Aquaculture and environmental microbiology: PhD student in bioinformatics

 

The Faculty of Chemistry, Biotechnology and Food Science (KBM) at the Norwegian University of Life Sciences (NMBU) has vacant a 3-year position for a PhD student as part of the project “On-site monitoring of aquaculture impact on the environment by open-source nanopore eDNA analyses”.  

The project is funded by the Research Council of Norway (NFR 320076), and coordinated by NMBU with partners from both the aquaculture industry and reseacrh institutes.

The project involves building and systemizing a fundamental understanding of microbial processes in the seafloor, with the goal of establishing indexes that reflect the environmental conditions.

The project is about developing tools to determine the environmental impact of aquaculture so that Norway can secure a sustainable aquaculture industry.  

Main tasks

Analysis  of nanopore DNA sequencing data

Development of algorithms for taxonomic assignment Characterization  of seafloor microorganisms

Relate microbiota function to chemical and macrofauna composition

Derive environmental classification indexes based on multivariate data

Write and publish high-level scientific publications

Tasks will be conducted in research environments at NMBU with  expertise and multiple ongoing projects in microbial ecology, bioinformatics, and the development of novel in vitro diagnostic tools. Together with the industrial partners partners in the project the aim is to implement a new standard for environmental monitoring connected to aquaculture, based on on-site sequencing.

Bygninger  Tivoli Circus med sitteplasser

Competence

The successful PhD applicant must meet the conditions defined for admission to a PhD programme at NMBU. The applicant must have an academically relevant education corresponding to a five-year Norwegian degree programme, where 120 credits are at master's degree level. The applicant must have a documented strong academic background from previous studies (B as average grade for the MSc studies, or better) and be able to document proficiency in both written and oral English. For more detailed information on the admission criteria please see the PhD Regulations and the relevant PhD programme description

Required academic qualifications:

MSc degree in bioinformatics, or related fields

Experiences and skills with at least 2 of the following are desirable:

Use and understand algorithms for taxonomic classification

Experience with NGS sequencing data and high-performance computing (UNIX)

Experience in developing web interfaces (e.g shiny apps)

Good programming skills in R

Personal qualities:

We are looking for a candidate who is ambitious, curious, motivated and able to work in a strong research environment. The ideal candidate will combine the following personal qualities:

Good communicative skills in English, orally and written

Able to work interdisciplinary

Hard-working and accurate

Creative and independence

Genuinely interested in scientific research and its applications

Good social and collaborative skills

Remuneration and further information

The position is placed in government pay scale position code 1017 PhD Fellow, pay scale 20. PhD Fellows are normally placed in pay grade 54 (NOK 482.200, -) on the Norwegian Government salary scale upon employment and follow ordinary meriting regulations.

Employment is conducted according to national guidelines for University and Technical College PhD scholars.

For further information, please contact Professor Knut Rudi (knut.rudi@nmbu.no) or Associate professor Lars Snipen (lars.snipen@nmbu.no)

Information for PhD applicants and general Information to applicants

Laboratoriearbeid

Application

To apply online for this vacancy, please click on the 'Apply for this job' button above. This will route you to the University's Web Recruitment System, where you will need to register an account (if you have not already) and log in before completing the online application form.

Application deadline: 01.07.2021

In the application, the candidate must confirm that information and documentation (in the form of attachments) submitted via the job application can also be used by NMBU in a possible admission process.

Applicants invited for an interview are expected to present original diplomas and certificates.

The following documents must be attached to the application:

Motivation letter

Complete CV  

Certified copies of academic diplomas and certificates. Applicants from universities outside Norway are kindly requested to send a di-ploma supplement, or a similar document, which describes in detail the study program and grading system

Diplomas/certificates (i.e. Diploma, transcript. Diploma supplement for both bachelor and master). (Diplomas, transcripts and diploma supplements that are not in Norwegian or English must be uploaded in the original language. An English translation of these documents must also be attached.)

Documentation of proficiency in written and oral English

About The Faculty of Chemistry, Biotechnology and Food Science

The Faculty of Chemistry, Biotechnology and Food Science (KBM) employs about 160 people. Currently about 50 PhD students are enrolled into our PhD program. KBM represents a broad range of scientific fields encompassing basic natural sciences such as microbiology, chemistry, biochemistry as well as the application of these towards food chemistry, technology and safety, biotechnology, bioprocessing and environmental issues. The Faculty is responsible for education, research and information within our fields of expertise and also has state-of-the-art instrumentation to perform research within these fields. KBM collaborates in networks and research projects both nationally and internationally. 

