8.8.2017 | Ajankohtaista
Position open in the doctoral student program of Department of Biological and Environmental Science, In University of Jyväskylä
The full description of the project can be found in:
https://www.jyu.fi/bioenv/en/study/doctoral-programme/phd-posts/2018/call#Project4
This PhD project aims to unravel the structural changes of chromatin and viral egress dynamics during the lytic infection with HSV-1. In continuation of our prior studies on HSV-1 reorganization of chromatin architecture, we will further analyze the mechanisms of viral impact on chromatin structure and detailed dynamics of viral nuclear exit. These studies are done in close collaboration with Prof. Carolyn Larabell (National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, CA, USA; 1, 3) and other collaboration partners with expertise in advanced imaging, modeling, biophysics, virology and viral therapy.
We are looking for a highly motivated PhD candidate with a Master’s degree and background in one or several of these areas or a related field: cell biology / microbiology / virology / advanced imaging including live cell imaging, confocal microscopy, EM etc. / biophysics, to conduct the experimental work.
· Contact person: Group leader, Adjunct Professor Maija Vihinen-Ranta, maija.vihinen-ranta@jyu.fi
8.8.2017 | Ajankohtaista
The University of Cologne, Faculty of Medicine, posts the position of Professorship (W2) for Clinical Nursing as per the requirements outlined in § 36 of the Universities act of North Rhine-Westphalia (HG NRW). The position is to be filled by Oct. 1st, 2017. The initial appointment will be for 5 years with an option for tenure.
The professorship will be affiliated with the Institute of Health Economics and Clinical Epidemiology. The main objective of this new position is to establish an international competitive
teaching and research program of nursing science with a primary focus on clinical nursing within a high-performance health care system.
Close cooperation, in particular with the Institute of Health Economics and Clinical Epidemiology, the Institute of Medical Sociology, Health Services Research, and Rehabilitation Science (IMVR),
the University Hospital’s Nursing School as well as with actors of the main research areas of the Medical Faculty is explicitly desired.
We are looking for a scientifically established person in the development of clinical nursing. Candidates should have an excellent scholarly record in developing and evaluating nursing
interventions as well as transferring new research findings into nursing practice. She / He possesses profound knowledge of epistemology and research methods, as for example
epidemiological, experimental and mixed-methods as well as qualitative and quantitative methods of health services research.
The successful applicant will be responsible for the design, implementation and preparation of the evaluation of the new dual Bachelor program in clinical nursing. It is the objective of research
and teaching to expand nursing competencies to respond to changing patients’ needs and to establish new interdisciplinary care approaches with better patient outcomes. Therefore,
profound teaching experiences as well as commitment to qualify and encourage nursing students are mandatory. Close cooperation with the University Hospital of Cologne is essential for success of the Bachelor program.
The Faculty of Medicine seeks to appoint a candidate with an excellent track record in research and teaching. Publications in international journals, social skills, the capacity to work in
multidisciplinary teams and to apply for third-party research funds are prerequisites.
The University of Cologne is committed to increase the percentage of women in research and teaching. Applications of women are specifically encouraged. In the case of equal qualifications,
competence, and specific achievements, women will be considered on preferential terms within the framework of the legal possibilities.
The University of Cologne is an equal opportunity employer in compliance with the German disabilities laws. Candidates with disabilities are therefore strongly encouraged to apply.
Further requirements for application include an academic qualification in nursing science as well as postdoctoral lecture qualification (Habilitation/PhD or equivalent) and background in managing
research projects as well as academic teaching experience. We expect a solid professional experience in nursing practice, preferably in an academic setting. Applicants should have very
good command of the German language.
Applications including a letter of motivation, a curriculum vitae, including publication list and a list of third-party grants, reprints of the five most important publications, teaching record, teaching
concept, concepts of research and clinical activities and credentials und records may be sent to the Dean of the Faculty of Medicine, University of Cologne, and submitted via our Academic
Job Portal (https://berufungen.uni-koeln.de ) no later than 31.8.2017.
