BMC Research Notes

http://link.springer.com/journal/13104

List of Papers (Total 5,987)

Analysis of gene expression patterns by microarray hybridization in blood mononuclear cells of SLA-DRB1 defined Canadian Yorkshire pigs

Background The Swine Leukocyte Antigen (SLA) system encodes molecules for self-nonself discrimination and is associated with immune responses and disease resistance. Three lines of pigs defined by their SLA-DRB1 alleles were developed at the University of Guelph for xenotransplantation and immune response studies. The aim of this project was to explore the potential association...

A sequencing strategy for identifying variation throughout the prion gene of BSE-affected cattle

Background Classical and atypical bovine spongiform encephalopathies (BSEs) are cattle prion diseases. Distinct bovine prion gene (PRNP) alleles have been associated with classical and atypical BSE susceptibility. However, the full extent of PRNP allele association with BSE susceptibility is not known. A systematic sequence-based genotyping method that detects variation...

PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data

Background We have created a software implementation of a published and verified method for assigning probabilities to potential phosphorylation sites on peptides using mass spectrometric data. Our tool, named PhosCalc, determines the number of possible phosphorylation sites and calculates the theoretical masses for the b and y fragment ions of a user-provided peptide sequence. A...

Lactogenic differentiation of HC11 cells is not accompanied by downregulation of AP-2 transcription factor genes

Background During pregnancy the mammary epithelium undergoes a complex developmental process which culminates in the generation of the milk-secreting epithelium. Secretory epithelial cells display lactogenic differentiation which is characterized by the expression of milk protein genes, such as beta-casein or whey acidic protein (WAP). Transcription factors AP-2alpha and AP...

The inverse starving test is not a suitable provocation test for Gilbert's syndrome

Background Introduction The aim of this study was to evaluate a simple diagnostic test for Gilbert's syndrome (GS), which avoids hospitalization and exposure to toxic test substrates. GS is the most frequent cause of isolated unconjugated hyperbilirubinemia. The nicotinic acid test and the starving test are established approaches to diagnose GS. However, these tests cause...

Chocolate bar as an incentive did not increase response rate among physiotherapists: a randomised controlled trial

Background The aim of this study was to assess the effect of a small incentive, a bar of dark chocolate, on response rate in a study of physiotherapy performance in patients with knee osteoarthritis. Findings Norwegian physiotherapists from private practice were randomised in blocks to an intervention group (n = 1027) receiving a bar of dark chocolate together with a data...

Evidence for bacteriophage T7 tail extension during DNA injection

Background Electron micrographs of bacteriophage T7 reveal a tail shorter than needed to reach host cytoplasm during infection-initiating injection of a T7 DNA molecule through the tail and cell envelope. However, recent data indicate that internal T7 proteins are injected before the DNA molecule is injected. Thus, bacteriophage/host adsorption potentially causes internal...

Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA

Background We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis was restricted to C→T and G→A miscoding lesions (the predominant manifestation of post mortem damage...

Sub-parts per billion detection of trace volatile chemicals in human breath using Selected Ion Flow Tube Mass Spectrometry

Background Selected ion flow tube mass spectrometry (SIFT-MS) allows the real time quantification of trace gases in air. Due to its tolerance of high humidity levels the technique is particularly suited to the chemical analysis of breath. The detection limit of SIFT-MS has previously reported to be approximately 5 – 10 PPBV which is insufficient for the measurement of some low...

Progress in the PRIDE technique for rapidly comparing protein three-dimensional structures

Background Accurate and fast tools for comparing protein three-dimensional structures are necessary to scan and analyze large data sets. Findings The method described here is not only very fast but it is also reasonable precise, as it is shown by using the CATH database as a test set. Its rapidity depends on the fact that the protein structure is represented by vectors that...

Biologically active fibroblast growth factor 1 tagged with various epitopes

Background Fibroblast growth factor (FGF) family members are involved in the regulation of a variety of biological phenomena. Because most of their activity is exerted via a signaling complex composed of FGF, heparin/heparan sulfate and FGF receptor tyrosine kinase, it is important to study the dynamic behavior of all the molecules in the complex without disturbing their...

Development and application of a microarray meter tool to optimize microarray experiments

Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter...

Stress regulated members of the plant organic cation transporter family are localized to the vacuolar membrane

Background In Arabidopsis six genes group into the gene family of the organic cation transporters (OCTs). In animals the members of the OCT-family are mostly characterized as polyspecific transporters involved in the homeostasis of solutes, the transport of monoamine neurotransmitters and the transport of choline and carnitine. In plants little is known about function...

