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Methods and Protocols, Volume 4, Issue 3

2021 September - 23 articles

Cover Story: The reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) opens up the possibility of modeling human diseases and developing new therapeutics. Using human iPSC-derived cells for preclinical and clinical research, however, requires a constant supply of well-characterized iPSC lines. To address this issue, we developed a multistep workflow to assess our newly generated iPSCs through growth rate profiling, testing of genome integrity, evaluation of pluripotency, and testing their ability to form the three germline layers, with a particular focus on cortical neurons of the ectodermal lineage. This workflow helps to streamline work processes and offers the potential to add new tests to it as technologies evolve, thus ensuring that researchers employ high-quality iPSCs for experimental reproducibility and robustness.View this paper
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Articles (23)

  • Protocol
  • Open Access
21 Citations
3,231 Views
10 Pages

Touch Imprint Intraoperative Flow Cytometry as a Complementary Tool for Detailed Assessment of Resection Margins and Tumor Biology in Liver Surgery for Primary and Metastatic Liver Neoplasms

  • Georgios S. Markopoulos,
  • Georgios K. Glantzounis,
  • Anna C. Goussia,
  • Georgios D. Lianos,
  • Anastasia Karampa,
  • George A. Alexiou and
  • George Vartholomatos

15 September 2021

Liver resection is the main treatment for primary and metastatic liver tumors in order to achieve long-term survival with good quality of life. The ultimate goal of surgical oncology is to achieve complete tumor removal with adequate clear surgical m...

  • Article
  • Open Access
7 Citations
5,231 Views
12 Pages

10 September 2021

In the food and pharmaceutical industries, evaluating the sterilization performance preceding aseptic production processes is of central importance. In the case of hydrogen peroxide sterilization of solid surfaces, bioindicators (BI) consisting of sp...

  • Study Protocol
  • Open Access
2,864 Views
10 Pages

10 September 2021

Asthma affects over 330 million people worldwide, with relatively higher disease burdens in Australia, New Zealand, Africa, the Middle East, and South America. The symptoms associated with asthma were reported to be prevalent in children from the per...

  • Protocol
  • Open Access
2 Citations
3,922 Views
14 Pages

Improvement of the Collection, Maintenance, and Analysis of Neoplastic Cells from Urine Specimens with the Use of CytoMatrix

  • Simone Minasi,
  • Daniela Bosco,
  • Bernardo Moretti,
  • Felice Giangaspero,
  • Antonio Santoro and
  • Francesca Romana Buttarelli

10 September 2021

Urine cytology is a non-invasive test used in combination with cystoscopy for screening and follow-up of urothelial carcinoma (UC). Although cytology can be used to efficiently identify high-grade UC, it has a lower accuracy for the diagnosis of low-...

  • Protocol
  • Open Access
5 Citations
3,935 Views
12 Pages

Effect of Oral Prophylactic Measures on the Occurrence of Pre-Eclampsia (OP-PE) in High-Risk Pregnant Women: A Cluster Randomized Controlled Trial

  • Aida Kanoute,
  • Jocelyne Gare,
  • Nicolas Meda,
  • Stephane Viennot,
  • Paul Tramini,
  • Laurie Fraticelli,
  • Florence Carrouel and
  • Denis Bourgeois

5 September 2021

Pre-eclampsia (PE), a pregnancy-specific hypertensive disorder, characterized by the development of placental endothelial dysfunction, remains a major source of maternal and perinatal morbidity and mortality, especially in low- and middle-income sett...

  • Review
  • Open Access
32 Citations
8,764 Views
27 Pages

5 September 2021

Alternative splicing (AS) is a crucial process to enhance gene expression driving organism development. Interestingly, more than 95% of human genes undergo AS, producing multiple protein isoforms from the same transcript. Any alteration (e.g., nucleo...

  • Protocol
  • Open Access
7 Citations
5,344 Views
13 Pages

Cluster Randomized Controlled Trial on the Effects of 12 Months of Combined Exercise Training during Hemodialysis in Patients with Chronic Kidney Disease—Study Protocol of the Dialysis Training Therapy (DiaTT) Trial

  • Gero von Gersdorff,
  • Pia von Korn,
  • André Duvinage,
  • Gabriele Ihorst,
  • Anika Josef,
  • Margit Kaufmann,
  • Thomas Baer,
  • Tim Fellerhoff,
  • Iris Fuhrmann and
  • Martin Halle
  • + 14 authors

Patients with chronic kidney disease (CKD) on hemodialysis (HD) experience treatment-related immobility and physical deconditioning, which is responsible for an increased risk of frailty and a high burden of multi-morbidity. Exercise has been shown t...

