Journal: BMC Research Notes

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BioMed Central

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1756-0500

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Publications1 - 10 of 16
  • Absence of nuclease activity in commonly used oxygen-scavenging systems
    Item type: Journal Article
    Gahlon, Hailey; Poudevigne-Durance, Paul; Rueda, David (2017)
    BMC Research Notes
    Objective Oxygen scavenging systems are routinely used during single-molecule imaging experiments to improve fluorescent dye stability. Previous work has shown nuclease contamination in the commonly used oxygen scavenging systems. This study evaluates the potential for nuclease contamination in these oxygen scavenging systems. Results Linear and plasmid DNA was incubated with two different oxygen scavenging systems (1) protocatechuic acid (PCA)-protocatechuate-3,4-dioxygenase (PCD) and (2) glucose-coupled glucose oxidase/catalase (GODCAT). No nucleic acid degradation was observed on single and double-stranded linear DNA and plasmid DNA, indicating the absence of nuclease contamination in these oxygen scavenging systems.
  • SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2
    Item type: Journal Article
    Szalkowski, Adam; Ledergerber, Christian; Krähenbühl, Philipp; et al. (2008)
    BMC Research Notes
    Background. We present swps3, a vectorized implementation of the Smith-Waterman local alignment algorithm optimized for both the Cell/BE and ×86 architectures. The paper describes swps3 and compares its performances with several other implementations. Findings. Our benchmarking results show that swps3 is currently the fastest implementation of a vectorized Smith-Waterman on the Cell/BE, outperforming the only other known implementation by a factor of at least 4: on a Playstation 3, it achieves up to 8.0 billion cell-updates per second (GCUPS). Using the SSE2 instruction set, a quad-core Intel Pentium can reach 15.7 GCUPS. We also show that swps3 on this CPU is faster than a recent GPU implementation. Finally, we note that under some circumstances, alignments are computed at roughly the same speed as BLAST, a heuristic method. Conclusion. The Cell/BE can be a powerful platform to align biological sequences. Besides, the performance gap between exact and heuristic methods has almost disappeared, especially for long protein sequences.
  • The transcriptome response of the ruminal methanogen Methanobrevibacter ruminantium strain M1 to the inhibitor lauric acid
    Item type: Journal Article
    Zhou, Xuan; Stevens, Marc J.A.; Neuenschwander, Stefan; et al. (2018)
    BMC Research Notes
    Objective Lauric acid (C12) is a medium-chain fatty acid that inhibits growth and production of the greenhouse gas methane by rumen methanogens such as Methanobrevibacter ruminantium. To understand the inhibitory mechanism of C12, a transcriptome analysis was performed in M. ruminantium strain M1 (DSM 1093) using RNA-Seq. Results Pure cell cultures in the exponential growth phase were treated with 0.4 mg/ml C12, dissolved in dimethyl sulfoxide (DMSO), for 1 h and transcriptomic changes were compared to DMSO-only treated cells (final DMSO concentration 0.2%). Exposure to C12 resulted in differential expression of 163 of the 2280 genes in the M1 genome (maximum log2-fold change 6.6). Remarkably, C12 hardly affected the expression of genes involved in methanogenesis. Instead, most affected genes encode cell-surface associated proteins (adhesion-like proteins, membrane-associated transporters and hydrogenases), and proteins involved in detoxification or DNA-repair processes. Enrichment analysis on the genes regulated in the C12-treated group showed a significant enrichment for categories ‘cell surface’ and ‘mobile elements’ (activated by C12), and for the categories ‘regulation’ and ‘protein fate’ (represssed). These results are useful to generate and test specific hypotheses on the mechanism how C12 affects rumen methanogens.
