Extensive Method Development Research Articles

Probing the role of ligation and exonuclease digestion towards non-specific amplification in bioanalytical RCA assays.

Non-specific amplification (NSA, amplification in the absence of a target analyte) in bioanalytical rolling circle amplification (RCA) assays, especially those involving pre-synthesized circular DNA (cDNA), affects its analytical sensitivity. Despite extensive development of RCA-based bioanalytical methods, the NSA in RCA remains uncharacterized in terms of its magnitude or origin. NSA may originate from inefficient ligation or succeeding cDNA purification steps. This study comprehensively quantifies NSA across several ligation and digestion techniques for the first time since the innovation of RCA. To quantify the NSA in RCA, cDNAs were prepared using self-annealing, splint-padlock, or cohesive end ligations. The cDNAs were then subjected to nine different exonuclease digestion steps and quantified for NSA under linear as well as hyperbranched RCA conditions. We investigated buffer compositions, divalent ion concentrations, single or dual enzyme digestion, cohesive end lengths, and splint lengths. The optimized conditions successfully mitigated absolute NSA by 30-100-fold and relative NSA (normalized against primer-assisted RCA) to ∼5%. Besides understanding the mechanistic origin of NSA, novel aspects of enzyme-substrate selectivity, buffer composition, and the role of divalent ions were discovered. With increasing bioanalytical RCA applications, this study will help standardize NSA-free assays.

Data-Driven Monitoring and Predictive Maintenance for Engineering Structures: Technologies, Implementation Challenges, and Future Directions

Estimating engineering structures’ health conditions and predicting their future behaviors are fundamental problems for a city’s safe and efficient operations. Data-driven solutions estimate the health conditions using statistical models generated from measurement data. They have attracted growing interest recently because advances in information and communication technologies (ICT) have enabled numerous real-world measurement data, and the flourishing big data community has provided enormous state-of-the-art data analytics algorithms. Nevertheless, most existing studies remain in numerical simulation while neglecting their real-world implementation, restricting the extensive development of data-driven methods. In this survey, we provide a structural overview of the past decade’s data-driven structural health monitoring (SHM) systems and algorithms from the perspective of real-world implementation. Specifically, we cover various aspects of the design and implementation of monitoring systems, including sensing technologies, communication technologies, and processing software. In addition, we classify the used data sources and statistical models with fined details. Under the proposed taxonomy, their limitations and advantages are thoroughly discussed. Based on our insights into existing studies, we clarify two major implementation challenges: the digressive performance in the real-world environment and inefficient computing systems for real-time data analytics. Possible solutions are then proposed to mitigate those challenges and promote the implementation of data-driven methods. Finally, we raise our outlook on future trends and suggest promising directions for further investigation.

Theoretical charge plots as a tool for targeted and accelerated ion exchange chromatography method development of NANOBODYⓇ molecules

NANOBODYⓇ molecules are an innovative class of biotherapeutics based on heavy chain only VHH immunoglobulins. Much like canonical antibodies, they are prone to the formation of charge variants and other post-translational modifications, which can potentially impact their critical quality attributes. Therefore, establishing high-resolution product-specific methods, such as IEX chromatography, is essential for evaluating the purity of these molecules. However, due to the lower surface charge of NANOBODYⓇ molecules, their charge-based elution behavior can differ considerably from that of classical antibodies, resulting in a more extensive method development set-up for these smaller molecules. Using an initial pH screening gradient based on theoretical protein charge plots, we investigated the IEX retention behavior of eight NANOBODYⓇ molecules with a wide range of pI values (pI 5.0 to 10.0). Our findings reveal that the charge-based chromatographic behavior of NANOBODYⓇ molecules cannot be solely attributed to the isoelectric point (pI) of the protein. Rather, a molecule-specific charge threshold was identified as a critical parameter for NANOBODYⓇ molecule retention. Furthermore, the protein charge plot also showed that NANOBODYⓇ molecule elution can be characterized by a charge plateau where the net charge of the protein remains constant over a certain pH range (∼ pH 5.5 to pH 8.0), further challenging the paradigm that elution pH and pI are fixed values. The application of this theoretical approach using protein charge plots to define NANOBODYⓇ molecule charge threshold and charge plateau parameters, can reduce overall IEX method development turnaround time by at least 2-fold.

