Participants: Dr. Mihaela Silion
Participation to online webinar "The real impact of HPLC and column parameters" organized by Thermo Fisher Scientific, 04.12.2024. In this webinar, strategic approaches for the development, optimization, and transfer of legacy and modern HPLC methods utilizing gradient elution were presented. The discussion covered various topics and data, including effective strategies for modifying gradient methods and adapting to evolving regulations for method transfer.
It was also discussed how to use the right tools to reduce the impact of method transfer on HPLC platforms, along with scalable parameters for pharmacopeia method modernization, as well as tips and tricks for method development and transfer.
Speakers:
James Grinias, Associate Professor Department of Chemistry & Biochemistry, Rowan University;
Frank Steiner, Sr. Manager of Product Applications and Scientific Advisor, Chromatography and Mass Spectrometry, Analytical Instrument Thermo Fisher Scientific

Participants: Prof. Aatto Laaksonern, PhD student Narcis Cibotariu
The MACCS1 conference was hosted by the University of Cagliari on and gathered scientists from Italian, Swedish and Chinese educational institutions aiming to share knowledge on the understanding the behaviour of complex systems in materials science, biotechnology and environmental chemistry through experiments combined with multi-scale modeling.
The event consisted of 16 oral presentations, each 20 minutes in duration. Among the most interesting talks was that of Prof. Xiaoyan Ji, who presented the models developed by her group for the thermodynamic properties of ionic liquids employing theories such as statistical associating fluids theory (SAFT) and machine learning (ML) to provide accuracy and predictive power to such models. Prof. Xiaohua Lu pointed out in his presentation the transition to green electricity, essential for carbon neutrality and the significant challenges in industrial processes, and Prof Aatto Laaksonen explained how the water molecules come into play to explain muscle contraction. Other exciting presentations were those of Dr. Leon De Villiers Engelbrecht on the properties of a type III eutectic solvent named ethaline in mixtures with water and methanol, and that of Dr. Cristina Carucci on the use of lipid nanoparticles as drug delivery systems. I also enjoyed Prof. Feng Lu's presentation, who spoke about the Chinese education system, taking Nanjing Tech University as a case study. Finally, the MACCS1 conference turned out to be a fruitful event for sharing knowledge and further promoting interdisciplinarity – a good opportunity for becoming one of the contributors and get involved in the development of science. Prof Aatto Laaksonen presented a lecture: “On the role of restrained water in biology – muscle contraction as example”

More info: https://convegni.unica.it/maccs1/

Participant: Dr. Mihaela Silion
In this webinar, we learned how mass spectrometry is used to study aging and inflammation. First, information was presented about analysing aging signatures, fibrosis, and cellular senescence in various tissues (breast, muscle, lung, and spinal cord) using Zeno SWATH DIA for detailed proteome coverage and biomarker discovery. We also explored new fragmentation methods for optimal coverage of peptides and glycans to better understand the molecular pathways involved in inflammation
Speakers:
o Birgit Schilling, Professor, Director of the Mass Spectrometry Technology Center Buck Institute for Research on Aging
o Shelley Jager, Ph.D. Candidate Utrecht University

Participant: PhD Student Narcis Cibotariu
This eSSENCE-EMMC meeting have feature two excellent speakers on the topic of multiscale modelling, one focussing on the "smaller entities", one on the "larger entities" along the multiscale ladder.
o Professor James Kermode (School of Engineering, The University of Warwick, UK): "Modelling at the Atomistic and Electronic Structure Scales − enhanced by Machine Learning"
o Professor Wolfgang Wenzel (Institute of Nanotechnology, Karlsruhe Institute of Technology, DE): "Virtual materials design beyond the Atomic Scales"
The following topics have been integrated into the lectures: Efficient surrogates for electronic structure models; Are there already universal force-fields ("foundation models") that can describe everything?; The importance of robust uncertainty estimates; From atomisticto continuum via kinetic Monte Carlo; Do we/people have realistic expectations of what multiscale modelling can achieve?; Fundamental aspects and industrially relevant applications.; Physics-based versus data-driven modelling

Participants: Dr. Tudor Vasiliu, Dr. Dragos Isac, Dr. Andrei Neamtu, Dr. Dragos Peptanariu, Razvan Puf, Narcs Cibotariu
In April 2024, part of the BioMat4CAST team attended a focused two-day training series dedicated to the latest advances in artificial intelligence applied to protein structure prediction presented by Prof. Anna MARABOTTI, "A. Zambelli" University of Salerno, Italy.

On April 18, the session “Artificial Intelligence (AI) Applications on Protein Structure Predictions” provided an overview of how state-of-the-art AI algorithms are transforming the way researchers approach biomolecular modelling. The presentation highlighted the revolutionary impact of deep learning methods, which now allow scientists to achieve unprecedented accuracy in predicting complex protein structures, thereby accelerating biomedical research and drug discovery.