  • DNA barcode trnH-psbA is a promising candidate for efficient identification of forage legumes and grasses
    Item type: Journal Article
    Loera-Sánchez, Miguel; Studer, Bruno; Kölliker, Roland (2020)
    BMC Research Notes
  • Differences in classification of COPD patients into risk groups A-D
    Item type: Journal Article
    Zogg, Stefanie; Dürr, Selina; Miedinger, David; et al. (2014)
    BMC Research Notes
    Background: The Global Initiative for Chronic Obstructive Lung Disease proposed in 2011 a new system to classify chronic obstructive pulmonary disease (COPD) patients into risk groups A-D, which considers symptoms and future exacerbation risk to grade disease severity. The aim of this study was to investigate the agreement between COPD risk group classifications using COPD assessment test (CAT) or modified Medical Research Council (mMRC) and severity grades or past-year exacerbations. Furthermore, physical activity across risk groups was examined. Methods: 87 patients with stable COPD were classified into risk groups A-D. CAT and mMRC were completed. Severity grades I-IV were determined using spirometry and the number of past-year exacerbations was recorded. To test the interrater agreement, Cohen’s Kappa was calculated. Daily physical activity was measured by the SenseWear Mini armband. Results: Using CAT, 65.5% of patients were in high-symptom groups (B and D). With mMRC, only 37.9% were in B and D. Using severity grades, 20.7% of patients were in high-exacerbation risk groups (C and D). With past-year exacerbations, 9.2% were in C and D. Interrater agreement between CAT and mMRC (κ = 0.21) and between severity grades and past-year exacerbations (κ = 0.31) was fair. Daily steps were reduced in risk groups B and C + D compared to A (p < 0.01), using either classification. Conclusions: When classifying COPD patients into risk groups A-D, the use of CAT or mMRC and severity grades or past-year exacerbations does not provide equal results. Daily steps decreased with increasing COPD risk groups.
  • Characterisation of five candidate genes within the ETEC F4ab/ac candidate region in pigs
    Item type: Journal Article
    Jacobsen, Mette; Cirera, Susanna; Joller, David; et al. (2011)
    BMC Research Notes
    Background: Enterotoxigenic Escherichia coli (ETEC) that express the F4ab and F4ac fimbriae is a major contributor to diarrhoea outbreaks in the pig breeding industry, infecting both newborn and weaned piglets. Some pigs are resistant to this infection, and susceptibility is inherited as a simple dominant Mendelian trait. Indentifying the genetics behind this trait will greatly benefit pig welfare as well as the pig breeding industry by providing an opportunity to select against genetically susceptible animals, thereby reducing the number of diarrhoea outbreaks. The trait has recently been mapped by haplotype sharing to a 2.5 Mb region on pig chromosome 13, a region containing 18 annotated genes. Findings: The coding regions of five candidate genes for susceptibility to ETEC F4ab/ac infection (TFRC, ACK1, MUC20, MUC4 and KIAA0226), all located in the 2.5 Mb region, were investigated for the presence of possible causative mutations. A total of 34 polymorphisms were identified in either coding regions or their flanking introns. The genotyping data for two of those were found to perfectly match the genotypes at the ETEC F4ab/ac locus, a G to C polymorphism in intron 11 of TFRC and a C to T silent polymorphism in exon 22 of KIAA0226. Transcriptional profiles of the five genes were investigated in a porcine tissue panel including various intestinal tissues. All five genes were expressed in intestinal tissues at different levels but none of the genes were found differentially expressed between ETEC F4ab/ac resistant and ETEC F4ab/ac susceptible animals in any of the tested tissues. Conclusions: None of the identified polymorphisms are obvious causative mutations for ETEC F4ab/ac susceptibility, as they have no impact on the level of the overall mRNA expression nor predicted to influence the composition of the amino acids composition. However, we cannot exclude that the five tested genes are bona fide candidate genes for susceptibility to ETEC F4ab/ac infection since the identified polymorphism might affect the translational apparatus, alternative splice forms may exist and post translational mechanisms might contribute to disease susceptibility
  • The constancy of gene conservation across divergent bacterial orders
    Item type: Journal Article
    Silander, Olin K.; Ackermann, Martin (2009)
    BMC Research Notes
    Background. Orthologous genes are frequently presumed to perform similar functions. However, outside of model organisms, this is rarely tested. One means of inferring changes in function is if there are changes in the level of gene conservation and selective constraint. Here we compare levels of gene conservation across three bacterial groups to test for changes in gene functionality. Findings. The level of gene conservation for different orthologous genes is highly correlated across clades, even for highly divergent groups of bacteria. These correlations do not arise from broad differences in gene functionality (e.g. informational genes vs. metabolic genes), but instead seem to result from very specific differences in gene function. Furthermore, these functional differences appear to be maintained over very long periods of time. Conclusion. These results suggest that even over broad time scales, most bacterial genes are under a nearly constant level of purifying selection, and that bacterial evolution is thus dominated by selective and functional stasis.
