Highlights

Every year, a committee of experts sits down with a tough job to do: from among all ICREA publications, they must find a handful that stand out from all the others. This is indeed a challenge. The debates are sometimes heated and always difficult but, in the end, a shortlist of  the most outstanding publications of the year is produced. No prize is awarded, and the only additional acknowledge is the honour of being chosen and highlighted by ICREA. Each piece has something unique about it, whether it be a particularly elegant solution, the huge impact it has in the media or the sheer fascination it generates as a truly new idea. For whatever the reason, these are the best of the best and, as such, we are proud to share them here.

LIST OF SCIENTIFIC HIGHLIGHTS

Format: yyyy

  • Uncovering the drivers of cancer   (2021)

    López-Bigas, Núria (IRB Barcelona)

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    Uncovering the drivers of cancer  

    Most mutations detected in cancer genes in cancer patients are of uncertain significance. Knowing which mutations are responsible for the development of a tumor (drivers) is key to select the best way to target it. Although impressive strides have been made in the identification of the genes that when mutated contribute to tumor emergence and growth, recognizing the specific driver mutations in these genes is still far from resolved. 

     

    We reasoned that the mutations identified in thousands of patients in cancer genes may be used to solve this problem. We derived 185 machine learning models inspired in evolutionary biology to identify which mutations in each cancer gene are able to drive tumorigenesis in different cancer types. We showed that these models can effectively identify driver mutations. Applying them to all possible mutations in these cancer genes we have generated driver potential blueprints available at intogen.org/boostdm (see Figure). 

     

    These models, named collectively BoostDM, help to interpret variants of uncertain significance in a clinical setting. The incorporation of boostDM models to our Cancer Genome Interpreter (cancergenomeinterpreter.org) system improves the interpretation of the mutations detected in a patient’s tumor. For more on boostDM, see nature.com/articles/s41586-021-03771-1 and youtube.com/watch?v=1Nq_rm_yudk&t=29s.

     

  • Progress in the development of cutting-edge High Performance Computing tools for modelling of fusion multiphysics phenomena (2021)

    Mantsinen, Mervi Johanna (BSC-CNS)

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    Progress in the development of cutting-edge High Performance Computing tools for modelling of fusion multiphysics phenomena

    The final goal of fusion power plants is to produce electricity in the grid. This is planned to be done by heating up water as with fission power plants or thermal power stations. In the case of magnetically confined fusion, neutrons released from the hot fusion plasma escape the magnetic confinement and finish in the wall heating up water. In the case of DEMO (DEMOnstration power plant), the neutron production will be large and the reactor materials have to be neutron-resistant. Thereby, neutronics becomes an increasingly important field of study.

    To simulate the neutron transport in a fusion reactor, we have developed NEUTRO [1], a new module inside the Alya framework [2]. Alya is one of the largest and most advanced computational mechanics codes developed at Barcelona Supercomputing Center. Alya has been applied to many domains thanks to the multi-physics approach and has been developed to solve complex coupled problems such as combustion or cardiovascular system simulation. In our recent journal paper, we have validated NEUTRO and included nuclear data, which brings the code forward and improves it significantly. We are currently working to couple NEUTRO with the various other physics modules available in Alya to solve coupled high fidelity and high demanding computational problem of the first wall for the realization of DEMO.

  • The Vertebrates Genome Project introduces the era of the reconstruction of the genetic representation for all species (2021)

    Marquès Bonet, Tomàs (UPF)

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    The Vertebrates Genome Project introduces the era of the reconstruction of the genetic representation for all species

    The Vertebrate Genomes Project (VGP) Consortium published this year their flagship study focused on genome assembly quality and standardization for the field of genomics. This study includes 16 diploid high-quality, near error-free, and near complete vertebrate reference genome assemblies for species across all taxa with backbones (i.e., mammals, amphibians, birds, reptiles, and fishes) from five years of piloting the first phase of the VGP project. 

    Growing out of the decade-old mission of Genome 10K Community of Scientists (G10K) to sequence the genomes of 10,000 vertebrate species and other comparative genomics efforts, the VGP is taking advantage of dramatic improvements in sequencing technologies in the last few years to begin production of high-quality reference genome assemblies for all ~70,000 living vertebrates. Specific to conservation and in collaboration with the Māori in New Zealand and officials in Mexico, genomic analyses of the kākāpō, a flightless parrot, and the vaquita, a small porpoise and the most endangered marine mammal, respectively, suggest evolutionary and demographic histories of purging harmful mutations in the wild. The implication of these long-term small population sizes at genetic equilibrium gives hope for these species’ survival.

