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Methods and Protocols, Volume 3, Issue 4

2020 December - 21 articles

Cover Story: E. coli strains and T7-promoter-based plasmids have been widely used for the expression of recombinant proteins. However, the limited amount of soluble protein fused with core-streptavidin made it challenging for the immobilization of protein on biotinylated materials. In this study, a T7-promoter-based pET-30a(+) plasmid encoded with a chimeric thymidine phosphorylase (TP)-coreSA gene was constructed as a model system for the expression of TP-coreSA fusion protein. Various bacterial strains with the T7 expression system were used to analyze the expression of soluble fusion protein, with the goal of minimizing time- and cost-consuming steps of protein purification. Our results indicate that the pET-30a(+)-TP-coreSA/Lemo21(DE3) system could provide efficient expression of soluble TP-coreSA fusion protein for purification. The eluted fusion protein tethered on biotinylated A549 cancer cells revealed its functionality by effectively killing cells after loading with prodrug 5′-DFUR.
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Articles (21)

  • Protocol
  • Open Access
7 Citations
4,271 Views
14 Pages

Digital Approach for the Rehabilitation of the Edentulous Maxilla with Pterygoid and Standard Implants: The Static and Dynamic Computer-Aided Protocols

  • Alessio Franchina,
  • Luigi Vito Stefanelli,
  • Simone Gorini,
  • Simone Fedi,
  • Giuseppe Lizio and
  • Gerardo Pellegrino

21 December 2020

A full-arch rehabilitation of the edentulous upper jaw without grafting procedures exploits the residual alveolar or the basal bone, with the necessity of long implants placed with a particular orientation. The precision in planning and placing the f...

  • Study Protocol
  • Open Access
11 Citations
3,723 Views
12 Pages

A Personalized Patient-Centered Intervention to Empower through Physical Activity the Patient in the Dialysis Center: Study Protocol for a Pragmatic Nonrandomized Clinical Trial

  • Fabio Manfredini,
  • Nicola Lamberti,
  • Yuri Battaglia,
  • Sofia Straudi,
  • Martino Belvederi Murri,
  • Maria Donadi,
  • Giovanni Piva,
  • Fabio Fabbian,
  • Pablo Jesús López-Soto and
  • Alda Storari
  • + 3 authors

6 December 2020

Sedentariness of patients affected by end-stage kidney disease (ESKD) expose them to high risk of unfavorable clinical outcomes. Exercise training is effective in improving physical function, quality of life (QoL) and long-term outcomes. However, the...

  • Protocol
  • Open Access
7 Citations
6,455 Views
15 Pages

1 December 2020

The limited amount of fusion protein transported into cytosol milieu has made it challenging to obtain a sufficient amount for further applications. To avoid the laborious and expensive task, T7 promoter-driving pET-30a(+) coding for chimeric gene of...

  • Article
  • Open Access
4 Citations
3,315 Views
13 Pages

Quantitative, High-Throughput Assays for Proteolytic Degradation of Amylin

  • Caitlin N. Suire,
  • Monica K. Brizuela and
  • Malcolm A. Leissring

24 November 2020

Amylin is a pancreatic peptide hormone that regulates glucose homeostasis but also aggregates to form islet amyloid in type-2 diabetes. Given its role in both health and disease, there is renewed interest in proteolytic degradation of amylin by insul...

  • Protocol
  • Open Access
3 Citations
3,131 Views
9 Pages

In Situ DNA/Protein Interaction Assay to Visualize Transcriptional Factor Activation

  • Michela Corsini,
  • Emanuela Moroni,
  • Cosetta Ravelli,
  • Elisabetta Grillo,
  • Marco Presta and
  • Stefania Mitola

21 November 2020

The chick embryo chorioallantoic membrane (CAM) represents a powerful in vivo model to study several physiological and pathological processes including inflammation and tumor progression. Nevertheless, the possibility of deepening the molecular proce...

  • Feature Paper
  • Review
  • Open Access
11 Citations
7,853 Views
28 Pages

18 November 2020

While clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing techniques have been widely adapted for use in immortalised immune cells, efficient manipulation of primary T cells has proved to be more challenging. Nonet...