  • Chlamydia in canine or feline coronary arteriosclerotic lesions
    Item type: Journal Article
    Sostaric-Zuckermann, Ivan C.; Borel, Nicole; Kaiser, Carmen; et al. (2011)
    BMC Research Notes
    Background: There are numerous reports linking Chlamydia infection to human coronary atherosclerosis. However, there is a lack of data regarding this correlation in dogs and cats, and there are no reports investigating coronary arteriosclerosis and Chlamydia in these species. The aim of the present study was to examine whether there is a correlation between canine and feline spontaneous atherosclerosis or arteriosclerosis and the presence of Chlamydia. Archived histopathological samples of dogs (n = 16) and cats (n = 13) with findings of atherosclerosis or arteriosclerosis in heart tissue were examined for the presence of Chlamydiaceae using real-time PCR, ArrayTube Microarray and immunohistochemistry. Additionally, arteriosclerotic lesions of all cases were histologically classified and graded. Results: Both canine atherosclerotic cases, and all 14 canine arteriosclerotic cases were negative for Chlamydia. Only one of the 13 arteriosclerotic feline cases was positive for Chlamydia by real-time PCR, revealing C. abortus by ArrayTube Microarray. To our knowledge, this is the first description of C. abortus in a cat. Overall, the type and grade of canine and feline arteriosclerotic lesions revealed similarities, and were predominantly moderate and hyperplastic. Conclusions: These findings suggest that there is no obvious correlation between canine and feline coronary arteriosclerosis and the presence of Chlamydia. In order to draw final conclusions about the correlation between Chlamydia and canine atherosclerosis, examination of more samples is required.
  • Pilot study: validity and reliability of textile insoles used to measure the characteristics of landing tasks during rehabilitation and artistic gymnastics
    Item type: Journal Article
    Schümperlin, Delia; Schärer, Christoph; Kalberer, Luzia; et al. (2023)
    BMC Research Notes
    Objectives: Artistic gymnastics is a sport where most athletes start at an early age and training volumes are high. Hence, overuse and acute injuries are frequent due to the load endured during landing tasks. During landing, the ground reaction force (GRF) is up to 15.8 times the body weight and therefore reliable GRF measurements are crucial. The gold standard for GRF measurements are force plates. As force plates are mostly used in a constrained laboratory environment, it is difficult to measure the GRF in representative training settings. Textile insoles (novel GmbH, Munich, Germany) exist, which can be used to measure dynamic GRF. Hence, the motivation of this study is to test the validity and reliability of these insoles during landing tasks. GRF was measured during four different exercises, in two test subjects and compared to concurrent force plate data. Results: Twelve out of 16 statistical parametric mapping plots showed no significant difference between the measured force curves of insoles and force plates. Across conditions, the root mean square error of the maximal vertical GRF was 21 N/kg and an impulse 0.4 Ns/kg. The intraclass correlation coefficient (ICC 2,1) ranged from 0.02 to 0.76 for maximal vertical GRF and from − 0.34 to 0.76 for impulse. The insoles are a valid measurement tool for GRF curve progression and impulse during landing but underestimate the maximal vertical GRF.
  • Pilot study: is there an influence of lower limb positioning during magnetic resonance imaging on muscle cross section shape assessment in the thigh?
    Item type: Journal Article
    Oberhofer, Katja; Blum, Matthias; Achermann, Basil; et al. (2023)
    BMC Research Notes
    Positioning in an MRI can influence quantitative measures of the muscle. The goal of this pilot study was to assess the influence of different levels of knee elevation during MRI on the predicted cross-sectional muscle shape in the thigh. Data were acquired in three healthy male participants (age: 29.3 ± 5.1y, height: 181.3 ± 6.4cm, weight: 85.1 ± 3.7kg). For each participant, three MRI scans were taken by a trained radiographer with low, moderate and high knee elevation. The shape of the anatomical cross-sectional areas of the hamstrings and quadriceps in three leg positionings were compared by fitting ellipsoidal functions to the segmented MRI data and calculating the so-called J index for every image slice using the Python scripting language. Different levels of knee elevation resulted in apparent changes in J index for all muscles except vastus medialis. Thereby, the changes were overall more pronounced in the hamstrings compared to the quadriceps. Particularly, by elevating the knee from 8 to 15 degree, the percentage changes in J index were between 7.2 and 13.6% for the hamstrings and between 0.5 and 3.3% for the quadriceps, respectively. For assessing the musculoskeletal properties by means of MRI, a standardized positioning of the leg is required and the knee joint angle should be controlled.
Publications1 - 10 of 16