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Talanta

Elsevier BV

Preprints posted in the last 90 days, ranked by how well they match Talanta's content profile, based on 12 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit.

1
Ni2+ And Zn2+-Binding DNA Motifs Revealed In DNA Aptamers To African Swine Fever Virus

Aliyeva, R.; Mushenkov, V.; Meshcheryakova, N.; Zaborova, O.; Oleynikov, I.; Mukhametova, L.; Eremin, S.; Koltsova, G.; Nechaev, A.; Zavyalova, E.

2026-05-07 synthetic biology 10.64898/2026.05.05.722837 medRxiv
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Rapid and specific diagnosis of viral and bacterial infections is a significant challenge in medicine and veterinary science, especially in the case of epidemically dangerous pathogens. The African swine fever virus (ASFV), for example, causes annual outbreaks among livestock, resulting in significant economic losses for farmers. DNA aptamers have been identified as a promising tool for point-of-care diagnostics, being highly specific to the target and stable ambient temperatures during storage. In this study, we describe the selection of DNA aptamers targeting the p54 viral protein using a single-round selection process. These aptamers were able to bind both to recombinant protein and inactivated ASFV viral particles. Analysis of the newly generated aptamers revealed a dependence of affinity and thermal stability on Ni2+ content, which was a dopant in the selection process. In some cases, the affinity increased 100 times, and melting temperature increased by 30{degrees}C. We have identify two novel DNA motifs that bound 2-3 Ni2+ or Zn2+ ions.

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CLIAMDK: A Modular Smartphone Platform Matching Plate Reader Performance for Chemiluminescent Immunoassay Development

Wood, C. S.; Abele, S. M.; Alsbach, J.; Gervalla, A.; Meinel, D. M.; Cuny, A. P.

2026-03-28 cardiovascular medicine 10.64898/2026.03.26.26348440 medRxiv
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The development of chemiluminescent immunoassays (CLIAs) is a complex and iterative process that relies on costly laboratory infrastructure, limiting its accessibility and application across healthcare settings and disease areas. Here, we detail the CLIA Mobile Development Kit (CLIAMDK) a modular, mobile, and inexpensive platform to assess image sensors, smartphones and data processing workflows for CLIA development. For its demonstration, we developed two CLIAs targeting renin and aldosterone, key biomarkers for diagnosing primary aldosteronism. The results from our performance study, including 50 patient samples, demonstrate the potential of our platform in a real-world scenario. We found that the performance of our mobile reader platform is comparable to that of a state-of-the-art plate reader, with a Lower Limit-of-Detection (LLoD) approaching 41 femtomolar. We envision that our platform will help accelerate CLIA development, make it more accessible, and lay the foundations for novel, distributed, yet highly sensitive diagnostic tests.

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Improved adenine-HPLC method for quantifying yeast based on cellular DNA content

Ohyama, Y.; Shimamura, M.; Asami, Y.; Tourlousse, D. M.; Togawa, N.; Narita, K.; Hayashi, N.; Terauchi, J.; Sekiguchi, Y.; Kawasaki, H.; Miura, T.

2026-03-14 microbiology 10.64898/2026.03.13.711611 medRxiv
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Accurate quantification of fungi is important for a myriad of applications but remains challenging. Previously, we demonstrated that an approach called the adenine-HPLC method can quantify bacteria, including those with aggregating properties that are difficult to quantify using conventional methods, by measuring cellular adenine derived from DNA and converting the adenine amount to genome copy number, without being influenced by cell morphology. However, in this study, when this adenine-HPLC method was applied to the quantification of budding yeast as a model fungus, accurate measurement proved impossible. This limitation was attributed to adenine release from other adenine-containing biomolecules, such as RNA and ATP, and we therefore developed a method that suppresses adenine release from these molecules. This method involves reducing the temperature of the acid treatment and prewashing the cells before acid treatment. In addition, we incorporated a process that corrects for the naturally occurring free adenine level as background during total adenine measurement. The improved adenine-HPLC method based on these modifications enables accurate quantification of budding yeast using genomic DNA content in whole cells as the quantification unit.

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Extending the limits of 3D printed polymers on paper towards bioanalytical sensing

Ngaju, P.; Pandey, R.; Kim, K.

