Articles

Reviewer acknowledgement 2013

A peer-reviewed journal would not survive without the generous time and insightful comments of the reviewers, whose efforts often go unrecognized. Biological Procedures Online has been blessed by the support of h...

Authors: Daniel Shanahan

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples

DNA methylation plays crucial roles in epigenetic gene regulation in normal development and disease pathogenesis. Efficient and accurate quantification of DNA methylation at single base resolution can greatly ...

Authors: Yew Kok Lee, Shengnan Jin, Shiwei Duan, Yen Ching Lim, Desmond PY Ng, Xueqin Michelle Lin, George SH Yeo and Chunming Ding

Fast automated yeast cell counting algorithm using bright-field and fluorescence microscopic images

The faithful determination of the concentration and viability of yeast cells is important for biological research as well as industry. To this end, it is important to develop an automated cell counting algorit...

Authors: Dongpyo Hong, Gwanghee Lee, Neon Cheol Jung and Moongu Jeon

Exploration of two methods for quantitative Mitomycin C measurement in tumor tissue in vitro and in vivo

Two methods of quantifying Mitomycin C in tumor tissue are explored. A method of ultraviolet-visible absorption microscopy is developed and applied to measure the concentration of Mitomycin C in preserved mous...

Authors: Lee MacKenzie Fischer, Juan Luis Vásquez, Julie Gehl, Gregers G Hermann and Niels B Larsen

Solution casting of chitosan membranes for in vitro evaluation of bioactivity

Considerable research is focusing on the surface modification of titanium implants for the treatment of orthopaedic tissue injuries to increase the success of orthopaedic fixations. Chitosan is one of the natu...

Authors: Ramona Lieder, Mariam Darai, Gissur Örlygsson and Olafur E Sigurjonsson

Expression, purification and molecular analysis of the human ZNF706 protein

The ZNF706 gene encodes a protein that belongs to the zinc finger family of proteins and was found to be highly expressed in laryngeal cancer, making the structure and function of ZNF706 worthy of investigation. ...

Authors: Jucimara Colombo, Paola Jocelan Scarin Provazzi, Marilia Freitas Calmon, Lilian Campos Pires, Nathália Campos Rodrigues, Paulo Petl Jr, Marcelo Andrés Fossey, Fátima Pereira de Souza, Fernanda Canduri and Paula Rahal

Simultaneous splicing of multiple DNA fragments in one PCR reaction

Rapid and simultaneous splicing of multiple DNA fragments is frequently required in many recombinant DNA projects. However, former overlap extension PCRs, the most common methods for splicing DNA fragments, ar...

Authors: Wei-Gui Luo, Hui-Zhen Liu, Wan-Huang Lin, Mohammed Humayun Kabir and Yi Su

Quantification of bone changes in a collagen-induced arthritis mouse model by reconstructed three dimensional micro-CT

Inflammatory arthritis is a chronic disease, resulting in synovitis and subchondral and bone area destruction, which can severely affect a patient’s quality of life. The most common form of inflammatory arthri...

Authors: Shu Yang, Anne M Hollister, Elysse A Orchard, Shubnum I Chaudhery, Dmitry V Ostanin, Stephen J Lokitz and J Michael Mathis

Increasing the library size in cDNA display by optimizing purification procedures

The library size is critical for selection in evolutionary molecular engineering (directed evolution). Although cDNA display has become a promising in vitro display technology by overcoming the instability of mRN...

Authors: Yuki Mochizuki, Shigefumi Kumachi, Koichi Nishigaki and Naoto Nemoto

An evaluation of the reliability of muscle fiber cross-sectional area and fiber number measurements in rat skeletal muscle

The reliability of estimating muscle fiber cross-sectional area (measure of muscle fiber size) and fiber number from only a subset of fibers in rat hindlimb muscle cross-sections has not been systematically ev...

