Archive for the ‘Workshops’ category

MGI4

March 11th, 2014

Comparative Genomics of Eukaryotic Microorganisms

August 6th, 2013

July 19th, 2013

March 13th, 2013

Effector Wisdom

January 20th, 2013

30th New Phytologist Symposium: Immunomodulation by Plant-associated Organisms

Meeting Report by Amy Huei-Yi Lee, Benjamin Petre, David L. Joly

Many organisms such as bacteria, fungi, oomycetes, nematodes and insects grow, feed and/or reproduce in close association with plant hosts. To establish such intimate interactions, symbionts (either mutualistic or parasitic) secrete effectors into host tissues, which are molecules that modulate plant cell structures and processes (Win et al., 2012a). This last decade, advances in genomics have revealed that symbionts possess dozens to hundreds of effectors. Currently, the field is moving rapidly from effector identification towards effector characterization, which provides a better understanding of how these effectors promote the establishment of a successful relationship with host plants. The 30th New Phytologist Symposium clearly illustrated this theme, as an international panel of c. 150 scientists was brought together to discuss current efforts to decipher effector functions within a wide range of biological systems. The remote location of the meeting in the Sierra Nevada mountains of California, USA, promoted lively discussions between participants during and after the sessions, but also via social networks (the whole conference was covered by a twitter feed, #30NPS tag, available onhttp://storify.com/KamounLab/30th-new-phytologist-symposium-immunomodulation-by). Read more …

Mycorrhizal Genomes Medley

November 1st, 2012

In less than two weeks, mycorrhizasts will gather at the INRA in Nancy, to enjoy an exciting workshop on the mycorrhizal genomes. So much novel and unexpected information is emerging from these genome and transcriptome exploration. That’s like exploring a Terra Incognita.

Below is the agenda;

2nd Mycorrhizal Genomics Initiative (MGI) Workshop

INRA-Nancy, November 13 & 14, 2012

Tuesday 13 November

  • 9:00 – 9:15     Opening remarks
  • 9:15 – 9:40     Exploring the genome diversity of mycorrhizal fungi. Project status. By F Martin
  • 9:40 – 10:00   The MycoCosm database & Fungal Genomics at JGI. By I Grigoriev
  • 10:00 – 10:30 Annotation and analysis of ECM genomes. By A Kuo
  • 11:00 – 11:20 Identifying transposable elements and other repeated elements in mycorrhizal genomes. By C Murat
  • 11:20 – 11:40 A new approach to infer protein function based on whole genomes and phylogenetic information. By L.G. Nagy
  • 11:40 – 12:00 Analysis of multigene families and duplications in mycorrhizal genomes. By E Morin
  • 12:00 – 12:20 CAZYmes and FOLymes in mycorrhizal genomes. By B Henrissat
  • 12:20 – 12:40 The secretome in mycorrhizal genomes. By C Fourrey
  • 14:00 – 14:20 The MGI transcriptome databases. By E Tisserant
  • 14:20 – 14:40 Identifying symbiosis-regulated genes by RNA-Seq. By A Kohler

14:40 – 15:30 Genome descriptions by species

  • Paxillus involutus & P. rubicundulus By A Tunlid & M Gardes
  • Hebeloma cylindrosporum By G Gay & J Doré
  • Amanita muscaria & A. thiersii By A. Pringle/J Hess

16:00 – 18:00 Genome descriptions by species

  • Laccaria amethystina By F Martin
  • Piloderma croceum By  M Tarkka et al.
  • Suillus luteus By J Colpaert et al.
  • Scleroderma citrinum By A Deveau
  • Pisolithus tinctorius & P. microcarpus By A Kohler
  • Sebacina vermifera By A Zuccaro
  • Tulasnella calospora By M Girlanda

18:00 – End

Wednesday 14 November

9:00 – 11:00   Genome descriptions by species

  • Cenococcum geophilum By M Peter
  • Oidiodendron maius By S Perotto et al.
  • Meliniomyces bicolor, M. variabilis By G Grelet
  • Tuber species By C Murat & R Ballestrini et al.
  • Terfezia boudierii By Y Sitrit

11:00 – 11:30 New Mycorrhizal Genomes Projects

CSP2012 #570 – Metatranscriptomics of Forest Soil Ecosystems: C Murat, M Buée, F Martin

CSP2013 #978 – MGI: Exploring the Symbiotic Transcriptomes: A Kohler, F Buscot, A Tunlid, F Martin

11:30 – 12:30 Discussions: MGI: Papers & Future activities

Photo: One of the sequenced ectomycorrhizal basidiomycete, the Amethyst Deceiver (Laccaria amethystina) (© F Martin)

Exploring the Mycorrhizal Genomes

September 9th, 2012

 

I hope you are wrapping up a good summer. I’m touching base to update you on our Mycorrhizal Genomics Initiative (MGI).

