Completion of FP7 IBD-BIOM project

By 30th September 2016 we reached the end of FP7 IBD-BIOM project. It was a successful and productive project that is somehow continuing with our new HORIZON2020 project SYSCID (A SYStems medicine approach to Chronic Inflammatory Disease) that is about to start. With the end of IBD-BIOM we have lost two members of our team – Paula and Dora. We are missing them, however, we see the rearrangements in the group as a new beginning. Paula is looking forward to going abroad, and Dora will still be “hanging” with us for a couple of month in order to finish her PhD thesis. “The Only Thing that is Constant is Change” (Heraclitus) – Change is really the true constant in life, without change you don’t grow, learn or fully develop into who you are as a person. Therefore, Paula and Dora we wish you good luck in the process of growing.

web-site-publications

Vanja is at Sanquin!

I apologise to Vanja for being late in updating the world about her recent activities:) So, Vanja is at Sanquin, already spending her fifth week there! She is getting experience in lentiviral transduction of primary B-cells in culture, and HEK293 Free Style cells, expressing IgG, our new model in studying regulation of IgG glycosylation. She is trying to insert our CRISPR/Cas9 constructs for the MGAT3 and BACH2 genes in these type of cells . She already did a lot and we hope she will have some nice results till the end of her stay at Sanquin. Good luck, Vanja!

Or, French people would say “Merde“:)

The origin of the French term ‘merde’ (shit) to say good luck

Wellcome Zeynep and Ceyda!

We have in the group two students from Koç University School of Medicine, Istanbul, Turkey. They are joining our group for a month to learn about epigenetic CRISPR technology. Wellcome Zeynep and Ceyda, we hope you will enjoy working with us and our company:)

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Zeynep Kutlu

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Ceyda Akartuna

 

Wellcome Josip!

We have a new team member in our group! Josip Madunić, a post-doc, has joined our group and enjoys in cloning, mini-preping, and all the beautiful inspiring bench work:)

Wellcome Josip, I hope we will not fail your expectations:)

Collection of publications on CRISPR biology

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The last Editorial of Nucleic Acids Research, written by the editors of this journal, Barry L. Stoddard and Keith Fox, describes CRISPR/Cas9 gene targeting system as a new revolution in the academic and commercial biotech community. The authors of the Editorial made a special online collection of over 70 articles on CRISPR biology – the studies that either  continue to unravel details of the formation of CRISPR loci and their subsequent mechanisms of surveillance and action, and studies that describe the application of CRISPR for targeted gene modification and genome engineering. This collection of publications is  organized here. Included in this special online issue is our paper “Repurposing the CRISPR/Cas9 system for targeted DNA methylation“.

More information: http://nar.oxfordjournals.org/content/44/11/4989

GlycoIgG – brainstorming meeting on IgG glycosylation

When and Where: June 22-25, 2016, Dubrovnik, Croatia

Who participated: 44 scientists from the glycobiology field with overlaping specialities in biochemistry, analytical chemistry, immunology, genetics and epigenetics, epidemiology and clinical medicine.

Organized by: prof. Gordan Lauc, meeting financed from FP7 RegPot Integra-Life project

Vlatka Zoldoš delivered talk entitled “Molecular models and tools for studying of regulation of IgG glycosylation“.

Cover page of BBA General subjects special issue “Glycans in personalised medicine”

June, 2016: We published paper “Glyco-genes change expression in cancer through aberrant methylation” in a special issue of BBA General Subjects “Glycans in personalised medicine”. In this work we:

  • identified glyco-genes that show changed expression and methylation in different types of cancer;
  • showed that a subset of ten glyco-genes consistently show both aberrant expression and CpG methylation;
  • showed that some of the identified genes show potential as prognostic markers in certain types of cancer.

The cover-page of this special issue presents our Venn diagrams which show the number of overlapping genes found as the most differentially methylated or the most differentially expressed in hepatocellular carcinoma, breast cancer, cervical cancer and melanoma.

More information:

http://www.sciencedirect.com/science/article/pii/S0304416516301891

Addgene Newsletter Hot Plasmids

What’s new: June, 2016, Addgene Newsletter published news in the field of epigenetic CRISPR/Cas9-based tools and cited our new released paper “Repurposing the CRISPR-Cas9 system for targeted DNA methylation“. The vectors containing inactive Cas9 (dCas9) and the catalytic domain of DNMT3A, co-expressed along with sgRNA for targeting specific region of interest, are available in Addgene.

More information: Addgene

Game of Epigenomics

Event: International Meeting “Game of Epigenomics

Vlatka Zoldoš delivered 30 min oral presentation entitled “Epigenetic deregulation is an important mechanism leading to aberrant protein glycosylation in human complex diseases“. She presented new results from her group that have been published recently within three papers: Vojta et al. 2016, BBA General Subjects; Vojta, Dobrinić et al. 2016, NAR; Klasić et al. 2016, Scientific Reports. In the same meeting Melanija delivered oral presentation entitled “A splicing switch of the histone variant MACROH2A couples the chromatin state to energy metabolism“.

When and Where: April, 24-28, 2016, Dubrovnik, Croatia

Organised by: Institute Rudjer Bošković

More information: http://goe.irb.hr