Phage Scientist – DuPont

DuPont Nutrition & Health is a USD 4.7 billion global business and one of the world’s largest producers of specialty food ingredients, developing and manufacturing solutions for the global food & beverage, nutrition and pharma market. With more than 8,500 employees, 50+ manufacturing sites and 20+ R&D centres across the world, N&H is on a mission to make food safer, more sustainable, better tasting and more nutritious.
N&H is part of DowDuPont, a globally listed company, which came to life following the merger of Dow Chemical and DuPont in 2017. DowDuPont has a turnover of approximately $62 billion, employs around 98,000 FTEs and is headquartered in Wilmington, USA.  The Upstream Culture Development group is part of the R&D Department of its Culture Development and Food Protection Division. The group is strongly involved in knowledge development and is responsible for selecting strains of microorganisms to be used in the design of starter cultures for dairy and other fermentation industries.

The group, which is based in France (86), is seeking a Phage Scientist

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Eligo Bioscience is hiring

“Eligo Bioscience is a VC-backed biotech startup, cofounded by professors and scientists from MIT and Rockefeller (Lu and Marraffini labs). We are developing next-gen therapeutics for precision microbiome engineering and bacteria-associated diseases. Our technology is based on the delivery of genetic circuits (notably CRISPR-Cas) to the microbiome via engineered phage particles.” They can be contacted here.

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Postdoctoral Researcher in Foodborne Pathogen Bioinformatics

Responsibilities:
Work with microbiologists to develop a pipeline for analysis of Campylobacter spp. whole genome sequencing data. This will involve processing of raw sequencing reads, genome assembly, submission of data to public databases, variant mapping, and phylogenetic analysis. The individual will also work with public health professionals at the Tennessee Department of Health (TDH). The role in this joint effort will be to provide data based on outputs from the pipleline, which will inform TDH investigations of campylobacteriosis within Tennessee. Additionally, the individual will assist with knowledge transfer by participating as part of a team in workshop and webinar development and delivery.

Required Qualifications: An earned doctorate in Bioinformatics, Computational Biology, Statistics, Microbiology, Food Science, or other relevant field. Demonstrated knowledge of bioinformatics and basic knowledge of relevant computer programming languages (such as Python, Perl, Bash, R, etc). Proven excellence in verbal and written communication skills, including a strong scientific, peer-reviewed publication record in bioinformatics and/or computational biology-related topics. Communicate effectively with non-computational researchers and be time-responsive

Application:

The University of Tennessee, Institute of Agriculture is seeking candidates who have the ability to contribute in meaningful ways to the diversity and intercultural goals of the University. Applicants should submit: 1) a letter of application, 2) a curriculum vitae detailing education background qualifications, research and teaching experience, and publications, 3) unofficial transcripts of all college course work, and 4) names and contact information (including e-mail addresses) of three individuals who will serve as references.

Submit all application materials using the following link:
https://ut.taleo.net/careersection/ut_knoxville/jobdetail.ftl?job=17000001BA&tz=GMT-04%3A00

More information can be found in this flier here

Opportunités de carrière : Doctoral Student SNSF (12249)

Introduction

The University of Lausanne is a higher teaching and research institution composed of seven faculties where approximately 14,300 students and nearly 3,900 collaborators, professors, and researchers work and study. Ideally situated along the lake of Geneva, near Lausanne’s city center, its campus brings together over 120 nationalities.

Presentation

The Department of Fundamental Microbiology offers a position of Doctoral Student SNSF (on bacteriophage therapy for Staphylococcus aureus infections).

Job information

Expected start date in position : 01.01.2018

Contract length : 1 year, maximum 4 years

Activity rate : 100%

Workplace : University of Lausanne until 31/12/2018 and then either in Lausanne or at the Bern University Hospital – Department of Intensive Care Medicine.

Your responsibilities

The Resch group (https://www.unil.ch/dmf/en/home/menuinst/research-units/gregory-resch.html) aims at developing new therapeutic phages and phage-lysins in a rational approach. Specifically, we isolate new bacteriophages active against the ESKAPE pathogens and evaluate their efficacity in different rodent models of infectious diseases amongst which infective endocarditis in rats. We also address fundamental aspects of phage-bacteria interactions such as bacterial resistance to phages and phage adaptation. The research project of the Doctoral Student SNSF will be on the development of new S. aureus therapeutic phages with a focus on the study of resistance mechanisms. A wide array of methods and technologies in microbiology, phage research and genomics will be applied. The project will provide an excellent scientific training with many opportunities for collaborations in a stimulating environment.