The list of taxa of mycorrhizal fungi for the first series of analyses aiming to identify symbiotic traits has now been “frozen”. Thanks to Igor Grigoriev’s JGI team, this list includes an outstanding series of annotated genomes and transcriptomes from ectomycorrhizal, ericoid and orchid symbionts:

  • Amanita muscaria Koide
  • Hebeloma cylindrosporum h7  (v2.0),
  • Laccaria bicolor (v2.0),
  • Oidiodendron maius Zn,
  • Paxillus involutus,
  • Paxillus rubicundulus,
  • Piloderma croceum F 1598,
  • Pisolithus microcarpus 441,
  • Pisolithus tinctorius 270,
  • Scleroderma citrinum FougA,
  • Sebacina vermifera MAFF 305830,
  • Suillus luteus UH-Slu-Lm8-n1,
  • Tulasnella calospora AL13/4D,

In addition, the following available transcriptomes will also be mined for symbiotic-related features:

  • Cenococcum geophilum
  • Cortinarius glaucopus,
  • Laccaria amethystina 08-1,
  • Lactarius quietus,
  • Meliniomyces bicolor,
  • Meliniomyces variabilis, and
  • Tricholoma matsutake 945.

Finally, we will add the unpublished genomes of five saprotrophic agaricomycotina (including leaf-litter species) that we will use for identifying potential common genomic features in litter-borne and mycorrhizal fungi:

  • Jaapia argillacea MUCL-33604,
  • Hydnomerulium pinastri MD-312,
  • Plicaturopsis crispa FD-325 SS-3,
  • Hypholoma sublateritium FD-334 SS-4, and
  • Gymnopus luxurians FD-317 M1

JGI has (or will soon) publicly released the web portals with the annotation for the above-mentioned fungal species. Visit the JGI Mycocosm database. In addition, we have released web sites for the corresponding transcriptome annotation at the Mycorhiza Genomics Initiative portal [restricted].

To make good use of this tremendous genomic resource, we are organizing the 2nd MGI Workshop at the INRA-Nancy center in Champenoux (France), on November 13-14, 2012. The aim of the workshop is to bring together the consortium teams for discussing our findings. The format of the workshop will be roughly equally split between informal presentations summarizing the current findings and brainstorming about how to take advantage of the genome sequences to inform our understanding of symbiosis and fungal biology.

On the following days, we will organize a New Phytologist Workshop entitled ‘ Bridging Mycorrhizal Genomics, Metagenomics & Forest Ecology‘. The workshop will also take place at INRA-Nancy over two days (Thursday 15 & Friday 16 November). The aim is to bring together a small group of MGI PI’s, fungal biologists and ecologists (20-25 attendees) to explore the future use of mycorrhizal genomes in order to both maximize the efficacy with which the community utilizes these technological breakthroughs in biology, ecology, phylogenetics, and forestry.

Photo: Larch Bolete (Suillus grevellei) (Boletales), a close relative of the sequenced slippery Jack (Suillus luteus) (© F Martin).

IMC10

August 20th, 2012

Planning is in full swing for the next International Mycological Congress, IMC10 in Bangkok, Thailand, August 3-8, 2014.

Point your web browser to: http://www.imc10.kasetsart.org/

Now, just 24 months to Bangkok 2014, is the time for you to suggest topics for Sessions and Symposia using the form on the website or right here:

Submit your ideas now, the committee will begin choosing topics in just 90 days, on November 1, 2012.

