Feature Papers 2021

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 30921

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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
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Special Issue Information

Dear Colleagues,

This Special Issue will be a collection of "Feature Papers" that contain either cutting-edge research results or comprehensive reviews. The accepted papers will be published free of charge in the open access journal MPs. Authors will be the Editorial Board Members and the researchers invited by the Editorial Office on behalf of Editor-in-Chief.

Prof. Dr. Fernando Albericio
Guest Editor

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.

Published Papers (6 papers)

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Research

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13 pages, 1525 KiB  
Article
Harnessing Intronic microRNA Structures to Improve Tolerance and Expression of shRNAs in Animal Cells
by Arjun Challagulla, Mark L. Tizard, Timothy J. Doran, David M. Cahill and Kristie A. Jenkins
Methods Protoc. 2022, 5(1), 18; https://doi.org/10.3390/mps5010018 - 10 Feb 2022
Cited by 1 | Viewed by 2527
Abstract
Exogenous RNA polymerase III (pol III) promoters are commonly used to express short hairpin RNA (shRNA). Previous studies have indicated that expression of shRNAs using standard pol III promoters can cause toxicity in vivo due to saturation of the native miRNA pathway. A [...] Read more.
Exogenous RNA polymerase III (pol III) promoters are commonly used to express short hairpin RNA (shRNA). Previous studies have indicated that expression of shRNAs using standard pol III promoters can cause toxicity in vivo due to saturation of the native miRNA pathway. A potential way of mitigating shRNA-associated toxicity is by utilising native miRNA processing enzymes to attain tolerable shRNA expression levels. Here, we examined parallel processing of exogenous shRNAs by harnessing the natural miRNA processing enzymes and positioning a shRNA adjacent to microRNA107 (miR107), located in the intron 5 of the Pantothenate Kinase 1 (PANK1) gene. We developed a vector encoding the PANK1 intron containing miR107 and examined the expression of a single shRNA or multiple shRNAs. Using qRT-PCR analysis and luciferase assay-based knockdown assay, we confirmed that miR30-structured shRNAs have resulted in the highest expression and subsequent transcript knockdown. Next, we injected Hamburger and Hamilton stage 14–15 chicken embryos with a vector encoding multiple shRNAs and confirmed that the parallel processing was not toxic. Taken together, this data provides a novel strategy to harness the native miRNA processing pathways for shRNA expression. This enables new opportunities for RNAi based applications in animal species such as chickens. Full article
(This article belongs to the Special Issue Feature Papers 2021)
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10 pages, 2775 KiB  
Article
Method for Zero-Waste Circular Economy Using Worms for Plastic Agriculture: Augmenting Polystyrene Consumption and Plant Growth
by Samuel Ken-En Gan, Ser-Xian Phua, Joshua Yi Yeo, Zealyn Shi-Lin Heng and Zhenxiang Xing
Methods Protoc. 2021, 4(2), 43; https://doi.org/10.3390/mps4020043 - 21 Jun 2021
Cited by 7 | Viewed by 6322
Abstract
Polystyrene (PS) is one of the major plastics contributing to environmental pollution with its durability and resistance to natural biodegradation. Recent research showed that mealworms (Tenebrio molitor) and superworms (Zophobas morio) are naturally able to consume PS as a [...] Read more.
Polystyrene (PS) is one of the major plastics contributing to environmental pollution with its durability and resistance to natural biodegradation. Recent research showed that mealworms (Tenebrio molitor) and superworms (Zophobas morio) are naturally able to consume PS as a carbon food source and degrade them without observable toxic effects. In this study, we explored the effects of possible food additives and use of worm frass as potential plant fertilizers. We found that small amounts of sucrose and bran increased PS consumption and that the worm frass alone could support dragon fruit cacti (Hylocereus undatus) growth, with superworm frass in particular, supporting better growth and rooting than mealworm frass and control media over a fortnight. As known fish and poultry feed, these findings present worms as a natural solution to simultaneously tackle both the global plastic problem and urban farming issue in a zero-waste sustainable bioremediation cycle. Full article
(This article belongs to the Special Issue Feature Papers 2021)
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Review

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13 pages, 1990 KiB  
Review
In Vitro Methods for Measuring the Permeability of Cell Monolayers
by Radoslaw Bednarek
Methods Protoc. 2022, 5(1), 17; https://doi.org/10.3390/mps5010017 - 09 Feb 2022
Cited by 17 | Viewed by 9070
Abstract
Cell monolayers, including endothelial and epithelial cells, play crucial roles in regulating the transport of biomolecules to underlying tissues and structures via intercellular junctions. Moreover, the monolayers form a semipermeable barrier across which leukocyte transmigration is tightly regulated. The inflammatory cytokines can disrupt [...] Read more.
Cell monolayers, including endothelial and epithelial cells, play crucial roles in regulating the transport of biomolecules to underlying tissues and structures via intercellular junctions. Moreover, the monolayers form a semipermeable barrier across which leukocyte transmigration is tightly regulated. The inflammatory cytokines can disrupt the epithelial and endothelial permeability, thus the reduced barrier integrity is a hallmark of epithelial and endothelial dysfunction related with numerous pathological conditions, including cancer-related inflammation. Therefore, the assessment of barrier function is critical in in vitro models of barrier-forming tissues. This review summarizes the commercially available in vitro systems used to measure the permeability of cellular monolayers. The presented techniques are separated in two large groups: macromolecular tracer flux assays, and electrical impedance measurement-based permeability assays. The presented techniques are briefly described and compared. Full article
(This article belongs to the Special Issue Feature Papers 2021)
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Other