8.8.2017 | Ajankohtaista
PhD student position_Pulliainen
6.7.2017 | Ajankohtaista
The Department of Biological and Environmental Science (University of Jyväskylä, Finland) seeks to recruit 4 doctoral students into the Doctoral Programme in Biological and Environmental Science, starting earliest 1.1.2018. The student should complete the doctoral degree in 4 years. Applications, together with all relevant enclosures, should be submitted using electronic application form at latest 31.8.2017 (in Finnish, in English). After the deadline, each supervisor will select one best candidate for their own project. These top candidates will be asked to write a 2-page long research plan on the thesis topic and will be interviewed. Applications sent by email will not be considered. Only one application per candidate is accepted.
For further information on the project, please contact the supervisor (see below).
Further information on the positions and application form: in Finnish, in English.
Descriptions of the projects (Cell and molecular biology):
2. Evolutionary obstacles and opportunities that govern the dynamics of mobile genetic elements in microbial communities
Resistance to antibiotics along with increased virulence has turned bacterium Klebsiella pneumoniae into one of the most notorious hospital pathogens. Genetically it is a complex puzzle: K. pneumoniae strains carry large conjugative and smaller non-conjugative plasmids; the number of integrated viruses and integrative and conjugative elements (ICEs) vary between bacteria, and some isolates have multiple CRISPR-loci defending the host against external genetic invaders whereas others have none. While the bacterial chromosome provides much of the genetic background for the mobile elements to operate in, it is usually the mobile elements that determine the resistance and virulence of individual strains. This interaction between chromosomal background (that drift away from each other due to neutral mutations) and mobile elements (that often change from one background to another) is understood only to some extent. Elements that are not adapted to the host induce fitness costs and thus are selected against. On the other hand, acquiring a novel element at the right moment can rescue the strain from otherwise lethal situation (for example during antibiotic therapy) or provide unique openings for reproduction (for example by providing genes that allow exploitation of host resources). Mobile elements can also force their uptake even in conditions where it is not favorable to the host.
In the proposed PhD project, the interaction of conjugative elements acquired from epidemic K. pneumoniae against novel genetic backgrounds (other hosts) are mapped in an attempt to understand evolutionary obstacles and opportunities that govern the dynamics of mobile genetic elements in microbial communities. This research provides insights to the emergence of novel hospital pathogens as well as helps determine fundamental eco-evolutionary rules behind inter-host genetic exchange. Methodologically, the project involves microbiology with bacteria, molecular biology, genetics and some bioinformatics. Also, if the applicant is interested, there are opportunities for developing computational models. The applicant would join a dynamic research group that studies antibiotic resistant bacteria originating from hospitals across the world. The project is done in collaboration with researchers from Karolinska Institute (Sweden), National Center for Biotechonology Information (NCBI, USA) and University of Cambridge (UK).
A successful applicant would have a background in cellular and molecular biology, evolutionary genetics, or a related field.
Further information: Academy Research Fellow Matti Jalasvuori, Email: matti.jalasvuori@jyu.fi.; mattijalasvuoriresearch.blogspot.fi.
References
Jalasvuori M. & Koonin E. (2015) Classification of prokaryotic genetic replicators: Between selfishness and altruism. Annals of the New York Academy of Sciences 1341: 96–105.
Ojala V., Mattila S., Hoikkala V., Bamford J.K.H., Hiltunen T. & Jalasvuori M. (2016) Scoping the effectiveness and evolutionary obstacles in utilizing plasmid-dependent phages to fight antibiotic resistance. Future microbiology. 11: 999–1009.
3.Structural and functional characterization of M23 family metalloendopeptidases that lyse bacterial cell wall peptidoglycans
Staphylococcus aureus is a major human and veterinary pathogen. The evident increase in S. aureus resistance to antibiotics demands for the development of new, efficient and cost-effective chemotherapeutics. The use of autolysins (bacterial peptidoglycan hydrolases) for the prevention and treatment of S. aureus infections has been under vivid research and shown very promising results. Autolysins play an important role in the maintenance of the bacterial cell wall. The S. aureus cell wall is composed of two polymers, peptidoglycan and teichoic acid. The former provides the structural framework of the bacterium and protects against turgor pressure, whereas the latter controls the overall surface charge affecting e.g. the activity of peptidoglycan hydrolases and surface adherence ability of the bacterium. To date, two autolysins have been tested as potential staphylolytic agents, S. simulans lysostaphin and Pseudomonas aeruginosa LasA. These cleave pentaglycine bridges present in peptidoglycan. Lysostaphin and LasA belong to the M23 family of zinc-dependent peptidases. Other M23 family members that have been structurally and/or functionally characterized are ALE-1 from S. capitis, LytM and LytU from S. aureus, and NMB0315 from Neisseria meningitidis. The overall structures of the enzymes are strikingly similar, the catalytic efficiencies are, nevertheless, markedly different.
