BMC Research Notes

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

List of Papers (Total 6,019)

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...

The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes

Background Wheat, barley, and rye, of tribe Triticeae in the Poaceae, are among the most important crops worldwide but they present many challenges to genomics-aided crop improvement. Brachypodium distachyon, a close relative of those cereals has recently emerged as a model for grass functional genomics. Sequencing of the nuclear and organelle genomes of Brachypodium is one of...

Are residential and nursing homes adequately screening overseas healthcare workers?

Background There has been significant growth in the number of healthcare workers born outside the UK or recruited to the UK from countries with a high prevalence of TB, Hepatitis and other blood borne infections. Government policy recognises the need for occupational health procedures to facilitate treatment for these individuals and to reduce the risk of transmission of disease...

SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences

Background Chromosome location is often used as a scaffold to organize genomic information in both the living cell and molecular biological research. Thus, ever-increasing amounts of data about genomic features are stored in public databases and can be readily visualized by genome browsers. To perform in silico experimentation conveniently with this genomics data, biologists need...

Streptococcus pneumoniaeearly response genes to human lung epithelial cells

Background Streptococcus pneumoniae infection starts from colonization of the host respiratory tract where interaction with host respiratory tract epithelial cells occurs. To investigate pneumococcal genes that are involved in the early stage of interaction with host epithelial cells, transcriptional responses of an encapsulated pathogenic pneumococcal strain TIGR4 upon exposure...

Power of grammatical evolution neural networks to detect gene-gene interactions in the presence of error

Background With the advent of increasingly efficient means to obtain genetic information, a great insurgence of data has resulted, leading to the need for methods for analyzing this data beyond that of traditional parametric statistical approaches. Recently we introduced Grammatical Evolution Neural Network (GENN), a machine-learning approach to detect gene-gene or gene...

Salvaging Affymetrix probes after probe-level re-annotation

Background Affymetrix GeneChips can be re-annotated at the probe-level by breaking up the original probe-sets and recomposing new probe-sets based on up-to-date genomic knowledge, such as available in Entrez Gene. This results in custom Chip Description Files (CDF). Using these custom CDFs improves the quality of the data and thus the results of related gene expression studies...

GPCRTree: online hierarchical classification of GPCR function

Background G protein-coupled receptors (GPCRs) play important physiological roles transducing extracellular signals into intracellular responses. Approximately 50% of all marketed drugs target a GPCR. There remains considerable interest in effectively predicting the function of a GPCR from its primary sequence. Findings Using techniques drawn from data mining and...

The transcriptional cofactor MIER1-beta negatively regulates histone acetyltransferase activity of the CREB-binding protein

Background Mier1 encodes a novel transcriptional regulator and was originally isolated as a fibroblast growth factor early response gene. Two major protein isoforms have been identified, MIER1α and β, which differ in their C-terminal sequence. Previously, we demonstrated that both isoforms recruit histone deacetylase 1 (HDAC1) to repress transcription. To further explore the role...

Comparative phylogenomics and multi-gene cluster analyses of the Citrus Huanglongbing (HLB)-associated bacterium Candidatus Liberibacter

Background Huanglongbing (HLB, previously known as citrus greening), is associated with Candidatus Liberibacter species and is a serious threat to citrus production world-wide. The pathogen is a Gram negative, unculturable, phloem-limited bacterium with limited known genomic information. Expanding the genetic knowledge of this organism may provide better understanding of the...

Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon

Background PCR inhibition by nucleic acid extracts is a well known yet poorly described phenomenon. Inhibition assessment generally depends on the assumption that inhibitors affect all PCR reactions to the same extent; i.e. that the reaction of interest and the control reaction are equally susceptible to inhibition. To test this assumption we performed inhibition assessment on...

Barriers to healthy eating by National Health Service (NHS) hospital doctors in the hospital setting: results of a cross-sectional survey

Background With high levels of obesity and related illness, improving the health of the nation is a major public health concern. This study aimed to identify factors that prevent healthy eating among doctors, and that are associated with satisfaction with catering services. Findings Methods: Cross-sectional survey of 328 NHS doctors working in two NHS Trusts with on-site hospital...

Quantification of circulating endothelial and progenitor cells: comparison of quantitative PCR and four-channel flow cytometry

Background Circulating endothelial cells (CEC) and endothelial precursor cells (CEP) have been suggested as markers for angiogenesis in cancer. However, CEC/CEP represent a tiny and heterogeneous cell population, rendering a standardized monitoring in peripheral blood difficult. Thus, we investigated whether a PCR-based detection method of CEC/CEP might overcome the limitations...

Drosophila phosphopantothenoylcysteine synthetase is required for tissue morphogenesis during oogenesis

Background Coenzyme A (CoA) is an essential metabolite, synthesized from vitamin B5 by the subsequent action of five enzymes: PANK, PPCS, PPCDC, PPAT and DPCK. Mutations in Drosophila dPPCS disrupt female fecundity and in this study we analyzed the female sterile phenotype of dPPCS mutants in detail. Results We demonstrate that dPPCS is required for various processes that occur...

Characteristics of TIA and its management in a tertiary care hospital in Pakistan

Background Transient ischemic attack (TIA) is described as a brief episode of neurological dysfunction caused by focal brain ischemia, with clinical symptoms typically lasting less than an hour, and without evidence of acute infarction. Recent studies depict TIA as a particularly unstable condition. Risk of stroke is greater than 10% in the first 90 days after an index TIA. The...

Knowledge and attitudes towards HIV vaccines among Soweto adolescents

Background To explore adolescent HIV risk perception, HIV vaccine knowledge, willingness to participate in future HIV vaccine clinical trials, and the factors that influence willingness to participate among high school students in Soweto, South Africa, we recruited school-going youth through randomly selected local high schools. All pupils within the selected schools from whom...

Characterization of endemic Shigella boydii strains isolated in Iran by serotyping, antimicrobial resistance, plasmid profile, ribotyping and pulsed-field gel electrophoresis

Background Shigellosis is one of the major causes of morbidity in children with diarrhea in Iran. The present study was undertaken to characterize apparently sporadic Shigella boydii strains isolated from pediatric patients in Iran. Findings Ten S. boydii strains isolated from pediatric cases of gastroenteritis and acute diarrhea in Tehran between December 2002 and November 2003...

Development of a nutrition and physical activity booklet to engage seniors

Background This paper describes the development and process evaluation of an interactive booklet aimed at motivating older adults to improve their nutrition and physical activity. Findings The booklet was developed in consultation with seniors via focus groups, individual interviews and self administered questionnaires. The booklet was disseminated to a group of 114 seniors as...

Identification of a non-purple tartrate-resistant acid phosphatase: an evolutionary link to Ser/Thr protein phosphatases?

Background Tartrate-resistant acid phosphatases (TRAcPs), also known as purple acid phosphatases (PAPs), are a family of binuclear metallohydrolases that have been identified in plants, animals and fungi. The human enzyme is a major histochemical marker for the diagnosis of bone-related diseases. TRAcPs can occur as a small form possessing only the ~35 kDa catalytic domain, or a...