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Methods and Protocols 2022
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Methods and Protocols 2022

A special issue of Methods and Protocols (ISSN 2409-9279).

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 41640

Special Issue Editors

Prof. Dr. Fernando Albericio

E-Mail Website
Guest Editor
1. School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
2. Department of Organic Chemistry, University of Barcelona, Barcelona, Spain
Interests: antimicrobial peptides; solid-phase chemistry; combinatorial chemistry; drug delivery systems; peptide drug conjugates; orthogonal chemistry; drug discovery; biomaterials
Special Issues, Collections and Topics in MDPI journals
Dr. Jongik Hwang

E-Mail Website
Guest Editor
‎Graduate School of Biomedical Science, College of Medicine, Korea University, 145 Anam-ro, Anam-dong, Seongbuk-gu, Seoul 02841, Republic of Korea
Interests: GPCR signaling; drug development; inflammation

Special Issue Information

Dear Colleagues,

We are pleased to announce a Special Issue entitled “Methods and Protocols 2022”, which will be the New Year Special Issue Series of Methods and Protocols.

For this Special Issue, we are seeking the submissions from our Academic Editors, authors, and reviewers. The papers in this Special Issue will be published via our open-access platform after a thorough peer review.

We look forward to receiving your excellent work.

Prof. Dr. Fernando Albericio
Dr. Jongik Hwang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Methods and Protocols is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

New Year Special Issue Series

This Special Issue is a part of Methods and Protocols’s New Year Special Issue Series. The series reflects on the achievements, scientific progress, and “hot topics” of the previous year in the journal. Submissions of articles whose lead authors are our Editorial Board Members are highly encouraged. However, we welcome articles from all authors.

Published Papers (15 papers)

