en News - BIOINFORMATICS BARCELONA News Tue, 11 Aug 2020 09:48:40 +0000 Tue, 11 Aug 2020 09:48:40 +0000 Houdini 2 (http://houdini.antaviana.cat/) http://www.bioinformaticsbarcelona.eu/news Phylloxera genome that took over European vineyards in the 19th century, deciphered

The genome of the phylloxera, an insect that caused plagues that ended with the European vineyards in the 19th century, has been deciphered by an international team in which the experts Julio Rozas and Alejandro Sánchez-Gracia, from the Faculty of Biology and the Biodiversity Research Institute of the UB (IRBio) take part, together with other members from the platform Bioinformatics Barcelona (BIB).


The study, published in the journal BMC Biology, affirms the plague comes from North America and likely from wild populations located over the upper course of the Mississippi River. The conclusions of the study helped to reconstruct the biological invasion that unchained mortal plagues on the European vineyards in the 19th century and to advance in the strategies to improve the productivity in viticulture.


The sequencing of the new genome has been promoted by the international consortium -more than seventy experts from eight countries worldwide- created in 2011 and led by the French National Research Institute for Agriculture (INRAE). The study counts on the technical support of the INRAE-BIPAA platform, which enabled the access to genomic resources on insects associated with agricultural ecosystems.


The experts Silvia Hinojosa-Alvarez, Jose F. Sánchez-Herrero, Paula Escuer and Pablo Librado take part in the UB-IRBio team as well. The team focused its scientific contribution in the genomic annotation and analysis of several families of genes of the olfactory system of the phylloxera. The general study, led by researchers François Delmotte and Denis Tagu (INRAE), counts on the participation of the experts from the Centre for Genomic Regulation (CRG) and UPF, apart from the Science Park of the University of Valencia. 


Phylloxera: from Mississippi riverbanks to the French vineyards


The grape phylloxera (Daktulosphaira vitifoliae) is a hemipteran insect from the family Phylloxeridae, which feeds from the sap of the roots in the vineyards. Described for the first time in 1854 by the entomologist Asa Fitch in the United States, which originated the first infection outbreaks in France in 1863 until it was identified in 1868 by Bazille, Planchon and Sahut, members of the Chambre d'Agriculture de l'Hérault in Montpellier.


The intense trade of vines between the United States and Europe could have been the open doors for the insect, which spread widely around France -the most affected country by this plague-, and other European areas. 


A new genic family with more than 2,700 genes


The DNA nuclear genomic analyses of the phylloxera reveal the existence of the largest genic family ever identified with a genome -with about 2,700 genes, when the average does not go over 200-, which would account for a 10% of the genome of this insect.


Researchers believe these genes are essential for the interaction between the phylloxera and the vineyard: they code the small secreted proteins -known as effectors- that could take part in the deactivation of the basic defenses of the plant. In the region of origin, the coevolution between the plant and the plague could have enabled the vineyards to be resistant to the insect. However, the vineyards in Europe did not have such a defense system to fight the threat of the new plague and the effectors.


The study has worked on sample campaigns of the plague in Europe and the United States, and it affirms the phylloxera that invaded Europe comes from the species Vitis riparia, a wild type from American vineyards. "As expected, the study reveals there is a great genetic variability among the native species of D. vitifoliae compared to the European strains. In particular, the comparison of these patterns of genetic variability is what enabled researchers to trace the geographical routes of the biological invasion", note the experts Julio Rozas and Alejandro Sánchez-Gracia, heads of the Research Group on Evolutionary Genomics and Bioinformatics UB-IRBio. 


From basic research to an improvement of wine production


Promoting knowledge on basic research is the most direct ccontribution of the studies that finish with genomic sequencing of a new species. "These new findings provide many biological information and basic knowledge on the evolution of insects -specially the aphids-, and about the genetics and selection of roots of those phylloxera-resistant plants", notes Professor Julio Rozas.


From an applied field, the genomic data of the new study will enable the promotion of genetic improvement in the practice of viticulture. Therefore, a better knowledge of the evolution and action mechanisms of the new family of effector genes will help design strategies to block the action through interventions on the plant or the parasite.


"The new study is an advance in our understanding of biological invasions and the potentially disastrous consequences on agriculture, and therefore, on the important social and economic sectors", notes researcher Alejandro Sánchez-Gracia.


