This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ http://www.biomedcentral.com/bmcresnotes/mostviewed/ Most viewed articles in last 30 days from BMC Research Notes (ISSN 1756-0500) published by BioMed Central 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.FindingsNorwegian physiotherapists from private practice were randomised in blocks to an intervention group (n=1027) receiving a bar of dark chocolate together with a data-collection form, and a control group (n=1027) that received the data-collection form only. The physiotherapists were asked to prospectively complete the data-collection form by reporting treatments provided to one patient with knee osteoarthritis through 12 treatment sessions. The outcome measure was response rate of completed forms. Out of the 510 physiotherapists that responded, 280 had completed the data-collection form by the end of the study period. There was no difference between the chocolate and no-chocolate group in response rate of those who sent in completed forms. In the chocolate group, 142 (13.8%) returned completed forms compared to 138 (13.4%) in the control group, ARR = 0.4 (95% CI: -3.44 to 2.6). Conclusions: A bar of dark chocolate did not increase response rate in a prospective study of physiotherapy performance. Stronger incentives than chocolate seem to be necessary to increase the response rate among professionals who are asked to report about their practice. Trial Registration: Current Controlled Trials register: ISRCTN02397855 http://www.biomedcentral.com/1756-0500/1/34 Gro Jamtvedt, Sarah Rosenbaum, Kristin Thuve Dahm and Signe Flottorp BMC Research Notes 2008, 1:34 Number of accesses: 192 2008-06-24 doi:10.1186/1756-0500-1-34 BMC Research Notes 1756-0500 1 34 2008-06-24 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-2gamma are downregulated during lactation, and their overexpression in transgenic mice impaired the secretory differentiation of the mammary epithelium, resulting in lactation failure. To explore whether the downregulation of AP-2alpha and AP-2gamma is of functional significance for lactogenic differentiation, we analyzed the expression of the AP-2 family members during the lactogenic differentiation of HC11 mammary epithelial cells in vitro. Differentiation of HC11 cells was induced following established protocols by applying the lactogenic hormones prolactin, dexamethasone and insulin.FindingsHC11 cells express all AP-2 family members except AP-2delta. Using RT-PCR we could not detect a downregulation of any of these genes during the lactogenic differentiation of HC11 cells in vitro. This finding was confirmed for AP-2alpha and AP-2gamma using Northern analysis. Differentiating HC11 cells displayed lower expression levels of milk protein genes than mammary glands of mid-pregnant or lactating mice. Conclusions: The extent of lactogenic differentiation of HC11 cells in vitro is limited compared to mammary epithelium undergoing secretory differentiation in vivo. Downregulation of AP-2 transcription factor genes is not required for lactogenic differentiation of HC11 cells but may functionally be involved in aspects of lactogenic differentiation in vivo that are not reflected by the HC11 system. http://www.biomedcentral.com/1756-0500/1/29 Richard Jager, Leontios Pappas and Hubert Schorle BMC Research Notes 2008, 1:29 Number of accesses: 171 2008-06-23 doi:10.1186/1756-0500-1-29 BMC Research Notes 1756-0500 1 29 2008-06-23 Background: Flavonoids are abundant plant phenolic compounds. More than 6000 have been identified to date, and some have been shown to possess antiparasitic activity. Here we investigate the effects of a range of common dietary flavonoids on the growth of two strains of the human malaria parasite Plasmodium falciparum.FindingsA chloroquine-sensitive (3D7) and a chloroquine-resistant (7G8) strain of P. falciparum were tested for in vitro susceptibility to a range of individual dietary flavonoids and flavonoid combinations. Parasite susceptibility was measured in 96-well plates over 96 h using a previously described [3H]hypoxanthine incorporation assay. Of the eleven flavonoids tested, eight showed antiplasmodial activity against the 3D7 strain (with IC50 values between 11 and 66 microM), and all showed activity against the 7G8 strain (with IC50 values between 12 and 76 microM). The most active compound against both strains was luteolin, with IC50 values of 11 +/- 1 microM and 12 +/- 1 microM for 3D7 and 7G8, respectively. Luteolin was found to prevent the progression of parasite growth beyond the