High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers

Aptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. 'High-throughput sequencing fluorescent ligand interaction profiling' (HiTS-FLIP) significantly increases the selection efficiency and is consequently a very powerful and versatile technology for the selection of high-performance aptamers. It is the first experiment to allow the direct and quantitative measurement of the affinity and specificity of millions of aptamers simultaneously by harnessing the potential of optical next-generation sequencing platforms to perform fluorescence-based binding assays on the clusters displayed on the flow cells and determining their sequence and position in regular high-throughput sequencing. Many variants of the experiment have been developed that allow automation and in situ conversion of DNA clusters into base-modified DNA, RNA, peptides, and even proteins. In addition, the information from mutational assays, performed with HiTS-FLIP, provides deep insights into the relationship between the sequence, structure, and function of aptamers. This enables a detailed understanding of the sequence-specific rules that determine affinity, and thus, supports the evolution of aptamers. Current variants of the HiTS-FLIP experiment and its application in the field of aptamer selection, characterisation, and optimisation are presented in this review.

GMP compliant isolation of mucosal epithelial cells and fibroblasts from biopsy samples for clinical tissue engineering

Engineered epithelial cell sheets for clinical replacement of non-functional upper aerodigestive tract mucosa are regulated as medicinal products and should be manufactured to the standards of good manufacturing practice (GMP). The current gold standard for growth of epithelial cells for research utilises growth arrested murine 3T3 J2 feeder layers, which are not available for use as a GMP compliant raw material. Using porcine mucosal tissue, we demonstrate a new method for obtaining and growing non-keratinised squamous epithelial cells and fibroblast cells from a single biopsy, replacing the 3T3 J2 with a growth arrested primary fibroblast feeder layer and using pooled Human Platelet lysate (HPL) as the media serum supplement to replace foetal bovine serum (FBS). The initial isolation of the cells was semi-automated using an Octodissociator and the resultant cell suspension cryopreservation for future use. When compared to the gold standard of 3T3 J2 and FBS containing medium there was no reduction in growth, viability, stem cell population or ability to differentiate to mature epithelial cells. Furthermore, this method was replicated with Human buccal tissue, providing cells of sufficient quality and number to create a tissue engineered sheet.

Analytical Performance Evaluation of Automated Coagulation Analyzer CP3000 for Routine and Special Coagulation Assays

CP3000 coagulation analyzer is a high-throughput, fully automated coagulation analyzer. The objective of this study was to evaluate the analytical performance of CP3000 coagulation system for general and special coagulation analyses. Quality control materials and patient samples were used to evaluate the analytical performance of CP3000 coagulation system. Precision, carryover, linearity, comparability with ACL-TOP 700 coagulation system, and verification of reference range were evaluated or performed according to Clinical and Laboratory Standards Institute guidelines. Within-run and between-run precisions were below 5% for both normal and abnormal ranges. There was no detectable carryover. The linearity of antithrombin and fibrinogen were excellent. The comparability between CP3000 and ACL-TOP 700 coagulation systems was acceptable except for activated partial thromboplastin time and thrombin time due to differences in reagent composition. Reference ranges proposed by the manufacturer were verified to be acceptable. CP3000 coagulation system is a reliable system that can be used to perform routine and special coagulation tests rapidly and accurately. Because of its small footprint as an additional advantage, the implementation of CP3000 coagulation system can be efficient in hospital laboratories of various sizes.

Hemoglobin point-of-care testing in rural Gambia: Comparing accuracy of HemoCue and Aptus with an automated hematology analyzer

Background

Anemia is one of the most impactful nutrient deficiencies in the world and disproportionately affects children in low-resource settings. Point-of-care devices (PoCDs) measuring blood hemoglobin (Hb) are widely used in such settings to screen for anemia due to their low cost, speed, and convenience. Here we present the first iteration of Aptus, a new PoCD which measures Hb and hematocrit (HCT).

Aim

To evaluate the accuracy of Aptus and HemoCue® Hb 301 against an automated hematology analyzer (Medonic®) in Gambian children aged 6–35 months and the Aptus’ usage in the field.

Methods

Aptus, HemoCue® and Medonic® were compared using venous blood (n = 180), and Aptus and HemoCue® additionally using capillary blood (n = 506). Agreement was estimated using Bland-Altman analysis and Lin’s concordance. Usage was assessed by error occurrence and user experience.

Results

Mean Hb values in venous blood did not significantly differ between Aptus and HemoCue® (10.44±1.05 vs 10.56±0.93g/dl, p>0.05), but both measured higher Hb concentrations than Medonic® (9.75±0.99g/dl, p<0.0001). Lin’s coefficient between Aptus and Medonic® was r_c = 0.548, between HemoCue® and Medonic® r_c = 0.636. Mean bias between the PoCDs venous measurements was -0.11g/dl with limits of agreement (LoA) -1.63 and 1.40g/dl. The bias was larger for the comparisons between the Medonic® and both Aptus (0.69g/dl, LoA 0.92 and 2.31g/dl) and HemoCue® (0.81g/dl, LoA 0.17 and 1.78g/dl). ROC curves showed an AUC of 0.933 in HemoCue® and 0.799 in Aptus. Capillary Hb was higher with Aptus than HemoCue® (10.33±1.11g/dl vs 10.01±1.07g/dl, p<0.0001). Mean bias was 0.32g/dl with LoA of -1.91 and 2.54g/dl. Aptus‘ usage proved intuitive, yet time-to-results and cuvettes could be improved.

Conclusion

Both PoCDs showed a relatively limited bias but large LoA. Aptus and HemoCue® showed similar accuracy, while both overestimated Hb levels. Aptus showed promise, with its operation unimpaired by field conditions as well as being able to show HCT values.

A machine-vision approach for automated pain measurement at millisecond timescales

Objective and automatic measurement of pain in mice remains a barrier for discovery in neuroscience. Here, we capture paw kinematics during pain behavior in mice with high-speed videography and automated paw tracking with machine and deep learning approaches. Our statistical software platform, PAWS (Pain Assessment at Withdrawal Speeds), uses a univariate projection of paw position over time to automatically quantify seven behavioral features that are combined into a single, univariate pain score. Automated paw tracking combined with PAWS reveals a behaviorally divergent mouse strain that displays hypersensitivity to mechanical stimuli. To demonstrate the efficacy of PAWS for detecting spinally versus centrally mediated behavioral responses, we chemogenetically activated nociceptive neurons in the amygdala, which further separated the pain-related behavioral features and the resulting pain score. Taken together, this automated pain quantification approach will increase objectivity in collecting rigorous behavioral data, and it is compatible with other neural circuit dissection tools for determining the mouse pain state.

High-throughput in situ experimental phasing

In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom solutions, using a Labcyte Inc. Echo 550 Liquid Handler, in a highly controlled and optimized fashion in order to generate derivatized and isomorphous crystals. Partial data sets obtained on MX beamlines using an in situ setup for data collection are processed with the aim of producing good-quality anomalous signal leading to successful experimental phasing.