Decipgering the genome of living beings


The Research Group on Evolutionary Genomics and Bioinformatics UB-IRBio has a significative experience in international studies which allowed them to decipher the genome of several organisms of scientific interest. Therefore, they are the co-authors of the genetic sequencing of the genome of the spider Dysdera sylvatica Schmidt 1981 -an endemic species of the Canary Island forests- (GigaScience, 2019); the plant varieties of the avocado Persea Americana var. drymifolia and Persea Americana Mill. Cv. Hass (Proceedings of the National Academy of Science, 2019); the tick Ixodes scapular, of great interest in public and veterinary health (Nature Communications, 2016); the myriapod Strigamia maritima, a common centipede in the coasts of northern Europe (PLOS Biology, 2014), and the coffee plant Coffea canephora (Science, 2014). 


In the field of insect genomics, they also took part in the decipherment of the pea aphid genome (Acyrthosiphon pisum),  -a parasite of legume plants that causes serious agricultural plagues-, published in the journal PLoS Biology  in 2010 by an international consortium that gave way to the scientific platform to decipher the genome of the phylloxera.


Tue, 11 Aug 2020 09:48:40 +0000 http://www.bioinformaticsbarcelona.eu/news//news/167/phylloxera-genome-that-took-over-european-vineyards-in-the-19th-century-deciphered http://www.bioinformaticsbarcelona.eu/news/167 0
Debate on The COVID-19 and its consequences

It is a series of debates on current and most interesting topics, in which personalities from different parts of the world participate with the aim to share and disseminate knowledge.

The first of the debates, to be held on the 12th, is titled "The Covid-19 and its health and social implications" and will count with the following speakers:

Ms. Rosalía Arteaga -  Lawyer, writer, former president of Ecuador

Ms. Maria Àngels Calvo  Pharmaceutical and veterinary, professor of microbiology

Mr. Manuel Carballo Epidemiologist and psychologist

Mr. José Becerra Epidemiologist doctor

Mr. LLuís Serra: Doctor. Professor of Public Health at the ULPGC

Mr. José Ramon Calvo Doctor. Strategic advisor at the BSC-CNS

Registration and confirmation through this link.

Limited places.

Registered people will receive a link to connect from 15 minutes before the start time.

Tue, 12 May 2020 15:03:38 +0000 http://www.bioinformaticsbarcelona.eu/news//news/165/debate-on-the-covid-19-and-its-consequences http://www.bioinformaticsbarcelona.eu/news/165 0
BIB invited at the AI World Team

Dr. Josep Lluis Arcos, researcher at the Artificial Intelligence Research Institute (IIIA-CSIC), will be the leading representative of the BIB within the AI World Team community.

The aim will be to promote the opportunities and initiatives of the AI World Team towards the BIB bioinformatics community as strategic in the Artificial Intelligence subject in the biomedicine.

Fri, 08 May 2020 10:15:32 +0000 http://www.bioinformaticsbarcelona.eu/news//news/163/bib-invited-at-the-ai-world-team http://www.bioinformaticsbarcelona.eu/news/163 0
"BioS - Digital skills on Computational Biology for Health Professionals": New article in the Faseb Journal

The 4emedicine: Emergency, Environmental, Electronics and Extreme medicine. Overview of the available and on‐going related controlled trials with a survey on the overlap areas and on the use of bioinformatics.

This article is written by Guglielmo Trovato, MD, Professor of Medicine, the EMA Director for Media, e-learning and e-medicine.

Prof. Trovato is actively working, in his medical and academic practice, now dealing with medical and research topics related to the current COVID-19 outbreak, also with active campaigns of dissemination using all the EMA social media.

Information about "BioS - Digital skills on Computational Biology for Health Professionals": https://www.bios-project.eu/site/es/index.html

Thu, 07 May 2020 15:33:46 +0000 http://www.bioinformaticsbarcelona.eu/news//news/161/bios-digital-skills-on-computational-biology-for-health-professionals-new-article-in-the-faseb-journal http://www.bioinformaticsbarcelona.eu/news/161 0
Bioinformatics is revolutionizing biology

Ana Ripoll interviewed in El Periodico de Catalunya.

In this interview, she explains why Bioinformatics emerges as a key discipline in the field of health to diagnose and find the best treatment.

Mon, 04 May 2020 15:55:28 +0000 http://www.bioinformaticsbarcelona.eu/news//news/159/bioinformatics-is-revolutionizing-biology http://www.bioinformaticsbarcelona.eu/news/159 0
COVID-19: EU Extraordinary Collaboration Call

The purpose of this call is to facilitate the standardization of this data in order to accelerate the extraction of evidence that allows to improve the clinical management of coronavirus-infected patients, anticipate their evolution and extend the effectiveness and safety of different treatments. For this purpose, the project has a strategy of mass standardization and analysis of data that acts remotely and allows the data to never leave the local environment where they are located.

