SciLifeLab

CSI Seminar: ‘Burnout and Stress’
2023-10-17 14:00 - 14:30 (Europe/Stockholm) | Hybrid event in Gamma 2 lunchroom and zoom, Tomtebodavägen 23 B, Solna, 17165, Sweden
We are excited to host a new Coaching in Science Initiative (CSI) Seminar titled: ‘Burnout and Stress’
The number of people with a burnout diagnosis has sky-rocketed during the last decade and it is now considered to be one of our major national diseases. Stress is a natural and important reaction but when the response is kept active for too long it can have negative effects. In this seminar, we will cover some basic aspects of stress and burnout, and share personal experiences of going through a burnout process. Together we’ll discuss where we currently experience negative stress and what measures we can take to find and keep a sustainable balance in life.
Date: 17/10/2023
Time: 14:00 – 14:30
Zoom link: https://kth-se.zoom.us/j/68847309081
On-site location: Gamma 2 lunch room
We will begin with a ca 20 min talk, held in Solna and over zoom. Then proceed with a reflection and discussion held only on-site. We encourage other sites to form watch parties, by listening in together to the talk and then hold their own discussion afterwards. Hopefully seeding many local chapters of CSI.
To help facilitate discussion and reflection, consider the follow starter questions:
Awareness: where do we experience high risk for negative stress in our lives?
Analysis: how well do I currently handle negative stress?
Alternative: how can we relate to burnout/stress, in ourselves and others?
Action: how will knowledge of burnout/stress change my decisions going forward?

Introduction to Data Management Practices - Cancelled
2023-10-17 08:00 - 2023-10-19 17:00 | Uppsala University, Uppsala and Chalmers University, Gothenburg
This national workshop in Data Management is a co-arranged event between Uppsala University and Chalmers University, and provides an introduction for PhD students, postdocs, researchers, and other employees within all Swedish universities. The workshop will introduce important aspects of research data management through a series of lectures, demonstrations, and hands-on computer exercises. The course is intended for researchers that want to take the first steps towards a more systematic and reproducible approach to analysing and managing research data. CANCELLED – next time (preliminary) in Stockholm, April 2024

Topics covered will include:

Open Science and FAIR in practice

Organising data, files and folders in research projects

Describing data with metadata

Publishing data to public data repositories

Cleaning tabular data and metadata with OpenRefine

Writing basic recipes for data analysis and visualisation with R

Versioning data, documents and scripts

Writing Data Management Plans

Important dates

Application opens: now

Application closes: 2023-09-27

Information to accepted students will be sent: 2023-09-29

Contact

edu.intro-dm@nbis.se

Application

Course website

Format

This workshop runs in parallel on-site in Uppsala, and Göteborg. Lectures will be streamed online from our Uppsala site (mainly) to the Gothenburg classrooms, and vice versa. Teachers and teaching assistants will be present at both locations all week to help with exercises and questions. When registering you will be asked to select a preferred site.

Venues

Uppsala

Trippelrummet (E10:1307-1309), SciLifeLab Navet, Entrance C11, Biomedical Centre (BMC)

Husargatan 3, 752 37 Uppsala

Gothenburg

CLS Room Scrum 1, University library, 2nd floor

Hörsalsvägen 2 (entrance), 412 96 Gothenburg

Course fee

This on-site training event costs 2000 SEK invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 2000 SEK. Please note that NBIS cannot invoice individuals.

Entry requirements

No previous programming experience is required but you are required to bring your own laptop with the required software pre-installed. Installation instructions will be provided before the course starts, and the course organisers arrange a pre-course event approximately one week prior to first course day.

Credits & Certificate

Please note that NBIS training events do not provide any formal university credits. Attendees with full attendance and completion of tasks will be issued a certificate of participation indicating topics covered and duration of the workshop.

Due to limitations in space and capacity the course can accommodate a maximum of 25 participants per site. If we receive more applications, participants will be selected based on several criteria, including correct entry information, motivation to attend the course, as well as gender and geographical balance.

For more detailed information about the workshop, please visit the workshop website.

Cryo-EM sample preparation and data collection
2023-10-17 08:00 - 2023-10-19 17:00 | KBC Building Umeå, Linneaus Väg 6, Umeå
The purpose of the course is to prepare and train Cryo-EM facility users in sample preparation methods, introduce users to the image data acquisition workflow, expand knowledge about cryo-EM methods among researchers and show that everyone can learn how to use cryo-EM for structure and cell biology.

The course is open for facility users or potential facility users, such as PhD students, postdocs, and researchers within the life sciences who are curious and will profit from cryo-EM skills. Swedish and international course participants are welcome. To attend, the course participants must have experience in basic electron microscopy and be familiar with structure or cell biology.

This course is supported by SciLifeLab, CryoNET and Umeå University and organized by the SciLifeLab Cryo-EM facility, both UmU and SU nodes together.

Read more

Application deadline

Application should be submitted before September 29, 2023

Course organizers

Michael Hall

Location

UCEM and Chemical Biological Centre (KBC) BuildingUmeå University, Linnaeus väg 6

Teachers and course instructors

Linda Sandblad

Michael Hall

Lars-Anders Carlson

Additional teachers t.b.a

Social program

A social program depending on the current corona restriction will be communicated to the participants after acceptance.

Course content

This course will cover practical aspects of cryo-EM sample preparation and data acquisition.

Topics covered

Basic theory of vitreous water, how to handle a cryo sample and consequences

Plunge freezing methods, tools and cryo-transfer

Sample and instrument requirements for single particle and tomography methods

Image data acquisition, concept of low dose and the cryo-specific workflow

Introduction to automatic data acquisition software, EPU, Tomography

Introduction to cryo-EM image processing methods

The course consists of lectures, cryo lab work, demonstrations and practical exercises for all participants, hands-on experiences of microscopy operation and discussions. A detailed schedule will be provided to accepted participant.

Course literature

Handouts and material online.

Entry requirements

Priority will be given to researchers involved in project where the use of cryo-EM is needed, which are to be briefly described upon application.

The course will be held at an advanced level, assuming that participants have a master’s degree or equivalent in a technical life science discipline. It aims to be relevant for a broad research community, also to participants not working in research environments using cryo-EM today.

A maximum of 15 participants will be admitted. Selection criteria include correct entry requirements, motivation to attend the course as well as gender balance.

Examination

Participation in all parts of the course, lectures, lab, microscopy demonstrations and evaluation are mandatory. SciLifeLab and Umeå University will provide successful participants with a course certificate and a recommendation for 1 ECTS

Campus Solna Seminar Series: Annika Bendes & Alexander Petri
2023-10-12 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Annika Bendes

Jochen Schwenk – alpha 2

Proteome profiling of self-sampled dried blood spots to enhance population-based studies and precision medicine

Alexander Petri

Kristoffer Sahlin – gamma 6

isONform: reference-free transcriptome reconstruction from Oxford Nanopore data

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

Metabolomics at speed – can direct analysis fingerprinting metabolomics be used for rapid sample screening?
2023-10-11 12:00 - 13:00 | Online event via Zoom
On-line seminar by Alastair Ross, Senior researcher/Metabolomics team lead at AgResearch, New Zealand.

Arranged by Otto Savolainen, Head of Unit, Chalmers Mass Spectrometry Infrastructure (CMSI), Metabolomics Platform.

Registration

SciLifeLab Day Linköping
2023-10-10 08:00 - 17:00 | Campus US, Linköping University, Lasarettsgatan 20, Linköping, Sweden
This event is a kick-off for the national SciLifeLab site in Linköping.

Learn more about the services and capabilities that are offered from SciLifeLab, both nationally and locally, and how you can participate in the activities.

Welcome to the SciLifeLab Day in Linköping. Here, life-science researchers will have a unique opportunity to meet experts in research infrastructure, participate in discussions on societal challenges and learn about what SciLifeLab have to offer both locally and nationally.

Exhibition, poster session, and mingle

Show your research in a poster and take the opportunity to discuss how you can implement SciLifeLab’s advanced technologies with the infrastructure experts and visit the exhibitions or posters from the infrastructure units to learn what services they can offer you.

Read more and find the program

SciLifeLab etablerar nytt forskningssäte i Linköping

Program

Detailed-program-SciLifeLab-Day-LinkopingDownload

Contact

linkoping@scilifelab.se

Josefine SandströmLinköping UniversitySite Coordinator SciLifeLab Linköpingjosefine.sandstrom@liu.se

SciLifeLab Days on the national sites

Gothenburg, April 17

Umeå, September 11

Lund, September 28

Linköping, October 10

Python programming with applications to bioinformatics
2023-10-09 09:00 - 2023-10-13 17:00
National course open for PhD students, postdocs, researchers and other employees in need of fundamental Python skills within all Swedish universities

Responsible teachers: Nina Norgren, Dimitris Bampalikis, Jeanette Tångrot

Contact information: edu.intro-python@nbis.se

Venues: SciLifeLab Uppsala, Trippelrummet, BMC & Umeå University, Naturvetarhuset, room NAT.D.370

Application

Course Website

Important dates

Application open: June 15

Application deadline: September 8

Confirmation to accepted participants: September 15

Course fee

A course fee* of 3000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks, and course dinner

*Please note that NBIS cannot invoice individuals

Course description

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs.

