BMC Research Notes

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

List of Papers (Total 6,571)

Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments

Background The recent determination of the complete nucleotide sequence of several Mycobacterium tuberculosis (MTB) genomes allows the use of comparative genomics as a tool for dissecting the nature and consequence of genetic variability within this species. The multiple alignment of the genomes of clinical strains (CDC1551, F11, Haarlem and C), along with the genomes of...

Cloning, expression and location of RNase9 in human epididymis

Background Mammalian spermatozoa become fully motile and fertile during transit through the luminal fluid of the epididymis. At least 200 proteins are present in the epididymal lumen, but the potential roles of these luminal proteins in male fertility are unknown. Investigation of the function of these proteins will elucidate the mechanism of sperm maturation, and also provide...

Global gene expression profiling of oral cavity cancers suggests molecular heterogeneity within anatomic subsites

Background Oral squamous cell carcinoma (OSCC) is a frequent neoplasm, which is usually aggressive and has unpredictable biological behavior and unfavorable prognosis. The comprehension of the molecular basis of this variability should lead to the development of targeted therapies as well as to improvements in specificity and sensitivity of diagnosis. Results Samples of primary...

Survival of pneumococcus on hands and fomites

Background Pneumococcal hand contamination in Indigenous children in remote communities is common (37%). It is not clear whether this requires frequent inoculation, or if pneumococci will survive on hands for long periods of time. Thus the aim of this study was to determine the survival time of pneumococci on hands and fomites. Findings The hands of 3 adult volunteers, a glass...

Protein subfamily assignment using the Conserved Domain Database

Background Domains, evolutionarily conserved units of proteins, are widely used to classify protein sequences and infer protein function. Often, two or more overlapping domain models match a region of a protein sequence. Therefore, procedures are required to choose appropriate domain annotations for the protein. Here, we propose a method for assigning NCBI-curated domains from...

Intrauterine growth restriction, visceral blood flow velocity and exocrine pancreatic function

Background Animal models and observations in human neonates suggest fetal exocrine pancreas vulnerability to reduced maternofetal blood flow. We investigated the relationship between superior mesenteric artery blood flow velocity (sma bfv) and exocrine pancreatic function, in a cohort of very low birth weight (VLBW) babies. Group 1: 9 babies < 3rd percentile for birth weight...

Interpreting missense mutations in Human TRIM5alpha by computational methods

Background The human restriction factor TRIM5α may play an important role in regulation of the human immunodeficiency virus (HIV). It is unclear whether non-synonymous single nucleotide polymorphisms (nsSNP) in TRIM5α affect the clinical course of HIV infection. Findings We surveyed the literature for TRIM5α nsSNPs and used comparative sequence analysis to predict the effect of...

The effect of the new GMS contract on GP appointment provision in Wales: postal questionnaire survey of practice managers

Background Access to health professionals is a key UK NHS priority, and meeting access targets is rewarded through the new General Medical Services (GMS) contract in the UK. We sought to determine the current state of appointment provision in Wales and any changes resulting from the need to meet indicators in the new GMS contract. We undertook a postal questionnaire study of...

Mapping of the spontaneous deletion in the Ap3d1 gene of mocha mice: fast and reliable genotyping

Background The mocha mouse carries a spontaneous deletion in the Ap3d1 gene, encoding the delta 1 subunit of the adaptor related protein complex 3, (Ap3d1), and subsequently lack the expression of functional AP-3. This leads to a deficiency in vesicle transport and storage, which affects neurotransmitter vesicle turnover and release in the central nervous system. Since the...

Purification and partial genome characterization of the bacterial endosymbiont Blattabacterium cuenoti from the fat bodies of cockroaches

Background Symbiotic relationships between intracellular bacteria and eukaryotes are widespread in nature. Genome sequencing of the bacterial partner has provided a number of key insights into the basis of these symbioses. A challenging aspect of sequencing symbiont genomes is separating the bacteria from the host tissues. In the present study, we describe a simple method of...

Impact of prior outpatient antibiotic use on mortality for community acquired pneumonia: a retrospective cohort study

Background The purpose of this study was to examine whether prior outpatient antibiotic use is associated with increased 30-day mortality, after adjusting for potential confounders, for those subsequently hospitalized with pneumonia. Methods A retrospective cohort study conducted at two tertiary teaching hospitals. Eligible subjects were admitted with a diagnosis of, and had a...

Vitamin K epoxide reductase complex subunit 1 (Vkorc1) haplotype diversity in mouse priority strains

BackgroundPolymorphisms in the vitamin K-epoxide reductase complex subunit 1 gene, Vkorc1, could affect blood coagulation and other vitamin K-dependent proteins, such as osteocalcin (bone Gla protein, BGP). Here we sequenced the Vkorc1 gene in 40 mouse priority strains. We analyzed Vkorc1 haplotypes with respect to prothrombin time (PT) and bone mineral density and composition...

HIV and AIDS-related knowledge among women in Iraq

Background Individuals who are aware of the risk of infection and perceive themselves to be at risk of infection are more likely to take action to prevent HIV infection. The aim of this study was to assess the knowledge of HIV/AIDS among Iraqi women. Methods A secondary analysis of the 2000 Multiple Cluster Indicator Survey (MICS) for Iraq was carried out to assess the extent of...

