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1.  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 gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC) are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.
PMCID: PMC3055252  PMID: 21406065
ocular proteomics; sample preparation; 2D-PAGE; 2D-DIGE; mass spectrometry
2.  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 differentially expressed genes. This makes it more difficult to identify unique or target-orientated expressed genes. In this study, we developed a novel method for subtraction at mRNA level by integrating magnetic particle technology into driver preparation and tester–driver hybridization to facilitate uniquely expressed gene discovery between peanut immature pod and leaf through a single round subtraction. The resulting target clones were further validated through polymerase chain reaction screening using peanut immature pod and leaf cDNA libraries as templates. This study has resulted in identifying several genes expressed uniquely in immature peanut pod. These target genes can be used for future peanut functional genome and genetic engineering research.
PMCID: PMC3055529  PMID: 21406066
Peanut; subtraction; gene discovery; cDNA library; hybridization; mRNA
3.  Change in Hemoglobin Levels due to Anesthesia in Mice: An Important Confounder in Studies on Hematopoietic Drugs 
Biological Procedures Online  2009;11:325-330.
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 (Hypnorm and Dormicum) has an influence on measurements of hemoglobin in mice. In a cross-over study, we have compared hemoglobin levels in two groups of mice: anesthetized versus non-anesthetized and found significant decrease in hemoglobin levels in the anesthetized group (p < 0.05) unrelated to which group received the anesthesia. The mean hemoglobin levels after intraperitoneal administration of Hypnorm and Dormicum was 8.7 mmol/L compared to mean hemoglobin 9.9 mmol/L before anesthesia (p < 0.001), and the decrease lasted for more than 30 min. These results show that anesthesia can be an important confounder in studies involving measurements of hemoglobin, and this should be taken into account when planning studies and analyzing data.
PMCID: PMC3056022  PMID: 19957064
anesthesia; hemoglobin; in vivo; fentanyl; midazolam
4.  Critical Appraisal of the MTT Assay in the Presence of Rottlerin and Uncouplers 
Biological Procedures Online  2009;11:227-240.
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 number of biological actions, including mitochondrial uncoupling effects. We recently found that Rottlerin inhibits the transcription factor nuclear factor κB in different cell types, causing downregulation of cyclin D1 and growth arrest. The present study was carried out to clarify the surprising lack of effect of Rottlerin on MCF-7 cell viability, assessed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) test. We found that Rottlerin causes overestimation of the MTT test, leading to inconsistent results between cell number and cell viability. Rottlerin, however, strongly differs from other antioxidant polyphenols, which directly reduce tetrazolium salts, since it does not exhibit any reactivity toward the tetrazolium salts in vitro nor does it modulate lactate dehydrogenase activity. The interference in the MTT assay occurred only in cultured cells, concomitantly with a decrease in the energy charge. Because the same MTT overestimation was observed in the presence of uncoupling agents, we conclude that the Rottlerin artifact is linked to its uncoupling action that, by accelerating oxidative chain, accidentally results in enhanced MTT reduction. These results suggest caution in the use of the MTT assay in the presence of Rottlerin and uncouplers in general.
PMCID: PMC3056051  PMID: 19957063
Rottlerin; MCF-7 cell; MTT; LDH; FCCP; mitochondrial uncoupling
5.  A Practical Guide to Rodent Islet Isolation and Assessment 
Pancreatic islets of Langerhans secrete hormones that are vital to the regulation of blood glucose and are, therefore, a key focus of diabetes research. Purifying viable and functional islets from the pancreas for study is an intricate process. This review highlights the key elements involved with mouse and rat islet isolation, including choices of collagenase, the collagenase digestion process, purification of islets using a density gradient, and islet culture conditions. In addition, this paper reviews commonly used techniques for assessing islet viability and function, including visual assessment, fluorescent markers of cell death, glucose-stimulated insulin secretion, and intracellular calcium measurements. A detailed protocol is also included that describes a common method for rodent islet isolation that our laboratory uses to obtain viable and functional mouse islets for in vitro study of islet function, beta-cell physiology, and in vivo rodent islet transplantation. The purpose of this review is to serve as a resource and foundation for successfully procuring and purifying high-quality islets for research purposes.
