Articles

Reliable FASP-based procedures for optimal quantitative proteomic and phosphoproteomic analysis on samples from acute myeloid leukemia patients

Satisfactory sample preparation for mass spectrometry-based analysis is a critical step in the proteomics workflow. The quality and reproducibility of sample preparation can determine the coverage and confiden...

Authors: Maria Hernandez-Valladares, Elise Aasebø, Olav Mjaavatten, Marc Vaudel, Øystein Bruserud, Frode Berven and Frode Selheim

Expression of Concern: The functional role of long non-coding RNAs and epigenetics

Authors: Shulin Li

Extracting functional trends from whole genome duplication events using comparative genomics

The number of species with completed genomes, including those with evidence for recent whole genome duplication events has exploded. The recently sequenced Atlantic salmon genome has been through two rounds of...

Authors: Russell A. Hermansen, Torgeir R. Hvidsten, Simen Rød Sandve and David A. Liberles

Endothelial Mesenchymal Transition: Comparative Analysis of Different Induction Methods

Endothelial-Mesenchymal-Transition (EndMT) plays an essential role in cardiovascular development, and recently became an attractive therapeutic target based on evidence supporting its involvement in fibrosis a...

Authors: Mariana T. Pinto, Dimas T. Covas, Simone Kashima and Claudia O. Rodrigues

A Modified Coupled Spectrophotometric Method to Detect 2-5 Oligoadenylate Synthetase Activity in Prostate Cell Lines

2’-5’ oligoadenylate synthetases (OAS) are interferon inducible enzymes that polymerizes ATP to 2’-5’-linked oligomers of adenylate (2-5As). As part of the innate immune response, these enzymes are activated b...

Authors: Sushma M. Bhosle, Aisha Hunt and Jaideep Chaudhary

MicroRNA biogenesis and their functions in regulating stem cell potency and differentiation

Stem cells are unspecialized/undifferentiated cells that exist in embryos and adult tissues or can be converted from somatic differentiated cells. Use of stem cells for tissue regeneration and tissue engineeri...

Authors: Shaomian Yao

Thanks to all those who reviewed for Biological Procedures Online in 2015

A peer-reviewed journal would not survive without the generous time and insightful comments of the reviewers, whose efforts often go unrecognized. Although final decisions are always editorial, they are greatl...

Authors: Shulin Li

Characterising protein/detergent complexes by triple-detection size-exclusion chromatography

In vitro investigations of membrane proteins usually depend on detergents for protein solubilisation and stabilisation. The amount of detergent bound to a membrane protein is relevant to successful experiment ...

Authors: Katharina Gimpl, Jessica Klement and Sandro Keller

A BioBrick™-Compatible Vector for Allelic Replacement Using the XylE Gene as Selection Marker

Circular plasmid-mediated homologous recombination is commonly used for marker-less allelic replacement, exploiting the endogenous recombination machinery of the host. Common limitations of existing methods in...

Authors: Michela Casanova, Lorenzo Pasotti, Susanna Zucca, Nicolò Politi, Ilaria Massaiu, Cinzia Calvio, Maria Gabriella Cusella De Angelis and Paolo Magni

Lambda Red-mediated Recombineering in the Attaching and Effacing Pathogen Escherichia albertii

The ability to introduce site-specific mutations in bacterial pathogens is essential towards understanding their molecular mechanisms of pathogenicity. This has been greatly facilitated by the genetic engineer...

Authors: Marisa Egan, Jasmine Ramirez, Christian Xander, Chirag Upreti and Shantanu Bhatt

Vectors for Genetically-Encoded Tags for Electron Microscopy Contrast in Drosophila

One of the most notable recent advances in electron microscopy (EM) was the development of genetically-encoded EM tags, including the fluorescent flavoprotein Mini-SOG (Mini-Singlet Oxygen Generator). Mini-SOG...

Authors: Marco Man Kin Tsui, Anri Itoh, Mohamed Amgad, Shao-Fang Wang and Toshio Sasaki

Lipase catalysis in organic solvents: advantages and applications

Lipases are industrial biocatalysts, which are involved in several novel reactions, occurring in aqueous medium as well as non-aqueous medium. Furthermore, they are well-known for their remarkable ability to c...

Authors: Ashok Kumar, Kartik Dhar, Shamsher Singh Kanwar and Pankaj Kumar Arora

Evaluation of local trace element status and 8-Iso-prostaglandin F_2α concentrations in patients with Tinea pedis

Tinea pedis (TP) is an infection of the feet caused by fungi. The infectious diseases caused by dermatophytes are mainly related to the enzymes produced by these fungi. Up to the now, the local 8-iso-prostagla...