The aim of the project is to unravel underlying structural basis for different substrate specificities, catalytic efficiencies as well as the catalytic mechanism of these very similar enzymes by using various biophysical and biochemical approaches. These studies pave the way for development of new therapeutic agents to treat S. aureus infections. The PhD student will engage in structural and functional characterization of this enzyme family by collecting and analyzing data on protein structure and dynamics along with substrate interactions and kinetics. The Permi Lab is the main user of a recently installed, state-of-the-art Bruker Avance III HD NMR spectrometer operating at 800 MHz of 1H frequency, and has access also to a recently upgraded Bruker Avance III 500 MHz NMR spectrometer. The group has also modern facilities for protein production and purification.
We are looking for a motivated PhD applicant having a Master’s degree in Biology/Chemistry or a related field, and some experience at least in one of the following topics: Structural biology/structural bioinformatics, protein biochemistry, biophysical characterization of proteins, NMR spectroscopy, X-ray crystallography. Additional experience on MD simulations, programming, statistics or bioinformatics is beneficial but not essential.
Further information: Professor Perttu Permi, Email: Perttu.Permi@jyu.fi, Tel. +358 (0)40 8054288
References:
Szweda et al. (2012) Peptidoglycan hydrolases-potential weapons against Staphylococcus aureus. Appl Microbiol Biotechnol. 96: 1157–74.
4. Virus-nucleus interactions
Understanding of virus-nucleus interactions is essential for discovering improvements and novel strategies in development of herpes simplex virus type 1 (HSV-1) anti-virals and HSV-1 mediated gene therapy. Moreover, viral infections manipulate the nucleus, and serve as excellent model systems for the characterization of nuclear processes. Our studies advance the current research of virus-nucleus interactions by an interdisciplinary approach involving cell biology and biophysics, combined with state-of-the-art techniques of microscopy imaging, advanced image analysis, and biophysical modeling.
This PhD project aims to unravel the structural changes of chromatin and viral egress dynamics during the lytic infection with HSV-1. In continuation of our prior studies on HSV-1 reorganization of chromatin architecture (1, 2), we will further analyze the mechanisms of viral impact on chromatin structure and detailed dynamics of viral nuclear exit. These studies are done in close collaboration with Prof. Carolyn Larabell (National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, CA, USA; 1, 3) and other collaboration partners with expertise in advanced imaging, modeling, biophysics, virology and viral therapy.
The doctoral student will benefit from supportive research training environment and receive co-supervision by group leader and the senior members of the research team. He/she will use state-of-the-art imaging techniques in University of Jyväskylä, Tampere and Helsinki, attend advanced practical courses on imaging (e.g. EMBO) and national and international scientific meetings, and do site visits in international labs.
We are looking for a highly motivated PhD candidate with a Master’s degree and background in one or several of these areas or a related field: cell biology / microbiology / virology / advanced imaging including live cell imaging, confocal microscopy, EM etc. / biophysics, to conduct the experimental work.
Further information: Group leader, senior lecturer Maija Vihinen-Ranta, Email: maija.vihinen-ranta@jyu.fi
Our most recent publications
Aho V., Myllys M., Ruokolainen V., Hakanen S., Mäntylä E.,Virtanen J.,Hukkanen V., Kühn T., Timonen J.,Mattila K.,Larabell C.& Vihinen-Ranta M (2017). Chromatin organization regulates viral egress dynamics Sci Rep 16(7): 3692.
Pyöriä L., Toppinen M., Mäntylä E., Hedman L., Aaltonen L.-M., Vihinen-Ranta M., Söderlund-Venermo M., Hedman K. & Perdomo M.F. (2017). Extinct type of human parvovirus B19 persists in tonsillar B cells. Nat Commun 4(8): 14930.
Myllys M., Ruokolainen V.,Aho V., Smith E., Hakanen S., Peri P.,Salvetti A., Timonen J., Hukkanen V.,Larabell C.& Vihinen-Ranta M. (2016).Herpes simplex virus 1 induces egress channels through marginalized host chromatin. Sci Rep, 28(6): 28844.