PMCID: PMC3056052  PMID: 19957062
islets of Langerhans; pancreatic islets; beta-cell; beta cells; cytokines; transplantation; calcium; insulin; apoptosis; necrosis; isolation; islet isolation; collagenase; rodent; mouse; rat; islet
6.  A Modified Coupled Enzyme Method for O-linked GlcNAc Transferase Activity Assay 
Biological Procedures Online  2009;11:170-183.
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 product generated in transglycosylation reaction. In the assay, UDP was coupled to the conversion of phosphoenolpyruvate to pyruvate using pyruvate kinase. Using a commercial pyruvate assay kit, the pyruvate was converted to a red terminal product, which could be photometrically measured at 570 nm or fluorometrically measured at 587 nm (Em = 535 nm) on a microplate reader. Kinetic study of a truncated recombinant mOGT and quantitative analysis of OGT in two biological samples indicated that this method was practical and competitive for quantitative analysis of OGT.
PMCID: PMC3056017  PMID: 19957065
O-linked GlcNAc transferase (OGT); coupled enzyme method; MS-glycosylation assay; kinetic study
7.  Dynamic Monitoring of Cellular Remodeling Induced by the Transforming Growth Factor-β1 
Biological Procedures Online  2009;11:316-324.
The plasticity of differentiated adult cells could have a great therapeutic potential, but at the same time, it is characteristic of progression of serious pathological states such as cancer and fibrosis. In this study, we report on the application of a real-time noninvasive system for dynamic monitoring of cellular plasticity. Analysis of the cell impedance profile recorded as cell index using a real-time cell analyzer revealed its significant increase after the treatment of prostate epithelial cells with the transforming growth factor-β1. Changes in the cell index profile were paralleled with cytoskeleton rebuilding and induction of epithelial–mesenchymal transition and negatively correlated with cell proliferation. This novel application of such approach demonstrated a great potential of the impedance-based system for noninvasive and real-time monitoring of cellular fate.
PMCID: PMC3056018  PMID: 19756912
real-time cell analysis; cell plasticity; epithelial–mesenchymal transition; transforming growth factor-β1; F-actin; cytoskeleton remodeling
8.  The Possible Cellular Mechanism for Extending Lifespan of Mice with Rapamycin 
PMCID: PMC3056009  PMID: 19728006
9.  MicroRNA Expression Profiling by Bead Array Technology in Human Tumor Cell Lines Treated with Interferon-Alpha-2a 
Biological Procedures Online  2009;11:113-129.
MicroRNAs are positive and negative regulators of eukaryotic gene expression that modulate transcript abundance by specific binding to sequence motifs located prevalently in the 3' untranslated regions of target messenger RNAs (mRNA). Interferon-alpha-2a (IFNα) induces a large set of protein coding genes mediating antiproliferative and antiviral responses. Here we use a global microarray-based microRNA detection platform to identify genes that are induced by IFNα in hepatoma- or melanoma-derived human tumor cell lines. Despite the enormous differences in expression levels between these models, we were able to identify microRNAs that are upregulated by IFNα in both lines suggesting the possibility that interferon-regulated microRNAs are involved in the transcriptional repression of mRNA relevant to cytokine responses.
PMCID: PMC3055981  PMID: 19629613
MicroRNAs; Oligonucleotide Array Sequence Analysis; Interferons; Melanoma; Hepatoma; Reverse Transcriptase Polymerase Chain Reaction; Suppressor of Cytokine Signaling Proteins
10.  Lentiviral-Mediated Transgene Expression Can Potentiate Intestinal Mesenchymal-Epithelial Signaling 
Biological Procedures Online  2009;11:130-144.