2026-03-31 molecular biology 10.64898/2026.03.27.714910 medRxiv
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Polymeric 3D printing of microfluidic devices for biosensing is an appealing fabrication alternative for rapid manufacturing of biosensing devices with complex geometry in a streamlined, repeatable and cost-effective manner without the need for expensive instrumentation such as those employed in photochemical etching and soft lithography. Hybrid 3D printed paper-based microfluidics is an emerging area which harnesses the unique properties of both, merging the construction of microfluidic structures and the inherent capillary-driven flow within paper substrates. In this work, we have fabricated hydrophobic barriers by 3D printing a single layer of machinable wax, thermoplastic polyurethane, polylactic acid and polypropylene directly on chromatography paper to create open microchannels and determine the most suitable material. Characterization of each open microchannel using the four materials revealed polypropylene as the most reliable material with high hydrophobic barrier integrity and resolution. Polypropylene achieved functional microchannels with a resolution of 621 {+/-} 33{micro}m, hydrophobic barrier integrity of (93.75 {+/-} 9.16%), wicking speed of 0.38mm/s and optimal hydrophilicity of channels (51.4 {+/-} 8.36 {degrees}) with minimal embedding during thermal curing. To demonstrate proof of principle, a fluorescence assay demonstrating the formation of a dimeric g-quadruplex structure from a g-rich sequence which significantly enhances fluorescence of thioflavin T was implemented.

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miRNova: A Next-Generation Platform for Ultra-Precise and Highly Specific MicroRNA Quantification Integrating a Tailored Stem Loop RT-qPCR and a Robust Analytical Framework

VAN, T. N. N.; Van Der Hofstadt, M.; Houot-Cernettig, J.; Thibal, C.; Nguyen, H. S.; Marcelin, C.; Ouedraogo, A.; Champigneux, P.; Molina, L.; Kahli, M.; Molina, F.

2026-04-04 bioengineering 10.64898/2026.04.01.715903 medRxiv
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MicroRNAs (miRNAs) are ultra-short RNA molecules characterized by high sequence homology, frequent post-transcriptional modifications, and typically low abundance, particularly in circulating biofluids. These inherent biological features present substantial technical challenges for RT-qPCR- based quantification. Consequently, the development of miRNA RT-qPCR assays has required architectural adaptations at the reverse transcription (RT) stage to generate extended cDNA templates, thereby enabling effective downstream quantitative PCR amplification. One widely adopted approach involves the enzymatic addition of a poly(A) tail to the 3' end of miRNAs, followed by poly(T)-primed universal reverse transcription, which has gained broad acceptance due to its perceived sensitivity and simplified workflow. However, independent experimental evidence indicates that this architecture does not consistently provide the level of specificity required for reliable single-nucleotide (SN) discrimination, particularly when quantifying low-abundance circulating miRNA targets, as demonstrated in our previous study. An alternative strategy relies on miRNA-specific reverse transcription using stem-loop priming has been equally well accepted. When generically generated, this approach offers certain improved specificity, but its performance in resolving single-nucleotide differences remains limited. In this article, we employed precision engineering to maximize specificity for both reverse transcription and qPCR steps. By tailoring both primer design and reaction architecture to the specific sequence features of each miRNA, we enable robust single nucleotide discrimination among these ultra-short targets. Prototype of ten different miRNova assays quantifying miRNAs whose sequences are differed in various configurations were tested on synthetic miRNA targets. For miRNova assay validation, saliva samples were elite rugby players submitted to small RNA extraction, then RT-qPCR. Spike-in of synthetic targets was applied for each quantification point to characterized the sensitivity, specificity and accuracy of the assays. Comparative analysis was performed between miRNova and two commercially available kits on the same sample set. The obtained results show a superior performance of miRNova assays allowing for sensitive and accurate quantification of miRNAs in saliva samples. Altogether, this results in modular, reproducible assays optimized for low-abundance miRNA detection in challenging biofluids, including saliva, positioning the platform beyond existing sensitivity-focused solutions toward true diagnostic-grade specificity.