Aho V., Mattila K., Kühn T., Kekäläinen P., Pulkkinen O., Brondani Minussi R., Vihinen-Ranta M. & Timonen J. (2016). Diffusion through thin membranes: Modeling across scales. Phys Rev E 93: 043309.
5.7.2017 | Ajankohtaista
1.Job/ project description:
The postdoc could choose between three main research projects:
a. Mathematical modeling of phenotypic evolution in populations with embryonic development.
b. Mathematical modeling of gene network and embryonic development evolution.
c. Mathematical modeling of organ development and their evolution in mammalian teeth or Drosophila wing.
The actual project will be chosen together with the candidate depending on his/her interests and skills.
The research will take place in the Isaac Salazar-Ciudad’s group in the Center of Excellence in Experimental and computational developmental biology of the Biotechnology Institute of the University of Helsinki, Finland.
The job is for 1 year and renewable for 1 extra year.
2. Background:
Why organisms are the way they are?
Can we understand the processes by which complex organisms are build in each generation and how these evolved?
The process of embryonic development is now widely acknowledged to be crucial to understand evolution since any change in the phenotype in evolution (e.g. morphology) is first a change in the developmental process by which this phenotype is produced. Over the years we have come to learn that there is a set of developmental rules that determine which phenotypic variation can possibly arise in populations due to genetic mutation (the so called genotype-phenotype map). Since natural selection can act only on existing phenotypic variation, these rules of development have an effect on the direction of evolutionary change.
Salazar-Ciudad’s group is devoted to understand these developmental rules and how these can help to better understand the direction of evolutionary change. The ultimate goal is to modify evolutionary theory by considering not only natural selection in populations but also developmental biology in populations. For that aim we combine mathematical models of embryonic development that relate genetic variation to morphological variation with population models. The former models are based on what is currently known in developmental biology.
Salazar-Ciudad’s group is in close collaboration with Jukka Jernvall’s group and other groups within the center of excellence in experimental and computational developmental biology. The center includes groups working in tooth, wing, hair and mammary glands development. In addition to evolutionary and developmental biologists the center of excellence includes bioinformaticians, populational and quantitative geneticists, systems biologists and paleontologists.
“The Academy of Finland’s Centres of Excellence are the flagships of Finnish research. They are close to or at the very cutting edge of science in their fields, carving out new avenues for research, developing creative research environments and training new talented researchers for the Finnish research system.”
3. Requirements:
The applicant must hold a PhD in either evolutionary biology, developmental biology or, preferably, in evolutionary developmental biology (evo-devo). Applicants with a PhD in theoretical or mathematical biology are also welcome.
Programming skills or a willingness to acquire them is required.
The most important requirement is a strong interest and motivation on science and evolution. A capacity for creative and critical thinking is also required.
4. Description of the position:
The fellowship will be for a period of up to 1+1 years (100% research work: no teaching involved). Salary according to Finnish postdoc salaries.
5. The application must include:
-Motivation letter including a statement of interests
-CV (summarizing degrees obtained, subjects included in degree and grades, average grade).
-Summary of PhD project, its main conclusions and its underlying motivation.
No official documents are required for the application first stage but these may be required latter on.
6. Deadline:
There is no specific deadline, the position will be filled as soon as a suitable candidate is found.
7. Examples of recent publications by Isaac Salazar-Ciudad group.
– Brun-Usan M, Marín-Riera M, Grande C, Truchado-Garcia M, Salazar-Ciudad I. A set of simple cell processes is sufficient to model spiral cleavage. Development. 2017 Jan 1;144(1):54-62.
– Salazar-Ciudad I, Marín-Riera M. Adaptive dynamics under development-based genotype-phenotype maps. Nature. 2013 May 16;497(7449):361-4.
– Salazar-Ciudad I, Jernvall J. A computational model of teeth and the developmental origins of morphological variation. Nature. 2010 Mar 25;464(7288):583-6.
8. Interested candidates should check our group webpage:
5.7.2017 | Ajankohtaista
Pulliainen-laboratory aims to understand i) how bacterial toxins/effector proteins are secreted, ii) how bacterial toxins/effector proteins recognize and enter the target host cell and iii) how bacterialtoxins/effector proteins manipulate host cell signaling to ultimately influence the disease progression. Our ultimate goal is to gain insights that allow development of new antimicrobials for emerging antibiotic resistant bacteria. The laboratory is currently funded by the Academy of Finland and the Sigrid Jusélius Foundation (– 2020).
