K2 Nytt

The Respiratory Research group is organising the workshop

Bioinformatic analysis of the airway microbiome: A QIIME2 workshop

16th – 20th of March 2020

This five-day workshop focuses on applied bioinformatics in the field of microbiome data mainly for non-computer scientists using QIIME2. The QIIME2 developers Greg Caporaso and Matthew Ryan Dillon will teach at the workshop.

Participants are required to have some experience with QIIME2 prior to attending the workshop, as no introduction to QIIME2 will be given. Examples used in the workshop will be from the MicroCOPD study, which is data consisting of 16S-rRNA (bacterial) and ITS (fungal) sequencing data from lung samples. Since these samples are low biomass, an emphasis will be on the challenges related to contamination in microbiome analysis.

Participants can bring their own data, but workshop datasets will also be provided. The sessions in the workshop include interactive discussions on several related topics such as different denoising strategies, bioinformatic identification and handling of contaminants, filtering strategies, diversity analyses, differential abundance testing, statistics interpretation, and visualisation and presentation of data.

The spaces are limited, and priority will be given to applicants with relevant background. If you are interested in attending the course, check out the information here:

https://www.digitallifenorway.org/arrangementer/bioinformatic-analysis-of-the-airway-microbiome-a-qiime2-workshop

[:no]Dette er en påminnelse om innsending av forskerlinjeprosjekt.

PROSJEKTER BES SENDT PÅ EPOST TIL marianne.stien@uib.no.

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[:no]CamBioScience are organising courses and conferences that might be of interest. Courses include: Data Analysis, CRISPR and Organoids. More information about each course can be found on their website.

Use the promo code DEP05MW0709 during registration to get a 5% discount.[:en]CamBioScience are organising courses and conferences that might be of interest. Courses include: Data Analysis, CRISPR and Organoids. More information about each course can be found on their website.

Use the promo code DEP05MW0709 during registration to get a 5% discount.[:]

[:no]Priyanthi Borgen Gjerde will defend her PhD thesis on Wednesday 29th January 2020

Trial lecture: Wednesday 29th January 2020 at 09.15.
Topic: “Lipid metabolism in physical health promotion and follow up of treatment response in psychotic disorders”
Place:Auditorium, Armauer Hansens hus, Haukelandsveien 28

Public defense: Wednesday 29th January 2020 at 11.15.
Title of dissertation: “Lipid effects during antipsychotic drug treatment and their relevance for clinical outcomes”
Place: Auditorium, Armauer Hansens hus, Haukelandsveien 28

1st opponent: professor Olli Kampman, Universitetet i Tampere, Finland
2nd opponent: førsteamanuensis Eva Malt, Universitetet i Oslo
3rd member of the comittee: professor II Jørn V. Sagen, Universitetet i Bergen

The defense will be led by professor Francisco Gomez Real[:en]Priyanthi Borgen Gjerde will defend her PhD thesis on Wednesday 29th January 2020

Trial lecture: Wednesday 29th January 2020 at 09.15.
Topic: “Lipid metabolism in physical health promotion and follow up of treatment response in psychotic disorders”
Place:Auditorium, Armauer Hansens hus, Haukelandsveien 28

Public defense: Wednesday 29th January 2020 at 11.15.
Title of dissertation: “Lipid effects during antipsychotic drug treatment and their relevance for clinical outcomes”
Place: Auditorium, Armauer Hansens hus, Haukelandsveien 28

1st opponent: professor Olli Kampman, Universitetet i Tampere, Finland
2nd opponent: førsteamanuensis Eva Malt, Universitetet i Oslo
3rd member of the comittee: professor II Jørn V. Sagen, Universitetet i Bergen

The defense will be led by professor Francisco Gomez Real

 [:]

[:no]Kan du fortelle litt om arbeidet ditt? Hva er de konkrete arbeidsoppgavene dine?
Jeg er ansatt i 100% stilling som professor ved Klinisk institutt 2, så hovedjobben min er jo i prinsippet todelt, å drive med forskning og med undervisning av medisinstudentene.
Forskningsmessig så har jeg i alle de år arbeidet hovedsakelig med dyreeksperimentell forskning med fokus på hjertefunksjon og sirkulasjon. Jobben innebærer å være både tilrettelegger, forskningsveileder samt prosjektmedarbeider i pågående doktorgradsprosjekter og forskergrupper.