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10 pages, 1580 KiB  
Article
Test−Retest Reliability of Isokinetic Ankle, Knee and Hip Strength in Physically Active Adults Using Biodex System 4 Pro
by Juho Tuominen, Mari Leppänen, Heidi Jarske, Kati Pasanen, Tommi Vasankari and Jari Parkkari
Methods Protoc. 2023, 6(2), 26; https://0-doi-org.brum.beds.ac.uk/10.3390/mps6020026 - 09 Mar 2023
Cited by 5 | Viewed by 3214
Abstract
Background: The isokinetic dynamometry is considered a gold standard in muscle strength testing. The reliability of lower limb isokinetic strength measurements has not been thoroughly evaluated. Objective: To examine the test−retest reliability of isokinetic ankle plantar and dorsiflexion, ankle inversion and eversion, knee [...] Read more.
Background: The isokinetic dynamometry is considered a gold standard in muscle strength testing. The reliability of lower limb isokinetic strength measurements has not been thoroughly evaluated. Objective: To examine the test−retest reliability of isokinetic ankle plantar and dorsiflexion, ankle inversion and eversion, knee extension and flexion and hip abduction and adduction strength in physically active adults using Biodex System 4 Pro. Methods: Peak torques (PTs) and average peak torques (APTs) of the dominant and nondominant lower limbs were tested twice in 19 physically active adults 7 to 14 days apart. Results: The intraclass correlation coefficients (ICC) values varied from excellent to moderate and coefficient of variation of typical error (CVTE) values were 6.6–19.5%. Change in the mean expressed as a percent varied from −3.1% to 9.6%. There was no difference in the reliability between PT and APT values. Dominant lower limb was more reliable in every case if there was difference between limbs. Conclusion: Test−retest reliability of isokinetic ankle, knee and hip strength in physically active adults using Biodex System 4 is mostly good or excellent. However, the observed range of the random variation has to be noted when using it in scientific follow-up studies or evaluation of patient progress in clinical settings. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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13 pages, 34735 KiB  
Article
Quantitative 1H Nuclear Magnetic Resonance (qNMR) of Aromatic Amino Acids for Protein Quantification
by Teodor Tchipilov, Klas Meyer and Michael G. Weller
Methods Protoc. 2023, 6(1), 11; https://0-doi-org.brum.beds.ac.uk/10.3390/mps6010011 - 23 Jan 2023
Viewed by 2560
Abstract
Hydrolysis of protein samples into amino acids facilitates the use of NMR spectroscopy for protein and peptide quantification. Different conditions have been tested for quantifying aromatic amino acids and proteins. The pH-dependent signal shifts in the aromatic region of amino acid samples were [...] Read more.
Hydrolysis of protein samples into amino acids facilitates the use of NMR spectroscopy for protein and peptide quantification. Different conditions have been tested for quantifying aromatic amino acids and proteins. The pH-dependent signal shifts in the aromatic region of amino acid samples were examined. A pH of 12 was found to minimize signal overlap of the four aromatic amino acids. Several aromatic compounds, such as terephthalic acid, sulfoisophthalic acid, and benzene tricarboxylic acid, were applied as internal standards. The quantification of amino acids from an amino acid standard was performed. Using the first two suggested internal standards, recovery was ~97% for histidine, phenylalanine, and tyrosine at a concentration of approximately 1 mM in solution. Acidic hydrolysis of a certified reference material (CRM) of bovine serum albumin (BSA) and subsequent quantification of Phe and Tyr yielded recoveries of 98% ± 2% and 88% ± 4%, respectively, at a protein concentration of 16 g/L or 250 µM. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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16 pages, 2733 KiB  
Article
Engineering Ag43 Signal Peptides with Bacterial Display and Selection
by Darius Wen-Shuo Koh, Jian-Hua Tay and Samuel Ken-En Gan
Methods Protoc. 2023, 6(1), 1; https://0-doi-org.brum.beds.ac.uk/10.3390/mps6010001 - 23 Dec 2022
Viewed by 2387
Abstract
Protein display, secretion, and export in prokaryotes are essential for utilizing microbial systems as engineered living materials, medicines, biocatalysts, and protein factories. To select for improved signal peptides for Escherichia coli protein display, we utilized error-prone polymerase chain reaction (epPCR) coupled with single-cell [...] Read more.
Protein display, secretion, and export in prokaryotes are essential for utilizing microbial systems as engineered living materials, medicines, biocatalysts, and protein factories. To select for improved signal peptides for Escherichia coli protein display, we utilized error-prone polymerase chain reaction (epPCR) coupled with single-cell sorting and microplate titer to generate, select, and detect improved Ag43 signal peptides. Through just three rounds of mutagenesis and selection using green fluorescence from the 56 kDa sfGFP-beta-lactamase, we isolated clones that modestly increased surface display from 1.4- to 3-fold as detected by the microplate plate-reader and native SDS-PAGE assays. To establish that the functional protein was displayed extracellularly, we trypsinized the bacterial cells to release the surface displayed proteins for analysis. This workflow demonstrated a fast and high-throughput method leveraging epPCR and single-cell sorting to augment bacterial surface display rapidly that could be applied to other bacterial proteins. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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15 pages, 2354 KiB  
