We are running a fortnightly SciLifeLab Site Umeå / KBC Infrastructure Seminar Series. The seminar series will be held in Glasburen KBC, and online attendance is available via Zoom.
Time: Tuesdays, 12:00-13:00
Place: Glasburen, KBC, and Zoom
For the following seminars, registration will be open ca 2 weeks before the scheduled date of the event:
18 April - Biochemical Imaging Centre Umeå (BICU)
Presenters:
Irene Martinez Carrasco, BICU facility manager and Senior research engineer at the Department of Medical Biochemistry and Biophysics, Department of Integrative Medical Biology (IMB)
Naga Venkata Gayathri Vegesna, Senior research engineer at the Department of Integrative Medical Biology (IMB)
Johan Olofsson Edlund, Research engineer at the Department of Medical Biochemistry and Biophysics
More information about the infrastructure: Homepage
2 May - Focused Electron and Ion Beam Microscopy (FIB-SEM)
Presenters:
Cheng Choo (Nikki) Lee, Research Engineer, Umeå Centre for Electron Microscopy (UCEM)
Sara Henriksson, Senior research engineer, Umeå Centre for Electron Microscopy (UCEM)
More information about the Umeå Centre for Electron Microscopy (UCEM): Homepage
16 May - Computational Analytics Support Platform (CASP) and National Bioinformatics Infrastructure Sweden (NBIS)
Presenters:
Kate Bennett, CASP Platform Manager and Research coordinator at the Department of Chemistry
Jeanette Tångrot, NBIS expert and Senior research engineer at the Department of Molecular Biology
More information about CASP: Homepage
More information about NBIS: Homepage
30 May - Structural Mass Spectrometry
Presenter:
Simon Ekström, Head of Unit, Structural Proteomics, SciLifeLab, and BioMS, Lund University
More information about Structural Proteomics, SciLifeLab: Homepage
13 June
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Towards the routine data collection from pico-gram crystals using MicroED - 28 March 2023
Title: Towards the routine data collection from pico-gram crystals using MicroED
Presenter: Johan Unge, MicroED core manager and collaborator with the Gonen lab at UCLA, Los Angeles
Abstract: Although electron crystallography has been known almost a century, the current success for organic and biological samples started only a decade ago. The theoretical complications from effects such as for instance dynamical scattering can be largely overcome using continuous rotation as in MicroED or cRED. Today an exponentially growing number of structures are deposited to PDB and CSD from MicroED data collections. The technique has several advantages and is a sample saving addition to the structural biology toolbox. The ability to collect a full data set from crystals 100 nm thick has allowed the structure determination of several proteins from nano sized crystals as well as small molecules directly from powder. The ability to see electrostatic potential as well as hydrogen atoms is useful for many functional studies. Recent experiences, advantages and complications as well as newest developments towards an automatic, accessible and efficient crystal structure determination is presented.
High Performance Computing Centre North (HPC2N) - 21 March 2023
Title: Are your simulations saturating your PC or do you need more computing power?: HPC2N as an alternative
Presenter: Pedro Ojeda May, Senior research engineer at High Performance Computing Centre North
Abstract: The High Performance Computing Center North (HPC2N) is a local/regional resource for researchers at HPC2N's partners (IRF, LTU, Mittuniversitetet, SLU and UmU). Our Director of HPC2N is Professor Paolo Bientinesi from the Computing Science Department.
We offer different types of hardware for computing and visualization, including standard CPUs and Graphical Processing Units (GPU)s. Most common packages for Scientific Research are installed on our cluster, for instance, GROMACS, VASP, MATLAB, and R/Rstudio, among others.
To get started with our system, we offer different types of training courses, including introductory courses and more specialized courses in topics such as Molecular Dynamics, QM/MM, Git, R, Machine Learning, MPI, Julia, and OpenMP (Recorded courses: https://www.youtube.com/@HPC2N). We provide general support through a ticket system and more advanced support for specific questions from researchers on-demand.
General questions: info@hpc2n.umu.se
Specific questions: support@hpc2n.umu.se
Website: https://www.hpc2n.umu.se/
MAX IV for new users: introduction and updates - 21 February 2023
Presenter: Alexandr Talyzin, Associate professor at the Department of Physics, Umeå University
Title: MAX IV for new users: introduction and updates
Abstract:
The main purpose of my presentation is to encourage more users (physics, chemistry and bioscience) to submit proposals to the MAX IV synchrotron facility. I will provide short summary of available beamlines and access schemes and give some advice related to the preparation of proposals. Some recent research highlights will be used to illustrate the possibilities of MAX IV in all branches of science. The presentation is addressed first of all to new users, but it could be of interest to everybody interested in exploring research possibilities at MAX IV. The next call has a deadline on the 7th of March 2023, and it is now the right time to prepare proposals. Currently, 16 beamlines are opened for standard proposals. Some beamlines are still under construction, and some beamlines are expanding the range of their experimental possibilities with every call. Therefore, it is important to follow updates and learn about current opportunities.
