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Methods and Protocols, Volume 6, Issue 5

2023 October - 31 articles

Cover Story: Although 2D in vitro cancer cell cultures have been used for decades to investigate antitumoral treatments, their use presents many drawbacks, including a poor resemblance of in vivo tumors. To mitigate these drawbacks, 3D culture models have emerged as a more representative alternative that more closely resembles solid tumors in their architecture and resistance to chemotherapeutic drugs. Additionally, they create a more physiological environment for the study of immune cell invasion and migration. In our paper, we describe a fast and cost-effective protocol for the generation of 3D spheroids. Using this protocol, spheroids of different human cancer cell lines can be obtained and characterized based on their morphology, viability, and expression of specific markers. View this paper
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Articles (31)

  • Study Protocol
  • Open Access
2 Citations
5,372 Views
23 Pages

Safeguarding against Dementia in Aboriginal and Torres Strait Islander Communities through the Optimisation of Primary Health Care: A Project Protocol

  • Yvonne C. Hornby-Turner,
  • Sarah G. Russell,
  • Rachel Quigley,
  • Veronica Matthews,
  • Sarah Larkins,
  • Noel Hayman,
  • Prabha Lakhan,
  • Leon Flicker,
  • Kate Smith and
  • Edward Strivens
  • + 6 authors

19 October 2023

This protocol describes the methodology and methods for a collaborative project with eight Aboriginal and Torres Strait Islander primary health care (PHC) organisations, across three Australian states and one territory, to increase clinical service p...

  • Article
  • Open Access
2 Citations
3,363 Views
12 Pages

19 October 2023

The sarcoendoplasmic reticulum Ca2+-ATPase (SERCA) is a membrane protein that is destabilized during purification in the absence of calcium ions. The disaccharide trehalose is a protein stabilizer that accumulates in the yeast cytoplasm when under st...

  • Systematic Review
  • Open Access
5 Citations
6,305 Views
14 Pages

17 October 2023

Concept mapping is a phased, mixed-method approach that is increasingly used in health research to develop an understanding of complex phenomena. The six phases of concept mapping are preparation, idea generation, structuring (clustering and prioriti...

  • Protocol
  • Open Access
3 Citations
6,348 Views
11 Pages

12 October 2023

Drosophila melanogaster is an excellent model for dissecting innate immune signaling and functions. Humoral and cellular immune mechanisms in the fly take place in the hemolymph, where host defense components are secreted and act in response to micro...

  • Study Protocol
  • Open Access
2 Citations
8,501 Views
11 Pages

Efficacy of Sonic-Powered and Manual Toothbrushes on Plaque-Induced Gingivitis in Pregnant Women: A Randomized Controlled Trial

  • Céline Clément,
  • Denis Bourgeois,
  • Flavia Vitiello,
  • Herve Perrier,
  • Ariane Tabary and
  • Florence Carrouel

12 October 2023

Hormonal changes and physiological alterations in pregnancy increase the susceptibility of the woman to oral diseases such as plaque-induced gingivitis. In individual oral prophylaxis, effective tooth brushing can reduce gingival inflammation. Theref...

  • Study Protocol
  • Open Access
3 Citations
3,375 Views
16 Pages

Maternal Antibiotic Exposure and the Risk of Developing Antenatal or Postpartum Depressive Symptoms: The Maternal Experience Study Protocol

  • Mahsa Pouranayatihosseinabad,
  • Maggie Taylor,
  • Jason Hawrelak,
  • Gregory M. Peterson,
  • Felicity Veal,
  • Tristan Ling,
  • Mackenzie Williams,
  • Megan Whatley,
  • Kyan Ahdieh and
  • Corinne Mirkazemi

11 October 2023

Limited epidemiological evidence suggests a link between antibiotic use and developing depression. This study seeks to investigate this association in depth, using a cohort of pregnant individuals. The primary aim is to explore any association betwee...

  • Article
  • Open Access
9 Citations
3,648 Views
21 Pages

Development of Solid Lipid Nanoparticles for Controlled Amiodarone Delivery

  • Andreea Creteanu,
  • Gabriela Lisa,
  • Cornelia Vasile,
  • Maria-Cristina Popescu,
  • Adrian Florin Spac and
  • Gladiola Tantaru

In various drug delivery systems, solid lipid nanoparticles are dominantly lipid-based nanocarriers. Amiodarone hydrochloride is an antiarrhythmic agent used to treat severe rhythm disturbances. It has variable and hard-to-predict absorption in the g...

