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Methods and Protocols, Volume 5, Issue 1

2022 February - 19 articles

Cover Story: New biomaterials for bone tissue engineering (BTE) applications need to be tested in a reliable model of bone microenvironment, and in vitro tests with bone cells represent worthy systems. Herein, a clear protocol to set up an indirect co-culture system of human-derived osteoblasts (OBs) and osteoclasts (OCs), reporting cell seeding density, cell:cell ratio, culture medium, and proofs of differentiation, is provided. The material to be tested is easily introduced in the system and the physical separation of OBs and OCs allows distinguishing the effects of the material on the two cell types via direct/indirect interaction between material and cells. The system is an in vitro model of bone coupling, useful in testing innovative materials for bone regeneration, and potentially exploitable in different application fields. View this paper
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Articles (19)

  • Protocol
  • Open Access
4 Citations
4,335 Views
15 Pages

16 February 2022

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...

  • Article
  • Open Access
1 Citations
4,134 Views
13 Pages

Harnessing Intronic microRNA Structures to Improve Tolerance and Expression of shRNAs in Animal Cells

  • Arjun Challagulla,
  • Mark L. Tizard,
  • Timothy J. Doran,
  • David M. Cahill and
  • Kristie A. Jenkins

10 February 2022

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 na...

  • Review
  • Open Access
53 Citations
20,457 Views
13 Pages

9 February 2022

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...

  • Protocol
  • Open Access
7 Citations
3,682 Views
9 Pages

Development of Primary Monolayer Cell Model and Organotypic Model of Uterine Leiomyoma

  • Natalia Shved,
  • Anna Egorova,
  • Natalia Osinovskaya and
  • Anton Kiselev

6 February 2022

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 signifi...

  • Communication
  • Open Access
6 Citations
3,631 Views
9 Pages

5 February 2022

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 f...

  • Article
  • Open Access
9 Citations
5,374 Views
25 Pages

Knotify: An Efficient Parallel Platform for RNA Pseudoknot Prediction Using Syntactic Pattern Recognition

  • Christos Andrikos,
  • Evangelos Makris,
  • Angelos Kolaitis,
  • Georgios Rassias,
  • Christos Pavlatos and
  • Panayiotis Tsanakas

2 February 2022

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 clu...

  • Protocol
  • Open Access
22 Citations
7,657 Views
7 Pages

A One-Stop Protocol to Assess Myocardial Fibrosis in Frozen and Paraffin Sections

  • Divya Sridharan,
  • Nooruddin Pracha,
  • Julie A. Dougherty,
  • Ali Akhtar,
  • Syed Baseeruddin Alvi and
  • Mahmood Khan

27 January 2022

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, an...

  • Article
  • Open Access
10 Citations
8,004 Views
17 Pages

A Simple and Effective Bioassay Method Suitable to Comparative In Vitro Study of Tomato Salt Tolerance at Early Development Stages

  • Marat R. Khaliluev,
  • Liliya R. Bogoutdinova,
  • Galina N. Raldugina and
  • Ekaterina N. Baranova

19 January 2022

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...

  • Article
  • Open Access
5 Citations
4,684 Views
14 Pages

PCA-Assisted Raman Analysis of Osteonecrotic Human Femoral Heads

  • Eiji Ishimura,
  • Wenliang Zhu,
  • Elia Marin,
  • Taigi Honma,
  • Nobuhiko Sugano,
  • Wataru Ando and
  • Giuseppe Pezzotti

17 January 2022

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 lif...

  • Systematic Review
  • Open Access
45 Citations
7,217 Views
12 Pages

A Systematic Review of Cementation Techniques to Minimize Cement Excess in Cement-Retained Implant Restorations

  • Rodolfo Reda,
  • Alessio Zanza,
  • Andrea Cicconetti,
  • Shilpa Bhandi,
  • Renzo Guarnieri,
  • Luca Testarelli and
  • Dario Di Nardo

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...

  • Protocol
  • Open Access
15 Citations
9,355 Views
25 Pages

Protocol of Co-Culture of Human Osteoblasts and Osteoclasts to Test Biomaterials for Bone Tissue Engineering

  • Giorgia Borciani,
  • Giorgia Montalbano,
  • Nicola Baldini,
  • Chiara Vitale-Brovarone and
  • Gabriela Ciapetti

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...

  • Protocol
  • Open Access
10 Citations
5,198 Views
11 Pages

Measurement of Physical Fitness and 24/7 Physical Activity, Standing, Sedentary Behavior, and Time in Bed in Working-Age Finns: Study Protocol for FINFIT 2021

  • Pauliina Husu,
  • Henri Vähä-Ypyä,
  • Kari Tokola,
  • Harri Sievänen,
  • Ari Mänttäri,
  • Sami Kokko,
  • Kaisu M. Kaikkonen,
  • Kai Savonen and
  • Tommi Vasankari

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...

  • Article
  • Open Access
4 Citations
4,937 Views
12 Pages

Comparability of CMV DNA Extraction Methods and Validation of Viral Load

  • Théophile Uwiringiyeyezu,
  • Bouchra El Khalfi,
  • Rachid Saile,
  • Jamal Belhachmi and
  • Abdelaziz Soukri

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 i...

  • Protocol
  • Open Access
5 Citations
9,781 Views
17 Pages

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 b...

  • Article
  • Open Access
5 Citations
4,122 Views
12 Pages

Near-Infrared Spectroscopy (NIRS) as a Method for Biological Sex Discrimination in the Endangered Houston Toad (Anaxyrus houstonensis)

  • Li-Dunn Chen,
  • Mariana Santos-Rivera,
  • Isabella J. Burger,
  • Andrew J. Kouba,
  • Diane M. Barber and
  • Carrie K. Vance

30 December 2021

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-inf...

  • Protocol
  • Open Access
1 Citations
4,371 Views
10 Pages

29 December 2021

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 lon...

  • Protocol
  • Open Access
8 Citations
4,205 Views
12 Pages

21 December 2021

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 recor...

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Methods Protoc. - ISSN 2409-9279