SciLifeLab

BAM Seminar: Grant opportunities for PhDs and Postdocs
2022-11-15 13:00 - 14:00 (Europe/Stockholm) | Gamma 2 Lunchroom, SciLifeLab, Tomtebodavägen 23, Solna, Sweden
As part of our “Biology At Most” seminar series we invite speakers from all types of life science career paths. They will share their visions, perspectives and expertise in their field in a informal environment.

Today’s Guests

Representatives of the scholarship offices from Stockholm University, Kungliga Tekniska Högskolan and Karolinska Institutet: Carina Lindblad (SU), Veronica Haegeland (KTH) and Daniela Strodthoff (KI)

These speakers will inform us about the grant opportunities available from our three universities for researchers at the PhD or Postdoc level. As researchers in academia we all rely on grants to carry out our research or to attend workshops and conferences. The seminar will cover topics and discussions that will be helpful for PhD students and Postdocs to further their research interests and consider new avenues to expand into high quality research ideas.

This event is mainly aimed at PhD students and Postdocs, but researchers in all stages of their career are of course welcome to attend.

You can join the meeting in person or via zoom (Meeting ID: 651 4642 5776).

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

DDLS Annual Conference
2022-11-15 12:30 - 2022-11-16 12:30 | Eva & Georg Klein, Solnavägen 9, Stockholm, 17165, Sweden
Welcome to a lunch-to-lunch conference focused on Data-driven Life Science. Listen to the DDLS Fellows and take part in social activities onsite.

The Data-Driven Life Science conference on November 15-16, 2022, is the first in-person conference of the DDLS program. This meeting brings together the community in biomolecular data science and AI, introduces newly appointed DDLS fellows, and provides opportunities for networking across the research community and SciLifeLab infrastructures. We are excited to host two international keynote speakers and welcome the community to join us. We are excited to meet in person at the poster session and other social events.

DDLS Annual Conference Poster session

Lightning talk and Poster session

The lightning talk is 1 minute and will be strictly timed. No slides. Please, indicate in the registration if you like to present a poster with, or without, a 1 min lightning talk.

DDLS Annual Conference Best Poster Award

The DDLS Annual Conference Best Poster Award encourages the submission and exhibition of high-quality posters carried out by young scientists, including Ph.D. students, post-doctoral researchers, etc. The poster should be on a topic related to data-driven life science. The Prize, which is based upon the decision of a Scientific Committee-appointed Jury, consists of a certificate and a travel grant of up to 5 000 SEK. The travel must be booked and ordered through the DDLS Support team and follow regular University travel policy. The trip should be completed before 2023-12-31.

Target group: We welcome all researchers interested in the DDLS program and data-driven life science.

Participants onsite: Venue Eva & Georg Klein, Floor 3 (ground floor), Biomedicum, Stockholm

Participate online: Online participation info, e.g, zoom link will be sent out upon registration

Organizer: SciLifeLab, host of SciLifeLab & Wallenberg National Program for Data-Driven Life Science.

Register here

Onsite: Register before November 9 at 12:00, so we can order coffee and lunch.

Download Flyer

Download Program

Agenda

Tuesday, November 1511:45Drop-in Registration with Coffee and WrapsArea: Social area directly to the right of the entrance. You can leave your coat and bag in the Lecture Hall. We ask the participants to be seated at 12:30.12:30WelcomeTuuli Lappalainen, KTH/SciLifeLabDDLS updatesOlli Kallioniemi, SciLifeLab13:00Keynote: Samuli Ripatti, Institute for Molecular Medicine, University of HelsinkiGenetic variation and risk of common diseases over the life course13:45Coffee break14:15DDLS Fellow Talk: Tom van der Valk, Museum of Natural HistoryEnvironmental DNA in the genomic decade14:35Infrastructures for data-driven life scienceJohan Rung, SciLifeLab Data CentreSciLifeLab Data Centre14:45Ola Spjuth, SciLifeLab Data CentreManaging the life cycle of AI models and apps15:00Matts Karlsson, Linköping UniversityNAIS, Berzelius and the road ahead15:15Poster lightning talks (1 minute per poster)Poster session with snacks and beverage17:30End of Day 1Wednesday, November 1609:00Keynote: Cecilia Clementi, Freie Universität BerlinDesigning molecular models with machine learning and experimental data09:45DDLS Fellow Talk: Johan Bengtsson-Palme, Chalmers University of TechnologyUnderstanding the Evolution of Pathogenicity: Predicting and Preventing the Disease Threats of the Future10:05Announcement of DDLS Annual Conference Best Poster Award10:15Coffee break10:45DDLS Fellow Talk: Tobias Andermann, Uppsala UniversityBig data approaches for assessing biodiversity value and potential11:05DDLS Fellow Talk: Fredrik Edfors, Royal Institute of Technology, KTHHarnessing the promise of next-generation plasma profiling for pan-cancer diagnostics11:25DDLS Fellow Talk: Clemens Wittenbecher, Chalmers University of TechnologyMetabolomics profiling generates candidate biomarkers for precision nutrition approaches11:45Panel discussion: Training in Data Driven Life ScienceChair: Carolina Wählby, Uppsala UniversityPanelists: Leslie Solorzano Vargas, postdoc at KINina Norgren, coordinator for DDLS education and training, Umeå UniversityKrzysztof Jurdzinski, PhD student at KTHDaniel Gedon, PhD student at UU12:30Joint conference lunchProgram updated 2022-11-12

Abstract

Cecilia Clemens
Designing molecular models with machine learning and experimental data. Cecilia Clemens.

The last years have seen an immense increase in high-throughput and high-resolution technologies for experimental observation as well as high-performance techniques to simulate molecular systems at a microscopic level, resulting in vast and ever-increasing amounts of high-dimensional data. However, experiments provide only a partial view of the molecular processes and are limited in their temporal and spatial resolution. On the other hand, simulations are still not able to completely characterize large and/or complex molecular processes over long timescales, thus leaving significant gaps in our ability to study these processes at a physically relevant scale. We present our efforts to bridge these gaps, by combining statistical physics with state-of-the-art machine-learning methods to design optimal coarse models for complex macromolecular systems. We derive simplified molecular models to reproduce the essential information contained both in microscopic simulation and experimental measurements.

Samuli Ripatti
Genetic variation and risk of common diseases over the life course. Samuli Ripatti.

Past 15 years have seen tremendous success in identifying genetic loci associated with common diseases and traits. Much of the current activities focus on strategies for inferring causal variants and genes driving these associations and on the potential translational opportunities arising from the genetic discoveries. I will highlight some of the opportunities, risks and gaps in our knowledge related to both causal inference and genetic prediction and translation. I will provide examples from FinnGen study (www.finngen.fi) consisting of genome wide profiles and longitudinal health registry data for half a million Finns and from a network on biobanks and machine learning/AI -methods developers in INTERVENE Consortium (https://www.interveneproject.eu).

Johan Bengtsson-Palme
Predicting the disease threats of the future. Johan Bengtsson-Palme

Our inability to restrain covid-19 to remain a local disease outbreak highlighted an important vulnerability in our preparedness for new infectious diseases – our inability to predict what the future disease agents might look like. This inability makes it impossible to preemptively monitor for potential future pathogens and makes it harder to quickly adapt existing disease surveillance to novel outbreaks. There is no guarantee that the next major outbreak will be viral – with increasing antibiotic resistance, multidrug-resistant bacteria may very well be the next pandemic. In this talk, I will discuss how we can predict which genes to look for to find future pathogens before they become widespread in clinics or among the general population, both in terms of genes responsible for pathogenicity and in terms of antibiotic resistance genes. I will also outline how surveillance for antimicrobial resistance could be adapted to also include markers for pathogenicity and thus allow us to prevent or constrain disease outbreaks early.