Experimental setup and image processing method for automatic enumeration of bacterial colonies on agar plates

Automated colony counting methods have long been known in Microbiology. Numerous methods for automated image analysis have been described and a wide range of commercial products exists. Known advantages are saving cost by reducing enumeration time, automatic documentation, reproducibility, and operator independence. Still, even today the realization of all advantages of automated image analysis makes it necessary to either invest in an expensive, high performance commercial system, or to acquire expert knowledge in image processing. This is a considerable obstacle for many laboratories, and the reason why manual colony counting is still done frequently. This article describes an easy to apply automatic colony counting system–including suggestions for sample preparation–that can be put into operation with basic knowledge of image processing and low budget.

Interferents of Automated Reticulocyte Analysis Integrated with Relevant Clinical Cases

BACKGROUND

Reticulocyte count (RET) has been used for many years to estimate the erythropoietic activity of the bone marrow. Fully automated methods not only provide enhanced precision and accuracy, but also enable reliable measurements of mRNA content and cellular indices. However, problems still exist, such as interference. The aim of the present study was to investigate the interferents of Sysmex XN 9000 reticulocyte analysis and ensure the accuracy of the results.

METHODS

We collected a total of 510 specimens from normal control patients and patients with various diseases including anemias, leukemias, infectious diseases, immune diseases, kidney disease, etc. Correlation of the agreement for reticulocytes between the new methylene blue (NMB) visual microscopy method and automated reticulocyte counting was evaluated by paired sample method according to the CLSI-ICSH document H44-A2-Methods for Reticulocyte Count. Blood smear microscopic examination was carried out on the disturbed samples, and the interferents were analyzed with the medical history, flagging algorithms, the warning information, and the microscopic examination.

RESULTS

A total of 44 (8.6%) cases exhibited interference. The main interferents of spuriously high reticulocyte count were caused by parasites, such as malaria, as well as suspicious autofluorescence due to drugs, while the main interferents of spuriously low reticulocyte count were caused by RBC fragments.

CONCLUSIONS

Detection of potential interferences may be accomplished through alarm information and flagging algorithms incorporated into the instrument and by examination of a blood film to ensure absence of relevant interferences.

Protocol development for discovery of angiogenesis inhibitors via automated methods using zebrafish

Their optical clarity as larvae and embryos, small size, and high fecundity make zebrafish ideal for whole animal high throughput screening. A high-throughput drug discovery platform (HTP) has been built to perform fully automated screens of compound libraries with zebrafish embryos. A Tg(kdrl:EGFP) line, marking endothelial cell cytoplasm, was used in this work to help develop protocols and functional algorithms for the system, with the intent of screening for angiogenesis inhibitors. Indirubin 3’ Monoxime (I3M), a known angiogenesis inhibitor, was used at various concentrations to validate the protocols. Consistent with previous studies, a dose dependant inhibitory effect of I3M on angiogenesis was confirmed. The methods and protocols developed here could significantly increase the throughput of drug screens, while limiting human errors. These methods are expected to facilitate the discovery of novel anti-angiogenesis compounds and can be adapted for many other applications in which samples have a good fluorescent signal.

Evaluation of Bio-Rad® discs for antimicrobial susceptibility testing by disc diffusion and the ADAGIO™ system for the automatic reading and interpretation of results

The disc diffusion test is used for antimicrobial susceptibility testing worldwide. In this study, the performance of both Bio-Rad® antibiotic discs (as compared with Oxoid® discs) and the ADAGIO™ automated system for the reading of disc diffusion test results was evaluated with American Type Culture Collection (ATCC) quality control (QC) and wild strains of bacteria. Inhibition zones of both disc brands were read manually and through use of the ADAGIO™ system. Categorized interpretation of the results for each strain and antibiotic combination was summarized according to the Clinical Laboratory Standards Institute MS-100 (2017 update) manual and ADAGIO™ readings. Eight ATCC QC strains and 120 different wild strains were evaluated, to give a total of 1226 antibiotic/bacteria combinations and 2486 manual readings. One major error and four minor errors (0.08% and 0.34%, respectively) were detected via manual readings of the Bio-Rad® discs as compared with the Oxoid® discs. For the same number of antibiotic/bacteria combinations, five minor errors and one major error (0.42% and 0.08%, respectively) were detected with the Bio-Rad® discs read by the ADAGIO™ system. In addition, the number of times the automatic reading needed manual edition with Bio-Rad® discs was statistically lower than it did with Oxoid® discs (3.7% vs. 5.7%, p < 0.05). These findings support the hypothesis that Bio-Rad discs are not inferior to Oxoid® discs, and the performance of the ADAGIO™ system is comparable to that of manual readings with both disc brands.

A Clinical Trial to Verify the Efficiency of the LC-1000 Exfoliative Cell Analyzer as a New Method of Cervical Cancer Screening

OBJECTIVE

The exfoliative cell analyzer, LC-1000 (Sysmex Corporation, Japan), is a medical device that presents the cell proliferation index and 23 research parameters as indicators of cellular proliferative potential. The objective was to evaluate the clinical usability of qualitative assessment by LC-1000 compared with cytology, the human papillomavirus (HPV) test, and histology as gold standard.

STUDY DESIGN

Women that visited 3 sites between July 2015 and March 2017 were registered. The primary endpoint in this study was the comparison between LC-1000 measurement and HPV test for sensitivity and specificity for cervical intraepithelial neoplasia 2+ (CIN2+). A tree model algorithm was newly constructed by a statistical method and its relationship with histological results was evaluated.

RESULTS

The sensitivity and specificity of LC-1000 were 78.3 and 74.1%, while those of the HPV test were 94.7 and 85.4%, respectively. A tree model comprising five categories was constructed. The proportion of advanced lesions was higher with the change in the rank classification results from 1 to 5. The positive predictive values of CIN2+ in the categories 4 and 5 were high. Despite the small number of subjects, cancer was undetected in categories 1 and 2. In addition, the comparison with follow-up results in 19 women assessed as CIN1 showed that the rate of progression in the categories 3-5 was 50% (7/14); progression in the categories 1 and 2 was 0% (0/5).

CONCLUSIONS

LC-1000 may be useful for cervical cancer screening as an index to qualitatively evaluate CIN and cancer based on the changes in characteristics of cells.

DIY Automated Feeding and Motion Recording System for the Analysis of Fish Behavior

Fish species such as medaka or zebrafish are widely used as animal models to study physiology, disease development, and treatment efficacy. They are also used to study the rapidly growing field of behavior research, such as social interactions, anxiety, and the influence of environmental factors. Here we describe an automated experimental setup allowing the recording of general locomotor activity in combination with a food-on-demand system. It can simply be built with some basic electronic knowledge. Our setup enables the recording of locomotor and feeding activity of several fish for long-term studies, excluding disturbing external influences. A description of the automated recording system is given, as well as examples of recordings to illustrate its applicability for the study of fish behavior. The construction manual and operation instructions can be downloaded for free.

