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Methods Protoc., Volume 2, Issue 4 (December 2019) – 13 articles

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Cover Story (view full-size image) Hypertrophic cardiomyopathy is a prevalent and complex cardiovascular disease with no effective [...] Read more.
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Open AccessArticle
Using DosiVox to Reconstruct Radiation Transport through Complex Archaeological Environments
Methods Protoc. 2019, 2(4), 91; https://doi.org/10.3390/mps2040091 - 11 Dec 2019
Viewed by 193
Abstract
The DosiVox programme is used to reconstruct radiation transport in complex depositional environments. Using two archaeological case studies from ancient Egypt, the burial environments for a selection of ceramic vessels are reconstructed using the DosiVox programme, allowing the simulation of the emission and [...] Read more.
The DosiVox programme is used to reconstruct radiation transport in complex depositional environments. Using two archaeological case studies from ancient Egypt, the burial environments for a selection of ceramic vessels are reconstructed using the DosiVox programme, allowing the simulation of the emission and transport of radiation throughout these burial environments. From this simulation we can extract the external dose rate of the archaeological samples, a measurement necessary for determine a luminescence age. We describe in detail how DosiVox can be used to best advantage at sites with complex depositional histories and highlight that DosiVox is a valuable tool in luminescence dating. This work illustrates that DosiVox is, at present, unparalleled in reconstructing a more accurate and detailed external gamma dose rate which can significantly improve upon simplistic scaled geometric models. Full article
(This article belongs to the Special Issue Methods in Dating and Other Applications using Luminescence)
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Open AccessArticle
Testing Luminescence Dating Methods for Small Samples from Very Young Fluvial Deposits
Methods Protoc. 2019, 2(4), 90; https://doi.org/10.3390/mps2040090 - 06 Dec 2019
Viewed by 287
Abstract
The impetus behind this study is to understand the sedimentological dynamics of very young fluvial systems in the Amazon River catchment and relate these to land use change and modern analogue studies of tidal rhythmites in the geologic record. Initial quartz optically stimulated [...] Read more.
The impetus behind this study is to understand the sedimentological dynamics of very young fluvial systems in the Amazon River catchment and relate these to land use change and modern analogue studies of tidal rhythmites in the geologic record. Initial quartz optically stimulated luminescence (OSL) dating feasibility studies have concentrated on spit and bar deposits in the Rio Tapajós. Many of these features have an appearance of freshly deposited pristine sand, and these observations and information from anecdotal evidence and LandSat imagery suggest an apparent decadal stability. The characteristics of OSL from small (~5 cm) sub-samples from ~65 cm by ~2 cm diameter vertical cores are quite remarkable. Signals from medium-sized aliquots (5 mm diameter) exhibit very high specific luminescence sensitivity, have excellent dose recovery and recycling, essentially independent of preheat, and show minimal heat transfer even at the highest preheats. These characteristics enable measurement of very small signals with reasonable precision and, using modified single-aliquot regenerative-dose (SAR) approaches, equivalent doses as low as ~4 mGy can be obtained. Significant recuperation is observed for samples from two of the study sites and, in these instances, either the acceptance threshold was increased or growth curves were forced through the origin; recuperation is considered most likely to be a measurement artefact given the very small size of natural signals. Dose rates calculated from combined inductively coupled plasma mass spectrometry/inductively coupled plasma optical emission spectrometry (ICP-MS/ICP-OES) and high-resolution gamma spectrometry range from ~0.3 to 0.5 mGya−1, and OSL ages for features so far investigated range from 13 to 34 years to several 100 years. Sampled sands are rich in quartz and yields of 212–250 μm or 250–310 μm grains indicate high-resolution sampling at 1–2 cm intervals is possible. Despite the use of medium-sized aliquots to ensure the recovery of very dim natural OSL signals, these results demonstrate the potential of OSL for studying very young active fluvial processes in these settings. Full article
(This article belongs to the Special Issue Methods in Dating and Other Applications using Luminescence)
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Open AccessProtocol
Optimized Extraction of Insect Genomic DNA for Long-Read Sequencing
Methods Protoc. 2019, 2(4), 89; https://doi.org/10.3390/mps2040089 - 23 Nov 2019
Viewed by 461
Abstract
Long-read sequencing technologies continue to increase the length of reads, and at present can average read lengths of >20 kb up to 60–80 kb. Now the challenge is to extract genomic DNA of sufficient fragment size and quality to support longer read lengths. [...] Read more.