Fredrik Edfors
Harnessing the promise of next-generation plasma profiling for pan-cancer diagnostics. Fredrik Edfors

Cancer is one of our biggest worldwide health problems, causing almost 10 million deaths annually. Despite significant advancements in cancer therapy over the past three decades, diagnosis and treatment still have a great deal of opportunity for improvement.

Here, a total of 12 prevalent cancer types represented by more than 1,400 cancer patients’ plasma profiles of 1,463 proteins were evaluated in trace amounts of blood plasma taken at the time of diagnosis and prior to treatment. A group of proteins linked to each of the examined malignancies was found using ML-based disease prediction models. This precision medicine strategy has the potential to benefit from advances in proteomics and precision and personalized medicine.

Tobias Andermann
Big data approaches for assessing biodiversity value and potential. Tobias Andermann

Our human societies worldwide are having a profound negative impact on the natural world surrounding us, leading to experts declaring the current biodiversity crisis. However, to date it is difficult if not impossible to actually quantify the magnitude of our impact on biodiversity. This is largely due to the overwhelming complexity of biodiversity, which is not easily summarized and reduced into manageable metrics. Yet, solving this task is necessary and is arguably one of the biggest and most urgent contemporary challenges for the biological research community. In this talk I will discuss the utility of environmental DNA (eDNA) sequencing as a tool for gathering comprehensive biodiversity data in the field. I will touch upon the challenges and possibilities regarding the application of eDNA data for this purpose, in particular how these data can be applied to train AI models with the ability to model biodiversity and simulate changes thereof.

Scientific Committee

Tuuli Lappalainen, chair and DDLS Steering group member, Clemens Wittenbecher, DDLS Fellow, Simon Olsson, WASP and Johan Rung, Data Centre.

Organizing Committee

Project leader Erika Erkstam, Operations office, and the DDLS support team Heidi T Persson, Ulrika Wallenquist, Titti Ekegren.

Spatial and Single Cell Biology Webinar
2022-11-14 13:00 - 15:00 | Online event via Zoom
The Spatial and Single Cell Biology Platform at SciLifeLab invites you to a virtual event where you can learn about the service we provide within the field of spatial and single cell omics. Take the opportunity to learn about cutting edge methods including spatial transcriptomics with Visium, in situ sequencing, spatial proteomics using highly multiplexed imaging, spatial metabolomics with MALDI imaging and advanced FISH technologies. The presentations will be given by our experts in there respective methods, working within the platform.

The event is open for anyone to attend, who are interested in including spatial omics in their research projects or with a general interest to learn about the methods.

register here

TEM sample preparation practical course part II
2022-11-14 08:00 - 2022-11-18 17:00 | Kemiskt Biologiskt Centrum, Umeå University, Linnaeus väg 6, Umeå, 90736
TEM sample preparation course – Chemical fixation, high pressure freezing, plastic embedding and staining methods including practice on ultra-microtome sectioning, TEM imaging and an introduction to CLEM (Correlative Light and Electron Microscopy), FIB-SEM (Focused Ion Beam) and electron tomography.

Read more

Pre-requisite criterion: Basic EM course at UCEM or equal previous experiences of EM methods.

Participants will practice EM sample preparation and EM imaging with one sample from their own project. Our lab space limits the number of participants to 8 so we will select participants based on your motivation and how your project aims fits to the course content. Please write a short project description, a motivation for participating and what sample you would like to process during the course.

Please, look at the program and the methods that are covered in this course. Make sure you have time to participate full days and the entire week. Since the fixation and plastic embedding takes time, you should bring one test-sample to Agnieszka on Monday 7 of November, and a new test-sample on the first course day, 14 November.

Preliminary Program:The course preliminary program will be announced here once it is organised.

Location:Lectures at KBC and laboratory demonstrations at UCEM – Level 5, 6 + new EM building (Level 1), Umeå University.

Participants:8 persons. Open to all research students, postdocs and staff.

Instructors:

Sara Henriksson – EM research engineerGayathri Vegesna – EM research engineerAgnieszka Ziolkowska – EM research engineerCamilla Holmlund – EM research engineerLinda Sandblad – EM facility director

Duration:5 days

Breaks/Refreshments:Coffee, cookies and fruit will be served.

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

Credits:Students that attend all theoretical and practical parts of the course, will receive a certificate for 1,5 hp.

[Clinical Talks] Combining AI and in situ sequencing to explore the tumor micro-environment
2022-11-11 09:00 - 09:30 | Online event via Zoom
Carolina Wählby

Professor in quantitative microscopy, SciLifeLab and Dept. IT, Uppsala University

Carolina Wählby is professor in Quantitative Microscopy at the Dept. of Information Technology, Uppsala University, and Scientific Director of the National SciLifeLab Bioimage Informatics Unit. Her research is focused on developing computational approaches for extracting information from image data with focus on precision medicine and life science. Methods include traditional image analysis as well as AI and deep learning for understanding dynamics of cancer tissue, antibiotics susceptibility and spatial transcriptomics, funded primarily by the ERC TissUUmaps project and the Swedish Foundation for Strategic research. She received the SBI2 President’s innovation award in 2014 for her work on in situ sequencing, and the Thuréus prize in 2015 for development of open tools for image analysis. She is a member of the Royal Society of Sciences at Uppsala and the Royal Swedish Academy of Engineering Sciences. She has a MSc in molecular biotechnology and a PhD in digital image analysis, and carried out postdoc research within genetics and pathology. She was part of the Imaging Platform of the Broad Institute of Harvard and MIT in 2009-2015 and became full professor at Uppsala University in 2014. She is a member of the steering group of a 300M€ effort on Data Driven Life Science, funded by the Knut and Alice Wallenberg Foundation, with the ambitious goal of training the next generation of life scientists. Her heart lies in the intersection between life science and computational image analysis, and she is intrigued by the possibilities of technological developments and convergence of the scientific fields.

register to receive zoom link

Moderator: Päivi Östling, SciLifeLab

Clinical Talks

Clinical Talks is back for more! With a brand new and shiny Season 6. After successfully completing 5 seasons with > 70 enthusiastic Clinical Talkers to our record, we have barely scratched the surface of all the amazing work our clinical, academic and industry Life Science community has to offer. More about the upcoming events is available here.

These events are co-organized by Karolinska Institutet Innovations AB and SciLifeLab, and brought to you by Colibri Ventures.

Workshop on biomolecular simulations
2022-11-09 08:00 - 17:00 | Inghesalen, Tomtebodavägen 18a,, Solna, 171 65 171 65, Sweden
The main focus of ‘Biomoelcular simulations workshop’ is on molecular dynamics simulations of biomolecular systems. The target audience of this workshop is the researchers working in Sweden on biomolecular simulations. The goal of this workshop is to bring together all the researchers from Sweden interested in biomolecular simulations and to provide an opportunity to junior researchers in the field to present their work. This will be a single day event with some talks by other researchers from abroad and ample opportunities for discussion and interactions among the people in the field.

Confirmed speakers

Simon Olsson, Chalmers, GothenburgMilosz Wieczor, IRB BarcelonaMercedes Alfonso-Prieto, Forschungszentrum Jülich

Program and abstracts are collapsible items – click to expand.