Your qualifications

Applicants should have a Master in biological science with experience in microbiology. Further experience with bacteriophages, animal experimentation, molecular biology, bacterial genomics and computational biology is an asset. The candidate should have a good command of English and be highly motivated to learn new experimental techniques to study phage-bacteria interactions.

What the position offers you

We offer a nice working place in a multicultural, diversified and dynamic academic environment, opportunities for professional training.

Possibilities of continuous training, a lot of activities and other benefits to discover.

Contact for further information

Dr. Grégory Resch

Phone number : 0041 21 692 56 09

Your application

Deadline : 30.11.2017

Please include your full application (motivation letter, CV, list of publications and the contact details of two referees) in Word or PDF.
Only applications through this website will be taken into account.

We thank you for your understanding.

Additional information

Seeking to promote an equitable representation of men and women among its staff, the University encourages applications from women.

PhD SCHOLARSHIP – VIRUS STRUCTURE, Massey University, New Zealand

Project title: Solving the end-cap structure of a biological nanorod derived from the Ff bacteriophage (f1, M13 or fd)

Academic mentors: A/Prof Jasna Rakonjac; A/Prof Andrew Sutherland-Smith

This project aims to determine the cap structure of a versatile biological filament (Ff filamentous bacteriophage). Ff (M13, f1 or fd) phage is a natural and affordable platform for a wide array of technologies, from nano-scale batteries to cancer therapies and treatment of Alzheimer’s disease. Detailed structure of the end-caps will help understand how the Ff filamentous phage is formed naturally and will aid in developing/improving filamentous phage applications.

Fig1
The fine structure of the Ff end-caps has remained a mystery, as they constitute only 2% of the phage filament mass. We overcome this problem by assembling short rods (we named Ff-nano) where the end-caps amount to as much as 40% of the total particle mass. An interesting property of the Ff-nano particles is that they easily form 2D crystals. The Ff-nano particles will therefore enable analyses of the end-cap structure at a near-atomic resolution using cryo-electron microscopy and at atomic resolution using X-ray crystallography.

Fig2
Candidates with a BSc or MSc degree (1st class or high upper 2nd class Honours degree) in biochemistry, biotechnology, molecular biology or microbiology, with interest in structural biology, bacteriophage or nanotechnology are encouraged to apply.

Scholarship is for three years, covering the stipend (NZ$ 25,000 per annum, non-taxable), fees (tuition) and medical insurance. Palmerston North is a lively student city in the Central North Island, close to the ski fields, kayaking and fishing spots, beaches and tramping areas, as well as to Wellington, the New Zealand Capital.

Institute of Fundamental Sciences at Massey University is equipped with a modern structural biology suite and has access to the Australian Synchrotron.

The deadline for the application is 08/05/2017. Applications will be considered on a rolling basis until the studentship is filled.

Filamentous phage topic:
http://journal.frontiersin.org/researchtopic/2352/filamentous-bacteriophage-in-bionanotechnology-bacterial-pathogenesis-and-ecology

Contacts:
A/Prof Jasna Rakonjac; j.rakonjac@massey.ac.nz
https://scholar.google.com/citations?user=N6BHLWoAAAAJ

A/Prof Andrew Sutherland-Smith; A.J.Sutherland-Smith@massey.ac.nz
https://scholar.google.com/citations?user=yHcnJ2wAAAAJ&hl=en

Massey University PhD programme:
http://www.massey.ac.nz/massey/learning/programme-course/programme.cfm?prog_id=-1005

PhD available studying co-evolutionary dynamics at the Max Planck Institute for Evolutionary Biology in Plön, Germany

We are seeking a motivated PhD student to join our research team working
on eco-evolutionary dynamics at the Max Planck Institute for Evolutionary
Biology in Plön, Germany.