Mesenchymal-epithelial signaling is essential for the development of many organs and is often disrupted in disease. In this study, we demonstrate the use of lentiviral-mediated transgene delivery as an effective approach for ectopic transgene expression and an alternative to generation of transgenic animals. One benefit to this approach is that it can be used independently or in conjunction with established transgenic or knockout animals for studying modulation of mesenchymal-epithelial interactions. To display the power of this approach, we explored ectopic expression of a Wnt ligand in the mouse intestinal mesenchyme and demonstrate its functional influence on the adjacent epithelium. Our findings highlight the efficient use of lentiviral-mediated transgene expression for modulating mesenchymal-epithelial interactions in vivo.
PMCID: PMC3055996  PMID: 19597903
lentivirus; mesenchymal-epithelial signaling; intestine; transgene expression; Wnt signaling; mouse
11.  Segmentation of Extrapulmonary Tuberculosis Infection Using Modified Automatic Seeded Region Growing 
Biological Procedures Online  2009;11:241-252.
In the image segmentation process of positron emission tomography combined with computed tomography (PET/CT) imaging, previous works used information in CT only for segmenting the image without utilizing the information that can be provided by PET. This paper proposes to utilize the hot spot values in PET to guide the segmentation in CT, in automatic image segmentation using seeded region growing (SRG) technique. This automatic segmentation routine can be used as part of automatic diagnostic tools. In addition to the original initial seed selection using hot spot values in PET, this paper also introduces a new SRG growing criterion, the sliding windows. Fourteen images of patients having extrapulmonary tuberculosis have been examined using the above-mentioned method. To evaluate the performance of the modified SRG, three fidelity criteria are measured: percentage of under-segmentation area, percentage of over-segmentation area, and average time consumption. In terms of the under-segmentation percentage, SRG with average of the region growing criterion shows the least error percentage (51.85%). Meanwhile, SRG with local averaging and variance yielded the best results (2.67%) for the over-segmentation percentage. In terms of the time complexity, the modified SRG with local averaging and variance growing criterion shows the best performance with 5.273 s average execution time. The results indicate that the proposed methods yield fairly good performance in terms of the over- and under-segmentation area. The results also demonstrated that the hot spot values in PET can be used to guide the automatic segmentation in CT image.
PMCID: PMC3055983  PMID: 19597904
Seeded Region Growing; Segmentation; Dual Modality Imaging; Positron Emission Tomography; Computed Tomography
12.  A Modified Protocol for Bisulfite Genomic Sequencing of Difficult Samples 
The bisulfite genomic sequencing protocol is a widely used method for analyzing DNA methylation. It relies on the deamination of unmethylated cytosine residues to uracil; however, its high rates of DNA degradation and incomplete cytosine to uracil conversion often lead to failed experiments, uninformative results, and false positives. Here, we report the addition of a single-step multiple restriction enzyme digestion (MRED) designed to differentially digest polymerase chain reaction products amplified from unconverted DNA while leaving those of converted DNA intact. We show that for our model system, RARB2 P2 promoter, use of MRED increased informative sequencings ninefold, and MRED did not alter the clonal representation in one fully methylated cell line, H-596, treated or not with 5-azadeoxycytidine, a methylation inhibitor. We believe that this method may easily be adapted for analyzing other genes and provide guidelines for selecting the most appropriate MRED restriction enzymes.
PMCID: PMC3055914  PMID: 19551458
bisulfite genomic sequencing; multiple restriction enzyme digestion; methylation
13.  A Method for Structure–Activity Analysis of Quorum-Sensing Signaling Peptides from Naturally Transformable Streptococci 
Biological Procedures Online  2009;11:207-226.