Program
09:30Morning Coffee, MingleInghesalen, Karolinska Institutet09:55Welcome from organizersOrganizing Committee10:00Multiscale simulations to study proton transfer: from enzymes to membrane proteinsMercedes Alfonso-Prieto, Forschungszentrum Jülich, Germany10:40Exploring the selectivity profile of plant UDP dependent glycosyl transferases (UGTs) by computational and experimental studiesJunhao Li, Uppsala University11:00Multi-scale Modeling of Axonal Injury (coupling of finite element analysis with molecular dynamics simulations)Maryam Majdolhosseini, KTH Royal Institute of Technology11:20Coffee Break11:40A Machine-Learned Atomistic Force Field for Nucleic AcidsMiłosz Wieczór, IRB Barcelona12:20Combining evolution and physics with coevolution-powered machine learningDarko Mitrovic, KTH Royal Institute of Technology12:40Lipid-ethanol mixtures for topical drug delivery applications: A molecular dynamics and NMR studyAmanda Quinones Vallin, Stockholm University13:00Lunch14:00Machine learning to reconcile experiment and simulationSimon Olsson, Chalmers University of Technology14:40Effective Molecular Dynamics from Neural-Network Based Structure Prediction ModelsAlexander Jussupow, Stockholm University15:00Opportunities and Challenges in GPCR SBDD: Finding the Sweet SpotsPierre Matricon, Sosei Heptares15:20Wrap up, Thank youOrganizing Committee

Multiscale simulations to study proton transfer: from enzymes to membrane proteins
Mercedes Alfonso-Prieto, Assistant Professor, Forschungszentrum Jülich, Germany

Proton transfer (PT) is one the most common processes in biology. Studying PT at the molecular level is a challenging task, due to the intrinsic complexity of proteins, including their functional dynamics and the presence of several titratable residues. Therefore, combination of experimental and computational techniques is needed to obtain a more comprehensive picture. Recent methodological and software advancements have enabled the efficient application of quantum mechanics/molecular mechanics (QM/MM) simulations to (large) biological systems. This multiscale approach allows treating the region of the protein where PT takes place at the QM level, while including the effect of the rest of the protein and its environment at the MM level. In this talk, I will show some examples of QM/MM simulations applied to PT processes in different systems, from enzymes to membrane proteins. Such hybrid simulations have provided atomistic insights complementary to experiments.

A Machine-Learned Atomistic Force Field for Nucleic Acids
Miłosz Wieczór, Postdoctoral fellow, IRB Barcelona

We present a new paradigm for the parametrization of nonbonded interactions in molecular force fields directly from quantum chemical data. The proposed machine-learned force field (ML-FF) accurately reproduces well-validated quantum chemical interaction energies, as well as allows for the systematic incorporation of experimental data such as measured affinity constants. Contrary to many recently published general ML-FFs, our force field ensures stability in molecular dynamics simulations thanks to a combination of regularization and active learning, and permits gradual upgrades should issues arise in previously untested systems. Meanwhile, a simple embedding scheme allows the parameters learned from minimal methyl-nucleobase systems to be employed in simulations of large biomacromolecules at virtually no computational overhead. We also present several key directions for the future evolution of our force field, both in terms of accuracy and applicability.

Machine learning to reconcile experiment and simulation
Simon Olsson, Assistant Professor, Chalmers University of Technology

Long-time-scale and enhanced sampling molecular dynamics simulations reveal the approximations of classical molecular dynamics force fields disagreeing with experimental data. However, under ideal conditions, experiments and simulations observe the same process — consequently, by optimally balancing experimental and simulation data, we may build models extracting helpful information from both. In this talk, I will overview efforts in this direction and talk about Augmented Markov models, and their recent extension dynamic Augmented Markov models.

Registration

NBIS - Bioinformatics and data support at SciLifeLab
2022-11-08 12:00 - 13:00 | Birgit Thilander Lecture Hall, Academicum, Medicinaregatan 3, Gothenburg
NBIS – Bioinformatics and data support at SciLifeLab

Thomas Svensson

NBIS, National Bioinformatics Infrastructure Sweden, is a distributed national research infrastructure. We are the SciLifeLab bioinformatics platform and the Swedish node in Elixir, a European intergovernmental organisation bringing together life science resources from across Europe. We offer bioinformatics support, infrastructure and training.

SciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started 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.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

Assembly Room Birgit Thilander, Medicinaregatan 3

SciLifeLab Uppsala PhD&Postdoc Online Seminar Series - Immunology Theme
2022-11-08 11:00 - 12:00 | Online event via Zoom
Welcome back to the SciLifeLab Uppsala PhD&Postdoc seminar series!

This seminar will take place on Tuesday November 8th from 11h to 11:50h on Zoom (https://uu-se.zoom.us/j/66489618700)

For this occasion the speakers will be:

1. Tiarne van de Walle, PhD Student at Anna Dimberg and Magnus Essand’s Labs (Vascular Biology & Cancer Immunotherapy), Dept. of Immunology, Genetics and Pathology, Uppsala University

Title: Shining the LIGHT on Glioblastoma

Summary:
Glioblastoma is the most aggressive primary brain cancer and is resistant to immunotherapy, which is largely due to poor T cell infiltration. Here, we screened a panel of lymphoneogenic cytokines, from which we selected LIGHT/TNFSF14 as the most promising candidate for treatment of glioma. Then, we utilized a brain endothelial cell-targeted vector to express LIGHT on the glioma vasculature. Systemic treatment with this novel therapeutic agent resulted in prolonged survival, and promoted efficient T cell infiltration and anti-tumour immune responses. As such, our work demonstrates that tailoring the vascular phenotype through vessel-targeted expression of LIGHT is a promising therapeutic strategy, which has broader implications for treatment of other immunotherapy-resistant cancers.

2. Miguel Vizoso Patiñoi, Researcher at Mia Phillipson’s Lab (Immunology), Dept. of Medical Cell Biology, Uppsala University

Title: Uncovering the role of the innate immune cells in vascular remodeling during menstruation and associated pathologies

Summary:
More than 10% of women worldwide suffer from abnormal uterine bleeding (AUB). Current standardized therapies for AUB include ovulation blockade and hysterectomy, which both are highly aggressive and interfere with fertility. Thus, there is an unmet clinical need for more effective and non-invasive treatments. The scarcity of efficient therapies is at least partly due to the lack of reproductive experimental models, as well as that the underlying mechanisms resulting in AUB are largely unknown. However, innate immune cells have been documented to be actively recruited to the endometrium during physiological menstrual cycle and pregnancy. Based on our recent discoveries of a pro-angiogenic subpopulation of neutrophils, in addition to novel functions of macrophages important for blood-vessel maturation, I will in this project, define the contribution of innate immune cells in the vascular phenotype of AUB. The main goals addressed by 2 work packages (WPs) are:

To develop the first humanized murine uterus to characterize how human endometrial epithelial cells (hEECs) participate of the vascular network remodeling in vivo. To this end, EECs from healthy and AUB donors will be orthotopically transplanted in immunocompromised mice and its impact on vasculature remodeling will be measurable in real time by intravital microscopy upon menstrual cycle induction. Samples will be also submitted for scRNAseq to reveal the transcriptomic networks connecting the epithelium (human-origin) and stroma/endothelium (murine-origin) compartments at different time points of the menstrual cycle.
To assess whether the role of the innate immune cells in endometrial angiogenesis and vascular pruning differs depending on their interaction with healthy or pathogenic (AUB) derived hEECs.

Thus, this project will provide a novel model to study endometrial human physiology in vivo, to enable the discovery of new mechanisms involved in AUB. Generated insights will then be used to pursue opportunities to translate the findings into clinical practice and provide non-invasive therapies to treat AUB disorders.