Format

This course runs in parallel both on-site in Uppsala and in Umeå. Lectures will be streamed online from our Uppsala site to the Umeå site. Several teaching assistants will be present both in the Umeå and Uppsala classroom all week to help with exercises and questions. When registering you will be asked to which site you apply.

The course consists of a mix of presentations, demonstrations, and practical exercises (either in the lab with assistants or on your own). Prior to the course, you can read a companion book “Programming Python”, or “Learning Python”. Such a book will also prove useful for your programming tasks, after the course is over. It is however not required, and material will be presented in class.

Course content

Core concepts about Python syntax: Data types, blocks and indentation, variable scoping, iteration, functions, methods and arguments

Different ways to control program flow using loops and conditional tests

Regular expressions and pattern matching

Writing functions and best-practice ways of making them usable

Reading from and writing to files

Code packaging and Python libraries

How to work with biological data using external libraries.

Learning outcomes

Describe and apply basic concepts in Python, such as:LoopsIf/else statementsFunctions

Reading/writing to files

Being able to edit and run Python code

Write file-processing Python programs that produce output to the terminal and/or external files

Create stand-alone python programs to process biological data

Know how to develop your skills in Python after the course (including debugging)

Entry requirements

The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage, such as navigating through folders and issuing commands at a shell prompt. We will not teach UNIX in detail: Other courses are available at SciLifeLab for it. Make sure your laptop has python installed for the practical exercises.

Selection criteria

Due to limited space the course can accommodate a maximum of 25 participants in Uppsala and 15 in Umeå. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to 1.5 hp credits, however the estimated credits are just recommendations. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Seminar "Stereo-Seq to study the brain gene expression across species" - Prof. Wei-Wu
2023-10-06 15:30 - 16:30 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Speaker: Prof. Wei-Wu

Title of Talk: Stereo-Seq to study the brain gene expression across species

The whole-brain single-cell spatial transcriptome atlas and cross-species comparisonThe brain is the most complex organ of humans with the highest heterogeneity of cell types. The composition and spatial location of different neuron subtypes, as well as their precise connections, are the basis for brain functions. Rapid advances in spatial transcriptomic technologies allow spatial mapping of gene expression as well as cellular subtypes at single-cell resolution of brain sections. We applied Stereo-Seq technology developed by BGI, to construct the whole-brain cell atlas for macaques, marmoset, and mice, with hundreds of coronal slices of spatial transcriptome across the whole brain per animal. Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex and cross-species comparative analysis identified primate-specific cell types enriched in cortical layer 4, whose marker genes are expressed in a region-dependent manner (Chen et al., Cell 2023). Whole-brain cell atlas provides the cellular and molecular basis for understanding the function, evolution, development, aging, and pathogenesis of the brain.

Host: Vicent Pelechano & Claudia Kutter

From sequences to structures, from structures to biology - On homo-oligomers and co-translational assembly
2023-10-06 11:00 - 12:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Emmanuel Levy, Weizmann

Host: Arne Elofsson

In this talk, I will provide an overview of our research, emphasizing two recent pieces of work. The first goes from sequences to structures, with the development of an atlas of homo-oligomerization spanning proteomes and lineages (https://www.biorxiv.org/content/10.1101/2023.06.09.544317v1). The second goes from structures to biology, leveraging protein complexes’ structures to crack the code of co-translational assembly.

Campus Solna Seminar Series: Daniela Almeida & May Britt Rian
2023-10-05 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Daniela Almeida

Marc Friedländer – gamma 5

Exploring bioactive peptides from Octopus vulgaris proteome after bacterial challenge

May Britt Rian

Jonathan Martin – alpha 1

Nontarget Analysis of Organic Micropollutants in Swedish Waters

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

6th CryoNET Symposium in Stockholm
2023-10-04 09:00 - 2023-10-05 17:00 | Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16C, Stockholm
We are very much looking forward to seeing you all in Stockholm on Wednesday. We’ll have a full house of around 200 participants, some 50 posters and a bunch of exciting speakers. It will be two intense and, we hope, enjoyable days!

CryoNet is a Nordic network in Cryo-electron microscopy that aims to promote collaboration and knowledge sharing across national borders. A main goal is to help establish state-of-the-art cryo-electron microscopy as a strong pillar of Nordic life science research.

The core of the network is formed by the Cryo-EM facilities at the University of Copenhagen, Aarhus University, Stockholm University and Umeå University. The network also reaches out to Cryo-EM sites in Norway and Finland.

The 6th CryoNET Symposium will take place October 4-5 2023 at Stockholm University. Take the opportunity to hear from world leaders in the field and network with students and researchers!

Participation in the symposium is free of charge and includes two days of lectures and a symposium dinner on October 4. We will start at 9:00 on Wednesday 4 October and finish 16:30 on Thursday 5 October.

We strongly encourage students and postdocs to submit an abstract about their research project. A number of abstracts will be selected for short talks and there will be a poster session for everyone during the symposium.

OrganizersGunnar von Heijne, Marta Carroni, Arne Elofsson och Xiaodong ZouContact: Gunnar von Heine

Program & Abstracts

Cryonet_program_abstracts_finalDownload

Keynote Speakers

Tamir Gonen, UCLA, USA

Ellen Zhong, Princeton University, USA

Confirmed Speakers

Henriette Autzen, Univ. Copenhagen, Denmark

Tristan Croll, Altos Labs, Cambridge, UK

Friedrich Förster, Utrecht Bioinformatic Center, The Netherlands

Emil Kristoffersen, Aarhus University

Karin Lindkvist, Lund University, Sweden

Misha Kudryashev, Max Delbrück Center, Berlin, Germany

Shintaro Aibara, AstraZeneca, UK

Ville Paavilainen, University of Helsinki, Finland

Anastassis Perrakis, NKI, Amsterdam, The Netherlands

Suparna Sanyal, Uppsala University, Sweden

Ludovic Sauguet, Institut Pasteur, Paris, France

Suyang Zhang, LMB-MRC, Cambridge UK

Exhibition in Navet at BMC
2023-10-03 09:00 - 2023-10-05 15:00 | Navet, SciLifeLab Uppsala, SciLifeLab Uppsala, BMC C11, Husargatan 3, Uppsala, 75237, Sweden
On October 3-5, between 09.00-15.00, you have a new opportunity to visit our exhibition in Navet at BMC. This is a chance to receive information and updates from 30 of the leading life science companies in Sweden. The entrance to Navet will be open between 09:00-10:00 and 13:00-14:00 for external visitors.

Tuesday, Oct 3

AH DiagnosticsWe help laboratories within life science and diagnostics to reach optimal performance by providing innovative quality products and full workflow solutions.

Bio-TechneBio-Techne´s family of brands includes R&D Systems, Novus Biologicals, Tocris, Protein Simple, ACD and Exosome Dx, creating a unique portfolio of products & services to empower researchers in Life Science & Clinical Diagnostics.

BioNordika

EppendorfEppendorf in the house, Navet October 3rd!

Move-it pipettes, first centrifuge with “green cooling”, lab consumables made from recycled cooking oils, new PCR and competitions.

Kem-En-Tec Nordic

SENSE Multilabel Plate Reader, Mirus Transfection reagents Efficient, Low Toxic, Instant Coomasie Stain 15 min w/o washes, Antibodies and ELISA kits, Metabolomic kits, DNA/RNA extraction kits

MercodiaFocuses on the development and manufacturing of immunoassays for research and clinical diagnostics, as well as offering bioanalytical services to pharma- and biotech companies.

MicromedicMicromedic provides a range of products for microscopy. The portfolio includes brands like Leica Microsystems (microscopes), Ibidi (consumable for live cell imaging) and SunJinLab (clearing reagents).

Nordic BioLabsDistributor representing e.g. Promega (enzymes, reagents), Active Motif (epigenetics), Lexogen (RNA-seq), Invitek (kits), Biosearch Technologies (enzymes, competent cells), Cytiva and Capricorn (cell culture)

PeproTech

RAMCON ABKombinerar globala produkter och expertis med lokal kunskap för att garantera att våra kunder uppnår bättre resultat på kortare tid. Vi riktar oss till forskare och tillverkare inom industrin, läkemedel, kemi och bioteknik.