Integrated routine workflow using next-generation sequencing and a fully-automated platform for the detection of KRAS, NRAS and BRAF mutations in formalin-fixed paraffin embedded samples with poor DNA quality in patients with colorectal carcinoma

Background

KRAS and NRAS mutations are identified resistance mutations to anti-epidermal growth factor receptor monoclonal antibodies in patients with metastatic colorectal cancer. BRAF status is also routinely assessed for its poor prognosis value. In our institute, next-generation sequencing (NGS) is routinely used for gene-panel mutations detection including KRAS, NRAS and BRAF, but DNA quality is sometimes not sufficient for sequencing. In our routine practice, Idylla platform is used for the analysis of samples that don’t reach sufficient quality criteria for NGS assay.

Methods

In this study, data from mCRC samples analyzed from May 2017 to 2018 were retrospectively collected. All samples with a poor DNA quality for sequencing have been assessed using Idylla platform. First, KRAS Idylla assay cartridge has been used for the determination of KRAS mutational status. All KRAS wild-type samples have then been analyzed using NRAS-BRAF assay. Among 669 samples, 67 samples failed the DNA quality control and have been assessed on Idylla KRAS mutation test.

Results

Among 67 samples, 50 (75%) samples had a valid result with Idylla KRAS mutation test including 22 carrying a KRAS mutation. For 28 samples, NRAS and BRAF mutational statuses have been assessed using Idylla NRAS-BRAF mutation test. Among 28 samples, 27 (96%) had a valid result including 2 samples bearing a NRAS mutation and 3 samples bearing a BRAF mutation.

Conclusions

Our study shows that an integrated workflow using NGS and Idylla platform allows the determination of KRAS, NRAS and BRAF mutational statuses of 651/669 (97.3%) samples and retrieve 49/67 (73.1%)samples that don’t reach DNA quality requirements for NGS.

Automated in vitro evolution of a translation-coupled RNA replication system in a droplet flow reactor

Automation is a useful strategy to make laborious evolutionary experiments faster and easier. To date, several types of continuous flow reactors have been developed for the automated evolutionary experiments of viruses and bacteria. However, the development of a flow reactor applicable to compartmentalized in vitro self-replication systems is still a challenge. In this study, we demonstrate automated in vitro evolution of a translation-coupled RNA system in a droplet flow reactor for the first time. This reactor contains approximately 1010 micro-scale droplets (average diameter is approximately 0.8 μm), which continuously fuse and divide among each other at a controllable rate. In the droplets, an RNA (artificial genomic RNA) replicate through the translation of self-encoded RNA replicase with spontaneously appearing parasitic RNA. We performed two automated replication experiments for more than 400 hours with different mixing intensities. We found that several mutations displayed increased frequencies in the genomic RNA populations and the dominant RNA mutants acquired the ability to replicate faster or acquired resistance to the parasitic RNA, demonstrating that Darwinian evolution occurred during the long-term replication. The droplet flow reactor we developed can be a useful tool to perform in vitro evolutionary experiments of translation-coupled systems.

Interchangeability of Procalcitonin Measurements Using the Point of Care Testing i-CHROMATM Reader and the Automated Liaison XL

BACKGROUND

Our aim was to verify if procalcitonin (PCT) measurements using the new point-of-care testing i-CHROMATM are interchangeable with those of Liaison XL.

METHODS

One hundred seventeen serum samples were processed sequentially on a Liaison XL and i-CHROMATM. Statistical analysis was done using the Passing-Bablok regression, Bland-Altman test, and Cohen's Kappa statistic.

RESULTS

Proportional and constant differences were observed between i-CHROMATM and Liaison XL. The 95% CI of the mean bias% was very large, exceeding the maximum allowable TE% and the clinical reference change value. However, the concordance between methods at the clinical relevant cutoffs was strong, with the exception of the 0.25 ng/mL cutoff which was moderate.

CONCLUSIONS

Our data suggest that i-CHROMATM is not interchangeable with Liaison XL. However, while the strong concordance at the clinical relevant cutoffs allows us to consider i-CHROMATM a suitable option to Liaison XL to support clinicians' decision-making; nevertheless, the moderate agreement at the 0.25 ng/mL cutoff recommends caution in interpreting the data around this cutoff.

Fully automated, on-site isolation of cfDNA from whole blood for cancer therapy monitoring

The potential utility of circulating tumour DNA (ctDNA) in patient blood for cancer diagnostics and real-time monitoring of disease progression is highly recognized. However, the lack of automated and efficient methods for cell-free DNA (cfDNA) isolation from peripheral blood has remained a challenge for broader acceptance of liquid biopsy in general clinical settings. Here, we demonstrate a lab-on-a-disc system equipped with newly developed, electromagnetically actuated, and reversible diaphragm valves that allows fully automated and rapid (<30 min) isolation of cfDNA from whole blood (>3 ml) to achieve high detection sensitivity by minimizing the degradation of fragile ctDNA as well as contamination of wild-type DNA from abundant blood cells. As a proof of concept study, we used the lab-on-a-disc to isolate cfDNA from patients with non-small cell lung cancer and successfully detected epidermal growth factor receptor gene mutations (L858R, T790M) during targeted drug therapy. The proposed lab-on-a-disc enables a fully automated, rapid, and point-of-care cfDNA enrichment starting from whole blood to facilitate the wide use of liquid biopsy in routine clinical practice.

Novel flowcytometry-based approach of malignant cell detection in body fluids using an automated hematology analyzer

Morphological microscopic examinations of nucleated cells in body fluid (BF) samples are performed to screen malignancy. However, the morphological differentiation is time-consuming and labor-intensive. This study aimed to develop a new flowcytometry-based gating analysis mode “XN-BF gating algorithm” to detect malignant cells using an automated hematology analyzer, Sysmex XN-1000. XN-BF mode was equipped with WDF white blood cell (WBC) differential channel. We added two algorithms to the WDF channel: Rule 1 detects larger and clumped cell signals compared to the leukocytes, targeting the clustered malignant cells; Rule 2 detects middle sized mononuclear cells containing less granules than neutrophils with similar fluorescence signal to monocytes, targeting hematological malignant cells and solid tumor cells. BF samples that meet, at least, one rule were detected as malignant. To evaluate this novel gating algorithm, 92 various BF samples were collected. Manual microscopic differentiation with the May-Grunwald Giemsa stain and WBC count with hemocytometer were also performed. The performance of these three methods were evaluated by comparing with the cytological diagnosis. The XN-BF gating algorithm achieved sensitivity of 63.0% and specificity of 87.8% with 68.0% for positive predictive value and 85.1% for negative predictive value in detecting malignant-cell positive samples. Manual microscopic WBC differentiation and WBC count demonstrated 70.4% and 66.7% of sensitivities, and 96.9% and 92.3% of specificities, respectively. The XN-BF gating algorithm can be a feasible tool in hematology laboratories for prompt screening of malignant cells in various BF samples.

