Ferrobotic swarms enable accessible and adaptable automated viral testing.

Expanding our global testing capacity is critical to preventing and containing pandemics1-9. Accordingly, accessible and adaptable automated platforms that in decentralized settings perform nucleic acid amplification tests resource-efficiently are required10-14. Pooled testing can be extremely efficient if the pooling strategy is based on local viral prevalence15-20; however, it requires automation, small sample volume handling and feedback not available in current bulky, capital-intensive liquid handling technologies21-29. Here we use a swarm of millimetre-sized magnets as mobile robotic agents ('ferrobots') for precise and robust handling of magnetized sample droplets and high-fidelity delivery of flexible workflows based on nucleic acid amplification tests to overcome these limitations. Within a palm-sized printed circuit board-based programmable platform, we demonstrated the myriad of laboratory-equivalent operations involved in pooled testing. These operations were guided by an introduced square matrix pooled testing algorithm to identify the samples from infected patients, while maximizing the testing efficiency. We applied this automated technology for the loop-mediated isothermal amplification and detection of the SARS-CoV-2 virus in clinical samples, in which the test results completely matched those obtained off-chip. This technology is easily manufacturable and distributable, and its adoption for viral testing could lead to a 10-300-fold reduction in reagent costs (depending on the viral prevalence) and three orders of magnitude reduction in instrumentation cost. Therefore, it is a promising solution to expand our testing capacity for pandemic preparedness and to reimagine the automated clinical laboratory of the future.

Bioeconomy triple factor nexus through indicator analysis.

The transition to a sustainable bioeconomy by a customized approach would speed up its development and make it more targeted. There is still no common international method for determining, measuring and comparing the extent of sustainability. The aim of this research is to develop a methodology for the assessment of bioeconomy-influencing factor interlinkages, and creation of benchmarks through a top-down approach. The main output is the assessment of factor interlinkages that could be further used for composite index creation. A case of triple factor nexus is presented: policy, research and innovations, and technology nexus for EU countries. As a result, the empirical model presents the mathematical description of policy, research and innovation, and technology link benchmark.

Budget Impact of Improved Diabetes Management by Utilization of Glucose Meters With a Color-Range Indicator-Comparison of Five European Healthcare Systems.

BACKGROUND AND AIM: Costs for the treatment of diabetes and its comorbidities are a major international issue. A recent randomized clinical trial showed that the introduction of color range indicator (CRI)-based glucose meters (GMs) positively affects the HbA1c of patients with type 1 and type 2 diabetes, when compared to GMs without a CRI. This budget impact analysis aimed to translate this beneficial effect of CRI-based GMs, OneTouch Verio Flex and OneTouch Verio, into potential monetary impact for the healthcare systems of five European countries, Germany, Spain, Italy, France, and the United Kingdom. MATERIAL AND METHODS: Data from a randomized controlled trial, evaluating the effect of CRI-based GMs, were used to estimate the ten-year risk of patients for fatal myocardial infarction (MI) as calculated by the UK Prospective Diabetes Study (UKPDS) risk engine. On the basis of assessed risks for MI, the potential monetary impact for the healthcare systems in five European countries was modeled. RESULTS: Based on a mean HbA1c reduction of 0.36%, as demonstrated in a randomized controlled trial, the UKPDS risk engine estimated a reduction of 2.4% of the ten-year risk of patients for fatal MI. When applied to our economic model, substantial potential cost savings for the healthcare systems of five European countries were calculated: €547 472 (France), €9.0 million (Germany), €6.0 million (Italy), €841 799 (Spain), and €421 069 (United Kingdom) per year. CONCLUSION: Improving metabolic control in patients with diabetes by the utilization of CRI-based GMs may have substantial positive effects on the expenditure of the healthcare systems of several European countries.

Evaluation of whole genome sequencing and software tools for drug susceptibility testing of Mycobacterium tuberculosis.

OBJECTIVES: Culture-based assays are currently the reference standard for drug susceptibility testing for Mycobacterium tuberculosis. They provide good sensitivity and specificity but are time consuming. The objective of this study was to evaluate whether whole genome sequencing (WGS), combined with software tools for data analysis, can replace routine culture-based assays for drug susceptibility testing of M. tuberculosis. METHODS: M. tuberculosis cultures sent to the Finnish mycobacterial reference laboratory in 2014 (n = 211) were phenotypically tested by Mycobacteria Growth Indicator Tube (MGIT) for first-line drug susceptibilities. WGS was performed for all isolates using the Illumina MiSeq system, and data were analysed using five software tools (PhyResSE, Mykrobe Predictor, TB Profiler, TGS-TB and KvarQ). Diagnostic time and reagent costs were estimated for both methods. RESULTS: The sensitivity of the five software tools to predict any resistance among strains was almost identical, ranging from 74% to 80%, and specificity was more than 95% for all software tools except for TGS-TB. The sensitivity and specificity to predict resistance to individual drugs varied considerably among the software tools. Reagent costs for MGIT and WGS were €26 and €143 per isolate respectively. Turnaround time for MGIT was 19 days (range 10-50 days) for first-line drugs, and turnaround time for WGS was estimated to be 5 days (range 3-7 days). CONCLUSIONS: WGS could be used as a prescreening assay for drug susceptibility testing with confirmation of resistant strains by MGIT. The functionality and ease of use of the software tools need to be improved.

