Optimization of Automated Sample Preparation for Vitamin D Determination on a Biomek i7 Workstation

Vitamin D belongs to the fat-soluble vitamins and is an integral part of bone metabolism. In the human body, a decreased vitamin D level can be an additional risk factor for diseases like cancer, diabetes, and mental diseases. As a result, an enormous increase in the demand for vitamin D testing has been observed in recent years, increasing the demand for powerful methods for vitamin D determination at the same time. Automation is the key factor in increasing sample throughput. This study compares three fully automated sample preparation methods for the determination of 25(OH)D2 and 25(OH)D3 in plasma and serum samples. Starting from a semiautomated reference method, the method is tested manually and subsequently fully automated on the Biomek i7 Workstation by integrating a centrifuge and a positive pressure extractor into the workstation. Alternatively, the centrifugation for the separation of protein aggregates and supernatant is replaced by a filter plate. Finally, the sample throughput is further increased by using phospholipid removal cartridges. The results show that phospholipid removal significantly increases the recovery rates in liquid chromatography–mass spectrometry. With the phospholipid removal cartridges, recovery rates of 97.36% for 25(OH)D2 and 102.5% for 25(OH)D3 were achieved, whereas with the automated classic automated preparation method, the recovery rates were 83.31% for 25(OH)D2 and 86.54% for 25(OH)D3. In addition to the technical evaluation, the different methods were also examined with regard to their economic efficiency. Finally, the qualitative and quantitative performance of the developed methods is benchmarked with a selected semiautomatic reference method.

Quantification of Fructans in Bioethanol Stillage Based On a Simplified Analytical Method

Bioethanol stillage, the main by-product of industrial bioethanol production, is a potential substrate for fructans. However, the determination and quantification of fructans in such complex sample matrices is still a challenge for the corresponding analytics to be overcome in order to allow for the identification and utilisation of such unused fructan sources. Especially a possible utilisation or rather the corresponding process development requires appropriate analytics first. Thus, this paper aims to illuminate the basics of fructan quantification in stillage and the corresponding challenges particularly arising with widely used HPLC-RID systems. On this basis, a new approach for fructan quantification is presented based on such HPLC-RID systems allowing for a reliable and especially simple fructan determination in bioethanol stillage for comparably high sample throughput. The developed method performs fructan quantification by determination of fructose and glucose equivalents after a targeted acidic hydrolysis adapted to the respective sample matrix. By means of two different stationary phases, the problem of limited resolution in case of HPLC-RID is overcome and thus measurement errors are reduced. The approach towards the adapted analytical method can be transferred easily to comparable complex sample matrices.

Automation of On-Resin Enrichment of S-Nitrosylated Proteins for Oxidized Cysteine-Selective cPILOT

S-Nitrosylation (SNO) is a cysteine post-translational modification that increases with normal aging and is present in Alzheimer’s disease and other aging-related illnesses. Detection of SNO-modified proteins can be challenging; however, we previously developed a robust quantitative proteomics approach termed “Oxidized Cysteine-Selective combined precursor isobaric labeling and isobaric tagging (OxcyscPILOT)” that allows for detection of endogenous SNO-modified proteins. OxcyscPILOT involves enrichment of SNO-modified proteins using a thiol-based resin. This enrichment is performed manually, and wash stages with the resin require numerous steps and buffer reagents. The goal of this study is to transfer the manual protocol to an automated liquid handler system in order to reduce wash steps, increase sample throughput, and minimize experimental error. In order to accomplish this, we evaluated the Biomek i7 liquid handler automated workstation and a Positive Pressure ALP (PPA) apparatus as a means to conduct automated on resin enrichment. Our findings provide starting pressure conditions for the use of PPA in an automated OxcyscPILOT proteomics workflow that could be transferred to other robotic liquid handling systems.

Large field of view-spatially resolved transcriptomics at nanoscale resolution

ABSTRACTHigh-throughput profiling of in situ gene expression represents a major advance towards the systematic understanding of tissue complexity. Applied with enough capture area and high sample throughput it will help to define the spatio-temporal dynamics of gene expression in tissues and organisms. Yet, current technologies have considerable bottlenecks that limit widespread application. Here, we have combined DNA nanoball (DNB) patterned array chips and in situ RNA capture to develop Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing). This approach allows high sample throughput transcriptomic profiling of histological sections at unprecedented (nanoscale) resolution with areas expandable to centimeter scale, high sensitivity and homogenous capture rate. As proof of principle, we applied Stereo-seq to the adult mouse brain and sagittal sections of E11.5 and E16.5 mouse embryos. Thanks to its unique features and amenability to additional modifications, Stereo-seq can pave the way for the systematic spatially resolved-omics characterization of tissues and organisms.

