Methods Protoc., Volume 5, Issue 1 (February 2022) – 19 articles

Members of the saposin-fold protein family and related proteins sharing a similar fold (saposin-like proteins; SAPLIP) are peripheral-membrane binding proteins that perform essential cellular functions. Saposins and SAPLIPs are abundant in both plant and animal kingdoms, and peripherally bind to lipid membranes to play important roles in lipid transfer and hydrolysis, defense mechanisms, surfactant stabilization, and cell proliferation. However, quantitative studies on the interaction between proteins and membranes are challenging due to the different nature of the two components in relation to size, structure, chemical composition, and polarity. Using liposomes and the saposin-fold member saposin C (sapC) as model systems, we describe here a method to apply solution NMR and dynamic light scattering to study the interaction between SAPLIPs and synthetic membranes at the quantitative level. Specifically, we prove with NMR that sapC binds reversibly to the synthetic membrane in a pH-controlled manner and show the dynamic nature of its fusogenic properties with dynamic light scattering. The method can be used to infer the optimal pH for membrane binding and to determine an apparent dissociation constant (K_Dapp) for protein-liposome interaction. We propose that these experiments can be applied to other proteins sharing the saposin fold. Full article

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

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

Cellular technologies are one of the most promising areas of biomedicine, which is based on the isolation of cells of various types, followed by their cultivation and use, or the use of their metabolic products, for medical purposes. Today, a significant part of biomedical research is carried out in vitro. On the other hand, organotypic culture can be used as a powerful model system and can complement cell culture and in vivo studies in different biomedical applications. Uterine leiomyoma (UL) is a very common benign tumor and often leads to many reproductive complications. Herein we describe a fast and reliable method of isolation and UL primary cells culturing along with the development of a UL organotypic model. We propose the usage of UL primary cells in experimental work at a first passage to prevent loss of driver mutations in MED12 and HMGA2 genes. New optimized conditions for the growth and maintenance of 2D and 3D models of uterine leiomyoma in vitro are suggested. Full article

Proteasomes hydrolyze most cellular proteins. The standard reaction to determine proteasome activity in cellular lysate or elsewhere contains AMC-conjugated peptide substrate, ATP, Mg²⁺, and DTT. ATP and Mg²⁺ are included to maintain 26S proteasome functionality. However, most cellular proteasomes are 20S proteasomes, and the effects of ATP on the turnover of fluorogenic substrates by 20S complexes are largely unknown. Here, we evaluated the effect of ATP alone or in combination with Mg²⁺ on the degradation of AMC-conjugated fluorogenic substrates by purified 20S proteasomes. Degradation of substrates used to determine chymotrypsin-, caspase- and trypsin-like proteasome activities was gradually decreased with the rise of ATP concentration from 0.25 to 10 mM. These effects were not associated with the blockage of the proteasome catalytic subunit active sites or unspecific alterations of AMC fluorescence by the ATP. However, ATP-induced peptide degradation slowdown was rescued by the addition of Mg²⁺. Moreover, the substrate degradation efficacy was proportional to the Mg²⁺/ATP ratio, being equal to control values when equimolar concentrations of the molecules were used. The obtained results indicate that when proteasome activity is assessed, the reciprocal effects of ATP and Mg²⁺ on the hydrolysis of AMC-conjugated fluorogenic substrates by the 20S proteasomes should be considered. Full article