The research focus for the PhD student position is on type IV secretion systems (T4SSs) – multiprotein megadalton complexes that span the cell envelope of clinically significant bacteria including generaBrucella, Helicobacter, Legionella, Bartonella and Bordetella. T4SSs translocate a multitude of different toxins/effector proteins, such as pertussis toxin or CagA oncoprotein, into to the extracellular space or directly into the cytosol of host cells. Type IV secretion systems also mediate bacterial conjugation and therefore they are key players in the spread of antibiotic resistance determinants.
The person selected for the position studies the secretion mechanism of T4SSs as well as the elusive host cell recognition process of T4SS pilus structures. The project also involves drug discovery approaches. T4SSs are ideal drug targets since no analogous counterparts are known from eukaryotes.
To qualify for the position, the candidate needs: 1) high motivation level, work morale and independent initiative, and 2) completed or nearly completed MSc or an equivalent degree.
Please send your application in English as a single PDF document to Arto Pulliainen (arto.pulliainen@utu.fi ), 31.8.2017 at the latest. The application has to contain: i) one page motivation letter, and ii)CV with contact information of at least two references.
The start time is negotiable, but September 2017 is preferable. The position includes a 4-month trial period.
Further information:
Arto Pulliainen, PhD, Docent/Adjunct professor
Institute of Biomedicine
University of Turku
Kiinamyllynkatu 10
FI-20520 TURKU
tel. +358 40 1586044
4.7.2017 | Ajankohtaista
Two postdoctoral fellow positions are available in the Dhvanit Shah Laboratory (www.shahlaboratory.org) at the Division of Hematology, Brigham and Women’s Hospital (BWH) & Harvard Medical School (HMS), Boston MA, United States.
The Shah laboratory is located in a dynamic Harvard Medical Area that offers excellent opportunities for intellectual exchange and collaborations among investigators from diverse fields. We investigate the origin, development, and differentiation of hematopoietic stem cells (HSCs), and their utility in treating patients with blood and bone-marrow diseases. We have expertise in utilizing zebrafish, mice, and human induced pluripotent stem (iPS) cells to analyze novel genes and mechanisms important for blood formation. Our goals are to utilize our knowledge in developing cellular- and mechanism-based therapies as well as generating functional HSCs for the treatment of hematological diseases.
Position # 1: Hematopoietic Stem Cell Development and Disorders
Ideal candidate will have Ph.D., M.D., or M.D./Ph.D. in Regenerative Medicine, Stem Cells, Immunotherapy, Hematology, Oncology, and/or Biology. This position offers an excellent opportunity to learn and apply skills in directed differentiation of mouse embryonic stem cells and/or human induced pluripotent stem cells, epigenetics, HSC transplant, xenograft, computational biology, high-throughput screening, gene-editing, and/or molecular and cellular biology techniques. Strong background in one or more of these areas is preferred. Qualified candidate should be able to work independently as well as in a group environment.
Position # 2: Bioengineering of 3D Scaffold Development
Ideal candidate will have Ph.D., M.D., or M.D./Ph.D. in Tissue Engineering, Biomaterials, Biophysics, Machine Learning, Systems Biology, Chemical Engineering, and/or Drug Development. This position offers an excellent opportunity to learn and apply skills in organoid development, 3D bio-printing, Bio-MEMS, artificial intelligence, microfluidics, proteomics, and/or medicinal chemistry. Strong background in one or more of these areas is preferred. Qualified candidate should be able to work independently as well as in a group environment.
Interested candidates should send their cover letter, CV, and contact details of three references to:
Dr. Dhvanit I. Shah
Division of Hematology,
Brigham and Women’s Hospital &
Harvard Medical School
One Blackfan Circle, Karp 06.211
Boston, MA 02115
BWH & HMS are an affirmative action/equal opportunity employers.
4.7.2017 | Ajankohtaista
PhD student position in structural biology and drug discovery; University of Oulu, Finland
4.7.2017 | Ajankohtaista
Medical Science Liaison; Chiesi Group, Finland
4.7.2017 | Ajankohtaista
Senior Clinical Research Associate/Start-up Specialist