QuARC

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The Queensland Area RNA Club (QuARC) is an informal organization of scientists fascinated by the emerging, and ever expanding, world of RNA biology. We are interested in transcription and the extent of the transcriptome, long non-protein-coding RNAs, microRNAs, piRNAs, structure, splicing, subcellular localization, computational analysis and prediction, and the discovery of new classes of RNA - although this list is by no means comprehensive.

We hold monthly meetings at the Institute for Molecualar Bioscience (@ UQ) or other institutions in Southeast Queensland.

Talks are given by lab heads, principal investigators, postdocs and graduate students. We don't care who you are - just how exciting your research is!

Meetings begin at 4:00 PM, followed by snacks and beer. (Or begining with snacks and beer if you get there early enough.) We aim to keep the meetings informal and to encourage lively(!) discussion.

If you're interested in staying in contact with us, getting tips from your colleagues about great RNA papers, or hearing about the next meeting please join our Google Group:

http://groups.google.com/group/QuAreaRNAclub


Contents


Our Sponsors

QuARC's snacks, beer and (sometimes) pizza is proudly sponsored by

image:ABI_IVGN_LifeTech_logo_small.jpg


Next Meeting

21 October

Dr. Tanja Gesell Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), Vienna, Austria.. For more information please see [1].

A Phylogenetic Structure (PS) and its Application to Gene Predictions
To date, the evolution of molecular structure has not been sufficiently considered with respect to the understanding of the intertwined relationship between structure and the substitution process. I will therefore be introducing a phylogenetic structure (PS) as an abstract object that is defined by a neighbourhood system, a substitution model and a phylogenetic tree. So as to mimic sequence evolution under structural constraints, we have developed SISSI (Simulating Site-Specific Interactions). SISSI makes it possible to study the influence of phylogenetic relationships among sequences on approaches that predict their secondary structure, including thermodynamics and covariance methods. We have shown that the inclusion of phylogenetic information in comparative structure prediction is helpful for distinguishing ancestral and functional constraints, leading to improved predictions. We have also developed a variant of a thermodynamic structure-based RNA gene-finding program that relies on SISSI and is not biased by the dinucleotide content (SISSIz). In a further step, a different view on sequence evolution will be discussed to include all aspects of a PS in one substitution matrix, on the way to a new phylogenetic structure conservation index for future research on structure evolution. Finally, based on a PS, we can now redefine structure changes as lineage specific neighbourhood systems (LSN) along the phylogenetic tree – which might help to resolve another problem currently encountered in the definition of structure conservation and genes respectively.

Upcoming 2010 Meetings

25 November: TBA

News / Announcements

April 23rd, 2009 At our last meeting we a great discussion about RNAi therapeutics. Our sponsor, Invitrogen, wanted to make sure we're aware of Invivofectamine. Invitrogen's Invivofectamine™ gives customers the ability to perform in vivo RNAi experiments that have so far been nearly impossible due to the lack of an effective and easy-to-use delivery reagent. Invivofectamine™ is a lipid-based reagent that when complexed with siRNA is a key component to successful knockdown experiments in vivo. Please feel free to contact your local Invitrogen representative (Daphne Kusters or Natalie Judge) for an introductory discount. Online manual [2]. Product page [3].

Feb 23rd, 2009 Check out our new mailing list and discussion board at http://groups.google.com/group/QuAreaRNAclub. Join today!

October 27th, 2008 Check out the latest edition of Quest Magazine from Invitrogen. This edition is focused on epigenetics and features an interview with John Mattick. You can find it here!

Meeting Location

Meeting are currently held in the Large Seminar Room on Level 3 at the Institute for Molecular Bioscience. If you are coming from outside the IMB please enter the building from the bus terminal side. Don't go into the lobby - instead, head up the ramp next to the auditorium (the pointy building) directly to the seminar rooms. Please see the map here and click on the blue pin.

Our Mission

Our hope is to foster collaboration and discussion between Queensland area labs that don't usually have the chance or time to connect. With recent advances in genomics and deep sequencing, and the explosion of RNA-centered publications, such collaborations are essential to stay abreast of recent findings and generating high quality research.

A few tips for speakers

  • Please have a few minutes at the beginning of your talk devoted to background information and how your project fits into the larger biological picture.
  • Present your work in progress! Please do not feel compelled to have a "flash" presentation - share some of your results and ideas! We also encourage "chalk talks".
  • Be prepared to be stopped in the middle of your talk if a member of the audience has a question.
  • Have fun! This is a great forum to get feedback from a diverse group.

Contact Us

For more information please contact Ryan Taft (Mattick Lab, IMB, UQ) at r.taft@imb.uq.edu.au or Paulo Amaral (Mattick Lab, IMB, UQ) at p.amaral@imb.uq.edu.au.

