13 June 2017
Recent publications in the school
Caing-Carlsson, R., Goyal, P.,
North, R.A., Friemann, R. and
Ramaswamy, S. (2017). Crystal structure of N-acetylmannosamine kinase from Fusobacterium nucleatum. Structural Biology Communications F73: 356-362.
Collings, D., Garrill, A. and Johnston, L. (2017). Student application for special consideration for examination performance following a natural disaster. Assessment & Evaluation in Higher Education doi:org/10.1080/02602938.2017.1332755.
Leung, D.W.M. (2017). Potential of plant tissue culture research conributing to combating arsenic pollution. In: Arsenic Contamination in the Environment: The Issues and Solutions. D.K. Gupta and S. Chatterjee, eds. Springer International: 187-194.
Lindsay, A., Petersen, C., Blackwell, G., Ferguson, H., Parker, G., Steyn, N. and Gieseg, S.P. (2017). The effect of 1 week of repeated ischaemic leg preconditioning on simulated Keirin cycling performance: a randomised trial. BMJ Open Sport & Exercise Medicine 3(e000229): doi:10.1136/bmjsem-2017-000229.
This is a first publication for Beth Jose (PhD candidate), Jasper Perry, Zoe Smeele and Jack Aitken (MSc candidates). Congratulations to all!
Osborne, A.J., Jose, B.R., Perry, J., Smeele, Z., Aitken, J., Gardner, P.P. and Slow, S. (2017). Complete genome sequences of two geographically distinct Legionella micdadei clinical isolates. American Society for Microbiology 5(22): e00436-17.
Recent PhD oral exam completed
Pictured: Jason Tylianakis (Oral Organiser), Kim Baronian (Supervisor), Jonathan and Richard Weld (Supevisor)
Jonathan Williams, had his oral exam on Wednesday 31st May. The title of his thesis is 'An investigation into the use of the yeast Arxula adeninivorans as the catalyst for a microbial fuel cell'. The Oral Examiner, Dr. Frédéric Barrière, University of Rennes was present via video link. Congratulations Jonathan!
Nicole McRae, had her oral exam on Wednesday 31st May via video link. The title of her thesis is 'Mechanisms of trace metal and diclofenac toxicity in Inanga (Galaxius maculatus): contextualising responses of a non-model native New Zealand species to standard fish models'. Chris Glover was her primary supervisor and her other supervisor was Sally Gaw from the Department of Chemistry, who were both present. Nicole had glowing reports from her examiners and the Australasian examiner, Prof Anu Kumar, who was present for the oral exam. Islay Marsden chaired the oral which went really well. [no photo available]. Congratulations Nicole!
Marta Gallart Diumenge, successfully got through her PhD oral on Monday 12th June and the degree is awarded subject to some revisions. Well done Marta! The title of her PhD is 'Genetic and environmental influences on tree nutrition in Pinus radiata (D. Don)'.
The oral was unusual these days in having everyone there in person rather than on video link.
(L to R): Senior supervisor Matthew Turnbull, NZ examiner Ian Dickie (was at Lincoln Univ when he examined it, has now moved to UC), Marta, associate supervisor Peter Clinton (SCION). Absent: assoc supervisor Paula Jameson.
It has been a pleasure to have your style and Catalonia flair about the School. Congratulations Marta!
In the spotlight
Teaching award - Pieter Pelser
On Tuesday 6th June Dr Pieter Pelser was finally awarded his Teaching Award. Teaching awards recognise significant teaching-related achievements in both undergraduate and graduate programmes (including thesis supervision). Teaching Innovation awards recognise a substantial contribution in a particular new area.
Pieter believes that “teaching is most effective when learning takes place in an environment in which students feel supported and receive the personal attention and encouragement that they need to excel.”
His nominators confirm: “Pieter has developed ways of instilling in students a higher personal commitment to engagement, not through cajoling or pressure, but through targeted feedback that results in improved learning outcomes. He brings a warm and personal approach to students, starting by getting to know each student by name.” One of his students says: “Pieter is one of the best teachers I have had. He genuinely cares about students learning, the way he answers questions shows that he doesn’t just want me to do well in assessments, but to actually understand the concepts he is teaching.”