Article
Comparison of Different Fixation Methods for Combined Histological and Biomolecular Analysis of Fixed and Decalcified Bone Samples
by Sarah Al-Maawi, Priscilia Valenzuela, Eva Dohle, Anja Heselich, Robert Sader and Shahram Ghanaati
Methods Protoc. 2022, 5(4), 64; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5040064 - 21 Jul 2022
Viewed by 3072
Abstract
The combination of histological and biomolecular analyses provides deep understanding of different biological processes and is of high interest for basic and applied research. However, the available analytical methods are still limited, especially when considering bone samples. This study compared different fixation media [...] Read more.
The combination of histological and biomolecular analyses provides deep understanding of different biological processes and is of high interest for basic and applied research. However, the available analytical methods are still limited, especially when considering bone samples. This study compared different fixation media to identify a sufficient analytical method for the combination of histological, immuno-histological and biomolecular analyses of the same fixed, processed and paraffin embedded bone sample. Bone core biopsies of rats’ femurs were fixed in different media (RNAlater + formaldehyde (R + FFPE), methacarn (MFPE) or formaldehyde (FFPE)) for 1 week prior to decalcification by EDTA and further histological processing and paraffin embedding. Snap freezing (unfixed frozen tissue, UFT) and incubation in RNAlater were used as additional controls. After gaining the paraffin sections for histological and immunohistological analysis, the samples were deparaffined and RNA was isolated by a modified TRIZOL protocol. Subsequently, gene expression was evaluated using RT-qPCR. Comparable histo-morphological and immuno-histological results were evident in all paraffin embedded samples of MFPE, FFPE and R + FFPE. The isolated RNA in the group of MFPE showed a high concentration and high purity, which was comparable to the UFT and RNAlater groups. However, in the groups of FFPE and R + FFPE, the RNA quality and quantity were statistically significantly lower when compared to MFPE, UFT and RNAlater. RT-qPCR results showed a comparable outcome in the group of MFPE and UFT, whereas the groups of FFPE and R + FFPE did not result in a correctly amplified gene product. Sample fixation by means of methacarn is of high interest for clinical samples to allow a combination of histological, immunohistological and biomolecular analysis. The implementation of such evaluation method in clinical research may allow a deeper understanding of the processes of bone formation and regeneration. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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13 pages, 3618 KiB  
Article
Development and Characterisation of a Four-Plex Assay to Measure Streptococcus pyogenes Antigen-Specific IgG in Human Sera
by Alexander J. Keeley, Martina Carducci, Luisa Massai, Mariagrazia Pizza, Thushan I. de Silva, Danilo G. Moriel and Omar Rossi
Methods Protoc. 2022, 5(4), 55; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5040055 - 27 Jun 2022
Cited by 5 | Viewed by 2205
Abstract
The measurement of antibodies to vaccine antigens is crucial for research towards a safe and effective vaccine for Streptococcus pyogenes (Strep A). We describe the establishment and detailed characterisation of a four-plex assay to measure IgG to the Strep A vaccine antigens SpyCEP, [...] Read more.
The measurement of antibodies to vaccine antigens is crucial for research towards a safe and effective vaccine for Streptococcus pyogenes (Strep A). We describe the establishment and detailed characterisation of a four-plex assay to measure IgG to the Strep A vaccine antigens SpyCEP, Slo, SpyAD and GAC using the Luminex multiplex platform. A standard curve was established and characterized to allow the quantification of antigen-specific IgG. Assay specificity, precision, linearity, reproducibility and repeatability were determined via the measurement of antigen-specific IgG from pooled human serum. The assay is highly specific, reproducible and performs well across a large range of antibody concentrations against all four antigens. It is, therefore, suitable for future clinical trials in humans with a four-component vaccine, as well as for seroepidemiological studies to gain insights into naturally occurring immunity. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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16 pages, 5645 KiB  
Article
A Polarized Raman Spectroscopic Method for Advanced Analyses of the Osteon Lamellar Structure of Human Bone
by Giuseppe Pezzotti, Eiji Ishimura, Ryosuke Inai, Wenliang Zhu, Taigi Honma, Nobuhiko Sugano, Wataru Ando, Ugo Pazzaglia and Elia Marin
