from biomolecules to the biosphere

Department of Biological Sciences Newsletter
“from biomolecules to the biosphere”
No. 13
April 4, 2014
Announcements
The NSERC DG results are finally available and I am pleased to say that our Department
did very well. CONGRATULATIONS to Peter Dunfield, Constance Finney, Lash Gedamu,
Sean Rogers, Jana Vamosi and Wic Wildering for each being awarded a five-year DG,
in many cases with a significant increase in funding. The Department went in with approximately $750K of total funding (over 5 years) and came out of the competition with
almost $1.2M! This is an excellent result. In addition, Sean Rogers was successful with an
RTI application. Many thanks to Doug Muench and all of the internal reviewers who provided valuable feedback on applications. Also, many thanks to Brian Keay for his workshops and reviews. Well done everyone! - Robert
Pictures from this year’s Graduate Student Poster Display
Important Dates
Apr 8th - “Special” Faculty Council Meeting with Dru Marshall - BI 587 2 PM
Apr 10th - Faculty Council Meeting - ST 141 9:30 AM
Apr 15th - Department Meeting - BI 211 2 PM
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June 12th - Convocation & Celebration Lunch
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Recent Publications
E. Snively, A. P. Russell, G. L. Powell, J. M. Theodor & M. J. Ryan 2013 The role of the neck
in the feeding behaviour of the Tyrannosauridae: inference based on kinematics and muscle
function of extant avians. Journal of Zoology.
doi:10.1111/jzo.12109
Philip, A., Jorgensen, E.H., Maule, A.G. and Vijayan, M.M. 2014. Tissue-specific molecular immune response to lipopolysaccharide challenge in emaciated anadromous Arctic charr. Developmental and Comparative Immunology 45: 133-140.
Sandhu, N., McGeer, J. and Vijayan, M.M. 2014. Exposure to environmental levels
of waterborne cadmium impacts corticosteroidogenic and metabolic capacities,
and compromises secondary stressor performance in rainbow trout. Aquatic Toxicology
146: 20-27.
Nesan, D. and Vijayan, M.M. 2013. The transcriptomics of glucocorticoid receptor signaling during zebrafish embryogenesis. PLoS ONE, 8: e80726.
Seminars
BCEM seminar - Tuesday at 16h00 in BI 499
April 8 - Michael Overduin - Intersection of kinase, phosphatase and membrane
protein structural biology and drug discovery
ICB seminars - Fridays at 14300 in BI 211
Apr 11 - Lianne Vachon - TBA
EEB seminar - Tuesday at Noon in BI 211
Apr 8 - Craig Scott - Palaeomammalogy in Alberta: New Insights from Old Fossils
EEB seminar - Friday at Noon in BI 211
Apr 11 - Sharon Strauss - TBA
ICB 601 seminars - Thursdays at 13h00 in BI 211
Apr 10 - Chinmayee Das - Rapid non-genomic cortisol signaling: mode of action
and cellular stress adaptation
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EEB 601 seminar - Monday at 12h00 in BI 211
Apr 7 - Soraya Villalobos - The role of pollinator specialization in the reproductive ecology of plants
Micro 601 seminars - Wednesdays at 12h00 in BI 211
Apr 9 - Roshan Khadka - TBA
Graduate Student Affairs
Research Proposals
None currently scheduled.
Ph.D. Candidacy Oral Examination - Candidacy Exams are Closed Exams.
Anne-Marie Labandera (Supervisor: G. Moorhead), will be holding her Candidacy Examination, in the area of “Biochemistry”, on May 5th, 2014 at 9:00 a.m. in BioSciences room
389. (Neutral Chair: V. Zaremberg).
Siyu Liang (Supervisor: M. Samuel), will be holding her Candidacy Examination, in the
area of “Physiology”, on May 9, 2014 at 10:00am in BioSciences room 312. (Neutral Chair:
A. Russell).
Yibo Wang (Supervisor: S. Noskov), will be holding his Candidacy Examination, in the
area of “Biophysical Chemistry”, on May 27, 2014 at 9:00am in BioSciences room 312.
(Neutral Chair: R. Edwards)
Ramya Singh (Supervisor: D. Hansen), will be holding her Candidacy Examination, in the
area of “Developmental Biology”, on June 23, 2014 at 10:00 a.m. in BioSciences room
312. (Neutral Chair: M. Samuel).
Thesis Oral Examinations - Exams are “Open” unless otherwise noted.
Please note: Pre-defense seminars are a degree requirement for all M.Sc. and Ph.D. students in
Biological Sciences. Typically, the seminar will take place immediately preceding the Oral Defense Exam.
