“The CardioSCOPE project enabled me to undertake a 30-day secondment at Biosfer Teslab in Reus, Spain, to gain expertise in mouse plasma NMR analysis. This initiative aimed to identify circulating metabolites resulting from changes in lipid metabolism. At the Genetic Regulation and Molecular Therapies Laboratory (GRMT Lab) of ICBP, Bucharest, Romania, where I am employed, our goal is to slow down plaque development by modulating the composition and functions of lipoproteins. Thus, the lipidomics and metabolomics data obtained from plasma analysis by NMR at Biosfer Teslab would provide essential insights for our research projects.
The 30-day secondment was conducted in two periods: February 19-29, 2024, and July 8-26, 2024. During the first phase of the secondment at Biosfer Teslab, I participated in analyzing human plasma samples using high-capacity 1H NMR spectroscopy with the BRUKER ULTRASHIELD 600PLUS NMR device. I learned about sample preparation, utilizing an automated liquid handling station with a robotic arm for plasma pipetting, and preparing samples for NMR analysis. The plasma was mixed with deuterium oxide in specific tubes compatible with the SampleJet device, which handles the samples within the Bruker Ultrashield Plus 600MHz NMR device. NMR detects transitions between nuclear spin states influenced by their environment. The resulting signals were recorded using Bruker TopSpin software, and the spectrograms were processed for peak correction and identification using the peak fitting method. The data set was then imported into R Software for statistical analysis.
From July 8-26, 2024, I completed a second 19-day secondment at Biosfer Teslab, Reus, Spain. During this time, along with the head of GRMT Lab, Dr. Anca Gafencu, I visited the new headquarters of Biosfer Teslab, where we analyzed the results we obtained in the first part of my internship in February 2024. Comparing the data obtained by NMR analysis with results obtained through FPLC and ultracentrifugation at the Laboratory of Gene Regulation and Molecular Therapies in Bucharest (IBPC) yielded interesting findings regarding lipoprotein analysis in plasma from apoE deficient mice. I also learned about the LIPOSCALE test (a trademark of Biosfer Teslab), which determines the lipoprotein profile in plasma using nuclear magnetic resonance. This test provides information on plasma cholesterol levels, the specific composition of lipoproteins such as VLDL, LDL, and HDL, and the number, size, and particle concentration of nine lipoprotein subclasses. Sample preparation for LIPOSCALE was similar to that used for metabolite identification, and the spectrogram peaks were analyzed with specialized software using the peak deconvolution method. Characterizing the lipoprotein profile in plasma samples through MRI analysis contributes to assessing the risk of developing atherosclerosis.
This secondment enhanced my understanding of NMR analysis of metabolites and plasma lipids, providing valuable insights into minor changes in plasma that significantly impact the metabolome. The knowledge gained, and information received during my visit to Biosfer Teslab in Reus has opened the prospect of collaboration with the company for NMR analysis of plasma from apoE-deficient mice in our ongoing projects at the GRMT laboratory in Bucharest.”
Dr Madalina Dumitrescu, ICBP “Nicolae Simionescu”
“During my first part of the secondment, I discussed with Dr. Nuria Amigo about the project progress and about the possible interactions with the people from my lab, in order to perform some analysis of the lipoproteins in plasma. In addition, we designed a frame of a manuscript and we planed some experiments. I gained a deeper understanding of high throughput NMR metabolomics. In addition, I worked together with the Biosfer Teslab team to examine some plasma samples to better understand this particular type of data obtained by NMR.
In the second part of the secondment, together with the PhD students from my lab from Romania, we visited the Center of Omics Science’s wet lab in Tarragona, where I saw some of the equipment and a part of the data processing. Together with the PhD from my lab, Irina Tudorache and Gabriela Ciumeica, we have very fruitful discussions with Dr. Maria Vainaxa and Dr. Nuria Amigo.
In the third part of the secondment together with Madalina Dumitrescu from my lab from Romania, we visited the new office of BioSper Teslab where we analyzed the results of the tests performed. The comparison of the data with the data that we obtained in Romania led to interesting results regarding the lipoprotein analysis. During this part of my secondment, I learned many details about Liposcale tests and NMR analysis of the lipoproteins. “
Dr Anca Gafencu, ICBP “Nicolae Simionescu”
“During the secondment, I was involved in various activities that significantly contributed to my professional growth.
The first major accomplishment was the development of a Python software tool specifically designed to assist laboratory staff by automating the generation of files used to track samples. This project required creating the software entirely from scratch and tailoring it to the lab’s needs. The result was a mini-software for sample management, improving efficiency and reducing the likelihood of human error in maintaining records.Next, I focused on translating MATLAB functions into R. This involved rewriting and optimizing these functions to enhance their performance. Additionally, I created R scripts for visualizing spectral plots and implemented the Statistical Total Correlation Spectroscopy (STOCSY) function to produce STOCSY plots. These tasks significantly made me acquire and refine my R programming skills. During the secondment, I attended a series of introductory seminars on statistical methodologies presented by a member of the hosting team. These seminars covered fundamental concepts, including Principal Component Analysis (PCA), an unsupervised technique, and Partial Least Squares Discriminant Analysis (PLS-DA), a supervised technique. These sessions provided foundational knowledge on how to choose appropriate models based on the structure of data and sample groups, which enhanced my understanding of statistical modeling and its applications in research.
I also had the opportunity to visit the laboratory where they process samples and observe their workflows. During this visit, I learned about the entire process, from sample preparation to analysis, and gained insights into the principles and operation of Nuclear Magnetic Resonance (NMR) devices. This included understanding the basics of how NMR works, such as the behavior of nuclei under a magnetic field and the information obtained from the resulting spectra. This hands-on exposure provided valuable context for the techniques and processes used in metabolomics research.
This secondment not only broadened my technical skills, particularly in Python and R programming, but also enhanced my understanding of statistical modeling, laboratory workflows, and advanced analytical techniques. It was an enriching and formative experience that will undoubtedly contribute to the quality of my future research. “
Madalin Ghinea, ICBP “Nicolae Simionescu”