Development of a cost effective and robust AlphaScreen® platform for application.

The use of AlphaScreen® detection has allowed researchers to examine a wide variety of molecular interactions for use in high-throughput screening. However, the cost of Alpha reagents can often be prohibitory for extended screening campaigns or for young investigators with limited funding. To reduce assay costs, many labs have focused on miniaturization, while there have been limited efforts to scale down Alpha reagents. Thus, we describe the optimization of an AlphaScreen detection platform by systematically reducing the Alpha reagents down to 2.5 µg/ml beads, without compromising assay integrity. We demonstrate that reducing bead concentration reduces detection costs substantially while yielding robust statistics. We believe this simple new protocol will enhance the future utilization of AlphaScreen technology in high-throughput screening.

A ten-color tube with dried antibody reagents for the screening of hematological malignancies.

INTRODUCTION: The workflow in clinical flow cytometry laboratories must constantly be reviewed to develop technical procedures that improve quality and productivity and reduce costs. Using the Beckman Coulter dry coating technology, we customized a ten-color tube with dried antibody reagents, designated the Duraclone screening tube (DST), for screening hematological malignancies. Here, we compared the applicability, clinical and numerical equivalence, and cost and time required for the technical procedures between the liquid reagents and the DST. METHODS: The DST contains CD4 + Kappa-FITC, CD8 + Lambda-PE, CD3 + CD14-ECD, CD33-PE-Cy5.5, CD20 + CD56-PE-Cy7, CD34-APC, CD19-APC-AlexaFluor700, CD10-APC-AlexaFluor750, CD5-Pacific Blue, and CD45-Krome Orange. We evaluated 20 bone marrow samples, 13 peripheral blood samples, 6 lymph node biopsy samples, 5 fine-needle aspirate samples, 5 cerebrospinal fluid samples, and 1 pleural fluid sample. RESULTS: The DST was useful for more than 60% of our samples. It was able to enumerate the majority of the populations in all types of samples with a statistically acceptable correlation with the liquid reagents. The use of the DST translated into significant time and cost savings of 15.8% and 12.3%, respectively, compared with the use of the liquid reagent. The cost was reduced by $14.36 per sample. CONCLUSIONS: The DST is an efficient solution for screening hematological malignancies with improved quality, productivity, standardization, and sustainability. These improvements could benefit patients by providing faster diagnoses using a higher quality and lower cost reagent.

Economical fermentation media for the production of a whole cell catalyst for the treatment of Cr(VI)-containing wastewaters.

The biotechnology sector is continually seeking sustainable and more economical bioprocesses. Fermentation media produced with cheap components or wastes reduce production costs. Moreover, if wastes are used, they contribute to avoid environmental pollution. In this work, microbial growth media based on molasses or acidified glycerol as carbon sources and fertilizer as nitrogen source were tested for the production of a whole-cell catalyst that could be used in Cr(VI)-containing wastewater treatments. Results showed that the highest biomass production yield was obtained with a medium containing acidified glycerol 5% v/v and fertilizer 0.6% v/v. The biomass produced using this medium was immobilized in calcium alginate beads and used as catalyst in the biotransformation of Cr(VI) into Cr(III). The catalyst could be efficiently used for 5 reduction cycles of 40mg/l Cr(VI) each. Cr(III) retention assays were performed to determine whether Cr(III) could be retained by the catalyst avoiding its solubilization in the supernatants. The retention capacity of the catalyst at 32°C and pH 3.0 was 3mg Cr(III)/g. Both an alternative and economical fermentation medium is here proposed for the optimization of Cr(VI)-containing wastewater treatment.

Price-Focused Analysis of Commercially Available Building Blocks for Combinatorial Library Synthesis.

Combinatorial libraries are synthesized by combining smaller reagents (building blocks), the price of which is an important component of the total costs associated with the synthetic exercise. A significant portion of commercially available reagents are too expensive for large scale work. In this study, 13 commonly used reagent classes in combinatorial library synthesis (primary and secondary amines, carboxylic acids, alcohols, ketones, aldehydes, boronic acids, acyl halides, sulfonyl chlorides, isocyanates, isothiocyanates, azides and chloroformates) were analyzed with respect to the cost, physicochemical properties (molecular weight and calculated logP), chemical diversity, and 3D-likeness using a large data set. The results define the chemical space accessible under a constraint of limited financial resources.

