Jonas Barandun featured in “Kemisk Tidskrift” article

In an article in the latest issue of “Kemisk Tidskrift” Jonas Baranduns “tiny” ribosome structure is shown together with an update on ISB in Umeå!!

New article in Nature Microbiology: Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome

A new study from the Barandun research group in collaboration with researchers at The Rockefeller University and The Connecticut Agricultural Experiment station uncovers the cryo-EM structure of the smallest known eukaryotic cytoplasmic ribosome. The structure visualizes the effect of extreme genome compaction on the translation machinery in microsporidia, uncovers a species-specific ribosomal protein and suggests a novel mode of ribosome inhibition in eukaryotes.

Manuscript:

Barandun, J., Hunziker, M., Vossbrinck, C. R. & Klinge, S. Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome. Nat. Microbiol. (2019). in press. doi:10.1038/s41564-019-0514-6

Involved research groups:

Barandun research group
The Laboratory for Molecular Infection Medicine Sweden (MIMS) and SciLifeLab National Fellow
Department of Molecular Biology

Klinge laboratory
Laboratory of Protein and Nucleic Acid Chemistry, Klinge Lab
The Rockefeller University, New York, USA

Vossbrinck laboratory
Department of Environmental Sciences 
The Connecticut Agricultural Experiment Station
New Haven, CT, USA

Image Attributions

  1. “Corn (Zea mays): Corn earworm (Helicoverpa zea)” by Plant pests and diseases is licensed under CC PDM 1.0 
  2. Vairimorpha necatrix spores, picture by Charles R. Vossbrinck

ISB Postdoctoral program – 2 postdoc positions available

The ISB Postdoctoral program is now open for interested applicants! This year we have 2 fully financed postdoctoral fellowships open – Please see here for more info.

Postdoctoral and PhD opening at Wu lab: Autophagy & Chemo-optogenetics

Umeå University is dedicated to providing creative environments for learning and work. We offer a wide variety of courses and programs, world leading research, and excellent innovation and collaboration opportunities. More than 4300 employees and 33979 students from over 60 nationalities have already chosen Umeå University. The recent breakthrough researches from Umeå include deciphering the molecular mechanisms of the bacterial CRISPR-Cas9 system and repurposing it into a tool for genome editing.

Umeå Campus

The Wu lab recently relocated from Max Planck Institute in Dortmund Germany to Umeå Sweden. The lab is located within the cross-disciplinary Chemical Biological Centre (video) (www.kbc.umu.se/english/) at Umeå University. The lab is fully equipped for biological and chemical researches with access to excellent facilities and state-of-art equipment and platforms in a creative, inspiring, international and highly interactive environment. Facilities include Protein Expertise Platform, X-ray, Proteomics, NMR (850-400 MHz), Cryo-EM and Biochemical Imaging Centre (confocal, FLIM, spinning disk, TIRF, STORM).

Project: Autophagy mechanisms

Autophagy is an evolutionarily conserved self-eating process mainly to eliminate or recycle dysfunctional cellular organelles or unused proteins. Autophagy plays an important role in physiology including development and ageing and has been associated with diverse human diseases, including cancer, neurodegeneration and pathogen infection. Autophagy modulation is implicated in the treatment of diseases such as neurodegeneration and cancer. Despite extensive work, the mechanisms of autophagosome formation and autophagy regulation are not yet well established. Our laboratory has elucidated fundamental mechanisms underlying autophagosome formation and bacterial escape from host autophagy using chemical genetic approaches (eLife 2017, Angew Chem 2017, Nat Chem Biol 2019). We will combine cell biological, biochemical, and novel chemical and chemo-optogenetic approaches to understand the mechanism of autophagic membrane morphogenesis and bacterial interaction with host autophagy.

Project: Chemo-optogenetics

Genetic perturbations such as knock-out or knock-down approaches is powerful for biological studies. However, traditional genetic approaches are chronic (hours to days). Consequently, the phenotype may not be detected due to adaptation and the dynamics of phenotypic change cannot be followed. Chemical genetic approaches using small molecules are acute, reversible, conditional and tunable and have been very useful to dissect the complexity of biological regulatory networks. However, many of these compounds have additional off-target effects that may confound elucidation of biological systems in certain contexts. Our laboratory has developed a set of chemical and photochemically induced dimerization (CID, pCID, psCID) system to spatiotemporally control cellular signaling and intracellular cargo transport (Angew Chem 2014, 2017, 2018, 2018). We will further develop novel chemo-optogenetic systems that enables the activity to be controlled by light with high spatial and temporal precision in live cells and organisms.

The projects are interdisciplinary with strong international collaborations across scientific disciplines. The European Research Council (ERC) and Wallenberg Foundation are funding the research in long term.

Requirements

The required qualification for postdoc is a doctoral degree in cell biology, biochemistry, chemical biology, or in another relevant field. The required qualification for PhD student is a master degree or equivalent in chemistry or biology related field. Highly motivated young talents are encouraged to apply.

