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.

Continue reading

Virion Location of Most Phage Depolymerases

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

Here is a something worth knowing about, from Pires, D.P., H. Oliveira, L.D. Melo, S. Sillankorva, and J. Azeredo. 2016. Bacteriophage-encoded depolymerases: their diversity and biotechnological applications.  Appl. Microbiol. Biotechnol. 100:2141-2151. [PubMed], (calls to figure and table excluded from quote):

Based on our search, the huge majority of phage depolymerases (126 proteins) are encoded in the same open reading frame of phage structural proteins (mostly on tail fibers, base plates, but sometimes also in the neck) or in close proximity to those genes, and were thus considered as structural proteins. Twenty other depolymerases found in this work might be soluble proteins since they are distant from any structural gene.

Depolymerases that are only soluble, that is, not virion attached, presumably are only useful in the immediate vicinity of phage-lysed bacteria, e.g., towards phage burrowing more deeply into biofilms. This perhaps means that phages don’t need depolymerases to initially infect biofilm bacteria (see here for that argument). Depolymerases that are associated with virions, by contrast, presumably are useful as well upon initial phage encounter with a biofilm bacterium.

That the majority of depolymerases are may not be soluble, but instead appear to be associated with virions, is suggestive that depolymerases are employed for the sake of initial encounter between virions and biofilm bacteteria. But this then begs the question of why more phages don’t encoded depolymerases?

Is it that we have trouble recognizing them in sequence data? Is it that bacteria are just too diverse in terms of extracellular polymers produced? (In addition to limiting utility, the latter may also interfere with our ability to detect depolymerase phenotypes during phage growth as plaques.) Is it because for the most part phages can infect biofilm bacteria sufficiently even without depolymerases? Or are there unexplored trade-offs associated with depolymerase encoding, perhaps especially when they are present as structural components of phage virions?

In the three previous paragraphs I am drawing on a tiny bit of past thought as to the role of depolymerases in phage interaction with biofilms, as can be found in my 2011 book, Bacteriophages and Biofilms. In particular, from p. 23 (of the revised pagination version, or p. 27 of the original… don’t ask…):

Ecologically, EPS depolymerases improve phage movement that occurs either adjacent to or distant from a phage’s parental infection. If distant, then movement towards bacteria will be enhanced by physical linkage between virions and depolymerases. Alternatively, for more localized movement, then soluble depolymerases may suffice, such as for phage dissemination out of biofilms [2004]. Scholl et al. [2005] thus found that efficiency of plating (EOP) was low for phages encoding a soluble EPS depolymerase when infecting a K1 capsule-producing strain and that an isogenic phage not encoding the depolymerase is “unable to form plaques on lawns of this strain” (p. 4872). This result is suggestive that though initiation of plaques occurred with low efficiency, once those infections commenced then subsequent EPS depolymerization presumably facilitated phage migration towards adjacent bacteria to complete plaque formation. In circumstances where enzymes may not be directly supplied, it should thus be advantageous for those enzymes to be carried by virion particles, if only to increase the efficiency of initial infection. That is, it should be advantageous to phages for enzymes to be present at the point of phage adsorption, by being virion attached, rather than present only immediately following the lyses of phage-infected bacteria [I then illustrate this argument with a figure…].

 

 

 

Attacking Biofilms: Another Quote, Plus Some Discussion

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

This quote is from Lee Watkins and J. W. Costerton (1984). Growth and biocide resistance of bacterial biofilms in industrial systems. Chemical Times and Trends (October):35-40.

The article has nothing to do with viruses. The quote is interesting, however, since it speaks to the question of how exactly to employ viruses in the biocontrol of microorganisms, specifically in the biocontrol and indeed elimination of biofilms from surfaces (quotation marks in the original):

lt is important to be able to answer that old question “Shall we slug with a biocide, shall we continuously treat with a biocide or shall we soak with a biocide—what is the best deal for the situation?”

To me these three alternatives are distinguishable in terms of how we might think about treatment of bacteria or biofilms with phages, that is, phage-mediated biocontrol of bacteria, or phage therapy.

The first alternative I interpret as the application of large amounts of biocide over short periods, perhaps in a single dose, i.e., slugging, or what we might describe as passive treatment in the case of phage therapy. Keep in mind that passive treatment should mean that for every bacterium targeted not only should at least 10 phages be added but at least 10 phages should be adsorbing, per adsorbable bacterium.

Continuous application, to me, would imply the application of lower but still minimally effective concentrations of biocide over longer periods. Continuous application represents an extreme of multiple dosing, i.e., where the time gap between applications is reduced to zero. Key here is that something other than overwhelming amounts of biocide is being applied, what many (unfortunately) would describe as something other than high multiplicities of infection (MOI) in the case of phage application. One can view such continuous application a preventive, or prophylactic.

