Slamovits Lab at Dalhousie University

Category: News

  • The Tree of Life, a poem by David Maddison

    The Tree of Life

    David R. Maddison

    I think that I shall never see
    A thing so awesome as the Tree
    That links us all in paths of genes
    Down into depths of time unseen;

    Whose many branches spreading wide
    House wondrous creatures of the tide,
    Ocean deep and mountain tall,
    Darkened cave and waterfall.

    Among the branches we may find
    Creatures there of every kind,
    From microbe small to redwood vast,
    From fungus slow to cheetah fast.

    As glaciers move, strikes asteroid
    A branch may vanish in the void:
    At Permian’s end and Tertiary’s door,
    The Tree was shaken to its core.

     

    The leaves that fall are trapped in time
    Beneath cold sheets of sand and lime;
    But new leaves sprout as mountains rise,
    Breathing life anew ’neath future skies.

    On one branch the leaves burst forth:
    A jointed limb of firework growth.
    With inordinate fondness for splitting lines,
    Armored beetles formed myriad kinds.

    Wandering there among the leaves,
    In awe of variants Time conceived,
    We ponder the shape of branching fates,
    And elusive origins of their traits.

    Three billion years the Tree has grown
    From replicators’ first seed sown
    To branches rich with progeny:
    The wonder of phylogeny

     
    © The Author(s) 2012. Published by Oxford University Press.
    This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits
    unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
    DOI:10.1093/sysbio/sys057

  • Protist Genomics, new open access journal

    PROTIST GENOMICS is a brand new open-access journal entirely dedicated to publishing research, news and review articles in the fiel of genomics of microbial eukaryotes. PG represents a much-needed option for many researchers who had to opt for either a general protistology, general genomics or molecular evolution journal to submit their work. This often results in less than satisfactory outcomes because reviewers or editors lack the specific background and expertise required to understand the specifics of genomics in protists. At PROTIST GENOMICS, manuscripts are managed and reviewed by scientists with the relevant knowledge.

    Some of the subtopics relevant to the journal are:

    • Analysis of whole and partial nuclear genome data
    • Studies on organellar genomes
    • Analysis of expressed data (e.g. RNA-seq, EST)
    • Comparative and evolutionary genomics, phylogenomics
    • Functional genomics, metabolomic and interactomic studies
    • Structural genomics, epigenomics
    • … and more

    The journal’s goal is providing a hub for researchers working in the growing field of protist genomics to present their research, discuss ideas, explore new concepts and hypotheses and review the status of particular areas and subjects.

    As a way to promote the journal, PG’s publishers will waive publication fees during the first two years, meaning that accepted manuscripts will be published, open-access at no cost until 2014.

    Protist Genomics counts on the support of a distinguished body of Editorial Advisors:

    • John M. Archibald, Dalhousie University, Canada
    • Sandra Baldauf, Uppsala University, Sweden
    • Gertraud Burger, Université de Montréal, Canada
    • Michael W. Gray, Dalhousie University, Canada
    • Christopher Howe, University of Cambridge, UK
    • Patrick J. Keeling, University of British Columbia, Canada
    • Franz Lang, Université de Montréal, Canada
    • Julius Lukeš, University of South Bohemia, Czech Republic
    • Geoffrey McFadden, University of Melbourne, Australia
    • Jan Pawlowski, University of Geneva, Switzerland
    • Andrew Roger, Dalhousie University, Canada
    • Najib El-Sayed, University of Maryland, USA
    • Dominique Soldati-Favre, University of Geneve, Switzerland

     

    For enquiries or submissions please contact cslamovits [at] versita.com

     

     

  • International Course in Automated Functional Annotation and Data Mining

    Blast2Go is organizing courses on automated functional annotation – Go here for info and registration

    Cost reduction in sequencing technologies is resulting in a growing number of laboratories getting involved in genome sequencing projects where a large amount of sequencing data is generated. After assembly, a large amount of unique sequences are obtained which need to be further characterized with putative functions. Good and sufficient functional annotations are decisive for follow up analyses such as gene expression, strain variations, tissue functional profiling, etc.