  • Article
  • Open Access
1 Citations
3,951 Views
17 Pages

A Novel and Quantitative Detection Assay (effluxR) for Identifying Efflux-Associated Resistance Genes Using Multiplex Digital PCR in Clinical Isolates of Pseudomonas aeruginosa

  • Nontaporn Rattanachak,
  • Sattaporn Weawsiangsang,
  • Robert A. Baldock,
  • Theerasak Jaifoo,
  • Touchkanin Jongjitvimol and
  • Jirapas Jongjitwimol

The rise of multidrug resistance of Pseudomonas aeruginosa highlights an increased need for selective and precise antimicrobial treatment. Drug efflux pumps are one of the major mechanisms of antimicrobial resistance found in many bacteria, including...

  • Article
  • Open Access
2 Citations
2,674 Views
22 Pages

Allergens and Other Harmful Substances in Hydroalcoholic Gels: Compliance with Current Regulation

  • Ana Castiñeira-Landeira,
  • Lua Vazquez,
  • Thierry Dagnac,
  • Maria Celeiro and
  • María Llompart

Hydroalcoholic gels or hand sanitisers have become essential products to prevent and mitigate the transmission of COVID-19. Depending on their use, they can be classified as cosmetics (cleaning the skin) or biocides (with antimicrobial effects). The...

  • Protocol
  • Open Access
4 Citations
5,591 Views
10 Pages

Although 2D in vitro cancer cell cultures have been used for decades as a first line-of-research tool to investigate antitumoral drugs and treatments, their use presents many drawbacks, including the poor resemblance of such cultures to the character...

  • Article
  • Open Access
16 Citations
6,284 Views
16 Pages

The aim of this research is to define optimal conditions to improve the stability of gold and silver nanoparticles’ anti-zearalenone antibody conjugates for their utilisation in lateral flow immunochromatographic assay (LFIA). The Turkevich&nda...

  • Protocol
  • Open Access
4 Citations
3,702 Views
16 Pages

A Simplified Microscopy Technique to Rapidly Characterize Individual Fiber Traits in Cotton

  • Quinn LaFave,
  • Shalini P. Etukuri,
  • Chaney L. Courtney,
  • Neha Kothari,
  • Trevor W. Rife and
  • Christopher A. Saski

Recent advances in phenotyping techniques have substantially improved the ability to mitigate type-II errors typically associated with high variance in phenotyping data sets. In particular, the implementation of automated techniques such as the High-...

  • Study Protocol
  • Open Access
2 Citations
3,581 Views
10 Pages

Diet and Depression during Peri- and Post-Menopause: A Scoping Review Protocol

  • Alexandra M. Bodnaruc,
  • Miryam Duquet,
  • Denis Prud’homme and
  • Isabelle Giroux

The aim of the proposed scoping review is to describe and summarize studies assessing the associations between diet-related variables and depression in peri- and post-menopausal women. Studies examining the associations between diet-related variables...

  • Technical Note
  • Open Access
2 Citations
2,972 Views
9 Pages

30 September 2023

Development of a rapid detection method for deoxycholic acid (DCA) is crucial for its diagnosis in the early stages of inflammation and cancer. In this study, we expressed a soluble recombinant anti-DCA single-chain variable fragment (scFv) in Escher...

  • Protocol
  • Open Access
14 Citations
8,910 Views
10 Pages

High-Efficiency Transformation and Expression of Genomic Libraries in Yeast

  • Mira Loock,
  • Luiza Berenguer Antunes,
  • Rhiannon T Heslop,
  • Antonio Alfonso De Lauri,
  • Andressa Brito Lira and
  • Igor Cestari

21 September 2023

Saccharomyces cerevisiae is a powerful system for the expression of genome-wide or combinatorial libraries for diverse types of screening. However, expressing large libraries in yeast requires high-efficiency transformation and controlled expression....

  • Study Protocol
  • Open Access
2,709 Views
9 Pages

Epidemiology of Maternal Nutritional Status and Risk of Adverse Birth Outcomes in Undernourished Mothers with Sickle Cell Disease: A Systematic Review and Meta-Analysis Protocol

  • Lauren J. Klein,
  • John Benaiah Ayete-Nyampong,
  • Annette M. Williams,
  • Lori A. Harding,
  • Samuel A. Oppong,
  • Sari Acra,
  • Michael R. DeBaun and
  • Aamer Imdad

17 September 2023

In pregnancies complicated by sickle cell disease (SCD), the maternal-fetal dyad is at high risk for mortality and morbidity. In healthy pregnancies, maternal nutritional status is a critical factor for the healthy growth and development of the fetus...