Long-read sequencing technologies continue to increase the length of reads, and at present can average read lengths of >20 kb up to 60–80 kb. Now the challenge is to extract genomic DNA of sufficient fragment size and quality to support longer read lengths. We developed a successful method to consistently obtain high-quality long genomic DNA from insects. The optimal developmental stage of insects for genomic DNA extraction was determined to be the pupal stage, eliminating DNA from ingested food and reducing contamination by chitinous material that can interfere with extraction. Improved results were obtained by a modified procedure of a commercial genomic DNA extraction kit. Initially, soft pupal tissue of the red flour beetle, Tribolium castaneum, was disrupted in the kit lysis buffer using Teflon micropestles. Modifications to the kit protocol also included gentle mixing by inversion of the tube, instead of harsh vortexing steps, and using wide-bore pipette tips in transferring fractions containing genomic DNA. Data from one sample were provided as an example of successful downstream library production and sequencing. While the technique has been optimized for insects, extractions from tissues of other organisms using these modified procedures also may improve long-read sequencing results. Full article
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Open AccessArticle
Sampling Methods for Luminescence Dating of Subsurface Deposits from Cores
Methods Protoc. 2019, 2(4), 88; https://doi.org/10.3390/mps2040088 - 22 Nov 2019
Viewed by 267
Abstract
Study of subsurface deposits often requires coring or drilling to obtain samples for sedimentologic and geochemical analysis. Geochronology is a critical piece of information for stratigraphic correlation and rate calculations. Increasingly, luminescence dating is applied to sediment cores to obtain depositional ages. This [...] Read more.
Study of subsurface deposits often requires coring or drilling to obtain samples for sedimentologic and geochemical analysis. Geochronology is a critical piece of information for stratigraphic correlation and rate calculations. Increasingly, luminescence dating is applied to sediment cores to obtain depositional ages. This paper provides examples and discussion of guidelines for sampling sediment core for luminescence dating. Preferred protocols are dependent on the extraction method, sedimentology, core integrity, and storage conditions. The methods discussed include subsampling of sediment in opaque core-liners, cores without liners, previously open (split) cores, bucket auger samples, and cuttings, under red lighting conditions. Two important factors for luminescence sampling of sediment core relate to the integrity of the natural luminescence signal and the representation of the dose rate environment. The equivalent dose sample should remain light-safe such that the burial dose is not reset (zeroed) by light exposure. The sediment sampled for dose rate analyses must accurately represent all units within at least 15 cm above and below the equivalent dose sample. Where lithologic changes occur, units should be sampled individually for dose rate determination. Sediment core extraction methods vary from portable, hand-operated devices to large truck- or vessel-mounted drill rigs. We provide recommendations for luminescence sampling approaches from subsurface coring technologies and downhole samplers that span shallow to deep sample depths. Full article
(This article belongs to the Special Issue Methods in Dating and Other Applications using Luminescence)
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Open AccessProtocol
Transferring Grains from Single-Grain Luminescence Discs to SEM Specimen Stubs
Methods Protoc. 2019, 2(4), 87; https://doi.org/10.3390/mps2040087 - 21 Nov 2019
Viewed by 318
Abstract
The grain transfer protocol presents a step-by-step guide on how to successfully transfer positioned grains from a single-grain luminescence disc to a scanning electron microscope (SEM) specimen stub and how to transport them between laboratories. Single-grain luminescence analysis allows the determination of luminescence [...] Read more.