    The course will teach on the principals and practical aspects of automated functional annotation of (novel) sequence data.
    Participants will learn how to :

    • Create and run standard or costumed pipelines for generating functional labels for sequence data.
    • Design annotation strategies and generate different annotation types
    • Create a local database installation for annotation speed up
    • Evaluate and report the results of the functional annotation pipeline
    • Perform data-mining and knowledge discovery using functional annotation and experimental data
    • Study similarities and differences between annotation datasets
    • Generate and modify knowledge-containing functional annotation graphs

    The course will be based on the use of Blast2GO application and will mainly comprise exercises and practical cases. Participants might bring their own data.

    Who should attend? Experimentalists and bioinformaticians working on EST, Next Generation Sequencing andmicroarray design projects, specially (but not exclusively) of non-model species.

  • What's up with microbes?

    Read about microbes and our work in the Winter issue of REACH, CIFAR’s publication about the exciting research being done by Program members. 

     

    CIFAR Reach Magazine

  • Two PhD-studentships in Exeter, UK

    A competition for two PhD studentships opened in the lab of Dr Mark van der Giezen, Exeter.

    1- Modelling early eukaryotic evolution using biogeochemical data – a systems approach
    Supervisors: Dr. Mark van der Giezen (Biosciences) & Prof. Tim Lenton (Geography)

    Information and application – click here

    2- An evolutionary fluke resulting in novel and safe drugs to protect crops and humans.
    Supervisors: Dr. Mark van der Giezen & Dr. David J. Studholme

    Information and application – click here

  • Postdoctoral and Short-Term Research Training Scholarships in Argentina

    The Department of Human Development, Education and Culture (DHDEC) presents its compliments to the Permanent Mission of the Organization of American States (OAS) and has the honor to inform about the scholarships opportunities offered by the OAS and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), in a joint effort to promote the education in the Americas by scholarships for Postdoctoral and Short Term Training and Research Scholarships.

    Scholarship Announcement

    Call for scholarship applications: starting December, 2011 and ending March 30th, 2012.

    Types of scholarships:

    • Postdoctoral Scholarships
    • Short Term Training and Research Scholarships

     

    Length of scholarship:

    The Postdoctoral Scholarships have a minimum duration of twelve (12) months and a maximum of twenty-four (24) months, not renewable and are designated to candidates which have finalized their doctoral training.

    The Short the Term Training and Research Scholarships have a duration of three (3) to six (6) months, are not renewable and are designated to candidates which have finalized their masters or doctoral training.

    General Requirements:

    • Be a national or a legal permanent resident of any OAS Member State with the exception of Argentina.
    • Have finalized a master’s or doctorate degree.
    • Be in generally good health to complete the program successfully.
    • Be fluent in Spanish.
    • Age limit: no older than 35 years old on or by December 31, 2011.
    • Agree to return to reside in the sponsoring country for a period of no less than 12 months after completing the program of study covered by the scholarship.
    • Submit the recommendation forms available through CONICET’s system. The OAS will not accept incomplete or late applications.

    Application Procedure

    All applicants must fill out the online application which needs to be printed once completed. The presentation and procedures of the applications will be processed through the CONICET’s SIGEVA database system.

    Applicants must send their complete and printed applications, by the established deadline, to: Organization of American States
    Department of Human Development, Education & Culture
    1889 F Street, NW, 6th Floor Washington DC, 20006 UNITED STATES

    Questions and Concerns

    Applicants should direct their questions to:
    becasoeaconicet@conicet.gov.ar indicating in the subject of the email “CONICET-OAS”

    Applicants who would like to verify if their printed application was received by the OAS should contact scholarships@oas.org indicating in the subject of the email “CONICET-OAS”

    Please find all the information about these programs in the attached announcement in Spanish and in the Educational Portal of the Americas: www.educoas.org

    The Department of Human Development, Education and Culture of the OAS is sending a copy of this official communication to the National Liaison Offices and the Offices of the OAS in the Member States for their information and for dissemination purposes only.

    The OAS/DHDEC reiterates to the Mission its sentiments of highest esteem and consideration. Washington DC, December 19th, 2011

  • Research Summer School for Undergrads – Apply now!