Authors: Meral Miraloglu, Ergul Belge Kurutas, Perihan Ozturk and Ozer Arican

Predicting Crystallization Propensity of Proteins from Arabidopsis Thaliana

Many studies have correlated characteristics of amino acids with crystallization propensity, as part of the effort to determine the factors that affect the propensity of protein crystallization. However, these...

Authors: Shaomin Yan and Guang Wu

A Medium-Throughput Single Cell CRISPR-Cas9 Assay to Assess Gene Essentiality

Target selection for oncology is a crucial step in the successful development of therapeutics. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 editing of specific loci offers an alterna...

Authors: A. R. Grassian, T. M. E. Scales, S. K. Knutson, K. W. Kuntz, N. J. McCarthy, C. E. Lowe, J. D. Moore, R. A. Copeland, H. Keilhack, J. J. Smith, J. A. Wickenden and S. Ribich

Detection of genetic variation using dual-labeled peptide nucleic acid (PNA) probe-based melting point analysis

Thermal denaturation of probe-target hybrid is highly reproducible, and which makes probe melting point analysis reliable in the detection of mutations, polymorphisms and epigenetic differences in DNA. To impr...

Authors: Deokhwe Hur, Myoung Sug Kim, Minsik Song, Jinwook Jung and Heekyung Park

Mitogen Activated Protein Kinase (MPK) Interacts With Auxin Influx Carrier (OsAux/LAX1) Involved in Auxin Signaling in Plant

Mitogen activated protein kinases (MPKs) are serine/threonine protein kinases that contain characteristic T-x-Y motif in the activation loop region. MPKs are important signaling molecules involved in diverse s...

Authors: Tapan Kumar Mohanta, Nibedita Mohanta, Pratap Parida and Hanhong Bae

A High-Throughput Assay for Screening of Natural Products that Enhanced Tumoricidal Activity of NK Cells

Recently, immunotherapy has shown a lot of promise in cancer treatment and different immune cell types are involved in this endeavor. Among different immune cell populations, NK cells are also an important com...

Authors: Chenyuan Gong, Zhongya Ni, Chao Yao, Xiaowen Zhu, Lulu Ni, Lixin Wang and Shiguo Zhu

CellProfiler: Novel Automated Image Segmentation Procedure for Super-Resolution Microscopy

Super resolution (SR) microscopy enabled cell biologists to visualize subcellular details up to 20 nm in resolution. This breakthrough in spatial resolution made image analysis a challenging procedure. Direct ...

Authors: Kareem Soliman

Chicken chorioallantoic membrane as a reliable model to evaluate osteosarcoma—an experimental approach using SaOS2 cell line

Osteosarcoma is the most common primary tumor that affects usually children. Due to its cellular complex and osteoid formation it is very difficult to understand the mechanism behind the progressiveness of ost...

Authors: Reji Manjunathan and Malathi Ragunathan

Erratum to: Model of Cation Transportation Mediated by High-Affinity Potassium Transporters (HKTs) in Higher Plants

Authors: Yi Su, Weigui Luo, Wanhuang Lin, Liying Ma and Mohammed Humayun Kabir

The diversity of fungal genome

The genome size of an organism varies from species to species. The C-value paradox enigma is a very complex puzzle with regards to vast diversity in genome sizes in eukaryotes. Here we reported the detailed ge...

Authors: Tapan Kumar Mohanta and Hanhong Bae

Evaluation of Epic® label-free technology to quantify functional recombinant hemagglutinin

Alternative methods are being sought to measure the potency of influenza vaccines. Label-free technologies that do not require the use of hemagglutinin (HA)-specific antisera are particularly attractive as the...

Authors: Lianlian Jiang and Maryna C Eichelberger

Recombinase-mediated cassette exchange (RMCE) system for functional genomics studies in Mycoplasma mycoides

We have previously established technologies enabling us to engineer the Mycoplasma mycoides genome while cloned in the yeast Saccharomyces cerevisiae, followed by genome transplantation into Mycoplasma capricolum

Authors: Vladimir N Noskov, Li Ma, Stephen Chen and Ray-Yuan Chuang

cDNA synthesis for BCR-ABL1 detection at the MMR level: the importance of using the appropriate kit

The synthesis of complementary DNA (cDNA) for use in the detection of BCR-ABL1 at the Major Molecular Response (MMR) level is a well-established method used by clinical laboratories world-wide. However, the quali...

Authors: Jianxiang Chi, Chryso Pierides, Andrie Mitsidou, Andri Miltiadou, Petroula Gerasimou and Paul Costeas

Evaluation of method performance for oxidative stress biomarkers in urine and biological variations in urine of patients with type 2 diabetes mellitus and diabetic nephropathy

Oxidative stress biomarkers such as superoxide dismutase (CuZnSOD), catalase (CAT) and malondialdehyde (MDA) play an important role in the pathogenesis or progression of numerous diseases. Data regarding the b...

