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8 Janelia Publications

Showing 1-8 of 8 results
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    Eddy/Rivas Lab
    01/01/09 | A survey of nematode SmY RNAs.
    Jones TA, Otto W, Marz M, Eddy SR, Stadler PF
    RNA Biology. 2009 Jan-Mar;6(1):5-8

    SmY RNAs are a family of approximately 70-90 nt small nuclear RNAs found in nematodes. In C. elegans, SmY RNAs copurify in a small ribonucleoprotein (snRNP) complex related to the SL1 and SL2 snRNPs that are involved in nematode mRNA trans-splicing. Here we describe a comprehensive computational analysis of SmY RNA homologs found in the currently available genome sequences. We identify homologs in all sequenced nematode genomes in class Chromadorea. We are unable to identify homologs in a more distantly related nematode species, Trichinella spiralis (class: Dorylaimia), and in representatives of non-nematode phyla that use trans-splicing. Using comparative RNA sequence analysis, we infer a conserved consensus SmY RNA secondary structure consisting of two stems flanking a consensus Sm protein binding site. A representative seed alignment of the SmY RNA family, annotated with the inferred consensus secondary structure, has been deposited with the Rfam RNA families database.

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    01/01/09 | Development of an implanted intramuscular EMG-triggered FES system for ambulation after incomplete spinal cord injury.
    Dutta A, Kobetic R, Triolo R
    Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society.. 2009;2009:6793-7. doi: 10.1109/IEMBS.2009.5333980

    Ambulation after spinal cord injury is possible with the aid of neuroprosthesis employing functional electrical stimulation (FES). Individuals with incomplete spinal cord injury (iSCI) retain partial volitional control of muscles below the level of injury, necessitating careful integration of FES with intact voluntary motor function for efficient walking. In this study, the intramuscular electromyogram (iEMG) was used to detect the intent to step and trigger FES-assisted walking in a volunteer with iSCI via an implanted neuroprosthesis consisting of two channels of bipolar iEMG signal acquisition and 12 independent channels of stimulation. The detection was performed with two types of classifiers- a threshold-based classifier that compared the running mean of the iEMG with a discrimination threshold to generate the trigger and a pattern recognition classifier that compared the time-history of the iEMG with a specified template of activity to generate the trigger whenever the cross-correlation coefficient exceeded a discrimination threshold. The pattern recognition classifier generally outperformed the threshold-based classifier, particularly with respect to minimizing False Positive triggers. The overall True Positive rates for the threshold-based classifier were 61.6% and 87.2% for the right and left steps with overall False Positive rates of 38.4% and 33.3%. The overall True Positive rates for the left and right step with the pattern recognition classifier were 57.2% and 93.3% and the overall False Positive rates were 11.9% and 24.4%. The subject showed no preference for either the threshold or pattern recognition-based classifier as determined by the Usability Rating Scale (URS) score collected after each trial and both the classifiers were perceived as moderately easy to use.

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    01/01/09 | Imaging informatics for personalised medicine: applications and challenges.
    Liu T, Peng H, Zhou X
    International Journal of Functional Informatics and Personalised Medicine. 2009;2(2):125-35. doi: 10.1007/s12021-010-9090-x

    Imaging informatics has emerged as a major research theme in biomedicine in the last few decades. Currently, personalised, predictive and preventive patient care is believed to be one of the top priorities in biomedical research and practice. Imaging informatics plays a major role in biomedicine studies. This paper reviews main applications and challenges of imaging informatics in biomedicine.

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    Simpson Lab
    01/01/09 | Mapping and manipulating neural circuits in the fly brain.
    Simpson JH
    Advances in Genetics. 2009;65:79-143. doi: 10.1016/S0065-2660(09)65003-3

    Drosophila is a marvelous system to study the underlying principles that govern how neural circuits govern behaviors. The scale of the fly brain (approximately 100,000 neurons) and the complexity of the behaviors the fly can perform make it a tractable experimental model organism. In addition, 100 years and hundreds of labs have contributed to an extensive array of tools and techniques that can be used to dissect the function and organization of the fly nervous system. This review discusses both the conceptual challenges and the specific tools for a neurogenetic approach to circuit mapping in Drosophila.

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    Looger Lab
    01/01/09 | Modulating protein interactions by rational and computational design.
    Marvin JS, Looger LL
    Protein Engineering and Design. 2009:343-66
    Chklovskii Lab
    01/01/09 | Reconstruction of sparse circuits using multi-neuronal excitation (RESCUME).
    Hu T, Chklovskii DB
    Neural Information Processing Systems. 2009;22:790-8

    One of the central problems in neuroscience is reconstructing synaptic connectivity in neural circuits. Synapses onto a neuron can be probed by sequentially stimulating potentially pre-synaptic neurons while monitoring the membrane voltage of the post-synaptic neuron. Reconstructing a large neural circuit using such a "brute force" approach is rather time-consuming and inefficient because the connectivity in neural circuits is sparse. Instead, we propose to measure a post-synaptic neuron's voltage while stimulating sequentially random subsets of multiple potentially pre-synaptic neurons. To reconstruct these synaptic connections from the recorded voltage we apply a decoding algorithm recently developed for compressive sensing. Compared to the brute force approach, our method promises significant time savings that grow with the size of the circuit. We use computer simulations to find optimal stimulation parameters and explore the feasibility of our reconstruction method under realistic experimental conditions including noise and non-linear synaptic integration. Multineuronal stimulation allows reconstructing synaptic connectivity just from the spiking activity of post-synaptic neurons, even when sub-threshold voltage is unavailable. By using calcium indicators, voltage-sensitive dyes, or multi-electrode arrays one could monitor activity of multiple postsynaptic neurons simultaneously, thus mapping their synaptic inputs in parallel, potentially reconstructing a complete neural circuit.

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    Eddy/Rivas Lab
    01/01/09 | Rfam: updates to the RNA families database.
    Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A
    Nucleic Acids Research. 2009 Jan;37(Database issue):D136-40. doi: 10.1093/nar/gkn766

    Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited taxonomic range and provide a limited number of annotations. Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/.

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    01/01/09 | Stochastic resonance-enhanced laser-based particle detector.
    Dutta A, Werner C
    Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society.. 2009;2009:785-7. doi: 10.1109/IEMBS.2009.5332748

    This paper presents a Laser-based particle detector whose response was enhanced by modulating the Laser diode with a white-noise generator. A Laser sheet was generated to cast a shadow of the object on a 200 dots per inch, 512 x 1 pixels linear sensor array. The Laser diode was modulated with a white-noise generator to achieve stochastic resonance. The white-noise generator essentially amplified the wide-bandwidth (several hundred MHz) noise produced by a reverse-biased zener diode operating in junction-breakdown mode. The gain in the amplifier in the white-noise generator was set such that the Receiver Operating Characteristics plot provided the best discriminability. A monofiber 40 AWG (approximately 80 microm) wire was detected with approximately 88% True Positive rate and approximately 19% False Positive rate in presence of white-noise modulation and with approximately 71% True Positive rate and approximately 15% False Positive rate in absence of white-noise modulation.

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