We are looking for a highly motivated ecologist or evolutionary biologist
to join our group Community Dynamics at the Max Planck institute for
Evolutionary Biology (http://web.evolbio.mpg.de/comdyn) and the Kiel
Evolution Center (http://www.kec.uni-kiel.de). The ideal candidate is
fascinated by evolutionary and ecological questions, independent and
creative. She/he has a background in evolutionary biology, population
or community ecology. A MSc (or equivalent) in Biology is required.

There is a continuing interest to identify the interactions and feedback
dynamics between ecological and evolutionary changes at the same time
scale. This interest in eco-evolutionary dynamics is fuelled by the
need to understand how populations and communities could adapt to rapid
environmental change such as warming, invasion and pollution. Despite
this pressing need to understand eco-evolutionary dynamics, they are
not well understood in complex systems. In the project we aim to (1)
identify rapid adaptive changes in coevolving host-virus populations in
different food webs that differ in the types of species interactions and
complexity and to (2) comprehend how the dynamics of adaptive changes
alter the ecological dynamics and potential feedbacks. We will combine
controlled laboratory experiments, whole genome sequencing of populations
across different time points and modeling to characterize and compare
the adaptive dynamics and their consequences within the different food
webs. For more information on potential the project contact Lutz Becks
(lbecks@evolbio.mpg.de).

The institute offers a stimulating international environment and
an excellent infrastructure with access to state‐of‐the-art
techniques. The town of Plön is in the middle of the Schleswig-Holstein
lake-district within a very attractive and touristic environment near the
Baltic Sea, close to the university towns of Lübeck and Kiel. Hamburg
and Lübeck are the closest airports.

The position is funded for three years.  We ask applicants to send
a PDF file containing their CV and letter of motivation as well
as contact information of two references by e-mail to Lutz Becks
(mailto:lbecks@evolbio.mpg.de). We will begin reviewing applications
starting March 22th until the position is filled.

The Max Planck Society is an equal opportunity employer.

PhD Student Position

Monash University: Microbiology in Bacteriophage

A PhD position is available to work with Dr Jeremy J. Barr at Monash University, School of Biological Sciences, in Melbourne, Australia. We are looking for motivated, talented and enthusiastic PhD students with an interest in microbiology. With cutting-edge interdisciplinary project, excellent resources, and a strong publication focus, the Barr Lab provides an outstanding opportunity for all students. To learn more, visit thebarrlab.org

Project details:
Bacteriophage are specialist viruses that infect bacteria and are the most abundant biological entities on the planet. Within our bodies, bacteriophages control and manipulate our bacterial microbiota, prevent infection and disease and have interactions with eukaryotic cells and surfaces. Our lab has demonstrated the interactions of bacteriophage with mucus layers that provides an antimicrobial layer (Barr et al., PNAS 2013, 2015). The aim of this PhD project is to investigate the interactions of bacteriophage with bacterial hosts and eukaryotic cells using in vitro experimental systems. In doing so, you will gain expertise in microbiology, bacteriophage biology, infectious diseases, next-generation sequencing, tissue culture, microfluidics and experimental biology.

Scholarship details:
The Barr Lab has three fully-funded scholarships available for domestic and international students interested in doing a PhD. The 3.5 year award includes all course fees and a $26,000 AUD per year tax-free stipend. Additional expenses for relocation, coursework and conference attendance will also be covered.

Monash and the School of Biological Sciences:
Monash is a member of the Group of Eight, a coalition of top Australian universities recognized for their excellence in teaching and research. The School of Biological Sciences is a dynamic unit with strengths in ecology, genetics and physiology and the nexus between these disciplines (monash.edu/science/about/schools/biological-sciences/). The University is located in Melbourne, one of the most liveable cities in the world and a cultural and recreational hub.

Application process:
Interested candidates should send their CV, academic transcripts and a brief outline of research interests and motivation to jeremy.barr@monash.edu Applicants must possess a Bachelor’s or equivalent degree with first-class Honours, MSc or MPhil degree in a relevant subject (e.g., microbiology, genetics, ecology). Review of applications will begin immediately and short-listed candidates will be contacted for more information and invited to interview.

Seeking PhD student in Molecular Biosciences (A)

Ref. No. SU FV-3912-16

at the Department of Molecular Biosciences, The Wenner-Gren Institute. Closing date: 20 January 2017.

