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1702 Publications visible to you, out of a total of 1702
Gravitational wave emission from dynamical stellar interactions

Abstract

Not specified

Authors: J. Moran-Fraile, F. Schneider, F. Roepke, S. Ohlmann, R. Pakmor, T. Soultanis, A. Bauswein

Date Published: 27th Feb 2023

Publication Type: Journal

ReStoRunT: Simple Recording, Storing, Running and Tracing changes in Spreadsheets

Abstract (Expand)

In addition to the ubiquitous big data, one key challenge indata processing and management in the life sciences is the diversity ofsmall data. Diverse pieces of small data have to be transformed … intostandards-compliant data. Here, the challenge lies not in the difficulty ofsingle steps that need to be performed, but rather in the fact that manytransformation tasks are to be performed once or only a few times. Thislimits the time that can be put into automated approaches, which inturn severely limits the verifiability of such transformations.As much of the data to be processed is stored in spreadsheets, withinthis paper we justify and propose a lightweight recording-based solutionthat works on a wide variety of spreadsheet programs, from MicrosoftExcel to Google Docs.

Authors: Wolfgang Müller, Lukrecia Mertova

Date Published: 23rd Feb 2023

Publication Type: Journal

FERM domains recruit ample PI(4,5)P2s to form extensive protein-membrane attachments

Abstract (Expand)

The four-point-one ezrin-radixin-moesin homology (FERM) protein domain is a multifunctional protein-lipid binding site, constituting an integral part of numerous membrane-associated proteins. Its … interaction with the lipid phosphatidylinositol-4,5-bisphosphate (PIP2), located at the inner leaflet of eukaryotic plasma membranes, is important for localization, anchorage, and activation of FERM-containing proteins. FERM-PIP2 complexes structurally determined so far exclusively feature a 1:1 binding stoichiometry of protein and lipid, with a few basic FERM residues neutralizing the −4 charge of the bound PIP2. Whether this picture from static crystal structures also applies to the dynamic interaction of FERM domains on PIP2 membranes is unknown. We here quantified the stoichiometry of FERM-PIP2 binding in a lipid bilayer using atomistic molecular dynamics simulations and experiments on solid supported membranes for the FERM domains of focal adhesion kinase and ezrin. In contrast to the structural data, we find much higher average stoichiometries of FERM-PIP2 binding, amounting to 1:3 or 1:4 ratios, respectively. In simulations, the full set of basic residues at the membrane interface, 7 and 15 residues for focal adhesion kinase and ezrin, respectively, engages in PIP2 interactions. In addition, Na ions enter the FERM-membrane binding interface, compensating negative PIP2 charges in case of high charge surpluses from bound PIP2. We propose the multivalent binding of FERM domains to PIP2 in lipid bilayers to significantly enhance the stability of FERM-membrane binding and to render the FERM-membrane linkage highly adjustable.

Authors: Thomas Ehret, Tim Heißenberg, Svenja de Buhr, Camilo Aponte-Santamaría, Claudia Steinem, Frauke Gräter

Date Published: 21st Feb 2023

Publication Type: Journal

Intrinsically disordered region of talin’s FERM domain functions as an initial PIP2 recognition site

Abstract (Expand)

Focal adhesions (FAs) mediate the interaction of the cytoskeleton with the extracellular matrix in a highly dynamic fashion. Talin is a central regulator, adaptor protein, and mechano-sensor of FA … complexes. For recruitment and firm attachment at FAs, talin’s N-terminal FERM domain binds to phosphatidylinositol 4,5-bisphosphate (PIP2)-enriched membranes. A newly published autoinhibitory structure of talin-1, where the known PIP2 interaction sites are covered up, lead us to hypothesize that a hitherto less examined loop insertion of the FERM domain acts as an additional and initial site of contact. We evaluated direct interactions of talin-1 with a PIP2 membrane by means of atomistic molecular dynamics simulations. We show that this unstructured, 33-residue-long loop strongly interacts with PIP2 and can facilitate further membrane contacts, including the canonical PIP2 interactions, by serving as a flexible membrane anchor. Under force as present at FAs, the extensible FERM loop ensures talin maintains membrane contacts when pulled away from the membrane by up to 7 nm. We identify key basic residues of the anchor mediating the highly dynamic talin-membrane interaction. Our results put forward an intrinsically disordered loop as a key and highly adaptable PIP2 recognition site of talin and potentially other PIP2-binding mechano-proteins.