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Barcode Crosstalk in ONT Multiplex Sequencing: Quantification and Mitigation Strategies

Scharf, S. A.; Spohr, P.; Ried, M. J.; Haas, R.; Klau, G. W.; Henrich, B.; Pfeffer, K.

2026-03-28 molecular biology 10.64898/2026.03.27.714689 medRxiv
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Multiplexing samples in long-read sequencing with Oxford Nanopore Next Generation Sequencing Technology (ONT) by ligating specific native barcodes to individual DNA samples enables significant increases of high throughput sequencing combined with a significant reduction of sequencing costs. However, this advantage carries the risk of barcode misassignment / crosstalk. Employing ONT multiplex sequencing with samples, we observed misassigned barcodes so called barcode crosstalk, after ONT library preparation according to the standard protocol, particularly in samples with low input DNA concentrations. We assumed that these barcode misassignments are largely due to misligation of remaining native barcodes during subsequent the subsequent sequencing adapter ligation. To systematically investigate and quantify barcode crosstalk, genomic DNA (gDNA) from four bacterial type strains with different DNA input concentrations was prepared using three protocols for library preparation: the Nanopore standard protocol (protocol A: version valid until July 2, 2025) the new Nanopore protocol (protocol B: version from July 2, 2025), and an in house protocol with pooling of the barcoded samples only after the sequencing adapter ligation step (protocol C: in house). All samples were sequenced on a Nanopore PromethIon device. The results clearly showed that the use of protocol A resulted in a pronounced barcode crosstalk especially detectable in samples with low DNA input concentrations (up to 2.4% misassigned reads). The ONT adjustment in protocol B (altered washing buffer vs. protocol A) significantly alleviated the barcode crosstalk to below 0.01%, whereas protocol C eliminated barcode crosstalk virtually completely. These observations emphasize that sequencing results obtained with older ONT native barcoding protocol variants should be critically reviewed. The newer ONT barcoding protocol is preferable for sequencing, but it does not completely eliminate the barcode crosstalk effect. In conclusion, for low DNA input and high accuracy sequencing, protocol C is recommended.

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A Spectrum of Possibilities: A Systematic Evaluation of Fluorescent Proteins in Cyanobacteria

Hasenklever, D.; Boecker, J.; Grankin, A.; Sener, F.; Axmann, I. M.; Behle, A.

2026-05-19 synthetic biology 10.64898/2026.05.18.725961 medRxiv
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Fluorescent reporters cover a wide range of applications in both basic and applied research. Whether a study involves microscopic imaging to study (co)-localization of proteins, FRET, biosensing, or quantifying gene expression, fluorophores are attractive reporter candidates due to their relatively straightforward in vivo readout. For microbiological applications, a wide variety of fluorescent proteins with varying excitation and emission wavelengths, brightness levels, and maturation times are available. Careful consideration is required when selecting from this large suite of proteins, especially when choosing multiple fluorophores. This is further complicated in phototrophic organisms, which exhibit strong autofluorescence, especially towards the red part of the spectrum, effectively eliminating common candidates such as mCherry. In this study, the specific properties and performance of a selection of fluorescent proteins are systematically evaluated against the background of photosynthetic pigment-derived autofluorescence in the cyanobacterium Synechocystis sp. PCC 6803. Specific readouts of different combinations of fluorescent proteins are also analyzed using high-throughput methods, namely plate reader fluorescent scans and single-cell flow cytometry to quantify fluorescence. The ultimate goal is to assess each fluorescent protein with regard to: 1.) Its ability to be discerned from cyanobacterial autofluorescence. 2.) Its compatibility with other fluorophores in this context. 3.) Its overall suitability in cyanobacterial research. Several highly suitable fluorescent proteins for use in cyanobacteria are identified, including mTagBFP2, mNeonGreen and mScarlet-I and suitable combinations, covering nearly the whole spectrum of visible light. This study expands the knowledge and toolset for current and future researchers and uncovers a whole spectrum of possibilities for fluorescent protein selection in cyanobacterial cell biology.

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Development of a Xylene-Free Sample Preparation Protocol for Quantitative Proteomics of Clinically Relevant Formaldehyde-Fixed Paraffin-Embedded Needle Biopsy Samples

Moagi, M.; Beke, L.; Mehes, G.; Kecskemeti, G.; Szabo, Z.; Turiak, L.; Csosz, E.