Leka Manoch and Morakot Tanticharoen
Co-Chairs, IMC10 Organizing Committee

 

JGI Summer 2012 Primer

August 2nd, 2012

The summer edition of the U.S Department of Energy (DOE) Joint Genome Institute (JGI) newsletter The Primer is now available for download: http://bit.ly/JGI-Summer-Primer-2012

…featuring articles and images:

Features include:

  • A summary of the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting
  • Comparative Genomics of White Rot Fungi Providing Insight into Selective Ligninolysis
  • The Omics Response to the Deepwater Oil Spill
  • Assembling the Switchgrass Genome
  • Single-cell Genomics @ the DOE JGI
  • Save the Date for the 8th Annual Genomics of Energy & Environment Meeting MARCH 25-29, 2013 in WALNUT CREEK, CA
  • Other Publication Highlights

 

 

8th JGI Users Meeting

August 2nd, 2012


Aboveground-belowground interactions

August 1st, 2012

The British Ecological Society, the Biochemical Society and the Society for Experimental Biology are organising a meeting entitled ‘Aboveground-belowground interactions: technologies and new approaches’, which is being held on 8-10 Oct 2012 in London.

The aim of the symposium is to promote cross-disciplinary collaboration by bringing together existing technology users and developers (e.g. biochemists, geneticists, bioinformaticists) who are interested in applying their skills to address research questions at the whole organism and ecological scales with above-belowground researchers working at biochemical, ecological, physiological, and molecular scales who have a desire to learn and apply new research technologies.

Plant Science For Future Needs

June 11th, 2012

The Linnean Centre invites plant scientists to Uppsala for a two-day conference October 11th and 12th, 2012. The conference aims to tackle upcoming challenges like climate change and food security by setting a foundation for future collaborations between different sub-disciplines of plant science. Eight scientific sessions with plenary presentations, short talks and posters will highlight prevailing directions and novel findings.

NOTE: Registration deadline 31st of August, 2012.

Confirmed speakers are:

  • Vincent Colot, Ecole Normale Supérieure Paris
  • Thomas Kraft, Syngenta Seeds
  • Cris Kuhlemeier, Bern University
  • Gary Loake, University of Edinburgh
  • Francis Martin, INRA, Nancy
  • John McKay, Colorado State University
  • Kalien A. Mooney, UC Irvine
  • Michele Morgante, University of Udine

More information about the plenary speakers can be found here.

 

JGI Spring 2012 Primer

May 29th, 2012

The Spring 2012 edition of the DOE Joint Genome Institute (DOE JGI) newsletter The Primer is now available for download:
http://1.usa.gov/JGI-Primer-Spring-2012
and features highlights from the DOE JGI Genomics of Energy & Environment Meeting #7.

Videos of the talks from Meeting #7 are posted here:
http://bit.ly/JGI_Mtg7Videos


Be sure to Save the Date for meeting #8 the week of March 25-29, 2013.

European Nitrogen Fixation Conference 2012

May 12th, 2012

The 10th European Nitrogen Fixation Conference (ENFC) will be held at the Ludwig-Maximilians-Universität München (LMU), Biozentrum in Martinsried near Munich, Germany, on 2-5 September 2012. This biennial congress series is always a big event for scientists working on nitrogen-fixing bacteria and the rhizobium-legume symbiosis. In addition, there will be sessions on the biochemistry of nitrogenase.

The 10th ENFC will start with a satellite meeting on “Genomics of Nitrogen Fixing Bacteria”. In addition, two satellite events will be organized for 6th/7th September: the “13th Symposium on Biological Nitrogen Fixation with Non-Legumes, focussing on the interaction of diazotrophic bacteria with practically most relevant Gramineae and the 1st “Molecular Mycorrhiza Meeting” (MMM).

Registration has recently opened on the conference web site: http://www.enfc2012.de , where you will also find an outline of the session topics and a list of confirmed speakers.

JGI Fungal Jamboree

March 19th, 2012

The annual JGI Fungal Jamboree will start on Monday 19th at the Marriott Hotel in Walnut Creek. During the workshop, attendees will:

  • provide an update on their JGI program’s development during the last year and future plans,
  • discuss several important questions, including: (1) How to address current bottlenecks for future scale-up (target selection, DNA samples, analysis, publications)? (2) How to reach new groups of users and coordinate with other large genomics initiatives (e.g., 1K Chinese Fungal Genomes)? (3) What products in addition to sequencing JGI should be working on for mycologists? (4) What informatics/analytical needs should be addressed?
  • discuss strategic partnerships.

I will report on our two fungal programs, i.e. the Mycorrhizal Genomics Initiative and the Metatranscriptomics of Forest Soils.

