a background for the experiment performed, I’ll introduce the science behind it. The telomeres are the structures at the end of linear chromosomes. In vertebrates, telomeres are made of kilobases of TTAGGG repeats in tandem. A protein complex called Shelterin binds to telomeres allowing a closed structure known as the t-loop, in which the ssDNA of the telomere invades the upstream telomeric dsDNA. In this way, the Shelterin complex prevents the telomeres to be recognized as DSBs. TRF2, a Shelterin protein, is the major player involved in this protection. Thus, by removing TRF2 a DDR is activated.
It has been shown in a recent publication from our lab (Francia S. et al Nature 2012) that the DDR cascade, downstream of H2AX phosphorylation, can only be activated in the presence of a novel class of short non-coding RNAs that we named DDRNAs. These are site-specific DROSHA and DICER RNA products that are necessary for the DDR focus assembly and maintenance. Hence, it is a reasonable hypothesis that a longer precursor is needed for the generation of DDRNAs. In our lab, we already have evidence of the existence of these precursor transcripts. Therefore, we wanted to confirm this finding by looking at the RNA in a Northern Blot.

During my secondment stay, I worked together with the CodeAge fellow at Joachim Lingner’s lab, Jana Majerská. Together with her, I implemented a protocol that is routinely used by several people in the lab in Lausanne. We used as starting material total MEF RNA samples that I previously produced in Milan. Two conditions were tested in the experiment: an induced TRF2 knock-out (KO) leading to telomeric DNA damage and a control set up in which TRF2 is expressed and telomeres are thus protected. We looked at different time points after KO induction and probed for G-rich and C-rich telomeric trancripts for each timepoint. As expected, we detected the presence of telomeric precursor transcripts only upon TRF2 KO. The Northern Blot data confirms the one I already obtained by real-time PCR and Next Generation Sequencing in the lab at IFOM, Milan.

The period spent in the Lingner laboratory has been very useful to learn a new technique and to use a different approach for the study and characterization of rare RNAs. The members of the lab have been friendly and always available to exchange thoughts and ideas relevant for our field of study.

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Secondment Report ESR7 (2)
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Date 2016-09-08 File Size 203.21 KB Download 0
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ntariESR 11
Lydia Ntari
Biomedcode Hellas S.A., Preclinical Drug Evaluation Unit, Greece

Seconded to: George Garinis, Institute of Molecular Biology and Biotechnology, Heraklion, Crete

For the Period: 15 March 2016 to 19 March 2016

As part of my CodeAge fellowship and PhD project, I spent my Secondment period in the laboratory of George Garinis’ at the Institute of Molecular Biology and Biotechnology, part of the FORTH institution in Crete. The duration of my visit was from 15th to 19th of March 2016. During my stay in the lab I had the opportunity to discuss and familiarise with the techniques and projects that have been carried out by Post-Docs and PhD students, as well as by my co-fellows in ITN programmes Kostis, Luca, Kyriakos and Christalla.

I had the opportunity to watch different techniques, such as pancreatic cells isolation from progeroid mouse models and to follow the protocol for further immunostaining analysis. In addition, I followed the protocol of White Adipose Tissue (WAT) and Brown Adipose Tissue (BAT) isolation from mouse and its further immunostaining as a whole mount tissue. Also, I had the chance to see an example of the analysis of this staining in the confocal microscope of IMBB. This technique will be very useful for my project as I am planning to carry out fat tissue stainings. Also, I had the chance to discuss some protocols regarding ways of cell death induction in in vitro fibroblasts cell cultures. Lastly, I was able to discuss my own project with the people of the lab and to get some new ideas on DNA damage response and the pathways involved in it, and to get new ideas of how to approach my own project in the future.

Overall, my Secondment was a very informative and rewarding experience, as I learned various techniques from experienced researchers. I would like to thank Dr. Garinis and all the people in his lab who were very friendly and kindly shared their expertise

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SR ESR 11
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Date 2016-11-25 File Size 286.15 KB Download 0
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majerskaESR 1
Jana Majerská
Ecole Polytechnique Federal de Lausanne, Switzerland

Seconded to: Fabrizio d'Adda di Fagagna, IFOM Fondazione Istituto Firc di Oncologia Molecolare, Milan, Italy

For the Period: 7 December 2015 to 11 December 2015

In December 2015, I had the opportunity to spend a week in the laboratory of Dr. Fabrizio d'Adda di Fagagna in Milan. There, I collaborated with Alessandro Galbiati to answer a question if our protein of interest (POI) localizes to telomeres, the protective structures at the ends of chromosomes (sometimes likened to the plastic tips that prevent a shoelace from fraying). We decided to use an in situ proximity ligation assay to visualize the interaction of POI with telomere-specific protein TRF2 in human cancer cells by microscopy. Unlike the classical immunofluorescence-based techniques, the readout in a proximity ligation assay is facilitated by detection of amplified DNA.

