Main Menu (Mobile)- Block

Main Menu - Block

janelia7_blocks-janelia7_fake_breadcrumb | block
Koyama Lab / Publications
custom | custom


facetapi-Q2b17qCsTdECvJIqZJgYMaGsr8vANl1n | block

Associated Lab

facetapi-PV5lg7xuz68EAY8eakJzrcmwtdGEnxR0 | block
facetapi-021SKYQnqXW6ODq5W5dPAFEDBaEJubhN | block
general_search_page-panel_pane_1 | views_panes

106 Publications

Showing 81-90 of 106 results
Your Criteria:
    04/12/07 | Straightening worm images.
    Peng H, Long F, Myers EW
    2007 4TH IEEE International Symposium on Biomedical Imagin : Macro to Nano, VOLS 1-3. 2007 Apr 12-15:292-5. doi: 10.1109/ISBI.2007.356846

    C. elegans, a roundworm in soil is widely used in studying animal development and aging, cell differentiation, etc. Recentlv, high-resolution fluorescence images of C. elegans have become available, introducing several new image analysis applications. One problem is that worm bodies usually curve greatly in images, thus it is highly desired to straighten worms so that they can be compared easily under the same canonical coordinate system. We develop a worm straightening algorithm (WSA) using a cutting-plane restacking method, which aggregates the linear rotation transforms of a continuous sequence of cutting lines/planes orthogonal to the "backbone" of a worm to best approximate the nonlinearly bended worm body. We formulate the backbone as a parametric form of cubic spline of a series of control points. We develop two minimum-spanning-tree based methods to automatically determine the locations of control points. Our experimental methods show that our approach can effectively straighten both 2D and 3D worm images.

    View Publication Page
    04/11/07 | Observability of Higgs produced with top quarks and decaying to bottom quarks
    Benedetti D, Cucciarelli S, Hill C, Incandela J, Koay SA, Riccardi C, Santocchia A, Schmidt A, Torre P, Weiser C
    Journal of Physics G: Nuclear and Particle Physics. 04/20027;34(5):N221 - N250. doi: 10.1088/0954-3899/34/5/N03

    The decay, , is dominant for a Standard Model Higgs boson in the mass range just above the exclusion limit of 114.4 GeV/c2 reported by the LEP experiments. Unfortunately, an overwhelming abundance of  events arising from more mundane sources, together with the lack of precision inherent in the reconstruction of the Higgs mass, renders this decay mode a priori undetectable in the case of direct Higgs production at the LHC. It is therefore of no small interest to investigate whether  can be observed in those cases where the Higgs is produced in association with other massive particles. In this note, the results of a study of Higgs bosons produced in association with top quarks and decaying via  are presented. The study was performed as realistically as possible by employing a full and detailed Monte Carlo simulation of the CMS detector followed by the application of trigger and reconstruction algorithms that were developed for use with real data. Important systematic effects resulting from such sources as the uncertainties in the jet energy scale and the estimated rates for correctly tagging b jets or mistagging non-b jets have been taken into account. The impact of large theoretical uncertainties in the cross sections for  plus N jets processes due to an absence of next-to-leading order calculations is also considered.

    View Publication Page
    Riddiford Lab
    04/01/07 | Size assessment and growth control: how adult size is determined in insects.
    Mirth CK, Riddiford LM
    BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology. 2007 Apr;29(4):344-55. doi: 10.1002/bies.20552

    Size control depends on both the regulation of growth rate and the control over when to stop growing. Studies of Drosophila melanogaster have shown that insulin and Target of Rapamycin (TOR) pathways play principal roles in controlling nutrition-dependent growth rates. A TOR-mediated nutrient sensor in the fat body detects nutrient availability, and regulates insulin signaling in peripheral tissues, which in turn controls larval growth rates. After larvae initiate metamorphosis, growth stops. For growth to stop at the correct time, larvae need to surpass a critical weight. Recently, it was found that the insulin-dependent growth of the prothoracic gland is involved in assessing when critical weight has been reached. Furthermore, mutations in DHR4, a repressor of ecdysone signaling, reduce critical weight and adult size. Thus, the mechanisms that control growth rates converge on those assessing size to ensure that the larvae attain the appropriate size at metamorphosis.