  • Protocol
  • Open Access
9 Citations
4,307 Views
9 Pages

DNA sequencing of whole bacterial genomes has revealed that the entire set of mobile genes (mobilome) represents as much as 25% of the bacterial genome. Despite the huge availability of sequence data, the functional analysis of the mobile genetic ele...

  • Protocol
  • Open Access
7 Citations
11,333 Views
7 Pages

Time Mating Guinea Pigs by Monitoring Changes to the Vaginal Membrane throughout the Estrus Cycle and with Ultrasound Confirmation

  • Rebecca L. Wilson,
  • Kristin Lampe,
  • Brad J. Matushewski,
  • Timothy R. H. Regnault and
  • Helen N. Jones

One of the greatest challenges to the development and implementation of pregnancy therapeutics is the ability to rigorously test treatments in clinically relevant animal models. Guinea pigs offer a unique advantage in studying the placenta, fetal dev...

  • Protocol
  • Open Access
4 Citations
5,032 Views
13 Pages

The VISTA Approach in Canine Disimpaction

  • Gabriella Galluccio,
  • Alessandra Impellizzeri,
  • Alessandra Pietrantoni,
  • Adriana De Stefano,
  • Gerardo La Monaca and
  • Roberto Pippi

Canine disimpaction is always a challenging orthodontic treatment overall, even when the impacted permanent canine is in a high position, especially when in tight relation with the upper incisors’ roots. Conventional treatment methods are usually not...

  • Protocol
  • Open Access
6 Citations
3,162 Views
15 Pages

Elastic fibres constitute an important component of the extracellular matrix and currently are the subject of intensive study in order to elucidate their assembly, function and involvement in cell–matrix interactions and disease. However, few studies...

  • Protocol
  • Open Access
7 Citations
4,853 Views
13 Pages

Effectiveness of Specialized Nutritious Foods and Social and Behavior Change Communication Interventions to Prevent Stunting among Children in Badakhshan, Afghanistan: Protocol for a Quasi-Experimental Study

  • Sajid Bashir Soofi,
  • Gul Nawaz Khan,
  • Shabina Ariff,
  • Arjumand Rizvi,
  • Mohammad Asif Hussainyar,
  • Cecilia Garzon,
  • Martin Ahimbisibwe,
  • Rafiullah Sadeed and
  • Ahmad Reshad

Stunting predominantly occurs during the first 1000 days of life and continues to the age of five years. We will aim to assess the effectiveness of specialized nutritious foods (SNF)and social and behavior change communication (SBCC) strategies durin...

  • Protocol
  • Open Access
6 Citations
4,905 Views
8 Pages

Three-dimensional (3D) printing is a leading manufacturing technique in the medical field. The constantly improving quality of 3D printers has revolutionized the approach to new challenges in medicine for a wide range of applications including otopla...

  • Protocol
  • Open Access
3 Citations
7,230 Views
18 Pages

Butterflies possess impressive cognitive abilities, and investigations into the neural mechanisms underlying these abilities are increasingly being conducted. Exploring butterfly neurobiology may require the isolation of larval, pupal, and/or adult b...

  • Study Protocol
  • Open Access
14 Citations
5,114 Views
14 Pages

The infant gut microbiome is shaped by numerous factors such as diet and the maternal microbiota and is also associated with later atopy and obesity. The Archive for Research in Child Health and Baby Gut (ARCHBG) cohort was established in 2015 to (1)...

  • Article
  • Open Access
3 Citations
5,287 Views
13 Pages

Pichia pastoris and the Recombinant Human Heterodimeric Amino Acid Transporter 4F2hc-LAT1: From Clone Selection to Pure Protein

  • Satish Kantipudi,
  • Daniel Harder,
  • Sara Bonetti,
  • Dimitrios Fotiadis and
  • Jean-Marc Jeckelmann

Heterodimeric amino acid transporters (HATs) are protein complexes composed of two subunits, a heavy and a light subunit belonging to the solute carrier (SLC) families SLC3 and SLC7. HATs transport amino acids and derivatives thereof across the plasm...