The project will fund the participating institutions with a sub-grant of between €30,000 and €50,000, depending on the degree of complexity of the data they can offer.

The call for collaboration, proposed in an agile working format in order to be able to provide the first results based on data from hundreds of thousands of COVID-19 infected, will remain open from 16th April to 14th May 2020.

For more information you can access the following LINK

Fri, 17 Apr 2020 10:48:58 +0000 http://www.bioinformaticsbarcelona.eu/news//news/157/covid-19-eu-extraordinary-collaboration-call http://www.bioinformaticsbarcelona.eu/news/157 0
New biocompatible nanoparticles for breast cancer therapy

According to data from the Spanish Association against Cancer (AECC) observatory, breast cancer is the second most common type of cancer in Spain with 33,307 new cases in 2019. The number of deceased has reached 6,689 this year. Many research groups are exploring new ways to fight against this disease.

Dasatinib, an FDA-approved compound for the treatment of chronic myeloid leukemia, has become a potential candidate for the treatment of other cancers. It has been recently demonstrated that it could have a relevant role in breast cancer therapy. However, the solubility of this compound is extremely low, leading to poor absorption by the organism. Thus, the administration of a higher dosage is needed in order to obtain a better effect.

An alternative solution to enhance its therapeutic effect is the development of polymeric nanoparticles for a sustained and controlled delivery of the drug.

Researchers from the University of Castilla La Mancha, the ALBA Synchrotron, the European Synchrotron Radiation Facility (ESRF) and the San Carlos Clinic Hospital in Madrid have used the polymer poly(cyclohexene phthalate), named also CHO/PA, to synthesize the nanoparticles to encapsulate the drug.

Thanks to the synchrotron light this team has analyzed and compared the structure between the polymer in bulk and in the form of nanoparticles. "Using synchrotron light techniques, such as the small-angle and wide-angle X-ray scattering (SAXS and WAXS), we can study the structure of the polymer to check if it changes its properties when forming the nanoparticles", Eduardo Solano, scientific of the ALBA Synchrotron's NCD-SWEET beamline, states.

The results demonstrate that the polymer maintains its properties when forming the nanoparticles. Moreover, the research has proved that CHO/PA is a biodegradable, non-toxic and blood compatible polymer. "Compared to other polymers, CHO/PA nanoparticles show a slower sustained release of Dasatinib. This means a potential increase of the drug's efficacy", says Carlos Alonso, members of the Castilla La Mancha University's research team.

"The next step is to study other compounds and investigate the efficacy of this particular one using in vivo models" adds Iván Bravo, also a member of the aforementioned University, "Which would improve its potential future use in patients" concludes Dr. Alberto Ocaña, an oncologist from the Hospital Clínico San Carlos in Madrid.


Up, 2D SAXS and WAXS patterns of the CHO/PA nanoparticles recorded at NCD-SWEET beamline, which confirm the lack of well-structured mesophase. Down, the research team at the NCD-SWEET beamline.

Smaller size for bigger results

Nanoparticles are particles with a size ranging between 1 and 100 nanometers (nm) (1 nanometer is the one thousand millionth part of a meter or 10-9 m). These units have the potential of revolutionizing medicine, since their characteristics make them ideal for encapsulating drugs extending their degradation time inside the body, and helping to make a targeted delivery, reducing toxicity and side effects.

Polymeric nanoparticles are considered one of the most promising drug delivery systems for use in oncology. This is due to the fact that they are made out of polymers. Polymers are macromolecules composed of long chains with many repeated subunits, called monomers. These materials are usually biodegradable and biocompatible and their release profiles can be modulated by the polymeric structure itself.

Reference: Enrique Niza, Cristina Nieto-Jiménez, María del Mar Noblejas-López, Iván Bravo, José Antonio Castro-Osma, Felipe de la Cruz-Martínez, Marc Martínez de Sarasa Buchaca, Daniel Hermida-Merino, Eduardo Solano, Alberto Ocaña, Carlos Alonso-Moreno. Poly(Cyclohexene Phthalate) Nanoparticles for Controlled Dasatinib Delivery in Breast Cancer Therapy. Nanomaterials 2019, 9, 1208. DOI: 10.3390/nano9091208.

