Category: HIV-1 genotypic resistance testing using the Vela automated next-generation sequencing platform
Centrifuge-free dispersive liquid-liquid microextraction coupled with thin-film microextraction for the preconcentration of molinate in real samples by ion mobility spectrometry
Quantitative Evaluation of a Telerobotic System for Vascular Ultrasound Measurement on a Short Arm Human Centrifuge
- Artificial Gravity generated by Short Arm Human Centrifuges is a promising multi-system countermeasure for physiological deconditioning during long duration space flights. To allow a continuous assessment of cardiovascular hemodynamics during centrifugation, a telerobotic robotic system holding an ultrasound probe has been installed on a Short Arm Human Centrifuge.
- A feasibility study was conducted to define the use capabilities and limitations of such a novel method. The objective of this study is to estimate the reproducibility and precision of remotely controlled vascular ultrasound assessment under centrifugation by assessing peripheral vascular diameter and wall distension. Four repeated centrifugation runs of 5 min, with 2.4 g at feet level, were performed including a 15 min rest between each run for a group of eight healthy male volunteers. Vascular diameter and distention were assessed for the common carotid artery (CCA) and the femoral artery (FA) by ultrasound imaging using a 10 MHz linear array probe (Mylab1, Esaote).
- Ultrasound measurements were consecutively performed: a) by an expert user in hand-held mode in standing as well as supine position, b) using the telerobotic arm without centrifugation as baseline and c) using the telerobotic arm during centrifugation. Vascular responses were compared between baseline and under centrifugation. Inter-, intra-registration and group variability have been assessed for hand-held and remotely controlled examination.
- The results show that intra-registration variability, σ h , was always smaller than inter-registration variability, σ m, that is in turned smaller than the inter-subject variability σ g (σ h < σ m < σ g). Centrifugation caused no significant changes in CCA diameter but a lower carotid distension compared to manual and robotic ultrasound in supine position (p < 0.05). Femoral diameter was significantly decreased in hypergravity compared to robotic sonography without centrifugation.
- A good reproducibility and precision of the remotely controlled vascular ultrasound assessment under centrifugation could be demonstrated. In conclusion, arterial wall dynamics can be precisely assessed for the CCA and femoral artery during centrifugation using a telerobotic ultrasound measurement system. Potential improvements to further enhance reproducibility and safety of the system are discussed.
Assessment of bridge natural frequency as an indicator of scour using centrifuge modelling
Microliter ultrafast centrifuge platform for size-based particle and cell separation and extraction using novel omnidirectional spiral surface acoustic waves
Superhydrophobic paper in the development of disposable labware and lab-on-paper devices.
Contaminating levels of zinc found in commonly-used labware and buffers affect glycine receptor currents.
Labware additives identified to be selective monoamine oxidase-B inhibitors
- 3D printing, also known as additive manufacturing, is the computer-guided process of fabricating physical objects by depositing successive layers of material. It has transformed manufacturing across virtually every industry, bringing about incredible advances in research and medicine. The rapidly growing consumer market now includes convenient and affordable “desktop” 3D printers.
- These are being used in the laboratory to create custom 3D-printed equipment, and a growing community of designers are contributing open-source, cost-effective innovations that can be used by both professionals and enthusiasts. User stories from investigators at the National Institutes of Health and the biomedical research community demonstrate the power of 3D printing to save valuable time and funding.
- While adoption of 3D printing has been slow in the biosciences to date, the potential is vast. The market predicts that within several years, 3D printers could be commonplace within the home; with so many practical uses for 3D printing, we anticipate that the technology will also play an increasingly important role in the laboratory.
Additive manufactured customizable labware for biotechnological purposes
- Yet already developed in the 1980s, the rise of 3D printing technology did not start until the beginning of this millennium as important patents expired, which opened the technology to a whole new group of potential users. One of the first who used this manufacturing tool in biotechnology was Lücking et al. in 2012, demonstrating potential uses 1, 2. This study shows applications of custom-built 3D-printed parts for biotechnological experiments.