Obtaining valuable clues for noncoding RNA (ribonucleic acid) subsequences remains a significant challenge, acknowledging that most of the human genome transcribes into noncoding RNA parts related to unknown biological operations. Capturing these clues relies on accurate “base pairing” prediction, also known as “RNA secondary structure prediction”. As COVID-19 is considered a severe global threat, the single-stranded SARS-CoV-2 virus reveals the importance of establishing an efficient RNA analysis toolkit. This work aimed to contribute to that by introducing a novel system committed to predicting RNA secondary structure patterns (i.e., RNA’s pseudoknots) that leverage syntactic pattern-recognition strategies. Having focused on the pseudoknot predictions, we formalized the secondary structure prediction of the RNA to be primarily a parsing and, secondly, an optimization problem. The proposed methodology addresses the problem of predicting pseudoknots of the first order (H-type). We introduce a context-free grammar (CFG) that affords enough expression power to recognize potential pseudoknot pattern. In addition, an alternative methodology of detecting possible pseudoknots is also implemented as well, using a brute-force algorithm. Any input sequence may highlight multiple potential folding patterns requiring a strict methodology to determine the single biologically realistic one. We conscripted a novel heuristic over the widely accepted notion of free-energy minimization to tackle such ambiguity in a performant way by utilizing each pattern’s context to unveil the most prominent pseudoknot pattern. The overall process features polynomial-time complexity, while its parallel implementation enhances the end performance, as proportional to the deployed hardware. The proposed methodology does succeed in predicting the core stems of any RNA pseudoknot of the test dataset by performing a 76.4% recall ratio. The methodology achieved a F1-score equal to 0.774 and MCC equal 0.543 in discovering all the stems of an RNA sequence, outperforming the particular task. Measurements were taken using a dataset of 262 RNA sequences establishing a performance speed of 1.31, 3.45, and 7.76 compared to three well-known platforms. The implementation source code is publicly available under knotify github repo. Full article

Masson’s Trichrome Staining (MTS) is a useful tool for analyzing fibrosis in a plethora of disease pathologies by differential staining of tissue components. It is used to identify collagen fibers in different tissues like heart, lung, skin, and muscles. Especially in cardiac fibrosis, MTS stains the collagen fibers (blue color), which helps in the distinction of scar area versus the healthy area (red color). However, there are several challenges to stain both paraffin-embedded sections and frozen (cryosections) using a single protocol. Therefore, the goal of this study was to develop a simple short protocol to assess cardiac fibrosis in both paraffin-embedded and cryo heart sections. MTS uses three different stains, i.e., Weigert’s Iron Hematoxylin, Biebrich scarlet-acid fuchsin, and aniline blue to detect nuclei, cytoplasm, and collagen, respectively. In this study, we developed a simple short protocol that can be adapted by any lab to easily assess cardiac fibrosis in paraffin and frozen heart sections. Furthermore, we have addressed the challenges that are commonly faced during the immunostaining process and troubleshooting techniques. Overall, we have successfully developed a simple one-step protocol to assess myocardial fibrosis in paraffin-embedded and frozen cryosections. Full article

In vitro evaluation of tomato seeds and seedlings for salt tolerance has undoubted advantages (high productivity, as well as stability and reproducibility of the obtained experimental data due to the maintenance of constant controlled conditions) in comparison with open-field system and pot experiments. However, even high-quality seeds greatly differ in the uniformity of germination capacity and germination energy. Heterogeneous germination in the habit and developmental stage of plant material significantly distorts the obtaining of relevant experimental data suitable for correct interpretation. In our study, we propose a simple and effective bioassay method suitable to comparative in vitro study of tomato salt tolerance using shoot apex of seedlings at the early first-true-leaf stage. Shoot apexes cultured the on the root induction medium (RIM) supplemented with 0.2 mg/L indole-3-butyric acid (IBA) and NaCl at different concentrations (0–250 mM NaCl) revealed significant differences between two tomato genotypes (line YaLF and cv. Rekordsmen) at the organismal (measurements of CO₂ gas exchange), organ (rhizogenesis frequency; number and length of de novo regenerated roots; root fresh (RFW) and dry (RDW) weights; shoot fresh (SFW) and dry (SDW) weights), tissue (the average cross-sectional area of epidermal and mesophylls cotyledonary cells) and cellular (ultrastructure of chloroplast and nuclear compartments) development levels. In addition, a quantitative comparison of proline and photosynthetic pigments contents under 75 and 150 mm NaCl treatments showed a different response between two tomato genotypes. The proposed methodological approach can be used for other plants with a high response to auxin-induced rhizogenesis in vitro, as well as for the comparative in vitro assessment of other abiotic stresses. Full article