Information

For how to apply: https://www.umu.se/en/work-with-us/fellowships-and-grants/6-1190-19/

For further information you are welcome to contact Prof. Yaowen Wu

Webpage: https://www.biostruct.umu.se/principal-investigators/yaowen-wu/

E-mail: yaowen.wu[at]umu.se

Press release:

https://www.kva.se/sv/pressrum/pressmeddelanden/goran-gustafssonpriser-2019-tre-miljoner-mer-till-yngre-forskarehttps://www.umu.se/en/news/yaowen-wu-is-awarded-the-goran-gustafsson-prize-in-molecular-biology_7673132/

F1-ATPase function uncovered with computational structural biology

In a computational study by ISB member Kwangho Nam (Umeå and UT Arlington) and Martin Karplus (Harvard University) a detailed model has been developed for the coupling between rotary motion and ATP hydrolysis in F1-ATPase.  The model predicts that F1-ATPase functions at near its maximum possible efficiency. The finding is published in PNAS.  https://www.pnas.org/content/116/32/15924.long

Mechanism of enzyme activation discovered

In an ISB effort the research groups lead by  Anna Linusson, Elisabeth Sauer-Eriksson and Magnus Wolf-Watz has discovered a key event in activation of the essential enzyme adenylate kinase. It was discovered that the large-scale and activating conformational change triggered by ATP binding is nucleated by a strong cation-PI interaction formed between the cationic sidechain of an arginine with the aromatic adenosine base of ATP. The discovery may pave way for future enzyme design efforts where recognition of aromatic systems is required. The finding was made possible through an integrative effort using DFT calculations, NMR spectroscopy and x-ray crystallography. The team consisted of Per Rogne, David Andersson, Christin Grundström, Elisabeth Sauer-Eriksson, Anna Linusson and Magnus Wolf-Watz. The finding is published in Biochemistry https://pubs.acs.org/doi/10.1021/acs.biochem.9b00538.

PhD position in Karina Persson’s group

A fully funded PhD position is available in Karina Persson’s group. The overall aim of the project is to obtain structural and functional data of bacterial fimbrial proteins and associated proteins involved in maturation of fimbria For more information and how to apply:

https://umu.mynetworkglobal.com/en/what:job/jobID:272296/

The closing date for applications is the 5th of Aug. 2019.

Postdoc position available in the Berntsson lab – study of adhesion proteins in G+ T4SSs

The Berntsson lab at the department of Medical Biochemistry and Biophysics at Umeå University, Sweden, is looking to recruit postdoctoral fellow (2-year fellowships, funded by the Kempe Foundation) to study the structural and functional aspects of Type 4 Secretion Systems. These large protein complexes are responsible for horizontal gene transfer between bacteria. As such, they facilitate the spread of, among other genes, antibiotic resistance between bacteria, both intra- and interspecies.

The overall goal of this project is to structurally and functionally characterize the adhesion proteins of G+ Type 4 Secretion Systems. These proteins are thought to be responsible for facilitating mating pair formation between the cells. We have the past years studied the T4SS from the pCF10 plasmid from Enterococcus faecalis, and we now understand the structural basis for how these cell-wall anchored proteins are involved both in biofilm formation and conjugation. However, there are numerous unanswered questions that we are still pursuing. The project will involve both functional assays in molecular biology, various biochemistry techniques (such as EMSAs and ITC) as well as protein structural determination via X-ray crystallography and/or single particle cryo EM. 

Qualifications

The applicants must possess a PhD, or another diploma deemed equivalent to a PhD, within molecular biology, biochemistry, structural biology or a related field. Furthermore, the applicant must have practical experience and expertise of cloning and protein production and purification in bacteria. The applicant must also have practical experience with either protein X-ray crystallography or cryo Electron Microscopy. Previous experience of working with Gram-positive bacteria is a merit. The applicants must have a very good level of English, both written and spoken. The applicants are also expected to be good team players, but should also be able to work independently. 

Application

The application should consist of the following:

  1. A motivation letter (max 1 A4), where you highlight why you want to join the laband study T4SSs. This letter must also include your contact information.
  2. The Curriculum Vitae of the applicant, including a list of published peer-reviewed articles.
  3. Copy of the PhD diploma (or equivalent).
  4. Contact details for three references, of which one should be your PhD supervisor.

The duration of the fellowship is 2 years. Your application should be written in English and prepared as a single package in PDF format, to be submitted to ronnie.berntsson@umu.se. Make sure touse the subject line: “postdoc application 2019-08” in the application email.Submit the applicationon August 19th, 2019 at the latest. The top ranked candidates will be contacted within two weeks from the closing date for an interview. Starting date according to agreement. For more information about the research or other details, do not hesitate to contact Dr. Ronnie Berntsson. 