  • Protocol
  • Open Access
21 Citations
7,389 Views
7 Pages

A Robust and Standardized Approach to Quantify Wound Closure Using the Scratch Assay

  • Stefan Balko,
  • Evan Kerr,
  • Edward Buchel,
  • Sarvesh Logsetty and
  • Afshin Raouf

17 September 2023

The scratch assay is an in vitro assay that allows for high-throughput quantification of wound closure by keratinocytes and fibroblasts with relative ease. However, this assay is amenable to experimental variables, which can result in false-positive...

  • Study Protocol
  • Open Access
6 Citations
2,381 Views
14 Pages

The European TauroPace™ Registry

  • Reinhard Vonthein,
  • Benito Baldauf,
  • Stefan Borov,
  • Ernest W. Lau,
  • Marzia Giaccardi,
  • Roberto Cemin,
  • Ojan Assadian,
  • Philippe Chévalier,
  • Kerstin Bode and
  • Hendrik Bonnemeier

15 September 2023

Background: Cardiac implantable electronic device (CIED) placement comes with certain complications. CIED infection is a severe adverse event related to CIED placement. In randomised controlled trials, the preoperative intravenous administration of a...

  • Study Protocol
  • Open Access
2 Citations
3,194 Views
7 Pages

11 September 2023

Tobacco use, particularly the initiation of smoking during adolescence and young adulthood, represents a significant public health concern in South Africa. The influence of socio-cultural factors, marketing strategies of the tobacco industry, and acc...

  • Study Protocol
  • Open Access
5 Citations
4,592 Views
11 Pages

Effect of Dietary Fiber Supplementation on Metabolic Endotoxemia: A Protocol for Systematic Review and Meta-Analysis of Randomized Clinical Trials

  • Yazan Ranneh,
  • Abdulmannan Fadel,
  • Abdah Md Akim,
  • Iskandar Idris,
  • Bolaji Lilian Ilesanmi-Oyelere and
  • Leila Cheikh Ismail

11 September 2023

Introduction: Metabolic endotoxemia (ME) is the main cause of sub-clinical chronic inflammation, which subsequently triggers the onset of several chronic diseases. However, recent reports have indicated that dietary fiber (DF) contributes significant...

  • Study Protocol
  • Open Access
4 Citations
5,225 Views
13 Pages

The Last Mile—Community Engagement and Conditional Incentives to Accelerate Polio Eradication in Pakistan: Study Protocol for a Quasi-Experimental Trial

  • Jai K. Das,
  • Amira Khan,
  • Farhana Tabassum,
  • Zahra Ali Padhani,
  • Atif Habib,
  • Mushtaq Mirani,
  • Abdu R. Rahman,
  • Zahid Ali Khan,
  • Arjumand Rizvi and
  • Zulfiqar Bhutta
  • + 1 author

8 September 2023

Poliomyelitis is a condition of great concern and is endemic in only two countries of the world: Pakistan and Afghanistan. Community mobilization plays a vital role in raising awareness and can help reduce polio vaccine refusals. The objective of thi...

  • Protocol
  • Open Access
3 Citations
8,187 Views
10 Pages

Improving 2-Chlorotrityl Chloride (2-CTC) Resin Activation

  • Tanya Román,
  • Gerardo Acosta,
  • Beatriz G. de la Torre,
  • Constanza Cárdenas,
  • Fanny Guzmán and
  • Fernando Albericio

8 September 2023

Used in solid-phase peptide synthesis (SPPS) for peptides with an acid termination, the 2-chlorotrityl chloride (2-CTC) resin is highly susceptible to moisture, leading to reduced resin loading and lower synthetic yields. It is therefore recommended...

  • Communication
  • Open Access
2 Citations
2,361 Views
11 Pages

5 September 2023

The black soldier fly (BSF) is well known for its ability to biologically convert organic waste into insect biomass, including protein and oil, which can be utilised as animal feed. Since raw BSF products, such as BSF powder, are difficult to differe...