  • Technical Note
  • Open Access
4 Citations
3,078 Views
9 Pages

Building Accurate Intracellular Polarity Maps through Multiparametric Microscopy

  • M. Carmen Gonzalez-Garcia,
  • Pilar Herrero-Foncubierta,
  • Emilio Garcia-Fernandez and
  • Angel Orte

11 November 2020

The precise knowledge of intracellular polarity, a physiological parameter that involves complex and intertwined intracellular mechanisms, may be relevant in the study of important diseases like cancer or Alzheimer’s. In this technical note, we...

  • Technical Note
  • Open Access
7 Citations
3,285 Views
9 Pages

Prediction of Lung Function in Adolescence Using Epigenetic Aging: A Machine Learning Approach

  • Md Adnan Arefeen,
  • Sumaiya Tabassum Nimi,
  • M. Sohel Rahman,
  • S. Hasan Arshad,
  • John W. Holloway and
  • Faisal I. Rezwan

9 November 2020

Epigenetic aging has been found to be associated with a number of phenotypes and diseases. A few studies have investigated its effect on lung function in relatively older people. However, this effect has not been explored in the younger population. T...

  • Protocol
  • Open Access
13 Citations
5,061 Views
10 Pages

Dynamic Navigation for Zygomatic Implants: A Case Report about a Protocol with Intraoral Anchored Reference Tool and an Up-To-Date Review of the Available Protocols

  • Gerardo Pellegrino,
  • Giuseppe Lizio,
  • Francesco Basile,
  • Luigi Vito Stefanelli,
  • Claudio Marchetti and
  • Pietro Felice

5 November 2020

Dynamic Navigation is a computer-aided technology that allows the surgeon to track the grip instruments while preparing the implant site in real time based on radiological anatomy and accurate pre-operative planning. The support of this technology to...

  • Article
  • Open Access
9 Citations
5,069 Views
12 Pages

Sustainable Management of Organic Wastes in Sharjah, UAE through Co-Composting

  • Md Maruf Mortula,
  • Aqeel Ahmed,
  • Kazi Parvez Fattah,
  • Ghina Zannerni,
  • Syed A. Shah and
  • Ahmed M. Sharaby

5 November 2020

Daily human activities and vast green areas produce substantial amounts of organic wastes that end up in landfills with minimal treatment. In addition to the problems associated with landfills, disposal through this method is unsustainable in the lon...

  • Review
  • Open Access
7 Citations
5,270 Views
12 Pages

Development of In Vitro Corneal Models: Opportunity for Pharmacological Testing

  • Valentina Citi,
  • Eugenia Piragine,
  • Simone Brogi,
  • Sara Ottino and
  • Vincenzo Calderone

2 November 2020

The human eye is a specialized organ with a complex anatomy and physiology, because it is characterized by different cell types with specific physiological functions. Given the complexity of the eye, ocular tissues are finely organized and orchestrat...

  • Protocol
  • Open Access
4 Citations
3,647 Views
14 Pages

Effects of Implementing the Timed and Targeted Counselling Model on Pregnancy Outcomes and Newborn Survival in Rural Uganda: Protocol for a Quasi-Experimental Study

  • Geoffrey Babughirana,
  • Sanne Gerards,
  • Alex Mokori,
  • Benon Musasizi,
  • Nathan Isabirye,
  • Isaac Charles Baigereza,
  • Grace Rukanda,
  • Emmanuel Bussaja,
  • Stef Kremers and
  • Jessica Gubbels

29 October 2020

Background: Although mortality rates have declined in Uganda over the last decade, maternal mortality is still high at 336 deaths per 100,000 live births, as is infant mortality at 43 deaths per 1000 live births. One in every 19 babies born in Uganda...

  • Protocol
  • Open Access
2 Citations
4,581 Views
11 Pages

28 October 2020

Butterflies are well known for their beautiful wings and have been great systems to understand the ecology, evolution, genetics, and development of patterning and coloration. These color patterns are mosaics on the wing created by the tiling of indiv...

