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Recombinant protein production for structural and functional studies
PRP@CERIC: Scientific Seminar Series
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Recombinant protein production for structural and functional studies

Biomedical research relies heavily on purified recombinant proteins, playing a crucial role in a wide spectrum of applications.

Their homogeneous nature allows for detailed reconstruction of their three-dimensional structures using techniques such as X-ray, cryoEM, and NMR, facilitating a deeper understanding of protein folding, conformational changes, molecular architectures, enabling studies of their function.

Additionally, these proteins are essential in investigating various interactions, such as protein-protein, protein-ligand, or protein-nucleic acid, and serve as critical tools in the field of therapeutics and diagnostics.

To guarantee the reliability of experimental data in these studies a good quality of recombinant protein is essential.

In this presentation the process of protein production is described, giving an overview of critical steps from construct design through expression, purification and quality control.

Speaker: Marta Semrau, RIT (Area Science Park)

PRP@CERIC: Scientific Seminar Series
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Regenerative Symphony: rigenerazione dei rifiuti elettronici tra arte e scienza
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Regenerative Symphony: rigenerazione dei rifiuti elettronici tra arte e scienza

Nasce una nuova residenza artistica in Area Science Park grazie alla collaborazione con MEET Digital Culture Center!

Nelle settimane scorse Area ha ospitato Studio Above&Below, il duo di artisti inglesi vincitore della sesta challenge di MEET all’interno del progetto “S+T+ARTS in the City”, promosso nel contesto del programma europeo STARTS.

Il progetto Regenerative Symphony si concentra sui materiali critici, sui diversi sistemi di intelligenza artificiale e sul riciclaggio dei rifiuti elettronici.

Dopo l’ideazione della challenge e della selezione dello Studio da parte di MEET, Area Science Park ha il compito di fornire ispirazione agli artisti attraverso l’accesso a risorse, piattaforme e dati aperti e al confronto con i nostri ricercatori, in particolare dei laboratori LADE e LAME, sul tema delle scienze dei materiali, dei dati e della vita.

Ne abbiamo parlato con Daria Jelonek e Perry-James Sugden, dello Studio Above&Below.

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From protein crystals to structural characterization
PRP@CERIC: Scientific Seminar Series
In questo video:
From protein crystals to structural characterization

Structural Biology is a consolidated scientific field that is critical for understanding of the molecular bases that lie behind the function of the different proteins, the investigation on the pathological impact of protein mutations and the development of new and better drugs.

One of the most long-standing disciplines of the field is protein crystallography, a technique that exploits single crystal x-ray diffraction to obtain atomic or near-atomic resolution models of the proteins that are investigated, allowing to delve into structure-activity relationship studies with final aims that may span from understanding the functioning of a biological process at molecular level, to the development of new therapeutic agents.

In the first part of the presentation some base concepts regarding protein crystallization are described, with a particular focus on how protein crystals can be optimized and on the techniques that may be used in order to obtain crystals, and then structures, of protein-ligand complexes.

In the second part a portion of a Structure Based Drug Design project is illustrated, providing an example of the data and results that can be obtained using single crystal x-ray diffraction, also focusing on the different approaches that might be used for the development of a drug candidate.

Speaker: Andrea Dalle Vedove, RIT (Area Science Park)

PRP@CERIC: Scientific Seminar Series
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Protein language models with structural alphabet
PRP@CERIC: Scientific Seminar Series
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Protein language models with structural alphabet

When trained on millions of protein sequences, large language models have been shown to develop emergent capabilities and to generalize across a range of applications, from prediction of mutational effects to long-range contact predictions.

Similarly, unsupervised machine learning tools are able to cluster protein sequences, identifying homologous domains and improving functional and evolutionary analyses.

In order to describe structural information, van Kempen et al. (2023) have recently introduced a discretized 20-letter structural alphabet (3Di) encoding the tertiary interactions between residues.

The 3Di alphabet allows the density peak clustering of structures starting from local Foldseek alignments, thus refining protein family classification in the twilight zone.

At the same time, new protein language models can be trained using this structure-aware vocabulary, finding applications, for instance, in protein stability due to point mutations.

Speaker: Marco Celoria, RIT (Area Science Park)

PRP@CERIC: Scientific Seminar Series
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AFM biomechanics at different scales: from tissues to cell membranes
PRP@CERIC: Scientific Seminar Series
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AFM biomechanics at different scales: from tissues to cell membranes

Atomic Force Microscopy (AFM) has got a fast development over the last decades mainly thanks to its versatility.

Indeed, AFM has shown unprecedented potential in the field of scanning probe microscopy, being able to operate in diverse environments and specimens, as well as to map simultaneously the topography and various physico-chemical properties of the scanned sample (e.g. adhesion, friction or elasticity) on different spatio-temporal scales, from µm to nm and from minutes to ms/µs.