Rapid direct detection of carbapenemase-producing Enterobacteriaceae in clinical urine samples by MALDI-TOF MS analysis

Objectives

Development of an automated MALDI-TOF MS-based method for the rapid, direct detection of carbapenemase-producing Enterobacteriaceae in clinical urine samples within 90 min of sample reception.

Methods

A total of 3041 urine samples were processed by flow cytometry, and a cut-off value of ≥1.5 × 10 5 bacteria/mL was used to select samples for the study. Following these criteria, 608 samples were selected for direct bacterial identification. Detection of carbapenemase activity by MALDI-TOF MS analysis was only performed after reliable direct identification of Gram-negative bacilli. A novel protocol was developed for extracting bacteria from urine samples by using the Sepsityper Kit (Bruker Daltonik, Germany). Carbapenem resistance was detected with imipenem as an antibiotic marker and the results were automatically interpreted using the STAR-BL module of MALDI-TOF Biotyper Compass software (Bruker Daltonik, Germany).

Results

The MALDI-TOF MS-based assay yielded direct reliable identification of 91% (503/553) of the samples. The assay showed 100% sensitivity (30/30) and specificity (454/454) for detecting carbapenemase activity within 90 min of sample reception. Isolates included in the study were further characterized by PCR and sequencing, and bla OXA-48 was detected from all isolates that tested positive in the MALDI-TOF MS-based resistance assay.

Conclusions

The proposed protocol for the direct analysis of urine samples by MALDI-TOF MS is suitable for use in clinical laboratories to identify bacteria and detect carbapenemase activity, thus saving at least 24-48 h relative to current routine methods.

Making It All Work: Functional Genomics and Reporter Gene Assays

Functional genomics is the study of the function of genes on a genome-wide level. Reporter gene assays can be utilized in this context to dissect signaling cascades, find new drug targets, or decipher the function of gene expression. The genome-wide scale of these experiments necessitates a different approach toward science than traditional single hypothesis driven research. High-throughput experimentation requires large project teams, automation, and discrete validation of each step in the automation and assay process. The purpose of this chapter is to provide a general outline of a standard functional genomics project with a reporter gene assay as readout, give an overview of the methodologies employed and familiarize the reader with the subsequent data analysis. The advantages of such high throughput experimentation are speed, quantitative results, and insights into biology on a genome-wide scale all of which enable a more rapid progress of science.

Contamination with HIV antibody may be responsible for false positive results in specimens tested on automated platforms running HIV 4th generation assays in a region of high HIV prevalence

INTRODUCTION

In South Africa where the prevalence of HIV infection is very high, 4th generation HIV antibody/p24 antigen combo immunoassays are the tests of choice for laboratory based screening. Testing is usually performed in clinical pathology laboratories on automated analysers. To investigate the cause of false positive results on 4th generation HIV testing platforms in public sector laboratories, the performance of two automated platforms was compared in a clinical pathology setting, firstly on routine diagnostic specimens and secondly on known sero-negative samples.

METHODS

Firstly, 1181 routine diagnostic specimens were sequentially tested on Siemens and Roche automated 4th generation platforms. HIV viral load, western blot and follow up testing were used to determine the true status of inconclusive specimens. Subsequently, known HIV seronegative samples from a single donor were repeatedly tested on both platforms and an analyser was tested for surface contamination with HIV positive serum to identify how suspected specimen contamination could be occurring.

RESULTS

Serial testing of diagnostic specimens yielded 163 weakly positive or discordant results. Only 3 of 163 were conclusively shown to indicate true HIV infection. Specimen contamination with HIV antibody was suspected, based on the following evidence: the proportion of positive specimens increased on repeated passage through the analysers; viral loads were low or undetectable and western blots negative or indeterminate on problem specimens; screen negative, 2nd test positive specimens tested positive when reanalysed on the screening assay; follow up specimens (where available) were negative. Similarly, an increasing number of known negative specimens became (repeatedly) sero-positive on serial passage through one of the analysers. Internal and external analyser surfaces were contaminated with HIV serum, evidence that sample splashes occur during testing.

CONCLUSIONS

Due to the extreme sensitivity of these assays, contamination with minute amounts of HIV antibody can cause a negative sample to test positive. Better contamination control measures are needed on analysers used in clinical pathology environments, especially in regions where HIV sero-prevalence is high.

An automated and portable microfluidic chemiluminescence immunoassay for quantitative detection of biomarkers

Microfluidic platforms capable of automated, rapid, sensitive, and quantitative detection of biomarkers from patient samples could make a major impact on clinical or point-of-care (POC) diagnosis. In this work, we realize an automated diagnostic platform composed of two main components: (1) a disposable, self-contained, and integrated microfluidic chip and (2) a portable instrument that carries out completely automated operations. To demonstrate its potential for real-world application, we use injection molding for mass fabrication of the main components of disposable microfluidic chips. The assembled three-layered chip with on-chip mechanical valves for fluid control consists of (1) a top silicone fluidic layer with embedded zigzag microchannels, reagent reservoirs and a negative pressure port, (2) a middle tinfoil layer with patterned antibody/antigen stripes, and (3) a bottom silicone substrate layer with waste reservoirs. The versatility of the microfluidics-based system is demonstrated by implementation of a chemiluminescence immunoassay for quantitative detection of C-reactive protein (CRP) and testosterone in real clinical samples. This lab-on-a-chip platform with features of quantitation, portability and automation provides a promising strategy for POC diagnosis.

A versatile and low-cost open source pipetting robot for automation of toxicological and ecotoxicological bioassays

In the past decades, bioassays and whole-organism bioassay have become important tools not only in compliance testing of industrial chemicals and plant protection products, but also in the monitoring of environmental quality. With few exceptions, such test systems are discontinuous. They require exposure of the biological test material in small units, such as multiwell plates, during prolonged incubation periods, and do not allow online read-outs. It is mostly due to these shortcomings that applications in continuous monitoring of, e.g., drinking or surface water quality are largely missing. We propose the use of pipetting robots that can be used to automatically exchange samples in multiwell plates with fresh samples in a semi-static manner, as a potential solution to overcome these limitations. In this study, we developed a simple and low-cost, versatile pipetting robot constructed partly using open-source hardware that has a small footprint and can be used for online monitoring of water quality by means of an automated whole-organism bioassay. We tested its precision in automated 2-fold dilution series and used it for exposure of zebrafish embryos (Danio rerio)-a common model species in ecotoxicology-to cadmium chloride and permethrin. We found that, compared to conventional static or semi-static exposure scenarios, effects of the two chemicals in zebrafish embryos generally occurred at lower concentrations, and analytically verified that the increased frequency of media exchange resulted in a greater availability of the chemical. In combination with advanced detection systems this custom-made pipetting robot has the potential to become a valuable tool in future monitoring strategies for drinking and surface water.

