Methods Protoc., Volume 5, Issue 5 (October 2022) – 17 articles

Introduction: Bangladesh introduced professional midwives in 2018 to address gaps in sexual and reproductive health services, focusing on improved maternity care. Facility mentoring has been introduced in selected facilities within the government to enable midwives as they move into their new roles. Objectives: To describe a protocol (1) to determine if introducing international standard midwives in rural sub-district hospitals in Bangladesh, both with and without facility mentoring, improve the availability and quality of maternal and newborn health care compared to the facility without midwives; and (2) to explore the experiences of the midwives, and the maternity staff and managers that they joined, following their introduction. Methods: This will be a mixed-methods study to examine differences between selected hospitals grouped into three categories: without midwives (only nurses), with midwives, and both with midwives and mentorship. Hospital selection will be based on choosing those with the highest birth caseload. The quantitative component will consist of facility observations and clinical data extraction to assess their (hospital and midwives) readiness (birth preparedness and complication readiness) and clinical care to explore whether facilities with newly introduced midwives have improved availability and quality of care. We will use facility assessment tools to extract clinical data. In addition, we will use a structured open-ended interview guideline to conduct focus groups and in-depth interviews to understand the perceptions, attitudes, and experiences among maternity staff (e.g., nurses and paramedics) and health managers (e.g., facility manager, residential medical officer, consultants), as well as the midwives themselves toward the newly introduced midwives and the quality of care. We plan to use a fixed effect logistic regression to compare the relationship between variables in the three hospital types for each observed data point. For analyzing qualitative data, we will adopt content analysis and use NVivo to identify themes related to perceptions, attitudes, and experiences. Expected results: The introduction of professional midwives may improve the quality of maternal health care in rural settings. The addition of a mentoring program can support midwives in transitioning into their new roles and introduce improved care quality. Full article

Despite various benefits of physical activity, children are increasingly inactive. Both school physical education classes and support from parents are important determinants of physical activity level of children and adolescents. We aim to develop a web-based intervention for physical education teachers and parents to teach them to be more need-supportive towards children when discussing physical activity and thus increase children’s autonomous motivation towards it. The study will adopt a waitlist-control design with cluster randomization by schools. The intervention content is based on self-determination theory. Specifically, the teachers and parents will be introduced to a series of motivation and behavior change techniques to help them satisfy the children’s psychological needs for autonomy, competence, and relatedness in physical activity. The targeted group in the six-week intervention is comprised of students aged 12–14 years. The primary outcome variable, physical activity of students, will be assessed via self-report questionnaires at baseline, post-intervention, one-month and six-month follow-up. Web-based intervention programs are cost-effective, allow self-paced learning and enable reaching larger audiences. If this project proves to be effective, a highly valuable web-based solution would be available for PE teachers and parents to help increase students’ physical activity levels. Full article

Due to their extensive use and the globalized commerce of agricultural goods, pesticides have become a global concern. Despite the undoubtful advantages of their use in agricultural practices, their misuse is a threat to the environment and human health. Their analysis in environmental samples and in food products continues to gain interest in the analytical chemistry community as they are challenging matrices, and legal concentration limits are particularly low (in the order of ppb). In particular, the use of solid-phase microextraction (SPME) has gained special attention in this field thanks to its potential to minimize the matrix effect, while enriching its concentration, allowing very low limits of detection, and without the need of a large amount of solvents or lengthy procedures. Moreover, its combination with gas chromatography (GC) can be easily automated, making it a very interesting approach for routine analysis. In this review, advances and analytical strategies for the use of SPME coupled with GC are discussed and compared for the analysis of pesticides in food and environmental samples, hopefully encouraging its further development and routine application in this field. Full article

Alanine aminotransferase (ALT) levels are frequently determined in serum and plasma samples and are a primary measure to quantitate hepatocellular injury in rodents, humans, and other organisms. An accurate, reliable, and scalable assay is hence of central importance. Here, we describe a methodology that fulfills those requirements, and demonstrates an excellent performance similar to a commercial ALT kit, with a long stable performance over several subsequent runs. Further, anticoagulation of blood samples with ethylenediaminetetraacetic acid (EDTA) or heparin results in similar ALT concentrations with this assay, whereas no anticoagulation significantly increases ALT levels. Mild hemolysis does not significantly increase ALT levels; however, moderate to severe hemolysis does lead to higher ALT levels. The assay provides stable results over a wide range of associated triglyceride concentrations that can be expected in serum and plasma samples from rodents and humans with dyslipidemia. It also performs well in diluted samples with a reduction of ALT levels corresponding to the factor used to dilute the samples. The described ALT reagent is also very affordable, costing less than 1/80 of comparable commercial kits. Based on the characteristics above, this methodology is suitable for a broad spectrum of applications in mice and possibly humans, where ALT concentrations need to be determined. Full article