The exponential nature of DNA amplification means that a limited number of interacting molecules can produce a strong, visible signal. This is especially important when we want to detect transient regulatory or signaling interactions that affect telomere homeostasis. To process the collected microscopic data, Alessandro introduced me to CellProfiler, an open-source software ideal for high-throughput quantitative cell image analysis.

Apart from learning new wet and dry lab techniques, I attended their lab meeting and was involved in many lively discussions about our ongoing projects, ideas, ambitions and frustrations. Overall, the lab atmosphere was focused yet very friendly, and I feel fortunate to have experienced it.

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princzESR 5
Andrea Princz
Institute of Molecular Biology and Biotechnology – FORTH, Greece

Seconded to: Björn Schumacher CECAD, Cologne, Germany

For the Period: 20 September 2015 to 23 October 2015

As part of my PhD project I’ve spent 1 month in Björn Schumacher’s lab in CECAD, in Germany. The goal of the visit was to learn new techniques used in this lab related to DNA damage responses and posttranslational modifications in C. elegans. The expertise of Björn Schumacher’s lab in addressing the DNA damage response and the proteomics facility at CECAD made this secondment very successful. After my arrival to Cologne I participated in the 3rd Annual Meeting of CodeAge from 21-23 September. I started to work in the lab from the 24th September until 23rd October.

During this one month I learned a lot about the aforementioned topics and I was even able to carry out experiments, gaining more practice. This knowledge is very useful for my PhD, and I will repeat these experiments again on Crete, in my host institute. Since I already have 7 years of working experience with C. elegans, this visit helped me to learn even more techniques and extend my knowledge even further concerning this model organism.

I also had the chance to participate in lab meetings and exchange ideas about projects. I’m very grateful for everybody for the fruitful scientific discussions, they were an important part of my secondment, since science is about exchanging ideas, and improvement can be achieved through discussions. CECAD has an excellent scientific community, and I’m very happy that I could be a part of that for one month.

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Secondment Report ESR 5
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Date 2015-11-09 File Size 86.58 KB Download 0
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perezESR 7
Julio Aguado Pérez
IFOM - The FIRC Institute of Molecular Oncology Foundation, Italy

Seconded to: Piero Carninci, Division of genomic technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan

For the Period: 29 July 2015 to 30 August 2015

Within my PhD project, I have completed a secondment in Yokohama (Japan) in the laboratory of Piero Carnici at the RIKEN Center for Life Science Techologies. The purpose of my four-week stay at RIKEN was to understand and improve my knowledge in the non-coding transcriptome through next-generation sequencing (NGS). In particular, I have implemented a protocol that allows the detection of rare functional RNA species; a method named as Targeted Sequencing of Small RNAs (TSSR).
Briefly, TSSR works as follows. In order to amplify RNA molecules, two linkers are ligated to the two ends of the starting RNA material. Linkers enable cDNA synthesis and PCR amplification of small RNAs allowing the generation of an RNA library. Then, sequence-specific baits are hybridized with the library leading to a postcapturing library. Non-hybridized RNAs are washed away, while bait-hybridized RNA molecules are retained and sequenced by an Illumina MiSeq sequencer.

To set up a background for the experiment performed, I’ll introduce the science behind it. The telomeres are the structures at the end of linear chromosomes. In vertebrates, telomeres are made of kilobases of TTAGGG repeats in tandem. A protein complex called Shelterin binds to telomeres allowing a closed structure known as the t-loop, in which the ssDNA of the telomere invades the upstream telomeric dsDNA. In this way, the Shelterin complex prevents the telomeres to be recognized as DSBs. TRF2, a Shelterin protein, is the major player involved in this protection. Thus, by removing TRF2 a DDR is activated.