Automating mouse weighing in group homecages with Raspberry Pi micro-computers

BACKGROUND

Operant training systems make use of water or food restriction and make it necessary to weigh animals to ensure compliance with experimental endpoints. In other applications periodic weighing is necessary to assess drug side-effects, or as an endpoint in feeding experiments. Periodic weighing while essential can disrupt animal circadian rhythms and social structure.

NEW METHOD

Automatic weighing system within paired mouse homecages. Up to 10 mice freely move between two cages (28×18×9cm) which were connected by a weighing chamber mounted on a load cell. Each mouse was identified using an RFID tag placed under the skin of the neck. A single-board computer (Raspberry Pi; RPi) controls the task, logging RFID tag, load cell weights, and time stamps from each RFID detection until the animal leaves the chamber. Collected data were statistically analyzed to estimate mouse weights. We anticipate integration with tasks where automated imaging or behaviour is assessed in homecages.

RESULTS

Mice frequently move between the two cages, an average of 42+-16 times/day/mouse at which time we obtained weights. We report accurate determination of mouse weight and long term monitoring over 53days. Comparison with existing methods Although commercial systems are available for automatically weighing rodents, they only work with single animals, or are not open source nor cost effective for specific custom application.

CONCLUSIONS

This automated system permits automated weighing of mice ∼40 times per day. The system employs inexpensive hardware and open-source Python code.

Performance Evaluation of a Newly Developed and Fully Automated Bacteriological Analyzer "RAISUS ANY" for Antimicrobial Susceptibility Testing of Fastidious Bacteria Haemophilus influenzae and Streptococcus pneumoniae

OBJECTIVE

Antimicrobial susceptibility testing for fastidious bacteria, such as Haemophilus influenzae (H. influenzae) and Streptococcus pneumoniae (S. pneumoniae) has been performed manually. We evaluated the performance of a newly developed fully automated system for rapid bacterial identification and antimicrobial susceptibility testing "RAISUS ANY" (Nissui Pharmaceutical Co., Ltd.).

METHODS

We evaluated the performance of "RAISUS ANY" for measurement of minimal inhibitory concentrations (MICs) of H. influenzae and S. pneumoniae, in comparison with the manual method (DP34, Eiken Chem. Co., Ltd.). The repeatability of MICs was studied using the reference strain of these bacteria, obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA).

RESULTS

The comparison with the manual method for 35 and 36 clinical strains of H. influenzae and S. pneumonia showed 62.9-100% and 86.1-100% agreement, respectively. Five of 35 H. influenzae strains that showed a trailing effect were stably and accurately measured for MICs without a variation among the examiners.

CONCLUSION

In conclusion, the automated system "RAISUS ANY" provided a reliable MICs data for H. influenzae and S. pneumonia, suggesting its improvement in performance and reliability for routine antimicrobial susceptibility testing in clinical bacteriological laboratories.

The microINR portable coagulometer: analytical quality and user-friendliness of a PT (INR) point-of-care instrument

Regular measurement of prothrombin time as an international normalized ratio PT (INR) is mandatory for optimal and safe use of warfarin. Scandinavian evaluation of laboratory equipment for primary health care (SKUP) evaluated the microINR portable coagulometer (microINR^®) (iLine Microsystems S.L., Spain) for measurement of PT (INR). Analytical quality and user-friendliness were evaluated under optimal conditions at an accredited hospital laboratory and at two primary health care centres (PHCCs). Patients were recruited at the outpatient clinic of the Laboratory of Medical Biochemistry, St Olav's University Hospital, Trondheim, Norway (n = 98) and from two PHCCs (n = 88). Venous blood samples were analyzed under optimal conditions on the STA-R^®Evolution with STA-SPA + reagent (Stago, France) (Owren method), and the results were compared to capillary measurements on the microINR^®. The imprecision of the microINR^® was 6% (90% CI: 5.3-7.0%) and 6.3% (90% CI: 5.1-8.3) in the outpatient clinic and PHCC2, respectively for INR ≥2.5. The microINR^® did not meet the SKUP quality requirement for imprecision ≤5.0%. For INR <2.5 at PHCC2 and at both levels in PHCC1, CV% was ≤5.0. The accuracy fulfilled the SKUP quality goal in both outpatient clinic and PHCCs. User-friendliness of the operation manual was rated as intermediate, defined by SKUP as neutral ratings assessed as neither good nor bad. Operation facilities was rated unsatisfactory, and time factors satisfactory. In conclusion, quality requirements for imprecision were not met. The SKUP criteria for accuracy was fulfilled both at the hospital and at the PHCCs. The user-friendliness was rated intermediate.

High-throughput transformation of Saccharomyces cerevisiae using liquid handling robots

Saccharomyces cerevisiae (budding yeast) is a powerful eukaryotic model organism ideally suited to high-throughput genetic analyses, which time and again has yielded insights that further our understanding of cell biology processes conserved in humans. Lithium Acetate (LiAc) transformation of yeast with DNA for the purposes of exogenous protein expression (e.g., plasmids) or genome mutation (e.g., gene mutation, deletion, epitope tagging) is a useful and long established method. However, a reliable and optimized high throughput transformation protocol that runs almost no risk of human error has not been described in the literature. Here, we describe such a method that is broadly transferable to most liquid handling high-throughput robotic platforms, which are now commonplace in academic and industry settings. Using our optimized method, we are able to comfortably transform approximately 1200 individual strains per day, allowing complete transformation of typical genomic yeast libraries within 6 days. In addition, use of our protocol for gene knockout purposes also provides a potentially quicker, easier and more cost-effective approach to generating collections of double mutants than the popular and elegant synthetic genetic array methodology. In summary, our methodology will be of significant use to anyone interested in high throughput molecular and/or genetic analysis of yeast.

Automated Gravimetric Calibration to Optimize the Accuracy and Precision of TECAN Freedom EVO Liquid Handler

High-throughput screening technologies are increasingly integrated into the formulation development process of biopharmaceuticals. The performance of liquid handling systems is dependent on the ability to deliver accurate and precise volumes of specific reagents to ensure process quality. We have developed an automated gravimetric calibration procedure to adjust the accuracy and evaluate the precision of the TECAN Freedom EVO liquid handling system. Volumes from 3 to 900 µL using calibrated syringes and fixed tips were evaluated with various solutions, including aluminum hydroxide and phosphate adjuvants, β-casein, sucrose, sodium chloride, and phosphate-buffered saline. The methodology to set up liquid class pipetting parameters for each solution was to split the process in three steps: (1) screening of predefined liquid class, including different pipetting parameters; (2) adjustment of accuracy parameters based on a calibration curve; and (3) confirmation of the adjustment. The run of appropriate pipetting scripts, data acquisition, and reports until the creation of a new liquid class in EVOware was fully automated. The calibration and confirmation of the robotic system was simple, efficient, and precise and could accelerate data acquisition for a wide range of biopharmaceutical applications.