- It gives an overview about the objects’ computer-aided design (CAD) followed by its manufacturing process and basic studies on the used printing material in terms of biocompatibility and manageability. Using the stereolithographic (SLA) 3D-printing technology, a customizable shake flask lid was developed, which was successfully used to perform a bacterial fed-batch shake flask cultivation. The lid provides Luer connectors and tube adapters, allowing both sampling and feeding without interrupting the process. In addition, the digital blueprint the lid is based on, is designed for a modular use and can be modified to fit specific needs.
- All connectors can be changed and substituted in this CAD software-based file. Hence, the lid can be used for other applications, as well. The used printing material was tested for biocompatibility and showed no toxic effects neither on mammalian, nor on bacteria cells. Furthermore an SDS-PAGE-comb was drawn and printed and its usability evaluated to demonstrate the usefulness of 3D printing for everyday labware. The used manufacturing technique for the comb (multi jet printing, MJP) generates highly smooth surfaces, allowing this application.
Whatman FTA cards versus plasma specimens for the quantitation of HIV-1 RNA using two real-time PCR assays
- Dried blood spots (DBS) are frequently used in clinical testing for biosurveillance, infectious disease and confirmatory testing, and clinical trials, particularly for populations in remote areas. The HemaSpot-HF blood collection device (HS) provides an alternative format to the Whatman 903 cards (903) to simplify sample collection and processing. In this study, the performance of the HS was compared to that of the 903 using previously characterized clinical specimens and HIV seroconversion panels known to exhibit markers of early human immunodeficiency virus (HIV) infection.
- HS and 903 samples were prepared and tested by Bio-Rad GS HIV Combo Ag/Ab enzyme immunoassay (EIA), GS HIV-1/-2 Plus O EIA, GS HIV-1 Western blot, and HIV-1 Geenius assays. Both HS and 903 performed well for up to 6 months at room temperature, but a marked loss of Western blot and low titer antibody signals from early infection samples was observed in samples stored for 180 days at elevated (37 to 45°C) temperatures and high humidity (95%).
- HemaSpot samples placed in sealed bags with additional desiccant were protected from degradation and showed improved signal recovery relative to that of the 903. HS was easier to use than the 903 and showed higher sensitivity and reproducibility for early infection samples and improved stability.
Whatman Protein Saver Cards for Storage and Detection of Parasitic Enteropathogens.
Comparison of stool collection and storage on Whatman FTA Elute cards versus frozen stool for enteropathogen detection using the TaqMan Array Card PCR assay.
Detection of anti-hepatitis C virus and hepatitis C virus RNA in dried blood spot specimens using Whatman No. 1 filter paper.
HIV-1 genotypic resistance testing using the Vela automated next-generation sequencing platform

The feasibility of producing mitochondrial DNA (mtDNA) knowledge has expanded significantly with the introduction of next-generation sequencing (NGS), particularly in the technology of whole mtDNA genome (mitogenome) sequences. However, the evaluation of those knowledge has emerged as the best problem to implementation in forensics.
To deal with this want, a customized toolkit to be used in the CLC Genomics Workbench (QIAGEN, Hilden, Germany) was developed by means of a collaborative effort between the Armed Forces Medical Examiner System – Armed Forces DNA Identification Laboratory (AFMES-AFDIL) and QIAGEN Bioinformatics.
Versatile ion S5XL sequencer for focused subsequent technology sequencing of strong tumors in a scientific laboratory
The AFDIL-QIAGEN mtDNA Expert, or AQME, generates an editable mtDNA profile that employs forensic conventions and consists of the interpretation vary required for mtDNA knowledge reporting. AQME additionally integrates an mtDNA haplogroup estimate into the evaluation workflow, which gives the analyst with phylogenetic nomenclature steerage and a profile high quality verify with out the use of an exterior software.

