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CBMR researchers develop computer tool to facilitate data analysis in Stem Cells related research

A group of researchers from CBMR developed a computer tool that allows access and analysis of transcriptomic datasets. Assuming that transcriptomic data have become a fundamental resource for stem cell biologists as well as for a wider research audience studying stem cell related processes such as aging, embryo development and prevalent diseases including cancer, diabetes and neurodegenerative diseases, one of the problems  is the access and the delay in the analysis of the information.

Creating StemMapper, a gene expression database, the group of researchers, led by Matthias Futschik, aims to simplify the task of thousands of scientists who collect and analyze this type of data.

This computer tool allows each integrated dataset to be individually inspected and manually curated enabling fast querying, comparison and interactive visualization by the user.  

A proof-of-principle analysis discovering novel putative astrocyte/neural Stem Cells lineage markers exemplifies the utility of this integrated data resource.

We believe that StemMapper, a free resource, available at https://stemmapper.sysbiolab.eu, can open the way for new insights and advances in Stem Cells research.

The article presenting the tool is already accepted and would be published soon by Nucleid Acids Research (NAR) – Oxford University Press.

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CBMR Science Platform featured on the radio

The radio program “Os Dias do Futuro” wanted to know the new CBMR Science Platform. In an interview with the journalist Edgar Canelas, Isa Mestre (CBMR Communication Officer) and Ana Teresa Maia (CBMR Vice-Director) explained all the details of this science communication project.

Listen the interview here.

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CBMR researcher won 22.000 euros to study rare neurological disease

Clévio Nóbrega, CBMR researcher and professor at the Department of Biomedical Sciences and Medicine (University of Algarve), obtained a 22.000 euros grant to study, over the next two years, Type 2 Cerebellar Ataxia, a rare neurological disease, without cure, that affects balance, coordination and speech.

The project, entitled “Neuroprotective therapeutic approach of Spinocerebellar ataxia type 2: pharmacological targeting of AMPK,” is funded by ATAXIA UK, a private, non-profit institution, that seeks to help patients and families affected by the disease.

The objective of the research, to be developed at the CBMR, in collaboration with the CNC – Center for Neurosciences and Cell Biology, is ambitious: to test an existing drug authorized for human use, in order to delay the progression of the disease.

At the moment there isn’t no treatment for this disease, only symptomatic treatments, incapable of delaying or preventing its progression.

So, Clévio Nóbrega and his team may take an important step in the treatment of the disease since the applicability of the drug may be accelerated because it isn’t an experimental drug.

Starting in october 2017, the project of Clévio Nóbrega is part of a series of innovative projects around the world that seek, through the financing of their research, to develop treatments and alternatives in the scope of the various types of Ataxias.

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CBMR launches CBMR Science Platform

It is our pleasure to welcome you to the CBMR Science Platform for research and innovation communication. Here you will find the latest and most interesting content in the field of Medicine, Biomedicine and Cognitive Neuroscience.

The CBMR Science Platform mission is to provide reliable scientific information from around the world and Portugal, including the CBMR research topics Molecular and Cellular Mechanisms of DiseaseMolecular Biomedicine and TechnologyRegenerative Medicine and Translational Medicine in an accessible manner. We aim to raise science awareness and public engagement.

The CBMR Science Platform brings together national and international researcher centers and science communicators to build a digital science communication network.

It is our privilege to welcome you to the CBMR Science Platform that disseminates science and innovation in Portugal and the wider world. We wish you an exciting experience!

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HeartExpress – technology for the heart

Heart development is a highly complex process with a series of precisely spatially and temporally ordered events on molecular level. To understand how these events are controlled and coordinated, it is necessary to study the underlying gene expression and its regulation. To help researchers in this formidable task, we have established HeartEXpress, a web-based platform for the analysis of integrated expression datasets associated with cardiomyogenesis. The current version comprises human and murine gene expression data from independent microarray experiments for stem cell differentiation, in vitro or in vivo reprogramming, in the context of cardiomyogenesis, and heart development. We hope that this resource will support the development of new therapies in cardiac regenerative medicine.

What is HeartEXpress?
HeartEXpress is a database that comprises published human and murine gene expression data from various microarray experiments for stem cell differentiation, in vitro or in vivo reprogramming in the context of cardiomyogenesis as well as heart development.

Why HeartEXpress?
Genome wide expression profiling of cardiogenesis in vivo and surrogate processes in vitro have delivered a detailed picture of molecular events important for the constitution of heart cells. However, the generated data remained difficult to access and analyze for many individual researchers, as they were dispersed across various repositories. HeartExpress can help here by providing an unique platform integrating various microarray studies for human and mouse with relevance for cardiogenesis.

HeartEXpress Data
At present, HeartEXpress integrated expression data from 15 mouse studies and 8 human studies with a total of 131 experimental conditions. These expression datasets cover more than 20000 genes in mouse and more than 19000 genes in human. Data sets were classified according to organisms and types of experiment and integrated data from both organisms and different types of studies.