Comparing TSPOT assay results between an Elispot reader and manual counts

BACKGROUND

The interferon gamma release assay, TSPOT.TB (TSPOT) can be read by several methodologies, including an Elispot reader or manually by technician. We compared the results from these two counting methods.

METHODS

Automated and manual TSPOT results among 2481 United States health care workers were compared. Cohen's kappa coefficient was used to determine the inter-rater agreement. Univariate and multiple logistic regression were used to investigate selected variable contributions.

RESULTS

No prognostic factors were associated with agreement of TSPOT results between counting methods. Agreement between TSPOT results were 92.3%, 89.5%, 93.0%, and 93.1% at baseline, and at follow-up at 6, 12, and 18 months, respectively. The inter-rater agreement for all test results was good (kappa = 0.71). There was a significant difference between individual technicians kappa coefficients (p < 0.001), but no significant increase in agreement over time for technicians (p = 0.394).

CONCLUSION

Commercial Elispot readers and manual counts have good agreement of TSPOT results in a low TB burden setting. Levels of agreement differed between individual technicians and automated reader from moderate to very good, indicating borderline results may be misinterpreted due to inter-rater variability. With no latent tuberculosis infection (LTBI) gold standard, it cannot be determined if one TSPOT reading method is better than another.

Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth

Dynamic control of gene expression can have far-reaching implications for biotechnological applications and biological discovery. Thanks to the advantages of light, optogenetics has emerged as an ideal technology for this task. Current state-of-the-art methods for optical expression control fail to combine precision with repeatability and cannot withstand changing operating culture conditions. Here, we present a novel fully automatic experimental platform for the robust and precise long-term optogenetic regulation of protein production in liquid Escherichia coli cultures. Using a computer-controlled light-responsive two-component system, we accurately track prescribed dynamic green fluorescent protein expression profiles through the application of feedback control, and show that the system adapts to global perturbations such as nutrient and temperature changes. We demonstrate the efficacy and potential utility of our approach by placing a key metabolic enzyme under optogenetic control, thus enabling dynamic regulation of the culture growth rate with potential applications in bacterial physiology studies and biotechnology.

Screening of presumptive urinary tract infections by the automated urine sediment analyser sediMAX

BACKGROUND

Urinary tract infections (UTI) are among the most common bacterial infections and urine samples represent a large proportion of the specimens processed in clinical microbiology laboratories, up to 80% of which, however, yield negative results. Automated microscopy is widely used for urine sediment analysis and has recently been evaluated in a few studies for bacteriological screening of urine samples, achieving high levels of performance.

METHODS

We present a study in which urine samples from both inpatients and outpatients, with either clean-catch or indwelling catheter urine samples, were screened for UTI by urine culture, as the reference method, and the automated urine analyser sediMAX, for the detection of bacteria, leukocytes and yeasts.

RESULTS

In total, 3443 urine samples were evaluated. When a single algorithm was adopted for sediMAX to screen the total patient population, 96.4% sensitivity, 75.4% specificity, 57.8% positive predictive value, and 98.4% negative predictive value were found. However, for male outpatients and all patients with indwelling catheter other algorithms were necessary to improve performances. Altogether, with sediMAX false negative rate was 2.4% and false positive rate was 27.6%. In addition, 54% of the investigated samples could have avoided urine culture.

CONCLUSIONS

After the identification of specific algorithms for different patient subgroups, the automated urine analyser sediMAX can be reliably employed in the screening of UTI.

Lab-on-a-disc for simultaneous determination of total phenolic content and antioxidant activity of beverage samples

In this paper, we present a fully integrated and automated lab-on-a-disc for the rapid determination of the total phenolic content (TPC) and antioxidant activity (AA) of beverage samples. The simultaneous determinations of TPC and AA on a spinning disc were achieved by integrating three independent analytical techniques: the Folin-Ciocalteu method that is used to measure TPC, the 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) method and the ferric reducing antioxidant power method that are used to measure AA. The TPC and AA of 8 different beverage samples, including various fruit juices, tea, wine and beer, were analyzed. Unlike conventional labor-intensive processes for measuring TPC and AA, our fully automated platform offers one-step operation and rapid analysis.

[Automation of the Examination for Autoantibodies]

Antinuclear antibody (ANA) testing is indispensable for diagnosing and estimating clinical conditions of autoimmune diseases. This literature explains the usability and problem points regarding routine laboratory tests with examples of our own experiments regarding ANA diagnostics with some new technologies. The indirect immunofluorescence assay (IFA) is the gold standard for ANA screening, and it can detect more than 100 different antibodies, including the anti-proliferating cell nuclear antigen as well as anti- cytoplasmic antibodies. However, complicated procedures of conventional IFA and visual interpretation require highly skilled laboratory staff. The EUROPattern Cosmic IFA System (EUROIMMUN, Cosmic Corporation) and HELIOS* (Aesku Diag- nostics, MBL), which are computer-aided microscope systems for ANA testing, showed concordance of the positivity rate as high as 93.3 and 91.9%, respectively, and concordance of the antibody titer as high as 94.0 and 98.8%, respectively (within +/-1 titer) compared with the conventional method, on the measurement of different populations for each system. Although the computer-aided microscope system is not considered a complete system and laboratory staff should verify each result, it is a useful system for routine ANA analysis because it contributes to ANA stand- ardization and an efficient workflow. In our previous study, we demonstrated that BioPlex2200 (Bio-Rad), a fully automated immunoassay ana- lyzer using suspension bead array technology, was useful for the clinical diagnosis of autoimmune diseases. As an ANA screening test, the positive rate was low (7.2%) in healthy subjects, and comparable with that of IFA ( X160). The prevalence of disease-specific ANA in connective tissue disease patients was comparable with the general occurrence rate except for anti-dsDNA antibody in SLE. In accordance with the results of double immunodiffusion and Western blotting with the conventional method, the concordance rate between BioPlex2200 and conventional methods was high (95.0-100%) except for anti-dsDNA antibody. To provide high-quality and prompt clinical tests while considering the efficiency of working and cost reduc- tion, each laboratory should actively innovate and operate these advanced inspection technologies. [Review].