Our lab has recently published (Francia S. et al Nature 2012) that the DDR cascade, downstream of H2AX phosphorylation, can only be activated in the presence of a novel class of short non-coding RNAs that we named DDRNAs. These are site-specific DROSHA and DICER RNA products that are necessary for the DDR focus assembly and maintenance.
During my secondment stay at RIKEN, I worked together with Quan Nguyen, PhD, the scientist that developed TSSR. We used as starting material small RNA samples that I previously produced in Milan. Two conditions were tested in the experiment: an induced TRF2 knock-out (KO) leading to telomeric DNA damage and a control set up in which TRF2 is expressed and telomeres are thus protected. In Milan, I have already detected the presence of telomeric DDRNAs and their induction upon telomeric damage by a qRT-PCR method designed to quantify miRNAs. TSSR results showed a comparable induction of telomeric DDRNAs upon telomere uncapping confirming the qRT-PCR data.
The period spent at RIKEN has been very useful to learn a new technique and to use a different approach for the study and characterization of small non-coding RNAs. The scientific exchange of ideas with Quan Nguyen was critical to understand and optimize the protocol for small RNA detection.

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Secondment Report ESR 7 (2)
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Date 2016-02-29 File Size 327.13 KB Download 0
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rodriguesESR 2
Joana Cristina Pedro Rodrigues
University of Newcastle, United Kingdom

Seconded to: Joachim Lingner, EPFL, Lausanne, Switzerland

For the Period: 24 August 2015 to 29 August 2015

 

As part of my PhD plan, I spent a week (from 24 to 29 of August, 2015) in Joachim Lingner’s lab, in Lausanne, Switzerland. Prof. Lingner’s lab is part of the École Polytechnique Fédérale De Lausanne (EPFL) and by going there I aimed to get familiarized with the techniques used to study DNA damage in human cell lines.

In the laboratory I learnt how to measure telomere and telomeric overhang size and how to do Pulse-Field Gel Electrophoresis (PFGE). Getting familiarized with all the PFGE apparatus was extremely helpful since I intend to use a slightly modified version of this method to answer important questions in my project.
Moreover, I had the opportunity to speak and exchange ideas with some of the Post-Docs and PhD students working in Prof. Linger’s Lab. Seeing what they are doing helped me to get a broader idea of the varied ways of answering similar questions in different cell models: S. cerevisiae and human cell lines.

Overall, it was a rewarding experience that allowed me to learn about many different techniques and to exchange ideas with experienced researchers in the telomere field.

 

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Secondment Report ESR2
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Author Joana Rodrigues Date 2015-09-04 File Size 314.9 KB Download 1
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rieckherER
Matthias Rieckher
University of Cologne, Germany

Seconded to: Nektarios Tavernarakis, IMBB-FORTH, Greece

For the Period: 28 June 2015 to 5 July 2015

 

During my Secondment I visited the Tavernarakis lab, which is part of the Institute of Molecular Biology and Biotechnology (IMBB), Heraklion, Crete, Greece. Mainly, I used the time for scientific discussion and project planning to initiate collaborative projects with different labs and research fellows.

At the Tavernarakis lab I collaborate with Andrea Princz, fellow of the CodeAge Network. The aim of our corporate study is to decipher the regulation of eIF4E compartmentalization by the heat shock response pathway during ageing in C. elegans. We laid out a scientific plan and commenced work on various transgenic lines. Subsequently, Andrea Princz spent her Secondment at the CECAD Cologne (September 2015) to progress with the project. Also, I initiated work with Konstantinos Palikaras, which aims to investigate the role of mitophagy and autophagy in cellular maintenance in response to UVB irradiation.

The Tavernarakis lab has a long lasting collaboration “In vivo Imaging Lab”, headed by Giannis Zacharakis, as part of the Institute of Laser and Electronics (IESL), FORTH, Heraklion, Greece, who are experts on in vivo imaging techniques including “Optical Projection Tomography” and Light Sheet Microscopy. In an interdisciplinary approach we apply these novel microscopy methods for in vivo imaging of protein dynamics in C. elegans (Rieckher et al., 2015, PLoS ONE 10(5): e0127869). We developed a plan for continuation of our joint project, which aims to improve and publish algorithms for 3D reconstruction of our datasets, by beginning 2016. To this end, we evaluated and processed images of transgenic C. elegans expressing fluorescent fusion proteins.