Further information: https://www.nmbu.no/en/faculty/kbm 

Bioteknologibygningen NMBU

The Norwegian University of Life Sciences

NMBU has a particular responsibility for research and education that secures the basis for the life of future generations. Sustainability is rooted in everything we do and we deliver knowledge for life. NMBU has 1,800 employees of which about 250 phd scholarships and 6,000 students. The university is divided into seven faculties.

NMBU believes that a good working environment is characterised by diversity.

We encourage qualified candidates to apply regardless of gender, functional ability, cultural background or whether you have been outside the labour market for a period. If necessary, workplace adaptations will be made for persons with disabilities. More information about NMBU is available at www.nmbu.no.

Apply

Postdoc position in solid phase flow chemistry

 

A Postdoc position is available in the group of Prof. Dr. Nina Hartrampf in the Department of Chemistry at University of Zurich (Switzerland). The group is interested in the development of new methods for the chemical synthesis and modification of peptides, proteins and related biopolymers.
Chemical synthesis allows for the incorporation of non-canonical building blocks, backbone modifications, and functional handles, but also requires highly efficient transformations to ensure successful incorporation of every single building block. The Hartrampf group addresses these challenges by using flow-based synthesis methods.

Your responsibilities

The Postdoc project focusses on reaction development for solid phase synthesis. The project will also include the design/modification of a flow chemistry set up, and the screening and optimization of synthesis conditions.

Your profile

We are looking for a highly motivated and enthusiastic Postdoc to join our young and dynamic research group. The candidate must hold an excellent PhD in chemistry, chemical engineering, or related field, and must be fluent in oral and written English. A strong background in synthetic organic chemistry, as well as experience with solid phase synthesis, flow chemistry and/or programming (Python & LabView) is a plus.

What we offer

We offer an exciting position in a stimulating and challenging environment, and the opportunity to work with state-of-the-art SPS technology, flow chemistry equipment, and new instrumentation for purification and analysis.

Place of work

Hartrampf Research Group
University of Zurich - Irchel Campus
Department of Chemistry
Winterthurerstrasse 190
8057 Zurich

Start of employment

The employment should start as soon as possible (e.g. July 2021).
Your application should contain (as a single pdf document):

• letter of motivation
• curriculum vitae
• short summary of past research accomplishments
• transcripts of your academic records from your University, and a copy of your degree
• contact details of two referees (e.g. your PhD supervisor)

Incomplete applications will not be considered.

Apply

PhD Scholarship in Microbial Interspecies Interactions Involved in Seabed Methane Cycling

 

We invite applicants for a three-year PhD scholarship in microbial interactions involved in seabed methane cycling. The scholarship is partly funded by the Danish Research Council and partly by the Department of Biology and the Faculty of Science, University of Southern Denmark. The project will be based at the Nordcee section, Department of Biology, University of Southern Denmark (Principal Investigator: Amelia-Elena Rotaru). The project is a collaboration with the Department of Bioscience at Aarhus University (Co-PI: Bo Barker Jørgensen; Co-investigators: Kasper Urup Kjeldsen and Hans Røy). The starting date for the position is 1 September 2021 or soon thereafter. Application deadline: 31 July 2021.

Project background
In the seabed, microorganisms (archaea) produce large amounts of the greenhouse gas methane. Most methane is decomposed below the sediment surface, where it is oxidized with sulphate. We recently discovered a previously undetected production of methane in the sulfate methane transition zone. Here, anaerobic methane oxidizing archaea appear capable of reversing their metabolism and produce methane, possibly via syntrophic acetate oxidation. These archaea may exchange electrons through electrically conductive molecules on the cell surface or via conductive mineral particles naturally occurring in sediments. These results may be important for understanding how enhanced nutrient load and rising temperature could affect the seabed's natural methane filter in the future.

We will use sensitive analytical and experimental methods to study how electrons are transferred between microorganisms and how such electron transfer is regulated. The PhD project aims to explore the interspecies associations of archaea and bacteria from the sulfate-methane transition, then uncouple the organisms in bioelectrochemical reactors in the laboratory where we can test the reversibility of the process. 

Qualifications
Candidates are expected to have an MSc degree in a field relevant to the project, such as environmental microbiology, biogeochemistry or bioelectrochemistry. There is also the possibility of joining a four-year MSc-PhD programme. The candidate should preferably have experience in aquatic microbiology, microbial ecophysiology, or related fields. Experience with bioelectrochemical systems is desirable. We are looking for candidates who are enthusiastic about fundamental science, independent, and interested in working in an interdisciplinary environment, sharing ideas, and collaborating with people from different fields. The candidate should be proficient in spoken and written English.

