Of bits and bugs

Pur-α is a nucleic acid-binding protein involved in cell cycle control, transcription, and neuronal function. Initially no prediction of the three-dimensional structure of Pur-α was possible. However, recently we solved the X-ray structure of Pur-α from the fruitfly Drosophila melanogaster and showed that it contains a so-called PUR domain. Here we explain how we exploited bioinformatics tools in combination with X-ray structure determination of a bacterial homolog to obtain diffracting crystals and the high-resolution structure of Drosophila Pur-α. First, we used sensitive methods for remote-homology detection to find three repetitive regions in Pur-α. We realized that our lack of understanding how these repeats interact to form a globular domain was a major problem for crystallization and structure determination. With our information on the repeat motifs we then identified a distant bacterial homolog that contains only one repeat. We determined the bacterial crystal structure and found that two of the repeats interact to form a globular domain. Based on this bacterial structure, we calculated a computational model of the eukaryotic protein. The model allowed us to design a crystallizable fragment and to determine the structure of Drosophila Pur-α. Key for success was the fact that single repeats of the bacterial protein self-assembled into a globular domain, instructing us on the number and boundaries of repeats to be included for crystallization trials with the eukaryotic protein. This study demonstrates that the simpler structural domain arrangement of a distant prokaryotic protein can guide the design of eukaryotic crystallization constructs. Since many eukaryotic proteins contain multiple repeats or repeating domains, this approach might be instructive for structural studies of a range of proteins

Monitoring muscle fatigue following continuous load changes

Department of Human Factors EngineeringPrevious studies related to monitoring muscle fatigue during dynamic motion have focused on detecting the accumulation of muscle fatigue. However, it is necessary to detect both accumulation and recovery of muscle fatigue in dynamic muscle contraction while muscle load changes continuously. This study aims to investigate the development and recovery of muscle fatigue in dynamic muscle contraction conditions following continuous load changes. Twenty healthy males conducted repetitive elbow flexion and extension using 2kg and 1kg dumbbell, by turns. They performed the two tasks of different intensity (2kg intensity task, 1kg intensity task) alternately until they felt they could no longer achieve the required movement range or until they experienced unacceptable biceps muscle discomfort. Meanwhile, using EMG signal of biceps brachii muscle, fatigue detections were performed from both dynamic measurements during each dynamic muscle contraction task and isometric measurements during isometric muscle contraction right before and after each task. In each of 2kg and 1kg intensity tasks, pre, post and change value of EMG amplitude (AEMG) and center frequency were computed respectively. They were compared to check the validity of the muscle fatigue monitoring method using Wavelet transform with EMG signal from dynamic measurements. As a result, a decrease of center frequency in 2kg intensity tasks and an increase of center frequency in 1kg intensity tasks were detected. It shows that development and recovery of muscle fatigue were detected in 2kg and 1kg intensity tasks, respectively. Also, the tendency of change value of center frequency from dynamic measurements were corresponded with that from isometric measurements. It suggests that monitoring muscle fatigue in dynamic muscle contraction conditions using wavelet transform was valid to detect the development and recovery of muscle fatigue continuously. The result also shows the possibility of monitoring muscle fatigue in real-time in industry and it could propose a guideline in designing a human-robot interaction system based on monitoring user's muscle fatigue.clos

Real-World Repetition Estimation by Div, Grad and Curl

We consider the problem of estimating repetition in video, such as performing push-ups, cutting a melon or playing violin. Existing work shows good results under the assumption of static and stationary periodicity. As realistic video is rarely perfectly static and stationary, the often preferred Fourier-based measurements is inapt. Instead, we adopt the wavelet transform to better handle non-static and non-stationary video dynamics. From the flow field and its differentials, we derive three fundamental motion types and three motion continuities of intrinsic periodicity in 3D. On top of this, the 2D perception of 3D periodicity considers two extreme viewpoints. What follows are 18 fundamental cases of recurrent perception in 2D. In practice, to deal with the variety of repetitive appearance, our theory implies measuring time-varying flow and its differentials (gradient, divergence and curl) over segmented foreground motion. For experiments, we introduce the new QUVA Repetition dataset, reflecting reality by including non-static and non-stationary videos. On the task of counting repetitions in video, we obtain favorable results compared to a deep learning alternative

Abnormal oscillation modes in a waning light bridge

A sunspot acts as a waveguide in response to the dynamics of the solar interior; the trapped waves and oscillations could reveal its thermal and magnetic structures. We study the oscillations in a sunspot intruded by a light bridge, the details of the oscillations could reveal the fine structure of the magnetic topology. We use the Solar Dynamics Observatory/Atmospheric Imaging Assembly data to analyse the oscillations in the emission intensity of light bridge plasma at different temperatures and investigate their spatial distributions. The extreme ultraviolet emission intensity exhibits two persistent oscillations at five-minute and sub-minute ranges. The spatial distribution of the five-minute oscillation follows the spine of the bridge; whereas the sub-minute oscillations overlap with two flanks of the bridge. Moreover, the sub-minute oscillations are highly correlated in spatial domain, however, the oscillations at the eastern and western flanks are asymmetric with regard to the lag time. In the meanwhile, jet-like activities are only found at the eastern flank. Asymmetries in forms of oscillatory pattern and jet-like activities \textbf{are} found between two flanks of a granular light bridge. Based on our study and recent findings, we propose a new model of twisted magnetic field for a light bridge and its dynamic interactions with the magnetic field of a sunspot.Comment: 5 figures, Accepted version in A&