The grain transfer protocol presents a step-by-step guide on how to successfully transfer positioned grains from a single-grain luminescence disc to a scanning electron microscope (SEM) specimen stub and how to transport them between laboratories. Single-grain luminescence analysis allows the determination of luminescence characteristics for individual sand-sized grains. By combining such luminescence data with other grain properties such as geochemical composition, shape, or structure also at single-grain level, it is possible to investigate factors controlling luminescence signals or study other material properties. The non-luminescence properties are typically measured in another instrument; thus, grains need to be transferred between machines and sample holders, and sometimes also between laboratories. It is then important that the position of each grain is known and stable so that the properties from the same grain are compared. By providing an easily observable orientation marker on the specimen stub, the hundred numbered grains from the single-grain disc can be transferred and later identified when analyzed in the SEM. Full article
(This article belongs to the Special Issue Methods in Dating and Other Applications using Luminescence)
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Open AccessProtocol
A Method to Reuse Archived H&E Stained Histology Slides for a Multiplex Protein Biomarker Analysis
Methods Protoc. 2019, 2(4), 86; https://doi.org/10.3390/mps2040086 - 15 Nov 2019
Viewed by 342
Abstract
Archived Hematoxylin and Eosin (H&E) stained pathology slides are routinely stored to index formalin-fixed paraffin-embedded (FFPE) sample tissue blocks. FFPE blocks are clinically annotated human tumor specimens that can be valuable in studies decades after the tissue is collected. If stored properly, they [...] Read more.
Archived Hematoxylin and Eosin (H&E) stained pathology slides are routinely stored to index formalin-fixed paraffin-embedded (FFPE) sample tissue blocks. FFPE blocks are clinically annotated human tumor specimens that can be valuable in studies decades after the tissue is collected. If stored properly, they have the potential to yield a valuable number of serial sectioned slides for diagnostic or research purposes. However, some retrospective studies are limited in scope because the tissue samples have been depleted or not enough material is available in stored blocks for serial sections. The goal of these studies was to determine if archived H&E-stained slides can be directly reutilized by optimizing methods to de-stain and then re-stain the H&E stained slides to allow the detection of several biomarkers of interest using a conjugated antibody with chromogen multiplex immunohistochemistry procedure. This simple but innovative procedure, combined with image analysis techniques, demonstrates the ability to perform precise detection of relevant markers correlated to disease progression in initially identified tumor regions in tissue. This may add clinical value in retaining H&E slides for further use. Full article
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Open AccessProtocol
Characterising Mutational Spectra of Carcinogens in the Tumour Suppressor Gene TP53 Using Human TP53 Knock-in (Hupki) Mouse Embryo Fibroblasts
Methods Protoc. 2019, 2(4), 85; https://doi.org/10.3390/mps2040085 - 13 Nov 2019
Viewed by 353
Abstract
DNA in dividing cells is prone to mutagenesis, with mutations making key contributions to human disease including cancer. The tumour suppressor gene TP53 is the most frequently mutated gene in human tumours. Here, we present a robust protocol for studying TP53 mutagenesis utilising [...] Read more.
DNA in dividing cells is prone to mutagenesis, with mutations making key contributions to human disease including cancer. The tumour suppressor gene TP53 is the most frequently mutated gene in human tumours. Here, we present a robust protocol for studying TP53 mutagenesis utilising human TP53 knock-in (Hupki) mouse embryonic fibroblasts (HUFs). In the HUF immortalisation assay (HIMA), primary HUFs are treated with known or suspected carcinogens at 3% oxygen and then transferred to 20% atmospheric oxygen to induce senescence. Cells containing mutations (e.g., in TP53) that allow bypassing of senescence eventually emerge as immortalised clonal cell lines after 2–3 months of serial passaging. As not all immortalised HUF cells contain TP53 mutations, we developed a Nutlin-3a counter-screen to select for TP53-mutated clones prior to sequencing. TP53 mutation spectra generated can be compared with those of human tumours recorded in the International Agency for Research on Cancer TP53 mutation database. Environmental mutagens that have demonstrated and validated the utility of the HIMA include ultraviolet radiation, aristolochic acid, and benzo[a]pyrene. The TP53 mutation patterns induced by these mutagens in the HIMA corresponded to those found in human tumours from patients exposed to these mutagens. The approach presented helps to deepen our understanding of human cancer aetiology. Full article
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Open AccessFeature PaperArticle
Alkaline Extraction for Lead Determination in Different Types of Commercial Paints
Methods Protoc. 2019, 2(4), 84; https://doi.org/10.3390/mps2040084 - 01 Nov 2019
Viewed by 264
Abstract
In 2017, the World Health Organization and the United Nations Environment Programme formed the Global Alliance to Eliminate Lead Paint. All alliance member countries have pledged to develop control regulations that include lead threshold limits. To improve regulations and demonstrate compliance of paint [...] Read more.