Systematic Development of a Simultaneous Determination of Plastic Particle Identity and Adsorbed Organic Compounds by Thermodesorption–Pyrolysis GC/MS (TD-Pyr-GC/MS)

Micro-, submicro- and nanoplastic particles are increasingly regarded as vectors for trace organic chemicals. In order to determine adsorbed trace organic chemicals on polymers, it has usually been necessary to carry out complex extraction steps. With the help of a newly designed thermal desorption pyrolysis gas chromatography mass spectrometry (TD-Pyr-GC/MS) method, it is possible to identify adsorbed trace organic chemicals on micro-, submicro- and nanoparticles as well as the particle short chain polymers in one analytical setup without any transfers. This ensures a high sample throughput for the qualitative analysis of trace substances and polymer type. Since the measuring time per sample is only 2 h, a high sample throughput is possible. It is one of the few analytical methods which can be used also for the investigation of nanoplastic particles. Initially adsorbed substances are desorbed from the particle by thermal desorption (TD); subsequently, the polymer is fragmented by pyrolysis (PYR). Both particle treatment techniques are directly coupled with the same GC-MS system analyzing desorbed molecules and pyrolysis products, respectively. In this study, we developed a systematic and optimized method for this application. For method development, the trace organic chemicals phenanthrene, α-cypermethrin and triclosan were tested on reference polymers polystyrene (PS), polymethyl methacrylate (PMMA) and polyethylene (PE). Well-defined particle fractions were used, including polystyrene (sub)micro- (41 and 40 µm) and nanoparticles (78 nm) as well as 48-µm sized PE and PMMA particles, respectively. The sorption of phenanthrene (PMMA << PS 40 µm < 41 µm < PE < PS 78 nm) and α-cypermethrin (PS 41 µm < PS 40 µm < PE < PMMA < PS 78 nm) to the particles was strongly polymer-dependent. Triclosan adsorbed only on PE and on the nanoparticles of PS (PE < PS78).

Developing multiplex ddPCR assays for SARS-CoV-2 detection based on probe mix and amplitude based multiplexing

Multiplexing has been highlighted to save on costs, increase sample throughput, and maximize on the number of targets that can be sensitively detected within a small sample. With the ongoing SARS-CoV-2 pandemic, different articles have been published highlighting the superiority of droplet digital PCR (ddPCR) over the gold reverse transcription PCR (RT-PCR) in SARS-CoV-2 detection. However, few studies have been reported on developing multiplex ddPCR assays for SARS-CoV-2 detection and their performance. In this study, we developed simplex (1 target), duplex (2 targets), triplex probe mix (3 targets), and fourplex (4 targets) assays based on a two color ddPCR system for SARS-CoV-2 detection. Results showed that the fourplex assay had the similar limits of detection and accuracy to the lower multiplex assays. Analyzing 94 clinical isolates demonstrated that the ddPCR triplex probe mix assay had better sensitivity than the RT-qPCR assay. Additionally, the ddPCR multiplex assay showed that remdesivir could inhibit the growth of SARS-CoV-2 in vitro while another testing drug couldn’t. Conclusively, our research shows that developing multiplex ddPCR assays is possible by combing probe mix and amplitude based multiplexing, which will help in developing multiplexed ddPCR assays for different SARS-CoV-2 applications.

An inexpensive semi-automated sample processing pipeline for cell-free RNA

Despite advances in automated liquid handling and microfluidics, preparing samples for RNA sequencing at scale generally requires expensive equipment, which is beyond the reach of many academic labs. Manual sample preparation remains a slow, expensive, and error-prone process. Here, we describe a low-cost, semi-automated pipeline to extract cell-free RNA (cfRNA) that increases sample throughput by 12-fold while reducing time spent and cost by nearly 11-fold and 3-fold respectively. This pipeline is generalizable for many nucleic acid extraction applications, thereby increasing the scale of studies, which can be performed in small research labs.