Automated Specimen Preparation Research Articles

Creating Efficient Workflows for Electron Microscopy Laboratories with Automated Specimen Preparation

Abstract Electron microscopy (EM) is essential to the biological and biomedical sciences and clinical diagnostic pathology. Electron microscopy specimen preparation is laborious and time-consuming, with transmission EM (TEM) chemical preparation typically requiring 1–3 days, while volume electron microscopy (vEM) takes 3–5 days of tedious manual reagent exchanges every few minutes or hours. This places a considerable burden on laboratory scientists with the ongoing demand for TEM, and the rapidly growing demand for vEM due to its potential to revolutionize structural biology, connectomics, and related fields. This burden is exacerbated by a shortage of trained electron microscopy scientists as current staff retire, and few enter the workforce. This report provides four case studies to illustrate how automated and faster specimen preparation workflows using mPrep™ Automated Specimen Processors (ASP-1000™ and ASP-2000™, Microscopy Innovations, LLC) free electron microscopy staff in academic and pre-clinical research labs and a clinical pathology laboratory.

Comparative Evaluation of the Performance of the Abbott Real-Time Human Immunodeficiency Virus Type 1 (HIV-1) Assay for Measurement of HIV-1 Plasma Viral Load following Automated Specimen Preparation

The performance of the new Abbott real-time human immunodeficiency virus type 1 (HIV-1) assay for HIV-1 RNA load determination in plasma was compared to that of the Abbott LCx HIV-1 RNA quantitative assay following automated RNA isolation by the Abbott m1000 extractor. The measured viral loads of 89 clinical specimens differed by mean 0.19 log10 copies/ml (95% confidence interval, 0.12 to 0.26 log10 copies/ml). Although the difference in viral load determinations was positively skewed in favor of the LCx assay, it did not reach statistical significance (P = 0.42). Results were linearly associated (R2 = 0.94) and strongly correlated (R = 0.96). Good performance was observed with HIV-1 subtypes other than B and circulating recombinant forms, although results obtained with two subtype G specimens and one H specimen showed a more substantial difference.

Comparative evaluation of the Cobas Amplicor HIV-1 Monitor™ Ultrasensitive Test, the new Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor™ Ultrasensitive Test and the Versant HIV RNA 3.0 assays for quantitation of HIV-1 RNA in plasma samples

There are several commercially available assays for the quantitation of HIV RNA. A new automated specimen preparation system, the Cobas AmpliPrep, was developed to automate this last part of the PCR. We compared the results obtained by the Roche Cobas Amplicor HIV-1 Monitor Ultrasensitive Test (MCA, manual sample preparation) with those by the Versant HIV-1 RNA 3.0 assay (bDNA). Secondly we compared the MCA with the new Cobas AmpliPrep/Cobas Amplicor HIV Monitor Ultrasensitive Test (CAP/CA, automated specimen preparation) by investigating clinical patient samples and a panel of HIV-1 non-B subtypes. Furthermore, we assessed the assay throughput and workflow (especially hands-on time) for all three assays. Seventy-two percent of the 140 investigated patient samples gave concordant results in the bDNA and MCA assays. The MCA values were regularly higher than the bDNA values. One sample was detected only by the MCA within the linear range of quantification. In contrast, 38 samples with results <50 copies/ml in the MCA showed in the bDNA results between 51 and 1644 copies/ml (mean value 74 copies/ml); 21 of these specimens were shown to have detectable HIV RNA < 50 copies/ml in the MCA assay. The overall agreement between the MCA and the CAP/CA was 94.3% (551/584). The quantification results showed significant correlation, although the CAP/CA generated values slightly lower than those generated by the manual procedure. We found that the CAP/CA produced comparable results with the MCA test in a panel of HIV-1 non-B subtypes. All three assays showed comparable results. The bDNA provides a high sample throughput without the need of full automation. The new CAP/CA provides reliable test results with no HIV-subtype specific influence and releases time for other works in the laboratory; thus it is suitable for routine diagnostic PCR.

High throughput screening of 16 million serologically negative blood donors for hepatitis B virus, hepatitis C virus and human immunodeficiency virus type-1 by nucleic acid amplification testing with specific and sensitive multiplex reagent in Japan