Thermo Fisher Scientific

Wednesday, Oct 4

Akoya BiosciencesAkoya Biosciences offers comprehensive single-cell imaging solutions that allow researchers to phenotype cells with spatial context and visualize how they organize and interact to influence disease progression and response to therapy.

Beckman Coulter

Dedicated to developing and providing advanced technologies and equipment for research and discovery to explore new treatment methods.

Becton DickinsonBD Biosciences provides high-quality single cell multiomics (scM) instruments, reagents, and bioinformatics tools for reliable, reproducible scM data

Hyperfine studiosHyperfine Studios, an animation, video and illustration production studio. We produce visuals that are scientifically correct and visually appealing. The studio possesses expertise in both science and visual communication.

Meso Scale

Mettler Toledo

Nordic BioSiteNordic BioSite is a supplier of products for research & diagnostics throughout the Nordics. Let’s talk about your workflow for Genomics and Transcriptomics, antibodies available in BULK, and services.

QiagenQIAGEN delivers Sample to Insight solutions for molecular testing and offers products and services that enable our customers to gain valuable insights from any biological sample – from basic research to clinical healthcare.

Science ImagingDistributes selected Life Science Products mainly in Scandinavia and Finland. Our goal is to offer comprehensive solutions to the image related problems faced by today’s research communities

Tecan NordicTecan is a Swiss company founded in 1980, a world-leading provider of automated solutions for laboratories. We develop, manufacture and distribute our own products worldwide, with production in Switzerland, Austria and the USA.

Thursday, Oct 5

Bio-WorksWe supply the biopharmaceutical and biotech industry with WorkBeadsTM chromatography resins and GoBio™ prepacked columns for the purification of a wide range of biomolecules, e.g. proteins and peptides.

GenScriptGenscript biotech is global CRO provider of genes, protein, peptides and antibodies as a products and services for research and clinical use

Hamilton Nordic

Integrated DNA Technologies

LabLife NordicExciting news for cell- and molecular biosciences, Label-free cell characterization and sorting, NGS & single cell sample prep and target enrichment panels,Oligo synthesis, Cell assay sample prep, Cleanup and extraction, Western blot

NavinciNavinci is a Swedish biotech company that specializes in developing innovative solutions for the study of protein interactions based on our proprietary proximity ligation technology – Bringing Precision to Spatial Proteomics.

Pacific BiosciencesPacBio is a life science technology company that is providing advanced sequencing solutions that enable scientists to improve their understanding of the genome and ultimately, resolve genetically complex problems.

ShimadzuShimadzu Sweden provides a broad range of analytical instruments indispensable for research, development, and quality control in a variety of fields.

Takara Bio

Committed to helping scientists break new ground with innovative technologies. Our extensive portfolio offers solutions to support advancements across many areas of research, diagnostics, & clinical applications

Techtum LabA distributor of cutting-edge laboratory equipment and solutions for molecular biology research will exhibit at BMC Navet October 5. Live demos of a selection of our instruments!

Computational Enzymology - Identifying Catalytic Modules and predicting Mechanisms
2023-09-29 10:00 - 11:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Speaker: Janet Thornton, EBI

Computational Enzymology: Towards using knowledge of structure and function to predict enzyme transformations and mechanisms.

JM Thornton, AJM Ribeiro, Ioannis Riziotis, JD Tyzack, Neera Borkakoti, Roman Laskowski. European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK

Enzymes catalyse most of the chemical reactions which are essential for life. They are powerful catalysts that have evolved over millions of years to perform the functions in an organism that are necessary for survival. Using structural data and computational biology we seek to understand and predict how enzymes work and how they evolve to perform new enzyme functions. In this talk I will present our ongoing work to ‘perform catalysis’ in the computer. Using methods developed in cheminformatics, combined with information derived from 3D enzyme structures, we are developing tools to predict transformations and mechanisms.

Host: Arne Elofsson

Dame Janet M Thornton has contributed significantly to structural bioinformatics by increasing our fundamental understanding of the structure and function of proteins and how they contribute to disease and ageing. She has uniquely combined the analysis of structural features with the development of prediction methods. Together with Christine Orengo, the popular database CATH was developed. Her studies of sidechain conformation and stereochemistry were developed with Roman Laskowski into a tool, PROCHECK, widely used for evaluating the quality of experimentally defined protein structures. With Orengo and David Jones she developed methods for protein structure prediction. She was the director of the European Bioinformatics Institute from 2001 to 2015 and initiated the European infrastructure ELIXIR.

Campus Solna Seminar Series: Lina Stepanauskaite & Guillem Marin Aguilera
2023-09-28 12:00 - 13:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Lina Stepanauskaite

Cecilia Williams – alpha 2

Inflammation effect on microbiota composition in mice

Guillem Marin Aguilera

Ilaria Testa – gamma 3

Novel methodology to measure rotational diffusivity with fluorescence photo-switching

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

SciLifeLab Day Lund
2023-09-28 08:00 - 17:00 | Forum Medicum, Fernströmsalen, Sölvegatan 19, Lund, Sweden
SciLifeLab has launched four new sites across Sweden in 2022. The sites, located in Gothenburg, Linköping, Lund, and Umeå, will be crucial in promoting scientific research and research infrastructure nationally, while also strengthening the collaboration between all Swedish universities.

The expansion of SciLifeLab’s network will provide researchers across Sweden with state-of-the-art research infrastructure and technology, enabling them to perform cutting-edge research in areas such as genomics, proteomics, and bioinformatics. This will not only help to advance scientific knowledge but also contribute to the development of innovative solutions to pressing societal challenges.

The launch of the national sites, in addition to existing ones in Stockholm and Uppsala, will also contribute to the development of a stronger research environment, crucial for attracting talented researchers and investment to the country, further cementing Sweden’s position as a leader in scientific research.

Throughout this year, each site arrange a whole day program to highlight the national and local perspectives of SciLifeLab.

Conference proceedings

SciLifeLab-Day-Lund-Booklet-finalDownload

Program

SciLifeLab-Day-in-Lund-ProgrammeDownload

Contact

lund@scilifelab.se

Esther González-PadillaLund UniversitySite Coordinator SciLifeLab Lundesther.gonzalez-padilla@scilifelab.se (+46) 76-517 38 35

Venue

SciLifeLab Days on the national sites

Gothenburg, April 17

Umeå, September 11

Lund, September 28

Linköping, October 10

Computational and chemical approaches to drug repurposing
2023-09-27 13:00 - 16:00 | Samuelssonsalen, Tomtebodavägen 6, Solna, Sweden
Welcome to Xuexin Li’s doctoral thesis defense 1 September at 09.00 in Samuelssonsalen, Tomtebodavägen 6, Solna

Title

“Computational and chemical approaches to drug repurposing”

Author

Xuexin Li, Department of Medical Biochemistry and Biophysics, Karolinska Institutet

Principal Supervisor

Prof. Oscar Fernandez-Capetillo, Department of Medical Biochemistry and Biophysics, Karolinska Institutet

Co-supervisor

Dr. Daniela Hühn, Department of Medical Biochemistry and Biophysics, Karolinska Institutet

Opponent

Dr. Brinton Seashore-Ludlow, Department of Oncology-Pathology, Karolinska Institutet

Examination Board

Prof. Per Svenningsson, Department of Clinical Neuroscience, Karolinska Institutet

Prof. Ernest Arenas, Department of Medical Biochemistry and Biophysics, Karolinska Institutet

Prof. Patrick Aloy, Structural Systems Biology lab, Institut de Recerca Biomèdica de Barcelona

Blending Chemistry and Biology to Enable Systems Pharmacology
2023-09-27 10:00 - 11:00 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
Patrick Aloy, Prof., Institute for Research in Biomedicine (IRB Barcelona)

Organizers

CBCS-KI and PhenoTarget Research Community Program

Join the seminar on Zoomhttps://ki-se.zoom.us/j/64473979770

Abstract

Big Data analytical techniques and AI have the potential to transform drug discovery, as they are reshaping other areas of science and technology, but we need to blend biology and chemistry in a format that is amenable for modern machine learning. In this talk, I will present the Chemical Checker (CC), a resource that provides processed, harmonized and integrated bioactivity data on small molecules. The CC divides data into five levels of increasing complexity, ranging from the chemical properties of compounds to their clinical outcomes. In between, it considers targets, off-targets, perturbed biological networks and several cell-based assays such as gene expression, growth inhibition and morphological profiles. I will also present the Bioteque, a resource of unprecedented size and scope that contains pre-calculated biomedical embeddings around 11 biological entities (e.g. genes, cells, tissues, disease, etc), derived from a gigantic knowledge graph, so that each entity can be described considering different contexts (e.g. interactions, expression, etc). With small molecule and biological bioactivity descriptors in hand, we now face a new scenario for chemical and biological entities where they both are translated into a common numerical format. In this computational framework, complex connections between entities can be unveiled by means of simple arithmetic operations. Indeed, we demonstrate and experimentally validate that these descriptors can be used to reverse and mimic biological signatures of disease models and genetic perturbations in vitro and in vivo, options that are otherwise impossible using chemical information alone.ReferencesDuran-Frigola et al. Extending the small molecule similarity principle to all levels of biology with the Chemical Checker. 2020. Nat Biotechnol. 38: 1087-1096.