Hepatic steatosis in patients with HIV-Hepatitis C Virus coinfection: is it associated with antiretroviral therapy and more advanced hepatic fibrosis?

Background and aims Patients with HIV and hepatitis C virus (HCV) coinfection are at increased risk of developing hepatic steatosis. The aims of this study were to assess the prevalence of steatosis in a cohort with HIV-HCV coinfection, and to determine an association, if any, between steatosis, antiretroviral therapy (ART), and advanced hepatic fibrosis. Patients and methods HIV...

Educational inequalities in self-reported health in a general Iranian population

Background The aim of this study was to investigate the relationship between educational level and self-reported health in an Iranian population, in order to provide evidence on social inequalities in health from a country in which such data need to be collected. Methods This population-based study was carried out in Tehran, Iran. Individuals aged 15 years and over were...

Prediction of protein secondary structures with a novel kernel density estimation based classifier

Background Though prediction of protein secondary structures has been an active research issue in bioinformatics for quite a few years and many approaches have been proposed, a new challenge emerges as the sizes of contemporary protein structure databases continue to grow rapidly. The new challenge concerns how we can effectively exploit all the information implicitly deposited...

Hand-held internet tablets for school-based data collection

Background In the last 20 years, researchers have been using computer self-administered questionnaires to gather data on a wide range of adolescent health related behaviours. More recently, researchers collecting data in schools have started to use smaller hand-held computers for their ease of use and portability. The aim of this study is to describe a new technology with wi-fi...

Cigarette smoking and associated factors among in-school adolescents in Jamaica: comparison of the Global Youth Tobacco Surveys 2000 and 2006

Background We conducted this study to estimate the correlates of current cigarette smoking among in-school adolescents in Jamaica 2006 and compare prevalence of smoking and associated factors between 2000 and 2006. Results In 2006, 1854 participated of whom 49.5 were males and 50.5% females. 1752 adolescents, 48.8% male and 51.2% females participated in the 2000 survey. Between...

Different media and supplements modulate the clonogenic and expansion properties of rabbit bone marrow mesenchymal stem cells

Background - Rabbits provide an excellent model for many animal and human diseases, such as cardiovascular diseases, for the development of new vaccines in wound healing management and in the field of tissue engineering of tendon, cartilage, bone and skin. The study presented herein aims to investigate the biological properties of bone marrow rabbit MSCs cultured in different...

A new approach to primer design for the control of PCR bias in methylation studies

Primer design for PCR-based methylation analysis following bisulfite conversion of DNA is considerably more complex than primer design for regular PCR. The choice of the optimal primer set is critical to the performance and correct interpretation of the results. Most methodologies in methylation analysis utilize primers that theoretically amplify methylated and unmethylated...

Whole genome amplification and its impact on CGH array profiles

Background Some array comparative genomic hybridisation (array CGH) platforms require a minimum of micrograms of DNA for the generation of reliable and reproducible data. For studies where there are limited amounts of genetic material, whole genome amplification (WGA) is an attractive method for generating sufficient quantities of genomic material from miniscule amounts of...

Conservation of CD44 exon v3 functional elements in mammals

Background The human CD44 gene contains 10 variable exons (v1 to v10) that can be alternatively spliced to generate hundreds of different CD44 protein isoforms. Human CD44 variable exon v3 inclusion in the final mRNA depends on a multisite bipartite splicing enhancer located within the exon itself, which we have recently described, and provides the protein domain responsible for...

Primary antimicrobial resistance among Mycobacterium tuberculosis isolates from HIV seropositive and HIV seronegative patients in Dar es Salaam Tanzania

Background The United Republic of Tanzania is one of the 22 high M. tuberculosis burden countries. Data collected between 2002 and 2007 indicate that the global prevalence of drug-resistant M. tuberculosis including MDR vary greatly. The varied drug-resistance patterns make continuous surveillance of drug resistance an essential component of tuberculosis control program. Findings...

Meta-analysis of SUMO1

An abundantly growing body of literature implicates conjugation of SUMO in the regulation of many proteins and processes, yet the regulation of SUMO pathways is poorly understood. To gain insight into the players in the SUMO1 pathway I have performed an in-silico co-expression meta-analysis of SUMO1, comparing many different multi-microarray studies of various normal and human...

Skateboards: Are they really perilous? A retrospective study from a district hospital

Background Skateboarding has been a popular sport among teenagers even with its attendant associated risks. The literature is packed with articles regarding the perils of skateboards. Is the skateboard as dangerous as has been portrayed? Methods This was a retrospective study conducted over a 5 year period. All skateboard related injuries seen in the Orthopaedic unit were...