SINGEK: New Early Stage Researcher SARA CASTILLO

New SINGEK Early Stage Researcher at UNEXE

We are very happy to welcome a new SINGEK Early Stage Researcher: Sara Castillo

Sara will be working on the research project “NOVEL MICROFLUIDICS FOR THE STUDY OF PREVIOUSLY UNCULTURED MICROEUKARYOTES” under the supervision of Dr. Stefano Pagliara (University of Exeter). In particular, she will use microfluidic devices in order to evaluate the single-cell behaviour and potential community linkages of the smallest free-living eukaryotic cell, Ostreococcustauri. This will provide an insight about population dynamics and the necessary understanding for its proper protection and conservation and applications in biotechnology.

We are looking forward to a successful research cooperation in the upcoming months!

L&O Special Issue: “Linking metagenomics to aquatic microbial ecology and biogeochemical cycles”

L&O Special Issue: “Linking metagenomics to aquatic microbial ecology and biogeochemical cycles”

 

Ramon Massana, SINGEK coordinator and supervisor of ESR1, will be Special Editor in the Limnology & Oceanography Special Issue entitled “Linking metagenomics to aquatic microbial ecology and biogeochemical cycles” and jointly edited by Special Editors Hans-Peter Grossart (Leibniz-Institute of Freshwater Ecology and Inland Fisheries), Katherine McMahon (University of Wisconsin-Madison) and David Walsh (Concordia University, Canada).

The emphasis of the 2020 Special Issue for Limnology and Oceanography will be on the use of metagenomics to increase our understanding of aquatic microbiology and ecosystem functioning. 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. However, a major challenge in microbial ecology remains. Many taxa that appear functionally redundant at the metabolic pathway level 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. The special issue will explore 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 and from viruses and microbes to protists. Reviews, meta-analyses, and perspectives are welcome in addition to standard manuscripts that use primary data.

Submissions from all interested researchers who work in this area are welcome!!

The deadline for manuscript submission is January 28, 2019. Manuscripts may be submitted earlier, and accepted papers will be published online upon acceptance with a print issue expected in January 2020. Articles should be submitted through ScholarOne at the Wiley Limnology & Oceanography website: https://mc.manuscriptcentral.com/lo. Please identify your submission for consideration in the “metagenomics” issue.

For more information: https://aslo.org/blog/2020-l&o-special-issue

 

SINGEK: New paper about Genome Analyses of the Microalga Picochlorum and evolution of thermotolerance in the green lineage

A collaboration between different SINGEK teams from the Ghent University (VIB) and the Observatoire Oceanologique de Banyuls sur mer (OBS Banyuls-CNRS) has been established. Within this context, François BUCCHINI (SINGEK ESR10) has developed code to assess the gene space completeness in the newly sequenced Picochlorum genome and compared it with genomes of other green algae. From that, it could be concluded that the new genome was of high quality and more complete than published Picochlorum genomes.

As a result of this analysis, a paper has recently been published in Genome Biology and Evolution:

“Genome Analyses of the Microalga Picochlorum Provide Insights into the Evolution of Thermotolerance in the Green Lineage”

M. Krasovec, E. Vancaester, S. Rombauts, F. Bucchini, S. Yau, C. Hemon, H. Lebredonchel, N. Grimsley, H. Moreau, S. Sanchez-Brosseau, K. Vandepoele, G. Piganeau

 

The Genome of a novel picoalga species, Picochlorum costavermella, provides insights into the Evolution of Thermotolerance in the Green lineage.

While the molecular events involved in cell responses to heat stress have been extensively studied, our understanding of the genetic basis of basal thermotolerance, and particularly its evolution within the green lineage, remains limited. Here, we present the 13.3-Mb haploid genome and transcriptomes of a halotolerant and thermotolerant unicellular green alga, Picochlorum costavermella (Trebouxiophyceae) to investigate the evolution of the genomic basis of thermotolerance. Differential gene expression at high and standard temperatures revealed that more of the gene families containing up-regulated genes at high temperature were recently evolved, and less originated at the ancestor of green plants. Inversely, there was an excess of ancient gene families containing transcriptionally repressed genes. Interestingly, there is a striking overlap between the thermotolerance and halotolerance transcriptional rewiring, as more than one-third of the gene families up-regulated at 35 °C were also up-regulated under variable salt concentrations in Picochlorum SE3. Moreover, phylogenetic analysis of the 9,304 protein coding genes revealed 26 genes of horizontally transferred origin in P. costavermella, of which five were differentially expressed at higher temperature. Altogether, these results provide new insights about how the genomic basis of adaptation to halo- and thermotolerance evolved in the green lineage.