Development and validation of a headspace GC-MS method to evaluate the interconversion of impurities and the product quality of liquid hand sanitizers

The COVID-19 pandemic has led to increased usage of hand sanitizer products by the public to prevent the spread of COVID-19 and decrease the likelihood of acquiring the disease. The increase in demand has also led to an increase in the number of manufacturers. This work describes the FDA’s Center for Drug Evaluation and Research (CDER) laboratories efforts to develop tests to assess the quality of hand sanitizer products containing ethanol or isopropanol as the primary active ingredient. The products were evaluated for the active ingredient content and determination of the 12 impurities listed in the FDA Hand Sanitizer Temporary Guidance, followed by a spike recovery assay performed to verify the test results. Extensive method development was conducted including an investigation into the stability of ethanol, isopropanol, and the 12 impurities. Stability and kinetic studies confirmed the instability of acetal in acidic liquid hand sanitizer products during spike recovery assay testing. The headspace GC-MS method was validated according to ICH Q2 (R1) guidelines and the spike recovery assay was validated using three concentrations of standards for the drug product. During method application, six liquid hand sanitizer products were tested and all were determined to have ethanol or isopropanol above 70% v/v. Two liquid hand sanitizer products were determined to contain acetaldehyde as an impurity above the FDA recommended safety levels.

Nanopore sequencing technology, bioinformatics and applications.

Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.

Verification benchmarks for single-phase flow in three-dimensional fractured porous media

Flow in fractured porous media occurs in the earth’s subsurface, in biological tissues, and in man-made materials. Fractures have a dominating influence on flow processes, and the last decade has seen an extensive development of models and numerical methods that explicitly account for their presence. To support these developments, four benchmark cases for single-phase flow in three-dimensional fractured porous media are presented. The cases are specifically designed to test the methods’ capabilities in handling various complexities common to the geometrical structures of fracture networks. Based on an open call for participation, results obtained with 17 numerical methods were collected. This paper presents the underlying mathematical model, an overview of the features of the participating numerical methods, and their performance in solving the benchmark cases.

Development of a simple liquid chromatography method for dissolution testing of low dose desogestrel and ethinylestradiol tablets

Accurate quantitation of low dose, multi-active dissolution samples poses unique challenges in the pharmaceutical industry, often resulting in separate HPLC methods for each active or the use of multiple detectors for increased sensitivity. In this study, we report a fast, isocratic HPLC method utilizing only UV detection for dissolution testing of low dose desogestrel and ethinylestradiol tablets. Rapid separation is completed in 5 min using isocratic elution at a flow rate of 0.45 mL/min, with a column temperature at 30 °C, an injection volume of 50 μL and the detection wavelength at 200 nm. After extensive method development and optimization, the cyano stationary phase was used to overcome the large difference in hydrophobicity for desogestrel and ethinylestradiol, providing balanced retention for both analytes under isocratic elution. Chromatography modeling software was used to provide a rapid analysis of multiple columns and chromatography conditions. The optimized method boasts fast and efficient separation through use of a short, small I.D. column and a large injection volume of dissolution solution to achieve high sensitivity. The stable baseline from an isocratic separation allows low detection wavelengths to be used, resulting in accurate and precise quantitation of both desogestrel and ethinylestradiol. The method has been successfully validated for specificity, linearity, accuracy and precision in the range of 75 – 600 ng/mL for desogestrel and 10 – 80 ng/mL for ethinylestradiol using both HPLC and UHPLC systems. The method robustness was characterized using a design of experiment approach, and the operational design region of the method was established.

An Accidental Genetic Epidemiologist.