The time at the IMBB in Crete was inspiring and I was able to initiate a number of collaborative projects. My hosts of the Tavernarakis lab gave me a warm welcome and made my stay an unforgettable experience, scientifically and personally. I thank the CodeAge Network for the possibility to further the collaborative spirit, which I consider to be the essence of scientific progress.

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Secondment Report ER
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Date 2015-12-02 File Size 110.84 KB Download 0
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bajwaESR 9
Seerat Bajwa
Leibniz Institute for Age research, Germany

Seconded to: Maria Denis, Biomedcode, Athens, Greece

For the Period: 28 May 2015 to 5 June 2015

 

As a requirement of CodeAge network, I planned a short secondment to Biomedcode, Athens, Greece in the lab of Dr. Maria Denis from 28-05-2015 to 05-06-2015. My aim was to do Immunohistochemistry for immune system related markers on paraffin embedded sections from mouse. As the lab working closely with partner institute Alexander Fleming and both are very experience in Inflammation and immune system related techniques, so I was interested as my project is based on immune system regulation in aging mouse model.


I took mice sections with me and used the expertise in the lab. I stained the sections with immune cell markers namely B cells, T cells, Macrophages, Granulocytes. During my stay there I got to know also about the projects they are working on, namely arthritis model, and how company works in general. I got really nice suggestions from the senior scientific members of the lab which broadens my prospect. I also discussed with them about expertise of my lab so that if they are interested in visiting us.

Overall it was very informative trip. It really helped me to figure out something really new and exciting. I would like to thanks all lab members specially Niki Karagianni and PhD students who helped me there both scientifically and personally to make my trip comfortable.

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Secondment Report ESR 9
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Date 2015-11-06 File Size 77.6 KB Download 0
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kenfackESR 12
Esther Nkuipou-Kenfack
Mosaiques Diagnostics GmbH, Germany

Seconded to: George Garinis, Institute of Molecular Biology and Biotechnology - FORTH, Greece

For the Period: 20 May 2015 to 23 May 2015

 

I have recently completed my first short term visit in the Institute of Molecular Biology and Biotechnology under the direction of Professor George Garinis. The duration of the visit was 3 days starting from the 20th to the 23rd of May 2015 followed by the EMBO meeting in Crete, Greece. The aim of the secondment was to get familiar with the research carried out under the supervision of George Garinis and also get more insight into different well established technologies used at the institute.


FORTH is a leading Institute not only in Greece but also in Europe and receiving training in such environment was amazing! I would really like to thank all the members of George Garinis’ lab. And especially to Anna, a PhD student who has been amazing and has allowed me to follow her everywhere she went! A special thank you to my CodeAge fellows Konstantinos and Luca who have really put me at ease and made the whole experience unforgettable. In my free time in Crete, with the help of a student in the lab, I was able to visit the Heraklion Archaeological museum which is one of the greatest museums in Greece. The environment at FORTH was really a unique one and I am grateful for the experience.

The training consisted in mouse handling. In addition, I also had experience with bone marrow cells extraction from a mouse, immunohistochemistry staining techniques and cell sorting using fluorescence-activated cell sorting (FACS), cell culture, DNA extraction and PCR. Learning these techniques has widened the scope of my understanding on how they can be used to understand DNA damage in ageing.

 

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Secondment Report ESR 12 #2
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Author Esther Nkuipou Kenfack Date 2015-09-03 File Size 48.89 KB Download 0
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markiewiczESR 3
Marta Markiewicz
University of Newcastle, United Kingdom

Seconded to: Lenhard Rudolph, Leibniz-Institute for Age Research-Fritz Lipmann Institute, Jena, Germany

For the Period: 4 November 2014 to 14 November 2014

 

 

According to my PhD project, I spent my Secondment in the laboratory of Lenhard Rudolph at the Leibniz-Institute for Age Research - Fritz Lipmann Institute e.V. (FLI) in Jena, Germany. I worked in FLI from 4th to 14th of November 2014, and the aim of the training was to gain some insights into methods used in Rudolph’s Lab based on in vitro culture of stem cell and cancer cell lines. During the training period I have been learning the applications of genetically modified cell line cultures in identifying and studying the function of genes associated with telomeres.