Nationwide nucleic acid amplification testing (NAT) for hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus type 1 (HIV-1) of blood donated voluntarily after serological screening was implemented on July 1st 1999 for transfusion and plasma fractionation by the Japanese Red Cross blood transfusion services. From February 1st 2000, HBV, HCV and HIV-1 NAT screening of pools of 50 negative serologically screened donated blood was started and the results were reported within 1 day after blood donation. Systems were established for rapid shipment, electronic communication, automated specimen preparation, pooling and automated amplification and detection. At present, NAT screening is carried out within 1 day after donation. This report describes the blood screening system by NAT and the results obtained from over 16 million blood samples using simultaneous screening for HBV, HCV and HIV-1 with multiplex reagent. Between February 1, 2000 and December 31, 2002, 16 012 175 serologically negative units were tested by NAT. 308 units with Hepatitis B virus DNA (HBV DNA) were detected. The sensitivity of 50 pool NAT screening with input volume of 0.2 ml is significantly higher than that of highly sensitive HBsAg testing. 46 cases with HCV RNA and six cases with HIV-1 RNA were detected. These cases were not detected by HCV antibody and HIV-1 antibody screening. The false positive rate was 0.18%. The NAT system was developed from serological screening test negative non-remunerated voluntary donations. We supply blood products to medical organizations after screening by NAT for HBV, HCV and HIV-1 for transfusion and source plasma for fractionation. This is the first automated integrated system for prevention of transfusion transmitted HBV, HCV and HIV-1 infections, by NAT screening.

Quantitative Assay of Hepatitis C Virus RNA Using an Automated Extraction System for Specific Capture with Probes and Paramagnetic Particle Separation

A commercially available automated specimen preparation instrument for specific probe capture and paramagnetic separation has been developed (AmpliCap/GT-12; Roche Molecular Systems). We evaluated assay performance of the AmpliCap/GT-12 in the quantitative assay for hepatitis C virus (HCV) RNA with the AMPLICOR HCV MONITOR Test (version 2.0). Assay linearity using serial dilutions from a serum panel was observed in the range of 500 to 850000 IU/ml, with a slightly compromised slope in the higher viral titers. The overall within-run and between-run reproducibility of the entire detection process for 3 and 5 log(10) (IU/ml) of HCV RNA in samples had a standard deviation of <0.2, which was comparable to a manual method based on organic extraction and isopropanol precipitation (Roche Molecular Systems). Comparison of the test results with those obtained by the manual method showed a good correlation (R(2) = 0.972, n = 86). Using heparin (3, 6.5, and 13 U/ml), dextran sulfate (0.1, 1, and 5 mM), hemoglobin (1.13, 2.25, and 4.5 g/liter), conjugated or unconjugated bilirubin (7.5, 15, and 30 mg/dl), and ATP (1.25, 2.5, and 5.0 mM) as known inhibitors, inhibition was only detected at a dextran sulfate concentration of 1 mM with the manual method but not with the AmpliCap/GT-12 extraction. In summary, the AmpliCap/GT-12 system was shown to permit a stable extraction process and accurate results for the quantitative assay of HCV RNA, successfully eliminating the inhibitory effect of dextran sulfate. This automated extraction system provides reliable and reproducible test results and saves labor; thus, it is suitable for routine diagnostic PCR.

Fully Automated Nucleic Acid Extraction: MagNA Pure LC

Kinetic PCR analysis by real-time monitoring of DNA amplification was first described 8 years ago (1). Recently, the LightCyclerTM instrument (Roche Molecular Biochemicals, Mannheim, Germany), which allows high-speed thermal cycling by use of air instead of thermal blocks and on-line real-time fluorescence monitoring, was introduced (2). Several reports have been published with regard to utilization of the LightCycler technology for detection of pathogens (3)(4)(5)(6)(7)(8)(9)(10)(11). Real-time PCR has greatly decreased the amount of hands-on time needed to generate and detect amplification products. Before amplification, pathogen-specific DNA or RNA must be extracted from the specimen. This procedure, also called sample preparation, remains the most labor-intensive and time-consuming part of widely automated molecular assays and may be considered the major weakness in most molecular assays today (12)(13). Therefore, a fully automated sample preparation system is urgently needed for the routine diagnostic laboratory. In this study, a fully automated specimen preparation instrument, the MagNA Pure LCTM (Roche) was evaluated. The new instrument was used for extraction of herpes simplex virus (HSV) DNA in combination with real-time PCR on the LightCycler instrument. In the first experiment, the interassay variation and the detection limit were tested. The Second European Union Concerted Action HSV Proficiency Panel, which consists of 12 vials with different concentrations of HSV type 1 (HSV-1), strain MacIntyre (American Type Culture Collection), HSV type 2 (HSV-2), strain MS (American Type Culture Collection), varicella-zoster virus, and negative samples, was used. Samples were analyzed three times on different days. Results were compared with a molecular assay, which consisted of an in-house DNA extraction protocol and real-time PCR. In the second experiment, intraassay variation of the new molecular assay was tested. Plasma was collected from a …

Automation of laboratory testing for infectious diseases using the polymerase chain reaction-- our past, our present, our future.