Authors: Jannik Buhr, Florian Franz, Frauke Gräter

Date Published: 21st Feb 2023

Publication Type: Journal

EnzymeML: seamless data flow and modeling of enzymatic data.

Abstract (Expand)

The design of biocatalytic reaction systems is highly complex owing to the dependency of the estimated kinetic parameters on the enzyme, the reaction conditions, and the modeling method. Consequently, … reproducibility of enzymatic experiments and reusability of enzymatic data are challenging. We developed the XML-based markup language EnzymeML to enable storage and exchange of enzymatic data such as reaction conditions, the time course of the substrate and the product, kinetic parameters and the kinetic model, thus making enzymatic data findable, accessible, interoperable and reusable (FAIR). The feasibility and usefulness of the EnzymeML toolbox is demonstrated in six scenarios, for which data and metadata of different enzymatic reactions are collected and analyzed. EnzymeML serves as a seamless communication channel between experimental platforms, electronic lab notebooks, tools for modeling of enzyme kinetics, publication platforms and enzymatic reaction databases. EnzymeML is open and transparent, and invites the community to contribute. All documents and codes are freely available at https://enzymeml.org .

Authors: S. Lauterbach, H. Dienhart, J. Range, S. Malzacher, J. D. Sporing, D. Rother, M. F. Pinto, P. Martins, C. E. Lagerman, A. S. Bommarius, A. V. Host, J. M. Woodley, S. Ngubane, T. Kudanga, F. T. Bergmann, J. M. Rohwer, D. Iglezakis, A. Weidemann, U. Wittig, C. Kettner, N. Swainston, S. Schnell, J. Pleiss

Date Published: 9th Feb 2023

Publication Type: Journal

Systems Biology in ELIXIR: modelling in the spotlight.

Abstract (Expand)

In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems … biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.

Authors: V. Martins Dos Santos, M. Anton, B. Szomolay, M. Ostaszewski, I. Arts, R. Benfeitas, V. Dominguez Del Angel, E. Dominguez-Romero, P. Ferk, D. Fey, C. Goble, M. Golebiewski, K. Gruden, K. F. Heil, H. Hermjakob, P. Kahlem, M. I. Klapa, J. Koehorst, A. Kolodkin, M. Kutmon, B. Leskosek, S. Moretti, W. Muller, M. Pagni, T. Rezen, M. Rocha, D. Rozman, D. Safranek, W. T Scott, R. S. M. Sheriff, M. Suarez Diez, K. Van Steen, H. V. Westerhoff, U. Wittig, K. Wolstencroft, A. Zupanic, C. T. Evelo, J. M. Hancock

Date Published: 8th Feb 2023

Publication Type: Journal

Modeling photometric reverberation mapping data for the next generation of big data surveys. Quasar accretion disks sizes with the LSST

Abstract (Expand)

Abstract Photometric reverberation mapping can detect the radial extent of the accretion disc (AD) in Active Galactic Nuclei by measuring the time delays between light curves observed in different …rves observed in different continuum bands. Quantifying the constraints on the efficiency and accuracy of the delay measurements is important for recovering the AD size-luminosity relation, and potentially using quasars as standard candles. We have explored the possibility of determining the AD size of quasars using next-generation Big Data surveys. We focus on the Legacy Survey of Space and Time (LSST) at the Vera C. Rubin Observatory, which will observe several thousand quasars with the Deep Drilling Fields and up to 10 million quasars for the main survey in six broadband filter during its 10-year operational lifetime. We have developed extensive simulations that take into account the characteristics of the LSST survey and the intrinsic properties of the quasars. The simulations are used to characterise the light curves from which AD sizes are determined using various algorithms. We find that the time delays can be recovered with an accuracy of 5 and 15% for light curves with a time sampling of 2 and 5 days, respectively. The results depend strongly on the redshift of the source and the relative contribution of the emission lines to the bandpasses. Assuming an optically thick and geometrically thin AD, the recovered time-delay spectrum is consistent with black hole masses derived with 30% uncertainty.

Authors: F Pozo Nuñez, C Bruckmann, S Desamutara, B Czerny, S Panda, A P Lobban, G Pietrzyński, K L Polsterer

Date Published: 6th Feb 2023

Publication Type: Journal

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