young trophozoite stage, and did not affect parasite susceptibility to the antimalarial drugs chloroquine or artemisinin. Combining low concentrations of flavonoids was found to produce an apparent additive antiplasmodial effect. Conclusions: Certain common dietary flavonoids inhibit the intraerythrocytic growth of the 3D7 and 7G8 strains of P. falciparum. Flavonoid combinations warrant further investigation as antiplasmodial agents. http://www.biomedcentral.com/1756-0500/1/26 Adele M Lehane and Kevin J Saliba BMC Research Notes 2008, 1:26 Number of accesses: 162 2008-06-18 doi:10.1186/1756-0500-1-26 BMC Research Notes 1756-0500 1 26 2008-06-18 Background: A recurrent somatic mutation, E17K, in the pleckstrin homology domain of the AKT1 gene, has been recently described in breast, colorectal, and ovarian cancers. AKT1 is a pivotal mediator of signalling pathways involved in cell survival, proliferation and growth. The E17K mutation stimulates downstream signalling and exhibits transforming activity in vitro and in vivo.FindingsWe developed a sensitive high resolution melting (HRM) assay to detect the E17K mutation from formalin-fixed paraffin-embedded tumours. We screened 219 non-small cell lung cancer biopsies for the mutation using HRM analysis. Four samples were identified as HRM positive. Subsequent sequencing of those samples confirmed the E17K mutation in one of the cases. A rare single nucleotide polymorphism was detected in each of the remaining three samples. The E17K was found in one of the 14 squamous cell carcinomas. No mutations were found in 141 adenocarcinomas and 39 large cell carcinomas. Conclusion: The AKT1 E17K mutation is very rare in lung cancer and might be associated with tumorigenesis in squamous cell carcinoma. HRM represents a rapid cost-effective and robust screening of low frequency mutations such as AKT1 mutations in clinical samples. http://www.biomedcentral.com/1756-0500/1/14 Hongdo Do, Benjamin Solomon, Paul L Mitchell, Stephen B Fox and Alexander Dobrovic BMC Research Notes 2008, 1:14 Number of accesses: 136 2008-05-16 doi:10.1186/1756-0500-1-14 BMC Research Notes 1756-0500 1 14 2008-05-16 Background: Some mutations in the internal regions of exons occur within splicing enhancers and silencers, influencing the pattern of alternative splicing in the corresponding genes. To understand how these sequence changes affect splicing, we created a database of these mutations.FindingsThe Alternative Splicing Mutation Database (ASMD) serves as a repository for all exonic mutations not associated with splicing junctions that measurably change the pattern of alternative splicing. In this initial published release (version 1.2), only human sequences are present, but the ASMD will grow to include other organisms, (see Availability and requirements section for the ASMD web address).This relational database allows users to investigate connections between mutations and features of the surrounding sequences, including flanking sequences, RNA secondary structures and strengths of splice junctions. Splicing effects of the mutations are quantified by the relative presence of alternative mRNA isoforms with and without a given mutation. This measure is further categorized by the accuracy of the experimental methods employed. The database currently contains 170 mutations in 66 exons, yet these numbers increase regularly.We developed an algorithm to derive a table of oligonucleotide Splicing Potential (SP) values from the ASMD dataset. We present the SP concept and tools in detail in our corresponding article. Conclusion: The current data set demonstrates that mutations affecting splicing are located throughout exons and might be enriched within local RNA secondary structures. Exons from the ASMD have below average splicing junction strength scores, but the difference is small and is judged not to be significant. http://www.biomedcentral.com/1756-0500/1/3 Jason M Bechtel, Preeti Rajesh, Irina Ilikchyan, Ying Deng, Pankaj K Mishra, Qi Wang, Xiaochun Wu, Kirill A Afonin, William E Grose, Ye Wang, Sadik Khuder and Alexei Fedorov BMC Research Notes 2008, 1:3 Number of accesses: 124 2008-02-26 doi:10.1186/1756-0500-1-3 BMC Research Notes 1756-0500 1 3 2008-02-26 Background: Vigna radiata, which is classified in the family Fabaceae, is an important economic crop and a dietary staple in many developing countries. The species radiata can be further subdivided into varieties of which the variety sublobata is currently acknowledged as the putative progenitor of radiata. EcoTILLING was employed to