I briefly describe my early life and how, through a series of serendipitous events, I became a genetic epidemiologist. I discuss how the Elston-Stewart algorithm was discovered and its contribution to segregation, linkage, and association analysis. New linkage findings and paternity testing resulted from having a genotyping lab. The different meanings of interaction-statistical and biological-are clarified. The computer package S.A.G.E. (Statistical Analysis for Genetic Epidemiology), based on extensive method development over two decades, was conceived in 1986, flourished for 20 years, and is now freely available for use and further development. Finally, I describe methods to estimate and test hypotheses about familial correlations, and point out that the liability model often used to estimate disease heritability estimates the heritability of that liability, rather than of the disease itself, and so can be highly dependent on the assumed distribution of that liability.

Smart stitching: adding lateral priors to ensemble inversions as a post-processing step

The last decade has seen extensive development of Bayesian geophysical inversion methods which produce ensembles of models as outputs. Many of these are limited to producing 1D or very simple and n...

Standardized, Scalable, and Timely Flexible Adeno-Associated Virus Vector Production Using Frozen High-Density HEK-293 Cell Stocks and CELLdiscs.

Adeno-associated virus (AAV) vectors currently represent the most attractive platform for viral gene therapy and are also valuable research tools to study gene function or establish disease models. Consequently, many academic labs, core facilities, and biotech/pharma companies meanwhile produce AAVs for research and early clinical development. Whereas fast, universal protocols for vector purification (downstream processing) are available, AAV production using adherent HEK-293 cells still requires time-consuming passaging and extensive culture expansion before transfection. Moreover, most scalable culture platforms require special equipment or extensive method development. To tackle these limitations in upstream processing, this study evaluated frozen high-density cell stocks as a ready-to-seed source of producer cells, and further investigated the multilayered CELLdisc culture system for upscaling. The results demonstrate equal AAV productivity using frozen cell stock–derived cultures compared to conventionally cultured cells, as well as scalability using CELLdiscs. Thus, by directly seeding freshly thawed cells into CELLdiscs, AAV production can be easily upscaled and efficiently standardized to low-passage, high-viability cells in a timely flexible manner, potentially dismissing time-consuming routine cell culture work. In conjunction with a further optimized iodixanol protocol, this process enabled supply to a large-animal study with two high-yield AAV2 capsid variant batches (0.6–1.2 × 1015 vector genomes) in as little as 4 weeks.

Development and validation of the RapidHIT™ 200 utilising NGMSElect™ Express for the processing of buccal swabs

The RapidHIT™ 200 System is a fully automated sample-to-DNA profile system designed to produce high quality DNA profiles within 2h. The use of RapidHIT™ 200 System within the United Kingdom Criminal Justice System (UKCJS) has required extensive development and validation of methods with a focus on AmpFℓSTR® NGMSElect™ Express PCR kit to comply with specific regulations for loading to the UK National DNA Database (NDNAD). These studies have been carried out using single source reference samples to simulate live reference samples taken from arrestees and victims for elimination. The studies have shown that the system is capable of generating high quality profile and has achieved the accreditations necessary to load to the NDNAD; a first for the UK.

High resolution separations of charge variants and disulfide isomers of monoclonal antibodies and antibody drug conjugates using ultra-high voltage capillary electrophoresis with high electric field strength

Ultra-high voltage capillary electrophoresis with high electric field strength has been applied to the separation of the charge variants, drug conjugates, and disulfide isomers of monoclonal antibodies. Samples composed of many closely related species are difficult to resolve and quantify using traditional analytical instrumentation. High performance instrumentation can often save considerable time and effort otherwise spent on extensive method development. Ideally, the resolution obtained for a given CE buffer system scales with the square root of the applied voltage. Currently available commercial CE instrumentation is limited to an applied voltage of approximately 30kV and a maximum electric field strength of 1kV/cm due to design limitations. The instrumentation described here is capable of safely applying potentials of at least 120kV with electric field strengths over 2000V/cm, potentially doubling the resolution of the best conventional CE buffer/capillary systems while decreasing analysis time in some applications. Separations of these complex mixtures using this new instrumentation demonstrate the potential of ultra-high voltage CE to identify the presence of previously unresolved components and to reduce analysis time for complex mixtures of antibody variants and drug conjugates.

Origins of mtDNA mutations in ageing.