Email: ronnie.berntsson@umu.se

Webpage: https://www.biostruct.umu.se/principal-investigators/ronnie-berntsson/

Postdoctoral program

We are happy to announce that the Kempe foundation is funding an ISB postdoc program with two fellowships 2019 and three fellowships 2020. Running costs are included for the positions. The program will fund new constellations that tackle interdisciplinary structural biology projects. For more information please go to the page ISB Postdoctoral program.

PhD position in the Andersson lab

We are seeking a PhD student in chemistry that will be part of a research team focused on understanding membrane protein transport using experimental techniques such as time-resolved X-ray scattering and biochemical assays, as well as computer simulation. Application deadline is 2019-06-03.

Project description
Biological membranes contain proteins that are necessary for all forms of Life – not least human beings. Development of structural characterization methods during the last 20 years has resulted in increased understanding of these membrane proteins, which in turn has increased production of new pharmaceuticals. We now face a major challenge – how can we take the next step and understand how proteins change their structures to perform their designated functions. By determining intermediate structures in the natural membrane environment, we could significantly increase the number of pharmaceutical targets. We will specifically characterize transport proteins in pathogenic bacteria, which are absent in humans, since such proteins are targets for development of new antibiotics that has potential to fight multi-drug resistance that pose a severe threat to humans, society, and health care.

Working tasks
The PhD student will be part of an existing research team that combines experimental methods and computer simulation to understand membrane protein transport. We have developed a combination of time-resolved X-ray scattering and computer simulation capable of determining transient intermediate states in the natural membrane environment. Our work is carried out on the absolute forefront of structural biology and will prepare the PhD student for a continued research career in academia or industry.

The PhD student will acquire a unique skillset with both experimental expertise and high-performance computing. The research spans molecular biology production and characterisation of proteins to development work at the synchrotrons MAXIV (Lund) and ESRF (Grenoble). The computer simulations will be performed on the national SNIC platform at the high-performance computing center HPC2N. The work will be performed within the context of Integrated Structural Biology (https://www.biostruct.umu.se) at Umeå University that provides seminar series as well as an exciting research environment.

Qualifications
To be admitted for studies at third-cycle level you are required to have completed a second-cycle level degree, or completed course requirements of at least 240 ECTS credits, of which at least 60 ECTS credits are at second-cycle level or have an equivalent education from abroad, or equivalent qualifications.

To fulfill the specific entry requirements to be admitted for studies at third-cycle level in chemistry, you are required to have completed first-cycle courses of at least 90 ECTS credits within the field of chemistry or another subject considered to be directly relevant to the specialization in question (such as physics, biology etc). Of those 90 ECTS credits, at least 15 ECTS credits shall have been acquired at second-cycle level within the specialization or an equivalent subject.

Good knowledge of the English language, both written and spoken, is required as well as a great interest within the field of biophysics and/or biochemistry. A suitable candidate must also be creative, have good collaboration skills, have a high degree of independence, and problem-solving analytical ability. Experience of protein production and characterization and/or Linux terminal/programming are considered as merits.

Terms of employment
The appointment aims at a PhD degree and the main task of the PhD student is to pursue their doctoral studies, which includes participation in research projects as well as postgraduate courses. In the assignments, teaching and other departmental work (up to a maximum of 20%) can be included. The employment is limited to four years full-time or up to five years when part-time teaching. The salary placement takes place according to the established salary level for doctoral employment.

Application
A complete application, written in English or Swedish, should contain a Curriculum Vitae, a cover letter including a description of your research interests and motivation for applying for this position, copies of degree certificates or equivalent, including documentation of completed academic courses and obtained grades, name and contact information of at least two reference persons.

Applications must be submitted via our e-recruitment system (link at https://www.umu.se/en/work-with-us/open-positions/phd-student-position-in-chemistry-with-focus-on-biophysical-chemistry_267035/). The last day to apply is 2019-06-03.

For more information about the research, position, or other details, please contact Docent Magnus Andersson
email: magnus.p.andersson@umu.se
webpage: https://www.biostruct.umu.se/principal-investigators/magnus-andersson/

About us
The Department of Chemistry is one of the largest departments within the Faculty of Science and Technology with approximately 200 employees, of which approximately 40 are PhD students, and constitutes a strong and expanding research environment. The Department has three major research areas: Biological Chemistry, Environmental and Biogeochemistry, and Technical Chemistry. We are also a strong partner in the Chemical-Biological Center (KBC), which provides excellent scientific infrastructure with several core facilities and technical platforms. You can find more information here: https://www.umu.se/en/chemical-biological-centre/. Information about the postgraduate education can be found on the Faculty of Science and Technology website: www.umu.se/en/faculty-of-science-and-technology/education/doctoral-studies/chemistry/. For more information about working at Umeå University, https://www.umu.se/en/work-with-us/.

Umeå University wants to offer an equal environment where open dialogue between people with different backgrounds and perspectives lay the foundation for learning, creativity and development. We welcome people with different backgrounds and experiences to apply for the current employment.