Methods Protoc. 2022, 5(3), 41; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5030041 - 20 May 2022
Cited by 1 | Viewed by 2322
Abstract
Raman spectroscopy has recently been used for quantitative analyses of cortical bone tissue and related materials, such as dentin and enamel. While those analyses have proven useful as potential diagnostic tools, the Raman spectrum of bone encrypts a wealth of additional molecular scale [...] Read more.
Raman spectroscopy has recently been used for quantitative analyses of cortical bone tissue and related materials, such as dentin and enamel. While those analyses have proven useful as potential diagnostic tools, the Raman spectrum of bone encrypts a wealth of additional molecular scale details about structure and crystal arrangement, which are yet to be unfolded. Such details directly link to both bone physiology and pathology. In this work, a triple monochromator spectrometer with high spectral resolution, employed in polarized light configurations, was used to extract quantitative details about the preferential crystallographic orientation of apatite and collagen components in a human proximal femoral cortical bone sample. This body of information was then used to model the bone structure at the nanometric scale through a methodology that could be key in assessments of bone structure in health and disease. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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16 pages, 3198 KiB  
Article
Capillary Western Immunoassay Optimization of Estrogen Related Factors in Human Subcutaneous Adipose Tissue
by Jessica L. Hill, Kara B. McIver, Kaleigh Katzer and Michelle T. Foster
Methods Protoc. 2022, 5(2), 34; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5020034 - 15 Apr 2022
Cited by 3 | Viewed by 3214
Abstract
Lipedema is a multifaceted chronic fat disorder characterized by the bilateral and disproportionate accumulation of fat predominantly in the lower body regions of females. Research strongly supports that estrogen factors likely contribute to the pathophysiology of this disease. We aim to help demonstrate [...] Read more.
Lipedema is a multifaceted chronic fat disorder characterized by the bilateral and disproportionate accumulation of fat predominantly in the lower body regions of females. Research strongly supports that estrogen factors likely contribute to the pathophysiology of this disease. We aim to help demonstrate this link by quantifying estrogen factor differences between women with and without lipedema. For time and lipedema adipose tissue conservation, the Protein Simple WES machine will be utilized in place of traditional western blotting. Here, we are interested in evaluating estrogen related factors, such as, but not limited to, estrogen receptors and enzymes involved in the successive conversions of cholesterol and androgens to estrogens in human subcutaneous adipose. Evaluation of these factors within adipose tissue, however, is novel for this instrument. Thus, we optimized tissue lysis and protein extraction for 11 proteins of interest. Antibodies and their working concentrations were determined based upon specific and distinguishable (signal-to-noise) peaks from electropherogram outputs across different tissue lysate concentrations. We found that overnight acetone precipitation proved to be the best procedure for extracting protein from lipid rich adipose tissue samples. Six of the eleven proteins were found to migrate to their expected molecular weights, however, five did not. For proteins that did not migrate as expected, overexpression lysates and empty vector controls were used to validate detection antibodies. Protein extract from subcutaneous adipose tissue and overexpression lysates were then combined to understand if migration was specifically altered by adipose tissue. From these results, we concluded that the lipid rich nature of adipose tissue in combination with the separation matrix designated for use with the WES were preventing the appropriate migration of some proteins rather than non-specific antibody binding or inappropriate preparation methods. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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8 pages, 3980 KiB  
Article
Assessment of Sodium Diamine Fluoride (SDF) with Light Curing Technique: A Pilot Study of Antimicrobial Effects
by Jens Wilson, Sarah Swanbeck, Gavin Banning, Tatiana Alhwayek, Victoria Sullivan, Katherine M. Howard and Karl Kingsley
Methods Protoc. 2022, 5(2), 31; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5020031 - 07 Apr 2022
Cited by 1 | Viewed by 2573
Abstract
Silver diamine fluoride (SDF) has been useful in clinical dentistry for the purpose of caries arrest and prevention. Although methods for the application of SDF are well-known among dental professionals, such as microbrush applications, few studies have explored the effect of light curing, [...] Read more.