MtDNA mutations are one of the hallmarks of ageing and age-related diseases. It is well established that somatic point mutations accumulate in mtDNA of multiple organs and tissues with increasing age and heteroplasmy is universal in mammals. However, the origin of these mutations remains controversial. The long-lasting hypothesis stating that mtDNA mutations emanate from oxidative damage via a self-perpetuating mechanism has been extensively challenged in recent years. Contrary to this initial ascertainment, mtDNA appears to be well protected from action of reactive oxygen species (ROS) through robust protein coating and endomitochondrial microcompartmentalization. Extensive development of scrupulous high-throughput DNA sequencing methods suggests that an imperfect replication process, rather than oxidative lesions are the main sources of mtDNA point mutations, indicating that mtDNA polymerase γ (POLG) might be responsible for the majority of mtDNA mutagenic events. Here, we summarize the recent knowledge in prevention and defence of mtDNA oxidative lesions and discuss the plausible mechanisms of mtDNA point mutation generation and fixation.

Quantitative Analysis of Mixed Halogen Dioxins and Furans in Fire Debris Utilizing Atmospheric Pressure Ionization Gas Chromatography-Triple Quadrupole Mass Spectrometry.

Residential and commercial fires generate a complex mixture of volatile, semivolatile, and nonvolatile compounds. This study focused on the semi/nonvolatile components of fire debris to better understand firefighter exposure risks. Using the enhanced sensitivity of gas chromatography coupled to atmospheric pressure ionization-tandem mass spectrometry (APGC-MS/MS), complex fire debris samples collected from simulation fires were analyzed for the presence of potentially toxic polyhalogenated dibenzo-p-dioxins and dibenzofurans (PXDD/Fs and PBDD/Fs). Extensive method development was performed to create multiple reaction monitoring (MRM) methods for a wide range of PXDD/Fs from dihalogenated through hexa-halogenated homologue groups. Higher halogenated compounds were not observed due to difficulty eluting them off the long column used for analysis. This methodology was able to identify both polyhalogenated (mixed bromo-/chloro- and polybromo-) dibenzo-p-dioxins and dibenzofurans in the simulated burn study samples collected, with the dibenzofuran species being the dominant compounds in the samples. Levels of these compounds were quantified as total homologue groups due to the limitations of commercial congener availability. Concentration ranges in household simulation debris were observed at 0.01-5.32 ppb (PXDFs) and 0.18-82.11 ppb (PBDFs). Concentration ranges in electronics simulation debris were observed at 0.10-175.26 ppb (PXDFs) and 0.33-9254.41 ppb (PBDFs). Samples taken from the particulate matter coating the firefighters' helmets contained some of the highest levels of dibenzofurans, ranging from 4.10 ppb to 2.35 ppm. The data suggest that firefighters and first responders at fire scenes are exposed to a complex mixture of potentially hundreds to thousands of different polyhalogenated dibenzo-p-dioxins and dibenzofurans that could negatively impact their health.

Development and beyond: Strategy for long-term maintenance of an online laser diffraction particle size method in a spray drying manufacturing process

The purpose of this manuscript is to present the intended use and long-term maintenance strategy of an online laser diffraction particle size method used for process control in a spray drying process. A Malvern Insitec was used for online particle size measurements and a Malvern Mastersizer was used for offline particle size measurements. The two methods were developed in parallel with the Mastersizer serving as the reference method. Despite extensive method development across a range of particle sizes, the two instruments demonstrated different sensitivities to material and process changes over the product lifecycle. This paper will describe the procedure used to ensure consistent alignment of the two methods, thus allowing for continued use of online real-time laser diffraction as a surrogate for the offline system over the product lifecycle.

Comorbidities in cerebrovascular diseases

Cerebrovascular diseases are the major cause of morbidity and mortality among adults. The extensive development of various diagnostic methods and their introduction into routine practice increased the detection of previously underappreciated and unknown neurological diseases. Comorbidity, i.e. the joining of various other disorders of nervous system (neurodegenerative or demyelinating) to cerebrovascular disease, often leads to a layering of additional symptoms which contribute to a significant decline of the quality of life and increase the costs of treatment. In this clinical analysis case histories of patients with combined disorders of the nervous system are reviewed. Approaches to the diagnostic strategy and the need for personalized treatment based on the identified comorbidity are discussed.