For tiden er jeg involvert i flere dyreeksperimentelle studier på griser i full narkose. I disse dyremodellene kan vi simulerer åpne hjerteoperasjoner, livstruende sviktende hjertefunksjon og hjertestans. Mange av studiene handler om bruk av mekanisk sirkulasjonsstøtte med forskjellig typer utstyr (hjerte-lungemaskin, ECMO og Impella-pumper) som midlertidig kan understøtte eller erstatte hjertefunksjonen. Dette utstyret brukes også på pasienter, og vi ønsker i våre dyreeksperimenter å studere hvordan vi kan optimalisere hjertefunksjonen og sirkulasjonen til hjertemuskelen under og etter denne typen behandling. Det blir ofte lange dager i Vivarium med forsøk som kan vare i 8-10 timer. Der disponerer vi en god del avansert registreringsutstyr for vurdering av hjertefunksjon og sirkulasjon. Så går det jo mye tid til å samle, systematisere og analysere data fra slike forsøk. I samarbeid med doktorgradskandidater og andre utarbeides det så manuskripter med tanke på publikasjon.

Siden jeg opp gjennom årene har samarbeidet mest med hjertekirurgene ved Haukeland Universitetssykehus når det gjelder forskningen, har det blitt naturlig at jeg har en del undervisning for medisinstudentene om tema som omhandler hjerte- og thoraxkirurgisk behandling. Både rene forelesninger og pasient-nær undervisning på Hjerte Post 4 er noe av det jeg driver med. Jeg er jo dessuten involvert i nye eksamensordninger (OSKE) og i den faglige planleggingen av undervisningen i fagområdet Sirkulasjon. Siden jeg har muligheten her i K2Nytt; jeg og mange med meg synes at det er avsatt alt for liten tid og ressurser til undervisning både i hjertesykdommer generelt og i hjerte-thoraxkirurgi spesielt i den nye studieplanen MED2015. Her må det gjøres noen endringer.

Hva liker du å arbeide med på K2?
Det er vel det å arbeide sammen med andre mot noen felles mål både hva gjelder å få til god forskning og god studentundervisning som er det viktigste og som jeg liker best med jobben. I mitt tilfelle så kan det være å samarbeide med forskere, teknikere og administrative både fra K2, fra K1, fra Haukeland Universitetssykehus og andre. I tillegg så er det jo mange hyggelige kollegaer og medarbeidere som en treffer på og omgås med i hverdagen på K2.[:en]Can you tell us something about your daily tasks and work in general?
As fulltime professor at the Dep. of Clinical Science, my job is divided into two main tasks; both research and teaching of medical students. For most of my professional life, I have been working with experimental animal research focusing on cardiac function, blood circulation and metabolism in the cardiac muscle. My job involves being both facilitator, research supervisor and project co-worker in ongoing PhD projects and in current research groups.

Nowadays, I am involved in several animal studies using anaesthetized pigs as experimental model. In these models, we can simulate open cardiac surgery procedures, life-threatening cardiac failure and cardiac arrest. The current studies involve the use of mechanical circulatory support (heart-lung machine, ECMO and Impella pumps) offering temporary cardiac support supplementing or fully substituting the cardiac function in the experimental animal. This kind of equipment is widely used treating patients both worldwide, also here at Haukeland University Hospital. In our experimental models we are studying if and how it is possible to optimize heart function and the circulation in the heart muscle both during and after this type of treatment. Often there will be long days in the core facility Vivarium (the university’s animal facility), performing experiments that could last for up to eight to ten hours. In the Vivarium we have access to advanced evaluation- and recording equipment for studying cardiac function and circulation. In addition, much of my working hours are spent collecting, systemizing and analyzing data from this type of experimental studies. Finally, in collaboration with PhD-candidates and other researchers much time is spent on drafting, correcting and finalizing manuscripts for submission to international scientific journals.

Over the years, I have collaborated with the cardiac surgeons at Haukeland University Hospital. For this reason, I teach medical students on issues related to cardiac and thoracic surgery. Both traditional lectures and bed-side teaching for groups of students are some of my activities. I am also involved in the new exam arrangements (OSCE) and in the academic planning of teaching in the subject “Circulation”. Given this opportunity here in K2Nytt, many of my colleagues and I will strongly argue that too little time in the curriculum and limited teaching resources have been allocated to teaching both in heart disease in general and in cardio-thoracic surgery in the MED2015 curriculum plan. Here, changes are needed.

What do you enjoy working at K2?
I like working together with other people towards some common goals, whether that is good research or good and relevant teaching and training for the medical students. In my situation, I it is enjoyable to collaborate with researchers, technicians and administrative personnel both from K2, from K1, from Haukeland University Hospital and others. In addition, there are many friendly and pleasant people whom I meet and interact with on a daily basis at K2.[:]

[:no]Kjære alle sammen.

Vennligst se under de oppdaterte lenkene for ekstern finansiering.

Eksterne finansieringsmuligheter

Finansieringsmuligheter for utdanning

Nettsidene oppdateres hver annen uke. Nye oppføringer er merket med NEW.

Best regards,
Amra, Ramune og Kaia[:en]Dear all,

Please see below the updated links for external funding:

External funding opportunities

Funding opportunities for education

The webpages are updated every second week. New calls are marked as NEW.

Kind regards,

Amra, Ramune and Kaia[:]