Research at the Department of Molecular Biosciences, The Wenner-Gren Institute (MBW) experimentally addresses fundamental problems in molecular cell biology, integrative biology, and infection and immunobiology. State-of-the art and advanced methodologies are applied in a professional research environment characterized by its well-established international profile. The institute has 30 research groups with a research staff of 170, of which 55 are PhD students. Read more about MBW on www.su.se/mbw.

Project description
A PhD position in bacteriophage (bacterial viruses or phages) biology is available in the laboratory headed by Associate professor Anders Nilsson. The general aim of the research carried out in the group is to investigate the coevolution of phages and their bacterial hosts while also investigating the function of uncharacterized phage genes.

The position will be located within the project “Bacteriophage lysins as Alternatives to Antimicrobial Treatment” funded by the Swedish research council FORMAS under Animal Health and Welfare (ANIHWA), a part of the EU collaborative ERA-NET. The main goal of this project is to develop phage derived lysins as potential alternatives to antibiotics in animal production. The research group’s part of the project involves isolation and characterization of novel phages from environmental samples, genome sequencing as well as bioinformatic identification and characterization of lysin genes.

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Cages of phages: improved production of hydrogen by enzymes encapsulated in phage capsids

A guest post by Dr. Paul Hyman,
Ashland University, Ashland, OH, USA
phyman@ashland.edu

Bacteriophage capsids have been studied as frameworks for the development of new materials. In part this is an outgrowth of phage display which allows the precise placement of binding elements on the phage surface. But another approach is to use the native capsids and to nonspecifically attach conductive metals to create wire-like structures or to capture and encapsulate molecules in the capsids as the capsids assemble. In a recent paper in Nature Chemistry, Trevor Douglas’ group at Indiana University and colleagues have shown that the efficiency of an enzyme that reduces protons to form hydrogen gas is more efficient and stable when enclosed in a bacteriophage capsid.

The bacteriophage they used is the Salmonella phage P22.  P22’s capsid is an icosahedron composed of a major coat protein assembled onto a scaffold protein. Coat protein and scaffold protein self-assemble into a procapsid that during a normal infection is then packaged with the phage DNA.  The researchers fused the two subunits of a hydrogenase protein to separate scaffold protein genes.  When expressed together with coat protein, procapsid self-assembled with the heterodimeric hydrogenase protein inside as outlined in this figure.

Hyman blog post

(modified from Jordan 2015)

When they tested for hydrogenase activity, the highest efficiency was found if the scaffold protein/hydrogenase subunits were expressed several hours before the coat protein (line one in the table).  This pre-encapsulation period presumably allowed the two hydrogenase subunits to assemble into the active heterodimer before being constrained by the coat protein.

pH 5 pH 8
P22 encapsulated with sequential expression 6118 nmol H2/mg min 3218 nmol H2/mg min
P22 encapsulated with simultaneous expression 757 nmol H2/mg min
Unencapsulated hydrogenase + scaffold without coat protein 46 nmol H2/mg min 12.6 nmol H2/mg min
Free hydrogenase 12-38 nmol H2/mg min (pH not specified)

Data from Jordan 2015

Additional experiments showed that the encapsulation also partially protected the hydrogenase against trypsin, heat denaturation (60°C for 45 min.) and air exposure.

The reason for the increased enzymatic activity is not entirely clear.  The increased activity and protection results suggest that the enzyme’s quaternary structure is stabilized in some way in the capsid.  It may also be that enzyme efficiency is higher when several hundred copies of the enzyme are in close proximity to each other in some sort of synergistic effect.

Overall, this paper demonstrates another way that phages can be used in non-biological technologies as well as biological.  Independent of the phage aspect, an improved catalyst for production of hydrogen gas could prove quite valuable as alternative fuels, such as hydrogen, are increasingly sought after.

Reference: Paul C. Jordan, Dustin P. Patterson, Kendall N. Saboda, Ethan J. Edwards, Heini M. Miettinen, Gautam Basu, Megan C. Thielges, and Trevor Douglas, “Self-Assembling Biomolecular Catalysts for Hydrogen Production”, Nature Chemistry doi:10.1038/nchem.2416, published on-line December 21, 2015.