Silver diamine fluoride (SDF) has been useful in clinical dentistry for the purpose of caries arrest and prevention. Although methods for the application of SDF are well-known among dental professionals, such as microbrush applications, few studies have explored the effect of light curing, which accelerates precipitation onto dentin, and whether this has any effect on the antimicrobial properties of SDF. To assess this technique, single (Streptococcus gordonii) and polymicrobial (mixed salivary) colonies were grown and plated using SDF applied to hydroxyapatite discs with and without treatment with curing light. Kirby–Bauer Zone of Inhibition assay results revealed no significant differences in the areas between the two treatment groups (SDF: 1.27 mm, SDF plus curing light: 1.25 mm), p = 0.887 in the single culture (S. gordonii) experiments. In addition, no significant differences were found between the two treatment groups (SDF: 1.26 mm, SDF plus curing light: 1.24 mm), p = 0.771 in the polymicrobial culture experiments. Although there may be specific properties associated with SDF induced following light curing, these differences do not appear to be associated with the antimicrobial properties affecting gram-positive or polymicrobial films. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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16 pages, 2471 KiB  
Protocol
Advanced Flow Cytometry Using the SYTO-13 Dye for the Assessment of Platelet Reactivity and Maturity in Whole Blood
by Oliver Buchhave Pedersen, Leonardo Pasalic, Erik Lerkevang Grove, Steen Dalby Kristensen, Anne-Mette Hvas and Peter H. Nissen
Methods Protoc. 2023, 6(1), 8; https://0-doi-org.brum.beds.ac.uk/10.3390/mps6010008 - 13 Jan 2023
Cited by 1 | Viewed by 2008
Abstract
Newly produced immature platelets are larger, contain higher amounts of residual RNA, and are more reactive than mature platelets. Flow cytometry using the SYTO-13 dye is a method for the subdivision of immature platelets from mature platelets based on the labelling of intracellular [...] Read more.
Newly produced immature platelets are larger, contain higher amounts of residual RNA, and are more reactive than mature platelets. Flow cytometry using the SYTO-13 dye is a method for the subdivision of immature platelets from mature platelets based on the labelling of intracellular platelet RNA, enabling the simultaneous investigation of the reactivity of each platelet population. This method provides detailed information on several aspects of platelet physiology using a combination of platelet surface markers and agonists. Currently, no standardized protocol exists across laboratories. Here, we describe a flow cytometry protocol in detail to investigate platelet reactivity and its relation to platelet maturity. We analyzed 20 healthy individuals with the protocol and compared the platelet subpopulation with the highest SYTO-13 labelling (in the first quintile, “SYTO-high”) corresponding to the most immature platelets (highest RNA content) with the platelet subpopulation with the lowest SYTO-13 labelling (in the fifth quintile, “SYTO-low”) corresponding to the mature platelets with the lowest RNA content. SYTO-high platelets had overall significantly increased platelet reactivity compared with that of SYTO-low platelets. The presented method may be a valuable research tool for the analysis of platelet reactivity and its relation to platelet maturity. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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26 pages, 3266 KiB  
Protocol
Studying miRNA–mRNA Interactions: An Optimized CLIP-Protocol for Endogenous Ago2-Protein
by Sophie Stebel, Janina Breuer and Oliver Rossbach
Methods Protoc. 2022, 5(6), 96; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5060096 - 30 Nov 2022
Cited by 1 | Viewed by 2544
Abstract
Transcriptome-wide analysis of RNA-binding partners is commonly achieved using UV crosslinking and immunoprecipitation (CLIP). Individual-nucleotide-resolution CLIP (iCLIP)enables identification of the specific position of the protein–RNA interaction. In addition to RNA-binding proteins (RBPs), microRNA (miRNA)–mRNA interactions also play a crucial role in the regulation [...] Read more.
Transcriptome-wide analysis of RNA-binding partners is commonly achieved using UV crosslinking and immunoprecipitation (CLIP). Individual-nucleotide-resolution CLIP (iCLIP)enables identification of the specific position of the protein–RNA interaction. In addition to RNA-binding proteins (RBPs), microRNA (miRNA)–mRNA interactions also play a crucial role in the regulation of gene expression. Argonaute-2 (Ago2) mediates miRNA binding to a multitude of mRNA target sites, enabling the identification of miRNA–mRNA interactions by employing modified Ago2-CLIP protocols. Here, we describe an Ago2-specific CLIP protocol optimized for the use of small quantities of cell material, targeting endogenous Ago2 while avoiding possible methodological biases such as metabolic labeling or Ago2 overexpression and applying the latest advances in CLIP library preparation, the iCLIP2 protocol. In particular, we focus on the optimization of lysis conditions and improved radioactive labeling of the 5′ end of the miRNA. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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12 pages, 8104 KiB  
Protocol
Laser Microdissection-Mediated Isolation of Butterfly Wing Tissue for Spatial Transcriptomics
by Tirtha Das Banerjee, Shen Tian and Antόnia Monteiro
Methods Protoc. 2022, 5(4), 67; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5040067 - 11 Aug 2022