    MOMY in Woods Hole

    February 17th, 2012

    Dear Mycology Investigator,

    The Molecular Mycology summer course at the Marine Biological Laboratories in Woods Hole provides an opportunity for researchers to learn new concepts and techniques relating to the study fungal pathogenesis and the discovery of novel antifungal strategies. Many course graduates are now leading medical mycology research efforts around the world. We depend upon the members of the medical mycology community to encourage outstanding applicants. We hope that you can identify at least one prospective course participant who would benefit from the experience and encourage them to apply.

    This dynamic course provides state-of-the-art training in molecular methods and assays for studying fungal pathogens and fungi-host interactions. In addition, it provides opportunities to interact with colleagues from academia and industry with different areas of expertise relevant to the study of fungal diseases. The upcoming Molecular Mycology course promises to be exceptional. See the course website to see the list of interactive visiting and resident faculty who will make up the course curriculum.

    Laboratory exercises, demos, lectures, and informal panel discussions make up the curriculum. Laboratory exercises focus on Candida, Aspergillus, and Cryptococcus, and include genetic manipulation, discussion of new genetic tools, genetic screening strategies, cell culture and animal models, host response assays, antifungal susceptibility assays and live cell imaging of fungi. Additional topics include current research problems and strategies in medical mycology and topics relating to careers in fungal pathogenesis. Among the topics to be addressed in lectures include new animal models, immunology and fungal diseases, and fungi within microbial communities.

    The course is an intensive, two-week research training program, and its content is designed for advanced graduate students, post-docs, fellows, early independent investigators or PIs new to the field. The course runs from August 1-17, 2012.

    **Students accepted to the course often receive GENEROUS scholarships towards tuition and travel. **

    The course website and on-line application can be found at:

    http://www.mbl.edu/education/courses/special_topics/momy.html

    The application deadline is April 11, 2012.

    Thanks!

    Deb Hogan and Andy Alspaugh

    MBL Molecular Mycology Course co-Directors

    Lab of Excellence for Advanced Research on the Biology of TRee and Forest Ecosystems

    February 15th, 2012

     

     

    Forests provide a wide range of services: wood products and biomass for bioenergy, as well as many ecosystem services, such as carbon sequestration, water and air quality, biodiversity preservation and amenities. The European forest area has been expanding over the last century and standing tree volume is increasing, but several models showed that the trend towards increased productivity might reverse after 2050. Today, forests face unprecedented changes, largely resulting from human activity. Forests will experience rapid changes in the near future, and characterising the ecological and evolutionary dynamics of their response to global change is an ongoing challenge. European forests are usually managed to provide multiple services, and are facing increasingly pressing demands from society to supply more products of higher quality to fuel and feed the ‘green’ economy of tomorrow, and to provide additional social and environmental services to satisfy populations. These sometimes conflicting injunctions are taking place within a context of weak timber markets, scarce public resources, and against a backdrop of unprecedented anthropogenic changes that question the very long-term sustainability of many forest ecosystems.

     

    The Lab of Excellence (LABEX) for Advanced Research on the Biology of FoRest Ecosystems (ARBRE) was granted yesterday with € 7.5 million by the ‘Investissement d’Avenir‘ programme. The LABEX ARBRE  is a consortium of labs from INRA, Université de Lorraine, and AgroParisTech to address issues challenging forests through an interdisciplinary approach. ARBRE covers a broad spectrum of expertise, and has the potential to create a unique scientific consortium for experimental tree biology, functional ecology, wood sciences, economics, and for transferring knowledge to partners in forest management, wood transformation and other activities. One of the main strengths is the presence within ARBRE of research and training capacities that cover the whole forest-wood chain from production to transformation and economic valuation, which is a unique feature across Europe. Moreover, the contributions from the Office National des Forêts (ONF), Centre National de la Propriété Forestière (CNPF) and EFICENT-Observatory of European Forests (EFICENT-OEF) will facilitate knowledge transfer and help the emergence of novel research questions. ARBRE will support ~ 100 scientists.


    The main research objectives of ARBRE are to further the understanding of biological, ecological and evolutionary processes that affect interactions between organisms in temperate forest ecosystems, and to develop new approaches to address key questions related to nutrient cycling, carbon storage and cycling, forest productivity, wood products, ecosystem services and sustainable forest management. We will implement a wide range of disciplines – from genomics to functional ecology and economics – to understand, monitor and predict community structures, dynamics and processes in forest ecosystems. ARBRE will also address significant questions in forest ecology and evolution through synthesis of existing data or development of novel theory, design novel wood products and make policy recommendations based on scientific data.