Pieter has worked with Student Care and the Māori Development Team to organise four extra-curricular Positive Learning Workshops targeted to meet the needs of ‘at risk’ students. He is currently working on ‘5-minute Secrets to Success’ in his first year lectures to improve student well-being, academic skills and the transition from high school to university. He has also shown a strong commitment to course design and in particular to incorporating the UC graduate profile attributes.
Professor Jack Heinemann (Nominee), Dr Pieter Pelser (Awardee) and Professor Matthew Turnbull (Nominee)
Winners of the best poster in BIOL383
Aaron Wolfe and Andrew Brown for their poster, "How do slaters build their armour?"
Congratulations. They received 13 votes and $$.
Second place went to Fleur van Eyndhoven and Jenny Edwards (6 votes) for their poster, "Off the beaten track". An excellent poster as well. The display of posters was particularly of high quality this year, and it was also great to see a large turn-out staff and students outside the course. The poster presentation was worth 20% for the course.
Post antibiotic era is business as usual
Jack Heinemann and Brigitta Kurenbach wrote an article for the Alliance for the Prudent Use of Antibiotics (APUA) newsletter
The post-antibiotic era is more than the loss of existing antibiotics; it is the entrenchment of systems that threaten the effectiveness
of new antibiotics and transition to a post postantibiotic era. These systems include unprecedented reliance on manufactured chemical substances, where most of the ~8 million in commerce have neither been adequately evaluated for effects on human health nor for effects on microbes. Another is a social priority to use profit-generating inventions to direct both public and private sector research and development.
Check out the full article/newsletter here.
What Goes On In The Minds Of Spiders?
There are some very cool projects going on in spider science these days.
In one study, jumping spiders are induced to climb small viewing towers to contemplate experimentally manipulated images of prey. In another, wolf spiders are invited to assess visual and vibratory signals, digitally altered in various ways, that represent qualities of their potential mating partners.
Innovative methods are being used to ask the question, "What goes on in the mind of spiders?" The results suggest that the answer is "quite a lot."
Fiona Cross and Robert Jackson at the University of Canterbury in New Zealand discovered that jumping spiders of the species Portia africana display a sort of numerical competence. Read the full article at the National Public Radio, United States.
UC joins the Bio-Protection Research Centre
The Bio-Protection Research Centre (BPRC) is focused on novel research to develop sustainable solutions for controlling plant pests, weeds and diseases in New Zealand. UC will extend the BPRC’s capability in ecology, genomics, biological control and computational biology.
University of Canterbury Professor Matthew Turnbull, Head of the School of Biological Sciences, says UC officially became a partner following a formal invitation from the BPRC in April. Read the full article at UC Communications.
Jumping spiders can count 1, 2, and many
Portia’s capacity to represent exact numbers of prey has now featured in a new article in the Royal Society’s journal Interface Focusby Fiona Cross and Robert Jackson from the University of Canterbury and the International Centre of Insect Physiology and Ecology. Experiments were based on showing Portia a specific number of prey (ranging between 1–6) that could only be accessed by walking along a detour path that first went directly away from the prey. Read the full article at the Royal Society of New Zealand.
Mitja Remus-Emsermann, has secured 4 years of research funding to support a PhD project hosted by ESR entitled “Studying Legionella mobility and persistence in plumbing systems using micro-mimics”. The value of the funding is $82,500 (June 2017 – May 2020).
Ian Dickie, has secured 5 years of research funding within a Landcare-based MBIE contract “Winning against the wildings”. The value of the funding is $1,250,000 (June 2017 – Sept 2021).
David Schiel, has secured a 5-yr extension (Oct 2016 – Sept 2021) to a continuing NIWA subcontract “Maintenance & Rehabilitation of Aquatic Ecosystems”. The value of the extension is $1,216,000. This is contract that has been running since 2010, so it is great to see the relationship continue well into the future.
PhD student Phoebe Argylle, who with supervisor Islay Marsden has secured $3,800 from the Ministry of Foreign Affairs and Trade through the “New Zealand Aid Programme Awards for Postgraduate Field Research”. Her project is “The ecology and toxin production of Gambierdiscus species from the Kingdom of Tonga”.