Bertoni et al. Bioactivity descriptors for uncharacterized chemical compounds. 2021. Nat Commun. 12: 3932.

Pauls et al. Identification and drug-induced reversion of molecular signatures of Alzheimer’s disease onset and progression in AppNL-G-F, AppNL-F, and 3xTg-AD mouse models. 2021. Genome Med. 13:168.

Fernández-Torras et al. Connecting chemistry and biology through molecular descriptors. 2022. Curr Opin Chem Biol, 66: 102090.

Fernández-Torras et al. Integrating and formatting biomedical data in the Bioteque, a comprehensive repository of pre-calculated knowledge graph embeddings. 2022. Nat Commun. 13: 5304.

FAIRPoints 'Ask Me Anything' webinar on Equitable and transparent access to information
2023-09-26 14:00 - 15:30 | Online event via Zoom
Welcome to join SciLifeLab Data Centre for this virtual FAIRPoints ‘Ask Me Anything’ event. The theme of this session is “FAIRPoints ‘Ask Me Anything’ on Equitable and transparent access to information“. A discussion about the role of infrastructure for open and equitable access of information, how this reflects in design decisions and how open and FAIR relate to or mean to the rest of the world.

Speakers: Sharif Islam; DiSSCo (Distributed System of Scientific Collections), and Karl Meyer; GÉANT. The event is moderated by Emma Wilson.

When: Sept 26th 14.00-15.30 CEST virtual event.

This event is hosted by SciLifeLab Data Centre in collaboration with FAIRPoints, RDA, EOSC and FDO.

Register

For more information or inquiries please contact: Sara El-Gebali, SciLifeLab Data Centre, Project leader, Metadata and curation, sara.elgebali@scilifelab.uu.se or fairpoints@protonmail.com

Learn more about FAIRPoints, an event series highlighting pragmatic measures developed by the community towards the implementation of the FAIR (Findable, Accessible, Interoperable, Reusable) data principles here.

Basic Course in Scanning and Transmission Electron Microscopy for Life Sciences
2023-09-26 08:00 - 2023-09-28 17:00 | KBC Building Umeå, Linneaus Väg 6, Umeå
This course covers lectures and practical demonstrations in SEM and TEM techniques, specifically for life science applications. The contents include principles of electron microscopy, specimen preparation, cryo-electron microscopy and correlative light-electron microscopy. For electron microscopy in physical science applications, there will be a similar-content basic course in early 2024.

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Application deadline: The registration closes on September 15 2023.

Location: Lectures at KBC Building and laboratory demonstrations at UCEM.

Participants: 18 persons

Instructors: UCEM staff

Duration: 3 days

Breaks/Refreshments: Coffee, cookies and fruit.

Costs: No course fee, but full attendance is required!

Examination/Credits

Oral and practical examinations are conducted during laboratory demonstrations. A course certificate will be given after participants attend all lectures and laboratory demonstrations for this 3-day course. UCEM recommends PhD program examiners to give 1 ECTS after successful participation.

[The Svedberg seminar] - Targeting Non-Coding RNAs Using Synthetic Small Molecules: Original Targets for Innovative Therapies
2023-09-25 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Dr Maria Duca

CNRS Research Director, Université Côte d’Azur, FranceWebsite: icn.univ-cotedazur.fr/tna

Host: Duc Duy Vo duc.duy.vo@kemi.uu.se, UU

Bio

Dr. Maria Duca is head of Targeting of Nucleic Acids research group in the Institute of Chemistry of Nice (Université Côte d’Azur – CNRS). After undergraduate studies in Pharmacy and Medicinal Chemistry (Faculty of Pharmacy, University of Bologna, Italy), she obtained her PhD in Molecular Biochemistry under the supervision of Dr. Paola B. Arimondo (National Natural History Museum, Paris, France) working on topoisomerase II inhibitors. A 2-year post-doctoral training in Sydney Hecht’s lab (Department of Chemistry, University of Virginia, USA) allowed her to pursue the study of nucleic acids working on targeted protein mutagenesis. After CNRS recruitment as a Research Scientist in 2008 and promotion to Director of Research in 2022, her research activities focus on the targeting of non-coding RNAs using synthetic small molecules toward innovative therapeutic approaches for anticancer, antiviral and antimicrobial applications. She has been awarded the Michel Delalande award from the Académie de Pharmacie as well as national and international grants including H2020 grants. She is Associate Editor for RSC Medicinal Chemistry journal, chair of the Chemical Biology Initiative of EFMC as well as vice-president of the French medicinal chemistry society.

Targeting Non-Coding RNAs Using Synthetic Small Molecules: Original Targets for Innovative Therapies

RNA is one of the most intriguing and promising biological targets for the discovery of innovative drugs in a large number of pathologies and various biologically relevant RNAs that could serve as drug targets have already been identified.1 Among the most important ones, it is worth to mention prokaryotic ribosomal RNA which is the target of a number of currently employed antibiotics, viral RNAs such as TAR, RRE and DIS RNA of HIV-1 or oncogenic microRNAs that are tightly involved in the development and progression of various cancers.2 However, difficulties in the rational design of strong and specific small-molecule ligands renders this kind of molecules relatively rare.

In this presentation, the structure-based design of new RNA ligands targeting oncogenic RNAs will be illustrated together with the identification of new compounds bearing a promising biological activity.3 Also, it will be shown how the active binders can be employed as chemical tools for a better understanding of the formed interactions toward the design of optimized compounds.4 Finally, the use of RNA binders for the validation of new antibacterial targets against resistant bacterial strains will be described to highlight the potential of the small-molecule approach in RNA targeting.

References

[1] J. Childs-Disney, X. Yang, Q. Gibaut, Y. Tong, R. Batey, M. Disney, Nat. Rev. Drug. Discov. 2022, 21, 736.

[2] J. Falese, A. Donlic, A. Hargrove, Chem. Soc. Rev. 2021 50, 2224.

[3] D. D. Vo, C. Becquart, T. Tran, A. Di Giorgio, F. Darfeuille, C. Staedel, M. Duca, Org. Biomol. Chem. 2018 16, 6262; C. Staedel, T. Tran, J. Giraud, F. Darfeuille, A. Di Giorgio, N. Tourasse, F. Salin, P. Uriac, M. Duca, Sci. Rep. 2018 8, 1667.

[4] Maucort, C., Vo, D.D., Aouad, S., Charrat, C., Azoulay, S., Di Giorgio, A., Duca, M. ACS Med. Chem. Lett. 2021 12, 899; Tran, T.P.A., Poulet, S., Pernak, M., Rayar, A., Azoulay, S., Di Giorgio A., Duca, M. RSC Med. Chem. 2022 13, 311; Scheheoleva I., Fernandez-Remacha, D., Estrada-Tejedor, R., Duca, M., Michelet, V. Chem. Eur. J. 2023 doi.org/10.1002/chem.202300825

Dissecting peripheral protein-membrane interfaces
2023-09-25 10:00 - 11:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Speaker: Nathalie Reuter, Department of Chemistry and Computational Biology Unit, University of Bergen

Host: Arne Elofsson

Abstract

Peripheral membrane proteins (PMPs) are soluble proteins that bind transiently to the surface of cell membranes. Peripheral membrane proteins include a wide variety of proteins including membrane-targeting domains such as C1, C2, FYVE, PH, PX, ENTH and GLA, enzymes involved in lipid metabolism such as phospholipases, membrane remodeling. machines such as BAR domains or ESCRTIII, and lipid-transfer proteins to name a few. Having the ability to exist in both a soluble and a membrane-bound form their membrane-binding region is constrained to retain a fine balance of polar and hydrophobic character, which makes it difficult to distinguish it from the rest of their surface. As a result peripheral membrane-binding sites are notoriously difficult to predict.

We collected and curated a dataset containing 2500 structures and compared their membrane-binding sites to the rest of their solvent-accessible surfaces, in order to reveal features of PMPs’membrane-binding sites. We find that, among positively charged amino acids, lysines are significantly more present than arginines. Protruding hydrophobes are a landmark of the interfacial binding sites of ca. 2/3 of peripheral membrane binding proteins, indicating that a majority of PMPs takes advantage of the hydrophobic effect while a non-negligeable minority (1/3) most likely relies on electrostatics interactions or other mechanisms. The IBS of peripheral membrane proteins contain significantly more glycines than the rest of their surface. Furthermore the analysis of 9 superfamilies revealed amino acid distribution patterns in agreement with their known functions and membrane-binding mechanisms.

