1- A fully-funded PhD student to work on environmental diversity of enigmatic lineages of microbial eukaryotes that diverged near the origin of Archaeplastida. Deadline: Oct-20:
Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 54,000 students, more than 7,500 employees and a turnover of around SEK 8 billion.
The Department of Organismal Biology teaches and explores the evolution, development and function on the organismal level.
The position is placed in the research group of Fabien Burki within the Systematic Biology program at the Department of Organismal Biology (Evolutionary Biology Center, Uppsala University). In the Burki lab, we study the broad diversity of eukaryotes, which is mainly microbial, to understand some of the main transitions in broad eukaryote evolution such as the origin of plastids. This position is within an ERC-funded project: Establishing a new framework of plastid evolution derived from the characterization of novel diversity of unicellular eukaryotes
Project description
The Burki lab was recently awarded an ERC Consolidator grant (PlastidOrigin) that aims to study one of the most transformative events in eukaryote evolution–the origin of the photosynthetic organelles (the primary plastids). The main aim of this PhD position is to characterize novel environmental diversity that diverged near the origin of Archaeplastida–the supergroup of eukaryotes where plastids were established more than 1.5 billion years ago. We aim to identify and phylogenetically resolve microbial lineages that have never been seen before in order to produce a comprehensive evolutionary framework for the origin of plastids that include this crucial environmental diversity. A suite of methods will be employed, including long-read metabarcoding, single-cell transcriptomics, metagenomics, phylogenomics, cultivation, microscopy.
Duties
The position involves lab work and bioinformatics. Lab work may include: sampling, cell isolation, imaging with advanced microscopy, cell-sorting, attempts for cultivation of interesting cells in enrichment cultures, and library preparation for metabarcoding and HTS sequencing. Bioinformatics includes analysis of diversity datasets, phylogenetics, analysis of genomic datasets, phylogenomic. Disseminate results in appropriate formats, including leading peer-reviewed publications and conferences. Training will be provided when necessary.
Requirements
Completed university education of 240 university points (högskolepoäng, hp) out of which 60 hp on advanced level corresponding to master degree in relevant field to the project. Expertise and knowledge in microbial sampling as well as handling and culturing protist cells are beneficial. Background in eukaryotic diversity will be seen as highly valuable. A suite of methodologies will be used as described in the project description and are desirable attributes of the candidate. In particular, proven expertise in bioinformatics (e.g. phylogeny, genomics) and use of a scripting language (Python, R) are essential. A global assessment of the expertise will be made based on the candidates.
Great emphasis is placed on personal qualities such as high-motivation, planning and organizational skills, problem solving and good collaborations and communication skills with team-members and other researchers. The applicant should have documented experience and proficiency in oral and written presentation in English.
Additional qualifications
In filling this position, the university aims to recruit the person who, in the combined evaluation of competence, skills and documented qualifications, is judged most suitable to carry out and develop the work-in-hand and to contribute to a positive development of the department.
Position
The PhD-student position is a 4-year appointment, and the candidate will primarily devote the time to his/her own research studies. Other departmental work, such as teaching or administration are typically part of the position (maximum 20 %). Salary placement is in accordance with local guidelines at Uppsala University. The applicant must be eligible for PhD studies at Uppsala University.
Information about research education can be found at the web site of the Faculty of Science and Technology,
Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University’s rules and guidelines.
About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date 2023-01-01 or as agreed. Placement: Uppsala
For further information about the position, please contact: Dr. Fabien Burki; fabien.burki@ebc.uu.se.
Please submit your application by 20th of October 2022, UFV-PA 2022/3349.
Are you considering moving to Sweden to work at Uppsala University?
Please do not send offers of recruitment or advertising services.
Submit your application through Uppsala University’s recruitment system.
Placement: Department of Organismal Biology
Type of employment: Full time , Temporary position longer than 6 months
Pay: Fixed salary
Number of positions: 1
Working hours: 100%
Town: Uppsala
County: Uppsala län
Country: Sweden
Union representative: ST/TCO tco@fackorg.uu.se
Seko Universitetsklubben seko@uadm.uu.se
Saco-rådet saco@uadm.uu.se
Number of reference: UFV-PA 2022/3349
Last application date: 2022-10-20
2- A fully-funded PhD student to study the roles of genetic transfers in the integration of an endosymbiont into an organelle using the amoeba Paulinella as a model. Deadline: Oct-17
Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 54,000 students, more than 7,500 employees and a turnover of around SEK 8 billion.