Room bookings for Student Meetings - It is the student’s responsibility to book the necessary
com-media equipment with either Benedicta (220-3578 [email protected]) or David (2208307) for their examination. Please book the equipment as soon as you have the date set for
your exam/proposal meeting. (defense seminars are held one hour before the stated defense
time in BI 211 unless noted otherwise)
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Eun Jee “Jenny” Kim (Supervisor: D. Morck), will be holding her M.Sc. Thesis Oral Examination,
in the area of “Molecular Microbiology”, on April 17, 2014 at 2:00 p.m. in BioSciences room 499.
(Neutral Chair: L. Gedamu).
Jane Fowler (Supervisor: L. Gieg), will be holding her Ph.D. Thesis Oral Examination, in
the area of “Environmental Microbiology” on April 21, 2014 at 2:00 p.m. in BioSciences room 312.
(Neutral Chair: C. Shemanko).
Gregory Earle (Supervisor: R. Cartar), will be holding his MS.c. Thesis Oral Examination, in the
area of “Ecology” on May 7, 2014 at 10:00 a.m. in BioSciences room 312. (Neutral Chair: D. Hansen).
Brian Kopach (Supervisor: J. Fox), will be holding his Ph.D. Thesis Oral Examination, in the area of
“Ecology” on May 13, 2014 at 10:00 a.m. in BioSciences room 389. (Neutral Chair: K. Ruckstuhl).
CLOSED EXAM
Jennifer Beatty (Supervisor: A. Buret), will be holding her Ph.D. Thesis Oral Examination, in the
area of “Host-Pathogen Interactions” on June 11, 2015 at 10:00 a.m. in BioSciences room 389.
(Neutral Chair: D.A. Syme).
Amol Bhargava (Supervisor: A. Buret), will be holding his M.Sc. Thesis Oral Examination, in the
area of “Host-Parasite Interactions” on June 13, 2015 at 10:00 a.m. in BioSciences room 389.
(Neutral Chair: K. Ruckstuhl).
Kristen Reti (Supervisor: A. Buret), will be holding her M.Sc. Thesis Oral Examination, in the area
of “Host-Pathsogen Interactions” on June 25, 2014 at 10:00 a.m. in BioSciences room 312. (Neutral Chair: K. Ruckstuhl).
Congratulations to….
Mark Mahadeo, who successfully defended his Candidacy Examination, in the area of
“Biophysical Chemistry”, on March 28, 2014!
“Piled Higher and Deeper”
by Jorge Cham
www.phdcomics.com
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“from biomolecules to the biosphere”
Behind the Leaf
News from the BGSA
April Events and Information;
• 2014-15 BGSA Elections;
We are still looking for candidates to run for the Secretary and Treasurer
positions. These are important positions needed for the BGSA to operate. We
will accept nominations (send to [email protected]) until Sunday, April 6th at
11:59 PM. Please include a profile picture, which position you are running for,
and a short platform.
Voting Days start next week (April 7th-11th). Voting can be done through the
BGSA Blackboard webpage under “Elections 2014.” Candidate platforms can
also be found here. If you would like to vote, but don’t have access to the
BGSA Blackboard webpage, please let us know ([email protected]).
Voting results will be announced April 12th at this year’s Graduate Retreat!
Good luck to all candidates.
• Graduate Retreat, April 12th-13th, Biogeoscience Institute, Kananaskis
There are only a few spots left for this year’s Graduate Retreat!
Cost: $10 (includes lodging, dinner and breakfast).
Guest Speaker (Jessie Kubes) from Innovate Calgary; “Life after Grad School –
Getting Involved in Industry” April 12th at 3:30 PM.
If you have any dietary restrictions, need transportation to the Retreat (or are
able to carpool others), please let us know ASAP.
-
BGSA – University
of Calgary
The BGSA ([email protected])
BGSA (if you don’t have
access, email us)
@biogsa
“from biomolecules to thewww.ucalgary.ca/bgsa
biosphere”
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Department of Biological Sciences
“The INs and OUTs in Adaptive Immunity and Viral Immune Evasion”
Dr. Robert Tampé
Institute of Biochemistry, Biocenter, Goethe-University Frankfurt
April 8, 2014 (11 a.m. – 12 p.m.) / BI 211
Abstract: The recognition and elimination of virally or malignantly transformed cells is the pivotal task
of the adaptive immune system. For immune surveillance, a snapshot of the cellular proteome is
displayed on major histocompatibility (MHC) class I molecules as immunodominant epitopes for
recognition by cytotoxic T-cells. The knowledge about the track from the equivocal protein to the
presentation of peptides has greatly expanded, leading to an astonishingly elaborated understanding of
the MHC I peptide loading pathway. This seminar will report on this complex process, which rests on
ABC transporters, chaperones, and ER quality control. The contribution of the individual proteins and
subcomplexes as well as the architecture and dynamics of the peptide-loading complex will be
discussed, including mechanisms of viral immune evasion.