Automated Microscopy: Macro Language Controlling a Confocal Microscope and its External Illumination: Adaptation for Photosynthetic Organisms

Photosynthesis research employs several biophysical methods, including the detection of fluorescence. Even though fluorescence is a key method to detect photosynthetic efficiency, it has not been applied/adapted to single-cell confocal microscopy measurements to examine photosynthetic microorganisms. Experiments with photosynthetic cells may require automation to perform a large number of measurements with different parameters, especially concerning light conditions. However, commercial microscopes support custom protocols (through Time Controller offered by Olympus or Experiment Designer offered by Zeiss) that are often unable to provide special set-ups and connection to external devices (e.g., for irradiation). Our new system combining an Arduino microcontroller with the Cell⊕Finder software was developed for controlling Olympus FV1000 and FV1200 confocal microscopes and the attached hardware modules. Our software/hardware solution offers (1) a text file-based macro language to control the imaging functions of the microscope; (2) programmable control of several external hardware devices (light sources, thermal controllers, actuators) during imaging via the Arduino microcontroller; (3) the Cell⊕Finder software with ergonomic user environment, a fast selection method for the biologically important cells and precise positioning feature that reduces unwanted bleaching of the cells by the scanning laser. Cell⊕Finder can be downloaded from http://www.alga.cz/cellfinder. The system was applied to study changes in fluorescence intensity in Synechocystis sp. PCC6803 cells under long-term illumination. Thus, we were able to describe the kinetics of phycobilisome decoupling. Microscopy data showed that phycobilisome decoupling appears slowly after long-term (>1 h) exposure to high light.

Our Fat Future: Translating Adipose Stem Cell Therapy

Human adipose stem cells (hASCs) have the potential to treat patients with a variety of clinical conditions. Recent advancements in translational research, regulatory policy, and industry have positioned hASCs on the threshold of clinical translation. We discuss the progress and challenges of bringing adipose stem cell therapy into mainstream clinical use.

SIGNIFICANCE

This article details the advances made in recent years that have helped move human adipose stem cell therapy toward mainstream clinical use from a translational research, regulatory policy, and industrial standpoint. Four recurrent themes in translational technology as they pertain to human adipose stem cells are discussed: automated closed-system operations, biosensors and real-time monitoring, biomimetics, and rapid manufacturing. In light of recent FDA guidance documents, regulatory concerns about adipose stem cell therapy are discussed. Finally, an update is provided on the current state of clinical trials and the emerging industry that uses human adipose stem cells. This article is expected to stimulate future studies in translational adipose stem cell research.

A portable blood plasma clot micro-elastometry device based on resonant acoustic spectroscopy

Abnormal blood clot stiffness is an important indicator of coagulation disorders arising from a variety of cardiovascular diseases and drug treatments. Here, we present a portable instrument for elastometry of microliter volume blood samples based upon the principle of resonant acoustic spectroscopy, where a sample of well-defined dimensions exhibits a fundamental longitudinal resonance mode proportional to the square root of the Young's modulus. In contrast to commercial thromboelastography, the resonant acoustic method offers improved repeatability and accuracy due to the high signal-to-noise ratio of the resonant vibration. We review the measurement principles and the design of a magnetically actuated microbead force transducer applying between 23 pN and 6.7 nN, providing a wide dynamic range of elastic moduli (3 Pa-27 kPa) appropriate for measurement of clot elastic modulus (CEM). An automated and portable device, the CEMport, is introduced and implemented using a 2 nm resolution displacement sensor with demonstrated accuracy and precision of 3% and 2%, respectively, of CEM in biogels. Importantly, the small strains (<0.13%) and low strain rates (<1/s) employed by the CEMport maintain a linear stress-to-strain relationship which provides a perturbative measurement of the Young's modulus. Measurements of blood plasma CEM versus heparin concentration show that CEMport is sensitive to heparin levels below 0.050 U/ml, which suggests future applications in sensing heparin levels of post-surgical cardiopulmonary bypass patients. The portability, high accuracy, and high precision of this device enable new clinical and animal studies for associating CEM with blood coagulation disorders, potentially leading to improved diagnostics and therapeutic monitoring.

Laboratory Automation and Middleware

The practice of surgical pathology is under constant pressure to deliver the highest quality of service, reduce errors, increase throughput, and decrease turnaround time while at the same time dealing with an aging workforce, increasing financial constraints, and economic uncertainty. Although not able to implement total laboratory automation, great progress continues to be made in workstation automation in all areas of the pathology laboratory. This report highlights the benefits and challenges of pathology automation, reviews middleware and its use to facilitate automation, and reviews the progress so far in the anatomic pathology laboratory.

Automation of a single-DNA molecule stretching device

We automate the manipulation of genomic-length DNA in a nanofluidic device based on real-time analysis of fluorescence images. In our protocol, individual molecules are picked from a microchannel and stretched with pN forces using pressure driven flows. The millimeter-long DNA fragments free flowing in micro- and nanofluidics emit low fluorescence and change shape, thus challenging the image analysis for machine vision. We demonstrate a set of image processing steps that increase the intrinsically low signal-to-noise ratio associated with single-molecule fluorescence microscopy. Furthermore, we demonstrate how to estimate the length of molecules by continuous real-time image stitching and how to increase the effective resolution of a pressure controller by pulse width modulation. The sequence of image-processing steps addresses the challenges of genomic-length DNA visualization; however, they should also be general to other applications of fluorescence-based microfluidics.

A novel experimental approach to investigate radiolysis processes in liquid samples using collimated radiation sources

Here is detailed a novel and low-cost experimental method for high-throughput automated fluid sample irradiation. The sample is delivered via syringe pump to a nozzle, where it is expressed in the form of a hanging droplet into the path of a beam of ionising radiation. The dose delivery is controlled by an upstream lead shutter, which allows the beam to reach the droplet for a user defined period of time. The droplet is then further expressed after irradiation until it falls into one well of a standard microplate. The entire system is automated and can be operated remotely using software designed in-house, allowing for use in environments deemed unsafe for the user (synchrotron beamlines, for example). Depending on the number of wells in the microplate, several droplets can be irradiated before any human interaction is necessary, and the user may choose up to 10 samples per microplate using an array of identical syringe pumps, the design of which is described here. The nozzles consistently produce droplets of 25.1 ± 0.5 μl.

[Evaluation of an automated streaking system of urine samples for urine cultures]

INTRODUCTION

Automated systems have simplified laboratory workflow, improved standardization, traceability and diminished human errors and workload. Although microbiology laboratories have little automation, in recent years new tools for automating pre analytical steps have appeared.

OBJECTIVES

To assess the performance of an automated streaking machine for urine cultures and its agreement with the conventional manual plating method for semi quantitative colony counts.

MATERIALS AND METHODS

495 urine samples for urinary culture were inoculated in CPS® agar using our standard protocol and the PREVI™ Isola. Rates of positivity, negativity, polymicrobial growth, bacterial species, colony counts and re-isolation requirements were compared.

