VI Edition Ramon Margalef Summer Colloquia

The Ramon Margalef Summer Colloquium (RMSC) has been running yearly since 2013 and aims at training young researchers in Ecology, as well as promoting their networking and debate with invited lecturers as well as among themselves. The Colloquium is inspired in the figure of Ramon Margalef (Barcelona, 1919-2004), who was one of the founders of modern ecology. He broke paradigms and contributed with innovative theories about the spatio-temporal structure of ecosystems, the relationships between diversity, biodiversity, stability and connectivity, the fundamental role of energy in biological productivity as well as the interrelationships between ecological succession and evolution. He recognized the importance of the physical environment to understand the behavior of species and ecosystems. He wrote ca. 400 papers and books, working for many years at the Institut de Ciències del Mar and the University of Barcelona.

This 6th Colloquium will, again, be an excellent opportunity to foster learning and discussions on the relevance of an interdisciplinary perspective in Ecology & Evolution.

 

Central topic: Ecology through the omics lens

The use of omics techniques has spread rapidly across the field of Ecology and Evolution during the last decade, but there is substantial work ahead to link the obtained results with the existent ecological theory. During the 2018 Ramon Margalef Summer Colloquium, we will make an effort to bridge this gap, aiming to inspire attending students to move from “what” to “why” when using omics approaches to study the ecosystem, as well as to frame their omics-based research in a theoretical ecological framework. The course will cover different environments (marine, terrestrial, host associated) as well as organismal sizes (from microbes to plants and animals), thus becoming an excellent opportunity to bring together researchers with similar questions, but working in fields that seldom communicate between each other. Furthermore, this edition of the course will focus on the feedbacks between ecology and evolution, and how the processes studied by both disciplines shape the structure of life on earth.

 

The scientific organization of the RMSC 2018 will be provided by Institut de Ciències del Mar (ICM-CSIC) and the logistics will be taken care by the Catalan Association of Oceanographers (ACOIO). The course organizers are Javier del Campo, Ramiro Logares (SINGEK Project Supervisor of ESR2) and Cèlia Marrasé.

 

More information at the website of the Colloquia.

ASLO 2018 Summer Meeting

WATER CONNECTS !!

ASLO 2018 Summer Meeting, 10th-15th June, Victoria (Canada)

Water connects everything and everyone! Water transcends and connects all spheres: the lithosphere, atmosphere, and biosphere – from fresh to salty, from microscopic to macroscopic. Water connects us to each other and to resources – across cultures and society, across politics and international boundaries. However, these elements are too frequently studied in isolation. This meeting will encourage you to bring your knowledge, curiosity, and creativity to connect with each other and to share your passion for water!

From the SINGEK Team, Ramon Massana (Project Coordinator and supervisor of ESR1), will participate in the following session:

SS53: Linking Metagenomics to Aquatic Microbial Ecology and Biogeochemical Cycles

Hans-Peter Grossart, Leibniz Institute for Freshwater Ecology and Inland Fisheries (hgrossart@igb-berlin.de)
David Walsh, Concordia University (david.walsh@concordia.ca)
Ramon Massana, Institut de Ciencies del Mar-CMIMA CSIC (ramonm@icm.csic.es)
Rebecca Vega Thurber, Oregon State University (Rebecca.Vega-Thurber@oregonstate.edu)
Marguerite Xenopoulos, Trent University (mxenopoulos@trentu.ca)

A general aim of microbial ecology is to observe, understand, and predict the distribution and interactions of microorganisms in the context of environmental conditions. Taxonomic profiling of different microbial communities often reveals significant but unexplained variations across aquatic environments both in space and time. Functional differences among organisms are often invoked as an explanation; and variation in gene content (assessed by metagenomics) often reveals dynamic relationships between metabolic pathways and environmental conditions, the strength of which typically depends on the magnitude of the environmental change between communities in different ecosystems. However, a major challenge in microbial ecology remains. Many taxa that appear functionally redundant at the metabolic pathway level do show significant variation across environments with different ecological features. Possible explanations include dispersal limitation, biotic interactions, and rapid adaptation to environmental conditions that are not easily predictable based on gene content alone. In this session, we will explore and discuss recent advances and current limitations about how large-scale meta-omics analyses can be integrated into biogeochemical and eco-evolutionary frameworks to better predict taxonomic and functional diversity patterns across aquatic ecosystems from lakes and rivers to oceans. This session will be the seed for a 2020 special issue of Limnology and Oceanography.

 

See you in Victoria or follow updates from the ASLO 2018 Summer Meeting in its Website or via Twitter.

 

SINGEK: Training workshop for ESRs on Genome Annotation

Workshop on Genome Annotation: Challenges in Eukaryotes and Consequences Evolutionary Genomics

13th-16th February 2018, Observatoire Oceanologique de Banyuls sur mer

This week, SINGEK ESRs have attended to this workshop on genomic annotation organized by Gwenaël PiganeauI (OBS Banyuls-CNRS) and Klaas VANDEPOELE (Ghent University, VIB), supervisors of the SINGEK individual research projects: “ESR9 – Genomic insights into interactions in green microalgae” and “ESR10 – New tools for genome annotation in unknown microeukaryote lineages“, respectively.

Among the lecturers and experts, François BUCCHINI (ESR10 at Ghent University, VIB) contributed to this training activity as a trainer during the hands-on sessions on the TRAPID tool for comparative and functional annotations.

Everybody made a great job!