Authors: Ergul Belge Kurutas, Yakup Gumusalan, Ali Cetinkaya and Ekrem Dogan

Thanks to all those who reviewed for Biological Procedures Online in 2014

A peer-reviewed journal would not survive without the generous time and insightful comments of the reviewers, whose efforts often go unrecognized. Although final decisions are always editorial, they are greatl...

Authors: Shulin Li

Comparison of Vibratome and Compresstome sectioning of fresh primate lymphoid and genital tissues for in situ MHC-tetramer and immunofluorescence staining

For decades, the Vibratome served as a standard laboratory resource for sectioning fresh and fixed tissues. In skilled hands, high quality and consistent fresh unfixed tissue sections can be produced using a V...

Authors: Hadia M Abdelaal, Hyeon O Kim, Reece Wagstaff, Ryoko Sawahata, Peter J Southern and Pamela J Skinner

Model of Cation Transportation Mediated by High-Affinity Potassium Transporters (HKTs) in Higher Plants

Trk/Ktr/HKT transporters probably were evolved from simple K⁺ channels KcsA. HKT transporters, which mediate Na⁺-uniport or Na⁺/K⁺-symport, maintain K⁺/Na⁺ homeostasis and increase salinity tolerance, can be clas...

Authors: Yi Su, Weigui Luo, Wanhuang Lin, Liying Ma and Mohammed Hunayun Kabir

The functional role of long non-coding RNAs and epigenetics

Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, invo...

Authors: Jinneng Cao

A novel model of appendicitis and appendectomy to investigate inflammatory bowel disease pathogenesis and remediation

The appendix contains copious lymphoid tissue and is constantly exposed to gut flora. Appendicitis and appendectomy (AA) has been shown to prevent or significantly ameliorate ulcerative colitis. In our novel m...

Authors: Rajkumar Cheluvappa

A convenient, optimized pipeline for isolation, fluorescence microscopy and molecular analysis of live single cells

Heterogeneity within cell populations is relevant to the onset and progression of disease, as well as development and maintenance of homeostasis. Analysis and understanding of the roles of heterogeneity in bio...

Authors: Jordan R Yaron, Colleen P Ziegler, Thai H Tran, Honor L Glenn and Deirdre R Meldrum

Integration of bioinformatics to biodegradation

Bioinformatics and biodegradation are two primary scientific fields in applied microbiology and biotechnology. The present review describes development of various bioinformatics tools that may be applied in th...

Authors: Pankaj Kumar Arora and Hanhong Bae

A novel recombinant baculovirus overexpressing a Bacillus thuringiensis Cry1Ab toxin enhances insecticidal activity

Baculoviruses have been genetically modified to express foreign genes under powerful promoters in order to accelerate their speed of killing. In this study a truncated form of cry1Ab gene derived from Bacillus th...

Authors: Wael El-Menofy, Gamal Osman, Abdulrahman Assaeedi and Mohamed Salama

Real-time vascular mechanosensation through ex vivo artery perfusion

Cell-based perfusion studies have provided great insight into fluid-sensing mechanisms, such as primary cilia in the renal and vascular systems. However, the intrinsic limitations of in vitro cell culture, such a...

Authors: Rahul M Prasad, Xingjian Jin, Wissam A AbouAlaiwi and Surya M Nauli

Detection and quantification of extracellular microRNAs in murine biofluids

MicroRNAs (miRNAs) are short RNA molecules which regulate gene expression in eukaryotic cells, and are abundant and stable in biofluids such as blood serum and plasma. As such, there has been heightened intere...

Authors: Thomas C Roberts, Anna M L Coenen-Stass, Corinne A Betts and Matthew J A Wood

Isolation of T cells from mouse oral tissues

Utilizing mouse models provides excellent immunological and experimental tools to study oral immune responses. However for functional assays, isolating T lymphocytes from the oral tissues has proved to be chal...

Authors: Pushpa Pandiyan, Natarajan Bhaskaran, Yifan Zhang and Aaron Weinberg

Generation of a monoclonal antibody against the glycosylphosphatidylinositol-linked protein Rae-1 using genetically engineered tumor cells

Although genetically engineered cells have been used to generate monoclonal antibodies (mAbs) against numerous proteins, no study has used them to generate mAbs against glycosylphosphatidylinositol (GPI)-ancho...

Authors: Jiemiao Hu, Long T Vien, Xueqing Xia, Laura Bover and Shulin Li

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