RESULTS

Agreement was achieved in 98.97% of the positive/negative results, in 99.39% of the polymicrobial growth, 99.76% of bacterial species isolated and in 98.56 % of colony counts. The need for re-isolation of colonies decreased from 12.1% to 1.1% using the automated system.

DISCUSSION

PREVI™ Isola's performance was as expected, time saving and improving bacterial isolation. It represents a helpful tool for laboratory automation.

An overview of the Progenika ID CORE XT: an automated genotyping platform based on a fluidic microarray system

Automated testing platforms facilitate the introduction of red cell genotyping of patients and blood donors. Fluidic microarray systems, such as Luminex XMAP (Austin, TX), are used in many clinical applications, including HLA and HPA typing. The Progenika ID CORE XT (Progenika Biopharma-Grifols, Bizkaia, Spain) uses this platform to analyze 29 polymorphisms determining 37 antigens in 10 blood group systems. Once DNA has been extracted, processing time is approximately 4 hours. The system is highly automated and includes integrated analysis software that produces a file and a report with genotype and predicted phenotype results.

An inter-machine comparison of tobacco smoke particle deposition in vitro from six independent smoke exposure systems

There are several whole smoke exposure systems used to assess the biological and toxicological impact of tobacco smoke in vitro. One such system is the Vitrocell® VC 10 Smoking Robot and exposure module. Using quartz crystal microbalances (QCMs) installed into the module, we were able to assess tobacco smoke particle deposition in real-time. We compared regional deposition across the module positions and doses delivered by six VC 10s in four independent laboratories: two in the UK, one in Germany and one in China. Gauge R&r analysis was applied to the total data package from the six VC 10s. As a percentage of the total, reproducibility (between all six VC 10s) and repeatability (error within an individual VC 10) accounted for 0.3% and 7.4% respectively. Thus Gauge R&r was 7.7%, less than 10% overall and considered statistically fit for purpose. The dose-responses obtained from the six machines across the four different locations demonstrated excellent agreement. There were little to no positional differences across the module at all airflows as determined by ANOVA (except for one machine and at three airflows only). These results support the on-going characterisation of the VC 10 exposure system and suitability for tobacco smoke exposure in vitro.

An adjustable gas-mixing device to increase feasibility of in vitro culture of Plasmodium falciparum parasites in the field

A challenge to conducting high-impact and reproducible studies of the mechanisms of P. falciparum drug resistance, invasion, virulence, and immunity is the lack of robust and sustainable in vitro culture in the field. While the technology exists and is routinely utilized in developed countries, various factors–from cost, to supply, to quality–make it hard to implement in malaria endemic countries. Here, we design and rigorously evaluate an adjustable gas-mixing device for the in vitro culture of P. falciparum parasites in the field to circumvent this challenge. The device accurately replicates the gas concentrations needed to culture laboratory isolates, short-term adapted field isolates, cryopreserved previously non-adapted isolates, as well as to adapt ex vivo isolates to in vitro culture in the field. We also show an advantage over existing alternatives both in cost and in supply. Furthermore, the adjustable nature of the device makes it an ideal tool for many applications in which varied gas concentrations could be critical to culture success. This adjustable gas-mixing device will dramatically improve the feasibility of in vitro culture of Plasmodium falciparum parasites in malaria endemic countries given its numerous advantages.

A fully automated dual-online multifunctional ultrahigh pressure liquid chromatography system for high-throughput proteomics analysis

A fully automated dual-online multifunctional ultrahigh pressure liquid chromatography (DO-MULTI-UPLC) system has been developed for high throughput proteome analyses of complex peptide mixtures. The system employs two online solid phase extraction (SPE) columns (150μm inner diameter×3cm), two capillary reverse phase (RP) columns (75μm×100cm) and a strong cation exchange (SCX) column (150μm×15cm) on a single system utilizing one binary pump and one isocratic pump. With the automated operation of six switching valves, the selection of LC experiments between single-dimensional RPLC and online two-dimensional SCX/RPLC were achieved automatically, without manual intervention, while two RPLC columns were used independently and alternatively. By essentially removing the dead time for column equilibration between experiments, in either 1D mode or 2D experimental mode, the current system was demonstrated to increase the experimental throughput by about two folds, while keeping the inter-column reproducibility of peptide elution time in less than 1% of gradient time. The advantageous features of the proposed system were demonstrated by its application to proteome samples of varying complexities.

[Classifier of domestic pig (Sus scrofa domesticus) automatic chromosome identification]

Automated chromosome classification is an essential task in cytogenetics of animals and plants. Until now the automatic karyotyping systems were obtained only for human chromosomes. The main aim of this study was to develop the automatic pig chromosome classifier using image processing software "VideoTest-Karyo 3.1". To solve this problem 1578 chromosomes from 47 metaphases were used. The constructed classifier was checked with the use of additional sample of metaphases classified in fully automatic regime: error rate was 8.2%, this corresponds to 3.12 ± 0.26 errors per metaphase plate (these values are within acceptable limits for such kind of studies). In further studies the extra sample of pig acrocentric chromosomes was added to classifier up to 1807 chromosomes. This addition reduced the error rate up to 6.1%, which correspondes to 2.78 ± 0.18 errors per metaphase plate. It should be underlined that the revealed errors can immediately be corrected by an operator on every stage of analysis. The classifier was also verified using the chromosomes of boar with rcp(1p-; 11p+) in fully automatic regime and routine stained metaphases of Siberian minipigs with rob(16;17) in semi automatic regime. In both cases the chromosomes were identified correctly. The area of application of obtained pig automatic chromosome classifier is discussed.

A review of in vitro cigarette smoke exposure systems

In vitro test methods may be vital in understanding tobacco smoke, the main toxicants responsible for adverse health effects, and elucidating disease mechanisms. There is a variety of 'whole smoke' exposure systems available for the generation, dilution and delivery of tobacco smoke in vitro; these systems can be procured commercially from well-known suppliers or can be bespoke set-ups. These exposure technologies aim to ensure that there are limited changes in the tobacco smoke aerosol from generation to exposure. As the smoke aerosol is freshly generated, interactions in the smoke fractions are captured in any subsequent in vitro analysis. Of the commercially available systems, some have been characterised more than others in terms of published scientific literature and developed biological endpoints. Others are relatively new to the scientific field and are still establishing their presence. In addition, bespoke systems are widely used and offer a more flexible approach to the challenges of tobacco smoke exposure. In this review, the authors present a summary of the major tobacco smoke exposure systems available and critically review their function, set-up and application for in vitro exposure scenarios. All whole smoke exposure systems have benefits and limitations, often making it difficult to make comparisons between set-ups and the data obtained from such diverse systems. This is where exposure and dose measurements can add value and may be able to provide a platform on which comparisons can be made. The measurement of smoke dose, as an emerging field of research, is therefore also discussed and how it may provide valuable and additional data to support existing whole smoke exposure set-ups and aid validation efforts.