These findings and the collected dataset will be useful for the development of prediction models for membrane-binding sites of PMPs.

Metabolomics for the masses
2023-09-21 12:00 - 13:00 | Birgit Thilander Lecture Hall, Academicum, Medicinaregatan 3, Gothenburg
Metabolites reflect the interaction between the gene cascade and surrounding exposures and are therefore essential components in all living organisms. Metabolites can be used to identify biomarkers of both health conditions and environmental exposures. The SciLifeLab Metabolomics platform offers a range of services, which will be presented during this talk, for researchers interested in metabolomics.

The presenter, Otto Savolainen, is head of the Swedish Metabolomics Centre (SMC), which offers small molecule, lipid and metabolomics analysis in biological tissues and fluids using mass spectrometry methods, in Gothenburg. The SciLifeLab site in Gothenburg includes units at both the University of Gothenburg and Chalmers University of Technology and has a strong connection to Sahlgrenska University Hospital. The SMC unit in Gothenburg is part of the Chalmers Mass Spectrometry Infrastructure (CMSI).

A light lunch will be offered for those attending onsite.

registration

Deadline for registration is 19/9.

Campus Solna Seminar Series: Irene Stevens & Charlotta Heningson
2023-09-21 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Irene Stevens

Vicente Pelechano – gamma 5

The co-translational degradome provides a readout of Fluconazole response in Candida albicans

Charlotta Heningson

Iskra Pollak Dorocic – gamma 5

The effect of SSRIs on the spatio-molecular organization of the serotonin system

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

Computational Methods in Evolution and Biodiversity
2023-09-21 09:00 - 17:00 | Vivi Täckholmsalen (Q-salen), NPQ-huset, Stockholm University, Svante Arrhenius väg 20, Stockholm, Sweden
This symposium and workshop will showcase the latest computational methods for analysing big data in evolution and biodiversity and provide an opportunity for participants to gain hands-on experience in these methods. Two keynote speakers will discuss a) new advances in using image recognition to analyse biodiversity and b) population genomics approaches to understand the effects of climate adaptation on genetic diversity. In addition, there will be three parallel computer workshops focused on the application of computational and machine learning methods to genome variation and biodiversity data. Participants should bring their own computers to join these workshops. This symposium is organised by the DDLS Evolution and Biodiversity expert group in conjunction with the SciLifeLab summit on Genomics of Biodiversity and Evolution.

Post-symposium material from the Workshops

We have the workshop leaders’ permission to share links to the material for the workshops in the DDLS symposium Computational Methods in Evolution and Biodiversity. Feel free to do tutorials from the other workshops than the one you attended.

Tobias Andermann’s workshop (slides, tutorial, and data): https://github.com/tandermann/ai_workshop

Per Unneberg’s workshop: https://percyfal.github.io/workshop-biodiversity-summit/lab/index.html

Marcin Kierczak’s workshop: https://github.com/mkierczak/autoencoders_workshop

Program

09:00Welcome and introduction09:10Challenges in Fine-Grained Image Analysis. Keynote speaker: Serge Belongie, Pioneer Center for AI, Denmark09:50Computational methods give insight into paradigms and paradoxes in landscape genomics. Keynote speaker: Katie E. Lotterhos Northeastern University, USA10:30CoffeeIntroduction to Workshop x 311:00Looking at population structure from a machine learning perspective, Marcin Kierczak11:25Neural Networks for biodiversity research: challenges and opportunities, Tobias Andermann11:50Inference of ancestral recombination graphs for population genomics, Per Unneberg12:15Lunch13:30Workshop x 3; parallel sessions:Room P232, P224, P216. (Guidance on site)From PCA to Generative Deep Learning Models for better understanding population structure, Marcin KierczakBuilding your own customized neural network model (bring your own data if you want), Tobias AndermannIntroduction to whole genome tree sequence inference with tsinfer, Per Unneberg17:00End of DayVenue: Vivi Täckholmsalen (Q-salen), NPQ-huset, Svante Arrhenius väg 20, Stockholm University

Abstract Serge Belongie, Pioneer Center for AI, Denmark
Challenges in Fine-Grained Image Analysis

Fine-grained image analysis (FGIA) is a longstanding and fundamental problem in computer vision and pattern recognition, and underpins a diverse set of real-world applications. The task of FGIA is concerned with visual objects from subordinate categories, e.g., species of birds or models of cars. The small inter-class and large intra-class variation inherent to fine-grained image analysis makes it a challenging problem. Capitalizing on advances in deep learning, in recent years we have witnessed remarkable progress in deep learning powered FGIA. In this talk we review representative examples in the context of recognition, retrieval, and generation/synthesis. In addition, we also review other key issues of FGIA, such as publicly available benchmark datasets, related domain-specific applications, and connections with other modalities including text and audio. We conclude by highlighting several research directions and open problems.

Abstract Katie E. Lotterhos, Northeastern University, USA
Computational methods give insight into paradigms and paradoxes in landscape genomics

Predicting organisms’ vulnerabilities to rapid and multivariate climate change is a major scientific challenge. A hurdle to addressing this challenge arises from evolution in multivariate environments. This talk will highlight how adaptation in multivariate environments can lead to unexpected patterns at the alleles under selection, which has implications for the inference of the genetic basis of adaptation and for predicting vulnerability to environmental change.

Workshop

From PCA to Generative Deep Learning Models for better understanding population structure, Marcin Kierczak

The workshop will focus on looking at different ways of modelling and visualising population structure based on genomic kinship. Starting from more traditional approaches like PCs or MDS as a benchmark, we will build more complex deep learning-based models and discuss when such approach can be beneficial. Finally, we will see how deep learning can potentially be used to augment original input data with some artificially-generated individuals with desired pre-defined kinship relations. Throughout this workshop, we will be using Python and keras interface to Tensorflow.

Building your own customized neural network model (bring your own data if you want), Tobias Andermann

In this workshop we will cover some computational and data processing tools that will come in handy when working with neural network models. The workshop is focused on implementing your own custom-built neural network model for a chosen task. The provided examples will be from the field of biodiversity research, but you can apply the tools we cover during the workshop to problems in other research fields. In general this is an easy to follow and hands-on introduction to using neural network models. The workshop requires very basic familiarity with Python, as the model will be implemented using the Python tensorflow library.

Introduction to whole genome tree sequence inference with tsinfer, Per Unneberg

In this workshop, we will introduce tree sequence (a.k.a. ARG) inference using the tsinfer library. We will build tree sequences from input variation data and look at some applications and analyses using the resulting tree sequences. As the exercises will be performed in jupyter notebooks in Python, basic familiarity with Python is required.

Scientific Committee

Fredrik Ronquist, NRM

Tanja Slotte, SU

Matthew Webster, UU

Data-driven Evolution and biodiversity

The DDLS subject area concerns research that takes advantage of the massive data streams offered by techniques such as high-throughput sequencing of genomes and biomes, continuous recording of video and audio in the wild, high-throughput imaging of biological specimens, and large-scale remote monitoring of organisms or habitats. This research subject area aims to lead the development or application of novel methods relying on machine learning, artificial intelligence, or other computational techniques to analyze these data and take advantage of such methods in addressing major scientific questions in evolution and biodiversity.

The research area Expert Group arranges symposia and workshops and welcomes interested to join the activities. More information about the research area Evolution and Biodiversity here.

SciLifeLab Science Summit 2023
2023-09-20 09:00 - 17:00 | Aula Magna, Frescativägen 6, Stockholm, 114 18 Stockholm, Sweden
Genomics of Biodiversity and Evolution

In an era characterized by extinction and habitat loss, it is crucial to explore biological diversity on our planet and understand the evolutionary processes that generate it. Genome sequencing has generated numerous insights into how species form and how they adapt to their environments, which is vital to understand in a changing world. As sequencing technologies improve and become less expensive it becomes feasible to produce high-quality genome assemblies and analyze genetic diversity in a huge number of species, which has led to a number of ambitious projects including the Earth BioGenome Project to sequence all known Eukaryotes.

Swedish scientists and SciLifeLab are at the forefront of this field, with genome projects including spruce, herring, Arctic fox and 240 mammals, advancing knowledge of topics including population genetics, adaptation, speciation, convergent evolution, and functional constraint.

In this SciLifeLab Science Summit, we have gathered several leading researchers who use genomics to learn about the diversity of life!

We invite you to Stockholm and Aula Magna for a full-day conference program with ample time for discussions, mingling, and networking.

This event is open to anyone interested in the topic and is free of charge.