The Department of Organismal Biology teaches and explores the evolution, development and function on the organismal level. The position is placed in the research group of Fabien Burki within the Systematic Biology program at the Department of Organismal Biology (Evolutionary Biology Center, Uppsala University). In the Burki lab, we study the broad diversity of eukaryotes, which is mainly microbial, to understand some of the main transitions in broad eukaryote evolution such as the origin of plastids.
Project description
The Burki lab was recently awarded an ERC Consolidator grant (PlastidOrigin) that aims to study one of the most transformative events in eukaryote evolution–the origin of the photosynthetic organelles (the primary plastids). The main aims of this PhD position are to study the roles of genetic transfers in the integration of an endosymbiont into an organelle. For this we will study the lineage Paulinella–a lineage of amoebae (unicellular eukaryotes) that established primary plastids relatively recently.
While most of the research on Paulinella has been done on the photosynthetic species, i.e. the species that diverged after the establishment of plastids, we will instead look at the heterotrophic species that diverged close but before plastid establishment to test the hypothesis that gene transfers facilitating the endosymbiotic integration occurred before the establishment of the plastids from varying food sources. A suite of methods will be employed, including long-read metabarcoding, transcriptomics, phylogenomics, cultivation, microscopy.
Duties
The position involves lab work and bioinformatics. Lab work includes: field trips, sampling, cell isolation, imaging with advanced microscopy, attempts for cultivation of interesting cells in enrichment cultures, and library preparation for metabarcoding and HTS sequencing. Bioinformatics includes analysis of diversity datasets, phylogenetics, analysis of transcriptomic datasets, gene-tree species tree reconciliation. Disseminate results in appropriate formats, including leading peer-reviewed publications and conferences. Training will be provided when necessary.
Requirements
Completed university education of 240 university points (högskolepoäng, hp) out of which 60 hp on advanced level corresponding to master degree in relevant field to the project. The selected candidate must possess expertise and knowledge in microbial sampling as well as identifying and handling protist cells. Experience in culturing of microbial eukaryotes is required. Background in eukaryotic diversity will be seen as highly valuable.
A suite of methodologies will be used as described in the project description and are desirable attributes of the candidate. In particular, proven expertise in bioinformatics (e.g. phylogeny, genomics) and use of a scripting language (Python, R) are essential. Great emphasis is placed on personal qualities such as high-motivation, planning and organizational skills, problem solving and good collaborations and communication skills with team-members and other researchers. The applicant must have documented experience and proficiency in oral and written presentation in English.
Additional qualifications
In filling this position, the university aims to recruit the person who, in the combined evaluation of competence, skills and documented qualifications, is judged most suitable to carry out and develop the work-in-hand and to contribute to a positive development of the department.
Position
The PhD-student position is a 4-year appointment, and the candidate will primarily devote the time to his/her own research studies. Other departmental work, such as teaching or administration are typically part of the position (maximum 20 %). Salary placement is in accordance with local guidelines at Uppsala University. The applicant must be eligible for PhD studies at Uppsala University.
Information about research education can be found at the web site of the Faculty of Science and Technology,
Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University’s rules and guidelines.
About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date 2023-01-01 or as agreed. Placement: Uppsala
For further information about the position, please contact: Dr. Fabien Burki; fabien.burki@ebc.uu.se.
Please submit your application by 17th of October 2022, UFV-PA 2022/3359.
Are you considering moving to Sweden to work at Uppsala University?
Please do not send offers of recruitment or advertising services.
Submit your application through Uppsala University’s recruitment system.