2026-05-14 molecular biology 10.64898/2026.05.12.724492 medRxiv
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Fresh-frozen tissues are considered the gold standard for proteomic analyses due to superior preservation of protein integrity; however, their use is limited by the logistical and financial requirements of long-term storage. Formaldehyde-fixed paraffin-embedded (FFPE) tissues provide a practical alternative owing to their stability and widespread availability in clinical settings. A critical step in FFPE proteomics is deparaffinization, which traditionally relies on organic solvents such as xylene, along with efficient reversal of formaldehyde-induced crosslinks. In this study, we evaluated multiple FFPE protein extraction and digestion workflows including chaotropic, surfactant-based, and detergent-free approaches in combination with xylene-free deparaffinization strategies, using label-free data-independent acquisition (DIA) LC-MS/MS. Among the tested methods, a chaotropic-, reductant-, and surfactant-free in-solution digestion workflow demonstrated robust protein and peptide recovery. A modified version of this protocol further improved peptide coverage while maintaining comparable protein depth. The applicability of the optimized workflow was assessed using FFPE needle biopsy samples from control, hepatic steatosis, and liver fibrosis groups. Distinct proteomic patterns were observed across conditions, with hepatic steatosis associated with early activation of stress-response pathways, while fibrosis showed evidence suggesting altered lipid metabolism. Overall, this study presents a simple, xylene-free, and MS-compatible workflow for FFPE proteomics that is suitable for low-input clinical samples and may support broader application of archival tissues in proteomic research.

9
A tool to shoot genes with massive air from a compressor (TSGMAC)

Tsugama, D.

2026-03-26 plant biology 10.64898/2026.03.24.713841 medRxiv
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Particle bombardment systems are widely used for plant transformation, but commercial devices are expensive and rely on high-pressure helium gas. This study aimed to develop a cost-effective and helium gas-free alternative using an air duster gun connected to a commercial compressor. A nozzle (for DNA with transgenes), gold particles (as DNA carriers), nozzle-to-sample distance, and a method for coating gold particles with DNA were optimized to yield better transformation efficiency in targeting onion epidermal cells and rice calli. From the rice calli transformed with the newly developed system (a tool to shoot genes with massive air from a compressor: TSGMAC), stable transgenic plants could be obtained. TSGMAC offers a low-cost and helium gas-free solution for plant transformation and genome editing and can enhance accessibility to particle bombardment-based techniques.

10
Label-free toehold mediated strand displacement on 3D printed hybrid paper-polymer platform for protein sensing

Ngaju, P.; Kakadiya, D.; Abdollahi, S.; Kim, K.; Pandey, R.

2026-03-28 molecular biology 10.64898/2026.03.27.714923 medRxiv
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A programmable 4-input cascade DNA logic gate utilizing toehold mediated strand displacement (TMSD) was implemented on a 3D printed hybrid paper-polymer vertical flow device (3D HPVF) for on/off sensitive and specific fluorescence detection of platelet derived growth factor BB (PDGF BB). Polypropylene was 3D printed directly on paper and thermally cured to create micro paper analytical devices ({micro}PADs). The 3D HPVF comprised of three layers of {micro}PADs enclosed in a casing that clamped each {micro}PAD securely to ensure seamless and efficient wicking between layers. In the presence of PDGF BB, a partially complementary strand to a PDGF B aptamer (PDGF B Apt), cApt, was liberated from a PDGF B Apt/cApt duplex in solution. The solution was then deposited on the 3D HPVF with a dimeric g-quadruplex hairpin. The 4-nucleotide toehold region on the cApt started the hybridization reaction with the dimeric g-quadruplex hairpin (dGH) opening it up allowing formation of a dimeric g-quadruplex structure that binds with thioflavin T (ThT) with enhanced fluorescence intensity at room temperature. The 3D HPVF exhibits a pico molar range of detection from 10pM to 100pM with a 10pM limit of detection (LOD) for PDGF BB concentrations relevant for pregnant women predisposed to early-onset preeclampsia with clear differentiation when compared to similarly competing analytes PDGF AA and AB.