KBC DAYS 2022
2022-11-08 08:00 - 2022-11-09 17:00 | Carl Kempe-salen, KBC Building, Umeå University, Umeå, Sweden
We cordially invite you to join us for the Celebration of the 15th anniversary of KBC on 8 November and to attend the KBC DAYS 2022 conference with the main theme “Big data” on 8-9 November!

When: Tuesday, 8 November – Wednesday, 9 November 2022

Where: Carl Kempe salen (KB.E3.03) (MAP) and other locations at KBC

We invite you to participate in the KBC DAYS, an annual interdisciplinary conference, which will be back to a physical format this year after two years of digital events! Our aim is to foster collaborations between different departments and research centres affiliated with the Chemical Biological Centre, KBC, including departments from two faculties from Umeå University as well as from the Faculty of Forest Sciences from SLU.

A scientific focus this year will be on “Big Data“. We welcome you to listen to the plenary lectures and other presentations discussing different aspects, advantages and challenges of analysing, interpreting and handling big data.

Update yourself about the research infrastructures available in Umeå, get to know more about their services and join the guided tours to their facilities!

Come and listen to exciting scientific talks from new faculty members of the KBC environment, awardees and researchers that received major grants in the last year, presentations by PhD students and selected talks by young researchers from the Umeå Postdoc Society (UPS)!

We invite postdoctoral researchers from Umeå University and SLU Umeå to give a scientific talk during this year’s KBC DAYS. We especially encourage submissions from research related to this year’s topic, Big Data. We have a total of four 15-minutes slots (12 minutes talk + 3 minutes Q&A). Interested in presenting your work? Fill in the form and hit submit (before 20 October): https://forms.office.com/r/YFHYHXDuyF

This year, two special events will be dedicated to celebrating the 15th anniversary of KBC! Join for the panel discussion with those who contributed to the establishment and development of KBC to reminisce about how it all started, highlight what has been achieved, and discuss future visions for research and collaboration at KBC! The celebration gala dinner will be held on the evening of 8 November (more details and the program will be announced later).

In the frame of the celebration activities, we open a photo contest, “KBC is…” and invite you to express in 1-3 photos and share your vision of what KBC is for you.

Check your photo archives or shoot new ones and submit your photo(s) already now but no later than Monday, 7 November (23:59h) following this link: https://pollunit.com/polls/kbc_photo_contest_2022. You will also find detailed rules of the contest on this webpage.

The voting will take place, and the winner will be announced during the KBC DAYS, 8-9 November.

The contest is open to the participants of the KBC DAYS and everyone else related to the KBC environment!

If you have more photos related to the KBC history and past events in your archives, we will be more than happy to use these photos in a slide show during the KBC anniversary celebration! Please send these photos to info.kbc@umu.se!

[The Svedberg] - Studying microRNA functions at the single-cell level
2022-11-07 15:15 - 16:15
MicroRNAs are gene regulatory molecules that play important roles in numerous biological processes including human health. The function of a given microRNA is defined by its selection of target transcripts, yet current state-of-the-art experimental methods to identify microRNA targets are laborious and require millions of cells – hampering the entry of the microRNA field into the single-cell era. We have overcome these limitations by fusing the microRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing for the first time the detection of microRNA targets transcriptome-wide in single cells. Our agoTRIBE method reports functional microRNA targets which are additionally supported by evolutionary sequence conservation. As a proof-of-principle, we study microRNA interactions in single cells, and find substantial differential targeting across the cell cycle. In addition to presenting this single-cell project, I will talk about our recent efforts to sequence RNA fragments from ancient animal samples that are preserved in the Siberian permafrost.

Marc Friedländer is an associate professor at Stockholm University, Department of Molecular Biosciences. He graduated from his master’s thesis under the supervision of Anders Krogh in Copenhagen and his PhD in the group of Nikolaus Rajewsky in Berlin. He founded his own lab in Stockholm with funding from a SciLifeLab Fellowship and an ERC starting grant. His team is balanced between wet-lab and dry-lab biologists, and they develop and apply experimental and computational methods to understand gene regulation – with particular emphasis on microRNAs. His lab has studied these molecules in the context of space exposure (a collaboration with NASA); in ancient animal samples preserved in permafrost; and in mammalian single cells.

Webpage: www.friedlanderlab.org

Campus Solna Seminar Series: Sami Saarenpää and Vaishnovi Sekar
2022-11-03 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:

Sami Saarenpää

Stefania Giacomello – alpha 3

Spatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics

Vaishnovi Sekar

Marc Friedländer – gamma 5

agoTRIBE detects miRNA-target interactions in single cells

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

Bioinformatics and Data Center - A bioinformatics hub supporting biomedical and clinical research
2022-11-01 12:00 - 13:00 | Birgit Thilander Lecture Hall, Academicum, Medicinaregatan 3, Gothenburg
Bioinformatics and Data Center – A bioinformatics hub supporting biomedical and clinical research

Marcela Davila / Per Sikora

In this seminar, we will present the new setup for bioinformatics and infrastructure support at Core Facilities. The Bioinformatics and Data Centre provides high-throughput techniques for biomedical, clinical and pre-clinical research; a wide range of support in bioinformatics and statistics is available – from short term consulting to long term project support and training; general consulting and support for HPC hardware and software infrastructure development and storage for “big data”.

SciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started 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.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

Assembly Room Birgit Thilander, Medicinaregatan 3

Long-Read Sequencing Uppsala Meeting 2022
2022-10-31 08:00 - 2022-11-02 17:00 | Universitetsaulan, Biskopsgatan 3, Uppsala, Sweden
In recent years, long-read DNA sequencing has replaced short-read technologies as the gold standard solution for a wide range of genomics applications. In addition to producing high quality de novo genome assembly, long-read technologies can be used to study complex structural variation, full-length RNA isoforms, detection of epigenetic signals, and much more. The adaptation of long-read sequencing is sweeping through several areas of the life sciences including agricultural, environmental, and medical research.

Join us in Uppsala for a three-day event to catch up with the latest developments in long-read sequencing technologies and their applications, get inspired by peers presenting their research, and enjoy discussions with leading experts and company representatives.

Read more

Seminar: Single cell and spatially resolved epigenomics
2022-10-28 10:20 - 11:00 | Online event via Zoom
Spatial omics has emerged as a new frontier of biological and biomedical research. In particular, spatial transcriptomics has enabled genome-scale gene expression mapping with spatial resolution in tissue sections. So far, the ability to capture spatial epigenetic information at the cellular level and genome scale has been lacking. This talk will describe recent advances in spatial epigenomics (ATAC-seq, CUT&Tag), single cell epigenomics, and how they can be applied to study multiple sclerosis.

Speaker

Prof. Gonçalo Castelo-Branco is the Professor of Glial Cell Biology at the Department of Medical Biochemistry and Biophysics at Karolinska Institutet, Stockholm, Sweden. Prof. Castelo-Branco received his PhD in Medical Biochemistry in 2005, working on development of dopaminergic neurons and neural stem differentiation. He completed post-doctoral fellowships first at the Karolinska Institutet and then at the University of Cambridge, United Kingdom, working in neural and pluripotent stem cells and chromatin. Prof. Castelo-Branco started his research group in 2012, focusing on the molecular mechanisms defining the epigenetic state of cells of the oligodendrocyte lineage. The main focus of Prof. Castelo-Branco’s research group is to investigate how distinct epigenetic states within the oligodendrocyte lineage are established, by identifying key transcription factors, chromatin modifying complexes and non-coding RNAs that are involved in epigenetic transitions, using technologies such as RNA-Seq (single-cell and bulk), quantitative proteomics and epigenomics, among others. The long term aim of this research group to design epigenetic based-therapies to induce regeneration (remyelination) in demyelinating diseases, such as multiple sclerosis.

