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

  • Single molecules show their colours (2016)

    van Hulst, Niek F. (ICFO)

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    Single molecules show their colours

    Molecules are composed of atoms and electrons; their arrangement determines the energy states and spectroscopy, i.e. the response of a molecule to incident colours of light. A specific molecule has a corresponding specific response, which underlies the essence of optical spectroscopy. Yet in the real world, in a liquid or solid host, molecules do change their conformation depending on the local “nano”-environment. As a result, even for chemically identical molecules, each molecule has a shifted absorption spectrum, and in a typical single molecule experiments an unknown fraction is easily missed. Capturing all molecules is challenging as they fluctuate, blink and bleach: one needs to keep track of all colours at the same time.

    To this end we have developed a novel approach based on interferometric white light excitation combined with confocal fluorescence detection, revealing the specific colour of each molecule individually and bringing single molecule excitation spectroscopy side-by-side to single molecule emission spectroscopy. The interferometric approach, exploiting broad-band femtosecond pulses and rapid delay line scanning, is resilient against blinking and bleaching as the entire excitation spectrum is probed at once. Unprecedented spectral heterogeneities of single molecules, with individual excitation spectra shifted in wavelength by more than 100 nm are revealed. Conventional narrow-band excitation techniques would be incapable to capture the whole extent of the spectral distribution and would meagerly miss out on molecules detected by the broad-band scheme.

    The new femtosecond single molecule excitation spectroscopy addresses the ultrafast dynamics in the electronic excited state, giving access to the interaction between individual molecules and their environment as well as biomolecules in more complex systems. Equally, the technique will prove useful to follow slow-occurring chemical reactions in time through changes in the molecular excitation spectrum both in solution and on the single-molecule level.

     

  • Coherence: distilled, diluted, weighed and measured (2016)

    Winter, Andreas (UAB)
    Lewenstein, Maciej Andrzej (ICFO)

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    Coherence: distilled, diluted, weighed and measured

    Every true quantum experiment relies on interference effects, which are the physical manifestation of the superposition principle of quantum mechanics. In our work [WY], for the first time, we are able to derive universal measures of how strong the coherence of superposition is in any given quantum state. We do this by viewing superposition as a resource, and consider how it can be manipulated under so-called 'incoherent' operations [BCP].

    Our main findings are simple formulas for how much pure coherence is contained in a given quantum state, by answering two fundamental questions: How efficiently can one transform the state into pure coherence (distillation)? And how efficient is the reverse process (formation)? It turns out that any quantum state that is not itself incoherent, however noisy it is, has some bit of pure coherence that can be extracted from it. At the same time, distillation and formation are in general not inverses to each other. Rather, there is irreversible loss of coherence in any cyclic process of first forming a noisy state from pure coherence and then distilling that coherence back to pure.

    Traditionally, the degree of coherence is linked to the visibility of interference fringes in characteristic standardized experiments: double or multi-slit setups, interferometers, etc. In contrast, our approach quantifies the strength of coherence not with respect to a certain standard task, but by the performance at the best experiment tailored to the specific resource state.

    In subsequent work [SCR+], we made a fruitful comparison between the resource of coherence, and another major manifestation of quantumness, entanglement, which intuitively is the natural form of quantum coherence as correlation. We did this by studying their interplay and mutual tradeoff in the basic quantum information task of "state merging", a fundamental primitive protocol unifying data compression and error correction. We found various bounds on the tradeoff, suggesting that entanglement can be much more powerful than mere coherence.

  • Ocean warming and acidification on calcareous phytoplankton alter its ability to sequester atmospheric CO2   (2016)

    Ziveri, Patrizia (UAB)

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    Ocean warming and acidification on calcareous phytoplankton alter its ability to sequester atmospheric CO2  

    More than a quarter of the anthropogenic CO2 emissions are absorbed by the ocean, changing the ocean chemistry and resulting in ‘ocean acidification’. Anthropogenic CO2 emission leads also to a rise in global average temperatures, including sea surface temperature at an unprecedented pace. The risks posed by warming and acidification are expected to become more acute in the next decades, as CO2 emissions into the atmosphere are accelerating.

    Coccolithophores are a very abundant marine calcifying phytoplankton group that plays a major role in biogeochemical cycles and in the regulation of climate. These tiny algae measuring a few thousands of a millimeter, form the base of the marine trophic web, and through calcification and photosynthesis contribute to the  regulation of the atmospheric and oceanic CO2 levels. The effects of acidification - and in particular warming - are rarely considered for the organism itself, and there is very little knowledge on how warming and acidification combined may affect their adaptation and evolution.

    Culture experiments were conducted on Mediterranean Sea and North Pacific Ocean strains of Emiliania huxleyi, the most abundant coccolitophore species. A main aim was to detect the effects of temperature, and secondarily of acidification, on the coccolithophore calcification and sinking rates.