In 2017, the World Health Organization and the United Nations Environment Programme formed the Global Alliance to Eliminate Lead Paint. All alliance member countries have pledged to develop control regulations that include lead threshold limits. To improve regulations and demonstrate compliance of paint industry products, it is necessary to have adequate, locally applicable methodologies. In this sense, the main objective of this research was to validate the methodology of alkaline extraction for the quantification of lead in ten different types of Ecuadorian commercial paints using flame atomic absorption spectrophotometry. Two hundred and fifty samples from different paint industry products were analyzed, and the results were used to evaluate the method’s performance and robustness. It was determined that the method could be applied for lead concentrations above 100 mg·kg−1, and results showed relative standard deviation values lower than 14.8% and fortification recoveries between 80.3 and 119.4%, fulfilling the acceptance criteria established in the Environmental Protection Agency’s lead-based Paint Laboratory Operations Guidelines. Full article
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Open AccessProtocol
High-Throughput Phenotyping Toolkit for Characterizing Cellular Models of Hypertrophic Cardiomyopathy In Vitro
Methods Protoc. 2019, 2(4), 83; https://doi.org/10.3390/mps2040083 - 26 Oct 2019
Viewed by 511
Abstract
Hypertrophic cardiomyopathy (HCM) is a prevalent and complex cardiovascular disease characterised by multifarious hallmarks, a heterogeneous set of clinical manifestations, and several molecular mechanisms. Various disease models have been developed to study this condition, but they often show contradictory results, due to technical [...] Read more.
Hypertrophic cardiomyopathy (HCM) is a prevalent and complex cardiovascular disease characterised by multifarious hallmarks, a heterogeneous set of clinical manifestations, and several molecular mechanisms. Various disease models have been developed to study this condition, but they often show contradictory results, due to technical constraints and/or model limitations. Therefore, new tools are needed to better investigate pathological features in an unbiased and technically refined approach, towards improving understanding of disease progression. Herein, we describe three simple protocols to phenotype cellular models of HCM in vitro, in a high-throughput manner where technical artefacts are minimized. These are aimed at investigating: (1) Hypertrophy, by measuring cell volume by flow cytometry; (2) HCM molecular features, through the analysis of a hypertrophic marker, multinucleation, and sarcomeric disarray by high-content imaging; and (3) mitochondrial respiration and content via the Seahorse™ platform. Collectively, these protocols comprise straightforward tools to evaluate molecular and functional parameters of HCM phenotypes in cardiomyocytes in vitro. These facilitate greater understanding of HCM and high-throughput drug screening approaches and are accessible to all researchers of cardiac disease modelling. Whilst HCM is used as an exemplar, the approaches described are applicable to other cellular models where the investigation of identical biological changes is paramount. Full article
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Open AccessArticle
Assessing Pancreas Transplant Candidate Cardiac Disease: Preoperative Protocol Development at a Rapidly Growing Transplant Program
Methods Protoc. 2019, 2(4), 82; https://doi.org/10.3390/mps2040082 - 17 Oct 2019
Viewed by 321
Abstract
Pancreas transplant rates, despite improving outcomes, have decreased over the past two decades. This is due, in part, to ageing, increasingly co-morbid pancreas transplant candidates. There is a paucity of published data regarding coronary artery disease (CAD) in this population. To inform peri-operative [...] Read more.