The project of my PhD concerns different types of damaged telomeres, therefore the knowledge and skills acquired in Rudolph’s Lab would allow me to consider the application of methods used for human cell lines in yeast culture.

During the training I followed a group of experts working on cell lines (consisted of senior scientists, postdocs, PhD students and technicians) who showed me techniques used in the Lab. They assisted me to complete the plan designed specifically for my interests and the main theme of my PhD – telomere maintenance. Thanks to the support of the Lab, I am now able to work in in vitro cell culture laboratory: identify different cell types based on their morphology, maintain and split cells, prepare the background for the cell-line based experiments and perform basic in vitro experiments on my own. I assisted during co-transfection method of various cell lines to check the level of co-activity of different genes, presumably important for telomere maintenance in eukaryotes (luciferase assay). Moreover, afterwards I moved to the proteomic level and measured the protein concentrations in collected samples. Using software tools for data analysisI was able to assess the Luciferase intensity per μg of protein. Also, I was taught a widely-used method Q-FISH (Quantitative Fluorescent In Situ Hybridization) applied on mice and human testis and mice small intestine for stem cell localization of proteins potentially co-localised at telomeres.

In Rudolph’s lab for the first time I had the opportunity to work with human stem cells and cancer cell lines. I also had the contact with another model organism, Mus musculus, which is currently studied in the Lab. Previously I had been working on model plant, Arabidopsis thaliana, and on different orders of bacteria. During my PhD I have been working on buddying yeast. Owing to the Secondment I was able to work on human cell lines and could understand the approaches carried out on mice. I could observe the staining methods of different mouse organs on slides, and used some samples for fluorescent staining. 10 days period in the CodeAge affiliated laboratory has proven to be very helpful and useful not only for my PhD studies, but also in the future. Gaining the basic knowledge of how to maintain and cultivate cell lines, and also knowing commonly used methods of transfection and assessing the level of genes activity, it will be of great benefit for me to apply for other positions of my interest in the future. Techniques which I have never used before (e.g. Q-FISH, luciferase assay) I could also apply in my current study.

All members of the lab were extremely helpful and patient, trying to show me the most important and critical methods in such a short time. The respect must be shown to the senior scientist, Dr Cagatay Günes, who had planned the set of actions that I could have completed and understand in such a short time.

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Secondment Report ESR 3
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Date 2015-01-09 File Size 128.2 KB Download 0
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kenfackESR 12
Esther Nkuipou-Kenfack
Mosaiques Diagnostics GmbH, Germany

Seconded to: Lenhard Rudolph, Leibniz-Institute for Age Research-Fritz Lipmann Institute, Jena, Germany

For the Period: 25 September 2014 to 29 September 2014

 

I have recently completed my first secondment in the Leibniz-Institute for Age Research under the direction of Professor Lenhard Rudolph. The duration of the secondment was 1 week starting from the 25th to the 29th of August 2014. The aim of the secondment was to gain experience in mouse handling especially in collecting urine samples and also to get more insight into different well established technologies used at the institute.

The Leibniz-Institute for Age Research is a first class research centre for ageing with cutting edge technologies and the training I received during my time there was proportional to the standards of the Institute. The training I received would not have been possible without the help of the whole team of scientists who made my time enjoyable and I am really thankful.

The training consisted in animal handling and especially the collection of urine samples. Urine samples from telomerase knock-out and wild type mice of 61 weeks old were colleted. These samples will be further analysed using capillary electrophoresis couple to mass spectrometry (CE-MS) at Mosaiques Diagnostics GmbH aiming at depicting a link between Telomere dysfunction and accelerated ageing at a peptide level. It was quite a challenging and time-consuming procedure to reach the minimum urine volume required for a CE-MS analysis due to the size of the animal.

In addition, I also had an experience with bone marrow cells extraction from a mouse, immunohistochemistry staining techniques and cell sorting using fluorescence-activated cell sorting (FACS). Learning these techniques has widened the scope of my understanding on how they can be used to understand ageing.

The secondment was really beneficial for me because working in a company; I had the opportunity to familiarise myself with not only with different techniques but also with the academic environment.  