identify single nucleotide polymorphisms (SNPs) and small insertion/deletions (INDELS) in a collection of Vigna radiata accessions. FindingsA total of 157 DNA polymorphisms in the collection were produced from ten primer sets when using V. radiata var. sublobata as the reference. The majority of polymorphisms detected were found in putative introns. The banding patterns varied from simple to complex as the number of DNA polymorphisms between two pooled samples increased. Numerous SNPs and INDELS ranging from 4-24 and 1-6, respectively, were detected in all fragments when pooling V. radiata var. sublobata with V. radiata var. radiata. On the other hand, when accessions of V. radiata var. radiata were mixed together and digested with CEL I relatively few SNPs and no INDELS were detected. Conclusions: EcoTILLING was utilized to identify polymorphisms in a collection of mung bean, which previously showed limited molecular genetic diversity and limited morphological diversity in the flowers and pod descriptors. Overall, EcoTILLING proved to be a powerful genetic analysis tool providing the rapid identification of naturally occurring variation. Furthermore, it can be effectively used as an efficient, rapid technique to identify DNA polymorphisms in populations with high genetic identity and to mine for SNPs in collections of plant germplasm. http://www.biomedcentral.com/1756-0500/1/28 Noelle A Barkley, Ming LI Wang, Athey G Gillaspie, Rob E Dean, Gary A Pederson and Tracie M Jenkins BMC Research Notes 2008, 1:28 Number of accesses: 120 2008-06-18 doi:10.1186/1756-0500-1-28 BMC Research Notes 1756-0500 1 28 2008-06-18 Background: Genetic make up had been known to influence pharmacokinetics and pharmacodynamics of psychotropic medications. Time separation in evolutionary trend in Africans, Orientals and Caucasians had been thought a possible explanation for the observed racial variation in activities of Cytochrome P 450 (CYP 450) enzymes, which are responsible for metabolism of psychotropic and other medications in human. Past studies on pharmacokinetics and pharmacodynamics of antipsychotic medications and socio-cultural factors influencing response to antipsychotic medications had consistently giving an inkling of possible racial difference in symptoms response to antipsychotic medications. Another growing body of evidence subscribing to possible racial difference in psychotic symptoms response to antipsychotic medications is the observed variation in antipsychotic medications prescription pattern and dosage across races and regions. Empirical observation had shown that dosage prescription pattern of antipsychotic medications in most Sub-Saharan African countries deviates from the standard prescription guidelines published for use in western parts of the world. Studies coming from the United States (U.S) had consistently reported a higher dosage of antipsychotic medications prescription for African-American patients compared to their Caucasian counterparts. Research on East Asia Psychotropic Prescription (REAP) study had also identified high dosage antipsychotic medications prescription pattern well above the recommended dose of 1,000 mg Chlorpromazine equivalent per day as common practices in some East Asian countries. Presentation of the Hypothesis The pertinent question is why the apparent differences in dosage prescription practices across races and regions? The possibility of racial differences in psychotic symptoms response to antipsychotic medications rather than clinicians' prescription attitudes was entertained. Testing the Hypothesis Future carefully controlled studies might be needed to test the proposed hypothesis of racial differences in psychotic symptoms response to antipsychotic medications. Implication of the Hypothesis There might be actual racial influence on psychotic symptoms response to antipsychotic medications. If future carefully controlled studies uphold the hypothesis of racial differences in psychotic symptoms response to antipsychotic medications, there might be need to draw up new treatment or prescription guidelines that would put into consideration variations in genetic make up and consequent racial differences in psychotic symptoms response to antipsychotic medications. http://www.biomedcentral.com/1756-0500/1/25 Muideen O Bakare BMC Research Notes 2008, 1:25 Number of accesses: 118 2008-06-12 doi:10.1186/1756-0500-1-25 BMC Research Notes 1756-0500 1 25 2008-06-12 Background: Alzheimer's disease (AD) is a progressive, neurodegenerative disease mostly affecting the basal