Pancreas transplant rates, despite improving outcomes, have decreased over the past two decades. This is due, in part, to ageing, increasingly co-morbid pancreas transplant candidates. There is a paucity of published data regarding coronary artery disease (CAD) in this population. To inform peri-operative management strategies, we sought to understand the frequency of CAD among recipients of pancreas transplants at our center. Informed by these data, we sought to develop a standard protocol for evaluation. A retrospective review of pancreas transplants (solitary pancreas and simultaneous pancreas-kidney) was undertaken at the University of Maryland. Transplant outcomes and frequency of cardiac disease were analyzed. Current data were compared with historic controls. Over the study period, 59 patients underwent pancreas transplantation. Coronary architecture was assessed in 38 patients (64.4%). Discrete evidence of CAD was present in 28 of 39 patients (71.7%). All pancreas candidates (n = 21) who underwent left heart catheterization (LHC) demonstrated CAD (100%). No patients experienced myocardial infarction (MI) and no deaths resulted from cardiac disease in the early post-transplant period. Pancreas transplant candidates are at high risk for CAD. At a center in which pancreas transplant rates are increasing, a rigorous cardiac work up revealed that 71.7% of assessed recipients had CAD. Although asymptomatic, 6.8% required coronary artery bypass graft (CABG). Despite increasing age and co-morbid status, pancreas transplant recipients can enjoy excellent results if protocolized preoperative testing is used. Full article
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Open AccessProtocol
Simple and Quick Visualization of Periodical Data Using Microsoft Excel
Methods Protoc. 2019, 2(4), 81; https://doi.org/10.3390/mps2040081 - 11 Oct 2019
Viewed by 831
Abstract
Actograms are well-established methods used for visualizing periodic activity of animals in chronobiological research. They help in the understanding of the overall characteristics of rhythms and are instrumental in defining the direction of subsequent detailed analysis. Although there exists specialized software for creating [...] Read more.
Actograms are well-established methods used for visualizing periodic activity of animals in chronobiological research. They help in the understanding of the overall characteristics of rhythms and are instrumental in defining the direction of subsequent detailed analysis. Although there exists specialized software for creating actograms, new users such as students and researchers from other fields often find it inconvenient to use. In this study, we demonstrate a fast and easy method to create actograms using Microsoft Excel. As operations in Excel are simple and user-friendly, it takes only a few minutes to create an actogram. Using this method, it is possible to obtain a visual understanding of the characteristics of rhythms not only from typical activity data, but also from any kind of time-series data such as body temperature, blood sugar level, gene expressions, sleep electroencephalogram, heartbeat, and so on. The actogram thus created can also be converted to the "heatogram” shown by color temperature. As opposed to conventional chronograms, this new type of chronogram facilitates easy understanding of rhythmic features in a more intuitive manner. This method is therefore convenient and beneficial for a broad range of researchers including students as it aids in the better understanding of periodic phenomena from a large amount of time-series data. Full article
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Open AccessEditorial
“Cell-Free Synthetic Biology”: Synthetic Biology Meets Cell-Free Protein Synthesis
Methods Protoc. 2019, 2(4), 80; https://doi.org/10.3390/mps2040080 - 08 Oct 2019
Viewed by 555
Abstract
Since Nirenberg and Matthaei used cell-free protein synthesis (CFPS) to elucidate the genetic code in the early 1960s [...] Full article
(This article belongs to the Special Issue Cell-Free Synthetic Biology) Printed Edition available
Open AccessProtocol
Isolation, Maintenance and Differentiation of Primary Tracheal Basal Cells from Adult Rhesus Macaque
Methods Protoc. 2019, 2(4), 79; https://doi.org/10.3390/mps2040079 - 01 Oct 2019
Viewed by 468
Abstract
In this report, we describe methodologies for the isolation and culture of primary rhesus macaque tracheal basal cells, their cryopreservation, long term storage and differentiation. These are comparable to state-of-the-art protocols that have been developed for mouse and human airway basal cells. This [...] Read more.
In this report, we describe methodologies for the isolation and culture of primary rhesus macaque tracheal basal cells, their cryopreservation, long term storage and differentiation. These are comparable to state-of-the-art protocols that have been developed for mouse and human airway basal cells. This method is based on the use of proprietary media, providing an easily reproducible and applicable protocol for usage in biosafety level 2 (BSL2) settings. Tracheas from rhesus macaques were isolated after animal euthanasia and subjected to enzymatic digestion overnight. Cells of the epithelial layer were scraped off of the trachea for cell culture. Twenty-four hours after plating basal cells had attached and nonadherent cells were removed. First passages of basal cells can be frozen for early passage storage in liquid nitrogen or propagated and differentiated on an air–liquid interface and in a tracheosphere assay up to passage seven. This protocol provides a platform for the analysis of basal cells from a close evolutionary relative to humans. Full article
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