Registration closed If you are interested in participating, please send an email to events@scilifelab.se.

Poster session, Flash Talk & Best Poster Award

Registration opens at 08:45. Please hang your poster on the poster boards upon arrival and in time before the Conference starts at 09:30. Pins are available. There are two poster sessions. Please remove your poster from the poster board after the second session or at 17:00. Any remaining posters after 17:15 will be discarded. The Scientific Committee´s Poster jury will nominate the Science Summit 2023 Best Poster and award the winner a 5 000 SEK Travel Grant. You must stay for the prize ceremony at the end of the conference.

SciLifeLab Science Summit 2023 Poster ListDownload

Four (4) submitted poster abstracts will be selected for Flash Talks à 5 minutes on stage.

The selected Flash Talks speakers are

Cynthia Perez Estrada. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Patrik Rödin Mörch. The Role of Population History in Shaping the Mutational Load of Structural Variants Relative to SNPs, in Distinct Island versus Continental Lagopus Lineages

Andreas Wallberg. New insights into the evolutionary history and adaptive potential of World Ocean krill using comparative population transcriptomics

Qiaoling Deng. Genetic parallelism and adaptation to brackish water bodies in sprat (Sprattus sprattus) and Atlantic herring (Clupea harengus)

Important dates

Sept 1. Registration deadline for posters! Poster submission closes, and the selection of Flash Talks will be made.

Sept 4. Poster submission approval email.

Sept 11. Invitation email to selected Flash talk speakers.

Sept 11 at 12:00. Registration for the SciLifeLab Science Summit closes

Sept 11. Poster Abstracts published as a PDF on the website

Free bus transportation

We offer free bus transportation from Uppsala (BMC Campus) at 08:00 to Aula Magna, (SU Campus Frescati) in the morning and back after the Conference at 17:00 and after the mingle at 18:30. Reserve your seat when filling in the registration form.

Satellite Symposium:Computational Methods in Evolution and Biodiversity

On September 21, the Data-Driven Life Science Expert group invites you to a full-day satellite symposium and workshop, “Computational Methods in Evolution and Biodiversity“

Read more

Speakers

Leif Andersson, Uppsala University, SWE

Richard Durbin, Wellcome Sanger Institute, UK

Tom Gilbert, University of Copenhagen, DK

Elinor Karlsson, University of Massachusetts Medical School & Broad Institute, USA

Karin Norén, Stockholm University, SWE

Karin Rengefors, Lund University, SWE

Tanja Slotte, Stockholm University, SWE

Tom van der Valk, Swedish Museum of Natural History, SWE

Please, see the abstracts below the Program

Program

Program Science Summit 2023Download

08:00Bus from BMC Uppsala to Aula Magna08:45Registration and coffee, hanging posters09:30Welcome WordsYlva Engström, Chair of the SciLifeLab BoardIntroduction to the ConferenceKerstin Lindblad-Toh, Chair of the Scientific CommitteeSession I: Moderator Kerstin Lindblad-Toh09:45Investigating mammalian evolution and human disease through comparative genomics in hundreds of speciesElinor Karlsson, UMass Chan Medical School and Broad Institute, USA10:15A Million-Year-Old Journey: Exploring Mammoth Speciation and Adaptive Evolution through timeTom van der Valk, Swedish Museum of Natural History10:40Coffee break and Poster session ISession II: Moderator Leif Andersson11:20Insights from high quality genome sequencing across the tree of lifeRichard Durbin, University of Cambridge, UK11:55Conservation genomics of the Scandinavian Arctic foxKarin Norén, Stockholm University12:20Lunch break and mingle, exhibitionsSession III: Moderator Love Dalén13:40Domestication hologenomics – what are we missing without taking this approach?Tom Gilbert, University of Copenhagen, DK14:15Sequencing the supergene that governs Darwin’s different forms of flowersTanja Slotte, Stockholm University14:40Flash Talks from Junior researchers (selected from submitted abstracts) 5-minute talk/researcher15:05Coffee break and Poster session IISession IV: Moderator Matthew Webster15:45The remarkable population structure of Atlantic and Baltic herring – selection, selection, selectionLeif Andersson, Uppsala University16:20Why cyanobacterial blooms produce toxins – unravelling the underlying genetic diversity in the microcystin gene clusterKarin Rengefors, Lund University16:45Best Poster Award ceremonyClosing words17:00End of ConferenceMeet the speakers and mingle; snacks and free beveragesBus to Uppsala departs at 17:00 and at 18:30

Speaker abstracts

Science Summit speaker abstracts 2023Download

Abstract Leif Andersson – The remarkable population structure of Atlantic and Baltic herring – selection, selection, selection
Initial genetic studies with a handful of neutral markers revealed no genetic differentiation among populations of Atlantic herring, not even between Atlantic and Baltic herring classified as distinct subspecies by Linnaeus. Whole genome sequencing has totally changed the picture. Atlantic herring can now be divided into many subpopulations (ecotypes). It is an adaptive radiation with incomplete reproductive isolation between ecotypes. We find strong genetic differentiation at loci under selection but minute genetic differentiation at neutral loci. The explanation for this is the huge population sizes minimizing drift, high fecundity allowing effective selection, a homing behavior but with gene flow. Herring is a broadcast spawner and it is probably no strong selection for prezygotic reproductive isolation. Ecological adaptation in Atlantic herring is related to a diversity of environmental conditions including salinity, temperature and light conditions as well as behavioral traits such as timing of reproduction and migration. Recently we used SNP-chip analysis to explore the population structure of Baltic herring in the Bothnian Sea. This analysis revealed two major subgroups: spring- and autumn-spawning Baltic herring. However, a third genetically distinct population was present among the spring-spawners. This ecotype had a three-fold larger body size than other populations spawning in the same area at the same time implying a marked difference in feeding behavior. This illustrates the adaptive differentiation occurring in the herring. The results have important implications for fishery management of the herring in the Baltic Sea and elsewhere.

Dr. Leif Andersson is a specialist in genetics and genome biology. He and his group have made ground-breaking studies on the relationship between genetic and phenotypic variation. He has been working on comparative genomics using domestic animals as models for phenotypic evolution. This has resulted in discoveries of genotype-phenotype relationships such as mutations affecting pigmentation, gaits in horses, comb morphology in chickens and muscle growth in pigs. He has also studied the genetic basis for domestication of rabbits, chickens and pigs. The research program has been expanded to natural populations as exemplified by studies of the evolution of Darwin’s finches and their beaks, a supergene controlling male mating strategies in the ruff and genetic basis of ecological adaptation in Atlantic herring. Leif Andersson is professor in Functional Genomics at Uppsala University and in Animal Genomics at Texas A&M University. He was awarded the Wolf prize in Agriculture 2014.

Abstract Richard Durbin – Insights from high quality genome sequencing across the tree of life
I will discuss progress in scaling up the generation of high quality reference genome sequences, and some of the insights that we have obtained from them. Using high accuracy PacBio CCS reads and paired end Illumina Hi-C data we are now obtaining essentially complete, high contiguity chromosomal assemblies at an increasing rate and decreasing cost, with more than a thousand assemblies completed within the Tree of Life programme at the Wellcome Sanger Institute. Because in most cases even heterochromatic repeat DNA is well assembled, we have been able to characterise turnover of centromere-associated repeates which are some of the most rapidly evolving seqence in the genome, observing repeated transitions in plants between satellite tandem repeats and transposon cluster patterns. Furthermore, by selection of very high confidence bases from the individual CCS sequencing reads, we are able to identify signatures of somatic mutations across a very wide range of species, suggesting previously unobserved mutational processes.

Richard Durbin works in computational genomics. He has been leader or co-leader of multiple large collaborative projects, including the 1000 Genomes Project, and more recently has worked on genome assembly and contributed to the Vertebrate Genomes Project and the Earth Biogenome Project. He has also introduced multiple bioinformatic methods and data structures, including bwa for read mapping and the BAM format for genomic data, and worked on evolutionary genomics in non-model vertebrate systems, and understanding human history from ancient and modern DNA data. Richard is a Fellow of the Royal Society of London (2004), a Member of EMBO (2009) and a Foreign Member of the American Academy of Arts and Sciences (2019).

Abstract Tom Gilbert – Domestication hologenomics – what are we missing without taking this approach?
Analyses that compare the genomes of contemporary domestic animals and plants with those of their wild relatives have provided a wealth of insights into not only when and where our ancestors started the process, but also what specific genetic variants are key to modern phenotypes. Furthermore, once coupled to palaeogenomic data, such datasets can also even reveal the order in which such variants arose, shedding further insights into the process itself. However while there is no doubt that we have learnt much about domestication in general, and indeed for most domestic species we can clearly document the genetic basis of why the end product differs from the start, I argue that there may be certain processes that were involved that have been largely overlooked, in particular related to the so-called hologenome.