Lab website

ZOOM link

Contact: Jakub Westholm, SciLifeLab Bioinformatics Long-term Support

Developing therapies for the inherited bone marrow failure syndrome diamond-blackfan anemia
2022-10-27 15:30 - 17:00 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Johan Flygare

Docent, MD and PhD, Department of Laboratory Medicine, Lund University

Host: Mikael Lindström, Docent and PhD

October 27 at 3.30 pm

Seminar room: Air & Fire

Organizers: CBCS-KI and PhenoTarget Research Community Program

Campus Solna Seminar Series: Kathleen Watt and Mateusz Garbulowski
2022-10-27 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:

Kathleen Watt

Ola Larsson – gamma 5

Hypoxia-induced transcription start site switching remodels 5’UTRs driving translational reprogramming in breast cancer

Mateusz Garbulowski

Erik Sonnhammer – gamma 7

Gene regulatory network inference of RNA binding proteins

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

Swedish Bioinformatics Workshop
2022-10-27 08:00 - 2022-10-28 17:00 | Naturvetarhuset, Umeå University, Umeå
This year SBW will take place at Umeå University, October 27-28. The two days will be filled with inspiring talks, including keynote talks by Kerstin Lindblad-Toh (Uppsala University/Broad Institute), Debora S. Marks (Harvard University), and Simon Anders (Heidelberg University). There will also be three parallel hands-on workshops, a poster session, and a social event.

The target group is traditionally PhD students and postdocs working with any kind of bioinformatics and computational biology. This workshop aims to bring together talented students and young researchers across faculties and universities from throughout the country.

Visit sbw2022.com to register and view the programme. Registration will be open until 23rd September.

Read more

6th Uppsala Transposon Symposium
2022-10-26 12:00 - 2022-10-28 12:00 | Friessalen, Evolutionary Biology Centre, Norbyvägen 14, ground floor, Uppsala, 75236, Sweden
We are excited to announce that the 6th Uppsala Transposon Symposium – integrating transposon and virus identification into evolution and disease research will be on October 26-28 in Uppsala. This year, we have an in-person symposium with abstract submission, a livestream for virtual attendance + questions, and an interactive workshop with tool developers. Day 3 will be dedicated to a tools and database workshop. This will be a unique opportunity to discuss ideas, meet experts, and showcase contributions. Tool developers from RepeatModeler/Masker, Repbase, dfam, TE-hub, etc. will all be in Uppsala!

Virtual attendants can ask written questions that the chair will read out for the in-person audience. You will have the chance for networking with fellow virtual attendants during the coffee breaks.

Abstract submission deadline is September 23, and we encourage especially early-career transposon researchers to submit an abstract for regular talk or lightning talk with poster.

As previously for this symposium, registration will be free of charge, and especially early-career scientists are encouraged to submit an abstract for a regular talk or poster with lightning talk. The free in-person attendance includes coffee/tea/snacks + >1 meal, (and other meals at a student-friendly price).

Please follow the link for a detailed program, more information and to register! The registration is open.

#UppTransposon2022

Event webpage more Information

If you are looking for a second reason (apart from Uppsala October weather) to travel to Uppsala, note that the Long-Read Uppsala meeting (Oct 31-Nov 02) will be directly after the Uppsala Transposon Symposium. Abstract submission deadline for LRUA2022 is September 01.

Confirmed speakers:

Irina Arkhipova (Marine Biological Laboratory) [keynote 1]John Coffin (Tufts University) [keynote 2]Kenji Kojima (Genetic Information Research Institute)Alice Eunjung Lee (Harvard University)Gayle McEwen (Leibniz Institute for Zoo and Wildlife Research)Arian Smit (Institute for Systems Biology)Björn Nystedt (SciLifeLab)

Organizing committee:

Alexander Suh (University of East Anglia and Uppsala University)Claudia Kutter (Karolinska Institute)Patric Jern (Uppsala University)

Contact us: transposonsymposium@gmail.com

XPS Platform: Nobel prized technique to study surface and interfaces
2022-10-25 12:00 - 13:00 | Glasburen Seminar Room, Chemical Biological Centre (KBC) Building, Umeå University, Umeå, 901 87, Sweden
In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”, the seminars will be organised every second Tuesday during autumn 2022. The seminars will be held in a hybrid format IRL in Glasburen, KBC, and online via Zoom. Take the chance to get information on facilities, possibilities and services that infrastructure, both SciLifeLab-associated and local, can offer! Learn more about the seminar series and the schedule for autumn 2022 here: https://www.umu.se/en/research/infrastructure/medicinska-fakulteten/u/umea-centre-for-electron-microscopy-ucem/scilifelab-in-umea/scilifelab-site-umea–kbc-infrastructure-seminar-series/

On October 25th, 12:00-13:00, you are welcome to participate in the seminar

XPS Platform: Nobel prized technique to study surface and interfaces

by Andrey Shchukarev, manager of the XPS Platform and research fellow at the Department of Chemistry, Umeå University

More information about the infrastructure: https://www.umu.se/en/research/infrastructure/xps/

Seminar description: XPS Platform seminar covers the basics of X-ray Photoelectron Spectroscopy (XPS or ESCA) and focuses on XPS applications to probe real surfaces and interfaces in nature and life.

Read more

Registration deadline: Monday, 24 October, 10:00.

Online attendance: You can also join the seminar on Zoom, https://umu.zoom.us/j/63138997026 (registration is not required)

Organisers: SciLifeLab Site Umeå and Chemical Biological Centre (KBC)

Swedish NMR Centre - NMR in life sciences
2022-10-24 12:00 - 13:00 | Birgit Thilander Lecture Hall, Academicum, Medicinaregatan 3, Gothenburg
Swedish NMR Centre – NMR in life sciences

Göran Karlsson, Swedish NMR Centre, SciLifeLab Göteborg

The Swedish NMR Centre is a national research infrastructure offering metabolomics, protein-drug interaction studies and protein structure and dynamics characterization.

SciLifeLab is a national infrastructure within life science with a wide range of advanced technology and expertise. The newly started 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.

A light lunch will be offered during the talks for those joining on site. Online participation via Zoom is also available, please click the zoom-link below to join the event at the appointed time.

Venue

Assembly Room Birgit Thilander, Medicinaregatan 3

Epigenomics Data Analysis: from Bulk to Single Cell (ONLINE)
2022-10-24 09:00 - 2022-10-28 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: 2022-09-23

Confirmation to accepted students: 2022-09-30

Responsible teachers

Agata Smialowska, Jakub Orzechowski Westholm, Vincent van Hoef

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

COURSE WEBSITE

APPLICATION

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.

3D-Equivariant Graph Neural Networks for Refining and Evaluating Protein Structures
2022-10-21 11:00 - 12:00 | Online event via Zoom
Speaker:

Jianlin Cheng, Department of Electrical Engineering and Computer Science at the University of Missouri, Columbia, USA.

Title3D-Equivariant Graph Neural Networks for Refining and Evaluating Protein Structures

Abstract

Deep learning is revolutionizing the prediction of protein structure and is close to solve this grand challenge hanging over the scientific world for many years. In this talk, I will describe how this technology emerged in the field, how it overcame various technical hurdles to reach a high accuracy of predicting protein structures as demonstrated by AlphaFold2, and where it is going now. I will present our latest work of applying 3D-equivariant graph neural networks with self- attention to evaluate and refine protein structural models. Our experiments demonstrate that 3D-equivariant graph network networks that are robust against the rotation and translation of 3D objects can evaluate and improve the quality of protein structures more effectively than the existing methods.