    The VGP involves hundreds of international scientists working together from more than 50 institutions in 12 different countries since the VGP was initiated in 2016 and is exemplary in its scientific cooperation, extensive infrastructure, and collaborative leadership. Additionally, as the first large-scale eukaryotic genomes project to produce reference genome assemblies meeting a specific minimum quality standard, the VGP has thus become a working model for other large consortia, including the Bat 1K, Pan Human Genome Project, Earth BioGenome Project, Darwin Tree of Life, and European Reference Genome Atlas, among others. 

     

     

  • Holography, Cosmological Phase Transitions and Gravitational Waves (2021)

    Mateos, David (UB)

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    Holography, Cosmological Phase Transitions and Gravitational Waves

    Phase transitions are ubiquitous in Nature. When we boil liquid water, bubbles of vapour appear and expand until the entire volume is filled by gas. It is conjectured that the Universe may have undergone a similar process many billions of year ago: As it expanded and cooled down, bubbles of a new phase may have appeared and expanded until the new phase filled the entire Universe. 

    This process, known as a cosmological phase transition, would have produced tiny ripples in the fabric of spacetime, known as Gravitational Waves, that would have been traveling through the Universe ever since they were emitted. The most exciting aspect is that we may be able to detect them in the near future. 

    Maximising the discovery potential requires the determination of a few parameters controlling the phase transition. The most important one is the bubble wall velocity, namely the velocity at which the bubbles of the new phase expand. This parameter is extremely challenging to compute with conventional methods because it involves out-of-equilibrium physics. For this reason, we have used a string-theoretical tool known as "holography", which maps the properties of the bubbles in our four-dimensional world to those of … a black hole in five dimensions! 

    By solving Einstein's equations in five dimensions we have determined the time evolution of the black hole horizon, and from this the wall velocity. We have been able to go even further and we are currently computing the spectrum of four-dimensional Gravitational Waves directly in terms of the five-dimensional black hole dynamics. 

  • Advanced nanobiosensors for diagnostics of COVID19 and more (2021)

    Merkoçi, Arben (ICN2)

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    Advanced nanobiosensors for diagnostics of COVID19 and more

    Nanobiosensors represent the next generation of biosensors that has emerged in the last two decades thanks to the contribution from new nanotechnologies and nanomaterials.  One of the urgent application of nanobiosensors is related to the diagnostics in various clinical scenarios of COVID19 pandemics for which we have shown the recent advanced of these devices, the raised issues and the work requested to implement them in the clinical practice. [1] We also reported an electrochemical aptamer-based (EAB) sensor for the rapid and efficient detection of the SARS-CoV-2 spike protein. The clinical potential of the sensor, was demonstrated in biological fluids (serum and artificial saliva) allowing for rapid (minutes) and single-step detection of the S protein in its clinical range. [2]

    The broad range of nanomaterials with interesting optical or electrical properties and nanotechnologies is allowing breakthrough achievements in the field of nanobiosensors reaching extremely low detection limits (attomolar levels). [3] Nanobiosensors are also expected to contribute as smart devices in food and agriculture areas thanks also to their combination with artificial intelligence and machine learning tools as discussed in our recent invited news & views article at Nature Food. [4]

  • Relationship between chromosomal instability and senescence revealed in the fly Drosophila (2021)

    Milán Kalbfleisch, Marco (IRB Barcelona)

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    Relationship between chromosomal instability and senescence revealed in the fly Drosophila

    Chromosomal instability (CIN), the continuous change in chromosome number and structure, is a feature of most solid tumours. Likewise, cellular senescence is a process that is highly related to cellular ageing and its link to cancer is becoming increasingly clear. The work carried out by Jery Joy and colleagues in the laboratory of Marco Milán has utilized Drosophila as model system to show that in an epithelial tissue with high levels of CIN those cells with an altered balance of chromosome number detach from their neighbouring cells and enter senescence. Senescent cells are characterised by a permanently halted cell cycle and by the secretion of a large number of proteins. This abnormal secretion of proteins alters the surrounding tissue, alerting the immune system and causing inflammation. Cells with an unbalanced number of chromosomes present high levels of proteotoxic stress, accumulate aberrant mitochondria and, therefore, a high level of oxidative stress, which in turn activates the  c-Jun N-terminal kinase (JNK) signalling pathway, triggering entry into senescence. Interestingly, removing dysfunctional mitochondria or reducing proteotoxic stress by different means rescue the deleterious effects of CIN. These findings open new avenues of research to find therapeutic targets and reduce senescence levels caused by chromosomal instability in solid tumours.

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