Tom Gilbert is Professor of Palaeogenomics at the University of Copenhagen, Professor II at NTNU University Museum, and Director of the DNRF Center for Evolutionary Hologenomics. He holds a PhD in the study of ancient DNA from the University of Oxford, and has been active in both trying to develop methods to both expand the potential of ancient DNA to our understanding of the past, as well as more recently leading research aimed at revisiting our understanding of ecological and evolutionary processes using hologenomic techniques – ie the integrative approach of combining host genomes with those of their microbiome.

Abstract Elinor Karlsson – Investigating mammalian evolution and human disease through comparative genomics in hundreds of species
A major challenge in genomics is discerning which bases among billions alter organismal phenotypes and affect health and disease risk. The Zoonomia project compared 240 different placental mammal species to detect which individual bases in the genome are exceptionally conserved (constrained) and likely to be functionally important. Eighty percent of the most constrained bases are outside protein-coding exons, and half have no functional annotations in the ENCODE project. By pairing Zoonomia’s genomic resources with phenotype annotations, we find genomic elements associated with phenotypes that differ between species, including olfaction, hibernation, brain size, and vocal learning. Comparative genomics is advancing human health today by identifying functionally important in both coding and noncoding regions. Exploring the genomic basis of phenotype diversity that has emerged across 100 millions of years of placental mammal evolution is a powerful tool for discovering the next generation of biotechnological advances.

Elinor Karlsson, PhD, is associate professor in Bioinformatics and Integrative Biology at the UMass Chan Medical School, and director of Vertebrate Genomics at the Broad Institute of MIT and Harvard. Her research combines new technology, community science and genomics to investigate diseases and discover the origins of exceptional mammalian traits. Dr. Karlsson’s research includes the Zoonomia project, an international effort to compare the genomes of over 240 mammals (from the African Yellow-spotted Rock Hyrax to the Woodland Dormouse), to identify segments of DNA that are important for survival and health. Dr. Karlsson has a special interest in dog and wolf genetics, and her international Darwin’s Ark project invites all dog owners to enroll their dogs in an open data research project exploring the genetic basis of behavior, as well as diseases such as cancer.

Elinor received her B.A. in biochemistry/cell biology and her B.F.A. (Bachelor of Fine Arts) from Rice University, and earned her Ph.D. in bioinformatics from Boston University. She was a postdoctoral fellow with Pardis Sabeti at Harvard University before starting her research group at UMass Chan in 2014.

Abstract Karin Norén – Conservation genomics of the Scandinavian Arctic fox
Over the past decade, whole genome sequencing has generated important insights about key processes in conservation genetics, e.g. inbreeding depression, genomic erosion and genetic rescue in small and threatened populations. The Scandinavian Arctic fox (Vulpes lagopus) was on the verge of extinction in the late 1990s. In response to efficient conservation actions, the population has increased, but studies have documented that the bottleneck, geographic fragmentation and long-term low population size resulted inbreeding depression and loss of genetic variation. To explore the dynamics of inbreeding, accumulation of deleterious genetic variation and genetic rescue, we assembled a draft reference genome and resequencing data of >80 complete Arctic fox genomes. We found alternating levels of genomic inbreeding and a short-term genetic rescue effect, operating over different time scales. An immigration event resulted in an increased mutational load where immigrant offspring displayed higher proportion of loss of function mutations compared to native individuals. Further, we established a link between deleterious genetic variation and individual fitness. The results from these studies play a fundamental role for making informed decisions in conservation of this particular population, but also make important contributions for conservation of other small and threatened populations and species.

Karin Norén is a researcher and docent in animal ecology at Department of Zoology, Stockholm University. She received a PhD from Stockholm University in 2011. Thereafter, she spent three years as a post-doctoral researcher at University of California, Davis. She is currently a PI in the Swedish Arctic Fox Project and her research is focused on conservation genomics, especially in carnivores, and genetic processes in fluctuating populations in northern ecosystems.

Abstract Karin Rengefors – Why cyanobacterial blooms produce toxins – unravelling the underlying genetic diversity in the microcystin gene cluster
Cyanobacterial blooms are a global threat to freshwater ecosystems since they produce cyanotoxins that are poisonous to humans, wildlife, and livestock. Microcystin is the most common and toxic among the cyanotoxins and induces liver failure and tumor promotion in mammals. However, its function in cyanobacteria is still contested. In Microcystis spp., the most common microcystin-producing genus, microcystin-producing and non microcystin-producing strains co-exist within populations. Moreover the proportions of the strain types vary in time and space. Microcystin is biosynthesized by the constitutively expressed mcy gene cluster consisting of ten modular genes (mcyA-J). Previous studies have suggested that non-producers lack the entire cluster. In the field, toxigenic strains are quantified using quantitative PCR targeting one of the genes in the microcystin gene cluster (usually mcyB or E). However, the number of gene copies are not always correlated with microcystin in the water. To better understand the underlying genotypes of microcystin producers and non-producers we sequenced the genomes of strains of Microcystis isolated from a single bloom. At the same time, the strains were phenotyped to determine microcystin variants. Unexpectedly, non microcystin-producing strains displayed a range of genotypes yet with a common pattern of mostly lacking mcyF, G, and J. Other genes in the cluster were either present or had partial hits against our custom-made microcystin gene database. We suggest that non microcystin-producing Microcystis are genotypically and phenotypically diverse and that genotype composition varies among populations. I will also discuss potential causes of mcy gene-loss and the way forward to unravel the function of microcystin.

Dr. Karin Rengefors is a professor of limnology at the Biology Department of Lund University, and her research interest is on phytoplankton ecology and evolution, with focus on freshwater harmful algal blooms. Currently her research group focuses on understanding the population dynamics and genetic diversity of toxin-producing cyanobacteria. Another research topic is investigating the processes underlying population differentiation and speciation in phytoplankton. Dr. Rengefors also has a strong interest in doctoral education and took the lead in developing and running GENECO, the Graduate Research School in Genomic Ecology at Lund university 2008-2013. For this work she was awarded the Lund University Pedagogical prize in 2012. She has also been a co-director of the internationally renowned Workshop on Genomics in Cesky Krumlow. Dr. Rengefors did her BSc as well as her PhD at Uppsala University, followed by two years postdoc at the Woods Hole Oceanographic Institution, USA. In 2001, she landed an Assistant Professorship at Lund University, and in 2005 a University Lecturer position. She was promoted full professor in 2008, thus becoming the first female professor in limnology in Sweden.

Abstract Tanja Slotte – Sequencing the supergene that governs Darwin’s different forms of flowers
Supergenes are genomic regions containing sets of tightly linked genes that control multi-trait phenotypic polymorphisms. Although supergenes are responsible for a wide variety of balanced polymorphisms in nature, our understanding of the origins and evolution of supergenes remains incomplete. We aim to fully characterize and study evolutionary processes at one of the first described supergenes, the S-locus that governs a floral polymorphism called distyly. We are doing so in Linum, wild flaxseed species, a system where Darwin himself described this floral polymorphism, but where its genetic basis remained unknown. To generate a genomic framework for the study of distyly, we assembled high-quality genomes of a diverse set of Linum species. We then identified the distyly supergene and showed that it harbors indel variation and not inversions, which is typical for many other supergenes. Our results have important implications for the evolution and breakdown of distyly supergenes, and shed light on the genetic architecture and evolution of the classic supergene that governs Darwin’s “different forms of flowers”.

Tanja Slotte is a professor in the Department of Ecology, Environment and Plant Sciences at Stockholm University. Her group works on the evolution of supergenes and plant mating systems primarily using evolutionary genomic analyses. A population geneticist by training, she received her PhD from Uppsala University, followed by a postdoc at the University of Toronto, Canada before starting her own group at Uppsala University. In 2014 she moved to Stockholm University to take up a SciLifeLab Fellow position and since 2022 she is Professor in Ecological Genomics at Stockholm University.

Abstract Tom van der Valk – A Million-Year-Old Journey: Exploring Mammoth Speciation and Adaptive Evolution through time
In this presentation, I will share our efforts over the past years in recovering genome-wide data from woolly mammoths and discuss how the genomic insights have advanced our understanding of evolutionary processes such as speciation and long-term adaptive evolution. Our research involved sequencing specimens from the Early and Middle Pleistocene subepochs, including some of the last surviving woolly mammoths. This work led to the identification of a previously unknown mammoth lineage, evidence of hybridization between different mammoth species, and the finding that most protein-coding changes linked to cold adaptation in woolly mammoths were already present one million years ago. I will show that the woolly mammoths had acquired a diverse array of positively selected genes associated with among others hair and skin development and fat storage at the time of its origin. Our research also identified genes that underwent recent positive selection, including those related to skeletal morphology, body size, and a gene potentially responsible for the small ear size observed in Late Quaternary woolly mammoths. Overall, our findings highlight the potential of palaeogenomics in enriching our understanding of speciation and long-term adaptive evolution.

