Biology subjects

Ainla, A.

Publications and source records attributed to Ainla, A..

4 recordsLinked to original sources

bioRxiv2026

Microfluidic Extraction of Extracellular Vesicle-Associated Nucleic Acids for Downstream Molecular Analysis

Aim: To develop a microfluidic workflow for extracting extracellular vesicle (EV)-associated nucleic acids (NAs) from biofluids, such as blood plasma and serum, for downstream molecular analysis. Methods: Healthy serum and plasma samples were spiked with EVs obtained from Hec-1-A cells carrying defined mutations and characterized in accordance with MISEV guidelines. The spiked samples were then processed using either the standard centrifugation-based ExoGAG protocol or a microfluidic workflow. The latter combines ExoGAG mediated aggregation of EVs with mechanical entrapment of the resulting EV aggregates in a microfluidic filtration device (EVNA-chip). The retained material was washed and on-chip lysed to release its NA cargo. NAs were subsequently purified using a commercial silica column, producing an output suitable for molecular analysis through droplet digital PCR (ddPCR). Results: The EVNA-chip recovery yield was 42.0 +/- 4.28% and 38.1 +/- 1.46% for double-stranded DNA (dsDNA) and microRNA respectively. The recovered dsDNA remained compatible with ddPCR detection of the KRAS p.G12D variant (c.35G>A) and with the assessment of MSI-associated alterations using BAT25, BAT26, NR21, NR24, and MONO27. The method was demonstrated for pilot cohort of patients with endometrial cancer. The RNA workflow supported reverse transcription and was demonstrated for the quantification of miR-X, a potential marker of Fabry disease, using patient samples and healthy controls. Conclusion: Although recovery was lower than with the standard protocol (~45% for DNA and for RNA), the centrifugation-free EVNA-chip workflow demonstrates the compatibility of the method with downstream NA molecular analyses and is advantageous for the development of an integrated, automated platform for EV-based liquid biopsy applications.

bioengineering↗

bioRxiv2025

Single cell-derived spheroids for real-time growth and metabolomic studies in breast cancer

Breast cancer remains a leading cause of cancer-related mortality, with disease progression and metastasis posing significant challenges in treatment. Three-dimensional (3D) cancer models have emerged as valuable tools for studying cancer cell biology in a physiologically relevant microenvironment. Studying the tumour heterogeneity and metabolic adaptations at the single-cell level can be crucial to identify factors driving metastatic progression. Here, we present a novel approach to generate single cell-derived breast cancer spheroids using cell lines (MCF-7 and MCF-10A) within a decellularised adipose tissue extracellular matrix (adECM). Spheroid culture conditions were optimised with integrated plasmonic nanosensors (gold nanostars - GNSs), to enable real-time surface-enhanced Raman scattering (SERS)-based measurements. Our results demonstrated that spheroid growth kinetics and viability in adECM were comparable to commonly used animal-derived matrices, validating its use as a reproducible ECM hydrogel. We further show that the concentration of plasmonic nanosensors used was compatible with cell culture and enabled SERS detection of a model reporter, paving the way for label-free, non-destructive analysis of cancer cell metabolism. This platform offers a promising approach to study cancer progression, including metabolic adaptations, with potential applications in biomarker discovery and preclinical research.

cancer biology↗

bioRxiv2024

A miniaturised semi-dynamic in-vitro model of human digestion

Reliable in-vitro digestion models that are able to successfully replicate the conditions found in the human gastrointestinal tract (GIT) are key to assess the fate and efficiency of new formulations aimed for oral consumption. However, current in-vitro models either lack the capability to replicate crucial dynamics of digestion or require large volumes of sample/reagents, which can be scarce when working with nanomaterials under development. Here, we propose a miniaturised digestion system, a digestion-chip, based on incubation chambers integrated on a polymethylmethacrylate (PMMA) device. The digestion-chip incorporates key dynamic features of human digestion, such as gradual acidification and gradual addition of enzymes and simulated fluids in the gastric phase, and controlled gastric emptying, while maintaining low complexity and using small volumes of sample and reagents. In addition, the new approach integrates real-time automated closed-loop control of two key parameters, pH and temperature, during the two main phases of digestion (gastric and intestinal) with an accuracy down to {+/-}0.1{degrees}C and {+/-}0.2 pH points. The experimental results demonstrate that the digestion-chip successfully replicates the gold standard static digestion INFOGEST protocol and that the semi-dynamic digestion kinetics can be reliably fitted to a first kinetic order model. These devices can be easily adapted to dynamic features in an automated, sensorised, and inexpensive platform and will enable reliable, low-cost and efficient assessment of the bioaccessibility of new and expensive drugs, bioactive ingredients or nano-engineered materials aimed for oral consumption, thereby avoiding unnecessary animal testing.

bioengineering↗

bioRxiv2020

Subcompartmentalization and pseudo-division of model protocells

Membrane enclosed intracellular compartments have been exclusively associated with the eukaryotes, represented by the highly compartmentalized last eukaryotic common ancestor. Recent evidence showing the presence of membranous compartments with specific functions in archaea and bacteria makes it conceivable that the last universal common ancestor and its hypothetical precursor, the protocell, could have exhibited compartmentalization. To our knowledge, there are no experimental studies yet that have tested this hypothesis. We report on an autonomous subcompartmentalization mechanism for protocells which results in the transformation of initial subcompartments to daughter protocells. The process is solely determined by the fundamental materials properties and interfacial events, and do not require biological machinery or chemical energy supply. In the light of our findings, we propose that similar events could have taken place under early Earth conditions, leading to the development of compartmentalized cells and potentially, primitive division.

biophysics↗