While it is an extremely powerful and versatile assay method, polymerase chain reaction (PCR) can be a labor-intensive process. Since the advent of commercial test kits from Roche and the semi-automated microwell Amplicor system, PCR has become an increasingly useful and widespread clinical tool. However, more widespread acceptance of molecular testing will depend upon automation that allows molecular assays to enter the routine clinical laboratory. The forces driving the need for automated PCR are the requirements for diagnosis and treatment of chronic viral diseases, economic pressures to develop more automated and less expensive test procedures similar to those in the clinical chemistry laboratories, and a shortage in many areas of qualified laboratory personnel trained in the types of manual procedures used in past decades. The automated Roche COBAS AMPLICOR system has automated the amplification and detection process. Specimen preparation remains the most labor-intensive part of the PCR testing process, accounting for the majority of the hands-on-time in most of the assays. A new automated specimen preparation system, the COBAS AmpliPrep, was evaluated. The system automatically releases the target nucleic acid, captures the target with specific oligonucleotide probes, which become attached to magnetic beads via a biotin-streptavidin binding reaction. Once attached to the beads, the target is purified and concentrated automatically. Results of 298 qualitative and 57 quantitative samples representing a wide range of virus concentrations analyzed after the COBAS AmpliPrep and manual specimen preparation methods, showed that there was no significant difference in qualitative or quantitative hepatitis C virus (HCV) assay performance, respectively. The AmpliPrep instrument decreased the time required to prepare serum or plasma samples for HCV PCR to under 1 min per sample. This was a decrease of 76% compared to the manual specimen preparation method. Systems that can analyze more samples with higher throughput and that can answer more questions about the nature of the microbes that we can presently only detect and quantitate will be needed in the future.

Microstructural Characterization of Automated Specimen Preparation for TEM Analysis

Automated specimen preparation for transmission electron microscopy has the obvious advantage of saving personnel time. While some people may perform labor intensive specimen preparation techniques quickly, automated specimen preparation performed in a timely and reproducible fashion can significantly improve the throughput of specimens in an industrial laboratory. The advent of focused ion beam workstations for the preparation of electron transparent membranes has revolutionized TEM specimen preparation. The FIB lift-out technique is a powerful specimen preparation method. However, there are instances where the “traditional” FIB method of specimen preparation may be more suitable. The traditional FIB method requires that specimens must be prepared so that the area of interest is as thin as possible (preferably less than 50 μm) prior to FIB milling. Automating the initial specimen preparation for brittle materials (e.g., Si wafers) may be performed using the combination of cleaving and sawing techniques as described below.

Automated specific capture of hepatitis C virus RNA with probes and paramagnetic particle separation.

We developed and evaluated a prototype automated specimen preparation instrument for the specific capture of hepatitis C virus (HCV) RNA with probes and magnetic bead-fluid separation. HCV RNA was isolated from serum by lysis of virus particles with a chaotropic agent, followed by hybridization of the RNA with biotinylated probes and capture of the hybridized RNA with streptavidin-coated paramagnetic particles. After washing of the hybrid-particle complexes to remove nonspecifically bound materials, the particles were resuspended in a specimen diluent and were then ready for amplification and detection with a fully automated PCR system (COBAS AMPLICOR; Roche Diagnostic Systems). The analytical sensitivity in the dilution series was 33 copies per ml or greater. Comparison of the test results with those obtained by a manual method based on organic extraction and precipitation of RNA (SepaGene RV-R; Sanko Junyaku Co., Ltd.) showed 93% (49 of 53 samples) sensitivity and 100% (12 of 12 samples) specificity. There was 94% overall agreement between results. When RNA was extracted by the manual method from serum containing 10(3) or 10(5) copies of HCV per ml in the presence of heparin, there was an inhibitory effect on detection of both HCV RNA and the internal control. In contrast, when RNA was extracted from the serum by the automated method, there was no inhibitory effect. This inhibitory effect of heparin on the manual method was also observed for a series of serum specimens from a hemodialysis patient, but the inhibitory effect was eliminated by the automated specimen preparation method. In summary, a fully automated RNA extraction system for PCR detection of HCV RNA by use of specific capture with probes and magnetic bead-fluid separation was shown to have performance similar to that of the conventional manual method. In addition, it successfully eliminated the inhibitory effect of the heparin in the serum and permitted the detection of HCV RNA in serum samples from a hemodialysis patient. The prototype automated RNA extraction system is suitable as a totally automated system, starting with RNA extraction to detection of HCV, if it was combined with the fully automated COBAS AMPLICOR PCR system.

An Automated Technique for the Analysis of Total Inorganic Iron by Atomic Absorption Spectroscopy

A fully automated method for the preparation of surface water specimens for total inorganic iron analysis by atomic absorption spectroscopy and a method for the aspiration of prepared specimens are described. The automated specimen preparation technique is compared with a standard method used for total iron analysis and is applied to iron, manganese, zinc, and copper. Standard Technicon AutoAnalyzer components and standard atomic absorption spectrophotometers were used. The automated specimen preparation technique will handle 60 samples per hour and is totally flexible as to sampling rates, sample ratios, added chemicals, and time for particulate settling.