[Clinical Talks] Stanford Ignite: Lessons learned from teaching entrepreneurs
2022-10-21 09:00 - 09:30 | Online event via Zoom
Yossi Feinberg

The Adams Distinguished Professor of Management and Professor of Economics at Stanford Graduate School of Business (GSB)

Yossi Feinberg received his PhD in Mathematics from the Hebrew University in Jerusalem in 1997. His thesis studied how differing prior beliefs of decision makers can be expressed by their disagreement on current (posterior) events. After completing his dissertation under the supervision of Nobel Laureate Professor Robert J. Aumann, Yossi began teaching economics at Kellogg Graduate School of Management. Yossi joined Stanford GSB in 1998.

Yossi’s teaching interests include Economics of Organization, Managerial Economics, Strategy, Information Markets, Game Theory and Applied Decision Making. In 2003 he received the MBA distinguished teaching award.

Yossi’s recent research interests include, for example, the analysis and implication of strategic decision making in the face of unawareness. He has modeled games with unawareness and their solutions. In these games each decision maker can reason about the extent to which others may only have a limited perception of the full scale of the economic interaction at hand. Yossi was an Associate Editor of the Journal of Economic Theory and is serving as a referee for all major microeconomics journals. He has given numerous invited seminars as well as multiple plenary talks at academic conferences.

He has been consulting in a wide range of industries including hi-tech, media and healthcare as well as giving invited talks on topics such as pricing, the sub-prime crisis, in-house vs. outsourcing, allocating decision power in organizations and strategic interactions.

He is the faculty director of Stanford Ignite, a global innovation program running on the Stanford Campus.

register to receive zoom link

Stanford Ignite

Stanford Ignite grew out of a new kind of entrepreneurial educational program initiated in 2006 and spearheaded by Professor Yossi Feinberg. In aggregate, about 1,600 past participants have started more than 100 successful companies since the program was introduced.

Stanford Ignite is a certificate program that provides the business fundamentals necessary to succeed at any entrepreneurial or intrapreneurial venture. Business concepts learned in the classroom span core business skills and functional skills, and are reinforced through practical application with team venture projects, where participants work by project-based learning approach, in teams of five or six to develop a new product or service for an existing organization or a new venture.Previous participants include graduate students currently pursuing a master’s, MD, PhD, or post-doc program in a nonbusiness field, with a strong representation from the Life Sciences area. A key attribute to of the success of the program is the close academic experience it offers. Participants engage directly with the same renowned faculty that teach in the Stanford MBA Program. Participation in real-time lectures, case evaluations, Q&A sessions, small group discussions, workshops, panels, and team projects. The program also features guest speakers from leading companies, many of whom become venture-project mentors.

Key Benefits

Stanford Ignite –is a certificate program that provides the business fundamentals to succeed at any entrepreneurial ventures.

Learn fundamental business concepts from core business frameworks to tactical skills.Reinforce and apply lessons learned by working on a team to develop a new product or service.Improve communication, elevator pitch, and presentation skills in a daylong communications bootcamp.Present your idea and get robust feedback from venture capitalists, angel investors, industry experts, and experienced entrepreneurs.

Clinical Talks

Clinical Talks is back for more! With a brand new and shiny Season 6. After successfully completing 5 seasons with > 70 enthusiastic Clinical Talkers to our record, we have barely scratched the surface of all the amazing work our clinical, academic and industry Life Science community has to offer. More about the upcoming events is available here.

These events are co-organized by Karolinska Institutet Innovations AB and SciLifeLab, and brought to you by Colibri Ventures.

Campus Solna Seminar Series: Simin Zhang
2022-10-20 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:

Simin Zhang

Sean Rudd – alpha 5

Targeting nucleotide catabolic enzymes to improve chemotherapies

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

The 8th RIKEN-KI-SciLifeLab Symposium
2022-10-20 09:30 - 16:30 | Air&Fire, SciLifeLab Stockholm, Tomtebodavägen 23A, Solna, Sweden
Preparing for the next pandemic

COVID-19 pandemic responses were organized by countries according to their needs. The preparations for responses to potential future pandemics are currently addressed by organizations including RIKEN, Karolinska Institutet and SciLifeLab with prominent roles in Japan and Sweden, respectively. This symposium event, which is part of the RIKEN-KI-SciLifeLab Symposium Series, addresses the political, organizational and practical aspects of preparedness for potentially upcoming pandemics with focus on Japan and Sweden.

This symposium is co-organized and sponsored by JSPS Stockholm Office.

Date and location 2022-10-20 (THU)

09:30-16:30 Symposium

16:30-18:00 Social mingle

Download Program (PDF)

Registration

Symposium history

Each symposium of the series is centered on one specific topic. Topics from previous years are: Molecular Imaging and Genomics (2014), Structural Biology for Drug Discovery (2015), Decoding Health and Disease with a) Imaging & Disease, b) RNA & Disease, c) Single, Rare and Stem cells & Disease (2016), Life Science Frontiers in Health, Disease and Aging, with sessions a) Gene Expression in Disease and Aging, b) Neural Function, Disease and Therapy, c) Molecular Aspects of Health, Disease and Aging, d) Visualizing Health, Disease and Aging, e) Molecular Network Control (2017), Artificial Intelligence meet Life Sciences (2018), and Biomedical Data for Artificial Intelligence (2019, 2020).

The Protein Expertise Platform - a Core Facility at the KBC and a node of PPS
2022-10-18 12:00 - 13:00 | Glasburen Seminar Room, Chemical Biological Centre (KBC) Building, Umeå University, Umeå, 901 87, Sweden
In the frame of the “SciLifeLab Site Umeå / KBC Infrastructure Seminar Series”, the seminars will be organised every second Tuesday during autumn 2022. The seminars will be held in a hybrid format IRL in Glasburen, KBC, and online via Zoom. Take the chance to get information on facilities, possibilities and services that infrastructure, both SciLifeLab-associated and local, can offer! Learn more about the seminar series and the schedule for autumn 2022 here: https://www.umu.se/en/research/infrastructure/medicinska-fakulteten/u/umea-centre-for-electron-microscopy-ucem/scilifelab-in-umea/scilifelab-site-umea–kbc-infrastructure-seminar-series/

On October 18th, 12:00-13:00, you are welcome to participate in the seminar

The Protein Expertise Platform – a Core Facility at the KBC and a node of PPS

by Uwe Sauer, Associate professor, PEP coordinator, Department of Chemistry, Umeå University

Read more

Seminar description: Proteins play a central role for most cellular processes. In order to study such processes, Swedish Life-Science researchers rely on high-quality protein reagents for their research. At the Protein Expertise Platform (PEP) at the Dept. of Chemistry and the KBC, we work with the custom production of recombinant proteins in E. coli and plant cell suspensions. We have teamed up with six other Swedish protein production platforms and, since 2022, are part of Protein Production Sweden (PPS), a national research infrastructure for protein production (www.gu.se/pps) funded by VR and the local Universities. PPS provides expert competence in a variety of expression systems, including E. coli, insect cells, P. pastoris, plant cells and cell-free translation. The PPS nodes collaborate in the form of a national distributed research infrastructure and provide expertise in gene and vector design, production and purification of the proteins, as well as methods for quality control. PPS can also produce proteins with different labels.

Researchers can apply for project support through a common application portal found on the PPS website.

