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Articles
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Citation: Biological Procedures Online 2016 18:12
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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...
Citation: Biological Procedures Online 2016 18:11 -
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...
Citation: Biological Procedures Online 2016 18:10 -
A Modified Coupled Spectrophotometric Method to Detect 2-5 Oligoadenylate Synthetase Activity in Prostate Cell Lines
2ā-5ā oligoadenylate synthetases (OAS) are interferon inducible enzymes that polymerizes ATP to 2ā-5ā-linked oligomers of adenylate (2-5As). As part of the innate immune response, these enzymes are activated b...
Citation: Biological Procedures Online 2016 18:9 -
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...
Citation: Biological Procedures Online 2016 18:8 -
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...
Citation: Biological Procedures Online 2016 18:7 -
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 ...
Citation: Biological Procedures Online 2016 18:4 -
A BioBrickā¢-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...
Citation: Biological Procedures Online 2016 18:6 -
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...
Citation: Biological Procedures Online 2016 18:3 -
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...
Citation: Biological Procedures Online 2016 18:5 -
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...
Citation: Biological Procedures Online 2016 18:2 -
Evaluation of local trace element status and 8-Iso-prostaglandin F2Ī± 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...
Citation: Biological Procedures Online 2016 18:1 -
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...
Citation: Biological Procedures Online 2015 17:16 -
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...
Citation: Biological Procedures Online 2015 17:15 -
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...
Citation: Biological Procedures Online 2015 17:14 -
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...
Citation: Biological Procedures Online 2015 17:13 -
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...
Citation: Biological Procedures Online 2015 17:12 -
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 ...
Citation: Biological Procedures Online 2015 17:11 -
Chicken chorioallantoic membrane as a reliable model to evaluate osteosarcomaāan 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...
Citation: Biological Procedures Online 2015 17:10 -
Erratum to: Model of Cation Transportation Mediated by High-Affinity Potassium Transporters (HKTs) in Higher Plants
Citation: Biological Procedures Online 2015 17:9 -
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...
Citation: Biological Procedures Online 2015 17:8 -
Evaluation of EpicĀ® 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...
Citation: Biological Procedures Online 2015 17:7 -
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
Citation: Biological Procedures Online 2015 17:6 -
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...
Citation: Biological Procedures Online 2015 17:4 -
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...
Citation: Biological Procedures Online 2015 17:3 -
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...
Citation: Biological Procedures Online 2015 17:5 -
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...
Citation: Biological Procedures Online 2015 17:2 -
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...
Citation: Biological Procedures Online 2015 17:1 -
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...
Citation: Biological Procedures Online 2014 16:42 -
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...
Citation: Biological Procedures Online 2014 16:10 -
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...
Citation: Biological Procedures Online 2014 16:9 -
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...
Citation: Biological Procedures Online 2014 16:8 -
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...
Citation: Biological Procedures Online 2014 16:7 -
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...
Citation: Biological Procedures Online 2014 16:6 -
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...
Citation: Biological Procedures Online 2014 16:5 -
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...
Citation: Biological Procedures Online 2014 16:4 -
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...
Citation: Biological Procedures Online 2014 16:3 -
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...
Citation: Biological Procedures Online 2014 16:2 -
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 ...
Citation: Biological Procedures Online 2014 16:1 -
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...
Citation: Biological Procedures Online 2013 15:13 -
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...
Citation: Biological Procedures Online 2013 15:12 -
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...
Citation: Biological Procedures Online 2013 15:11 -
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. ...
Citation: Biological Procedures Online 2013 15:10 -
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...
Citation: Biological Procedures Online 2013 15:9 -
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 patientās quality of life. The most common form of inflammatory arthri...
Citation: Biological Procedures Online 2013 15:8 -
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...
Citation: Biological Procedures Online 2013 15:7 -
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...
Citation: Biological Procedures Online 2013 15:6 -
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...
Citation: Biological Procedures Online 2013 15:5 -
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...
Citation: Biological Procedures Online 2013 15:4 -
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 ...
Citation: Biological Procedures Online 2013 15:3