Viewed by 2873
Abstract
The assignment of specific patterns of gene expression to specific cells in a complex tissue facilitates the connection between genotype and phenotype. Single-cell sequencing of whole tissues produces single-cell transcript resolution but lacks the spatial information of the derivation of each cell, whereas [...] Read more.
The assignment of specific patterns of gene expression to specific cells in a complex tissue facilitates the connection between genotype and phenotype. Single-cell sequencing of whole tissues produces single-cell transcript resolution but lacks the spatial information of the derivation of each cell, whereas techniques such as multiplex FISH localize transcripts to specific cells in a tissue but require a priori information of the target transcripts to examine. Laser dissection of tissues followed by transcriptome analysis is an efficient and cost-effective technique that provides both unbiased gene expression discovery together with spatial information. Here, we detail a laser dissection protocol for total RNA extraction from butterfly larval and pupal wing tissues, without the need of paraffin embedding or the use of a microtome, that could be useful to researchers interested in the transcriptome of specific areas of the wing during development. This protocol can bypass difficulties in extracting high quality RNA from thick fixed tissues for sequencing applications. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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14 pages, 4886 KiB  
Protocol
Measuring Electrical Responses during Acute Exposure of Roots and Rhizoids of Plants to Compounds Using a Flow-Through System
by Robin Lewis Cooper, Matthew A. Thomas, Rachael M. Vascassenno, Kaitlyn E. Brock and David Nicholas McLetchie
Methods Protoc. 2022, 5(4), 62; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5040062 - 18 Jul 2022
Cited by 2 | Viewed by 2743
Abstract
Monitoring electrical signals in plants allows the examination of their acute and chronic physiological changes and responses to stimuli. Understanding how plant roots/rhizoids respond to chemical cues in their environment will provide insight into how these structures acquire resources. Chronic exposure to L-glutamate [...] Read more.
Monitoring electrical signals in plants allows the examination of their acute and chronic physiological changes and responses to stimuli. Understanding how plant roots/rhizoids respond to chemical cues in their environment will provide insight into how these structures acquire resources. Chronic exposure to L-glutamate alters root growth and is known to alter Ca2+ flux inside roots. The ionic flux can be detected by electrical changes. A rapid and relatively easy approach is presented to screen the electrical sensitivity of roots/rhizoids to compounds such as amino acids and known agonists/antagonists to receptors and ion channels. The approach uses a background-flow system of basal salt or water; then, the administered compounds are added to the roots/rhizoids while monitoring their electrical responses. As a proof of concept, the response to flow-through of glutamate (1 mM) was targeted at the root/rhizoids of three plants (Arabidopsis thaliana, Pisum sativum and Marchantia inflexa). Both Arabidopsis thaliana and Pisum sativum produced rapid depolarization upon exposure to glutamate, while M. inflexa did not show an electrical response. In some experiments, simultaneous recordings with impedance measures for acute changes and glass electrodes for chronic electrical potential changes were used. The effect of potassium chloride (300 mM) as a depolarizing stimulus produced responses in both P. sativum and M. inflexa. The protocol presented can be used to screen various compounds in a relatively rapid manner for responsiveness by the roots/rhizoids of plants. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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19 pages, 6555 KiB  
Protocol
Impedance Measures for Detecting Electrical Responses during Acute Injury and Exposure of Compounds to Roots of Plants
by Robin Lewis Cooper, Matthew A. Thomas and David Nicholas McLetchie
Methods Protoc. 2022, 5(4), 56; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5040056 - 30 Jun 2022
Cited by 1 | Viewed by 3261
Abstract
Electrical activity is widely used for assessing a plant’s response to an injury or environmental stimulus. Commonly, a differential electrode recording between silver wire leads with the reference wire connected to the soil, or a part of the plant, is used. One method [...] Read more.