Registration: To register your physical attendance and reserve your free sandwich, please go to the registration Link: https://www.umu.se/en/chemical-biological-centre/kbc_events/registration-form-infrastructure-seminar/

Registration deadline: Monday, 17 October, 10:00.

Online attendance: You can also join the seminar on Zoom, https://umu.zoom.us/j/63138997026 (registration is not required)

More information about PEP: https://www.umu.se/en/research/infrastructure/pep/

Organisers: SciLifeLab Site Umeå and Chemical Biological Centre (KBC)

[The Svedberg] - Manfred Schartl
2022-10-17 15:15 - 16:15
Developmental Biochemistry, University of Würzburg, Germany

Time: 15:15Venue: C8:305, BMC, Uppsala

Host: Leif Andersson, Uppsala University

Title of the talk: Evolution of sex determination and sex chromosomes in fish

Bio: Prof. Manfred Schartl studied Biology and Chemistry at the University of Giessen, Germany, and graduated in Genetics. After postdoctoral research in Giessen and at the NIH in Bethesda he was team leader of a research group from 1985 to 1991 at the Gene Center of the Max Planck Institute for Biochemistry in Martinsried, Germany. Until 2019 he was full professor and chairman of Physiological Chemistry at the Biocenter of the University of Würzburg. Currently, he heads a research group as senior professor at the Biocenter and works as scholar in residence at the Xiphophorus Genetic Stock Center at Texas State University in San Marcos. He is member of the German Academy of Sciences, Leopoldina, and the European Academy of Sciences, Academia Europea. He holds an honorary doctorate from the University of Bergen, Norway.He uses the small aquarium fish biomedical models Xiphophorus and Medaka to understand molecular processes of organ development and their malfunction in disease with a focus on pigment cells and melanoma and another one on sex determination and gonad development. Key to his research is taking an evolutionary perspective to answer these questions on the basis of comparative genomics and molecular biology experimental studies.

Abstract: Sex determination (SD) is unique biological process in showing an astonishing plasticity of mechanisms. Fish present the greatest variability of SD amongst vertebrates. In the case of genetic SD this is linked to a similarly high variability of sex chromosome differentiation. While in a handful of species with genetic SD the master SD genes have been identified, their molecular function in directing the development of the bipotential gonad primordium towards testis or ovary is unclear in many cases or incompletely known in the others. To obtain a deeper understanding of this diversity we need a better knowledge of the molecular basis of SD mechanisms and the structure and genetic organization of sex chromosomes across a broad diversity of fish. To identify sex chromosomes and primary SD genes, we use high throughput RAD-tag marker mapping, transcriptomics, Pool-Seq and whole genome sequencing to identify sex-specific chromosomal regions and candidate SD genes in sharks, sturgeons and teleosts. This led to the identification of sex-specific markers, allowing to delineate the extent of recombination suppression, which turned out to be highly variable between species. We identified several species with clear cut XX/XY or ZZ/ZW monofactorial systems but also species with more complex sex-determination systems including species with a mix of genetic SD and environmental SD and species with potential polygenic systems. In species with available genomic resources, sex-specific markers could be used to assign scaffolds to regions that are supposed to contain the primary SD gene. We identified candidate genes in several species and find that most of them belong to already known factors of the primary SD regulatory network including candidate genes that have not been found so far as being SD genes. We also find that many species harbor very poorly differentiated sex-chromosomes. The SD variety does not follow a phylogenetic pattern, and turnovers of the genetic SD system from male to female heterogamety and vice versa are frequent in some groups, making the evolutionary instability of SD a spectacular trait whose biological meaning is not yet understood.

Facility Forum
2022-10-17 10:00 - 2022-10-18 14:00 | Djurönäset, Seregårdsvägen 1, Djurhamn
Facility Forum is a two-day event exclusively for the SciLifeLab infrastructure community, including platform and unit leadership, staff, and administrative personnel, as well as central management and support teams.

The event aims to bring everyone updated on what is cooking at SciLifeLab, promote cross-platform and cross-unit interactions, and enable discussions on urgent topics related to infrastructure operations. We offer inspiring talks, network activities, discussions in parallel sessions, and dinner with entertainment in the evening on day one. The second day is devoted to platform-wise activities and ends with a joint lunch. We have a maximum number of participants (400p).

Your participation includes the following:

Bus from/to Cityterminalen, Tomtebodavägen Solna or BMC Uppsala

Conference program

Lunches and coffee breaks

Teamwork activity

Conference dinner

Overnight stay in a single/double room (only for participants of Day 1+2)

Bus transport to Djurönäset, Oct 17

Departure from BMC Uppsala at exactly 07:15

Departure from Tomtebodavägen 23, Solna at exactly 08:00

Departure from Cityterminalen, Stockholm at exactly 08:30(Gate number is shown on the digital screens inside the terminal building, 30 minutes before departure)

Bus transport from Djurönäset, Oct 18

14:00 Busses to Cityterminalen, BMC Uppsala, and Tomtebodavägen departs from Djurönäset

Bus transport to Fågelbrohus, evening Oct 17 and morning Oct 18

The event is fully booked, and accommodation (single room) at Fågelbrohus (about 10 minutes by bus) has been arranged for the latest registered participants. The Fågelbrohus residents are welcome to use the SPA at Djurönäset before dinner.

22:00 Bus departs to Fågelbrohus

23:30 Bus departs to Fågelbrohus

08:30 Bus departs to Djurönäset from Fågelbrohus

Program

Download Program

Program
October 17

09:00Coffee, sandwich, and registration10:00Welcome. SciLifeLab talk show with guests, Stora KongressenShort break 11:00-11:30 and 12:00-12:10 12:45Conference lunch13:45Drop-in Poster session and coffee, Stora Kongressen14:30Teamwork activity, instructions from the stage, Stora KongressenCoffeeCheck-in15:30Parallel sessions (see Workshops A-G below) 17:00Free time, SPA available18:15Aperitif and music, Lounge, main building19:00Conference dinner and entertainment

October 18

09:00Platform-wise program09:00 Platform-wise programClinical Genomics, House 7, Room Lilla KongressenOperations office/SISU, Room 1K+1ASpatial and Single Cell Biology, Room 2AGenomics, Room 3ADDD, Room, 4ABioinformatics, Room 5AClinical Proteomics and Immunomonitoring, Room 6ACBGE, Room 1ECellular and Molecular Imaging, Room 2EIntegrated Structural Biology, Room 3EMetabolomics, Room 4EData center, Room 5E09:30Coffee is served in the lounge, outside the meeting rooms from 09:30-11:00. Special requirements in House 6.12:45Conference lunch14:00Bus transfer

Workshops

SciLifeLab Training Hub
Meet the team for the SciLifeLab Training Hub to discuss how training, courses, lifelong learning, and education of the infrastructure users should be organized in a nationally coordinated model to optimally serve both the platforms and the Swedish life science research community.

Location: ROOM 6A

Workshop leader

Jessica Lindvall

How do you reach out? – Improve your communication skills
Reflections and advice on reaching out to target groups outside science with a focus on presentation techniques.

Contents include

Five core principles of effective communication

Popularizing science – some hands-on advice

The Five Ps: Planning, Preparing and Performing Persuasive Presentations

Preparing an elevator pitch – a walkthrough

Practical advice for connecting with the audience

Location: ROOM 2A

Workshop leader

Olle Bergman

How to serve academic vs non-academic infrastructure users and the work towards harmonized SciLifeLab models
Meet the SciLifeLab External Relations Office and SciLifeLab/KTH lawyer to discuss models to interact with different user categories, user fee policies, priorities, contracts, legal aspects, and intellectual property rights.