Cranioplasty is a neurosurgical procedure in which the skull bone is repaired after craniectomy. Recently, studies have suggested that sonolucent synthetic materials are safe and useful for cranioplasty. Sonolucent cranioplasty (SC) implants provide unprecedented opportunity in adult neurosurgery to monitor neuroanatomy, assess hemodynamics, view devices located within the implant, and conduct focused ultrasound treatments. Current research on SC includes proof-of-concept cadaveric studies, patient-related safety and feasibility studies, and case series demonstrating transcranioplasty ultrasonography (TCUS). The purpose of this protocol is to investigate the current literature on SC use and outcomes in TCUS. We will perform a systematic literature search following PRISMA-ScR guidelines. The search will be conducted using Ovid Embase, Ovid Medline, and Web of Science Core Collection databases. Titles, abstracts, and full texts will be screened. Joanna Briggs Institute critical appraisal tools will be utilized. Data extraction points will include subject characteristics, SC implant characteristics, ultrasound characteristics, and sonographic findings. These findings will provide a comprehensive review of the literature on sonolucent cranioplasty and directions for future research. Full article

Until recently, the favored method for making directed modifications to the budding yeast genome involved the introduction of a DNA template carrying the desired genetic changes along with a selectable marker, flanked by homology arms. This approach both limited the ability to make changes within genes due to disruption by the introduced selectable marker and prevented the use of that selectable marker for subsequent genomic manipulations. Following the discovery of CRISPR-Cas9-mediated genome editing, protocols were developed for modifying any DNA region of interest in a similar single transformation step without the need for a permanent selectable marker. This approach involves the generation of a DNA double-strand break (DSB) at the desired genomic location by the Cas9 nuclease, expressed on a plasmid which also expresses the guide RNA (gRNA) sequence directing the location of the DSB. The DSB is subsequently repaired via homologous recombination using a PCR-derived DNA repair template. Here, we describe in detail an improved method for incorporation of the gRNA-encoding DNA sequences into the Cas9 expression plasmid. Using Golden Gate cloning, annealed oligonucleotides bearing unique single-strand DNA overhangs are ligated into directional restriction enzyme sites. We describe the use of this CRISPR-Cas9 genome editing protocol to introduce multiple types of directed genetic changes into the yeast genome. Full article

Breast cancer (BC) is a heterogeneous disease, affecting millions of women every year. Early diagnosis is crucial to increasing survival. The clinical workup of BC diagnosis involves diagnostic imaging and bioptic characterization. In recent years, technical advances in image processing allowed for the application of advanced image analysis (radiomics) to clinical data. Furthermore, -omics technologies showed their potential in the characterization of BC. Combining information provided by radiomics with –omics data can be important to personalize diagnostic and therapeutic work up in a clinical context for the benefit of the patient. In this review, we analyzed the recent literature, highlighting innovative approaches to combine imaging and biochemical/biological data, with the aim of identifying recent advances in radiogenomics applied to BC. The results of radiogenomic studies are encouraging approaches in a clinical setting. Despite this, as radiogenomics is an emerging area, the optimal approach has to face technical limitations and needs to be applied to large cohorts including all the expression profiles currently available for BC subtypes (e.g., besides markers from transcriptomics, proteomics and miRNomics, also other non-coding RNA profiles). Full article

In aging, the brain is more vulnerable to injury and neurodegenerative disease, but the mechanisms responsible are largely unknown. Evidence now suggests that neuroinflammation, mediated by resident brain astrocyte and microglia populations, are key players in the generation of inflammatory responses and may influence both age related processes and the initiation/progression of neurodegeneration. Consequently, targeting these cell types individually and collectively may aid in the development of novel disease-modifying therapies. We have optimized and characterized a protocol for the effective sequential isolation of both microglia and astrocytes from the adult mouse brain in young and aged mice. We demonstrate a technique for the sequential isolation of these immune cells by using magnetic beads technology, optimized to increase yield and limit potential artifacts in downstream transcriptomic applications, including RNA-sequencing pipelines. This technique is versatile, cost-effective, and reliable for the study of responses within the same biological context, simultaneously being advantageous in reducing mice numbers required to assess cellular responses in normal and age-related pathological conditions. Full article