Supplemental AQME outputs reminiscent of nucleotide-per-position metrics, configurable export information, and an audit path are produced to help the analyst throughout overview. AQME is utilized to straightforward CLC outputs and thus might be integrated into any mtDNA bioinformatics pipeline inside CLC no matter pattern sort, librarypreparation or NGS platform.
An analysis of AQME was carried out to exhibit its performance and reliability for the evaluation of mitogenome NGS knowledge. The research analyzed Illumina mitogenome knowledge from 21 samples (together with related controls) of various high quality and pattern preparations with the AQME toolkit.
A complete of 211 software edits had been routinely utilized to 130 of the 698 complete variants reported in an effort to stick to forensic nomenclature. Although further guide edits had been required for 3 samples, supplemental instruments reminiscent of mtDNA haplogroup estimation assisted in figuring out and guiding these essential modifications to the AQME-generated profile.
Along with profile technology, AQME reported correct haplogroups for 18 of the 19 samples analyzed. The single errant haplogroup project, though phylogenetically shut, recognized a bug that solely impacts partial mitogenome knowledge. Future changes to AQME’s haplogrouping software will deal with this bug in addition to improve the general scoring technique to raised refine and automate haplogroup assignments.
As NGS permits broader use of the mtDNA locus in forensics, the availability of AQME and different forensic-focused mtDNA evaluation instruments will ease the transition and additional help mitogenome evaluation inside routine casework. Toward this finish, the AFMES-AFDIL has utilized the AQME toolbox along with the CLC Genomics Workbench to efficiently validate and implement two NGS mitogenome strategies.
BACKGROUND
Next technology sequencing primarily based tumor tissue genotyping entails complicated workflow and a comparatively longer turnaround time. Semiconductor primarily based subsequent technology platforms assorted from low throughput Ion PGM to excessive throughput Ion Proton and Ion S5XL sequencer. In this research, we in contrast Ion PGM and Ion Proton, with a brand new Ion S5XL NGSsystem for workflow scalability, analytical sensitivity and specificity, turnaround time and sequencing efficiency in a scientific laboratory.
METHODS
Eighteen strong tumor samples constructive for numerous mutations as detected beforehand by Ion PGM and Ion Proton had been chosen for research. Libraries had been ready using DNA (vary10-40ng) from micro-dissected formalin-fixed, paraffin-embedded (FFPE) specimens using the Ion Ampliseq Library Kit 2.zero for complete most cancers (CCP), oncomine complete most cancers (OCP) and most cancers hotspot panel v2 (CHPv2) panel as per producer’s directions.
The CHPv2 had been sequenced using Ion PGM whereas CCP and OCP had been sequenced using Ion Proton respectively. All the three libraries had been additional sequenced individually (S540) or multiplexed (S530) using Ion S5XL. For S5XL, Ion chef was used to automate template preparation, enrichment of ion spheres and chip loading. Data evaluation was carried out using Torrent Suite 4.6 software program on board S5XL and Ion Reporter.
A restrict of detection and reproducibility research was carried out using serially diluted DLD1 cell line.RESULTSA complete of 241 variant calls (235 single nucleotide variants and 6 indels) anticipated in the studied cohort had been efficiently detected by S5XL with 100% and 97% concordance with Ion PGM and Proton, respectively. Sequencing run time was decreased from 4.5 to 2.5 hours with output vary of 3-5 GB (S530) and 8-9.3Gb (S540). Data evaluation time for the Ion S5XL is quicker 1 h (S520), 2.5 h (S530) and 5 h (S540) chip, respectively as in comparison with the Ion PGM (3.5-5 h) and Ion Proton (8h). A restrict detection of 5% allelic frequency was established together with excessive inter-run reproducibility.
CONCLUSION
SIon S5XL system simplified workflow in a scientific laboratory, was possible for operating smaller and bigger panels on the similar instrument, had a shorter turnaround time, and confirmed good concordance for variant calls with comparable sensitivity and reproducibility as the Ion PGM and Proton.