Articles

The Possible Cellular Mechanism for Extending Lifespan of Mice with Rapamycin

Authors: Shulin Li

MicroRNA Expression Profiling by Bead Array Technology in Human Tumor Cell Lines Treated with Interferon-Alpha-2a

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 targ...

Authors: Fredy Siegrist, Thomas Singer and Ulrich Certa

Segmentation of Extrapulmonary Tuberculosis Infection Using Modified Automatic Seeded Region Growing

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 i...

Authors: Iman Avazpour, M Iqbal Saripan, Abdul Jalil Nordin and Rajaa Syamsul Azmir Iman Abdullah

Lentiviral-Mediated Transgene Expression Can Potentiate Intestinal Mesenchymal-Epithelial Signaling

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 effecti...

Authors: Adria D Dismuke, Aimee D Kohn, Randall T Moon and Melissa H Wong

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 degrada...

Authors: Jane J Pappas, André Toulouse and WEC Bradley

A Method for Structure–Activity Analysis of Quorum-Sensing Signaling Peptides from Naturally Transformable Streptococci

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...

Authors: XiaoLin Tian, Raymond T Syvitski, TianLei Liu, Nadine Livingstone, David L Jakeman and Yung-Hua Li

A Framework for White Blood Cell Segmentation in Microscopic Blood Images Using Digital Image Processing

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...

Authors: Farnoosh Sadeghian, Zainina Seman, Abdul Rahman Ramli, Badrul Hisham Abdul Kahar and M-Iqbal Saripan

SDS-PAGE-Based Quantitative Assay for Screening of Kidney Stone Disease

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 prote...

Authors: Lau Wai-Hoe, Leong Wing-Seng, Zhari Ismail and Gam Lay-Harn

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 ...

Authors: Harold P Erickson

In Vivo Imaging of Far-red Fluorescent Proteins after DNA Electrotransfer to Muscle Tissue

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...

Authors: Pernille Hojman, Jens Eriksen and Julie Gehl

Detection and Processing Techniques of FECG Signal for Fetal Monitoring

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...

Authors: MA Hasan, MBI Reaz, MI Ibrahimy, MS Hussain and J Uddin

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 lis...

Authors: Jennifer Commins, Christina Toft and Mario A Fares

Comparison of Enzymatic and Non-Enzymatic Means of Dissociating Adherent Monolayers of Mesenchymal Stem Cells

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-fre...

Authors: Boon C Heng, Catherine M Cowan and Shubhayu Basu

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...

Authors: Alina Rodríguez-Mallon, Yamilet Cárdenas, Juana María Lugo, Aymé Oliva, Antonio Morales and Mario Pablo Estrada

Streptozotocin, Type I Diabetes Severity and Bone

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 requi...

Authors: Katherine Motyl and Laura R McCabe

Ultra-Fast and Optimized Method for the Preparation of Rodent Testicular Cells for Flow Cytometric Analysis

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, var...

Authors: Rosana Rodríguez-Casuriaga, Adriana Geisinger, Beatriz López-Carro, Valentina Porro, Rodolfo Wettstein and Gustavo A Folle

A method to generate human mesenchymal stem cell-derived neurons which express and are excited by multiple neurotransmitters

The present study describes a protocol to generate heterogenous populations of neurotransmitter-producing neurons from human mesenchymal stem cells (MSCs). MSCs are bone marrow (BM)-derived cells which undergo...

Authors: Steven J. Greco, Chunyi Zhou, Jiang-Hong Ye and Pranela Rameshwar

A rapid microwell fluorescence immunoassay for cellular protein detection

In this paper, we describe a simple, rapid, specific, sensitive, and reliable method, the FICP method (Fluorescence Immunoassay for Cellular Protein detection) which is readily applicable to the detection of p...

Authors: Carole Lavigne, Armèle de Guignée and Alain R. Thierry

Tracking and ablating subpopulations of epiblast cells in the chick embryo

The early chick embryo contains subpopulations of cells that express lineage-specific transcription factors. We have developed protocols to examine the role of these cells during development that involve label...

Authors: Jacquelyn Gerhart, Christine Neely, Jessica Pfautz and Mindy George-Weinstein

Characterizing gene family evolution

Gene families are widely used in comparative genomics, molecular evolution, and in systematics. However, they are constructed in different manners, their data analyzed and interpreted differently, with differe...

Authors: David A. Liberles and Katharina Dittmar

Cell culture-based analysis of postsynaptic membrane assembly in muscle cells

We report a method for studying postsynaptic membrane assembly utilizing the replating of aneural cultures of differentiated skeletal muscle cells onto laminin-coated surfaces. A significant limitation to the ...

Authors: Getu Teressa and Joav Prives

A method for purification, identification and validation of DNMT1 mRNA binding proteins

DNA methyltransferase 1 (DNMT1) is the enzyme responsible for the maintenance of DNA methylation patterns during cell division. DNMT1 expression is tightly regulated within the cell cycle. Our previous study s...