  • Protocol
  • Open Access
2 Citations
3,654 Views
12 Pages

4 September 2023

Advancements in single-cell-related technologies have opened new possibilities for analyzing rare cells, such as circulating tumor cells (CTCs) and rare immune cells. Among these techniques, single-cell proteomics, particularly single-cell mass spect...

  • Article
  • Open Access
6 Citations
3,062 Views
11 Pages

Quantitative Polymerase Chain Reaction System for Alongshan Virus Detection

  • Alexander G. Litov,
  • Egor V. Okhezin,
  • Ivan S. Kholodilov,
  • Alexandra E. Polienko and
  • Galina G. Karganova

4 September 2023

The recently discovered Jingmenvirus group includes viruses with a segmented genome, RNA of a positive polarity, and several proteins with distant homology to the proteins of the members of the genus Orthoflavivirus. Some Jingmenvirus group members,...

  • Study Protocol
  • Open Access
5,984 Views
19 Pages

Gathering the Evidence on Diet and Depression: A Protocol for an Umbrella Review and Updated Meta-Analyses

  • Alexandra M. Bodnaruc,
  • Coralie Vincent,
  • Carolina Soto,
  • Miryam Duquet,
  • Denis Prud’homme and
  • Isabelle Giroux

Our objectives are to perform (1) an umbrella review on diet and depression, (2) a systematic review update on dietary patterns and depression, and (3) updated meta-analyses using studies from the previous two objectives. Systematic reviews examining...

  • Protocol
  • Open Access
13 Citations
4,141 Views
18 Pages

Improvement of Targeted Fungi Secondary Metabolite Production Using a Systematic Experimental Design and Chemometrics Analysis

  • Lamonielli F. Michaliski,
  • Laura P. Ióca,
  • Leandro S. Oliveira,
  • Camila M. Crnkovic,
  • Mirelle Takaki,
  • Vitor F. Freire and
  • Roberto G. S. Berlinck

Fungi are well-known producers of chemically diverse and biologically active secondary metabolites. However, their production yields through fermentation may hamper structural analysis and biological activity downstream investigations. Herein, a syst...

  • Study Protocol
  • Open Access
3 Citations
4,665 Views
10 Pages

Health Benefits of Montmorency Tart Cherry Juice Supplementation in Adults with Mild to Moderate Ulcerative Colitis: A Protocol for a Placebo Randomized Controlled Trial

  • Jonathan Sinclair,
  • Stephanie Dillon,
  • Robert Allan,
  • Johanne Brooks-Warburton,
  • Terun Desai,
  • Charlotte Lawson and
  • Lindsay Bottoms

Ulcerative colitis, characterized by its relapsing and remissive nature, negatively affects perception, body image, and overall quality of life. The associated financial burden underscores the need for alternative treatment approaches with fewer side...

  • Protocol
  • Open Access
2,423 Views
10 Pages

Procuring high-grade RNA from mature coconut tissues is a tricky and labor-intensive process due to the intricate scaffold of polysaccharides, polyphenols, lipids, and proteins that form firm complexes with nucleic acids. However, we have effectively...

  • Protocol
  • Open Access
3,390 Views
16 Pages

Protocol Study: Resistance Training Program, Nutritional, Sleep, and Screen Use Recommendations in Schoolchildren from Educational Centers in the Extreme South of Chile

  • Javier Albornoz-Guerrero,
  • Olga Barceló,
  • Sonia García-Merino,
  • Guillermo García-Pérez-de-Sevilla,
  • Igor Cigarroa and
  • Rafael Zapata-Lamana

Background: Childhood obesity has tripled, reaching critical levels of malnutrition. This factor is directly associated with a poorer health-related quality of life of the child and adolescent population. This article presents the study protocol of t...

  • Protocol
  • Open Access
3 Citations
3,412 Views
9 Pages

Novel Protocol for the Preparation of Porcine Bone Marrow Primary Cell Culture for African Swine Fever Virus Isolation

  • Olga Puzankova,
  • Vera Gavrilova,
  • Roman Chernyshev,
  • Ivan Kolbin,
  • Alexey Igolkin,
  • Alexandr Sprygin,
  • Ilya Chvala and
  • Ali Mazloum

Isolation of African swine fever virus (ASFV) is a critical step towards the identification, titration, characterization, and even modification of the virus. Therefore, it is important to identify a suitable cell line that supports the efficient repl...

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Methods Protoc. - ISSN 2409-9279