Elissa Cameron, has secured $120,000 from Woolnorth Wind Farm Holdings and $25,000 from TasNetworks as industry partners for her project “Conservation ecology and response to disturbance of the Tasmanian Wedge Tailed Eagle”.
The funding is to support the expansion of the project, based at the University of Tasmania, which has previously been supported by other industry partners (Forestry Tasmania, Norske Skog and the Holsworth Foundation). The project is a collaboration between Elissa and the Tasmanian Forest Practices Authority, the Department of Primary Industries, Parks, Water & Environment, and the USGS in Boise, Idaho.
David Schiel, for securing a NSC Sustainable Seas contract: Project 4.1.1: Ecosystem connectivity: Tracking biochemical fluxes to inform Ecosystem Based Management. $52,766 (October 2016 to June 2019).
David Schiel, Islay Marsden and John Pirker, have secured a Ministry for Primary Industries grant. To quantify the impact of the Kaikōura earthquake on rocky reef infauna and monitor recovery. $528,936 (May 2017 to July 2018).
The Ngāi Tahu Research Centre invites you to attend the June seminar with Kelly Whitau presenting:
Protecting native forest birds in New Zealand beech forests
When: Friday 16 June, 3.00pm – 4.00pm
Where: Room 208, Level 2, Te Ao Marama Building, Arts Road, University of Canterbury
The Great Hall at the Arts Centre
Our all-day event is free, and suitable for adults and children alike, and we would love to see you there.
The Christchurch Maths Craft Day will feature seven craft creation stations as well as public talks by mathematician crafters, and the day-long celebration of maths promises to engage people of all ages. Make a Möbius strip, crochet a hyperbolic plane, build a fractal sculpture, fold an origami octahedron, and listen to talks about the connections between maths and crafts. Explore the newly opened Teece Museum at the Arts Centre and discover the ancient relationship between mathematics and craftsmanship. Open to everyone: experts and amateurs, maths-fans and maths-phobes, the crafty and the curious.
Genome Biology Symposium
3 - 4 September 2017, Rydges Hotel, Queenstown
Applications for studentship close 5pm on June 30th
The popular view that the sequence of the genome is the key to understanding many diseases and phenotypes is oversimplified. Genome biology is the complex intersection of the processes that are required to decode the DNA sequence. This symposium seeks to challenge our understanding of genome biology. In so doing it will provide an opportunity for researchers who are driven by a desire to collaborate across traditional disciplines to connect and develop new approaches to integrating the knowledge that each individual discipline has amassed.
International Society for Subsurface Microbiology conference (ISSM)
6-10 November 2017, Rotorua
Marsden Funded PhD Scholarship
Testing for Fishing-Induced Evolution using Genotyping-by-Sequencing of Ancient and Modern Snapper
The ideal starting date is 1 July 2017
We are seeking a highly-motivated PhD student for a project that aims to test for fishing-induced evolution in New Zealand Snapper (Chrysophrys auratus) using Genotyping-by-Sequencing (GBS) of modern and ancient DNA.
Dr. Peter Ritchie, Victoria University of Wellington (VUW), New Zealand
Dr. Nic Rawlence, Department of Zoology, University of Otago, New Zealand
Dr. Maren Wellenreuther, Plant and Food Research (PFR), Nelson, New Zealand
Fishing typically targets larger individuals and thus has the potential to increase the reproductive success of small fish that mature early. Numerous studies have reported a decrease in the average size of heavily fished species and the age of maturation, but there is uncertainty about whether this is caused by directional selection on allele frequencies (evolutionary change). The overall goal of this PhD project is to test for fishing-induced evolution in New Zealand snapper by comparing DNA isolated from contemporary populations, to the DNA isolated from bones of pre-industrial fish samples. New Zealand has a unique record of snapper bones that have been preserved in prehistoric New Zealand middens (i.e. places where food remains were dumped or buried). The successful candidate for this project will be responsible for collecting a GBS dataset of genome-wide SNPs using DNA extracted from contemporary samples. This position will be based at Victoria University of Wellington (New Zealand). The data set collected from contemporary samples will be combined with a comparable dataset recovered from snapper ancient DNA that will be obtained by researchers at the Otago Palaeogenetics Laboratory. The complete physical isolation of the ancient and modern part of the project will ensure there is minimal risk of cross-contamination. This ambitious and innovative approach will provide the level of resolution needed to identify genomic regions that have experienced selection and make precise population genetic and demographic inferences possible.