Thu, 28 Nov 2019 14:22:33 +0000 http://www.bioinformaticsbarcelona.eu/news//news/153/new-biocompatible-nanoparticles-for-breast-cancer-therapy http://www.bioinformaticsbarcelona.eu/news/153 0
Conference The opportunity for Big Data and Artificial Intelligence in clinical decision-making and health evaluation. Barcelona The Conference "The opportunity for Big Data and Artificial Intelligence in clinical decision-making and health evaluation" held in Barcelona, on November 6th, 2019, was organized by Bioinformatics Barcelona (BIB), the Faculty of Medicine and Health Sciences of the University of Barcelona (UB) and professional societies.

Dr Ana Ripoll, President at BIB, participated in the opening conference "Bioinformatics Barcelona (BIB): a strategic ecosystem in health as a 21st century vision of societies". Other representatives, members and collaborators at BIB participated in the following sessions: "Scientific and technical aspects in healthcare practice", "Ethical, social and legal aspects", and "The application of Big Data and Artificial Intelligence in clinical research and evaluation in Health".

Mon, 24 Feb 2020 16:22:06 +0000 http://www.bioinformaticsbarcelona.eu/news//news/151/conference-the-opportunity-for-big-data-and-artificial-intelligence-in-clinical-decision-making-and-health-evaluation-barcelona http://www.bioinformaticsbarcelona.eu/news/151 0
The mechanism of the most commonly used antimalarial drugs in near-native conditions unveiled

Plasmodium falciparum parasite, transmitted through mosquito sting, causes the malaria disease infecting red blood cells of its victim. In the last two decades, the parasite has evolved into drug-resistant strains. "Recently, the increasing geographical spread of the species, as well as resistant strains has concerned the scientific community, and in order to improve antimalarial drugs we need to know how they work precisely", explains Sergey Kapishnikov, from the University of Copenhagen in Denmark, and the Weizmann Institute, in Israel, and leader of the study.

Once inside red blood cells, Plasmodium ingests hemoglobin (the protein in charge of oxygen transport) as a nutrient.  After digesting, iron-containing heme molecules are released, which are toxic to the parasite. However, these molecules crystallise into hemozoin, a disposal product formed from the digestion of blood by the parasite that makes the molecules inert. As reported in previous studies, for the parasite to survive, the rate at which the heme molecules are liberated must be slower or the same as the rate of hemozoin crystallization. Otherwise there would be an accumulation of the toxic heme within the parasite.

Quinoline-family drugs, which include quinine-based antimalarial pills, effectively damage the parasite. The scientific community has suspected that the reason for their success is the inability of the heme to crystallise. Until today, all studies of the drug action on heme crystals have been done either on model systems or on dried parasites, which yielded limited data and opened room for speculation. Kapishnikov and his team, which include scientists from Denmark, Spain, Germany, Israel and France, decided to find out the mode of action of established drugs like chloroquine (although they used the analog bromoquine) in fully hydrated, rapidly frozen, Plasmodium falciparum-infected red blood cells. Rapid freezing creates instant snapshots of the living stage of the cells such that chemical distribution therein is unaltered by sample preparation.

Synchrotron complementary techniques

In this case, the same cells maintained under cryogenic conditions had to travel across Europe. The researchers brought them in and out of synchrotron facilities, in order for their structure to be mapped in three dimensions by soft X-ray cryo-tomography at the MISTRAL beamline from the ALBA Synchrotron and BESSY-II in Berlin. This technique, only available in four countries all over the world (UK, USA and these two mentioned in Germany and Spain), is the unique way to image whole cell samples in their native state without any chemical treatment or sectioning.

Finally, cells were brought to ESRF for mapping of bromine and iron distribution by the X-ray fluorescence nano-probe. The synchrotron data were analyzed back in Denmark where scientists determined the correlation between the different imaging modalities and they calculated and interpreted the concentrations of bromoquine at the surface of hemozoin crystals, at the membrane and within the lumen of the parasitic digestive vacuole - the site of the drug action.

The mapped infected red blood cells at the synchrotrons showed that bromoquine caps hemozoin crystals, thereby inhibiting the hemozoin crystal growth and hence, sabotaging heme detoxification. Surprisingly, they also found that bromoquine accumulates in the digestive system of the parasite, which enhances the drug's efficiency in depriving heme from docking onto the hemozoin crystal surface.

"These results show a model that can be generalized to all quinoline drugs, such as quinine, and our approach can be extended to other families of antimalarial drugs, such as artemisinins", explains Kapishnikov. Malaria remains one of the biggest killers in low-income countries, estimates of the number of deaths each year range from 450,000 to 720,000, with the majority of deaths happening in Africa. "We hope that this knowledge will let us go a step further in designing new, effective drugs against resistant malaria strains", he concludes.