Placement: Department of Organismal Biology
Type of employment: Full time , Temporary position longer than 6 months
Pay: Fixed salary
Number of positions: 1
Working hours: 100 %
Town: Uppsala
County: Uppsala län
Country: Sweden
Union representative: ST/TCO tco@fackorg.uu.se
Seko Universitetsklubben seko@uadm.uu.se
Saco-rådet saco@uadm.uu.se
Number of reference: UFV-PA 2022/3359
Last application date: 2022-10-17
3- A postdoc/researcher to perform whole-cell spatial proteomics of red algae; note that this is a 5-year position. Deadline: Nov-3:
Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 54,000 students, more than 7,500 employees and a turnover of around SEK 8 billion.
The Department of Organismal Biology teaches and explores the evolution, development and function on the organismal level.
The position is placed in the research group of Fabien Burki within the Systematic Biology program at the Department of Organismal Biology (Evolutionary Biology Center, Uppsala University). In the Burki lab, we study the broad diversity of eukaryotes, which is mainly microbial, to understand some of the main transitions in broad eukaryote evolution such as the origin of plastids
Project description
The Burki lab was recently awarded an ERC Consolidator grant (PlastidOrigin) that aims to study one of the most transformative events in eukaryote evolution–the origin of the photosynthetic organelles (the primary plastids) in Archaeplastida. The main aim of this postdoc/researcher position is to produce the first plastid proteomes for red algae using whole-cell spatial proteomics with the hyperLOPIT method (or alternatively LOPIT-DC). By combining this data to verified proteomes for other archaeplastids, and by searching for homologues in other eukaryotes and prokaryotes, we want to characterize the origin of plastid proteins and the size of the endosymbiotic vs non-endosymbiotic plastid proteomic fractions across archaeplastids. Depending on the expertise of the candidate, a training period may be organised abroad.
Duties
Establish the knowledge and workflow to run proteomic experiments in the lab in collaboration with a local proteomic core facility. Adapt hyperLOPIT to red algae. Bring red algal cultures to sufficient densities, and execute hyperLOPIT. Perform protein cellular location prediction by Machine Learning. Analyse the data in the context of plastid evolution. Disseminate results in appropriate formats, including leading peer-reviewed publications and conferences. Training of junior group members might also be involved, as well as other standard tasks related to a research group including providing operational support to the good functioning of the lab. The candidate should be willing to travel, for short (e.g. conference) or longer period if training is necessary.
Requirements
PhD in Biology, Chemistry or equivalent. We are looking for an enthusiastic individual with the desire to share and establish a novel methodology in the Burki lab. The successful candidate will have a strong record, appropriate for their career stage, of high-quality research publications. Great emphasis is placed on personal qualities such as high-motivation, planning and organizational skills, problem solving, stress management. We strive to create a friendly atmosphere among team-members and other employees in the work place, so a collegiate capacity to work as part of a team is necessary.
For this position, a proven experience in mass spectrometry and proteomics is absolutely essential, and must be demonstrated by scientific publications in these fields. A keen interest in evolution, especially in big transitions in eukaryote evolution such as the origin of plastids, is a desirable attribute of the candidates. The candidate should be proficient on the command line and R to perform quantification and statistical analysis, as well as have a good knowledge of at least one scripting language (eg Python). Proficiency in English, both oral and in writing, is required.
Additional qualifications
Prior knowledge on subcellular fractionation methods and on hyperLOPIT or LOPIT-DC will be seen as major quality. Prior experience in cell culturing, especially algae, will be a strong asset.
About the employment
The employment is a permanent position, probationary period may be applied. Scope of employment 100 %. Starting date 2023-01-01 or as agreed. Placement: Uppsala
For further information about the position, please contact: Fabien Burki, +46 18 471 2779, fabien.burki@ebc.uu.se
Please submit your application by the 3rd of November 2022, UFV-PA 2022/3361.
Are you considering moving to Sweden to work at Uppsala University?
Please do not send offers of recruitment or advertising services.
Submit your application through Uppsala University’s recruitment system.
Placement: Department of Organismal Biology
Type of employment: Full time , Permanent position
Pay: Individual salary
Number of positions: 1
Working hours: 100%
Town: Uppsala
County: Uppsala län
Country: Sweden
Union representative: Seko Universitetsklubben seko@uadm.uu.se
ST/TCO tco@fackorg.uu.se
Saco-rådet saco@uadm.uu.se
Number of reference: UFV-PA 2022/3361
Last application date: 2022-11-03