Background: The most used types of retention of implant-supported prostheses are screw-retained or cement-retained restorations. The advantages and disadvantages of both have been identified by various authors over the years. However, cement-retained implant crowns and fixed partial dentures are among the most used types of restorations in implant prostheses, due to their aesthetic and clinical advantages. When cemented prostheses are made on implants, the problem of cement residues is important and often associated with biological implant pathologies. The objective of this research was to establish to what extent the techniques to reduce excess cement really affect the volume of cement residues. Materials and Methods: This review was written following the PRISMA statement; a detailed search was carried out in three different electronic databases—PubMed, Scopus, and Cochrane Library. The inclusion criteria were prospective clinical studies, with at least 10 participants per group, and with at least 6 months of the follow-up period. Results: There have been many proposals for techniques supposed to reduce the amount of excess cement in the peri-implant sulcus and on the prosthetic components, but of these, which are exceptional in their in vitro capabilities, very few have been clinically validated, and this represents the real limitation and a great lack of knowledge regarding this topic. Three articles met the inclusion criteria, which were analyzed and compared, to obtain the information necessary for the purposes of the systematic review. Discussion: Extraoral cementation can reduce the excess cement, which, after a normal excess removal procedure, is, nevertheless, of such size that it does not affect the possibility of peri-implant pathologies developing. All these studies concluded that a small amount of cement residue is found in the gingival sulcus, and using eugenol-free oxide cements, the residues were only deposited on the metal surfaces, with a better peri-implant tissues health. Conclusion: Despite the limitations of this study, it was possible to carefully analyze these characteristics and obtain valuable suggestions for daily clinical practice. Resinous cements are considered, due to the free monomers present in them, toxic for the soft tissues. The provisional zinc-oxide cements, also eugenol-free, represent the ideal choice. The different grades of retentive forces provided by these cements do not seem to have clinical effects on the decementation of restorations. Full article

Osteonecrosis of the femoral head (ONFH) occurs frequently in adolescents and young adults and causes progressive deformation and destruction of the hip joint and impairs standing and walking, resulting in a significant decrease in the quality of life of patients. In addition, studies have shown that a history of corticosteroid administration and heavy alcohol consumption are closely related to the occurrence of ONFH. However, the detailed mechanism by which steroid administration and alcohol consumption are associated with the development of the disease is still unknown. With many researches still ongoing and without a clear biological pathway for osteonecrosis, effective preventive measures cannot be taken. Therefore, the current focus of ONFH treatment is to establish an early diagnosis and treatment strategy. We obtained the femoral heads of four patients with steroidal ONFH and three patients with alcoholic ONFH. We then compared the femoral heads of steroidal and alcoholic osteonecrosis by analyzing them at the molecular level by Raman spectroscopy. Crystallographic changes (deformations) in the mineral phase and fraction of organic material respect to the total mass were then plotted as a function. We found that changes in bone composition in ONFH were different in steroidal and alcoholic ONFH. We conclude that this suggests that the developmental mechanisms of steroidal and alcoholic ONFH may follow different paths. We also noticed that while steroid seem to lead to a more marked degradation of the tissue, alcohol seem to affect also the quality of the healthy tissue. Full article

New biomaterials and scaffolds for bone tissue engineering (BTE) applications require to be tested in a bone microenvironment reliable model. On this assumption, the in vitro laboratory protocols with bone cells represent worthy experimental systems improving our knowledge about bone homeostasis, reducing the costs of experimentation. To this day, several models of the bone microenvironment are reported in the literature, but few delineate a protocol for testing new biomaterials using bone cells. Herein we propose a clear protocol to set up an indirect co-culture system of human-derived osteoblasts and osteoclast precursors, providing well-defined criteria such as the cell seeding density, cell:cell ratio, the culture medium, and the proofs of differentiation. The material to be tested may be easily introduced in the system and the cell response analyzed. The physical separation of osteoblasts and osteoclasts allows distinguishing the effects of the material onto the two cell types and to evaluate the correlation between material and cell behavior, cell morphology, and adhesion. The whole protocol requires about 4 to 6 weeks with an intermediate level of expertise. The system is an in vitro model of the bone remodeling system useful in testing innovative materials for bone regeneration, and potentially exploitable in different application fields. The use of human primary cells represents a close replica of the bone cell cooperation in vivo and may be employed as a feasible system to test materials and scaffolds for bone substitution and regeneration. Full article