Tom completed his doctoral studies at Uppsala University, Sweden, with his thesis “Genomics of population decline,” which investigated the genomic consequences of rapid population declines in endangered mammals. He then worked as Postdoctoral Researcher at the Centre for Palaeogenetics in Stockholm, focusing on the computational analysis of ancient and historical genomes of multiple extinct and endangered species. He then served as a Bioinformatician at the National Bioinformatics Infrastructure Sweden, working on a large-scale conifer genome project. As of 2022, Tom is a Data-Driven-Life-Science fellow at the Centre for Palaeogenetics, where his research group focusses on the development of computational methods to analyze complex samples, with a priority on identifying the presence of species from minute amounts of DNA.

Science-Summit-Poster-abstracts-2023Download

Scientific Committee

Kerstin Lindblad-Toh (chair), Leif Andersson, Matt Webster, Love Dalén.

Operations office project leader: Erika Bergqvist Erkstam. Team: Maria Bäckström, David Gotthold, Isolde Palombo and Hampus Persson.

SciLifeLab Science Summit – Proposal for topic 2024

The SciLifeLab Science Summit is a one-day symposium, each year with a new topic. The Science Summit aims to create awareness about SciLifeLab research and researchers, promote collaborations within life science in Sweden, and be a day for the SciLifeLab community to meet and interact.

To SciLifeLab Group Leaders, Platform Directors and Head of Units,

Is your research the theme for SciLifeLab Science Summit in 2024? Send in your proposal now and take part as the scientific committee!

Read more

Neurodiversity in communication, relationships, academia & life
2023-09-19 14:00 - 14:30 | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
We are excited to host a new Coaching in Science Initiative (CSI) Seminar titled:
‘Neurodiversity in communication, relationships, academia & life’

Neurodiversity; to be outside of the category of people who are considered cognitive ‘normal’. But what is ‘normal’ really? And how broadly can we extend the concept of neurodiversity? On a personal level, perhaps it is more helpful to ask ourselves, what neurodiverse traits do I have in general, or in this particular group of people? Could they be different depending on whom I’m socializing with at work and at home?

Applying the CSI coaching model and our core values, we will explore who we are in relation to others, raise awareness of how we are different, learn more about the biology behind our emotional regulation and what to do when we find ourselves in difficult social interactions.

Date: 19/9/2023
Time: 14:00
On-site location: Gamma 2 lunch room
Zoom link: https://kth-se.zoom.us/j/65001858940

We will begin with a 15-20 min talk, held in Solna and over zoom. Then proceed with a reflection and discussion held only on-site. We encourage other sites to form watch parties, by listening in together to the talk and then hold their own discussion afterwards. Hopefully seeding many local chapters of CSI.

To help facilitate discussion and reflection, consider the follow starter questions:
Awareness: where do we experience neurodiversity in our lives already?
Analysis: how well do I currently interact with neurodiversity?
Alternative: how can we relate to neurodiversity, in ourselves and others?
Action: how will knowledge of neurodiversity change my decisions going forward?

[The Svedberg seminar] - Female sex hormones and the human microbiome
2023-09-18 15:15 - 16:15 | BMC Room C8:301, Husargatan 3, Uppsala, Sweden
Luisa Hugerth

Assistant ProfessorDDLS FellowDepartment of Medical Biochemistry and Microbiology, UU

Bio

Luisa Hugerth has a background in molecular biology and biomedicine, but got her PhD in 2016 at KTH Royal Institute of Technology with an analysis of microbial community time-series in the Baltic Sea. After that, Dr. Hugerth spent 6 years at the Centre for Translational Microbiome Research in Karolinska Institutet, where she studied the human microbiome in functional bowel disorders, before becoming deeply involved in research on the microbiome of pregnant and non-pregnant women. Since 2022, she is a DDLS fellow in epidemiology and biology of infection at Uppsala University’s Department of Medical Biochemistry and Microbiology, Imbim

Female sex hormones and the human microbiome

Estrogen and progesterone have pleitropic effects throughout the body. This includes mucosal surfaces and the diverse microbial communities that inhabit them. Microbiota can enhance or dampen these effects, thereby acting as risk mediating factors for various diseases, most notably gynecologic and periodontal inflammation. The vaginal microbiota has been epidemiologically linked to various outcomes, from STI acquisition to preterm birth. The oral microbiota has also been causally linked to as disparate outcomes as preterm birth and newly onset depression. Here, I will present ongoing work on the interplay between endogenous and exhogenous hormones on the oral, vaginal and gut microbiome, in women with a regular menstrual cycle as well as pregnant women. Additionally, since both sex hormones and the gut microbiome are implicated in mood disorders, I will touch upon the gut-brain axis in relation to pregnancy nausea and perinatal depression.

Host: Mikael Sellin mikael.sellin@imbim.uu.se, UU

Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE)
2023-09-18 08:00 - 2023-09-22 17:00 | Online event via Zoom
National workshop open for PhD students, postdocs, researchers and other employees within Swedish academia. This course is run by the National Bioinformatics Infrastructure Sweden (NBIS).

Important dates

Application opens: now

Application closes: 2023-09-04

Confirmation to accepted students: 2023-09-08

Responsible teachers

Agata Smialowska, Jakub Orzechowski Westholm, Vincent van Hoef

Please contact edu.epigenomics@nbis.se for course specific questions

Application

Course website

Workshop fee

This online training event has no fee. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2000 SEK.

*Please note that NBIS cannot invoice individuals.

Workshop content

This workshop aims to introduce the best practice bioinformatics methods for processing, analyses, visualisation and integration of epigenomics and functional genomics data.

Topics covered include:

Data processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;

ChIP-seq: peak calling, peak independent / dependent quality metrics, differential binding analysis; DNA motif enrichment;

ATAC-seq: peak calling, peak independent / dependent quality metrics, differential accessibility analysis;

Quantitative ChIP-seq using spike-ins;

CUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;

Functional analysis, including finding nearest genes and custom features, GO terms and Reactome pathways enrichment;

Basic multi-omics exploration and integration;

Visualisations of epigenomics datasets;

Introduction to analysis of single cell functional genomics data (scATAC-seq);

Introduction to nf-core pipelines for processing and analysis of epi- and functional genomics data : Methylseq, ChIP-seq, ATAC-seq.

Entry requirements

Required for being able to follow the workshop and complete the computer exercises:

BYOL, bring your own laptop with R and RStudio installed;

Basic knowledge in Linux;

Basic programming experience, preferably in R.

Desirable

Experience working on the SNIC center Uppmax or another HPC. We encourage participants to run the linked Uppmax tutorial before the workshop;

Previous experience with NGS data analyses;

Completing NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists” or equivalent.

Due to limited capacity the workshop can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the workshop as well as gender and geographical balance.

Please note that NBIS training events do not provide any formal university credits.

This training content is estimated to correspond to a 1.5 HPs, however the estimated credits are just guidelines. If formal credits are crucial, participants need to confer with the home department whether the course is valid for formal credits.

Campus Solna Seminar Series: Christian Sommerauer & Robin Ebbestad
2023-09-14 12:00 - 13:00 | Milkyway SciLifeLab Solna, Tomtebodavägen 23, Solna
Welcome to join the Campus Solna Seminar Series – an initiative to promote the fantastic science ongoing at Campus Solna and hopefully forge more internal communication and collaboration between within Campus Solna. The format consists of two 15 min talks (One speaker from the Alpha-building and one from the Gamma-building respectively), with an additional 5 min of questions. Presentation of ongoing (unpublished) projects is strongly encouraged.

The seminars are held Thursdays 12:00-13:00. You can bring your lunch to the seminar.

This week:

Christian Sommerauer

Claudia Kutter – gamma 5

Estrogen receptor activation remodels TEAD1 gene expression to alleviate nonalcoholic fatty liver disease

Robin Ebbestad

Hjalmar Brismar – gamma 3

High-resolution imaging and deep learning-based segmentation of glomerular pathologies in the kidney

This seminar series is organized by the PhD & Postdoc Council. For more information about the Council and other events check our page.

Beyond pharmacological inhibition of DNA repair
2023-09-14 08:00 - 17:00 | Atrium, Karolinska Institutet, Nobels väg 12, Solna, Sweden
A Mini-Symposium dedicated to the boosting and reprogramming of DNA repair as a novel technology and its implications in the treatment of human disease.Come and learn more about exciting opportunities in modulating DNA repair, discuss with experts and enjoy a classic swedish Fika.

registration for on-site participation

registration for on-line participation

InvitationDownload
