Graph-based modeling of tandem repeats improves global multiple sequence alignment

Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivates numerous studies of TRs and their evolution, requiring accurate multiple sequence alignment. TRs may be lost or inserted at any position of a TR region by replication slippage or recombination, but current methods assume fixed unit boundaries, and yet are of high complexity. We present a new global graph-based alignment method that does not restrict TR unit indels by unit boundaries. TR indels are modeled separately and penalized using the phylogeny-aware alignment algorithm. This ensures enhanced accuracy of reconstructed alignments, disentangling TRs and measuring indel events and rates in a biologically meaningful way. Our method detects not only duplication events but also all changes in TR regions owing to recombination, strand slippage and other events inserting or deleting TR units. We evaluate our method by simulation incorporating TR evolution, by either sampling TRs from a profile hidden Markov model or by mimicking strand slippage with duplications. The new method is illustrated on a family of type III effectors, a pathogenicity determinant in agriculturally important bacteria Ralstonia solanacearum. We show that TR indel rate variation contributes to the diversification of this protein famil

Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions

Intrinsically disordered proteins (IDPs) or proteins with disordered regions (IDRs) do not have a well-defined tertiary structure, but perform a multitude of functions, often relying on their native disorder to achieve the binding flexibility through changing to alternative conformations. Intrinsic disorder is frequently found in all three kingdoms of life, and may occur in short stretches or span whole proteins. To date most studies contrasting the differences between ordered and disordered proteins focused on simple summary statistics. Here, we propose an evolutionary approach to study IDPs, and contrast patterns specific to ordered protein regions and the corresponding IDRs.Two empirical Markov models of amino acid substitutions were estimated, based on a large set of multiple sequence alignments with experimentally verified annotations of disordered regions from the DisProt database of IDPs. We applied new methods to detect differences in Markovian evolution and evolutionary rates between IDRs and the corresponding ordered protein regions. Further, we investigated the distribution of IDPs among functional categories, biochemical pathways and their preponderance to contain tandem repeats. disorder prediction using a phylogenetic Hidden Markov Model based on our matrices showed a performance similar to other disorder predictors

KINETIC ANALYSIS OF LOWER BODY RESISTANCE TRAINING EXERCISES

This study evaluated and compared the peak vertical ground reaction force (GRF) and rate of force development (RFD) for the eccentric and concentric phases of 4 lower body resistance training exercises, including the back squat, deadlift, step-up, and forward lunge. Sixteen women performed 2 repetitions of each of the 4 exercises at a 6 repetition maximum load. Kinetic data were acquired using a force platform. A repeated measures ANOVA was used to evaluate the differences in GRF between the exercises. Results revealed significant main effects for GRF both the eccentric (p ≤ 0.001) and concentric (p ≤ 0.001) phases. Significant main effects were also found for RFD for the eccentric (p ≤ 0.001) and concentric phases (p ≤ 0.001). Force and power requirements and osteogenic potential differ between these resistance training exercises

ANTAGONIST CONDITIONING CONTRACTIONS IMPAIR AGONIST FUNCTIONING

This study assessed the effect of antagonist conditioning contractions (ACC) on the subsequent force and electromyography of an agonist. Twelve subjects performed isokinetic elbow flexion on a dynamometer in 4 test conditions including a baseline condition without, and 1, 3 and 6 seconds after, isometric triceps extension. Average peak torque (T), peak torque/body weight (T:BW), average power (P), and rate of torque development (RTD) were assessed. Electromyographic data were obtained from elbow extensors and flexors. A repeated measures ANOVA with post hoc analysis demonstrated that T, T:BW, P, and RTD were higher in the baseline, compared to the post ACC conditions (P ≤ 0.05), and appears to be due to higher brachioradialis activation in the baseline condition in compared to some post ACC conditions (P ≤ 0.05)

OMA 2011: orthology inference among 1000 complete genomes

OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline—in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org

Highly sensitive luminescence nanothermometry and thermal imaging facilitated by phase transition

Currently available temperature measurements or imaging at nano-micro scale are limited to fluorescent molecules and luminescent nanocrystals, whose spectral properties respond to temperature variation. The principle of operation of these conventional temperature probes is typically related to temperature induced multiphonon quenching or temperature dependent energy transfers, therefore, above 12%/K sensitivity and high thermal resolution remain a serious challenge. Here we demonstrate a novel class of highly sensitive thermographic phosphors operating in room temperature range with sub-kelvin thermal resolution, whose temperature readings are reproducible, luminescence is photostable and brightness is not compromised by thermal quenching. Corroborated with phase transition structural characterization and high spatio-temporal temperature imaging, we demonstrated that optically active europium ions are highly and smoothly susceptible to monoclinic to tetragonal phase transition in nanocrystalline (54 ± 14 nm) LiYO2 host, which is evidenced by changed number and the splitting of Stark components as well as by smooth variation of contribution between magnetic and electric dipole transitions. Further, reducing the size of phosphor from bulk to nanocrystalline matrix, shifted the phase transition temperature from 100 °C down to room temperature. These findings provide insights into the mechanism underlaying phase transition based luminescence nanothermometry and motivate future research toward new, highly sensitive, high temporal and spatial resolution nano-thermometers aiming at precise studying heat generation or diffusion in numerous biological and technology applications

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

<p>Abstract</p> <p>Background</p> <p>The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation.</p> <p>Results</p> <p>A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from <url>http://dna.uio.no/swipe/</url> under the GNU Affero General Public License.</p> <p>Conclusions</p> <p>Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.</p

Normal radial migration and lamination are maintained in dyslexia-susceptibility candidate gene homolog Kiaa0319 knockout mice

AbstractDevelopmental dyslexia is a common disorder with a strong genetic component, but the underlying molecular mechanisms are still unknown. Several candidate dyslexia-susceptibility genes, including KIAA0319, DYX1C1, and DCDC2, have been identified in humans. RNA interference experiments targeting these genes in rat embryos have shown impairments in neuronal migration, suggesting that defects in radial cortical migration could be involved in the disease mechanism of dyslexia. Here we present the first characterisation of a Kiaa0319 knockout mouse line. Animals lacking KIAA0319 protein do not show anatomical abnormalities in any of the layered structures of the brain. Neurogenesis and radial migration of cortical projection neurons are not altered, and the intrinsic electrophysiological properties of Kiaa0319-deficient neurons do not differ from those of wild-type neurons. Kiaa0319 overexpression in cortex delays radial migration, but does not affect final neuronal position. However, knockout animals show subtle differences suggesting possible alterations in anxiety-related behaviour and in sensorimotor gating. Our results do not reveal a migration disorder in the mouse model, adding to the body of evidence available for Dcdc2 and Dyx1c1 that, unlike in the rat in utero knockdown models, the dyslexia-susceptibility candidate mouse homolog genes do not play an evident role in neuronal migration. However, KIAA0319 protein expression seems to be restricted to the brain, not only in early developmental stages but also in adult mice, indicative of a role of this protein in brain function. The constitutive and conditional knockout lines reported here will be useful tools for further functional analyses of Kiaa0319