Authors: Alexander Unterberger, Jérôme Torrisani and Moshe Szyf

Optimized two-dimensional thin layer chromatography to monitor the intracellular concentration of acetyl phosphate and other small phosphorylated molecules

Acetyl phosphate (acetyl-P) serves critical roles in coenzyme A recycling and ATP synthesis. It is the intermediate of the Pta-AckA pathway that inter-converts acetyl-coenzyme A and acetate. Acetyl-P also can ...

Authors: David H. Keating, Ana Shulla, Adam H. Klein and Alan J. Wolfe

Identification of a calcitriol-regulated Sp-1 site in the promoter of human CD14 using a combined western blotting elect rophoresis mobility shift assay (WEMSA)

Calcitriol (1α, 25-dihydroxyvitamin D₃) induces the expression of CD14 in mononuclear phagocytes. The mechanisms accounting for this have been unclear since the promoter of CD14 does not contain a canonical vitam...

Authors: Alireza Moeenrezakhanlou, Devki Nandan and Neil E. Reiner

Quantitative evaluation of signaling events in Drosophila S2 cells

Drosophila activates a robust defense response to gram-negative bacteria through the Immune deficiency (Imd) pathway. Imd signaling proceeds through c-Jun N-terminal Kinase (JNK), NF-kB and caspa...

Authors: David Bond, David A. Primrose and Edan Foley

Recent advances in freeze-fracture electron microscop: the replica immunolabeling technique

Freeze-fracture electron microscopy is a technique for examining the ultrastructure of rapidly frozen biological samples by transmission electron microscopy. Of a range of approaches to freeze-fracture cytoche...

Authors: Horst Robenek and Nicholas J. Severs

In vivo and in vitro techniques for comparative study of antiviral T-cell responses in the amphibian Xenopus

Activation of lymphocytes in mammals is often quantified by measuring the amount of proliferation during the expansion phase of an immune response. Bromodeoxyuridine (BrdU) incorporation and carboxyfluorescein...

Authors: Heidi Morales and Jacques Robert

Development of human gene reporter cell lines using rAAV mediated homologous recombination

Understanding mechanisms of gene regulation has broad therapeutic implications for human disease. Here we describe a novel method for generating human cell lines that serve as reporters of transcriptional acti...

Authors: Sandra L. Fernandez, David W. Russell and Peter J. Hurlin

Micro-scale flow cytometry-based and biochemical analysis of lipid signaling in primary B cell subpopulations

B cell subpopulations in the spleen have been extensively characterized phenotypically; however, biochemical properties of these cell populations following B cell antigen receptor engagement have not been full...

Authors: Pierre Antony, Kristen Hoek, Bhaskarjyoti Sarmah and Wasif N. Khan

Improving image analysis in 2DGE-based redox proteomics by labeling protein carbonyl with fluorescent hydroxylamine

Recent advances in redox proteomics have provided significant insight into the role of oxidative modifications in cellular signalling and metabolism. At present, these techniques rely heavily on Western blots ...

Authors: H. Fai Poon, Laila Abdullah, Jon Reed, Sarah M. Doore, Cyndi Laird, Venkat Mathura, Michael Mullan and Fiona Crawford

Anin vitro method to study the effects of hematopoietic regulators during immune and blood cell development

In adults, hematopoiesis occurs in bone marrow (BM) through a complex process with differentiation of hematopoietic stem cells (HSCs) to immune and blood cells. Human HSCs and their progenitors express CD34. M...

Authors: Nitixa Patel, Marianne Castillo and Pranela Rameshwar

Multiplexed genotyping of ABC transporter polymorphisms with the Bioplex suspension array

We have developed and validated a consolidated bead-based genotyping platform, the Bioplex suspension array for simultaneous detection of multiple single nucleotide polymorphisms (SNPs) of the ATP-binding cass...

Authors: Seok Hwee Koo, Tan Ching Ong, Kok Ting Chong, Caroline Guat Lay Lee, Fook Tim Chew and Edmund Jon Deoon Lee

Rapid sitrapid site-directed domain scanning mutagenesis of enteropathogenic Escherichia coli espD

We developed a rapid mutagenesis method based on a modification of the QuikChange® system (Stratagene) to systemically replace endogenous gene sequences with a unique similar size sequence tag. The modificatio...

Authors: Qiwen Deng, Wensheng Luo and Michael S. Donnenberg

Generation of shrnas from randomized oligonucleotides

Suppression of gene expression by small interfering RNA (siRNA) has proved to be a gene-specific and cost effective alternative to other gene suppression technologies. Short hairpin RNAs (shRNAs) generated fro...

Authors: Hailong Wu, Anh Dinh and Yin-Yuan Mo

A method for detecting functional activity related expression in gross brain regions, specific brain nuclei and individual neuronal cell bodies and their projections

We have developed a system to visualize functionally activated neurons and their projections in the brain. This system utilizes a transgenic mouse, fos-tau-lacZ (FTL), which expresses the marker gene, lacZ, in ne...

Authors: Mark Murphy, Ursula Greferath and Yvette M. Wilson

Assessment of different protocols for the isolation and purification of gut associated lymphoid cells from the gilthead seabream (Sparus aurata L.)