     

    Relative to existing international research efforts in this field, ARBRE’s unique added value is its integrated approach aiming to: (i) develop a comprehensive molecular-level understanding of the forest soil microbiome, tree-microbe interactions, and tree development and functioning, to be achieved through the application of ‘-omics’ approaches and system biology; (ii) generate functional and mechanistic insights into the complex interactions between biogeochemical cycles, carbon sequestration and biodiversity in forests, including interspecific and intraspecific genetic variability. This will be achieved by using long-term observatories (LTO), dedicated field experiments including isotopes tracing and large database analysis; (iii) integrate biochemistry- and biophysics-based knowledge to understand wood formation and to produce timber with properties tailored for ‘green’ end-products; (iv) contribute to the broader development of social, economic, and regulatory policies related to forest sciences and innovation in France, focusing on biodiversity; (v) train highly qualified personnel for careers in France’s R&D-driven industries and institutions; (vi) disseminate scientific innovation rapidly to end users represented in the consortium [like Office National des Forêts (ONF), CNPF and others].

    ARBRE will couple bottom-up (from the understanding of processes to forest functions) and top down approaches (from the production of goods and services back to processes) within a series of interconnected task forces or  workpackages (WPs). WP1 will integrate genomics know-how and toolkits to identify major genetic factors controlling soil microbiomes, root-microbe interactions, tree root development and functioning, focusing on stress responses. WP2 will investigate the processes taking place at the interfaces (soil/microbe/tree and tree/atmosphere) in disturbed forest ecosystems and will forecast the state and future evolution of temperate forests. WP3 will link wood properties of the forest resource to the ‘green’ end-products that can be tailored from wood fibers and their chemical components. WP4 will develop biodiversity indicators and a new set of economic instruments (such as payment instruments) for motivating forest managers based on those indicators.

    ARBRE will also stimulate the development of educational programmes in tree and microbial biology, forest ecology and management, wood sciences and economic sciences. ARBRE will contribute to the development of a unique and coordinated training facility for engineering and research covering all fields relevant to the forest based sector, contributing to the development and recognition of Lorraine as one of the leading European Center for education in forest and wood sciences. ARBRE will open new positions for postdoctoral fellows and Ph.D. students in the coming months.

     

     

     

    EMBO Plant-Microbe Interactions

    February 6th, 2012

    Register now

    Mycorrhizal Genomics Initiative: an Update

    January 18th, 2012

    I am writing to touch base about our JGI Mycorrhizal Genomics Initiative. As of today, the genome annotations publicly released are those of:

    The genome of Piloderma croceum and Tulasnella calospora are in the JGI annotation pipeline and should (hopefully) be available in the coming weeks. Those of Cenococcum geophilum, Sebacina vermifera, and Pisolithus tinctorius are in the final phase of sequencing, but Cenococcum and Pisolithus are difficult (large and polymorphic) genomes and JGI cannot give an estimated date of release.

    The transcriptome of free-living mycelium of C. geophilum, H. cylindrosporum, O. maius, P. involutus, P. croceum, P. microcarpus, P. tinctorius, Scleroderma citrinum, Sebacina vermifera and T. calospora are sequenced (RNA-Seq) and a series of dedicated databases are under construction.

    Finally, Igor Grigoriev, Joey Spatafora and I would like to invite you to Walnut Creek in mid-March 2012 to participate in several important JGI meetings:

    • Fungal Jamboree (March 19, 2011 8am-8pm) to discuss progress and coordination of large scale initiatives in fungal genomics: (1) Genomic Encyclopedia of Fungi, (2) 1000 fungal genomes, and (3) Fungal model systems and metagenomes (including our Mycorrhizal Genome Initiative).
    • JGI User Meeting (March 20-22, 2012: http://www.jgi.doe.gov/meetings/usermeeting/) and workshops including MycoCosm Tutorial (March 20, afternoon)

    You could access our recently opened MycorWeb portal dedicated to this project, Mycorrhizal Genomics Initiative, for links and updates.

    Plant Biology Congress Freiburg 2012

    January 13th, 2012