In parallel, the research interest on biophysical topics for diagnostic and therapeutic purposes has been growing, along with the need for high resolution tools able to operate on biological systems in physiological conditions.

Particular attention has been paid to the field of mechanobiology, given the demonstrated correlation between mechanical properties and the patho-physiological state of many biological specimens.

In this context, AFM allows for the acquisition of simultaneous topographic and mechanical maps of several biological systems, ranging from the micro- to the nanoscale.

Recently, rising attention has been dedicated to the analysis of cellular membranes models and their interaction with small Extracellular vesicles (s-EVs), given the similarities of the latter to viral particles and their well-known capability to influence the fate of recipient cells.

This presentation gives some examples of AFM-based mechanobiology on cells, ECMs and tissues, as well as a quick review of the results obtained so far in the NanoInnovation Labs in Elettra on cellular membranes/s-EVs interactions.

Some future perspectives and the potential of the high-speed AFM acquired in the context of PRP project are also illustrated.

Speaker: Luca Puricelli, RIT (Area Science Park) – Elettra Sincrotrone Trieste

PRP@CERIC: Scientific Seminar Series
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Il riciclo perfettamente espresso
Pin of Innovation
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Il riciclo perfettamente espresso

Durante il processo di tostatura del caffè si forma uno scarto di lavorazione che si chiama silverskin. Il silverskin non possiede nessun tipo di impurità ma veniva smaltito come rifiuto speciale.

Grazie alla rete Enterprise Europe Network, Area Science Park, gli addetti regionali per la gestione dei rifiuti speciali e i torrefattori italiani si sono riuniti a un tavolo di lavoro per cercare di capire come poterlo riutilizzare.

Ne abbiamo parlato con Omar Zidarich, Presidente del Gruppo Italiano Torrefattori Caffè, Claudio Freddi del Corpo forestale regionale FVG e Francesca Marchi, EEN Project Manager in Area Science Park.

Pin of Innovation
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Dissecting an HPC data center, hardware, and the ground-level software that drives numerical research
PRP@CERIC: Scientific Seminar Series
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Dissecting an HPC data center, hardware, and the ground-level software that drives numerical research

High-Performance Computing (HPC) has become a cornerstone of scientific and industrial advancement, enabling breakthroughs in diverse fields such as drug discovery, material simulations, and neural network research.

However, the intricate web of components that make up an HPC infrastructure often remains obscured, hindering a comprehensive understanding of its inner workings.

This talk aims to dissect the complex tapestry of HPC infrastructure, shedding light on each component and elucidating the intricate relationships that drive computational power to new heights.

The presentation commences with a description of ORFEO, the hardware that enables its usage as an HPC facility, and the challenges that new projects pose to this facility.

Then, the discussion seamlessly moves into the software layer of HPC infrastructure, where it unravels the complexities of orchestrating computational tasks.

Notably, the role of resource managers like SLURM and container orchestration platforms like Kubernetes in efficiently allocating and managing computing resources is explored.

The talk addresses the challenges and advantages of these systems in coordinating parallel computations, optimizing job scheduling, and adapting to dynamic workloads.

Moving beyond resource management, exploring storage solutions and identity management solutions underscores the critical role they play in serving data and securing access within an HPC environment.

Finally, this talk presents VirtualOrfeo, the first iteration of a realistic virtual environment to play with the discussed technologies.

Speaker: Ruggero Lot, RIT – Area Science Park

PRP@CERIC: Scientific Seminar Series
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FAIR by design
PRP@CERIC: Scientific Seminar Series
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FAIR by design

FAIR-by-design approach is the worldwide Gold-Standard for what concerns public data collection, both in scientific research and in administrative processes.

This talk tries to contextualize the environment in which the FAIR-by-design concept was born by retracing the main stages of what we could address as the “Open Knowledge Movement”, that brought to the definition of Open Data and Open Access.

It is discussed how Open Data have a reason for being only if they satisfy the FAIR principles, and it is explained how to be fully compliant with them implies being collected through a FAIR-by-design approach.

It is also underlined that notwithstanding FAIR Data idea was introduced in tight connection with Open Data one, FAIRness is a broader concept that applies even to Data that are not Open.

Special attention is given to the reason why the only way to have Data fully compliant with FAIR principle is collecting them through a FAIR-by-design pipeline and what this implies for a scientific laboratory.

Speaker: Federica Bazzocchi, RIT – Area Science Park

PRP@CERIC: Scientific Seminar Series
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Nanofabrication: an essential tool for modern bio-science
PRP@CERIC: Scientific Seminar Series
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Nanofabrication: an essential tool for modern bio-science

Cryo-microscopy techniques are emerging as fundamental components for the future of scientific research.

Despite significant technological advancements on the instrumental front, numerous aspects in sample preparation methodologies still require refinement and standardization.

While progress has been made across all levels, from instrumentation to sample preparation, challenges persist, demanding continued attention.