Many species of streptococci secrete and use a competence-stimulating peptide (CSP) to initiate quorum sensing for induction of genetic competence, bacteriocin production, and other activities. These signaling molecules are small, unmodified peptides that induce powerful strain-specific activity at nano-molar concentrations. This feature has provided an excellent opportunity to explore their structure–function relationships. However, CSP variants have also been identified in many species, and each specifically activates its cognate receptor. How such minor changes dramatically affect the specificity of these peptides remains unclear. Structure–activity analysis of these peptides may provide clues for understanding the specificity of signaling peptide–receptor interactions. Here, we use the Streptococcus mutans CSP as an example to describe methods of analyzing its structure–activity relationship. The methods described here may provide a platform for studying quorum-sensing signaling peptides of other naturally transformable streptococci.
PMCID: PMC3055912  PMID: 19517207
Quorum sensing; Signaling peptides; Structure–activity analysis; Circular dichroism and nuclear magnetic resonance spectroscopy; Streptococcus mutans
14.  A Framework for White Blood Cell Segmentation in Microscopic Blood Images Using Digital Image Processing 
Biological Procedures Online  2009;11:196-206.
Evaluation of blood smear is a commonly clinical test these days. Most of the time, the hematologists are interested on white blood cells (WBCs) only. Digital image processing techniques can help them in their analysis and diagnosis. For example, disease like acute leukemia is detected based on the amount and condition of the WBC. The main objective of this paper is to segment the WBC to its two dominant elements: nucleus and cytoplasm. The segmentation is conducted using a proposed segmentation framework that consists of an integration of several digital image processing algorithms. Twenty microscopic blood images were tested, and the proposed framework managed to obtain 92% accuracy for nucleus segmentation and 78% for cytoplasm segmentation. The results indicate that the proposed framework is able to extract the nucleus and cytoplasm region in a WBC image sample.
PMCID: PMC3055951  PMID: 19517206
White blood cell segmentation; Active contours; Snake algorithm; Zack thresholding
15.  SDS-PAGE-Based Quantitative Assay for Screening of Kidney Stone Disease 
Biological Procedures Online  2009;11:145-160.
Kidney stone disease is a common health problem in industrialised nations. We developed a SDS-PAGE-based method to quantify Tamm Horsfall glycoprotein (THP) for screening of kidney stone disease. Urinary proteins were extracted by using ammonium sulphate precipitation at 0.27 g salt/mL urine. The resulted pellet was dissolved in TSE buffer. Ten microliters of the urinary proteins extract was loaded and separated on 10% SDS-PAGE under reducing condition. THP migrated as single band in SDS-PAGE. The assay reproducibility and repeatability were 4.8% CV and 2.6% CV, respectively. A total of 117 healthy subjects and 58 stone patients were tested using this assay, and a distinct cut-off (P < 0.05) at 5.6 μg/mL THP concentration was used to distinguish stone patients from healthy subjects. The sensitivity and specificity of the method were 92.3% and 83.3%, respectively.
PMCID: PMC3055900  PMID: 19495911
Kidney stone disease; SDS-PAGE; Tamm Horsfall Protein and diagnostic device
16.  Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy 
An important part of characterizing any protein molecule is to determine its size and shape. Sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural analysis. This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level. Readers are reminded that the Perrin equation is generally not a valid approach to determine the shape of proteins. Instead, a simple guideline is presented, based on the measured sedimentation coefficient and a calculated maximum S, to estimate if a protein is globular or elongated. It is recalled that a gel filtration column fractionates proteins on the basis of their Stokes radius, not molecular weight. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte. Finally, rotary shadowing and negative stain electron microscopy are powerful techniques for resolving the size and shape of single protein molecules and complexes at the nanometer level. A combination of hydrodynamics and electron microscopy is especially powerful.
PMCID: PMC3055910  PMID: 19495910
Protein shape; hydrodynamics; gel filtration; sedimentation; electron microscopy
17.  In Vivo Imaging of Far-red Fluorescent Proteins after DNA Electrotransfer to Muscle Tissue 
Biological Procedures Online  2009;11:253-262.