For further information, please contact: Associate Professor Amelia-Elena Rotaru, e-mail: arotaru@biology.sdu.dk, phone: +45 81920352.


Application, salary etc.
Appointment as a PhD Research Fellow is for three (students who have completed their MSc) or four years (students who have not yet completed their MSc). Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.

The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.

The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Application must be made in the form of a Declaration of Interest including the following:
• A research proposal/description of your approach to the above project (max one page excluding references)
• A letter stating your specific interest, motivation and qualifications for the project in question (max. two pages) (please attach this under box "Application form")
• Detailed CV, including personal contact information
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades
• At least two signed reference letters. Should your referees wish to send their letters directly to us, please have them use e-mail: anc@sdu.dk mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.

Shortlisting may be used in the assessment process.

Further information about the PhD-study can be found at the homepage of the University.

Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Further information for international applicants about entering and working in Denmark.

Send application

Deadline 2021-July-31

You can apply for the job at Faculty of Science by completing the application form

APPLY ONLINE

PhD Scholarship: The Ecological and Biogeochemical Consequences of Ecosystem Restoration at Gyldensteen Coastal Lagoon

 

Department of Biology is seeking to recruit a PhD student for the study of ecological and biogeochemical consequences when flora and fauna composition improve in Gyldensteen Coastal Lagoon after ecosystem restoration by sand-capping, eelgrass transplantation and stone reef establishment. The position is for three years and is supported by a grant from Aage V. Jensen Nature Foundation.  

Gyldensteen Coastal Lagoon is established as a large-scale restoration project where 214 ha agricultural land was flooded with seawater in 2014 by managed realignment. Now, six years after, the flora and fauna has not fully recovered as expected due to impenetrable clay-rich soils that together with resuspension and high water turbidity have hampered the development of the lagoon into a well-functioning ecosystem. To restore the coastal lagoon even further, 10 cm sand-capping, eelgrass transplantation and diffuse stone reefs will be established in several ha of the lagoon.    

The research of the candidate will focus on the ecological biogeochemical conditions expressed by changes in flora (seagrasses and macroalgae) and fauna (benthic infauna and mobile pelagic fauna) after the establishment of the three restoration approaches in the coastal lagoon. The research will include 1) flora and fauna dynamics inside and outside the restored areas within the coastal lagoon; 2) deciphering of changes to the food webs after the restoration efforts; 3) assessing biogeochemical changes in the soil associated with the potential changes in benthic flora and fauna. The selected candidate will be integrated in the research team that manages the large-scale ecosystem restoration project in Gyldensteen Coastal Lagoon.

The candidate must have an MSc degree in biology or equivalent and should have a background in marine ecology and/or biogeochemistry. The candidate will spend much time performing measurements in the field, and in laboratories situated at Gyldensteen Strand and the University of Southern Denmark. The candidate must be able to communicate the research results in Danish to the broader public.

Expected starting date: 1 October 2021. Application deadline: 2 August 2021.

For further information please contact Erik Kristensen, tel.: +45 6550 2754, e-mail: ebk@biology.sdu.dk.


Application, salary etc.
Appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.

The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.

The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Application must be made in the form of a Declaration of Interest including the following:
• A research proposal/description of your approach to the above project (max one page excluding references)
• A letter stating your specific interest, motivation and qualifications for the project in question (max. two pages) (please attach this under box "Application form")
• Detailed CV, including personal contact information
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades
• At least two signed reference letters. Should your referees wish to send their letters directly to us, please have them use e-mail: anc@sdu.dk mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.

Shortlisting may be used in the assessment process.

Further information about the PhD-study can be found at the homepage of the University.

Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Further information for international applicants about entering and working in Denmark.

Send application

Deadline 2021-Aug-02

You can apply for the job at Faculty of Science by completing the application form

APPLY ONLINE

Computational PhD Scholarship to Develop Novel Methods for Disentangling Transcriptional Regulation Using Advanced Functional Genomics

 

The Center for Functional Genomics and Tissue Plasticity (ATLAS) at the Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, invites applications from outstanding candidates who are interested in joining our team as a PhD fellow. The PhD fellow will be affiliated with the Madsen group. The position is available from 1 September 2021 or as soon as possible thereafter. Application deadline: 1 July 2021.