On April 19, the training continued with a more technical perspective through the session “An Automated Pipeline Integrating AlphaFold2 and MODELLER for Protein Structure Prediction.” This presentation showcased how combining AlphaFold2, a groundbreaking AI tool, with MODELLER, a powerful computational platform, can create efficient, automated workflows for generating and refining protein models. Such integrated approaches open the way to scalable, reproducible, and more reliable predictions, facilitating both fundamental research and applied projects in structural biology.
Together, the two sessions equipped the BioMat4CAST team with both conceptual understanding and practical insights into the transformative role of AI in structural biochemistry, reinforcing the project’s commitment to adopting cutting-edge computational methodologies.

Mass spectrometry (MS) has emerged as an indispensable tool for polymer analysis, facilitating the study of various aspects including polymer structure, composition, end-groups, additives, molecular weight distribution, and degree of polymerization. Its unparalleled sensitivity enables the detection and identification of minor polymer components, synthesis by-products, low-level impurities, and decomposition products. However, traditional MS analysis often relies on coupling with chromatographic techniques such as gas chromatography (GC-MS) or liquid chromatography (LC-MS) to separate complex mixtures prior to mass spectrometric analysis, resulting in a complex and time-consuming process.
To address these challenges, Bruker offers innovative solutions to streamline polymer analysis. Two complementary chromatography-free MS methods, Matrix Assisted Laser Desorption Ionization (MALDI) and Direct Analysis in Real Time (DART), are presented as alternatives to traditional chromatography-coupled MS approaches. MALDI employs a laser to desorb and ionize molecules from a matrix-coated sample target, enabling rapid and direct analysis across various fields including material science, metabolomics, forensics, and environmental analysis. Similarly, DART ionizes samples in open air or solvent-free environments, facilitating direct analysis of solids, liquids, and gases without the need for sample preparation or chromatographic separation. These chromatography-free MS methods offer simplified workflows, expedited analysis, and enhanced efficiency, thus revolutionizing polymer analysis in research and industrial applications.
Participants: Dr. Mihaela Silion

To remain competitive against other technologies, mass spectrometry (MS) needs to rise to the challenge of unprecedented throughput with very deep analyses of very complex samples. With analysis time reduced to several minutes by fast liquid separations, confident identification and quantitation over many orders of dynamic range still requires a generational leap in the sequencing performance of MS. The Thermo Scientific™ Astral™ analyzer is a novel class of high-resolution accurate-mass analyzer that compliments the Thermo Scientific™ Orbitrap™ analyzer to provide high speed and sensitivity measurements. This webinar will explore the underlying technology of the Thermo Scientific™ Orbitrap™ Astral™ mass spectrometer and its’ application to biomedical research. Rethink what is possible with a mass spectrometer including the analysis of 300 proteomics samples per day, measuring 5,000 proteins from a true single-cell, and collecting fragmentation data on over 90% of compounds in metabolomics experiments. Trainers: Dr. Alexander Makarov Director, Global Research LSMS, Thermo Fisher Scientific; Dr. Hamish Stewart Staff Scientist, Analytical Instruments Group, Thermo Fisher Scientific
Participants: Dr. Mihaela Silion

Razvan Puf and Narcis Ciubotariu participated to Proteomics and its Applications in Cancer. The training served as a comprehensive exploration of the advancements and applications of proteomics in cancer research. The event brought together three experts from Europe and America, each presenting their innovative research and methodologies in the context of breast cancer (BC) detection, diagnosis and understanding. Prof. Dr. Margrét Thorsteinsdóttir, a distinguished professor of pharmaceutical analytical chemistry at the University of Iceland, gave a presentation focusing on “Targeted proteomics for the discovery of protein biomarkers in human plasma for early diagnosis of breast cancer”. Her research interests are aimed on lipid metabolism in cancer cells and identification of plasma-derived biomarkers for early detection of BC. In her presentation, Prof. Dr. Thorsteinsdóttir highlighted the successful implementation of a targeted proteomics platform capable of quantifying 131 proteins in human plasma. In particular, 99 proteins were quantified in an Icelandic BC study cohort with remarkable precision and accuracy, showing minimal batch variation. Of particular importance is the evaluation through rigorous validation procedures, both internally, using the measured cohort, and externally, with a new set of samples to improve early detection of BC.

The webinar took place on September 25, 2023, and was organized by the ImagoMOL cluster, uniting experts from the realms of medical imaging and artificial intelligence (AI). Carmen Mihai, as manager of ImagoMOL cluster, opened the event with a brief overview of the activities carried out within the ImagoMOL cluster and its key role in the field of molecular and structural imaging.