  • Article
  • Open Access
50 Citations
8,726 Views
21 Pages

A Multistep Workflow to Evaluate Newly Generated iPSCs and Their Ability to Generate Different Cell Types

  • Carol X.-Q. Chen,
  • Narges Abdian,
  • Gilles Maussion,
  • Rhalena A. Thomas,
  • Iveta Demirova,
  • Eddie Cai,
  • Mahdieh Tabatabaei,
  • Lenore K. Beitel,
  • Jason Karamchandani and
  • Thomas M. Durcan
  • + 1 author

Induced pluripotent stem cells (iPSCs) derived from human somatic cells have created new opportunities to generate disease-relevant cells. Thus, as the use of patient-derived stem cells has become more widespread, having a workflow to monitor each li...

  • Protocol
  • Open Access
3 Citations
9,424 Views
19 Pages

HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells

  • Tomas Zelenka and
  • Charalampos Spilianakis

The functional implications of the three-dimensional genome organization are becoming increasingly recognized. The Hi-C and HiChIP research approaches belong among the most popular choices for probing long-range chromatin interactions. A few methodic...

  • Study Protocol
  • Open Access
13 Citations
6,657 Views
16 Pages

Experimental Protocol to Assess Neuromuscular Plasticity Induced by an Exoskeleton Training Session

  • Roberto Di Marco,
  • Maria Rubega,
  • Olive Lennon,
  • Emanuela Formaggio,
  • Ngadhnjim Sutaj,
  • Giacomo Dazzi,
  • Chiara Venturin,
  • Ilenia Bonini,
  • Rupert Ortner and
  • on behalf of the PRO GAIT Consortium
  • + 5 authors

Exoskeleton gait rehabilitation is an emerging area of research, with potential applications in the elderly and in people with central nervous system lesions, e.g., stroke, traumatic brain/spinal cord injury. However, adaptability of such technologie...

  • Protocol
  • Open Access
9 Citations
5,069 Views
8 Pages

Sensitive and Specific Immunohistochemistry Protocol for Nucleocapsid Protein from All Common SARS-CoV-2 Virus Strains in Formalin-Fixed, Paraffin Embedded Tissues

  • Yunguang Sun,
  • Linna Ge,
  • Sameer S. Udhane,
  • John F. Langenheim,
  • Mary J. Rau,
  • Mollie D. Patton,
  • Alexander J. Gallan,
  • Juan C. Felix and
  • Hallgeir Rui

Human coronavirus disease 2019 (COVID-19) is a life-threatening and highly contagious disease caused by coronavirus SARS-CoV-2. Sensitive and specific detection of SARS-CoV-2 viral proteins in tissues and cells of COVID-19 patients will support inves...

  • Protocol
  • Open Access
2 Citations
4,832 Views
14 Pages

Perilla Oil and Bifidobacterium for Alleviating Fear of Cancer Recurrence in Breast Cancer Survivors: Study Protocol for a Three-Arm Phase II Randomized Controlled Study (POB Study)

  • Yohei Sasaki,
  • Mina Honyashiki,
  • Takayuki Kinoshita,
  • Akira Matsui,
  • Ayako Nakashoji,
  • Takuma Inagawa,
  • Satoru Ikezawa,
  • Naoki Yoshimura,
  • Ryodai Yamamura and
  • Ryo Okubo
  • + 4 authors

The fear of cancer recurrence (FCR) is the most common and most severe unmet need among cancer survivors. Safe treatments for the FCR that are easily disseminated are greatly needed. Our primary aim is a preliminary evaluation of the efficacy and eff...

  • Protocol
  • Open Access
7 Citations
5,585 Views
43 Pages

The rates of translation elongation or termination in eukaryotes are modulated through cooperative molecular interactions involving mRNA, the ribosome, aminoacyl- and nascent polypeptidyl-tRNAs, and translation factors. To investigate the molecular m...

  • Article
  • Open Access
29 Citations
5,061 Views
13 Pages

Effect of Using Different Chemical Dispersing Agents in Grain Size Analyses of Fluvial Sediments via Laser Diffraction Spectrometry

  • Mubarak Abdulkarim,
  • Haruna M. Grema,
  • Ibrahim H. Adamu,
  • Daniela Mueller,
  • Melanie Schulz,
  • Marius Ulbrich,
  • Johannes M. Miocic and
  • Frank Preusser

Laser diffraction spectrometry allows for efficiently obtaining high-resolution grain size data. However, pretreatment and dispersion of aggregates in sediment samples are essential pre-requisites for acquiring accurate results using this method. Thi...

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Methods Protoc. - ISSN 2409-9279