DNA electrotransfer to muscle tissue yields long-term, high levels of gene expression; showing great promise for future gene therapy. We want to characterize the novel far-red fluorescent protein Katushka as a marker for gene expression using time domain fluorescence in vivo imaging. Highly efficient transgenic expression was observed after DNA electrotransfer with 100-fold increase in fluorescent intensity. The fluorescent signal peaked 1 week after transfection and returned to background level within 4 weeks. Katushka expression was not as stable as GFP expression, which was detectable for 8 weeks. Depth and 3D analysis proved that the expression was located in the target muscle. In vivo bio-imaging using the novel Katushka fluorescent protein enables excellent evaluation of the transfection efficacy, and spatial distribution, but lacks long-term stability.
PMCID: PMC3055792  PMID: 19495913
Electroporation; Gene delivery; Whole-body imaging; Katushka; Skeletal muscle
18.  Detection and Processing Techniques of FECG Signal for Fetal Monitoring 
Biological Procedures Online  2009;11:263-295.
Fetal electrocardiogram (FECG) signal contains potentially precise information that could assist clinicians in making more appropriate and timely decisions during labor. The ultimate reason for the interest in FECG signal analysis is in clinical diagnosis and biomedical applications. The extraction and detection of the FECG signal from composite abdominal signals with powerful and advance methodologies are becoming very important requirements in fetal monitoring. The purpose of this review paper is to illustrate the various methodologies and developed algorithms on FECG signal detection and analysis to provide efficient and effective ways of understanding the FECG signal and its nature for fetal monitoring. A comparative study has been carried out to show the performance and accuracy of various methods of FECG signal analysis for fetal monitoring. Finally, this paper further focused some of the hardware implementations using electrical signals for monitoring the fetal heart rate. This paper opens up a passage for researchers, physicians, and end users to advocate an excellent understanding of FECG signal and its analysis procedures for fetal heart rate monitoring system.
PMCID: PMC3055800  PMID: 19495912
19.  Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects 
Comparative genomics has become a real tantalizing challenge in the postgenomic era. This fact has been mostly magnified by the plethora of new genomes becoming available in a daily bases. The overwhelming list of new genomes to compare has pushed the field of bioinformatics and computational biology forward toward the design and development of methods capable of identifying patterns in a sea of swamping data noise. Despite many advances made in such endeavor, the ever-lasting annoying exceptions to the general patterns remain to pose difficulties in generalizing methods for comparative genomics. In this review, we discuss the different tools devised to undertake the challenge of comparative genomics and some of the exceptions that compromise the generality of such methods. We focus on endosymbiotic bacteria of insects because of their genomic dynamics peculiarities when compared to free-living organisms.
PMCID: PMC3055744  PMID: 19495914
Comparative Genomics; Orthologs search; BLAST; Functional Categories; Genomics Dynamics
20.  Comparison of Enzymatic and Non-Enzymatic Means of Dissociating Adherent Monolayers of Mesenchymal Stem Cells 
Biological Procedures Online  2009;11:161-169.
The dissociation of adherent mesenchymal stem cell (MSC) monolayers with trypsin and enzyme-free dissociation buffer was compared. A significantly lower proportion of viable cells were obtained with enzyme-free dissociation buffers compared to trypsin. Subsequently, the dissociated cells were re-seeded on new cell culture dishes and were subjected to the MTT assay 24 h later. The proportion of viable cells that reattached was significantly lower for cells obtained by dissociation with enzyme-free dissociation buffer compared to trypsin. Frozen–thawed MSC displayed a similar trend, yielding consistently higher cell viability and reattachment rates when dissociated with trypsin compared to enzyme-free dissociation buffer. It was also demonstrated that exposure of trypsin-dissociated MSC to enzyme-free dissociation buffer for 1 h had no significant detrimental effect on cell viability.