    The Vienna Biocenter Summer School provides a unique opportunity for 25 undergraduate students to work side by side with leading researchers in a dynamic scientific environment. This program aims to attract talented students from around the world, creating a vibrant and diverse atmosphere. It is the perfect preparation for those students who are interested in graduate study in the life sciences arena. Applicants who are successful are provided with accommodation, a travel allowance and a st stipend for the duration of the Scholarship.

    The program, starting on the 29 June and finish on the 31 August 2012

    Students from all around the world who are undergraduates, and have completed at least two years of university study are encouraged to apply. Applicants are expected to have a good academic record, provide a statement of their research interests, their curriculum vitae and evidence of enrolment at their institution.

    Arrangements will be made for applicants from overseas to secure the necessary visas. Applicants should be aware that the working language of the institutes is English.

    Applications are due on 17 February 2012. 
    Successful applicants will be notified by the end of February 2012.

    Click here to apply

  • Faculty Position in Marine Eukaryotic Microbial Ecology at UBC

    The Departments of Botany and Zoology at the University of British Columbia invite applications for a Tier 2 Canada Research Chair (CRC) in Marine Eukaryotic Microbial Ecology. This is a tenure track position, with initial appointment to be made at the Assistant Professor level, beginning no earlier than July 1, 2012. We seek an outstanding applicant whose research program examines the ecological functions of marine microbial eukaryotes (e.g., protists, protozoa, algae) in the context of their natural environment. The program should address fundamental ecological questions and include a strong field component.

    Applicants must have a PhD and preferably postdoctoral research experience. The successful applicant will be a member of the UBC Centre for Microbial Diversity and Evolution (http://www.cmde.science.ubc.ca) and will also be considered for appointment as a Scholar in the Canadian Institute for Advanced Research program in Integrated Microbial Biodiversity (http://www.cifar.ca/integrated-microbial-biodiversity).

    Responsibilities of the position include establishing and conducting an internationally competitive and externally funded research program, teaching at the undergraduate and graduate levels, supervising graduate students, and participating on service committees for the departments, university, and academic/scientific community.

    Applicants should send a cover letter, curriculum vitae, statement of research, statement of teaching accomplishments and/or interests, and up to four publications to Dr. Brian Leander at ecologysearch@zoology.ubc.ca. Letters of support from three referees should be sent to ecologyreferences@zoology.ubc.ca. Applications should be submitted on or before November 27, 2011.

    Canada Research Chairs are open to individuals of any nationality. The position is subject to review and final approval by the CRC Secretariat. More information about the CRC program can be found athttp://www.chairs.gc.ca.

    UBC hires on the basis of merit and is committed to employment equity. UBC is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, persons of any sexual orientation or gender identity, and others who may contribute to the further diversification of ideas.

  • Seeing biosphere's dark matter

    AAAS 2012 Meeting's Themes

    We are organizing a symposium within 2012 Annual Meeting of the American Association for the Advancement of Science (AAAS), which will take placein the City of Vancouver, Canada in February 2012. Our symposium will be part of a special, day-long seminar “Unlocking Biology’s Potential and will verse on the exploration of uncultured microbial diversity, its challenges and benefits.

    The symposium is organized by Claudio Slamovits and Patrick Keeling and sponsored by the Canadian Institute for Advanced Research. The speakers will be Alexandra Worden, Forest Rohwer and Patrick Keeling. A summary of the theme and links to more information follows below:

     

    Seeing Biosphere’s Dark Matter: Genomic Methods on Unculturable Microbial Diversity

    A decline in biodiversity poses dramatic consequences to almost every aspect of human development, either directly or indirectly, from food supply to global health, from climate change to the economy. Our ability to respond to these threats depends on efficient and thorough exploration, classification, and interpretation of biodiversity. Some components of the biosphere are visible to the eye, such as plants and animals, and have obvious importance. But microorganisms, the invisible majority of living forms on planet Earth, play critical roles in regulating global-scale processes and driving essential nutrient cycles that support all life forms. This session will illustrate the challenges of exploring microbial diversity in natural habitats such as the open oceans, deep into the ground, or inside our own bodies.

     

    AAAS website

     

    2012 Meeting

    2012 Meeting Seminars

     

     

  • Teach evolution not creationism

    Are you in the UK?

    Sign the Creationism In Schools Isn’t Science petition!