Professor Cipriana Ștefănescu presented a broad overview of the medical data collection process, highlighting the crucial importance of this process in the development of AI algorithms for nuclear imaging. Paul Herghelegiu pointed out the determinant role of the form and quality of input data in the design and development of AI algorithms. Professor Mihaela Breabăn and radiologist Roxana Balcan discussed the elaborated process of medical image processing and annotation for the development of advanced diagnostic paradigms. These presentations highlighted the importance of detail in obtaining relevant data and supporting medical doctors in their diagnostic process. As a final presentation, Bogdan Bercean, PhD student and co-founder of the start-up Rayscape, gave a talk on how to build and validate an AI model in radiology using only available online resources. He also underligned the significant potential of technology and online sources in the development of cutting-edge algorithms for medical image analysis.

This webinar provided an opportunity to disseminate critical milestones in the development of AI algorithms for medical imaging and highlighted the importance of continued research and collaboration in this emerging medical field.

Dr. Dragos Peptanariu participated at CADD. This course was of an introductory level and during it I learned several things about: Linux (OS Centos), introduction to CADD, Molecular Modeling, Molecular Energies, graphical visualization of ligand-receptor complexe, graphical analysis of the ligand-receptor interaction (Chimera Software), Molecular Mechanics, conformational search, receptor-based drug design. Theoretical notions were combined with practical exercises about: ligand-receptor interaction (Chimera Software), creating a compound database using MolBook UNIPI Software, pharmacophore-based drug design, and the exercises about docking a ligand into a protein (Software Dock 6) and pharmacophore modeling (software Pharmer). Theoretical concepts were also taught and practical exercises were done related to Molecular Dynamics (MD) simulation of a protein-ligand complex (Amber software), virtual screening in drug discovery and Machine Learning for drug discovery.

The program of the summer school was intense and consisted of a combination of theoretical and practical lessons. On the first day, the lessons started with introductory notes about the Linux operating system and continued with an introduction about CADD, molecular modeling energies, graphical visualization of ligand-receptor complexes and the analysis of their interaction with the Chimera software. In the following days Dr. Peptanariu learned about many other things: molecular mechanics, conformational search, receptor-based drug design, how to create a compound database using MolBook UNIPI software, docking a ligand into a protein, pharmacophore-based drug design, molecular dynamics simulation of a protein-ligand complex, virtual screening and machine learning in drug discovery.

Besides the actual participation in these courses, it was a very good opportunity to establish new professional links with the members of the teaching staff as well as with researchers from various places who came to this event.

The course was focused on innovative approaches to toxicity assessment using in vitro and in silico procedures and is open to toxicologists, risk assessors and other professionals and combines lectures by leading experts in the field of in vitro toxicology with interactive group exercises. Dr Dragos Peptanariu participate in the training. Lectures cover a wide range of topics related to regulatory, screening and investigative in vitro toxicology, while group exercises consist of real-life case studies in which participants apply the principles of in vitro toxicology to the risk assessment of chemicals. During this course dr Peptanariu learned about alternative testing methods and OECD (Organization for Economic Co-Operation and Development) testing guidelines.

The OECD program on chemical safety is: to help member and partner countries protect humans and the environment, to gain efficiency in chemicals management by developing and harmonizing testing and assessment methodologies, to avoid duplication of resources engaged by governments and industries and to integrate animal welfare and “3 Rs” considerations in developing these methodologies: Refinement alternatives: alleviate or minimize potential pain, suffering and distress; Reduction alternatives: obtain a comparable level of information from the use of fewer animals, or more information from the same number of animals; Replacement alternatives: permit a given purpose to be achieved without using animals.

The course also included practical hands-on sessions conducted by technology developers and was completed by an exam that Dr. Pieptanariu passed and received a certificate based on.

At the recommendation of Prof. Leif Eriksson (member of the International Advisory Board of BioMat4CAST), Dr. Dragos Pieptanariu have participate to the Online High Throughput and High Content Screening Workshop lasted 3 days (January 30, 31 and February 6) and provided an introduction to assay development for high throughput screening (HTS), high content screening (HCS), and lead discovery projects. It encompasses an overview, methods, and practical examples from the pharmaceutical industry, offering insights not commonly found in academic settings or literature. This workshop was led by Dr. Sheraz Gul who is Head of Assay Development and Drug Repurposing at Fraunhofer Institute for Translational Medicine and Pharmacology and is a seasoned pharmaceutical researcher. Refined over many years, this program was valuable for researchers embarking on the development of assays for high throughput screening, high content assays, and drug-discovery projects.

The event gave a comprehensive and practical view of assay development. This includes gaining a better understanding of the high throughput and high content screening/lead discovery process, knowing where to find additional information, and being able to create strong assays for new targets. Furthermore, participants had the chance to present their projects and engage in discussions to receive practical advice for overcoming challenges.

text