Secondments 8 and 9: University of Crete to BSN – Biological Sales Network

|
|
Secondments 8 and 9: University of Crete to BSN – Biological Sales Network

“During my secondment in BSN, I acquired working experience in a diagnostic laboratory.

The first day of my visit at BSN, I had an extensive tour of the facility, acquiring valuable understanding of the company’s structure and activities. Giacinto Guercilena kindly delivered a comprehensive overview of the company’s historical and present status in the market for designing, developing and producing in vitro diagnostic medical kits utilising HPLC and LC-MS technology.

Initially, I was introduced in HPLC and LC-MS/MS and learned about the different methods of sample analysis, in which I had no prior experience. I was trained in preparation of different kinds of biological samples (whole blood, urine, hair) using the proper preparation protocol for each method, as well as in the detection of different markers in these samples for various purposes. I learned about the detection of catecholamines and metanephrines, their metabolites, in urine and in plasma with HPLC and LC-MS and how their analysis can be used for the diagnosis of pheochromocytoma, neuroblastoma and other neuroectodermal tumours. I also learned about the detection of drugs of abuse in different kinds of biological samples, and the diagnosis of alcohol abuse from hair samples with LC-MS. Moreover, I learned about the detection of hydroxypyrene in urine with LC-MS, which can be used as a biomarker to assess the internal load of polycyclic aromatic hydrocarbons, formed by the absorption of carcinogenic or mutagenic substances. With this training I became familiar with the methodology and the pre-analytical, analytical and post-analytical requirements for good quality and was able to contribute to the establishment of pre-analytical standard operating procedures for human sample handling and processing (WP4).

Apart from the practical training in wet lab methods, I had the opportunity to learn about the line of work in a research company outside of academia, which I find really exciting. I participated in the preparation of reagents for HPLC and LC-MS kits, quality control of reagents prepared, and testing of reagents’ stability close to the expiration date. Furthermore, I got into troubleshooting processes for various customer requests, regarding modification of protocols or setup of equipment.

Another important part of my secondment was the collaboration with Mattia Albertini, Thomas Matulli Cavedagna, and Sara Marzatico to whom I am very grateful for walking me through protocols and analyses step by step and for entrusting me with performing all the beautiful work they do in the lab. The cooperative atmosphere in the lab was really inspiring and helped me enhance my interpersonal and collaborative skills. Overall, this experience was really valuable to me because not only did it expand my scientific knowledge by giving me a solid experience on HPLC and LC-MS, but also because I learned a lot about research outside of academia and teamwork.”

Elina Paflioti, PhD student from University of Crete

“During my secondment at the BSN S.R.L. I engaged in a range of activities that introduced me to HPLC and LC-MS techniques, expanded my skills, and allowed me to test my Computer Science expertise in the context of the company’s endeavours. Upon arrival on November 15th, I undertook a comprehensive tour of the facility, providing me with valuable insights into the company’s infrastructure and operations. 

Giacinto Guercilena kindly provided a very thorough presentation of the historical and current standing of the company in the market of design, development and production of in vitro diagnostic medical devices using chromatographic techniques. Subsequently, I delved into the world of chromatography which was an entirely new topic for me. This involved hands-on experience in analysis of samples, introduction to the various rigorous protocols used for sample collection, preparation and standardisation of results to ensure their high accuracy and quality. Not only did I learn and become familiar with the company protocols but also the internal workings of HPLC, the various Mobile Phases, their expected timely reactions with the static column to allow for the precise classification of samples. This both on a physical level but also in software through the usage of the Multi Quant Software, acquiring new practical skills in chromatographic analysis. 