    Using scanning electron microscopy, an increase in malformed and incomplete coccoliths in a warmer and more acidified ocean was shown. This will hamper the evolutionary success of these calcifiers and their role in regulating atmospheric carbon. In addition, using a novel approach to calculate sinking rate from cell-architecture,  the studies showed that a warmer and more acidic ocean will lead to an increase in their cell sinking rate. The faster sinking of this group of calcifying phytoplankton can have an impact on their survival.

  • The risk of metastatic disease in colorectal cancer is determined by a gene program expressed in the tumor stroma (2015)

    Batlle Gómez, Eduard (IRB Barcelona)

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    The risk of metastatic disease in colorectal cancer is determined by a gene program expressed in the tumor stroma

    About 40% of Colorectal Cancer (CRC) patients with locally advanced disease show resistance to therapy and eventually develop metastasis. Current CRC staging based on histopathology and imaging has limited ability to predict disease progression or patient prognosis. A major advance has been the recent elaboration of molecular classifications based on global gene expression profiles, which have defined CRC subtypes displaying resistance to therapy and poor prognosis. In this work, we evaluated various molecular classifications and discovered that in all cases, their predictive power arises from genes expressed by cancer-associated fibroblasts (CAFs) rather than by tumor cells themselves. We found that such stromal gene program is driven by TGF-beta signaling and is expressed by virtually all poor prognosis CRCs. Functional dissection of CRC progression demonstrated that the presence of CAFs facilitates tumor initiation, an effect that is dramatically enhanced by transforming growth factor (TGF)-ß  signaling. Using patient-derived tumor organoids and xenografts, we showed that the use of TGF-ß signaling inhibitors to block the cross-talk between cancer cells and the microenvironment prevented metastasis formation. Overall, our work reveals that CRC metastasis rely on a cancer cell non-autonomous program driven by TGF-ß in the tumor microenvironment. This dependency suggests that patients with advanced CRC cancers could benefit from the use TGF-ß signaling inhibitors. In addition, our work paves the way for new methods of patient classification based on the existence of distinct tumor microenvironments.     

  • A new light source with unprecedented sensitivity to molecular fingerprints of cancer cells (2015)

    Biegert, Jens (ICFO)

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    A new light source with unprecedented sensitivity to molecular fingerprints of cancer cells

    Researchers from the Attoscience and Ultrafast Optics Group led by ICREA Prof. at ICFO Jens Biegert, in collaboration with the Laboratory for Attosecond Physics at the Max Planck Institute for Quantum Optics (MPQ) and the Ludwig-Maximilians-Universität (LMU) in Munich, have developed a worldwide unique broadband and coherent infrared light source. The record peak brilliance of the light source makes it an ultrasensitive detector for the infrared molecular fingerprint region, ideal to detect minute changes in the spectral features from cells or tissue which are telltale signs of DNA mutation or the presence of cellular malfunctions such as cancer.

  • Nucleosomes arrange in clutches along the chromatin fiber; a novel model of chromatin fiber organization (2015)

    Cosma, Maria Pia (CRG)
    García Parajo, Maria F. (ICFO)

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    Nucleosomes arrange in clutches along the chromatin fiber; a novel model of chromatin fiber organization

    The chromatin fiber is formed by wrapping of the DNA around the nucleosome octamers composed of H2A, H2B, H3 and H4 core histones (Luger et al., Nature, 1997). Using X-ray diffraction, the chromatin fiber was seen as assembled into a hierarchical structure with the DNA double helix of 10 nm diameter compacted into a higher ordered fiber of 30 nm with a solenoid or two-start helix spatial arrangement (Finch et al., Proc Natl Acad Sci U S A, 1976; Dorigo et al., Science, 2004). The existence of the 30 nm fibers has however been challenged and the 10 nm fiber was postulated to occasionally assemble in more condensed areas (Fussner et al., EMBO Rep, 2012). Computational modeling indicated that the 30 nm spatial assembly is not compatible with efficient packaging of the fiber into the nucleus (Tokuda et al., Biophys J, 2012).

    Using quantitative super-resolution nanoscopy, we discovered that nucleosomes arrange in groups of various sizes along the chromatin fiber, which we named ‘nucleosome clutches’ (in analogy with clutches of eggs). Clutches are interspersed with nucleosome-free regions. Interestingly, we found that the median number of nucleosomes and their compaction inside the clutches is highly correlated with cellular state. Strikingly, ground-state pluripotent stem cells have, on average, clutches that are less dense and contain fewer nucleosomes. RNA polymerase II is associated with the smallest clutches, suggesting that small clutches are transcriptionally active. Moreover there is a high amount of linker histone H1 in the largest clutches, which form the heterochromatin.

    Our super-resolution studies, which involve Prof. Melike Lakadamyali (ICFO) and two ICREA Professors, María García Parajo (ICFO) and Maria Pia Cosma (CRG), provide key structural and functional information on the chromatin fiber and reveal a novel and essential feature of stem cells.

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