Multiple fluorochromes are extensively used to investigate different microalgal aspects, such as viability and physiology. Some of them can be used to stain nucleic acids (DNA). Well-known examples are SYBR Green I and SYTO 9, the latter of which offers several advantages, especially when combined with flow cytometry (FCM)—a powerful method for studying microalgal population heterogeneity and analyzing their cell cycles. However, the effects of these dyes on the microalgae cell physiology have not been fully elucidated yet. A statistical experimental design, using response surface methodology (RSM) with FCM was applied in this study to optimize the DNA staining of a non-conventional microalgae, Chromochloris zofingiensis, with SYBR Green I and SYTO 9, and to optimize the variables affecting staining efficiency, i.e., the dye concentration, incubation time and staining temperature. We found that none of these factors affects the staining efficiency, which was not less than 99.65%. However, for both dyes, the dye concentration was shown to be the most significant factor causing cell damage (p-values: 0.0003; <0.0001) for SYBR Green I and SYTO 9, respectively. The staining temperature was only significant for SYTO 9 (p-value: 0.0082), and no significant effect was observed regarding the incubation time for both dyes. The values of the optimized parameters (0.5 µM, 05 min and 25 °C) for SYTO 9 and (0.5 X, 5 min and 25 °C) for SYBR Green I resulted in the maximum staining efficiency (99.8%; 99.6%), and the minimum damaging effects (12.86%; 13.75%) for SYTO 9 and SYBR Green I, respectively. These results offer new perspectives for improving the use of DNA staining fluorochromes and provides insights into their possible side effects on microalgae. Full article

Introduction: Heart transplant (HT) survival has barely improved in the last decades, which is unsatisfactory for many HT recipients. The development of anti-human leukocyte antigen (anti-HLA) antibodies in HT patients is associated with a cardiac allograft dysfunction. The mechanisms leading to this damage are unclear. The Multimodality Evaluation Of Antibody-Mediated Injury In Heart Transplantation (LEONE-HT) study aimed to thoroughly describe the damage inflicted on the myocardium by anti-HLA antibodies. Methods and analysis: The LEONE-HT study is a cohort study with a cross-sectional approach in which HT patients with positive anti-HLA antibodies are compared with coetaneous HT patients with negative anti-HLA antibodies. All patients will undergo a state-of-the-art multimodal assessment, including imaging techniques, coronary anatomy and physiology evaluations and histological and immunological analyses. The individual and combined primary outcomes of structural graft injuries and longitudinal secondary outcomes are to be compared between the exposed and non-exposed groups with univariate and multivariable descriptive analyses. Ethics and dissemination: The LEONE-HT study is carried out in accordance with the principles set out in the Declaration of Helsinki and the International Conference on Harmonization guidelines for good clinical practice and following national laws and regulations. The study design, objectives and participant centers have been communicated to clinicaltrials.gov (NCT05184426). The LEONE-HT study counts on the support of patient associations to disseminate the objectives and results of the research. This study was funded by the Spanish Ministry of Science and Innovation and the Spanish Society of Cardiology. Full article

Studies in Saccharomyces cerevisiae and Schizosaccharomyces pombe have enhanced our understanding of the regulation and functions of histone H2B monoubiquitination (H2Bub1), a key epigenetic marker with important roles in transcription and other processes. The detection of H2Bub1 in yeasts using immunoblotting has been greatly facilitated by the commercial availability of antibodies against yeast histone H2B and the cross-reactivity of an antibody raised against monoubiquitinated human H2BK120. These antibodies have obviated the need to express epitope-tagged histone H2B to detect H2Bub1 in yeasts. Here, we provide a step-by-step protocol and best practices for the quantification of H2Bub1 in yeast systems, from cell extract preparation to immunoblotting using the commercially available antibodies. We demonstrate that the commercial antibodies can effectively and accurately detect H2Bub1 in S. cerevisiae and S. pombe. Further, we show that the C-terminal epitope-tagging of histone H2B alters the steady-state levels of H2Bub1 in yeast systems. We report a sectioned blot probing approach combined with the serial dilution of protein lysates and the use of reversibly stained proteins as loading controls that together provide a cost-effective and sensitive method for the quantitative evaluation of H2Bub1 in yeast. Full article

RT-PCR tests have become the gold standard for detecting the SARS-CoV-2 virus in the context of the COVID-19 pandemic. Because of the extreme number of cases in periodic waves of infection, there is a severe financial and logistical strain on diagnostic laboratories. For this reason, alternative implementations and validations of academic protocols that employ the lowest cost and the most widely available equipment and reagents found in different regions are essential. In this study, we report an alternative implementation of the EUA 2019-nCoV CDC assay which uses a previously characterized duplex PCR reaction for the N1 and RNAse P target regions and an additional uniplex reaction for the N2 target region. Taking advantage of the Abbott m2000 Sample Preparation System and NEB Luna Universal Probe One-Step RT-qPCR kit, some of the most widely available and inexpensive nucleic acid extraction and amplification platforms, this modified test shows state-of-the-art analytical and clinical sensitivities and specificities when compared with the Seegene Allplex-SARS-CoV-2 assay. This implementation has the potential to be verified and implemented by diagnostic laboratories around the world to guarantee low-cost RT-PCR tests that can take advantage of widely available equipment and reagents. Full article

