740 research outputs found
Titin visualization in real time reveals an unexpected level of mobility within and between sarcomeres
Contrary to prior models in which titin serves as a stable scaffold in sarcomeres, sarcomeric and soluble titin exchange dynamically in myofibers when calcium levels are low
The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species
Genes in durophage intersection set at 15 dpf. This is a comma separated table of the genes in the 15 dpf durophage intersection set. Given are edgeR results for each pairwise comparison. Columns indicating whether a gene is included in the intersection set at a threshold of 1.5 or 2 fold are provided. (CSV 13Â kb
Phylogenetic comparative assembly
Husemann P, Stoye J. Phylogenetic Comparative Assembly. Algorithms for Molecular Biology. 2010;5(1): 3.BACKGROUND:Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. RESULTS:Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a graph that contains the likelihood for each pair of contigs to be adjacent. Subsequently, this graph can be used to compute a layout graph that shows the most promising contig adjacencies in order to aid biologists in finishing the complete genomic sequence. The layout graph shows unique contig orderings where possible, and the best alternatives where necessary. CONCLUSIONS:Our new algorithm for contig ordering uses sequence similarity as well as phylogenetic information to estimate adjacencies of contigs. An evaluation of our implementation shows that it performs better than recent approaches while being much faster at the same tim
Next-generation sequencing of vertebrate experimental organisms
Next-generation sequencing technologies are revolutionizing biology by allowing for genome-wide transcription factor binding-site profiling, transcriptome sequencing, and more recently, whole-genome resequencing. While it is currently not possible to generate complete de novo assemblies of higher-vertebrate genomes using next-generation sequencing, improvements in sequence read lengths and throughput, coupled with new assembly algorithms for large data sets, will soon make this a reality. These developments will in turn spawn a revolution in how genomic data are used to understand genetics and how model organisms are used for disease gene discovery. This review provides an overview of the current next-generation sequencing platforms and the newest computational tools for the analysis of next-generation sequencing data. We also describe how next-generation sequencing may be applied in the context of vertebrate model organism genetics
Unusual explosive growth of a squamous cell carcinoma of the scalp after electrical burn injury and subsequent coverage by sequential free flap vascular connection – a case report
BACKGROUND: Squamous cell carcinomos may arise from chronic ulcerating wounds in scars, most commonly postburn scars. Tumour growth usually takes place over months to years. Localization on the scalp is a relatively rare condition. CASE PRESENTATION: This report presents the case of a 63-year-old man with chronic ulceration of a postburn scar of the scalp due to an electrical burn 58 years ago. Sudden tumour growth started within weeks and on presentation already had extended through the skull into frontal cortex. After radical tumour resection, defect was covered with a free radial forearm flap. Local recurrence occurred 6 weeks later. Subsequent wide excision including discard of the flap and preservation of the radial vessels was followed by transfer of a free latissimus dorsi muscle flap, using the radial vessels of the first flap as recipient vessels. The patient received radiotherapy post-operatively. There were no problems with flap survivals or wound healing. Due to rapidly growing recurrence the patient died 2 months later. CONCLUSION: Explosive SCC tumour growth might occur in post-burn scars after more than 50 years. As a treatment option the use of sequential free flap connections might serve in repeated extensive tumour resections, especially in the scalp region, where suitable donor vessels are often located in distance to the defect
A chromosomal reference genome sequence for the malaria mosquito Anopheles gambiae, Giles, 1902, Ifakara strain
We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length
Distribution of Class 1 Integrons with IS26-Mediated Deletions in Their 3′-Conserved Segments in Escherichia coli of Human and Animal Origin
Class 1 integrons play a role in the emergence of multi-resistant bacteria by facilitating the recruitment of gene cassettes encoding antibiotic resistance genes. 512 E. coli strains sourced from humans (n = 202), animals (n = 304) and the environment (n = 6) were screened for the presence of the intI1 gene. In 31/79 integron positive E. coli strains, the gene cassette regions could not be PCR amplified using standard primers. DNA sequence analysis of 6 serologically diverse strains revealed atypical integrons harboured the dfrA5 cassette gene and only 24 bp of the integron 3′-conserved segment (CS) remained, due to the insertion of IS26. PCR targeting intI1 and IS26 followed by restriction fragment length polymorphism (RFLP) analysis identified the integron-dfrA5-IS26 element in 27 E. coli strains of bovine origin and 4 strains of human origin. Southern hybridization and transformation studies revealed the integron-dfrA5-IS26 gene arrangement was either chromosomally located or plasmid borne. Plasmid location in 4/9 E. coli strains and PCR linkage of Tn21 transposition genes with the intI1 gene in 20/31 strains, suggests this element is readily disseminated by horizontal transfer
Lower trunk motion and speed-dependence during walking
Abstract Background There is a limited understanding about how gait speed influences the control of upper body motion during walking. Therefore, the primary purpose of this study was to examine how gait speed influences healthy individual's lower trunk motion during overground walking. The secondary purpose was to assess if Principal Component Analysis (PCA) can be used to gain further insight into postural responses that occur at different walking speeds. Methods Thirteen healthy subjects (23 ± 3 years) performed 5 straight-line walking trials at self selected slow, preferred, and fast walking speeds. Accelerations of the lower trunk were measured in the anterior-posterior (AP), vertical (VT), and mediolateral (ML) directions using a triaxial accelerometer. Stride-to-stride acceleration amplitude, regularity and repeatability were examined with RMS acceleration, Approximate Entropy and Coefficient of Multiple determination respectively. Coupling between acceleration directions were calculated using Cross Approximate Entropy. PCA was used to reveal the dimensionality of trunk accelerations during walking at slow and preferred speeds, and preferred and fast speeds. Results RMS acceleration amplitude increased with gait speed in all directions. ML and VT trunk accelerations had less signal regularity and repeatability during the slow compared to preferred speed. However, stride-to-stride acceleration regularity and repeatability did not differ between the preferred and fast walking speed conditions, partly due to an increase in coupling between frontal plane accelerations. The percentage of variance accounted for by each trunk acceleration Principal Component (PC) did not differ between grouped slow and preferred, and preferred and fast walking speed acceleration data. Conclusion The main finding of this study was that walking at speeds slower than preferred primarily alters lower trunk accelerations in the frontal plane. Despite greater amplitudes of trunk acceleration at fast speeds, the lack of regularity and repeatability differences between preferred and fast speeds suggest that features of trunk motion are preserved between the same conditions. While PCA indicated that features of trunk motion are preserved between slow and preferred, and preferred and fast speeds, the discriminatory ability of PCA to detect speed-dependent differences in walking patterns is limited compared to measures of signal regularity, repeatability, and coupling.</p
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