11
YY1 Binding Motif at Upstream of Rep/Cap Increases AAV Yield and Full Capsids

Ofusa, Y.; Nishio, S.; Enoki, T.; Mineno, J.; Ozawa, K.; Mizukami, H.; Ohba, K.

2026-05-22 microbiology 10.64898/2026.05.21.726733 medRxiv
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Adeno-associated virus (AAV) vectors are widely used in gene therapy, whereas low manufacturing efficiency and a large proportion of empty capsids are major obstacles. This study focused on the Yin Yang 1 (YY1) binding motif (YY1-motif) and investigated the effect of its presence or insertion at upstream of the Replicase (Rep)/Capsid Cap) gene on AAV vector production. We found that the YY1-motif incidentally presented in a Rep/Cap plasmid was associated with high vector production. We then designed several modified Rep/Cap (RC2) constructs. The YY1-motif insertion at the upstream of Rep/Cap gene increased vector yield in a repeat-number-dependent manner, and similar effects were not observed with other promoters insertion. Furthermore, the insertion of the YY1-motif reduced the amount of Cap protein per the same amount of full particle in supernatants on multiple serotypes, indicating the improvement in the empty/full capsid ratio. The YY1-motif insertion did not affect the AAV vector infectivity. These results denote that the YY1-motif has a universal regulatory function that optimizes the Rep/Cap expression balance, and simultaneously improves the production efficiency and full particle formation of AAV vectors. This finding could contribute to the development of highly efficient and high-quality AAV manufacturing processes.

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DropletFactory CORE - a droplet cytometry and sorting platform for fast and accessible screening in biotechnology

Veere, R.; Zenner, M. N.; Afroz, A.; Joemaa, R.; Olman, T.; Bartkova, S.; van der Hoek, S. A.; Melkic, A.; Zheng, A. J. L.; Laki, A. J.; Laki, M.; Pardy, T.; Scheler, O.

2026-03-12 microbiology 10.64898/2026.03.11.711014 medRxiv
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Droplet sorting technology has the potential to revolutionize the biotechnology sector as it provides massive high-throughput screening capacity, but the technology remains not accessible for a wider audience yet. There is a need for more affordable droplet sorting platforms to design cell factories and screen cell libraries. In here we demonstrate our droplet cytometry/sorter platform for single-cell screening of yeast cells based on their fluorescence signal.

13
Molecular Structure and DNA Binding Mode of Unsymmetric Cyanine Dyes RiboGreen and OliGreen

Blackford, N.; Nepal, S.; Zheng, L.; Yang, W.; Silvers, R.

2026-05-07 molecular biology 10.64898/2026.05.04.722657 medRxiv
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The binding of fluorescent dyes to nucleic acids and their fluorogenic properties are indispensable tools for nucleic acid detection, quantification, and imaging, yet the molecular structures of several widely used commercial dyes have remained unknown. Here, we de novo determined the molecular structures of RiboGreen and OliGreen and confirmed the previously proposed structure of PicoGreen using high-field NMR spectroscopy. All three dyes were identified as unsymmetric cyanine dyes, where a benzoxazole/benzothiazole moiety is linked to a 4-quinoline by a monomethine bridge. Complete 1H and 13C resonance assignments enabled us to expand the existing chemical shift reference set for this important class of dyes. Photophysical characterization with standardized single- and double-stranded DNA and RNA targets indicated that all dyes performed similarly upon binding despite being marketed towards different nucleic acid types. NMR spectroscopy and long-timescale molecular dynamics simulations showed that RiboGreen interacts with double-stranded DNA predominantly by two binding modes, electrostatic interactions with the phosphodiester backbone and {pi}-{pi} stacking with the ultimate and penultimate base pairs of the DNA molecule. These results establish the molecular structures of three widely used commercial dyes and provide a structural and mechanistic framework for understanding the fluorogenic properties of this class of dyes. HighlightsO_LIDetermination of the molecular structures of nucleic acid dyes RiboGreen, OliGreen, and PicoGreen C_LIO_LINMR spectroscopic characterization of all three dyes. C_LIO_LINMR and MD data indicate binding to be dominated by electrostatic and {pi}-{pi} stacking interactions C_LI

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Mechanistic Evaluation of Amplification Lag in Paper-Based Colorimetric Loop Mediated Isothermal Amplification (LAMP) and Its Reduction by BSA Pre-Coating

Kim, T.; Palla, G.; Raut, B.; Verma, M. S.; Ardekani, A. M.