Background: Population studies gathering measured data on fitness and physical behavior, covering physical activity, standing, sedentary behavior, and time in bed, are scarce. This article describes the protocol of the FINFIT 2021 study that measures fitness and physical behavior in a population-based sample of adults and analyzes their associations and dose–response relationships with several health indicators. Methods: The study comprises a stratified random sample of 20–69-year-old men and women (n = 16,500) from seven city-centered regions in Finland. Physical behavior is measured 24/7 by tri-axial accelerometry and analyzed with validated MAD-APE algorithms. Health and fitness examinations include fasting blood samples, measurements of blood pressure, anthropometry, and health-related fitness. Domains of health, functioning, well-being, and socio-demographics are assessed by a questionnaire. The data are being collected between September 2021 and February 2022. Discussion: The study provides population data on physical fitness and physical behavior 24/7. Physical behavior patterns by intensity and duration on an hour-by-hour basis will be provided. In the future, the baseline data will be assessed against prospective register-based data on incident diseases, healthcare utilization, sickness absence, premature retirement, and death. A similar study will be conducted every fourth year with a new random population sample. Full article

Human cytomegalovirus is a herpesvirus that has a worldwide seroprevalence of more than 60% of adults in developed countries and 90% in developing countries. Severe disabilities in newborns are characteristic of the human cytomegalovirus congenital infection, and this virus is implicated in graft rejection in transplant patients. To treat and follow-up the infection, the CMVPCR viral loads are required, and the DNA extraction step remains very important; however, the quantity, quality, and purity of extracted DNA from different biological fluids influence the results of PCR amplification, that is why for reliable results, the choice of nucleic acid extraction methods requires careful attention. Materials and methods: In this study, we compare 4 protocols, I (EZ1 DSP Virus kit), II (EZ1 Virus mini kit), III (QIAamp DSP virus kit), and IV (heating); the extractions are made from plasma collected on EDTA tubes, and the concentration of extracted DNA was measured on NanoDrop Lite followed by real-time CMVPCR using an Artus CMV QS-RGQ kit. All protocols are performed following the manufacturer’s instructions. Results: This study is conducted on the samples of 135 transplant patients whose follow-up medical tests related to human cytomegalovirus infection; since most of the CMVPCR results are negative, we have chosen the 10 CMVPCR positive samples and 2 negative samples as controls to conduct this comparison study. By using NanoDrop Lite to evaluate the DNA concentration, the yield of extracted DNA is higher in our heating protocol than other protocols, the EZ1 DSP virus kit and EZ1 Virus mini kit show homogeneous quantities, and the QIAamp DSP virus kit shows very low DNA yields. Comparing cycle threshold and viral loads by real-time PCR, all these protocols identified negative samples (100%), and the previously positive samples used were as follows: protocol IV (90%), protocol II (60%), and protocol I (40%). QIAamp DSP virus kit results were not real-time PCR applicable and were non-conclusive because of the low DNA yields. Conclusion: Our developed heating method (protocol IV) is very effective, reliable, simple, fast, and cheap compared to the other protocols in our study. Full article