  • Study Protocol
  • Open Access
2 Citations
3,108 Views
8 Pages

Study Protocol of a Randomized Controlled Trial of Home Modification to Prevent Home Fall Injuries in Houses with Māori Occupants

  • Michael Keall,
  • Hope Tupara,
  • Nevil Pierse,
  • Marg Wilkie,
  • Michael Baker,
  • Philippa Howden-Chapman and
  • Chris Cunningham

23 October 2020

Worldwide, injuries due to falls in the home impose a substantial burden and merit considerable effort to find effective prevention measures. The current study is one of very few randomized controlled trials that assess the effectiveness of home modi...

  • Protocol
  • Open Access
6 Citations
3,452 Views
8 Pages

Ultrasonic Navigation for the Treatment of Medication-Related Jaw Osteonecrosis Involving the Inferior Alveolar Nerve: A Case Report and Protocol Review

  • Gerardo Pellegrino,
  • Francesca Pavanelli,
  • Agnese Ferri,
  • Giuseppe Lizio,
  • Roberto Parrulli and
  • Claudio Marchetti

21 October 2020

Dynamic navigation (DN) is a computer-guided technique employed in different surgical fields and recently adopted in dental implantology to improve the accuracy of dental implant insertion. Medication-related osteonecrosis of the jaws (MRONJ) often r...

  • Protocol
  • Open Access
9 Citations
21,792 Views
9 Pages

An Efficient Method for Isolation of Plasmid DNA for Transfection of Mammalian Cell Cultures

  • Daniel V. Kachkin,
  • Julia I. Khorolskaya,
  • Julia S. Ivanova and
  • Aleksandr A. Rubel

14 October 2020

In this article, we present several protocols that describe the steps from cloning and obtaining a large amount of pure plasmid DNA to generation of lentiviruses based on these constructs. The protocols have been worked out on human cell culture HEK2...

  • Protocol
  • Open Access
13 Citations
3,961 Views
9 Pages

KidneyCare Guided Immuno-Optimization in Renal Allografts: The KIRA Protocol

  • Jennifer N. Gray,
  • Theresa Wolf-Doty,
  • Nimisha Sulejmani,
  • Osama Gaber,
  • David Axelrod,
  • Basmah Abdalla and
  • Gabriel Danovitch

30 September 2020

Immunosuppressant agents are essential in every transplant recipient’s care yet walking the fine line of over- or under-immunosuppression is a constant struggle for both patients and transplant providers alike. Optimization and personalization...

  • Protocol
  • Open Access
29 Citations
9,373 Views
12 Pages

Fibrin Clot Formation and Lysis in Plasma

  • Julie Brogaard Larsen and
  • Anne-Mette Hvas

25 September 2020

Disturbance in the balance between fibrin formation and fibrinolysis can lead to either bleeding or thrombosis; however, our current routine coagulation assays are not sensitive to altered fibrinolysis. The clot formation and lysis assay is a dynamic...

  • Protocol
  • Open Access
4 Citations
3,321 Views
9 Pages

Application of a Flow-Induced Stress Wave and Investigation of Associated Injuries on Cell Monolayers Using a Parallel Plate Flow Chamber

  • Samar Shurbaji,
  • Mahmoud Khatib A. A. Al-Ruweidi,
  • Fatma Hassan Ali,
  • Fatiha M. Benslimane and
  • Huseyin C. Yalcin

24 September 2020

Parallel plate flow chambers are widely used to expose cultured cells to physiological flows for the investigation of a variety of diseases. These applications usually involve the generation of continuous and steady fluid flow over cell monolayers fo...

  • Protocol
  • Open Access
36 Citations
6,340 Views
14 Pages

24 September 2020

Oxidative stress is prominent in many neurodegenerative diseases. Along with mitochondrial dysfunction and pathological protein aggregation, increased levels of reactive oxygen and nitrogen species, together with impaired antioxidant defense mechanis...

  • Article
  • Open Access
96 Citations
12,620 Views
30 Pages

23 September 2020

The boxplot is a powerful visualization tool of sampled continuous data sets because of its rich information delivered, compact size, and effective visual expression. The advantage of boxplots is not widely appreciated. Many top journals suggest that...

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Methods Protoc. - ISSN 2409-9279