2026-03-11 bioengineering 10.1101/2025.10.25.684418 medRxiv
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Colorimetric loop-mediated isothermal amplification (LAMP) on microfluidic paper-based analytical devices (PADs) offers a low-cost, disposable, and equipment-free alternative to liquid LAMP assays. However, amplification on PADs is consistently slower, by 5-46%, than reactions in tubes. To identify the origin of this delay, we evaluated heat transfer, diffusion in porous cellulose, and nonspecific adsorption of LAMP components across both high- and low-copy input regimes. Our results show that once thermal equilibrium is reached, reduced effective diffusion is the dominant contributor to the kinetic lag at low copy numbers, whereas nonspecific adsorption becomes the primary barrier at higher template concentrations. Pre-coating the paper with bovine serum albumin (BSA) mitigates adsorption. It narrows the tube-to-paper gap, thereby accelerating amplification of the SARS-CoV-2 ORF7ab synthetic gene by an average of 6 minutes, from 1E3 to 1E5 copies per reaction. These findings provide a mechanistic basis for the copy-number-dependent behavior of PAD LAMP and offer simple, low-cost strategies to improve the speed and reliability of PAD nucleic acid assays.

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Rapid and flexible assessment of gene functions in plant cells with particle bombardment and linear DNA

Weerasinghe, P. R.; Tsugama, D.

2026-05-18 plant biology 10.64898/2026.05.17.725698 medRxiv
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Biolistic transformation is a versatile tool in plant science, yet high equipment costs and tissue damage from high-pressure gas remain significant barriers. Building on our previously developed "TSGMAC", a low-cost, helium-free biolistic system, we report three major advancements to enhance its throughput, delivery quality, and quantitative capability. First, a "guide barrel" assembled from commercial DIY fittings was developed; it effectively eliminates physical tissue damage and ensures uniform particle distribution, even in soft tissues like bok choy (Brassica rapa subsp. chinensis). Second, a rapid gene expression platform using PCR products was characterized. Results demonstrate that linear DNA constructs are efficiently circularized via non-homologous end joining (NHEJ) in plant cells, and protein expression is robust regardless of the relative positions of the promoter, coding sequence, and terminator. This system bypasses time-consuming cloning. Third, a cost-effective, highly sensitive dual-luciferase assay system utilizing teal Luc (teLuc) and inexpensive firefly luciferase (FLuc) inhibitors was established. This integrated workflow enables rapid, quantitative molecular biology using supermarket-obtained materials and standard PCR reagents. Our findings provide a practical foundation for plant scientists, synergistically accelerating gene functional analysis and genetic tool development.

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Combining Anion Exchange and Size Exclusion Chromatography for Extracellular Vesicle Enrichment from Small Volumes of Human and Mouse Plasma for Quantitative Proteomics

Dunlop, F. M.; Mason, S.; Hafizi Rastabi, N.; Alexander, S. E.; Robatjazi, S.; Davis, J.; Laird, C.; Kang, T.; Mathivanan, S. E.; Russell, A. P.