Event free and open to the public / Host: Dr. Peter Tieleman
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“from biomolecules to the biosphere”
NEXT GENERATION
SEQUENCING
SYMPOSIUM
Tuesday April 22, 2014
Clara Christie Lecture Theatre in HSC
University of Calgary
Speakers: 8:30am-3:45pm
Lunch provided
Poster Session / Wine & Cheese Social: 3:45-6pm
*To register visit
canadangssymposia.com
or research4kids.ca
The symposium will provide an overview of NGS, and a forum to discuss the science,
applications, instrumentation, methods, and best practices in NGS.
Featured Speakers:

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Dr. François Bernier - Director, Clinical Genetics Unit, Dept. Head of Medical Genetics, University of
Calgary
Marc Strous, PhD - Professor, CAIP Chair, Energy Bioengineering Group, Dept. of Geoscience,
University of Calgary
Masoud Toloue, PhD - Vice-Pres. Genomic Technologies, Bioo Scientific Corp, Texas
Joe Harrison, PhD - Assistant Professor, CRC in Biofilm Microbiology and Genomics, Dept. of
Biological Sciences, University of Calgary
Sean Rogers, PhD - Assistant Professor, Dept. of Biological Sciences, University of Calgary
Paul Gordon, PhD - ACHRI Bioinformatics Support Specialist, University of Calgary
Scott Rose, PhD - Director of Product Development, Integrated DNA Technologies Inc, Iowa
Dr. Dan Gregson – Dept. of Pathology and Laboratory Medicine, University of Calgary
 Jillian Parboosingh, PhD - Laboratory Director, Molecular Diagnostic Laboratory, Alberta Children’s
Hospital; Associate Professor, Department of Medical Genetics, University of Calgary
*There is no fee to attend
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2nd Molecular Simulation Summer School
23rd - 27th June 2014
University of Calgary
WHAT: 2nd Molecular Simulation Summer School
WHEN: 23rd - 27th June 2014
WHERE: Centre for Molecular Simulation, University of Calgary
TOPICS: Combined quantum/molecular mechanics, molecular dynamics,
and coarse-grained molecular dynamics simulations
STRUCTURE: Two days of lectures delivered by experts in the field, followed
by three days of hands-on training in QM/MM and MD/Gromacs/Martini
FOR WHOM: Graduate students, postdoctoral fellows, and researchers
For more info and registration visit:
http://www.science.ucalgary.ca/molsim/summerschool
Registration deadline: 21st April 2014
No registration fee
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“from
Centre for Molecular Simulation
Graduate Student Positions in Molecular and Cellular Biology and Biochemistry / Biophysics Available University of Guelph There are two positions available for excellent graduate students in the Dawson laboratory at the University of Guelph to work on these projects: 1. Understanding how changes in muscle proteins lead to heart disease. Cardiovascular disease is the leading cause of death in Canada and the developing world, costing the Canadian economy more than $22 billion each year. Changes in the proteins of muscle sarcomeres lead to abnormal heart function, contributing to heart disease and heart failure; specifically, the development of either hypertrophic cardiomyopathy (HCM) or dilated cardiomyopathy (DCM). Our goal is to understand how changes in sarcomere proteins lead to heart disease, beginning with the central cardiac actin protein (ACTC) and building biological complexity to the organism. Currently, 16 known mutations in the ACTC gene have been uncovered in patients suffering from DCM or HCM. We will purify ACTC variants using the baculovirus expression system and then determine if interactions change between ACTC variant proteins and myosin alone, in reconstituted filaments or in reconstituted cardiomyofibres. At the organism level, we have established zebrafish (Danio rerio) as a model system and will characterize the impact of expressing variant ACTC proteins in embryos. This project is perfect for a highly-‐motivated student with an interest in disease development and molecular biology, cell biology and biochemistry skills. Experience with zebrafish is a plus, but not required. 2. Building short actomyosin complexes of defined length for biochemical and structural determination All living things move: to breath, to reproduce, for metabolism. When biological movement goes wrong, cells die or disease develops. All Biochemistry textbooks show models of the actomyosin complex and its force-‐
generating ATPase cycle, but what is missing in the field is a complete picture of how actin and myosin work together at the atomic level. The problem is that actin forms helical polymers of varying lengths and so it cannot be used for X-‐ray crystallography and structural determination. We have developed stable, short actin polymers that possess one myosin-‐binding site. We will now characterize the interactions between our short F-‐actin structure and myosin, determine the requirements for long-‐range F-‐actin allostery on the actomyosin complexes, and, ultimately, determine atomic-‐resolution structures of complexes containing our short F-‐actin structure. This work is of the highest international impact. This project requires a hard-‐working student with a biochemistry or biophysics degree and experience with protein purification and characterization skills. Send your resume along with the names of two references to: [email protected] For further information, check out the lab website at: http://www.uoguelph.ca/~jdawso01/ For information regarding the MCB graduate program and admission requirements see: http://mcb.cbs.uoguelph.ca/graduate/graduate.shtml Additional information about the programs, stipends, living costs in Guelph and fees, is available in the Graduate Student Handbook; written by Graduate Students for Graduate students, available at: http://www.uoguelph.ca/mcb/graduate/currentgrad.shtml GUELPH • ONTARIO • CANADA • N1G 2W1 TEL. (519) 824-4120, x53867 • FAX (519) 837-1802