Location: ROOM 4A

Workshop Leader

Josefin Lundgren Gawell

IT and data management services for SciLifeLab infrastructure
Meet representatives from SciLifeLab Data Centre to find out about services available for your platform/unit and to discuss future needs. Learn about the Data Centre plans and how to get involved in testing of upcoming systems and services.

Location: ROOM 3A

Workshop leader

Hanna Kultima

Precision medicine at SciLifeLab
How can the infrastructure contribute to implementation of precision medicine into routine clinical care in Sweden? An interactive workshop and discussion with representatives from the SciLifeLab Precision Medicine team.

Location: ROOM LILLA KONGRESSEN, 7A

Workshop leader

Åsa Johansson

Quality aspects of infrastructure operations, data handling and scientific output
In the light of the recommendations from our International Advisory Board, this workshop will focus on discussions on how to increase the quality of the research that is facilitated by the infrastructure. This involves among other things aspects of the service repertoire, modes of operation, cross-platform interactions, and data handling.

Location: ROOM 1A

Workshop leader

Annika Jenmalm Jensen

Planetary Biology – understanding ecosystems from molecular to planetary scale
Meet the scientific leads of the recently launched Planetary Biology capability at SciLifeLab and find out more about the mission and vision. Brainstorm with us about what technologies and methods in the SciLifeLab infrastructure toolbox could be of value to the target research community in visionary and forward-looking discussions.

Location: ROOM 5A

Workshop Leaders

Stefan Bertilsson & Olga Vinnare Pettersson

Important information

Registration: Registration has closed, and we have a waiting list. We have 400 p. registered for Facility Forum.

Cancellations: In the unfortunate case that you need to cancel your participation, send an email to infra@scilifelab.se ASAP so we can have someone from the waiting list take your place.

Parallel sessions: All the participants have been granted their first choice of workshop.

Overnight stay: Only participants of Day 2 are allowed the overnight stay. We have exceeded the number of rooms available at Djurönäset, så the last registered persons will stay at Hotel Fågelbrohus. A bus transfer from/to Djurönäset (about 10 minutes) will be provided in the evening and the morning. We have used the first-come-first-served principle, and a large number of people are accommodated with a roommate. All double rooms have separate beds. If you can stay in a double room, let us know your room mate.

Conference dinner: If necessary, priority will be given to people participating for two days.

Getting there by public transport: Visit www.sl.se and make a query for your journey – e.g. from T-centralen to Djurönäset. Bus 433 and bus 434 departs regularly from Slussen to Djurönäset.

For questions about Facility Forum, please contact infra@scilifelab.se

Organizing committee

Chair: Annika Jenmalm Jensen, SciLifeLab Infrastructure Director

Operations office: Erika Bergqvist Erkstam, project leader, Maria Bäckström, David Gotthold, Lars Johansson, Alice Sollazzo, Samuel Avraham, Charlotte Stadler, Björn Nystedt, and with fantastic support from the Platform Coordination Officers.

The Dark Side of Science: Misconduct in Biomedical Research
2022-10-14 15:30 - 17:00 | Online event via Zoom
Researchers in all stages of their career are welcome to attend and could find the talk useful. Kindly feel free to extend the invitation to your home universities.

Flyer-BAM-Elisabeth-BikDownload

Science builds upon science. Even after peer-review and publication, science papers could still contain images or other data of concern. If not addressed post-publication, papers containing incorrect or even falsified data could lead to wasted time and money spent by other researchers trying to reproduce those results. Several high-profile science misconduct cases have been described, but many more cases remain undetected. Elisabeth Bik is an image forensics detective who left her paid job in industry to search for and report biomedical articles that contain errors or data of concern. She has done a systematic scan of 20,000 papers in 40 journals and found that about 4% of these contained inappropriately duplicated images. In her talk she will present her work and show several types of inappropriately duplicated images and other examples of research misconduct. In addition, she will show how to report scientific papers of concern, and how journals and institutions handle such allegations.

Elisabeth Bik, PhD is a Dutch-American microbiologist who has worked for 15 years at Stanford University and 2 years in industry. Since 2019, she is a science integrity volunteer and consultant who scans the biomedical literature for images or other data of concern and has reported over 6,000 scientific papers. Her work has resulted in over 900 retracted and almost 1,000 corrected papers.

Who the event is aimed at i.e., who will attend: Researchers in all stages of their career are welcome to attend and could find the talk useful. Kindly feel free to extend the invitation to your home universities.

Speakers: Dr. Elisabeth Bik

[The Svedberg seminar] Prof. Jay Hinton
2022-10-13 15:15 - 16:30
University of Liverpool, UK

Time: 15:15Venue: C8:305, BMC, Uppsala

Host: Siv Andersson, Uppsala University

Prof. Jay Hinton is Professor of Microbial Pathogenesis at the University of Liverpool. Prof. Prof. Hinton has developed RNA-seq-based approaches for studying gene expression of in vitro-grown and intra-macrophage bacteria. He is currently using functional genomics methods to understand how new Salmonella pathovariants are causing endemic bloodstream infections across sub-Saharan Africa. This disease has killed around 500,000 people over the last decade.

Title of the talk: How has Salmonella become so dangerous in Africa?

With 3.4 million infections each year, invasive non-Typhoidal Salmonella (iNTS) is a major cause of illness worldwide. In Sub-Saharan Africa, bloodstream infections involving iNTS Salmonella enterica serovar Typhimurium are causing ~49,000 deaths annually. Co-infection with HIV or malaria in adults, and a young age (<5 years) are known risk factors. The main causative agent of iNTS is a pathovariant of Salmonella Typhimurium called ST313, which is multi-drug resistant and closely-related to the ST19 type of Salmonella responsible for gastroenteritis globally.

Using a combination of comparative genomics and comparative transcriptomics,we discovered phenotypic differences that distinguish African from global Salmonella pathovariants (Canals et al., 2019; Honeycutt et al., 2020).

Our analysis led us to identify a single core genome SNP responsible for the up-regulation of a single promoter in strain D23580 that controlled the expression of a Salmonella virulence factor (Hammarlöf et al., 2018), and offers part of the explanation of the pan-African epidemic of bloodstream infection.All of the Salmonella transcriptomic data we have generated are now available online in a user-friendly website that allows intra-strain and inter-strain comparisons of gene expression between African and global pathovariants ofS. Typhimurium: https://tinyurl.com/SalComD23580

Most recently, we used the combined power of genomics and epidemiology and thousands of historical and contemporary Salmonella isolates to understand the precise evolutionary trajectory of the S. Typhimurium ST313 pathogen in Africa. We identified a series of novel genome degradation events that impacted upon the function of Salmonella genes required for colonisation of the mammalian gut, providing evidence of niche adaptation and the continuing evolution of ST313 (Pulford et al., 2021).

I will summarise the evolutionary pathway of invasive S. Typhimurium across Africa, and explain the value of an integrated functional genomic analysis for understanding how bacterial pathogens cause disease.

ReferencesCanals et al. (2019) Adding function to genome of African Salmonella Typhimurium ST313. PLoS Biology 17(1): e3000059. DOI: 10.1371/journal.pbio.3000059

Hammarlöf et al. (2018) Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella. PNAS 115: E2614 – E2623.

DOI: 10.1073/pnas.1714718115

Honeycutt et al. Genetic variation in the MacAB-TolC efflux pump influences pathogenesis of invasive Salmonella isolates from Africa. PLoS Pathog. 2020 16:e1008763. DOI: 10.1371/journal.ppat.1008763

Pulford et al. (2021) Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nature Microbiology 6: 327–338.

DOI:10.1038/s41564-020-00836-1