Authors: Lisa Ceglia, Sathit Niramitmahapanya, Lori L Price, Susan S Harris, Roger A Fielding and Bess Dawson-Hughes

Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods

Specific applications and modern technologies, like non-invasive prenatal testing, non-invasive cancer diagnostic and next generation sequencing, are currently in the focus of researchers worldwide. These have...

Authors: Tatiana Sedlackova, Gabriela Repiska, Peter Celec, Tomas Szemes and Gabriel Minarik

Next generation sequencing in cancer research and clinical application

The wide application of next-generation sequencing (NGS), mainly through whole genome, exome and transcriptome sequencing, provides a high-resolution and global view of the cancer genome. Coupled with powerful...

Authors: Derek Shyr and Qi Liu

A do-it-yourself protocol for simple transcription activator-like effector assembly

TALEs (transcription activator-like effectors) are powerful molecules that have broad applications in genetic and epigenetic manipulations. The simple design of TALEs, coupled with high binding predictability ...

Authors: Claudia Uhde-Stone, Nilang Gor, Tiffany Chin, Joseph Huang and Biao Lu

Determine the quality of human embryonic stem colonies with laser light scattering patterns

With the prompt developments of regenerative medicine, the potential clinical applications of human embryonic stem cells have attracted intense attention. However, the labor-intensive and complex manual cell s...

Authors: Chi-Shuo Chen, Matthew Biasca, Catherine Le, Eric Y-T Chen, E Daniel Hirleman and Wei-Chun Chin

A new method of kidney biopsy using low dose CT-guidance with coaxial trocar and bard biopsy gun

To explore a new method of kidney biopsy with coaxial trocar and bard biopsy gun under low dose computed tomography (CT)-guidance and evaluate its accuracy, safety, and efficacy.

Authors: Xiao-ling Pi, Zhen Tang, Li-qian Fu, Mei-hua Guo, Mei-hua Shi, Lan Chen and Zheng-ying Wan

Spontaneous arthritis and ankylosis in male DBA/1 mice: further evidence for a role of behavioral factors in “stress-induced arthritis”

Ageing male DBA/1 mice spontaneously develop arthritis in the hind paws. We and others have demonstrated that this model shares striking features with human spondyloarthritis, in particular entheseal involveme...

Authors: Kirsten Braem, Shea Carter and Rik J Lories

Modified protocol for in vivo imaging of wild-type mouse retina with customized miniature spectral domain optical coherence tomography (SD-OCT) device

This protocol outlines and evaluates a modified scanning procedure for a customized spectral domain optical coherence tomography (SD-OCT) imaging apparatus within the wild-type C57Bl/6 mouse posterior segment....

Authors: Lee R Ferguson, Sankarathi Balaiya, Sandeep Grover and Kakarla V Chalam

A robust dual reporter system to visualize and quantify gene expression mediated by transcription activator-like effectors

Transcription activator-like effectors (TALEs) are a class of naturally occurring transcription effectors that recognize specific DNA sequences and modulate gene expression. The modularity of TALEs DNA binding...

Authors: Claudia Uhde-Stone, Joseph Huang and Biao Lu

Competitive DNA transfection formulation via electroporation for human adipose stem cells and mesenchymal stem cells

Adipose stem cells have a strong potential for use in cell-based therapy, but the current nucleofection technique, which relies on unknown buffers, prevents their use.

Authors: Michael Flanagan, Jeffrey M Gimble, Gang Yu, Xueqing Xia, Bruce A Bunnell and Shulin Li

Novel mouse mammary cell lines for in vivo bioluminescence imaging (BLI) of bone metastasis

Tumor cell lines that can be tracked in vivo during tumorigenesis and metastasis provide vital tools for studying the specific cellular mechanisms that mediate these processes as well as investigating therapeutic...

Authors: Celeste Bolin, Caleb Sutherland, Ken Tawara, Jim Moselhy and Cheryl L Jorcyk

A reinvestigation of somatic hypermethylation at the PTEN CpG island in cancer cell lines

PTEN is an important tumour suppressor gene that is mutated in Cowden syndrome as well as various sporadic cancers. CpG island hypermethylation is another route to tumour suppressor gene inactivation, however, th...