A pivotal moment in my secondment occurred on November 20th, where I successfully obtained data from the Multi Quant Software. Although this software also serves as a standalone analysis tool, harnessing my programming expertise, I analysed and visualised the data using a Python program developed from scratch, showcasing the intersection of my computational skills with biological research applications. This integration of programming into biological data analysis aligns with my extensive background in computer science. After being able to successfully parse the output coming from Multi Quant the next step was getting raw data from the SCIEX QTrap chromatography machine, which I also had the chance to do getting the raw .wiff and .wiff.scan files that are outputted by the machine. Although these are proprietary formats I was able to find documentation online and ended up using a combination of open source software, namely ProteoWizard and OpenMS in order to analyse the raw data from scratch and be able to detect and quantize the different chromatography peaks present at different times that corresponded to different molecule detections. This was a very rewarding exercise that also led to addressing 2 bugs on the OpenMS suite that initially, briefly prevented me from analysing the raw data. The github ticket for the resulting bug fix I identified was this ( https://github.com/OpenMS/OpenMS/issues/7220 ) and it ensures that future engineers and researchers using these open tools will be able to successfully perform similar tasks using open software and platforms. This both demonstrates my problem-solving abilities and commitment to improving software tools used in the industry as well as providing alternate open-source compatible tool-chains for B.S.N. that may be useful in the direction of future research of novel molecule classification techniques.

I observed the maintenance procedures of the Mass Spectrometry SCIEX QTrap machine, with the help of Bruno Casetta, who is an expert on this crucial instrument, broadening my knowledge. To improve my theoretical understanding through literature review, I immersed myself in papers such as “Deep Learning-Assisted Peak Curation for Large-Scale LC-MS Metabolomics” and “Deep Learning for the Precise Peak Detection in High-Resolution LC–MS Data.” This initiative underscores my effort to apply my Machine Learning / Artificial Intelligence knowledge stemming from my Computer Vision and Robotics background to apply novel methods to the problem in order to stay abreast of cutting-edge methodologies in the field.

In more practical aspects of data handling, I practised extracting, processing and storing analysis data in various standardised formats such as CSV and XLSX. This skill set is paramount for effective data management, aligning with the rigorous demands of biological R&D and the reduction of human error when dealing with manual processing of a large volume of measurement values from experiments.

Collaboration was another facet of my secondment. With the generous help of Mattia Albertini, Sara Marzatico and Thomas Matulli Cavedagna, evident in my involvement (despite not having prior experience) in preparing aliquot reagents such as for kit EUM-22100, or the preparation of the mobile phases for the kit EUM-17100 and its subsequent quality control. This teamwork experience enhanced my interpersonal and collaborative skills, while at the same time providing hands-on experience which is crucial to grasp the complexity of procedures that may affect the quality of analysed data in a research and development setting.

In summary, my secondment experience was marked by integration of my computational expertise into the biological research domain. From hands-on chromatography to data analysis and software debugging, I attempted to contribute to the best of my ability to the company’s projects. This interdisciplinary approach reflects my effort to bridge the gap between computer science and biology, leveraging my diverse skill set for contributions in a real-world laboratory setting.

These experiences align with my broader professional journey, reflecting a trajectory from already being a self-taught student programmer at the age of 14 to a seasoned PhD candidate researcher with a robust background in computer vision, robotics, and artificial intelligence. My commitment to continuous learning and integration of diverse skills will hopefully position me as a valuable asset in interdisciplinary research environments.”

Ammar Qammaz, PhD student from University of Crete

Latest Updates

As we approach the end of the second year and the midpoint of the project, our partner, the University of Belgrade – Faculty of Pharmacy,...
From 16th-18th September, 2024, we had the incredible opportunity to join forces between MSCA SE CardioSCOPE and COST Action AtheroNET, bringing the latest advances in...
IMG_0461
“I participated in a 3-month secondment in the Genetic Lab (GL) in Bucharest, from April 1st  2024 until the 30th of June 2024. During this...
OK1
“I was hosted in the Clinical Chemistry lab, led by prof. Tsatsanis, at the University of Crete School of Medicine (UOC). During my stay at...
MC1
“I spent two months (from July 2nd  to August 31st, 2024) at the Institute for Artificial Intelligence at Fondazione Bruno Kessler (FBK) in Trento, Italy....
“During my stay at the Genetic Lab SRL. I received extensive instruction on the general organization of the laboratory and the workflow when analyzing different...