SINGEK: New paper about evolutionary genomics of Metchnikovellidae, an early branching microsporidium

Congratulations Luis and Puri for that a new SINGEK paper published in Genome Biology and Evolution:

“Evolutionary genomics of Metchnikovella incurvata
(Metchnikovellidae), an early branching microsporidium”

L. J. Galindo, G. Torruella, D. Moreira, H. Timpano, G. Paskerova, A. Smirnov, E. Nassonova, P. López-García

 

Heatmap illustrating the conservation of pathways and structures in metchnikovellids
and neighbor lineages. It is based on 73 Gene Ontology terms (GO), identified using EggNOG
(Huerta-Cepas et al. 2017) for 12 Holomycota representative proteomes. Sequences obtained
in this study are highlighted in black. Colors indicate the percentage of annotated genes with
a GO term.

Metchnikovellids are highly specialized hyperparasites, which infect and reproduce inside gregarines (Apicomplexa) inhabiting marine invertebrates. Their phylogenetic affiliation was under constant discussion until recently, when analysis of the first near-complete metchnikovellid genome, that of Amphiamblys sp., placed it in a basal position with respect to most Microsporidia. Microsporidia are a highly diversified lineage of extremely reduced parasites related to Rozellida (Rozellosporidia = Rozellomycota = Cryptomycota) within the Holomycota clade of Opisthokonta. By sequencing DNA from a single-isolated infected gregarine cell we obtained an almost complete genome of a second metchnikovellid species, and the first one of a taxonomically described and well-documented species, Metchnikovella incurvata. Our phylogenomic analyses show that, despite being considerably divergent from each other, M. incurvata forms a monophyletic group with Amphiamplys sp., and confirm that metchnikovellids are one of the deep branches of Microsporidia. Comparative genomic analysis demonstrates that, like most Microsporidia, metchnikovellids lack mitochondrial genes involved in energy transduction and are thus incapable of synthesizing their own ATP via mitochondrial oxidative phosphorylation. They also lack the horizontally acquired ATP transporters widespread in most Microsporidia. We hypothesize that a family of mitochondrial carrier proteins evolved to transport ATP from the host into the metchnikovellid cell. We observe the progressive reduction of genes involved in DNA repair pathways along the evolutionary path of Microsporidia, which might explain, at least partly, the extremely high evolutionary rate of the most derived species. Our data also suggest that genome reduction and acquisition of novel genes co-occurred during the adaptation of Microsporidia to their hosts.

SINGEK: European Researchers’ Night 2018

Who is Who in European Science?

EUROPEAN RESEARCHERS’ NIGHT 2018

28th September, 20h @ ImaginCafe (Barcelona)

 

This year, the SINGEK team will participate in the European Researchers’ Night 2018. In particular, the Early Stage Researchers will collaborate in the activity called WHO is WHO in EUROPEAN SCIENCE?

This event will be held on Friday 28th of September (20:00h) at the ImaginCafe Barcelona within the framework of  “La Nit de la Recerca a Catalunya”. It will provide the opportunity to attendants to share some time (and even a drink) with a new generation of young researchers from seven European Innovative Training Networks:

Register here (limited places!!)

 

Royal Society International conference on developing single cell methods (UK, December 2018)

Royal Society International conference on developing single cell methods

December 2018, UK

As part of the SINGEK Research Program, an international conference on developing single cell methods will be held in the UK, December 2018. This prestigious event funded by the Royal Society will be a two-day meeting “Single cell ecology”   in central London at the Royal Society, followed by a two-day satellite meeting “Developing new approaches for the single cell manipulations and experimentation” at the Kavli Royal Society Centre, Chicheley Hall.

Both scientific discussion meetings are organised by Professor Thomas Richards (University of Exeter, supervisor of SINGEK ESR11), Dr Ramon Massana (Institute of Marine Sciences, SINGEK coordinator and supervisor of ESR1) and Professor Neil Hall (Earlham Institute, SINGEK Partner Organisation).