Authors: Luke B Hesson, Deborah Packham, Emily Pontzer, Pauline Funchain, Charis Eng and Robyn L Ward

A microplate technique to simultaneously assay calcium accumulation in endoplasmic reticulum and SERCA release of inorganic phosphate

Traditional analyses of calcium homeostasis have separately quantified either calcium accumulation or release mechanisms. To define the system as a whole, however, requires multiple experimental techniques to ...

Authors: David C McMullen, William S Kean, Ajay Verma, Jeffrey T Cole and William D Watson

An improved competitive inhibition enzymatic immunoassay method for tetrodotoxin quantification

Quantifying tetrodotoxin (TTX) has been a challenge in both ecological and medical research due to the cost, time and training required of most quantification techniques. Here we present a modified Competitive...

Authors: Amber N Stokes, Becky L Williams and Susannah S French

Enhancement of anti-murine colon cancer immunity by fusion of a SARS fragment to a low-immunogenic carcinoembryonic antigen

It is widely understood that tumor cells express tumor-associated antigens (TAAs), of which many are usually in low immunogenicity; for example, carcinoembryonic antigen (CEA) is specifically expressed on huma...

Authors: Chen-Si Lin, Shih-Han Kao, Yu-Cheng Chen, Chi-Han Li, Yuan-Ting Hsieh, Shang-Chih Yang, Chang-Jer Wu, Ru-Ping Lee and Kuang-Wen Liao

A method for non-invasive genotyping of APC^min/+ mice using fecal samples

The APC^min/+ mouse is commonly used in cancer research and is just one of many genetically altered models that is currently being developed. With high numbers of breeding programs, it is important to have a simpl...

Authors: Erin L Symonds and Michael Fenech

Gene-targeted embryonic stem cells: real-time PCR assay for estimation of the number of neomycin selection cassettes

In the preparation of transgenic murine ES cells it is important to verify the construct has a single insertion, because an ectopic neomycin phosphortransferase positive selection cassette (NEO) may cause a posit...

Authors: Cecilia Mancini, Erika Messana, Emilia Turco, Alessandro Brussino and Alfredo Brusco

An automated cell-counting algorithm for fluorescently-stained cells in migration assays

A cell-counting algorithm, developed in Matlab^®, was created to efficiently count migrated fluorescently-stained cells on membranes from migration assays. At each concentration of cells used (10,000, and 100,000 ...

Authors: Baraa K Al-Khazraji, Philip J Medeiros, Nicole M Novielli and Dwayne N Jackson

Rapid generation of long tandem DNA repeat arrays by homologous recombination in yeast to study their function in mammalian genomes

We describe here a method to rapidly convert any desirable DNA fragment, as small as 100 bp, into long tandem DNA arrays up to 140 kb in size that are inserted into a microbe vector. This method includes r olling...

Authors: Vladimir N Noskov, Nicholas CO Lee, Vladimir Larionov and Natalay Kouprina

Frequency shifting approach towards textual transcription of heartbeat sounds

Auscultation is an approach for diagnosing many cardiovascular problems. Automatic analysis of heartbeat sounds and extraction of its audio features can assist physicians towards diagnosing diseases. Textual t...

Authors: Farshad Arvin, Shyamala Doraisamy and Ehsan Safar Khorasani

Media composition influences yeast one- and two-hybrid results

Although yeast two-hybrid experiments are commonly used to identify protein interactions, the frequent occurrence of false negatives and false positives hampers data interpretation. Using both yeast one-hybrid...

Authors: Ying Liu, Zabeena Merchant, Hao-Ching Hsiao, Kim L Gonzalez, Kathleen S Matthews and Sarah E Bondos

A rapid and easy method for the DNA extraction from Cryptococcus neoformans

DNA isolation from C. neoformans is difficult due to a thick and resistant capsule. We have optimized a new and rapid DNA isolation method for Cryptococcus using a short urea treatment followed by a rapid method ...

