Capillary Electrophoresis with Interchangeable Cartridges for Versatile and Automated Analyses of Dried Blood Spot Samples.

A novel concept for highly versatile automated analyses of dried blood spot (DBS) samples by commercial capillary electrophoresis (CE) is presented. Two interchangeable CE cartridges with different fused-silica capillaries were used for the DBS elutions and the DBS eluate analyses, respectively. The application of one CE cartridge with a wide-bore capillary reduced DBS processing times to a minimum (1-2 min per sample) while fitting the other CE cartridge with a narrow-bore capillary served for highly efficient CE analyses. A comprehensive investigation of major variables affecting liquid handling in CE (capillary length, internal diameter, and temperature) was carried out with the aim of optimizing both procedures and enabling their maximum flexibility. The application of two CE cartridges also enabled the employment of CE detectors with different instrumental set-ups and/or principles as was demonstrated by the optical detection of nonsteroidal anti-inflammatory drugs (NSAIDs) and the conductivity detection of amino acids (AAs). The presented methods were optimized for the automated CE analyses of 36 DBS samples formed by a volumetric collection of 5 µL of capillary blood onto Whatman 903 discs and processed by direct in-vial elution using the CE instrument. The precision of liquid transfers for the automated DBS elutions was better than 0.9% and the precision of CE analyses did not exceed 5.1 and 12.3% for the determination of NSAIDs and AAs, respectively. Both methods were linear (R2 ≥ 0.996) over the therapeutic (NSAIDs) and the endogenous (AAs) concentration ranges, had limits of quantification below the typical analyte concentrations in human blood, and achieved sample throughputs of more than 6 DBSs per hour.

Autonomous capillary electrophoresis processing and analysis of dried blood spots for high-throughput determination of uric acid.

A new set-up for fully autonomous and high-throughput capillary electrophoresis (CE) analyses of dried blood spot (DBS) samples is presented. The DBS samples were prepared by collecting exactly 5 µL of capillary blood from a finger-prick onto a pre-punched DBS disc in a disposable plastic CE vial and by in-vial blood drying. The vials with the DBS samples were then loaded into a commercial CE instrument for a fully unmanned sample processing and analysis. A fused-silica capillary of the CE instrument was first used for the transfer of 100 µL of elution solvent to each vial, in-vial DBS elution, and in-vial eluate homogenization. The same capillary was also used for at-line injection, separation, and selective analysis of the resulting eluates. Novel CE sequences were tailor-programmed for consecutive processing and analyses of multiple DBSs, which facilitated a fully autonomous determination of uric acid with a throughput of 240 DBS samples per day (24 h). The presented analytical protocol (using 100 µm i. d./30 cm capillary; 30 mM 2-(N-morpholino)-ethanesulfonic acid, 30 mM l-histidine, and 30 µM cetyltrimethylammonium bromide background electrolyte solution; and UV detection at 292 nm) provided excellent precision at endogenous and spiked uric acid concentrations with RSD values of peak areas below 3.2%. Calibration curves were linear over the 33.3 - 1200 µM range (R2 better than 0.998), limits of detection and quantification in the original capillary blood were 10 and 33.3 µM, respectively, and were well below the uric acid clinical range (140-420 µM). The stability of uric acid in DBS samples stored at laboratory temperature for up to 2 months was also excellent demonstrating less than a 4.2% decrease in uric acid concentrations. The actual set-up might thus be highly attractive for clinical subjects and laboratories because it is minimally invasive and requires minimum intervention from laboratory staff.

Honeybee Iflaviruses Pack Specific tRNA Fragments from Host Cells in Their Virions.

The Picornavirales include viruses that infect vertebrates, insects, and plants. It was believed that they pack only their genomic mRNA in the particles; thus, we envisaged these viruses as excellent model systems for studies of mRNA modifications. We used LC-MS to analyze digested RNA isolated from particles of the sacbrood and deformed wing iflaviruses as well as of the echovirus 18 and rhinovirus 2 picornaviruses. Whereas in the picornavirus RNAs we detected only N6 -methyladenosine and 2'-O-methylated nucleosides, the iflavirus RNAs contained a wide range of methylated nucleosides, such as 1-methyladenosine (m1 A) and 5-methylcytidine (m5 C). Mapping of m1 A and m5 C through RNA sequencing of the SBV and DWV RNAs revealed the presence of tRNA molecules. Both modifications were detected only in tRNA. Further analysis revealed that tRNAs are present in form of 3' and 5' fragments and they are packed selectively. Moreover, these tRNAs are typically packed by other viruses.

LC/MS analysis and deep sequencing reveal the accurate RNA composition in the HIV-1 virion.

The mechanism of action of various viruses has been the primary focus of many studies. Yet, the data on RNA modifications in any type of virus are scarce. Methods for the sensitive analysis of RNA modifications have been developed only recently and they have not been applied to viruses. In particular, the RNA composition of HIV-1 virions has never been determined with sufficiently exact methods. Here, we reveal that the RNA of HIV-1 virions contains surprisingly high amount of the 1-methyladenosine. We are the first to use a liquid chromatography-mass spectrometry analysis (LC/MS) of virion RNA, which we combined with m1A profiling and deep sequencing. We found that m1A was present in the tRNA, but not in the genomic HIV-1 RNA and the abundant 7SL RNA. We were able to calculate that an HIV-1 virion contains per 2 copies of genomic RNA and 14 copies of 7SL RNA also 770 copies of tRNA, which is approximately 10 times more than thus far expected. These new insights into the composition of the HIV-1 virion can help in future studies to identify the role of nonprimer tRNAs in retroviruses. Moreover, we present a promising new tool for studying the compositions of virions.

AmtDB: a database of ancient human mitochondrial genomes.

Ancient mitochondrial DNA is used for tracing human past demographic events due to its population-level variability. The number of published ancient mitochondrial genomes has increased in recent years, alongside with the development of high-throughput sequencing and capture enrichment methods. Here, we present AmtDB, the first database of ancient human mitochondrial genomes. Release version contains 1107 hand-curated ancient samples, freely accessible for download, together with the individual descriptors, including geographic location, radiocarbon dating, and archaeological culture affiliation. The database also features an interactive map for sample location visualization. AmtDB is a key platform for ancient population genetic studies and is available at https://amtdb.org.