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10 pages, 551 KiB  
Protocol
Mind-Body Therapies for Cancer Patients Living with Depression, Anxiety or Insomnia (MIRACLE): A Systematic Review with Individual Participant Data Network Meta-Analysis
by Yoann Birling, Sarah Nevitt, Deep Jyoti Bhuyan, Mingxian Jia, Fan Feng, Linda Ellen Carlson, Tiffany Pham, Jing Liu, Zahra Ayati, Liyi Nyiam, Zhichao Yu and Paul Fahey
Methods Protoc. 2021, 4(4), 76; https://doi.org/10.3390/mps4040076 - 19 Oct 2021
Cited by 4 | Viewed by 4506
Abstract
Depression, anxiety, and insomnia are common in cancer patients. Mind-body therapies (MBTs) are promising forms of treatment for cancer patients living with depression, anxiety, and insomnia. The objective of this study is to assess the effectiveness and acceptability of MBTs in cancer patients [...] Read more.
Depression, anxiety, and insomnia are common in cancer patients. Mind-body therapies (MBTs) are promising forms of treatment for cancer patients living with depression, anxiety, and insomnia. The objective of this study is to assess the effectiveness and acceptability of MBTs in cancer patients living with depression, anxiety, or insomnia. EMBase, PubMed, Cinahl, PsychINFO, IndMED, CSI-NISCAIR, CNKI, Clinicaltrial.gov, ChiCTR, and CTRI will be searched until October 2020 for relevant studies. Randomized controlled studies in which MBTs were tested in a cancer population will be selected. The authors of the selected studies will be contacted to obtain individual participant data. The participants who reached a defined clinical threshold for depression, anxiety, or insomnia will be selected for the three sub-studies on depression, anxiety, and insomnia, respectively. Pairwise and network meta-analyses will be used to assess the changes in depression, anxiety, sleep quality, and completion rate. We will assess the effect of the treatment dose (number and frequency of interventions) on effectiveness. The results of this study will inform clinical decision-making for the treatment of psychological disturbances in cancer patients. If MBTs are found effective, they will potentially be recommended as treatments for cancer patients with psychological symptoms. Full article
(This article belongs to the Special Issue Feature Papers 2021)
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12 pages, 935 KiB  
Protocol
Effect of Oral Prophylactic Measures on the Occurrence of Pre-Eclampsia (OP-PE) in High-Risk Pregnant Women: A Cluster Randomized Controlled Trial
by Aida Kanoute, Jocelyne Gare, Nicolas Meda, Stephane Viennot, Paul Tramini, Laurie Fraticelli, Florence Carrouel and Denis Bourgeois
Methods Protoc. 2021, 4(3), 61; https://doi.org/10.3390/mps4030061 - 05 Sep 2021
Cited by 3 | Viewed by 2566
Abstract
Pre-eclampsia (PE), a pregnancy-specific hypertensive disorder, characterized by the development of placental endothelial dysfunction, remains a major source of maternal and perinatal morbidity and mortality, especially in low- and middle-income settings. Periodontal disorders during pregnancy, and particularly periodontal pathogens, may be related to [...] Read more.
Pre-eclampsia (PE), a pregnancy-specific hypertensive disorder, characterized by the development of placental endothelial dysfunction, remains a major source of maternal and perinatal morbidity and mortality, especially in low- and middle-income settings. Periodontal disorders during pregnancy, and particularly periodontal pathogens, may be related to the risk of PE. Standard oral hygiene methods, based mainly on the joint use of toothbrushes and interdental brushes, reduce periodontal inflammatory risk and modulate the dysbiosis of the oral microbiome. The aim of this trial is to compare the PE outcomes in high-risk pregnant women receiving oral prophylactic measures to a control group. This trial is designed as a two-arm, parallel, cluster randomized controlled trial with the antenatal obstetric clinic as the unit of randomization and an allocation ratio of 1:1. The pregnant women will be included at 3 months of pregnancy and will be followed throughout the pregnancy. The primary outcome measure will be the incidence of PE from a baseline during the pregnancy. Secondary outcomes measures will include changes from the baseline in quantification of the pathogenic bacterial load of the interdental microbiota, the severity scores of periodontal indicators, and the incidence of adverse perinatal outcomes. This trial should demonstrate that the implementation of daily oral hygiene reduces oral dysbiosis, the incidence of periodontal disease, and the risk of PE. Full article
(This article belongs to the Special Issue Feature Papers 2021)
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18 pages, 8329 KiB  
Protocol
Dissections of Larval, Pupal and Adult Butterfly Brains for Immunostaining and Molecular Analysis
by Yi Peng Toh, Emilie Dion and Antónia Monteiro
Methods Protoc. 2021, 4(3), 53; https://doi.org/10.3390/mps4030053 - 05 Aug 2021
Viewed by 4557
Abstract
Butterflies possess impressive cognitive abilities, and investigations into the neural mechanisms underlying these abilities are increasingly being conducted. Exploring butterfly neurobiology may require the isolation of larval, pupal, and/or adult brains for further molecular and histological experiments. This procedure has been largely described [...] Read more.
Butterflies possess impressive cognitive abilities, and investigations into the neural mechanisms underlying these abilities are increasingly being conducted. Exploring butterfly neurobiology may require the isolation of larval, pupal, and/or adult brains for further molecular and histological experiments. This procedure has been largely described in the fruit fly, but a detailed description of butterfly brain dissections is still lacking. Here, we provide a detailed written and video protocol for the removal of Bicyclus anynana adult, pupal, and larval brains. This species is gradually becoming a popular model because it uses a large set of sensory modalities, displays plastic and hormonally controlled courtship behaviour, and learns visual mate preference and olfactory preferences that can be passed on to its offspring. The extracted brain can be used for downstream analyses, such as immunostaining, DNA or RNA extraction, and the procedure can be easily adapted to other lepidopteran species and life stages. Full article
(This article belongs to the Special Issue Feature Papers 2021)
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