Probing of Actinobacillus pleuropneumoniae ApxIIIA toxin-dependent cytotoxicity towards mammalian peripheral blood mononucleated cells

Background Actinobacillus pleuropneumoniae, the causative bacterial agent of porcine pleuropneumonia, produces Apx toxins which belong to RTX toxin family and are recognized as the major virulence factors. So far, their target receptor(s) has not been identified and the disease cytopathogenesis remains poorly understood. Production of an active Apx toxin and characterization of...

Lack of anabolic response to skeletal loading in mice with targeted disruption of the pleiotrophin gene

Background In a previous study we showed, using the whole genome microarray approach, that pleiotrophin (PTN) expression was increased by 4-fold in response to mechanical loading (ML) in a good responder C57BL/6J (B6) mice. To address PTN role in mediating ML effects on bone formation, we first evaluated time course effects of ML on expression levels of PTN gene using real time...

Resveratrol prevents antibody-induced apoptotic death of retinal cells through upregulation of Sirt1 and Ku70

BackgroundTo determine whether resveratrol, a natural plant-derived drug, has protective effects against antibody-induced apoptosis of retinal cells in vitro and to provide insights on the mechanism of resveratrol protection.FindingsE1A.NR3 retinal cells pretreated with 40 μM resveratrol were grown in the presence of anti-recoverin (Rec-1), anti-enolase (Enol-1) antibodies, and...

Exploring the agreement between diagnostic criteria for IBS in primary care in Greece

Background Irritable Bowel Syndrome (IBS) is frequently diagnosed in primary care. Its diagnosis is based on diagnostic criteria but their use is limited in primary care. We aimed to assess the diagnostic agreement between the older (Manning's and Rome II) and the new (Rome III) criteria for the diagnosis of IBS in primary care in Greece. Methods Medical records of 5 Health...

Single nucleotide polymorphisms concordant with the horned/polled trait in Holsteins

Background Cattle that naturally do not grow horns are referred to as polled, a trait inherited in a dominant Mendelian fashion. Previous studies have localized the polled mutation (which is unknown) to the proximal end of bovine chromosome 1 in a region approximately 3 Mb in size. While a polled genetic test, Tru-Polled™, is commercially available from MetaMorphix Inc...

An Italian functional genomic resource for Medicago truncatula

Background Medicago truncatula is a model species for legumes. Its functional genomics have been considerably boosted in recent years due to initiatives based both in Europe and US. Collections of mutants are becoming increasingly available and this will help unravel the genetic control of important traits for many species of legumes. Findings Our report is on the production of...

Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases

Background Mass spectrometric analysis of peptides is an essential part of protein identification and characterization, the latter meaning the identification of modifications and amino acid substitutions. There are two main approaches for characterization: (i) using a predefined set of possible modifications and substitutions or (ii) performing a blind search. The first option is...

Gene expression in early and progression phases of autosomal dominant polycystic kidney disease

Background Little is known about the genes involved in the initial cyst formation and disease progression in autosomal dominant polycystic kidney disease (ADPKD); however, such knowledge is necessary to explore therapeutic avenues for this common inherited kidney disease. Findings To uncover the genetic determinants and molecular mechanisms of ADPKD, we analyzed 4-point time...

Using a commercially available DNA extraction kit to obtain high quality human genomic DNA suitable for PCR and genotyping from 11-year-old saliva saturated cotton spit wads

Background We sought to describe the integrity of human genomic DNA extracted from saliva saturated cotton spit wads stored at -20°C for approximately 11 years. 783 spit wad samples were collected from an ADHD sample population (Vermont Family Study) during 1996–2000. Human genomic DNA was extracted from the spit wads using a commercially available kit; QIAamp DNA Blood Midi Kit...

Synergistic effect of methyljasmonate and cyclodextrin on stilbene biosynthesis pathway gene expression and resveratrol production in Monastrell grapevine cell cultures

Background Plant cell cultures have been shown as feasible systems for the production of secondary metabolites, being the elicitation with biotic or abiotic stimuli the most efficient strategy to increase the production of those metabolites. Vitaceae phytoalexins constitute a group of molecules belonging to the stilbene family which are derivatives of the trans-resveratrol...

Is there an association between fibromyalgia and below-normal levels of urinary cortisol?

Background Adynamia in fibromyalgia (FM) may be an expression of a functional deficit of the hypothalamic-pituitary-adrenal axis and be associated with below-normal levels of urinary cortisol. Our aim was to demonstrate that urinary cortisol was lower in patients with FM than in healthy subjects. Findings We measured urinary cortisol levels for a sample of 47 women aged 29 to 64...

A set of vectors for introduction of antibiotic resistance genes by in vitro Cre-mediated recombination

Background Introduction of new antibiotic resistance genes in the plasmids of interest is a frequent task in molecular cloning practice. Classical approaches involving digestion with restriction endonucleases and ligation are time-consuming. Findings We have created a set of insertion vectors (pINS) carrying genes that provide resistance to various antibiotics (puromycin...