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FACULTY OF SCIENCE OFFICE OF THE DEAN International Programs Tel: 403-‐210-‐6757 Email: [email protected] Opportunity for Exchange Studies at Lund University
SCIENCE STUDENTS:
Lund University in Sweden is an exchange partner with the University of
Calgary faculty of Science through TASSEP (Trans-Atlantic Science Student
Exchange Program). Lund University is accepting applications between April
1-25 and they are offering many English-speaking courses in Sciences.
What does this mean for you?
•
•
•
•
You pay regular U of C tuition to U of C (no international fees!).
You get to work on your Science degree in Sweden and get
transfer credit.
You can go for one full year.
You can add "international experience" to your degree and your
resume.
A list of courses is found at: http://www.science.lu.se/education/studentexchange/find-a-course. The deadline to apply is April 25.
For questions/inquiries: please contact [email protected] or
T: 403.210.6757
If you would like to study somewhere other than Sweden, have a look at our
other partner universities at: http://studyabroad.unc.edu/tassep/
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“from biomolecules to the biosphere”
The University of Neuchâtel, Switzerland, invites applications for a position of
Assistant professor in Ecology
Job description : The candidate has experience, and international standing, in field-oriented
ecological research, preferably in the areas of vegetation, soil and/or ecosystem ecology. We
welcome applicants who take an experimental and/or theoretical/modelling approach to their research, and an interest in developing interdisciplinary approaches to the study of links between
vegetation, soil and ecosystem ecology. He/she will be integrated at the Institute of Biology at the
Faculty of Sciences. Further collaborations with other laboratories and Departments of the University of Neuchâtel (e.g., soil biology, microbiology, botany, hydrogeology, agro-ecology) and
beyond are desirable.
The successful candidate will teach at all levels of the biology curriculum (Bachelor, Master, Doctoral Program), and should be ready to teach in other curricula. Teaching at the Bachelor level
will be in French.
Starting date : February 1st, 2015 or upon agreement.
Requirement : PhD in biology and internationally recognized research record.
Deadline : May 10th, 2014.
Applications should be sent by regular mail to the Dean of the Faculty of Sciences, Prof. Peter
Kropf, Rue Emile Argand 11, Unimail, CH-2000 Neuchâtel – Switzerland ; as well as by email to
[email protected]
To apply, please send a letter of motivation, a CV, teaching and research statements (maximum
3 pages each), a list of publications and copies of academic degrees as a single PDF document
on the www.unine.ch/candis website. The candidates must have 3 reference letters sent directly
to the Dean.
The University of Neuchâtel encourages women to apply.
Additional information can be requested from the Dean, Prof. P. Kropf ([email protected]) or
from the head of the Hiring Committee, Prof. E. Mitchell ([email protected]); further details can be found at www.unine.ch/sciences - under “emploi”.
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Lethbridge Research Centre
5403 – 1 Avenue South
PO Box 3000
Lethbridge AB T1J 4B1
Tel: 403-317-2292
Email: [email protected]
Postdoctoral Positions Available
NSERC Visiting Fellowships in Canadian Government Laboratories
Two positions are available in the area of metatranscriptomics, microbial community analysis
and genome exploitation, beginning in April 2014. Applicants should have a recent (within 5
years) PhD in microbiology, biochemistry, molecular biology, or a related field. Applicants with
experience in any of the following areas are invited to apply:
- analysis of complex microbial communities, including metatranscriptomic library preparation
and analysis, Illumina NGS sequencing
- bioinformatics, sequence-based phylogenetic analysis, analysis of large datasets
-enzymology of plant polysaccharide degradation, including some or all of: screening of
metatranscriptomic/metagenomic libraries for specific enzyme activities, protein purification,
genetic/genomic analysis of enzyme biosynthetic pathways, gene cloning for targeted enzyme
expression
These positions are administered under the NSERC Visiting Fellowships in Canadian
Government Laboratories program, and application should be made through NSERC to establish
eligibility for the fellowship program, as well as to Dr. Forster. Currently two-thirds of the
awards must be made to Canadian citizens or permanent residents. Each successful candidate
must pass a reliability security screening. Appointments will be for a maximum of three years.