Authors: Fatma Mseddi, Mohammed Ali Jarboui, Amira Sellami, Hayet Sellami and Ali Ayadi

Quantitative Assessment of Mammary Gland Density in Rodents Using Digital Image Analysis

Rodent models have been used extensively to study mammary gland development and for studies of toxicology and carcinogenesis. Mammary gland gross morphology can visualized via the excision of intact mammary gl...

Authors: John N McGinley and Henry J Thompson

A quantitative PCR method for measuring absolute telomere length

We describe a simple and reproducible method to measure absolute telomere length (aTL) using quantitative real-time polymerase chain reaction (qPCR). This method is based on the Cawthon method for relative mea...

Authors: Nathan J O'Callaghan and Michael Fenech

Biological Procedures Online now publishing with BioMed Central

Authors: Shulin Li

Influence of RT-qPCR Primer Position on EGFR Interference Efficacy in Lung Cancer Cells

Real-time quantitative RT-PCR (RT-qPCR) is a “gold” standard for measuring steady state mRNA levels in RNA interference assays. The knockdown of the epidermal growth factor receptor (EGFR) gene with eight indi...

Authors: Gang Chen, Peter Kronenberger, Erik Teugels and Jacques De Grève

Influence of RT-qPCR primer position on EGFR interference efficacy in lung cancer cells

Real-time quantitative RT-PCR (RT-qPCR) is a "gold" standard for measuring steady state mRNA levels in RNA interference assays. The knockdown of the epidermal growth factor receptor (EGFR) gene with eight indi...

Authors: Gang Chen, Peter Kronenberger, Erik Teugels and Jacques De Grève

Utilization of IκB–EGFP Chimeric Gene as an Indicator to Identify Microbial Metabolites with NF-κB Inhibitor Activity

NF-κB regulates several important expressions, such as cytokine release, anti-apoptosis, adhesion molecule expression, and cell cycle processing. Several NF-κB inhibitors have been discovered as an anti-tumor ...

Authors: Yu-Ling Lin, Yen-Shun Chen, Jui-Hung Hsieh, Ching-Min Lin, Hsin-Yi Wu, Chen-Si Lin, Rea-Min Chu, Kuang-Wen Liao and Yuan-Hsun Hsu

A Method for Serial Tissue Processing and Parallel Analysis of Aberrant Crypt Morphology, Mucin Depletion, and Beta-Catenin Staining in an Experimental Model of Colon Carcinogenesis

The use of architectural and morphological characteristics of cells for establishing prognostic indicators by which individual pathologies are assigned grade and stage is a well-accepted practice. Advances in ...

Authors: John N McGinley, Matthew D Thompson and Henry J Thompson

A Method to Study the Epigenetic Chromatin States of Rare Hematopoietic Stem and Progenitor Cells; MiniChIP–Chip

Dynamic chromatin structure is a fundamental property of gene transcriptional regulation, and has emerged as a critical modulator of physiological processes during cellular differentiation and development. Ana...

Authors: Holger Weishaupt and Joanne L Attema

A New Microsphere-Based Immunoassay for Measuring the Activity of Transcription Factors

There are several traditional and well-developed methods for analyzing the activity of transcription factors, such as EMSA, enzyme-linked immunosorbent assay, and reporter gene activity assays. All of these me...

Authors: Yu-Ling Lin, Yun-Ju Lai, Nu-Man Tsai, Tai-Chu Peng, Yen-Ku Liu, Ru-Ping Lee, Chueh-Jen Tsai and Kuang-Wen Liao

Quick and Simple Detection Technique to Assess the Binding of Antimicrotubule Agents to the Colchicine-Binding Site

Development of antimitotic binding to the colchicine-binding site for the treatment of cancer is rapidly expanding. Numerous antimicrotubule agents are prepared every year, and the determination of their bindi...