The introduction of a nanofabrication approach for producing substrates used in biological applications of cryo-microscopy is crucial for enhancing the reproducibility and statistical validity of conducted analyses.

Nanofabrication can address existing gaps in this field, significantly contributing to the enhancement of sample preparation protocols. This technology plays a key role in streamlining workflows and optimizing the precision of procedures.

Furthermore, nanofabrication extends to the production of devices used in conjunction with cryo-microscopy. These devices, such as detectors and sensors, are essential for detecting and quantifying bacterial contaminations from samples of different types and for various applications.

At IOM, two primary technologies are emerging in this context, focusing on approaches based on the use of MEMS (Micro-Electro-Mechanical Systems) and purely optical readouts to improve the effectiveness of conducted analyses.

In summary, the application of nanofabrication not only addresses gaps in sample preparation protocols but also plays a crucial role in the development of advanced technologies for the detection and characterization of biological samples using cryo-microscopy.

Speaker: Simone Dal Zilio, CNR – IOM

PRP@CERIC: Scientific Seminar Series
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Intermolecular interactions characterization
PRP@CERIC: Scientific Seminar Series
In questo video:
Intermolecular interactions characterization

The research interest of the main group at the Institute of Crystallography (CNR) in Trieste is the structural and functional characterization of therapeutic targets and protein involved in human diseases.

The aim is to elucidate the structural basis of human pathologies and to develop effective drugs.

Structural studies are performed by means of X-ray crystallography and Small Angle X-ray scattering and in vitro functional characterization is mainly achieved by qualitative, semiquantitative and quantitative binding analysis.

This talk addresses the present state of the art of the intermolecular interactions characterization facility @ IC-CNR Trieste, discussing the applications and the potential of the core of the platform (i.e., Isothermal Titration Calorimetry and Grating Coupled Interferometry), and its upcoming improvements that will be achieved thanks to PRP@CERIC project.

Speaker: Sonia Covaceuszach, CNR – IC

PRP@CERIC: Scientific Seminar Series
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Sindrome metabolica: l’importanza del fattore alimentare
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Sindrome metabolica: l’importanza del fattore alimentare

La sindrome metabolica è una condizione che oggi coinvolge 2 – 3 italiani su 10 al di sotto dei 65 anni e quasi 1 su 2 dai 65 anni in su.

Questa condizione è caratterizzata dalla coesistenza di almeno tre dei seguenti fattori: aumento dell’obesità addominale, alterazione della glicemia, alterazione del colesterolo ed alterazione della pressione arteriosa.

Il Dr. Schär R&D Centre lavora allo sviluppo di nuovi prodotti alimentari che possano contrastare la sindrome metabolica e che abbiano un impatto positivo sul colesterolo e sulla glicemia.

Ne abbiamo parlato con Lucio Lucchin, per 21 anni Direttore dell’Unità Operativa Complessa di Dietetica e Nutrizione Clinica del Comprensorio Sanitario di Bolzano, e Aurore Ranchon, Director of Global Product Development Gluten Free & Conventional del Dr. Schär R&D Centre.

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Deep UV Raman spectroscopy for probing active eukaryotic viruses
PRP@CERIC: Scientific Seminar Series
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Deep UV Raman spectroscopy for probing active eukaryotic viruses

Deep Ultraviolet Resonance Raman Spectroscopy (DUVRR) is an emerging and powerful analytical tool used for detection and characterization of biological samples in a label-free and real time approach.

The excitation in the Deep UV provides specific resonance enhancement of biological moieties, especially protein, DNA and RNA structures, allowing to efficiently detect biological Raman markers in the spectra.

It is well known that DUV radiation is a genotoxic agent. Prolonged UV light exposition induces damage to the genomes of viruses, breaking bonds and forming photodimeric lesions in RNA.

These damages prevent both transcription and replication which leads to viral inactivation. Even though the effects of UV radiation on DNA of microorganisms have been well-recorded, its impact on RNA and RNA modifications is less known.

A sample that is prone to such a damage are viruses, and with the SARS-COV-2 (RNA virus) outbreak, the need of fast tools for viral characterization and classification became even more necessary.

In this work, we will show how to obtain stable, high quality and information-rich DUVRR spectra of active Vesicular Stomatitis Virus (VSV) without affecting its viability, RNA and protein integrity.

By opportunely tuning the excitation wavelength, we can detect and assign in the vibrational spectra specific markers of protein and RNA components useful to elucidate biochemical characteristics of active VSV virus.

In addition, we can study the effect of DUV irradiation in the mechanism of inactivation of VSV viruses in order to find the most damaging wavelength for the active VSV virus. This information can further be exploited to build an effective countermeasure tool for virus deactivation.

Speaker: Denis Rajnovic, ICGEB – Elettra Sincrotrone Trieste

PRP@CERIC: Scientific Seminar Series
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