2026-03-14 molecular biology 10.64898/2026.03.11.711200 medRxiv
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Extracellular vesicles (EVs) are promising biomarkers, yet their proteomic analysis from plasma is hampered by low abundance and co-purification of contaminants (e.g., lipoproteins, platelets) and technical variability, particularly in small-volume animal models. We developed and validated a modular protocol integrating Size Exclusion Chromatography (SEC) with Strong Anion Exchange (SEC-SAX) specifically tailored for quantitative LC-MS proteomics from small starting volumes (150 l of plasma). SEC alone successfully removed 99% of Albumin, and the SAX step significantly enriched EVs over contaminating lipoproteins. Downstream single pot solid phase enhanced (SP3) sample prep and STAGE tip solid phase extraction ensured maximum proteome depth. Critical confounding factors were objectively assessed: Platelet Factor 4 (PF4) was confirmed as a highly sensitive platelet marker, confirming the necessity of meticulous plasma preparation. Sample hemolysis impacted the plasma EV proteome data. As such, an objective measure (nanodrop spectrophotometer) of hemolysis and exclusion of hemolysed samples (heme >0.3 mg/ml) is recommended. The protocol is applicable to both human and mouse plasma as demonstrated by EV enrichment and quantification of biomarker proteins associated with neurodegenerative diseases from eight individual mouse plasma samples. Manuscript HighlightsO_LIDevelopmental workflow for a quantitative SEC-SAX protocol for EV proteomics from small plasma volumes (150 l). C_LIO_LIA range of variables tested including SAX beads amount, digestion buffer, digestion time, STAGE tip solid phase extraction, SAX elution buffer and sample filtration. C_LIO_LIThe SAX step significantly enhances EV proteome depth by increasing EV purity in relation to ApoB lipoproteins. C_LIO_LIShows the impact of the major confounding factors of sample hemolysis and platelet contamination on the EV proteome. C_LIO_LIPlatelet contamination increases the number and abundance of proteins detected including known disease biomarkers and sample hemolysis is associated with proteins derived from platelet and red blood cell derived EVs. C_LIO_LIPlatelet Factor 4 (PF4) is identified and confirmed as a sensitive marker for platelet contamination. C_LIO_LIApplicable to both human and mouse plasma. C_LI

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Unspecific Molecular Adsorption (UMA) sample preparation method for bottom-up and whole protein analysis. The foundation.

Zougman, A.

2026-03-05 biochemistry 10.64898/2026.03.02.709073 medRxiv
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The protein sample preparation methods for shotgun proteomics are nowadays well-established unlike the ones for whole protein analysis. The goal of my work has been to create a simple methodology which provides a single uncomplicated sample preparation tool for these two fields. Nowadays the bulk of proteomics work is done using detergents for protein solubilization. The presented concept, which is based on unspecific adsorption of protein molecules on wide pore materials, allows for protein capture and clean-up from solutions of the most commonly used sodium dodecyl sulfate detergent. It could also be applied to proteins in detergent-free solutions. After the capture and clean-up, proteins could be either cleaved for the downstream peptide analysis or eluted for the whole protein analysis. If required, the eluted whole proteins could be recaptured and cleaved into peptides. Depending on the experimental goals, the sample preparation device could be fitted with embedded proteolytic enzymes to simplify routine sample processing and/or reversed phase media for the downstream peptide or protein separation.

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Application of the Nicking Loop™ targeted library preparation method to DNBSEQ™ sequencing

Adamusova, S.; Korkiakoski, A.; Hirvonen, T.; Ren, H.; Laine, N.; Musku, A.; Rantasalo, T.; Kim, J.; Bloomster, J.; Laine, J.; Xu, C.; Tamminen, M.; Pursiheimo, J.-P.

2026-03-12 molecular biology 10.64898/2026.03.10.710732 medRxiv
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Nicking Loop is a PCR-free targeted library preparation method that combines conversion of linear target DNA into circular single-stranded DNA (CssDNA) library with early sample indexing in a single step. The resulting CssDNA libraries can be either directly sequenced or optionally amplified, offering maximum flexibility across sequencing applications. This study demonstrates the compatibility of Nicking Loop circular libraries with a MGIs DNBSEQ platform. Compatibility was evaluated against established linear Nicking Loop libraries sequenced on Illumina MiSeq platform. Using synthetic reference samples with defined variant allele frequencies, Nicking Loop method demonstrated matching performance across both library formats and sequencing platforms. Key quality metrics, including unique molecular identifier (UMI) distributions, error profiles and VAF detection, were all highly consistent. Both library types generated over 97% singleton UMIs, indicating uniform template sampling, and VAF measurements were strongly concordant across platforms (Spearmans {rho} = 0.939). Collectively, these findings demonstrate that Nicking Loop method is directly applicable to circular NGS platforms, such as DNBSEQ, strongly supporting its use as a platform-agnostic library preparation strategy for targeted sequencing applications.