Lastly there is soaking, which could also be viewed as continuous application, though this is an application that takes place over a relatively short period, i.e., days or weeks rather than months or years. This would be equivalent to the application of phages by soaking bandages, soaking various absorbent material (one sees mention of “tampons” in various places in the phage therapy literature, though it’s important to realize that the word has a medical definition), or instead via the application of, e.g., Phage Bioderm (for example, as discussed here).

What’s missing, of course, are any assumptions that the biocide will replicate in situ, i.e., so-called active treatment, which is typically considered to be a hallmark of phage-mediated biocontrol/phage therapy. That absence, though, is not unexpected given that this is from a discussion of chemical and physical anti-biofilm biocides rather than of phages.

Still, it once again is nice to see that there really is little that is new under the sun. When dealing with bacterial infections, particularly chronic ones which are associated with biofilms, it can be important to keep in mind these ideas:

  1. We can hit them very hard (literally overkill) over short periods,
  2. We can hit them less hard (minimally adequate biocide concentrations) but over long periods, perhaps particularly towards prevention, or
  3. We can soak the infections over intermediate periods, presumably with periodic re-invigoration of dosing, using antibacterial levels which, also presumably, are somewhat in excess of what might be viewed as minimally adequate.

Any other approach, unless backed by hard data, should be considered to represent mostly wishful thinking.

Some additional reading:

Abedon, S.T. 2016. Bacteriophage exploitation of bacterial biofilms: phage preference for less mature targets?  FEMS Microbiol. Lett. 363:fnv246. [PubMed]

Abedon, S.T. 2016. Commentary: phage therapy of staphylococcal chronic osteomyelitis in experimental animal model.  Front. Microbiol. 7:1251. [PubMed]

Abedon, S.T. 2016. Phage therapy dosing: The problem(s) with multiplicity of infection (MOI).  Bacteriophage 6:e1220348. [PubMed]

Abedon, S.T. 2014. Bacteriophages as drugs: the pharmacology of phage therapy., p. 69-100. In J. Borysowski, R. Miedzybrodzki, and A. Górski (eds.), Phage Therapy: Current Research and Applications. Caister Academic Press, Norfolk, UK.

Abedon, S. 2011. Phage therapy pharmacology: calculating phage dosing.  Adv. Appl. Microbiol. 77:1-40. [PubMed]

Abedon, S.T., S.J. Kuhl, B.G. Blasdel, and E.M. Kutter. 2011. Phage treatment of human infections.  Bacteriophage 1:66-85. [PubMed]

Abedon, S.T. and C. Thomas-Abedon. 2010. Phage therapy pharmacology.  Curr. Pharm. Biotechnol. 11:28-47. [PubMed]

Bacterial Lawns as Biofilm-Like Environments: A New Old Quotation

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

Way back in 2010 we (Abedon and Thomas-Abedon) suggested that the growth of phage plaques within bacterial lawns could serve as mimics of bacteriophage interaction with bacterial biofiolms. In fact, we made a rather extensive argument with six Roman numeraled points: (i) constraint of bacterial movement, (ii) bacterial growth within lawns as microcolonies, (iii) inhibition of phage movement, (iv) plaque-like phage growth within actual biofilms, (v) possible temporary shielding of bacteria within lawn microcolonies from phage attack, and (vi) variation in bacterial physiologies again as found within microcolonies within lawns and as potentially equivalent to bacterial microcolonies within biofilms. We concluded that, “Given these similarities, phage plaques as a facile laboratory model therefore could enrich our understanding of phage-bacterial interrelations as they may occur during the phage therapy of biofilm-producing bacterial infections.”

Indeed, we noted as well that Gallet et al. (2009) described phage formation of plaques also as phage growth within a “biofilm-like environment”.

Here I provide a quote from an earlier publication which serves to further these arguments. From Gilbert and Brown (1995) [Mechanisms of the protection of bacterial biofilms from antibacterial agents, p. 118-130. In J. W. Costerton and H. Lappin-Scott (ed.), Microbial biofilms. Cambridge University Press, Cambridge, UK.], p. 119:

The most simple in vitro method of generating biofilms to study antimicrobial sensitivity is to inoculate the surface of an agar plate to produce a confluent growth. Such cultures, whilst not fully duplicating the in vivo situation, have been suggested to model the close proximity of individual cells to one another and the various gradients found in biofilms. In this respect, colonies grown on agar may bе representative of biofilms at solid-air interfaces.

Of course, one cannot claim that bacteria growing within soft agar overlays are perfect representations of naturally occurring biofilm structures. Nonetheless, as we’ve noted previously, e.g., Abedon and Yin (2009), plaque formation within them is a lot more complex than people otherwise may realize.