Stabilization of human urine doping control samples: a current opinion

Transportation of doping control urine samples from the collection sites to the World Anti-doping Agency (WADA) Accredited Laboratories is conducted under ambient temperatures. When sample delivery is not immediate, microbial contamination of urine, especially in summer, is a common phenomenon that may affect sample integrity and may result in misinterpretation of analytical data. Furthermore, the possibility of intentional contamination of sports samples during collection with proteolytic enzymes, masking the abuse of prohibited proteins such as erythropoietin (EPO) and peptide hormones, is a practice that has already been reported. Consequently, stabilization of urine samples with a suitable method in a way that protects samples' integrity is important. Currently, no stabilization method is applied in the sample collection equipment system in order to prevent degradation of urine compounds. The present work is an overview of a study, funded by WADA, on degradation and stabilization aspects of sports urine samples against the above threats of degradation. Extensive method development resulted in the creation of a mixture of chemical agents for the stabilization of urine. Evaluation of results demonstrated that the stabilization mixture could stabilize endogenous steroids, recombinant EPO, and human chorionic gonadotropin in almost the entire range of the experimental conditions tested.

Development of a nasal cast model to test medicinal nasal devices

Bespak, a division of Consort Medical plc, and Queen's University Belfast have developed a viable and unique in-vitro testing capability for nasal drug delivery devices. The aim was to evaluate and optimize current and conceptual drug delivery devices by quantifying the deposition of drug in the various distinct regions of the nasal cavity. The development of this test apparatus employed computed tomography (CT) scan data of the human nasal cavity to construct an accurate representation of the human nasal airways. An investigation of suitable materials and manufacturing technologies was required, together with extensive analytical method development. It is possible for this technique to be further developed in an attempt to create a standardized apparatus based on nasal geometry that can be used to compare accurately deposition from drug delivery devices. This paper presents the issues encountered in the development of this test apparatus, including manufacturing and material limitations, investigation and choice of suitable materials, laboratory testing considerations, and the steps required to validate the analytical process.

Time-resolved diffraction studies into the pressure acid leaching of nickel laterite ores: a comparison of laboratory and synchrotron X-ray experiments

This paper compares time-resolved diffraction experiments that have been performed using laboratory and synchrotron X-ray sources. The experiments investigated the mechanism and kinetics of pressure acid leaching of nickel laterite ores. The sample environment was a purpose-built capillary reaction vessel, and extensive method development was conducted in the laboratory using Mo Kα radiation prior to repeating and extending the experiments at the Daresbury Synchrotron Radiation Source, beamline MPW6.2. In general, the synchrotron results confirmed the findings from previously reported laboratory work and also confirmed the presence of a minor phase that had been ambiguous in the laboratory experiments,i.e.the formation of hematite in the pressure acid leaching of saprolite. The synchrotron measurements also extended the experimental programme to include poorly diffracting laterite components that could not be examined in the laboratory,e.g.nontronite. The results from these components supported the reaction mechanisms determined fromex-situanalyses conducted in larger scale autoclaves.

Biotechnological Approach to the Synthesis of 9α‐Hydroxylated Steroids

The steroid 9α‐hydroxylase gene has been cloned from Mycobacterium smegmatis into Escherichia coli BL21. Progesterone added to bioreactors was subjected to in vivo transformation into 9α‐hydroxyprogesterone. In 7 days, 43.6 mg 9α‐hydroxyprogesterone was formed from 53.8 mg/L progesterone. The enzyme also has shown evidence of processing 4‐androstene‐3,17‐dione in vivo. An extensive analytical method development, including LLE, HPLC‐DAD, MS, and NMR was performed to verify the product and to enable a quantitative analysis. Protocols for analytical and preparative separation have been developed, using binaphtol as internal standard. Both the growth pattern and the bioconversion rate were unaffected by the presence of binaphtol in the bioreactor. The enzyme was purified by immobilised metal affinity and ion exchange chromatography, resulting in low in vitro activity.