Overview

Interdisciplinary meeting to explore the use of single cell technologies to understand the function, diversity and interactions of microbes. By bringing together physicists who manipulate cells, microbiologists who seek to understand the nature of microbial communities and genomicists who are developing new approaches to study individual cells we will achieve a greater understanding of the potential of this new field.

There will be a poster session at 16:15 on Monday 10 December. If you would like to apply to present a poster please submit your proposed title, abstract (not more than 200 words and in third person), author list, name of the proposed presenter and institution to the Scientific Programmes team with the subject heading “Single cell ecology: poster abstract” no later than Monday 22 October 2018. Please note that places are limited and posters are selected at the scientific organiser’s discretion. Poster abstracts will only be considered if the presenter is registered to attend the meeting.

Recorded audio of the presentations will be available here after the meeting has taken place.

Meeting papers will be published in a future issue of Philosophical Transactions B.

 

Single cell approaches are changing how we study many biological problems. This meeting will bring together biophysicists, molecular biologists and microbial ecologists who are using these technologies to understand the natural world. The aim of this satellite meeting is to report progress, identify areas for synergy and lay down the foundations for further developing this interdisciplinary science.

There will be a poster session at 16:15 on Wednesday 12 December. If you would like to apply to present a poster please submit your proposed title, abstract (not more than 200 words and in third person), author list, name of the proposed presenter and institution to the Scientific Programmes team with the subject heading “Single cell new approaches: poster abstract” no later than Monday 22 October 2018. Please note that places are limited and posters are selected at the scientific organiser’s discretion. Poster abstracts will only be considered if the presenter is registered to attend the meeting.

Recorded audio of the presentations will be available here after the meeting has taken place.

 

Both venues will be an exciting and stimulating meeting for all SINGEK members and participants.

Register now!

 

 

SINGEK: 3rd BCN Science Slam, 31st MAY 2018 – CALL OPEN

3rd BCN Science Slam 2018

31st May, 20h @ Bar mau mau (Barcelona)

 

The Center for Genomic Regulation (CRG) will organise in partnership with the Barcelona Institute of Science and Technology (BIST) the 3rd Barcelona Science Slam on Thursday 31st of May at 20:00 in Bar Mau Mau (Fontrodona 35, 08004 Barcelona). This time it is also a European Science Slam pre-final and the winner will participate in the European final in Toulouse on 7th of July 2018.

SINGEK CONTRIBUTION

SINGEK team will actively participate this time as well: Konstantina (ESR3) and Imer (ESR15) will be trainers in the science communication workshop previous to the Science Slam organized by Damjana Kastelic (CRG). In addition, Imer will be the moderator of the Science Slam on May 31st.

 

PRACTICAL INFORMATION

This 3rd Barcelona Science Slam encourages PhD students and postdoctoral researchers to participate, providing an exciting opportunity to learn about a broad range of scientific fields and to bring their research closer to society. Science Slam is a science communication contest where up to 8 scientists explain their research projects in 5 min engaging, clear and fun talks. You can see some examples of previous editions of the Barcelona Science Slam here.

How can you participate?

Option A: attend a free 2-day science communication workshop, which will prepare you for the slam
On this interactive workshop, you will learn how to communicate your complex research projects to the general public, and practice how to bring your science to life using simple, but strong storytelling techniques like metaphors. The ability to command core science communication tools will leave your audience spellbound; be it when you are giving a talk, or simply explaining your research to your friends or family members. In addition, you will also learn how to deal with a stage fright when presenting to a bigger  crowd of people. This very practical hands on training will prepare you how to be a confident science slammer and to be ready to hit the stage without any fear.

Duration of the course: 2 full days (29th and 30th May 2018) from 9:15 am to 5 pm
Venue: Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona
Registration: The number of participants is limited to 25. Registration deadline: 22nd May 2018

Option B: directly apply for the science slam
You can also directly apply for the science slam (without attending the science communication workshop) by uploading a one-minute video of you describing your research project by 22nd May 2018. You will be notified by 24th May 2018if your slam has been selected for the semifinal European slam on the 31st May 2018 in Bar Mau Mau at 20pm.

The call for the 3rd BCN Science Slam is now open til 22nd May 2018. Register HERE

VI Edition Ramon Margalef Summer Colloquia EXTENDED DEADLINE – MAY 10th

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!