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Evaluating the Utility of a Nanoscale Flow Cytometer for Detection of Surface Proteins on HIV and Extracellular Vesicles

Burnie, J.; Ouano, C.; Costa, V.; Castrosin, I.; Hammond, C.; Matthews, H.; Tigges, J.; Corbett-Helaire, K. S.

2026-03-10 microbiology 10.64898/2026.03.09.710614 medRxiv
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BackgroundFlow virometry (FV) - the application of flow cytometry to viruses - has historically been hindered by the inability of cytometers to detect particles below [~]300 nm in size. However, advances in optics and fluidics have enabled cytometers primarily designed for cells to detect viruses and extracellular vesicles (EVs) through light scatter alone. In 2024, the CytoFLEX nano was released, marketed for the detection of particles as small as 40 nm; however, its performance has yet to be compared to a conventional instrument for FV. MethodsFV was utilized to evaluate performance of the CytoFLEX nano and a conventional flow cytometer (CytoFLEX S). Instrument scatter sensitivity was assessed using NIST beads (40-400 nm), and virus stocks [human immunodeficiency virus (HIV), human coronaviruses (HCoV)-229E and HCoV-OC43]. For fluorescence analysis, HIV virions were stained with PE- and BV421-conjugated antibodies targeting virion incorporated proteins (CD38, CD44), individually and in combination. Finally, HIV stocks were labeled with antibodies against the envelope (Env) glycoprotein and tetraspanins (CD9, CD81) to assess EVs within virus preparations. ResultsCompared to the CytoFLEX S, the CytoFLEX nano exhibited substantially greater scatter sensitivity, reflected by up to 50-fold higher signal-to-noise ratio across NIST-traceable beads and virus samples. This enabled clearer resolution of smaller populations, including bead populations < 70 nm that were undetectable on the CytoFLEX S, as well as improved resolution across all viruses. While both instruments reliably detected stained proteins on HIV virions, the CytoFLEX nano revealed a distinct population of tetraspanin-positive EVs within HIV stocks that was undetected on the CytoFLEX S. Using GFP-tagged HIV, we identified Env+ particles lacking GFP, indicating the presence of Env on EVs. ConclusionsThe CytoFLEX nano exhibited markedly improved scatter sensitivity compared to the CytoFLEX S, improving detection of viruses and enabling detection of EV populations that were undetectable on the conventional instrument. While both platforms performed similarly for surface protein labeling, additional consideration of spectral overlap was needed with the CytoFLEX nano in multicolor experiments. These findings highlight that the complementary strengths of each platform can be utilized to more comprehensively characterize virus and EV populations, providing new opportunities to investigate nanoparticle heterogeneity.

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Identification of the siderophore schizokinen and its derivatives by LCHRMS and mass-tandem fragmentation

Sottorff, I.

2026-05-08 biochemistry 10.64898/2026.05.05.723046 medRxiv
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Biological metal chelators are of great interest for investigation due to their capacity to retain or mobilize metals from the environment. While some biological and bioinspired chelators find use in medical applications, others are promising platforms for the mining or recycling of technologically important metal ions. In particular, the siderophores, which are primarily iron chelators, have been studied. Four siderophores of relevance are schizokinen and its derivatives, which have been isolated from bacterial and algae cultures, in addition to soil. These siderophores have shown metal chelating activity with different metals such as iron, copper, and aluminum. In the time of metabolomics, it is required to unambiguously determine the identity of the produced siderophores as quickly as possible. Thus, Liquid Chromatography coupled to High Resolution Mass Spectrometry and mass-tandem fragmentation (LC-HRMS-MS) provides a quick and applicable alternative for identification of schizokinen and its derivatives. Here, we report an analytical method for the identification and potential quantification of the schizokinen siderophore series. We developed a working method through LC-HRMS-MS, which provides the unequivocal identification of the four schizokinen derivatives, which has not been reported to date. Additionally, we constructed the molecular network for the four molecules to enable their identification using the Global Natural Products Social Molecular Networking (GNPS) platform. Most importantly, this contribution can help speed up the characterization of schizokinen producers and facilitate the dereplication process of siderophores.