IBA student and the recipient of the IBA travel grant for research stays abroad, Erik Paulshus, has spent two months in the US working on his PhD (he is currently enrolled at NMBU, Ås). This is what he had to say about it!
My PhD project aims at identifying the major sources of antibiotic resistance in urban wastewaters. Approaching this issue, we have looked at phenotypic and resistance profiles in bacterial isolates cultivated from wastewater samples and measured the levels of antibiotics. The third approach was to look at the prevalence of antibiotic resistance genes (ARGs) in the corresponding samples. The project was initially run in parallel to a European project in which the same method for detecting ARGs was used. The European counterpart was however finished before my sampling campaign was ready, and the plan of shipping my samples alongside the European ones to MSU had to be altered. Since I had many samples to analyze, the research group at MSU offered to host me at their labs so that I could assist with the analysis to reduce the time needed as well as learn the methods.
IBA was very generous in accepting my application for a travel grant to stay the two months in Michigan to do the intended work. James Tiedje is a University Distinguished Professor and Director at MSU and has vast experience in the field of environmental microbiology. The method I would be using to analyze my samples involves a very large array of qPCR reactions that are run in parallel at the Research Technology Support Facility (RTSF). A very big thanks to Professor Syed Hashsham who leads the environmental engineering lab where the preparation of samples was performed and his colleagues for help with the lab work. Some thanks are also allotted to James Cole, director of the ribosomal database project for allowing me a desk space in his computer labs at times when my designated office area was completely uninhabited.
Several complications leading up to my stay at MSU and during my stay did make the whole experience a little bit less successful then we would have hoped, but I did learn a great deal about American bureaucracy! I was lucky enough to find a student housing options that relieved some of the strain on the IBA grant budget, and I was also able to travel a bit and see several places in Michigan, including a two-night stay in Chicago and a visit to my American second cousin Krista near Grand Rapids, whom I’ve not met in person until now.
I am very thankful for meeting so many positive and encouraging researchers in a country that has recently been given a very harsh reputation, and even though things don’t always work out as planned, I am also forever grateful to IBA for granting me this opportunity.
Just before the summer holidays, Oslo node of IBA had its first social meeting of the year!
We enjoyed good company, discussions, and planned future collaborations over good food in the beautiful Oslo fjord.
A unique intensive course on “Antibiotics and Antibiotic Resistance” is jointly organised by IBA and the National Doctoral Programme in Infections and Antibiotics (NDPIA) 26-30 November, 2018, at Hjortviken Konferens outside Gothenburg. The course features lectures by internationally leading scientists, opportunities for participants to present research in poster walks and ample time for networking. Scientific lectures describing antibiotic resistance from other perspectives focusing on ethics, public awareness and media are also included. The preliminary program is available here Preliminary Programme Antibiotics and Antibiotic Resistance NDPIA IBA
Registration deadline: 17 September 2018
For more details and information on how to apply see the course page.
Time and place: October 8-9 2018, Copenhagen, Denmark
The 1st Annual CryoNet Symposium will gather Scandinavian researchers, students and technical staff to discuss the latest advances in Cryo-electron microscopy with some of the world leading researchers in the field.
International participants are also welcome to register! The maximum number of attendees are 150.
Abstract deadline: Abstracts will be selected for short talks and/or poster presentation. Send your abstract (max 300 words) to firstname.lastname@example.org no later than August 31 2018.
This course is a continuation of TTA bioinformatics course level 1 and requires some basic knowledge of whole genome assembly, including quality assessment of raw data, trimming and contig assembly. Although not a strict requirement, we do recommend participants to attend in level 1 before signing up for this advanced course.
Participants of the hands-on session must bring their own laptops. A list of required preparations including instructions on how to install Geneious trial version will be provided end of August.
Part I: Seminars 11:00 – 12:30:
Theoretical introduction to the course and short repetition of required level 1 content.
11:00 – 11:30 Timo Lutter (TTA) – SNP calling, phylogenetic tree building and whole genome alignment
Nermin Zecic (TTA) – RNAseq and differential gene expression
11:30 – 12:00 Henrik Hasman – (Statens Serum Institut, DK) – Identification of acquired antibiotic resistance genes with ResFinder
12:00 – 12:30 Jon Bolin (FHI) – Mechanisms of foreign DNA acquisition and their detection in microbial genomes
12:30 – 13:00 Lunch
Part II: Hands-on exercises 13:00 – approx. 17:00:
Map to reference assembly and building SNP trees in Geneious with RAxML(using Ebola virus isolates as an example)
Basic alignments of bacterial genomes and draft genomes to detect large-scale evolutionary events (rearrangements/inversions) with Mauve
RNAseq and differential gene expression in Geneious
Introduction to Center for Genomic Epidemiology and ResFinder for identification of antimicrobial resistance genes
The National Doctoral Programme in Infections and Antibiotics (NDPIA)and the Swedish Society for Microbiology (SFM) are organizing a workshop on English writing and grant proposal writing followed by a one-day scientific meeting.
For additional information please see the events website.
These networking activities will be held outside Gothenburg and 5 IBA members (who have registered to NDPIA via http://ndpia.se/register/ by the time of registering to the activities) are very welcome to participate. Please note that abstract submission, poster presentation and participation in all activities 1-2 October is mandatory.
Interested IBA members are very welcome to contact Anna Holmström (email@example.com) by 25 June at the latest, but preferentially before that, and she will guide the first five to the proper registration link. Free participation and accommodation for 1 October (in shared double rooms) will automatically be booked via the registration link – there is a possibility to have a single room for SEK 625. IBA will cover travel costs.