PMCID: PMC3055293  PMID: 19495917
Dissociation; Enzyme; Mesenchymal; Stem cells; Trypsin
21.  Competitive RT-PCR Strategy for Quantitative Evaluation of the Expression of Tilapia (Oreochromis niloticus) Growth Hormone Receptor Type I 
Quantization of gene expression requires that an accurate measurement of a specific transcript is made. In this paper, a quantitative reverse transcription-polymerase chain reaction (RT-PCR) by competition for tilapia growth hormone receptor type I is designed and validated. This experimental procedure was used to determine the abundance of growth hormone receptor type I transcript in different tilapia tissues. The results obtained with this developed competitive RT-PCR were similar to real-time PCR results reported recently. This protocol provides a reliable alternative, but less expensive than real-time PCR to quantify specific genes.
PMCID: PMC3055623  PMID: 19495916
Tilapia; Receptors; Somatostatin
22.  Streptozotocin, Type I Diabetes Severity and Bone 
Biological Procedures Online  2009;11:296-315.
As many as 50% of adults with type I (T1) diabetes exhibit bone loss and are at increased risk for fractures. Therapeutic development to prevent bone loss and/or restore lost bone in T1 diabetic patients requires knowledge of the molecular mechanisms accounting for the bone pathology. Because cell culture models alone cannot fully address the systemic/metabolic complexity of T1 diabetes, animal models are critical. A variety of models exist including spontaneous and pharmacologically induced T1 diabetic rodents. In this paper, we discuss the streptozotocin (STZ)-induced T1 diabetic mouse model and examine dose-dependent effects on disease severity and bone. Five daily injections of either 40 or 60 mg/kg STZ induce bone pathologies similar to spontaneously diabetic mouse and rat models and to human T1 diabetic bone pathology. Specifically, bone volume, mineral apposition rate, and osteocalcin serum and tibia messenger RNA levels are decreased. In contrast, bone marrow adiposity and aP2 expression are increased with either dose. However, high-dose STZ caused a more rapid elevation of blood glucose levels and a greater magnitude of change in body mass, fat pad mass, and bone gene expression (osteocalcin, aP2). An increase in cathepsin K and in the ratio of RANKL/OPG was noted in high-dose STZ mice, suggesting the possibility that severe diabetes could increase osteoclast activity, something not seen with lower doses. This may contribute to some of the disparity between existing studies regarding the role of osteoclasts in diabetic bone pathology. Examination of kidney and liver toxicity indicate that the high STZ dose causes some liver inflammation. In summary, the multiple low-dose STZ mouse model exhibits a similar bone phenotype to spontaneous models, has low toxicity, and serves as a useful tool for examining mechanisms of T1 diabetic bone loss.
PMCID: PMC3055251  PMID: 19495918
streptozotocin; Diabetes mellitus; Type I; bone; mice; osteocalcin; adipocytes; osteoporosis
23.  Ultra-Fast and Optimized Method for the Preparation of Rodent Testicular Cells for Flow Cytometric Analysis 
Biological Procedures Online  2009;11:184-195.
Homogeneity of cell populations is a prerequisite for the analysis of biochemical and molecular events during male gamete differentiation. Given the complex organization of the mammalian testicular tissue, various methods have been used to obtain enriched or purified cell populations, including flow cell sorting. Current protocols are usually time-consuming and may imply loss of short-lived RNAs, which is undesirable for expression profiling. We describe an optimized method to speed up the preparation of suitable testicular cell suspensions for cytometric analysis of different spermatogenic stages from rodents. The procedure takes only 15 min including testis dissection, tissue cutting, and processing through the Medimachine System (Becton Dickinson). This method could be a substitute for the more tedious and time-consuming cell preparation techniques currently in use.
PMCID: PMC3055716  PMID: 19495915
Flow cytometry; Gene expression; Spermatogenesis

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