Electrical activity is widely used for assessing a plant’s response to an injury or environmental stimulus. Commonly, a differential electrode recording between silver wire leads with the reference wire connected to the soil, or a part of the plant, is used. One method uses KCl-filled glass electrodes placed into the plant, similar to recording membrane/cell potentials in animal tissues. This method is more susceptible to artifacts of equipment noise and photoelectric effects than an impedance measure. An impedance measure using stainless steel wires is not as susceptible to electrically induced noises. Impedance measurements are able to detect injury in plants as well as exposure of the roots to environmental compounds (glutamate). The impedance measures were performed in 5 different plants (tomato, eggplant, pepper, liverwort, and Coleus scutellarioides), and responses to mechanical movement of the plant, as well as injury, were recorded. Monitoring electrical activity in a plant that arises in a distant plant was also demonstrated using the impedance method. The purpose of this report is to illustrate the ease in using impedance measures for monitoring electrical signals from individual plants or aggregates of plants for potentially scaling for high throughput and monitoring controlled culturing and outdoor field environments. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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22 pages, 554 KiB  
Protocol
Healthcare Service Interventions to Improve the Healthcare Outcomes of Hospitalised Patients with Extreme Obesity: Protocol for an Evidence and Gap Map
by Caz Hales, Rebecca Chrystall, Anne M. Haase and Mona Jeffreys
Methods Protoc. 2022, 5(3), 48; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5030048 - 08 Jun 2022
Viewed by 2360
Abstract
Hospitalised patients with extreme obesity have poorer healthcare outcomes compared to normal weight patients. How hospital services are coordinated and delivered to meet the care needs of patients with extreme obesity is not well understood. The aim of the proposed evidence gap map [...] Read more.
Hospitalised patients with extreme obesity have poorer healthcare outcomes compared to normal weight patients. How hospital services are coordinated and delivered to meet the care needs of patients with extreme obesity is not well understood. The aim of the proposed evidence gap map (EGM) is to identify and assess the available evidence on healthcare interventions to improve healthcare outcomes for hospitalised patients with extreme obesity. This research will use standardised evidence gap map methods to undertake a five-stage process to develop an intervention–outcome framework; identify the current evidence; critically appraise the quality of the evidence, extract, code, and summarise the data in relation to the EGM objectives; and create a visualisation map to present findings. This EGM will provide a means of determining the nature and quality of health service initiatives available, identify the components of the services delivered and the outcome measures used for evaluation, and will identify areas where there is a lack of research that validates the funding of new research studies. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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8 pages, 227 KiB  
Protocol
Methods of Detecting Medication Administration Point-of-Care Errors in Acute Adult Inpatient Settings: A Scoping Review Protocol
by Julie-Anne Martyn, Angela Ratsch, Kaye Cumming and Jennifer Dredge
Methods Protoc. 2022, 5(2), 32; https://0-doi-org.brum.beds.ac.uk/10.3390/mps5020032 - 14 Apr 2022
Cited by 1 | Viewed by 2398
Abstract
Medication administration is recognized as a risk-prone activity where errors and near misses have multiple opportunities to occur along the route from manufacturing, through transportation, storage, prescription, dispensing, point-of-care administration, and post-administration documentation. While substantial research, education, and tools have been invested in [...] Read more.
Medication administration is recognized as a risk-prone activity where errors and near misses have multiple opportunities to occur along the route from manufacturing, through transportation, storage, prescription, dispensing, point-of-care administration, and post-administration documentation. While substantial research, education, and tools have been invested in the detection of medication errors on either side of point-of-care administration, less attention has been placed on this finite phase, leaving a gap in the error detection process. This protocol proposes to undertake a scoping review of the literature related to the detection of medication errors at the point-of-care to understand the potential size, nature, and extent of available literature. The aim is to identify research evidence to guide clinical practice and future research at the medication and patient point-of-care intersection. The search strategy will review literature from PubMed, CINAHL, Cochrane Collaboration, Embase, Scopus, PsychInfo, Web of Science, TRIP, TROVE, JBI Systematic Reviews, Health Collection (Informit), Health Source Nursing Academic, Prospero, Google Scholar, and graylit.org dated 1 January 2000–31 December 2021. Two independent reviewers will screen the literature for relevancy to the review objective, and critically appraise the citations for quality, validity, and reliability using the Joanna Briggs scoping review methodology and System for Unified Management, Assessment and Review of Information (SUMARI) tool. The data will be systematically synthesized to identify and compare the medication error administration detection method findings. A descriptive narrative discussion will accompany the findings. Full article
(This article belongs to the Special Issue Methods and Protocols 2022)
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