Herein we report a practical approach for peptide synthesis using second-generation fibrous polyacrylamide resin (Li-resin, “Li” is coming from the name of its inventor, Yongfu Li). This resin with the corresponding handle was used for solid phase peptide synthesis (SPPS) using a fluorenylmethoxycarbonyl (Fmoc) approach. We reveal that the most appropriate mixing and filtration strategy when using amino-Li-resin in SPPS is via shaking and gravity filtration, instead of mechanical stirring and suction filtration used with other resins. The strategy was demonstrated with the SPPS of H-Tyr-Ile-Ile-Phe-Leu-NH₂, which contains the difficult sequence Ile-Ile. The peptide was obtained with excellent purity and yield. We are confident that this strategy will be rapidly implemented by other peptide laboratories. Full article

Platelet–neutrophil complexes (PNCs) occur during the inflammatory response to trauma and infections, and their interactions enable cell activation that can lead to tissue destruction. The ability to identify the accumulation and tissue localisation of PNCs is necessary to further understand their role in the organs associated with blast-induced shock wave trauma. Relevant experimental lung injury models often utilise pigs and rats, species for which immunohistochemistry protocols to detect platelets and neutrophils have yet to be established. Therefore, monoplex and multiplex immunohistochemistry protocols were established to evaluate the application of 22 commercially available antibodies to detect platelet (nine rat and five pig) and/or neutrophil (four rat and six pig) antigens identified as having potential selectivity for porcine or rat tissue, using lung and liver sections taken from models of polytrauma, including blast lung injury. Of the antibodies evaluated, one antibody was able to detect rat neutrophil elastase (on frozen and formalin-fixed paraffin embedded (FFPE) sections), and one antibody was successful in detecting rat CD61 (frozen sections only); whilst one antibody was able to detect porcine MPO (frozen and FFPE sections) and antibodies, targeting CD42b or CD49b antigens, were able to detect porcine platelets (frozen and FFPE and frozen, respectively). Staining procedures for platelet and neutrophil antigens were also successful in detecting the presence of PNCs in both rat and porcine tissue. We have, therefore, established protocols to allow for the detection of PNCs in lung and liver sections from porcine and rat models of trauma, which we anticipate should be of value to others interested in investigating these cell types in these species. Full article

The liver is a complex organ that governs many types of metabolisms, including energy metabolism and other cellular processes. The liver also plays a crucial role in important functions in immunity, and the activity of liver tissue-associated immunity affects the outcome of many liver pathologies. A thorough characterization of the liver immune microenvironment may contribute to a better understanding of immune signaling, the mechanisms of specific immune responses, and even to improved predictions about therapy outcomes. In this paper, we present an optimized, simple, and rapid protocol to characterize the liver-associated immune cell milieu. We believe that the most suitable technique for obtaining a complex immune cell suspension and for removing contaminating blood cells is to perform mouse liver perfusion, using only phosphate buffer saline. Combining an enzymatic digestion and a mechanical dissociation of liver tissue, followed by cell purification, improves downstream applications. This combination is an essential prerequisite for immune cell determination and characterization. We then demonstrate a flow cytometry-based multiparametric immunophenotyping along with a gating strategy to detect and quantify liver endothelial cells, T cells (helper and cytotoxic), B cells, NK cells, NKT cells, neutrophils, monocytes (subsets included), dendritic cells (subsets included), macrophages and Kupffer cells. Full article

Crop improvement under changing climatic conditions is required to feed the growing global population. The development of transgenic crops is an attractive and conceivably the most effective approach for crop improvement with desired traits in varying climatic situations. Here, we describe a simple, efficient and robust in planta Agrobacterium-mediated genetic transformation method that can be used in most crops, including rice, wheat and cotton, and particularly in tissue culture recalcitrant crops, such as chickpea and pigeon pea. The protocol was successfully used for the development of transgenic chickpea and pigeon pea lines for resistance against pod borer. Transgenic lines in chickpea, pigeon pea and wheat were also developed for salt stress tolerance. These lines exhibited improved salt tolerance in terms of various physio-biochemical parameters studied. Since the protocol is rapid, as no tissue culture step is involved, it will significantly contribute to the improvement of most crops and will be of interest for plant biologists working with genetic engineering or genome editing. Full article

Macrophage activation refers to the enhanced functionality of macrophages in response to endogenous or exogenous stimuli. Due to the existence of limitless stimuli and a multitude of receptors on macrophage surfaces, the nature of activation (or acquired functioning) can be specific to the encountering stimulus. This article describes a macrophage-activation screening platform in a 96-well format. The methodology involves the generation of bone marrow-derived macrophages, their activation into two extreme activation states, and screening of activated macrophages for expression of bonafide protein biomarkers. A high-throughput and stringent assay to determine macrophage activation markers developed in this article can be adapted for biomarker determination in pathological conditions and toxicant/drug safety screening. Full article