forebrain, cortex and hippocampus whereas the cerebellum is relatively spared. The reason behind this region-specific brain damage in AD is not well understood. Here, we report our data suggesting "differential free fatty acid metabolism in the different brain areas" as a potentially important factor in causing the region-specific damage observed in AD brain.FindingsThe astroglia from two different rat brain regions, cortex (region affected in AD) and cerebellum (unaffected region), were treated with 0.2mM of palmitic acid. The conditioned media were then transferred to the cortical neurons to study the possible effects on the two main, AD-associated protein abnormalities, viz. BACE1 upregulation and hyperphosphorylation of tau. The conditioned media from palmitic-acid treated cortical astroglia, but not the cerebellar astroglia, significantly elevated levels of phosphorylated tau and BACE1 in cortical neurons as compared to controls (47 +/- 7% and 45 +/- 4%, respectively). Conclusions: The present data provide an experimental explanation for the region-specific damage observed in AD brain; higher fatty acid-metabolizing capacity of cortical astroglia as compared to cerebellar astroglia, may play a causal role in increasing vulnerability of cortex in AD, while sparing cerebellum. http://www.biomedcentral.com/1756-0500/1/20 Sachin Patil, Deebika Balu, Joseph Melrose and Christina Chan BMC Research Notes 2008, 1:20 Number of accesses: 112 2008-06-04 doi:10.1186/1756-0500-1-20 BMC Research Notes 1756-0500 1 20 2008-06-04 Background: Variance-stabilizing techniques have been used for some time in the analysis of gene expression microarray data. A new adaptation, the variance-stabilizing transformation (VST), has recently been developed to take advantage of the unique features of Illumina BeadArrays. VST has been shown to perform well in comparison with the widely-used approach of taking a log2 transformation, but has not been validated on a spike-in experiment. We apply VST to the data from a recently published spike-in experiment and compare it both to a regular log2 analysis and a recently recommended analysis that can be applied if all raw data are available. FindingsVST provides more power to detect differentially expressed genes than a log2 transformation. However, the gain in power is roughly the same as utilizing the raw data from an experiment and weighting observations accordingly. VST is still advantageous when large changes in expression are anticipated, while a weighted log2 approach performs better for smaller changes. Conclusions: VST can be recommended for summarized Illumina data regardless of which Illumina pre-processing options have been used. However, using the raw data is still encouraged whenever possible. http://www.biomedcentral.com/1756-0500/1/18 Mark J Dunning, Matthew E Ritchie, Nuno L Barbosa-Morais, Simon Tavare and Andy G Lynch BMC Research Notes 2008, 1:18 Number of accesses: 110 2008-06-04 doi:10.1186/1756-0500-1-18 BMC Research Notes 1756-0500 1 18 2008-06-04 Background: In Arabidopsis six genes group into the gene family of organic cation transporters (OCTs). The members of the OCT-family in animals 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, only one member of the organic cation transporter family, AtOCT1, has been characterized functionally as a carnitine transporter at the plasma membrane [1]. No information about the role, the subcellular localization or the gene regulation of the other five members in Arabidopsis is available up to now. FindingsWe localized the five uncharacterized members of the Arabidopsis OCT family, designated OCT2-OCT6, via GFP fusions and protoplast transformation to the tonoplast. Expression analysis with RNA Gel Blots showed a distinct, organ-specific expression pattern of the individual genes. With reportergene fusion of four members we analyzed the tissue specific distribution of OCT2, 3, 4, and 6. In experiments with salt, drought and cold stress, we could show that AtOCT4, 5 and 6 are up-regulated during drought stress, AtOCT2 and 5 during cold stress and AtOCT 5 and 6 during salt stress treatments. Conclusions: Localisation of the proteins at the tonoplast and regulation of the gene expression under stress conditions suggests a specific role for the transporters in plant adaptation to environmental stress. http://www.biomedcentral.com/1756-0500/1/43 Isabell Kufner and Wolfgang Koch BMC Research Notes 2008, 1:43 Number of accesses: 110 2008-07-11 doi:10.1186/1756-0500-1-43 BMC Research Notes 1756-0500 1 43 2008-07-11