The fellowships currently provide a stipend of $49,500/ year.
(http://www.nserc-crsng.gc.ca/students-etudiants/pd-np/laboratories-laboratoires/index_eng.asp)
Interested applicants are invited to apply to:
Dr. R. J. Forster
Lethbridge Research Centre
PO Box 3000, 5403 1st Ave. S.
Lethbridge, AB T1J 4B1
Telephone:
(403) 317-2292
Email: [email protected]
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“from biomolecules to the biosphere”
M.Sc. opportunities- Mount Allison University
Mount Allison University’s fish ecology and aquaculture lab (Dr. Matt Litvak’s lab) is looking to
recruit motivated graduate students at the M.Sc. level to begin in 2014, preferably May. We are
looking for students to work on several projects.
1) Sturgeon ecology in the Saint John, Petitcodiac and Miramichi rivers through the Ocean
Tracking Network (OTN: http://oceantrackingnetwork.org/)
We will tag Atlantic and shortnose sturgeon from the stock present in New Brunswick rivers
and from the mixed stock aggregation that migrates every summer, with acoustic codedpingers and archival tags Pop-up tags (for light based geolocation and measurement of
physical variables of the water column). Information from this project will allow us to
answer fundamental questions regarding the habitat use of juveniles, migratory behavior of
adults and origin of these enigmatic and threatened fish along the east coast of Canada and
the United States.
2) Early sex-determination in shortnose sturgeon
Sturgeon eggs, also known as caviar, and sturgeon meat are among the most highly valued
fish products in the world. Worldwide there are 27 species of sturgeon and almost all are
threatened or endangered. Demand for caviar and meat is extremely high and will grow as
stocks continue to be fished. Over the last 15 years, aquaculture production of sturgeon has
become an important contributor of caviar and fish flesh. This project involves a series of
experiments and models that aim to accelerate the development of shortnose sturgeon in
Canada, and encourage growth of the Canadian aquaculture industry by allowing for
diversification, expansion and sustainability. The objectives of the project are to develop
economically efficient techniques and technology to stimulate early maturation, detect
gender early in development, and determine physical and biological conditions, to maximize
growth for production of shortnose sturgeon for production of caviar.
For more information on the type of work we do see our website-https://sites.google.com/site/litvaklabsite/Home
Applicants must possess or be near completion of an undergraduate degree with honours in
biology or a related discipline. If you are interested in one or more of the projects above please
contact Dr. Matt Litvak at [email protected].
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Position: Research Associate in Plant Genomics/Phenomics Location: McGill University, Department Of Biology, Montreal, QC Canada Description and Duties: We seek a biologist to join a multidisciplinary team of plant biologists, genomicists, and bioinformaticians. Our project aims to identify functional domesticated transposable elements (DTEs) of agronomic importance in plants using comparative, population, and functional genomics (funded by Genome Quebec/Canada and NSERC). The candidate will conduct research using functional genomics to evaluate DTE function especially underlying agriculturally important phenotypes. The candidate will exploit a recently installed unique automated phenomics platform located in our department. This necessitates close collaboration with inter-‐ and intra-‐university researchers in functional genomics and phenomics. Qualifications: The successful candidate must hold a Ph.D. and have demonstrable postdoctoral experience in functional genomics, transposable elements, and high-‐throughput trait screening assays in plants. Salary: To be negotiable, according to qualifications and experience. Duration: The position is initially funded for two years with the potential for continuation pending available funds. Apply: Candidates should submit a letter of application, curriculum vita, and the names of two references before May 1, 2014. Contact Information: Prof. Thomas Bureau, McGill University, Department of Biology, 1205 Dr. Penfield Avenue, Montreal, Quebec, Canada H3A1B1 ([email protected]). McGill University is committed to diversity and equity in employment. It welcomes applications from: women, Aboriginal persons, persons with disabilities, ethnic minorities, persons of minority sexual orientation or gender identity, visible minorities, and others who may contribute to diversification. All qualified applicants are encouraged to apply; however, in accordance with Canadian immigration requirements, Canadians and permanent residents will be given priority. 14
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