Teleost gut associated lymphoid tissue (GALT) consists of leucocyte populations located both intraepithelially and in the lamina propria with no structural organization. The present study aims to assess differ...

Authors: Irene Salinas, José Meseguer and Maria Ángeles Esteban

The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the calgary biofilm device

Microbes frequently live within multicellular, solid surface-attached assemblages termed biofilms. These microbial communities have architectural features that contribute to population heterogeneity and conseq...

Authors: Joe J. Harrison, Howard Ceri, Jerome Yerly, Carol A. Stremick, Yaoping Hu, Robert Martinuzzi and Raymond J. Turner

Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR

Quantitative real-time PCR (qPCR) is a commonly used validation tool for confirming gene expression results obtained from microarray analysis; however, microarray and qPCR data often result in disagreement. Th...

Authors: Jeanine S. Morey, James C. Ryan and Frances M. Van Dolah

A statistical framework for genetic association studies of power curves in bird flight

How the power required for bird flight varies as a function of forward speed can be used to predict the flight style and behavioral strategy of a bird for feeding and migration. A U-shaped curve was observed b...

Authors: Min Lin, Wei Zhao and Rongling Wu

Techniques of EMG signal analysis: detection, processing, classification and applications (Correction)

This paper was originally published in Biological Procedures Online (BPO) on March 23, 2006. It was brought to the attention of the journal and authors that reference 74 was incorrect. The original citation for r...

Authors: M. B. I. Reaz, M. S. Hussain and F. Mohd-Yasin

Generation of gene deletions and gene replacements in Escherichia coli O157:H7 using a temperature sensitive allelic exchange system

In this work we describe protocols for the generation of gene deletions and gene replacements using a temperature sensitive plasmid in Escherichia coli O157:H7. This technology requires flanking DNA to be cloned ...

Authors: James R. Emmerson, David L. Gally and Andrew J. Roe

Addressing fluorogenic real-time qpcr inhibition using the novel custom excel file system ‘FocusField2-6GallupqPCRSet-upTool-001’ to attain consistently high fidelity qPCR reactions

The purpose of this manuscript is to discuss fluorogenic real-time quantitative polymerase chain reaction (qPCR) inhibition and to introduce/define a novel Microsoft Excel-based file system which provides a wa...

Authors: Jack M. Gallup and Mark R. Ackermann

Combining genetic and biochemical approaches to identify functional molecular contact points

Protein-protein interactions are required for many viral and cellular functions and are potential targets for novel therapies. Here we detail a series of genetic and biochemical techniques used in combination ...

Authors: Matthew P. Badtke, Feng Cao and John E. Tavis

Chromatin immunoprecipitation assay detects er recruitment to gene specific promoters in uterus

Chromatin immunoprecipitation (ChIP) technique allows detection of proteins that bind to chromatin. While this technique has been applied extensively in cell-based studies, its tissue-based application remains...

Authors: Sanhita Ray and Sanjoy K. Das

Practical three color live cell imaging by widefield microscopy

Live cell fluorescence microscopy using fluorescent protein tags derived from jellyfish and coral species has been a successful tool to image proteins and dynamics in many species. Multi-colored aequorea fluoresc...

Authors: Jianrun Xia, Song Hon H. Kim, Susan Macmillan and Ray Truant

Direct application of plasmid DNA containing type I interferon transgenes to vaginal mucosa inhibits HSV-2 mediated mortality

The application of naked DNA containing type I interferon (IFN) transgenes is a promising potential therapeutic approach for controlling chronic viral infections. Herein, we detail the application of this appr...

Authors: Bobbie Ann Austin, Cassandra M. James, Peter Härle and Daniel J. J. Carr

Use of chromatin immunoprecipitation (chip) to detect transcription factor binding to highly homologous promoters in chromatin isolated from unstimulated and activated primary human B cells

The Chromatin Immunoprecipiation (ChIP) provides a powerful technique for identifying the in vivo association of transcription factors with regulatory elements. However, obtaining meaningful information for promo...

Authors: Rebecca L. Dryer and Lori R. Covey

Cell-based expression cloning for identification of polypeptides that hypersensitize mammalian cells to mitotic arrest

Microtubule inhibitors such as Vinblastine and Paclitaxel are chemotherapy agents that activate the mitotic spindle checkpoint, arresting cells in mitosis and leading to cell death. The pathways that connect m...

Authors: Hiroshi Y. Yamada and Gary J. Gorbsky

Techniques of EMG signal analysis: detection, processing, classification and applications

Electromyography (EMG) signals can be used for clinical/biomedical applications, Evolvable Hardware Chip (EHW) development, and modern human computer interaction. EMG signals acquired from muscles require adva...

Authors: M. B. I. Reaz, M. S. Hussain and F. Mohd-Yasin

Rapid and simple comparison of messenger rna levels using real-time PCR

Real-time polymerase chain reaction (PCR) constitutes a significant improvement over traditional end-point PCR, as it allows the quantification of starting amounts of nucleic acid templates, in real-time. Howe...

Authors: Andrée-Anne Dussault and Marc Pouliot