Surface rendering, measured and simulated X-ray fluorescence maps of a bromoquine-treated infected red blood cell (iRBC) labeled A. (A) Surface rendering of a soft X-ray tomography segmentation. (B) Measured iron (Fe) X-ray fluorescence map.(C) Measured brome (Br) X-ray fluorescence map. (D) Simulated Br X-ray fluorescence map. Br atoms were evenly distributed over the surface of the digestive vacuole (DV) membrane, the parasite nucleus, and the parasite membrane with the density of 5·10^3 atoms per μm2, and on the surface of hemozoin (Hz) crystals with a density corresponding to 10% bromoquine surface coverage.

Reference: Sergey KapishnikovTrine StaalsøYang YangJiwoong LeeAna J. Pérez-BernáEva PereiroYang YangStephan WernerPeter GuttmannLeslie Leiserowitz, and Jens Als-Nielsen. Mode of action of quinoline antimalarial drugs in red blood cells infected by Plasmodium falciparum revealed in vivo. PNAS (2019). DOI: 1910123116.


Thu, 07 Nov 2019 09:52:02 +0000 http://www.bioinformaticsbarcelona.eu/news//news/149/the-mechanism-of-the-most-commonly-used-antimalarial-drugs-in-near-native-conditions-unveiled http://www.bioinformaticsbarcelona.eu/news/149 0
Artificial intelligence applied to the diagnosis of rare diseases associated with collagen VI

The system makes the diagnosis from images obtained with a confocal microscope located in the Hospital Sant Joan de Déu Barcelona and is based on artificial learning techniques, using cases previously diagnosed by IRSJD's specialists to generate a fully automatic diagnostic system with a reliability greater than 95%. This valuable tool will allow an objective evaluation of the effectiveness of any new therapy that can be developed to treat these diseases.

Deficiencies in the collagen VI' structure are a common cause of neuromuscular diseases with manifestations ranging from Bethlem myopathy to severe congenital muscular dystrophy Ullrich. Symptoms of these diseases include proximal and axial muscle weakness, distal hyperlaxity, joint contractures and critical respiratory failure that requires assisted ventilation, dramatically reducing life expectancy.

"Although we know that structural defects of collagen VI are related to mutations of the COL6A1, COL6A2 and COL6A3 genes. Diagnosis remains difficult, despite current genetic sequencing technologies." Comment Cecília Jiménez, PhD, research coordinator of the Neuromuscular Diseases Unit.

This difficulty generally occurs in diseases caused by dominant mutations, where there is no complete absence of a major protein, and when the effect of a genetic variant on the protein structure may not be evident. Currently, the diagnosis of dystrophies related to collagen VI is made from the analysis of the images of fibroblast cultures by specialists.

For this analysis, professionals take into account different aspects of the images: the coherence in the orientation of the collagen fibers, the distribution of the collagen network and the disposition of the cells in said network to identify potential patients. However, this evaluation is only qualitative, and regulatory agencies will not approve any treatment (such as genetic editing using CRISPR / Cas9 technology) without an objective methodology to assess its effectiveness.

For this reason, the system proposed in the work published in Applied Soft Computing will be a precise methodology to quantitatively monitor the effects of any new therapy. This system solves, on the one hand, the problem of the lack of data for typical learning in rare diseases; on the other, it indicates the possibly problematic areas in the query images. And it also provides a general quantitative evaluation of the condition of the patients.

Currently, the Neuromuscular Diseases Unit (Institut de Recerca Sant Joan de Déu · Hospital Sant Joan de Déu) is a national and international reference in research and diagnosis of neuromuscular diseases due to collagen deficiency VI.

In the study, researchers from the Neuromuscular Diseases Unit, the Paediatric Neurology Department and the Confocal Microscopy Unit (Daniel Bravo Center for Diagnosis and Research in Minority Diseases and Pediatric Institute of Rare Diseases) collaborated.

The Institute of Robotics and Industrial Informatics is a Joint Research Center of the Spanish Council for Scientific Research (CSIC) and the Technical University of Catalonia (UPC).

Image description: diagnosis display of a fibroblast culture image. The different areas of the image are evaluated independently which allows to quickly identify areas with defects in collagen VI. The system also provides a general diagnosis to track patients.

Thu, 07 Nov 2019 09:52:16 +0000 http://www.bioinformaticsbarcelona.eu/news//news/147/artificial-intelligence-applied-to-the-diagnosis-of-rare-diseases-associated-with-collagen-vi http://www.bioinformaticsbarcelona.eu/news/147 0