A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching

The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. Here, we designed a de novo strategy for detecting patterns that represent nested motifs based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories: motifs within other motifs, motifs flanked by other motifs, and motifs of large size. Our methodology, applied to genomic sequences from the plant species Aegilops tauschii and Oryza sativa, revealed that it is possible to find putative nested TEs by detecting these three types of patterns. The results were validated though BLAST alignments, which revealed the efficacy and usefulness of the new method, which we call Mamushka.Fil: Romero, José Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Carballido, Jessica Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Cs. E Ingeniería de la Computacion; ArgentinaFil: Garbus, Ingrid. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Ponzoni, Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Cs. E Ingeniería de la Computacion; Argentin

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA common to all chromosomes of a given species. In holocentric chromosomes, there is no primary constriction; the centromere is composed of many CenH3 loci distributed along the entire length of a chromosome. Using correlative fluorescence light microscopy and high-resolution electron microscopy, we show that pea (Pisum sativum) chromosomes exhibit remarkably long primary constrictions that contain 3-5 explicit CenH3-containing regions, a novelty in centromere organization. In addition, we estimate that the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp, several factors larger than any known centromere length. These domains are almost entirely composed of repetitive DNA sequences belonging to 13 distinct families of satellite DNA and one family of centromeric retrotransposons, all of which are unevenly distributed among pea chromosomes. We present the centromeres of Pisum as novel ``meta-polycentric'' functional domains. Our results demonstrate that the organization and DNA composition of functional centromere domains can be far more complex than previously thought, do not require single repetitive elements, and do not require single centromere domains in order to segregate properly. Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function

Generative theatre of totality

Generative art can be used for creating complex multisensory and multimedia experiences within predetermined aesthetic parameters, characteristic of the performing arts and remarkably suitable to address Moholy-Nagy's Theatre of Totality vision. In generative artworks the artist will usually take on the role of an experience framework designer, and the system evolves freely within that framework and its defined aesthetic boundaries. Most generative art impacts visual arts, music and literature, but there does not seem to be any relevant work exploring the cross-medium potential, and one could confidently state that most generative art outcomes are abstract and visual, or audio. It is the goal of this article to propose a model for the creation of generative performances within the Theatre of Totality's scope, derived from stochastic Lindenmayer systems, where mapping techniques are proposed to address the seven variables addressed by Moholy-Nagy: light, space, plane, form, motion, sound and man ("man" is replaced in this article with "human", except where quoting from the author), with all the inherent complexities

Molecular biology techniques as a tool for detection and characterisation of Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) is the causative agent of paratuberculosis, also known as Johne’s disease, a chronic intestinal infection in cattle and other ruminants. Paratuberculosis is characterised by diarrhea and weight loss that occurs after a period of a few months up to several years without any clinical signs. The considerable economic losses to dairy and beef cattle producers are caused by reduced milk production and poor reproduction performance in subclinically infected animals. Early diagnosis of infected cattle is essential to prevent the spread of the disease. Efforts have been made to eradicate paratuberculosis by using a detection and cull strategy, but eradication is hampered by the lack of suitable and sensitive diagnostic methods. This thesis, based on five scientific investigations, describes the development of different DNA amplification strategies for detection and characterisation of M. paratuberculosis. Various ways to pre-treat bacterial cultures, tissue specimens and fecal samples prior to PCR analysis were investigated. Internal positive PCR control molecules were developed and used in PCR analyses to improve the reliability and to facilitate the interpretation of the results. The sensitivity of the ultimate methods was found to be approximate that of culture and allowed detection of low numbers of M. paratuberculosis expected to be found in subclinically infected animals. Genomic DNA of a Swedish mycobacterial isolate, incorrectly identified by PCR as M. paratuberculosis was characterised. The isolate was closely related to M. cookii and harboured one copy of a DNA segment with 94% similarity to IS900, the target sequence used in diagnostic PCR for detection of M. paratuberculosis. This finding highlighted the urgency of developing or evaluating PCR systems based on genes other than IS900. A PCR-based fingerprinting method using primers targeting the enterobacterial intergenic consensus sequence (ERIC) and the IS900 sequence was developed and successfully used to distinguish M. paratuberculosis from closely related mycobacteria, including the above mentioned mycobacterial isolate. In conclusion, the molecular biology techniques developed in these studies have proved useful for accelerating the diagnostic detection and characterisation of M. paratuberculosis