National support with superresolution light microscopy
22 November 12:00-13:00
Speaker: Hans Blom, Royal Institute of Technology (KTH), Head of the Advanced Light Microscopy (ALM) Unit, SciLifeLab
About Hans Blom: https://www.kth.se/profile/hblom
Title: National support with superresolution light microscopy
More information about the national SciLifeLab facility Integrated Microscopy Technologies: https://www.scilifelab.se/units/integrated-microscopy-technologies/
XPS Platform: Nobel prized technique to study surface and interfaces
25 October 12:00-13:00
Presenter: Andrey Shchukarev, Research fellow at the Department of Chemistry, Umeå University, and manager of the XPS Platform
More information about the infrastructure: Homepage
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.
The Protein Expertise Platform - a Core Facility at the KBC and a node of PPS
18 October 12:00-13:00
Presenter: Uwe Sauer, Associate professor, Platform coordinator. Department of Chemistry, Umeå University
More information about the infrastructure: Homepage
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.
Vibrational Spectroscopy Core Facility - What’s in it for you?
Seminar description: The Vibrational Spectroscopy Core Facility provides in situ, non-destructive, label-free chemical compositional analysis in the form of FTIR and Raman spectroscopy and imaging. It is an open-access facility with many years of experience in a very broad spectrum of research areas, from plant sciences and medicine to environmental and material sciences.
Join this lunch seminar to see some examples of what this facility can provide for your research, ask questions and discuss possibilities.
A tour to the instruments is available after the seminar for those interested.
Instruments and methods at Umeå Centre for Electron Microscopy (UCEM)
NGS at NGI
Seminar description: Got samples? We’ve got the sequencing! NGI is one of the largest platforms at SciLifeLab and provides both established and cutting-edge genomics technologies to diverse user groups across Sweden and internationally. There’s a wide range of applications as NGI is equipped with both short- and long read technologies, as well as SNP genotyping- and DNA methylation arrays. The platform assists users in project design, data generation, analysis and management of data in order to support genomics research in all subject areas.
Prepare for your next (generation) sequencing experiment as we’ll get into the nitty-gritty of some different methods, sample types and requirements.
National NMR Infrastructure at KBC. What can we do for you?
Seminar description:
The KBC based central NMR facility provides access to one of the most powerful liquid and solid-state NMR infrastructures in the Nordic countries and expertise for all researchers in the KBC and Campus environment. The facility serves large user groups spanning a remarkably wide range of fields, such as materials science, chemical biology, organic synthesis, structural biology, plant- and environmental sciences, biogeochemistry and medical metabolomics. Local researchers profit strongly from the facility’s status as a national infrastructure and different structural biology facilities and expertise (“Integrated Structure Biology”) at UMU. Fragment-based screening is also offered as national support in collaboration with CBCS/LCBU, including comprehensive substance libraries. The facility is also closely linked to large research initiatives at the campus such as MIMS, UCMP, Bio4Energy, UPSC, the Swedish Metabolomics Center (SMC) and with SLU through collaborations and by offering service.
Activities: if required, a short guided tour to the NMR facility and drop-in discussions with NMR people about potential projects could be organised after the seminar.
Measuring metabolites, the building blocks of biology
The presentation will give an introduction to metabolomics, and small molecule analysis by mass spectrometry. We will present our different services and also give examples of different research projects in which SMC has been involved.
Unbiased characterization of cells using the single-cell facility
SciLifeLab Site Umeå / KBC Infrastructure Seminar Series presents a seminar by Johan Henriksson, Dept. Molecular Biology / Molecular Infection Medicine Sweden (MIMS), Umeå University. If you want to learn how you can benefit from single-cell analysis, join for 30 min presentation of cases & opportunities, followed by 30 min discussion of practicalities & project design.
Fluorescence In Situ Hybridization (FISH) – Advanced Technologies for Single Cell Visualization and Identification
SciLifeLab Site Umeå: Facilities, possibilities and services
UCEM is a joint resource for research and higher education in electron microscopy techniques.
SciLifeLab is a national center for molecular biosciences with focus on health and environmental research.
The Chemical Biological Centre is an interdisciplinary research centre for natural sciences and medicine.