Authors: Sébastien Fortin, Jacques Lacroix, Marie-France Côté, Emmanuel Moreau, Éric Petitclerc and René C-Gaudreault

Highly Efficient Stable Expression of Indoleamine 2,3 Dioxygenase Gene in Primary Fibroblasts

Indoleamine 2,3 dioxygenase (IDO) is a potent immunomodulatory enzyme that has recently attracted significant attention for its potential application as an inducer of immunotolerance in transplantation. We hav...

Authors: Alireza Moeen Rezakhanlou, Darya Habibi, Amy Lai, Reza B Jalili, Christopher J Ong and Aziz Ghahary

Optimized RNA Extraction and Northern Hybridization in Streptomycetes

Northern blot hybridization is a useful tool for analyzing transcript patterns. To get a picture of what really occurs in vivo, it is necessary to use a protocol allowing full protection of the RNA integrity a...

Authors: Marcello Tagliavia, Anna Taravella, Sandra Marineo, Anna Maria Puglia and Mario La Farina

Collection of Epithelial Cells from Rodent Mammary Gland Via Laser Capture Microdissection Yielding High-Quality RNA Suitable for Microarray Analysis

Laser capture microdissection (LCM) enables collection of cell populations highly enriched for specific cell types that have the potential of yielding critical information about physiological and pathophysiolo...

Authors: John N McGinley, Zongjian Zhu, Weiqin Jiang and Henry J Thompson

Comparison between Culture Conditions Improving Growth and Differentiation of Blood and Bone Marrow Cells Committed to the Endothelial Cell Lineage

The aim of this study was to compare different cell sources and culture conditions to obtain endothelial progenitor cells (EPCs) with predictable antigen pattern, proliferation potential and in vitro vasculoge...

Authors: Claudio Muscari, Chiara Gamberini, Ilaria Basile, Francesca Bonafé, Simond Valgimigli, Ombretta Capitani, Carlo Guarnieri and Claudio Marcello Caldarera

Ocular Proteomics with Emphasis on Two-Dimensional Gel Electrophoresis and Mass Spectrometry

The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide...

Authors: Nakul Mandal, Steffen Heegaard, Jan Ulrik Prause, Bent Honoré and Henrik Vorum

A Novel mRNA Level Subtraction Method for Quick Identification of Target-Orientated Uniquely Expressed Genes Between Peanut Immature Pod and Leaf

Subtraction technique has been broadly applied for target gene discovery. However, most current protocols apply relative differential subtraction and result in great amount clone mixtures of unique and differe...

Authors: Ning Wu, Kanyand Matand and Sonya Williams

Change in Hemoglobin Levels due to Anesthesia in Mice: An Important Confounder in Studies on Hematopoietic Drugs

Analgesic and anesthetic drugs may have an impact on the results achieved from animal experiments. In the study presented here, we try to enlighten whether anesthesia with fentanyl/fluniasone and midazolam (Hy...

Authors: Anita Gothelf, Pernille Hojman and Julie Gehl

Critical Appraisal of the MTT Assay in the Presence of Rottlerin and Uncouplers

Rottlerin is a natural product isolated from Mallotus philippinensis. This polyphenolic compound, originally described as a selective inhibitor of PKCδ, can inhibit many other PKC-unrelated kinases and has a numb...

Authors: Emanuela Maioli, Claudia Torricelli, Vittoria Fortino, Filippo Carlucci, Valentina Tommassini and Adriana Pacini

A Modified Coupled Enzyme Method for O-linked GlcNAc Transferase Activity Assay

In order to determine the activity of O-linked GlcNAc transferase (OGT), a modified coupled enzyme method was proposed. This method was based on the measurement of uridine 5'-(trihydrogen diphosphate) (UDP), a...

Authors: Lianwen Zhang, Feifei Ren, Jing Li, Xiaofeng Ma and Peng Wang