PhD Project Aims
1. To test whether size-selective industrial fishing is associated with a signature of genetic selection,
2. Determine levels of genetic diversity and differentiation,
3. Test for loci under selection and adaptive genetic variation.
This project will provide an excellent opportunity to develop skills in the areas of genomics, bioinformatics and population genetics, and how they can be used to support sustainable harvesting. The PhD student will gain experience working with collaborators in New Zealand (Professor Hamish Spencer), Australia (Professor Mike Bunce), and Norway (Dr. Bastiaan Star). The PhD student will be a member of a highly active and collaborative group of researchers, and help develop population genomics and an understanding of how human activity is changing the environment.
The successful candidate will be a highly-motivated researcher, with a strong background and interest in genomics and molecular evolution. Experience with a coding and/or scripting languages will be an advantage. This position will be based at Victoria University of Wellington and comes with a three-year scholarship that provides a stipend (NZ$27,500 pa) and university tuition fees. This project is supported by the New Zealand Marsden Fund.
Applicants should send a CV, contact details of two academic referees and a cover letter that states why you are interested in the position and how your qualifications and experience make you a good fit for the proposed research. Send these to Peter Ritchie (E-mail: Peter.Ritchie@vuw.ac.nz). Candidate selection will begin May, but applications will be considered until the position is filled. International applicants with strong academic record are encouraged to apply. For more information about studying at VUW and the entry requirements for the PhD program please see http://www.victoria.ac.nz/study/programmes-courses/postgraduates/phds-doctorates
Also see https://www.findaphd.com/search/ProjectDetails.aspx?PJID=84854
Blake DOC Ambassador
The Blake DOC Conservation Ambassador award provides an opportunity for young scientists and conservationists to work on a conservation project in New Zealand, annually. The Blake Ambassador partnership with DOC started in January 2015. DOC partners with other organisations to manage New Zealand’s conservation through habitat protection and restoration programmes, biodiversity inventory and monitoring research projects. This year there will be three Blake DOC Ambassador Programmes: The Rotoiti Nature Recovery Project, Great Barrier Island Black Petrel Seabird Monitoring Project and the Port Waikato Beach Care's Shorebird Protection Programme.
Check out the website and apply now.
Postdoctoral position, Bäurle lab, University of Potsdam
The role of chromatin in environmental stress memory
Applications will be accepted until the position is filled
The position is funded (according to TV-L E13, full time) by an ERC Consolidator Grant initially for two years with a possibility of extension: The successful candidate holds a PhD in biochemistry or molecular biology and is expected to have a proven track record in molecular biology, biochemistry or genetics, including publication(s) in major international journals. A demonstrated aptitude in chromatin biology or next generation sequencing methods is essential. A strong interest in the research question, flexibility, and the ability to work both independently and in a team are required. The working language of the laboratory is English.
PhD/PostDoc positions in Bern Switzerland
Applications close: 30 June
Applications are invited from Postdoctoral Scientists and PhD candidates who have a strong interest in applying genetic and genomic approaches to questions of ecology and evolution. We offer a creative and stimulating international scientific environment with high end facilities.You will join a small and active international group of scientists who address exciting research questions.
Name that song?
The words of the prophets are written on the subway walls.
402: Saunière closed his eyes, his thoughts a swirling tempest of fear and regret. The click of an empty chamber echoed through the corridor.
Answer: The Da Vinci Code
Guessed by: Juanita Miln
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Experienced editor available
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and now for something completely different...
Remembering the original Batman: Adam West
Those of a certain age will remember this character with glee, sitting in front of the TV after school to watch another ripping yarn of our favourite caped crusader.
Batman: Shark Attack - 1966
Batman: Fight scenes - POW!
The very best scenes as Mayor West - Family Guy
Thought for the Week
True black is rare; almost everything that looks black is actually some shade of gray. When everything seems dark, remember that however complicated, there is always a lighter shade to your difficulties.
If you have items of news or interest that you would like included in this newsletter, contact the admin office before noon on Friday at email@example.com or phone ext 6732.