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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
3,706 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 and ,
  • Anastasia Karampa,
  • George A. Alexiou and
  • George Vartholomatos
  • + 2 authors+ 0 author

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...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Article
  • Open Access
7 Citations
6,103 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
3,149 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...

(This article belongs to the Section Public Health Research)
  • Protocol
  • Open Access
3 Citations
4,292 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 and ,
  • Antonio Santoro and
  • Francesca Romana Buttarelli
  • + 1 author+ 0 author

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-...

(This article belongs to the Section Molecular and Cellular Biology)
  • Protocol
  • Open Access
6 Citations
4,234 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 and ,
  • Paul Tramini,
  • Laurie Fraticelli,
  • Florence Carrouel and
  • Denis Bourgeois
  • + 3 authors+ 0 author

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...

(This article belongs to the Special Issue Feature Papers 2021)
  • Review
  • Open Access
37 Citations
10,649 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...

(This article belongs to the Section Omics and High Throughput)
  • Protocol
  • Open Access
12 Citations
6,135 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 and ,
  • Anika Josef,
  • Margit Kaufmann,
  • Thomas Baer,
  • Tim Fellerhoff,
  • Iris Fuhrmann and
  • Martin Halle
  • + 19 authors+ 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...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Protocol
  • Open Access
10 Citations
4,756 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
13 Citations
13,266 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...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Protocol
  • Open Access
4 Citations
6,321 Views
13 Pages

The VISTA Approach in Canine Disimpaction

  • Gabriella Galluccio,
  • Alessandra Impellizzeri,
  • Alessandra Pietrantoni,
  • Adriana De Stefano and ,
  • Gerardo La Monaca and
  • Roberto Pippi
  • + 1 author+ 0 author

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...

(This article belongs to the Special Issue Digital Methods and Protocols in Implant Dentistry and Oral–Maxillofacial Surgery)
  • Protocol
  • Open Access
6 Citations
3,533 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...

(This article belongs to the Section Tissue Engineering and Organoids)
  • Protocol
  • Open Access
7 Citations
5,569 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 and ,
  • Mohammad Asif Hussainyar,
  • Cecilia Garzon,
  • Martin Ahimbisibwe,
  • Rafiullah Sadeed and
  • Ahmad Reshad
  • + 4 authors+ 0 author

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...

(This article belongs to the Section Public Health Research)
  • Protocol
  • Open Access
6 Citations
5,864 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
4 Citations
9,009 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...

(This article belongs to the Special Issue Feature Papers 2021)
  • Study Protocol
  • Open Access
16 Citations
5,578 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)...

(This article belongs to the Section Public Health Research)
  • Article
  • Open Access
3 Citations
6,526 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...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
  • Article
  • Open Access
61 Citations
10,737 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 and ,
  • Iveta Demirova,
  • Eddie Cai,
  • Mahdieh Tabatabaei,
  • Lenore K. Beitel,
  • Jason Karamchandani and
  • Thomas M. Durcan
  • + 6 authors+ 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...

(This article belongs to the Section Molecular and Cellular Biology)
  • Protocol
  • Open Access
6 Citations
11,238 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
14 Citations
7,413 Views
16 Pages

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

  • Roberto Di Marco,
  • Maria Rubega,
  • Olive Lennon,
  • Emanuela Formaggio and ,
  • Ngadhnjim Sutaj,
  • Giacomo Dazzi,
  • Chiara Venturin,
  • Ilenia Bonini,
  • Rupert Ortner and
  • on behalf of the PRO GAIT Consortium
  • + 10 authors+ 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...

(This article belongs to the Section Public Health Research)
  • Protocol
  • Open Access
10 Citations
5,601 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 and ,
  • Mary J. Rau,
  • Mollie D. Patton,
  • Alexander J. Gallan,
  • Juan C. Felix and
  • Hallgeir Rui
  • + 4 authors+ 0 author

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...

(This article belongs to the Section Public Health Research)
  • Protocol
  • Open Access
3 Citations
5,503 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 and ,
  • Ayako Nakashoji,
  • Takuma Inagawa,
  • Satoru Ikezawa,
  • Naoki Yoshimura,
  • Ryodai Yamamura and
  • Ryo Okubo
  • + 9 authors+ 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...

(This article belongs to the Section Biomedical Sciences and Physiology)
  • Protocol
  • Open Access
9 Citations
6,171 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...

(This article belongs to the Section Molecular and Cellular Biology)
  • Article
  • Open Access
36 Citations
6,432 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 and ,
  • Melanie Schulz,
  • Marius Ulbrich,
  • Johannes M. Miocic and
  • Frank Preusser
  • + 3 authors+ 0 author

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...

(This article belongs to the Section Biochemical and Chemical Analysis & Synthesis)
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Methods Protoc. - ISSN 2409-9279