 

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Secondment Report ESR 12
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Date 2014-12-18 File Size 48.24 KB Download 1
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bouzalasESR 8
Konstantinos Bouzalas
Institute of Molecular Biology and Biotechnology - FORTH, Greece

Seconded to: Bjoern Schumacher, CECAD University of Cologne, Germany

For the Period: 19 September 2014 to 26 September 2014

 

As part of my PhD project, I spent one week in the lab of Prof Schumacher, in CECAD Institute in Cologne, Germany.  I was there from the 19th of September till the 29th of the same month and I also participated in the Klenck Symposium “DNA Damage Response and Repair Mechanisms in Aging and Disease” organized by Prof Schumacher within CECAD, 19-21st of September 2014.

During my time at the lab of Prof Schumacher I got exposed to the biology of the C. elegans as an animal model and also to techniques of molecular biology related to C. elegans research. I also interacted with all the lab members and fellow PhD students, and I am grateful because they were very friendly, caring and eager to answer all my questions.

 

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Secondment Report ESR 8
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Date 2014-12-18 File Size 45.32 KB Download 1
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papandreouESR 6
Margarita-Elena Papandreou
Institute of Molecular Biology and Biotechnology - FORTH, Greece

Seconded to: Bjoern Schumacher, CECAD University of Cologne, Germany

For the Period: 23 June 2014 to 27 June 2014 

  

During my PhD, as part of my secondment, I visited the lab of Bjoern Schumacher located in Koln, Germany. I was in the lab between the 23rd and 27th June. During this time, the main aim was to

learn the different techniques used in the lab, specifically how to use UV-B and UV-C light to irradiate different C. elegans strains with differential sensitivity to UV irradiation, at different developmental stages, for different periods of time. Moreover, I was trained how set up the UV-B, system, which is quite complex, in my host lab, as we do not have expertise in DNA damage.

Finally, we were able to set up a collaboration with the other group focusing in DNA damage induced neurodegeneration. I will be soon visiting the lab again, to actually perform some of my experiments there and continue our collaboration.

 

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Secondment Report ESR 6
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Date 2014-12-18 File Size 45.55 KB Download 0
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edifiziESR 4
Diletta Edifizi
University of Cologne, Germany

Seconded to: George Garinis, Institute of Molecular Biology and Biotechnology, Heraklion, Crete

For the period: 16 June 2014 to 20 June 2014

  

As part of my PhD project, I have spent my Secondment period in Crete, in the laboratory of George Garinis at the Institute of Molecular Biology and Biotechnology, part of the FORTH institution. I worked in FORTH from 16th to 20th June 2014 aiming to improve my knowledge in proteomics techniques. During this period I have been mainly learning how to understand and analyze the data I have collected in Cologne, followed and mentored by experienced Postdocs and experts from the Mass Spectrometry (MS) field.

Thanks to the support received by this team of experienced scientists, I was able to rearrange the MS data by performing a deeper analysis of the proteins‘ sequences coupled with the specific peptides’ spectrum. I have been trained in the use of new tools for the data analysis such as the protein clustering program Perseus, the functional annotation website DAVID and Phosida, an updated posttranslational modification database.

Future work based upon this secondment will include the assessment of new data, improving the accuracy of the MS technique (using the ITRAQ 8plex) and applying the selection criteria I have learnt to mechanistically connect my functional assays.

Moreover in the Garinis laboratory I have had the chance to get in contact with different model organisms currently used in their studies: the Mus musculus. During my Bachelor degree I already experienced working with Rattus norvegicus concerning the breeding, the mating and the tissue extraction, however this was a good opportunity for me to understand how the approach is carried out on the mouse model. During this time, I observed the tailing procedure and the selection of the candidates for tissue extraction or further mating.

In the laboratory I have learnt how to genetically manipulate the mouse model, in particular the creation of special Biotag mouse, starting from the creation of the expression construct, to its injection into male mouse Embryonic Stem cells, that in the follow up will be inserted into fosters’ blastocysts.

The interesting aspect of this technique is that it allows the cloning of your protein of interest together with an Avidin-tag into the mouse, ideal for the protein pull down and the analysis of its expression in the different tissues of the animal before and after treatments.

This period in this CodeAge affiliated laboratory has been really useful to learn new techniques and to face a new approach in the Mass Spectrometry field. All the members of the lab have been friendly and always available to answer my questions; a common research project has been discussed in collaboration with George Garinis in order to translate their observation done in the mice model in the C.elegans.

 

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Secondment Report ESR 4
(0 votes)
Date 2014-12-18 File Size 48.24 KB Download 0
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