What is HeartEXpress useful for?
For genes of interest, HeartEXpress enables the simultaneous inspection of expression data from many individual experiments obtained with different transcriptomic technologies. It allows query for multiple gene symbols and offers the option to download data as table for further analysis or presentation.

Moreover, HeartEXpress provides clustered gene expression data and correlation between genes. These feature help to identifiy co-expression patterns of genes indicating a common regulation and function during differentiation, reprogram-ming or heart development. Such approach may be useful for:
– Assigning functions to genes that have not been yet associated to heart development or heart morphology;
– Prioritize genes for experimental characterization
– Generate new research hypotheses

HeartEXpress can be utilized in an intuitive way and has a “step-by-step” instructions on its Help page as well as a table containing information about the studies integrated in the database.

 

More information: http://heartexpress.sysbiolab.eu/

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Cláudia Florindo will be one of the teachers of the “III Quantitative Fluorescence Microscopy Course”

Cláudia Florindo, CBMR researcher, will be one of the teachers of the “III Quantitative Fluorescence Microscopy Course. The miscroscopy couse will be held from 18th to 22th September, at the Microscopy Imaging Center of Coimbra – Center for Neuroscience and Cell Biology (MICC-CNC).

The “III Quantitative Fluorescence Microscopy Course” is an one-week intensive microscopy course focused on the principles and high-end applications of quantitative fluorescence microscopy.

Attendees will gain a theoretical understanding and hands-on experience on state-of-the-art equipment such as widefield microscopy, laser scanning and spinning disk confocal microscopy, multi-photon microscopy, deconvolution methods, and digital image processing and analysis.

For more informations please visit the website: http://www.qfm.cnc.uc.pt/

 

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Medical students from UAlg stay as doctors in Algarve

Eight students who completed the Integrated Master’s Degree in Medicine at the University of Algarve in the academic year 2015/2016 completed the test that guarantees access to the specialty and are currently performing functions at Algarve Hospitals. With specialties ranging from Anesthesiology to Radiology, through General and Family Medicine and Urology, more and more are choosing the Algarve region to develop their professional career.

 

Know more here.

 

 

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CBMR students obtained doctoral and post-doctoral FCT research grants

Adriana Marcelo and Catarina Paulino obtained doctoral and post-doctoral FCT research grants for the development of their investigations over the next years. To the referred students CBMR wishes congratulations and all the success for the future!

Adriana Marcelo – Doctoral Research Grant FCT 2017 – Project “Stress granules as new players in Polyglutamine diseases: from pathogenesis to therapeutic strategies”

Catarina Paulino – Post-Doctoral Research Grant FCT 2016- “Anger vs. happiness: which comes first? The time course of emotional word recognition” (Supervisors: Alexandra Reis e Luís Faísca)

 

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Clévio Nóbrega publishes on British Medical Bulletin

Clévio Nóbrega, CBMR researcher, published recently on the British Medical Bulletin the article: “The contribution of genetics and environment to obesity”.

Know more about the article here.

Abstract: Obesity is a global health problem mainly attributed to lifestyle changes such as diet, low physical activity or socioeconomics factors. However, several evidences consistently showed that genetics contributes significantly to the weight-gain susceptibility.

Areas of controversy: After more than 10 years of investigation on the genetics of obesity, the variants found associated with obesity represent only 3% of the estimated BMI-heritability, which is around 47–80%. Moreover, genetic factors per sewere unable to explain the rapid spread of obesity prevalence.
Growing points: The integration of multi-omics data enables scientists having a better picture and to elucidate unknown pathways contributing to obesity.
Areas timely for developing research: New studies based on case–control or gene candidate approach will be important to identify new variants associated with obesity susceptibility and consequently unveiling its genetic architecture. This will lead to an improvement of our understanding about underlying mechanisms involved in development and origin of the actual obesity epidemic. The integration of several omics will also provide insights about the interplay between genes and environments contributing to the obese phenotype.

 

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Available postdoctoral position at “The Drosophila Development Laboratory”

A postdoctoral position is available at The Drosophila Development Laboratory for analysis of the epigenetic regulation of gene expression during oocyte reactivation and fast cell proliferation in Drosophila melanogaster and human cells. To bypass limitations of “standard” steady-state RNAseq approaches, we are currently optimising nascent RNA transcriptomics approaches for developing embryos.
Applications of highly motivated postdoctoral researchers, willing to learn state-of-the-art transcriptomics approaches, and not afraid of being involved in a international collaborative effort, are strongly encourage to apply. This project will be developed in close collaboration with Maria Carmo-Fonseca laboratory (IMM, Lisbon).
Ideal candidates should have: i) a previous experience with Drosophila melanogaster and/or tissue culture of human cells, qRT-PCR, chromatin purification, and RNAseq techniques; and/or ii) a strong background in computational biology and experience in the analysis of RNAseq datasets.
For more information please send email to: rgmartinho@ualg.pt