SciLifeLab course on Single Cell Genomics (Uppsala, March 2018)

SINGEK: New paper about comparative genomic analysis of the “pseudofungus” H. Catenoides

We are happy to announce that a new SINGEK paper is out in Open Biology:

“Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

G. Leonard, A. Labarre, D. S. Milner, A. Monier, D. Soanes, J. G. Wideman, F. Maguire, S. Stevens, D. Sain, X. Grau-Bové, A. Sebé-Pedrós, J. E. Stajich, K. Paszkiewicz, M. W. Brown, N. Hall, B. Wickstead and T. A. Richards

 

Schematic phylogenetic tree summarizing the evolution of cell and genomic characters relevant to the evolution of the Pseudofungi.

Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hyphochytrium
catenoides. Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.

SINGEK: Imer’s Video at 2nd BCN Science Slam

2nd BCN Science Slam 2017 (October, 2017)

Congratulations IMER!!

Imer Muhovic, SINGEK ESR15 based at aScidea (Barcelona), won the 2nd BCN Science Slam organized by the ITN DivIDE (Centre for Genomic Regulation, Barcelona).

His talk was entitled “Software for Humans” and here is his great performance at Black Lab bar:

Imer has been invited by the Marie Curie Alumni Association to present again at the Science Slam during their annual meeting on 2nd of February 2018 in Leuven, Belgium.
Good luck and thanks for spreading SINGEK to different audiences!!

SINGEK: Mid-Term Meeting & two training workshops

Mid-Term Meeting and two training workshops for ESRs in October 2017

Three relevant events were conducted within the SINGEK Consortium during this month:

– A Workshop on Genome Assembly was organized by the CNAG – CRG‘s Team: Ivo Gut, Holger Heyn (supervisors of ESR 6) and Tyler Alioto. This 3-day workshop, part of the training program for SINGEK ESRs, aimed to provide them an overview of bioinformatic assembly tools and hands-on experience through some examples.

– The SINGEK Mid-Term Meeting took place on October 24th at the Institute of Marine Sciences, Barcelona. During this meeting, the Coordinator of the Network, Ramon Massana, provided an update about the project progress and implementation. In addition, all 15 ESRs presented his/her individual research project and the results obtained so far. Several sessions were also devoted to discuss different aspects of the project with our Project Officer, Mrs. Giuliana Donini (Research Executive Agency), an external expert, Mr. Jean-Louis Marchal and an innovation expert, Mrs. Marusela Oliveras Salva.

– A Worshop on Scientific Writing was offered by the Partner Organisation ThePaperMill, in which all ESRs drew on experiences from well-written papers, learned to recognize common errors, and gained practical tools for writing in clear, simple language.

SINGEK: New Blog release

New SINGEK Blog

We are glad to announce that our SINGEK Blog has been released!

Do not miss our posts!

www.singek.eu/blog

CRG Symposium: 7th International Workshop on Genomic Epidemiology

7th International Workshop on Genomic Epidemiology

16th CRG Symposium, 20th-22nd September, PRBB, Barcelona

The 16th CRG Symposium: Seventh International Workshop on Genomic Epidemiology will take place at the PRBB Auditorium from 20 to 22 September 2017 will gather speakers to discuss about the progress in sequencing and with other technologies for biomolecular analysis, and their applications in research and clinical settings.

Solutions will be presented for the accumulation, handling and interpretation of huge data sets, including the identification of rare and common genetic variants associated with disease, functional evaluation of genetic variation, understanding of gene networks and epigenomic phenomena in health and disease, pharmacogenomics, gene-gene and gene-environment interactions. Examples of the application of these technologies for epidemiological scale studies in different disease areas will be presented.

Participants in the meeting are welcomed to present their research results with a short abstract of 300 words. A limited number of slots will be available in the programme for selected participants for short talks.

Organisers:

Registration deadline: August 31

Follow updates from this CRG Symposium in its website.

Open position at aScidea (TecnioSpring+ program)

OPEN POSITION AVAILABLE at aScidea: Bioinformatics R&D Scientist

aScidea Genomics & Bioinformatics CRO, a SINGEK hosting institution and Supervisor of the individual research project ESR15, offers a new position:

We are looking for a highly motivated and proactive person with a strong interest in learning and participating in an innovative and growing environment. This person will work as Bioinformatics R&D Scientist at our R&D Department and will develop its own research project in the framework of TecnioSpring+ program, and will be involved in current active projects in the company, such as SINGEK, aimed to develop single cell bioinformatics pipelines to advance the precision of the omics discoveries.

Tasks / responsibilities
– Develop Scientific Software and data analysis under the TecnioSpring+ program.

Requirements
– PhD in Computational Biology/Bioinformatics or similar.
– Prior experience of at least 2 years in Bioinformatics software and data analysis.
– Strong background in algorithms, statistics and data management and mining.
– Excellent programming skills. Experience in python.
– Familiar with Machine Learning techniques is a plus.
– Knowledge on SQL and noSQL databases.
– Knowledge on big data analytics.
– Fluent English (Catalan/Spanish is a plus).
– Working permit in the EU.

Offer
– Full time contract, starting at mid-January 2018.
– Flexible working
– Salary according to both candidate’s experience and company pay scales.
– An exciting and growing environment.

If you are interested in this position, please send a CV, a cover letter and 2-3 recommendation letters to: info@ascidea.com before August 15th.
Please write the tag [TECNIOSPRING] in the e-mail header.