Murine hepatitis virus (MHV) is a non-human pathogen betacoronavirus that is evolutionarily and structurally related to the human pathogenic viruses SARS-CoV, MERS-CoV, and SARS-CoV-2. However, unlike the human SARS and MERS viruses, MHV requires a biosafety level 2 laboratory for propagating and safe handling, making it a potentially suitable surrogate virus. Despite this utility, few papers discussed the propagation and quantification of MHV using cell lines readily available in biorepositories making their implementations not easily reproducible. This article provides protocols for propagating and quantifying MHV-A59 using the recommended NCTC clone 1469 and clone 929 cell lines from American Type Culture Collection (ATCC). More specifically, the methods detail reviving cells, routine cell passaging, preparing freeze stocks, infection of NCTC clone 1469 with MHV and subsequent harvesting, and plaque assay quantification of MHV using NCTC clone 929 cells. Using these protocols, a BSL-2 laboratory equipped for cell culture work would generate at least 6.0 log plaque-forming units (PFU) per mL of MHV lysate and provide an optimized overlay assay using either methylcellulose or agarose as overlays for the titration of infectious virus particles. The protocols described here are intended to be utilized for persistence and inactivation studies of coronaviruses. Full article

Biological sex is one of the more critically important physiological parameters needed for managing threatened animal species because it is crucial for informing several of the management decisions surrounding conservation breeding programs. Near-infrared spectroscopy (NIRS) is a non-invasive technology that has been recently applied in the field of wildlife science to evaluate various aspects of animal physiology and may have potential as an in vivo technique for determining biological sex in live amphibian species. This study investigated whether NIRS could be used as a rapid and non-invasive method for discriminating biological sex in the endangered Houston toad (Anaxyrus houstonensis). NIR spectra (N = 396) were collected from live A. houstonensis individuals (N = 132), and distinct spectral patterns between males and females were identified using chemometrics. Linear discriminant analysis (PCA-LDA) classified the spectra from each biological sex with accuracy ≥ 98% in the calibration and internal validation datasets and 94% in the external validation process. Through the use of NIRS, we have determined that unique spectral signatures can be holistically captured in the skin of male and female anurans, bringing to light the possibility of further application of this technique for juveniles and sexually monomorphic species, whose sex designation is important for breeding-related decisions. Full article

After a DNA double-strand break, cells utilize either non-homologous end joining or homologous recombination to repair the broken DNA ends. Homologous recombination requires extensive nucleolytic processing of one of the DNA strands, resulting in long stretches of 3′ single-strand DNA overhangs. Typically, single-stranded DNA is measured using immunofluorescence microscopy to image the foci of replication protein A, a single-stranded DNA-binding protein. Microscopy analysis of bromodeoxyuridine foci under nondenaturing conditions has also been used to measure single-stranded DNA. Here, we describe a proximity ligation assay which uses genome-wide bromodeoxyuridine incorporation to label single-stranded DNA in order to measure the association of a protein of interest with single-stranded DNA. This method is advantageous over traditional foci analysis because it is more direct and specific than traditional foci co-localization microscopy methods, uses only one color channel, and can reveal protein-single-stranded DNA interactions that are rare and potentially undetectable using traditional microscopy methods. We show here the association of replication protein A and bromodeoxyuridine as proof-of-concept. Full article

Physical activity is beneficial for improving health and reducing sick leave absences. This article describes a protocol for an intervention using an interactive accelerometer smartphone application, telephone counselling, and physical activity recordings to increase the physical activity of workers in the military and improve their health. Under the protocol, employees from six military brigades in Finland will be randomly assigned to intervention and control groups. The intervention group’s participants will use accelerometers to measure their daily physical activities and their quality of sleep for six months. They will receive feedback based on these measurements via a smartphone application. The intervention group’s participants will be encouraged to exercise for two hours per week during working hours, and to participate in telephone counselling. The control group’s participants will continue with their normal exercise routines, without the accelerometer or feedback. The participants of both groups will be measured at the baseline, after the intervention period, and six months after the end of the intervention. The measurements will include accelerometer recordings, biochemical laboratory tests, body composition measurements, physical fitness tests, and questionnaires on sociodemographic factors, physical activities, and health. The primary outcomes will indicate changes in physical activity, physical fitness, and sick leave absences. The findings will help to develop a straightforward and cost-effective model for supporting the health and working capabilities of employees in the military and other workplaces. Full article