Broad application of a simple and affordable protocol for isolating plant RNA.

BACKGROUND: Standard molecular biological methods involve the analysis of gene expression in living organisms under diverse environmental and developmental conditions. One of the most direct approaches to quantify gene expression is the isolation of RNA. Most techniques used to quantify gene expression require the isolation of RNA, usually from a large number of samples. While most published protocols, including those for commercial reagents, are either labour intensive, use hazardous chemicals and/or are costly, a previously published protocol for RNA isolation in Arabidopsis thaliana yields high amounts of good quality RNA in a simple, safe and inexpensive manner. FINDINGS: We have tested this protocol in tomato and wheat leaves, as well as in Arabidopsis leaves, and compared the resulting RNA to that obtained using a commercial phenol-based reagent. Our results demonstrate that this protocol is applicable to other plant species, including monocots, and offers yield and purity at least comparable to those provided by commercial phenol-based reagents. CONCLUSIONS: Here, we show that this previously published RNA isolation protocol can be easily extended to other plant species without further modification. Due to its simplicity and the use of inexpensive reagents, this protocol is accessible and affordable and can be easily implemented to work on different plant species in laboratories worldwide.

Reagent and labor cost optimization through automation of fluorescence in situ hybridization (FISH) with the VP 2000: an Italian case study.

In the modern molecular diagnostic laboratory, cost considerations are of paramount importance. Automation of complex molecular assays not only allows a laboratory to accommodate higher test volumes and throughput but also has a considerable impact on the cost of testing from the perspective of reagent costs, as well as hands-on time for skilled laboratory personnel. The following study tracked the cost of labor (hands-on time) and reagents for fluorescence in situ hybridization (FISH) testing in a routine, high-volume pathology and cytogenetics laboratory in Treviso, Italy, over a 2-y period (2011-2013). The laboratory automated FISH testing with the VP 2000 Processor, a deparaffinization, pretreatment, and special staining instrument produced by Abbott Molecular, and compared hands-on time and reagent costs to manual FISH testing. The results indicated significant cost and time saving when automating FISH with VP 2000 when more than six FISH tests were run per week. At 12 FISH assays per week, an approximate total cost reduction of 55% was observed. When running 46 FISH specimens per week, the cost saving increased to 89% versus manual testing. The results demonstrate that the VP 2000 processor can significantly reduce the cost of FISH testing in diagnostic laboratories.

Brewer's spent grain: a valuable feedstock for industrial applications.

Brewer's spent grain (BSG) is the most abundant by-product generated from the beer-brewing process, representing approximately 85% of the total by-products obtained. This material is basically constituted by the barley grain husks obtained as solid residue after the wort production. Since BSG is rich in sugars and proteins, the main and quickest alternative for elimination of this industrial by-product has been as animal feed. However, BSG is a raw material of interest for application in different areas because of its low cost, large availability throughout the year and valuable chemical composition. In the last decade, many efforts have been directed towards the reuse of BSG, taking into account the incentive that has been given to recycle the wastes and by-products generated by industrial activities. Currently, many interesting and advantageous methods for application of BSG in foods, in energy production and in chemical and biotechnological processes have been reported. The present study presents and discusses the most recent perspectives for BSG application in such areas.

Toward low-cost affinity reagents: lyophilized yeast-scFv probes specific for pathogen antigens.

The generation of affinity reagents, usually monoclonal antibodies, remains a critical bottleneck in biomedical research and diagnostic test development. Recombinant antibody-like proteins such as scFv have yet to replace traditional monoclonal antibodies in antigen detection applications, in large part because of poor performance of scFv in solution. To address this limitation, we have developed assays that use whole yeast cells expressing scFv on their surfaces (yeast-scFv) in place of soluble purified scFv or traditional monoclonal antibodies. In this study, a nonimmune library of human scFv displayed on the surfaces of yeast cells was screened for clones that bind to recombinant cyst proteins of Entamoeba histolytica, an enteric pathogen of humans. Selected yeast-scFv clones were stabilized by lyophilization and used in detection assay formats in which the yeast-scFv served as solid support-bound monoclonal antibodies. Specific binding of antigen to the yeast-scFv was detected by staining with rabbit polyclonal antibodies. In flow cytometry-based assays, lyophilized yeast-scFv reagents retained full binding activity and specificity for their cognate antigens after 4 weeks of storage at room temperature in the absence of desiccants or stabilizers. Because flow cytometry is not available to all potential assay users, an immunofluorescence assay was also developed that detects antigen with similar sensitivity and specificity. Antigen-specific whole-cell yeast-scFv reagents can be selected from nonimmune libraries in 2-3 weeks, produced in vast quantities, and packaged in lyophilized form for extended shelf life. Lyophilized yeast-scFv show promise as low cost, renewable alternatives to monoclonal antibodies for diagnosis and research.