ATLAS
Center for Functional Genomics and Tissue Plasticity (ATLAS) at University of Southern Denmark is supported by the Danish National Research Foundation. The aim of ATLAS is to obtain systems-level, mechanistic and cell type-resolved understanding of adipose and hepatic tissue plasticity in response to diet-induced obesity and regression in mouse models; and to translate this for in-depth understanding of the functional changes in human adipose and hepatic tissues in response to severe obesity and reversal. The centre applies a combination of functional genomics approaches including single cell sequencing, mouse models, proteomics, in vivo targeting, computational biology, and clinical studies.

The centre involves the following PIs:

Susanne Mandrup, Professor, Department of Biochemistry and Molecular Biology (Director) 
Søren Kragh Moestrup, Professor, Department of Molecular Medicine
Blagoy Blagoev, Professor, Department of Biochemistry and Molecular Biology
Aleksander Krag, Professor, Institute of Clinical Medicine & Odense University Hospital
Lars Grøntved, Associate Professor, Department of Biochemistry and Molecular Biology
Jonas Graversen, Associate Professor, Department of Molecular Medicine
Kim Ravnskjær, Associate Professor, Department of Biochemistry and Molecular Biology
Jesper Grud Skat Madsen, Assistant Professor, Department of Biochemistry and Molecular Biology

The Functional Genomics & Metabolism Research Unit
The Mandrup and Madsen groups as well as the centre administration of ATLAS are located in the Functional Genomics & Metabolism Research Unit at Department of Biochemistry and Molecular Biology, SDU. The research unit currently hosts eight independent research groups focusing on various aspects of functional genomics with focus on gene regulatory mechanisms controlling cellular identity, differentiation, and metabolism. The Research Unit constitutes an international, ambitious, highly dynamic, and well-equipped working environment. The unit and the department have state-of-the-art facilities for next generation sequencing, single-cell transcriptomics, flow cytometry, mass spectrometry, metabolomics, bioimaging and transgenic mouse work. Strategic research alliances exist with Odense University Hospital (OUH).

Research Project and Role
As a PhD fellow in ATLAS you will be engaged in a highly ambitious and interdisciplinary project covering gene regulatory mechanisms involved in liver and adipose tissue plasticity. You will interact and collaborate closely with other researchers in the Madsen group and the Mandrup group as well as with members of the other research groups within ATLAS and at the Department of Biochemistry and Molecular Biology.

The successful candidate will be responsible for developing new computational methods to obtain deeper insight into transcriptional regulation from both bulk and single cell -omics data. The project will use both public and internal data and there are rich possibilities to collaborate with wet-lab ATLAS scientists to use the computational models to push the boundaries of adipocyte and liver biology. Hands-on experience with bioinformatics, statistical programming (R or python) and machine learning is considered an advantage. 

Qualifications/requirements
We are looking for a highly motivated, dedicated, and ambitious candidate with:
• A Master’s degree in either Life, Data or Computer Science (e.g. Bioinformatics, Molecular Biology, Biomedicine, or Computational Systems Biology.
• Documented experience with statistical programming (e.g. R or Python).
• Documented experience with -omics data analysis (e.g. single-cell RNA-seq).
• Strong communication and collaborative skills and an interest in working in an interdisciplinary environment.
• Proficiency in spoken and written English.

We offer
• A three-year PhD position in a stimulating and supportive, international research environment.
• Access to state-of-the-art equipment, facilities, and infrastructure.
• Opportunity to interact with an extensive network of national and international collaborators.
• A competitive salary and social benefits (e.g. health coverage, parental leave, social security etc.).
• Dedicated assistance and support with various practical, social, and legal aspects (housing, visa, administration, tax etc.), especially for international candidates through our international staff office (ISO) and department.

For further information please contact Assistant Professor Jesper Grud Skat Madsen (jgsm@bmb.sdu.dk). 


Application, salary etc.
Appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.

The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.

The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Application must be made in the form of a Declaration of Interest including the following:
• A research proposal/description of your approach to the above project (max one page excluding references)
• A letter stating your specific interest, motivation and qualifications for the project in question (max. two pages) (please attach this under box "Application form")
• Detailed CV, including personal contact information
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades
• At least two signed reference letters. Should your referees wish to send their letters directly to us, please have them use e-mail: anc@sdu.dk mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.

Shortlisting may be used in the assessment process.

Further information about the PhD-study can be found at the homepage of the University.

Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Further information for international applicants about entering and working in Denmark.

Send application

Deadline 2021-July-01

You can apply for the job at Faculty of Science by completing the application form

APPLY ONLINE