Links

Our Sponsor (be sure to visit their display table at the QuARC meetings)

Invitrogen
Applied Biosytems

which are both part of Life Technologies

Partner Institutions (we are happy to add links - please contact us if your institution is missing)

University of Queensland
Griffith University
Queensland University of Technology

Australasian Organizations

Overseas RNA Clubs

Previous Meetings

Thursday October 23th, 2008

Professor John S. Mattick Ph.D. A.O (info here) Institute for Molecular Bioscience, University of Queensland

The modern RNA world

Elizabeth Murchinson Ph.D. (info here) Research School of Biological Sciences, The Australian National University

piRNAs, miRNAs and siRNAs: small RNA pathways in mammals

Thursday November 20th, 2008

Associate Professor Bernie Carroll Ph.D. (info here) School of Molecular and Microbial Sciences, School of Land, Crop and Food Sciences, University of Queensland

Intercellular RNA signalling in plants

Albert S Mellick Ph.D. GMRC Fellow, Head, Host Response to Cancer Lab, School of Medical Science, Griffith University

Small non coding RNAs, bone marrow stem cells and cancer

26 February, 2009

Dagmar Wilhelm (IMB bio here) Institute for Molecular Bioscience, University of Queensland

Non-coding RNAs and sex

Geoff Faulkner (bio here) Institute for Molecular Bioscience, University of Queensland

Novel retrotransposon promoters massively expand and regulate the mammalian transcriptome.

19 March, 2009

Assoc. Professor Nigel McMillan (http://www.di.uq.edu.au) Deputy Director and Principle Research Fellow, UQ Diamantina Institute for Cancer, Immunology and Metabolic Medicine

RNAi for cancer therapy

Sherry Wu Ph.D. (http://www.di.uq.edu.au) UQ Diamantina Institute for Cancer, Immunology and Metabolic Medicine

RNAi therapy for cancer: It's all about delivery!

30 April, 2009

Evgeny Glazov Ph.D. [4] UQ Diamantina Institute for Cancer, Immunology and Metabolic Medicine

Small regulatory RNA in vertebrates: exceptions rule!

Alistair Chalk Ph.D. [5] National Center for Adult Stem Cell Research, Griffith University, Brisbane, QLD, Australia

Transcriptome analysis of patient olfactory derived cell lines

21 May, 2009

Siew Ping, Ph.D. candidate UQ School of Chemistry & Molecular Bioscience

Evolution of the hnRNP A/B genes

Dr. Sassan Asgari [6] Senior Lecturer, UQ School of Biological Sciences

Role of viral and cellular microRNAs in insect host-virus interactions

18 June, 2009

Professor Tom Gonda [7] Head, Molecular Oncogenesis Laboratory, Diamantina Institute for Cancer, Immunology and Metabolic Medicine, University of Queensland

The ARVEC initiative: Development and Establishment of High-Throughput Functional Screening Technologies

Paulo Amaral, Ph.D. candidate Institute for Molecular Bioscience, University of Queensland

Noncoding RNAs and associated developmental genes: functional relationships and evolutionary implications

10 Sept, 2009

John Quackenbush (info [8]) Dana-Farber Cancer Institute and the Harvard School of Public Health

Network and State Space Models: Science and Science Fiction Approaches to Cell Fate Predictions

22 October, 2009

Sean Grimmond (more info here [9] and here [10]) Associate Professor, Institute for Molecular Bioscience, University of Queensland

Defining transcriptome content, complexity and dynamics with RNA-seq

19 November, 2009

Professor Emma Whitelaw (more info here [11] and here [12]) NHMRC Australia Fellow, Queensland Institute of Medical Research

Epigenetic reprogramming within and across generations

14 January, 2010

Dr Jessica Mar (more info here [13]) Jess is a postdoc in Prof John Quackenbush’s lab at the Dana-Farber Cancer Institute in Boston, MA.

Modeling Variance as a Measure of Network Topology in Waddington’s Canals

Dr Rohan Williams (more info here [14]) Group Leader at the John Curtin School of Medical Research at the Australian National University.

A gene set approach to understanding inter-individual variationin mRNA levels

18 February, 2010

Dr Pardis Sabetti and Dr John Rinn - canceled due to unforeseen circumstances.

25 March 2010

Dr Christine Wells (more info here [15]) Christine is a group leader in systems biology at the Eskitis Institute for Cell and Molecular Therapies at Griffith University.

Alternate splicing as a mechanism to diversify innate immune responses

29 April 2010

Lena Constantin (more info here [16]) Lena is a PhD candidate in Brandon Wainwright's laboratory at the IMB.

The cell-type specific role of microRNAs in medulloblastoma

Roberto Munita (more info here [17]) Roberto is a PhD candidate in Katia Gysling 's laboratory at the Pontifica Universidad Catolica de Chile and a current guest of the Mattick Laboratory and the IMB.

mirrorRNA and non-consensus splicing: Experimental artefact or sign of another biological surprise

1 June

Dirk Haussecker PhD (For more information please see his RNAi therapeutics blog [18]) Dirk, who was a post-doc at Stanford until 2009, is an expert consultant on RNAi therapeutics.

RNAi Therapeutics - where are we and where are we going?

24 June

Erin Poth Blackshaw laboratory, Department of Neuroscience, Johns Hopkins University School of Medicine. For more information please see [19].

Teaching an old dogma new tricks: The role of the long ncRNA Six3OS in retinal development

28 October

Marcel Dinger Institute for Molecular Bioscience. For more information please see [20].

Through a transcriptome, darkly: emergence of novel RNAs in disease and development

QuARC Secrets

We pronounce QuARC, "quark", which, as many of you know, is the name of a subatomic particle. BUT did you know there are other quarks!? (We didn't.) In German, the word Quark refers to a type of cheese [21], but is also used to denote "nonense" or "B.S." [22]. In light of this realization I propose we make In QuARC we never Quark reden our unofficial motto. (In QuARC we never speak rubbish.)

The word quark also makes an appearance in James Joyce's Finnegan's Wake, and is the name for the narrowest section of the Baltic sea between Finland and Sweden [23].

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