FastMotif: spectral sequence motif discovery.

MOTIVATION: Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, most of the existing motif finding algorithms are computationally demanding, and they may not be able to support the increasingly large datasets produced by modern high-throughput sequencing technologies. RESULTS: We present FastMotif, a new motif discovery algorithm that is built on a recent machine learning technique referred to as Method of Moments. Based on spectral decompositions, our method is robust to model misspecifications and is not prone to locally optimal solutions. We obtain an algorithm that is extremely fast and designed for the analysis of big sequencing data. On HT-Selex data, FastMotif extracts motif profiles that match those computed by various state-of-the-art algorithms, but one order of magnitude faster. We provide a theoretical and numerical analysis of the algorithm's robustness and discuss its sensitivity with respect to the free parameters. AVAILABILITY AND IMPLEMENTATION: The Matlab code of FastMotif is available from http://lcsb-portal.uni.lu/bioinformatics. CONTACT: vlassis@adobe.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Gait screening of a population of young, healthy athletes by means of a portable, low-cost device unveils hidden left-right asymmetries in both quadriceps and anterior cruciate ligament forces.

OBJECTIVE: The present study reports the on-field screening of a population of young soccer players in the pursuit of alterations in gait using a portable and low-cost gait analysis system composed of a Wii Balance Board and a webcam. RESULTS: Recordings of motion of the lower extremities along with vertical ground reaction force (GRF) were used to quantify coefficients of symmetry for the overall GRF and the forces exerted by the quadriceps femori and acting on the anterior cruciate ligament (ACL). Data show that, in face of a quite homogeneous symmetry of GRF during left and right stance phases of gait, quadriceps and ACL exert and are subjected to left-right asymmetrical forces that might prelude, especially in young athletes, later alterations of gait.

Expression of the Parkinson's Disease-Associated Gene Alpha-Synuclein is Regulated by the Neuronal Cell Fate Determinant TRIM32.

Alpha-synuclein is an abundant neuronal protein which has been associated with physiological processes like synaptic function, neurogenesis, and neuronal differentiation but also with pathological neurodegeneration. Indeed, alpha-synuclein (snca) is one of the major genes implicated in Parkinson's disease (PD). However, little is known about the regulation of alpha-synuclein expression. Unveiling the mechanisms that control its regulation is of high importance, as it will enable to further investigate and comprehend the physiological role of alpha-synuclein as well as its potential contribution in the aetiology of PD. Previously, we have shown that the protein TRIM32 regulates fate specification of neural stem cells. Here, we investigated the impact of TRIM32 on snca expression regulation in vitro and in vivo in neural stem cells and neurons. We demonstrated that TRIM32 is positively influencing snca expression in a neuronal cell line, while the absence of TRIM32 is causing deregulated levels of snca transcripts. Finally, we provided evidence that TRIM32 binds to the promoter region of snca, suggesting a novel mechanism of its transcriptional regulation. On the one hand, the presented data link the PD-associated gene alpha-synuclein to the neuronal cell fate determinant TRIM32 and thereby support the concept that PD is a neurodevelopmental disorder. On the other hand, they imply that defects in olfactory bulb adult neurogenesis might contribute to early PD-associated non-motor symptoms like hyposmia.