    View Publication Page
    Egnor Lab
    04/01/07 | Tracking silence: adjusting vocal production to avoid acoustic interference.
    Egnor SE, Wickelgren JG, Hauser MD
    Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology. 2007 Apr;193(4):477-83. doi: 10.1007/s00359-006-0205-7

    Organisms that use vocal signals to communicate often modulate their vocalizations to avoid being masked by other sounds in the environment. Although some environmental noise is continuous, both biotic and abiotic noise can be intermittent, or even periodic. Interference from intermittent noise can be avoided if calls are timed to coincide with periods of silence, a capacity that is unambiguously present in insects, amphibians, birds, and humans. Surprisingly, we know virtually nothing about this fundamental capacity in nonhuman primates. Here we show that a New World monkey, the cotton-top tamarin (Saguinus oedipus), can restrict calls to periodic silent intervals in loud white noise. In addition, calls produced during these silent intervals were significantly louder than calls recorded in silent baseline sessions. Finally, average call duration dropped across sessions, indicating that experience with temporally patterned noise caused tamarins to compress their calls. Taken together, these results show that in the presence of a predictable, intermittent environmental noise, cotton-top tamarins are able to modify the duration, timing, and amplitude of their calls to avoid acoustic interference.

    View Publication Page
    Eddy/Rivas Lab
    03/30/07 | Query-dependent banding (QDB) for faster RNA similarity searches.
    Nawrocki EP, Eddy SR
    PLoS Computational Biology. 2007 Mar 30;3(3):e56. doi: 10.1371/journal.pcbi.0030056

    When searching sequence databases for RNAs, it is desirable to score both primary sequence and RNA secondary structure similarity. Covariance models (CMs) are probabilistic models well-suited for RNA similarity search applications. However, the computational complexity of CM dynamic programming alignment algorithms has limited their practical application. Here we describe an acceleration method called query-dependent banding (QDB), which uses the probabilistic query CM to precalculate regions of the dynamic programming lattice that have negligible probability, independently of the target database. We have implemented QDB in the freely available Infernal software package. QDB reduces the average case time complexity of CM alignment from LN(2.4) to LN(1.3) for a query RNA of N residues and a target database of L residues, resulting in a 4-fold speedup for typical RNA queries. Combined with other improvements to Infernal, including informative mixture Dirichlet priors on model parameters, benchmarks also show increased sensitivity and specificity resulting from improved parameterization.

    View Publication Page
    Gonen Lab
    03/16/07 | Projection map of aquaporin-9 at 7 A resolution.
    Viadiu H, Gonen T, Walz T
    Journal of Molecular Biology. 2007 Mar 16;367(1):80-8. doi: 10.1016/j.jmb.2006.12.042

    Aquaporin-9, an aquaglyceroporin present in diverse tissues, is unique among aquaporins because it is not only permeable to water, urea and glycerol, but also allows passage of larger uncharged solutes. Single particle analysis of negatively stained recombinant rat aquaporin-9 revealed a particle size characteristic of the tetrameric organization of all members of the aquaporin family. Reconstitution of aquaporin-9 into two-dimensional crystals enabled us to calculate a projection map at 7 A resolution. The projection structure indicates a tetrameric structure, similar to GlpF, with each square-like monomer forming a pore. A comparison of the pore-lining residues between the crystal structure of GlpF and a homology model of aquaporin-9 locates substitutions in these residues predominantly to the hydrophobic edge of the tripathic pore of GlpF, providing first insights into the structural basis for the broader substrate specificity of aquaporin-9.

    View Publication Page
    03/13/07 | GSK-3/Shaggy regulates olfactory habituation in Drosophila.
    Wolf FW, Eddison M, Lee S, Cho W, Heberlein U
    Proceedings of the National Academy of Sciences of the United States of America. 2007 Mar 13;104(11):4653-7. doi: 10.1073/pnas.0700493104

    Habituation is a universal form of nonassociative learning that results in the devaluation of sensory inputs that have little information content. Although habituation is found throughout nature and has been studied in many organisms, the underlying molecular mechanisms remain poorly understood. We performed a forward genetic screen in Drosophila to search for mutations that modified habituation of an olfactory-mediated locomotor startle response, and we isolated a mutation in the glycogen synthase kinase-3 (GSK-3) homolog Shaggy. Decreases in Shaggy levels blunted habituation, whereas increases promoted habituation. Additionally, habituation acutely regulated Shaggy by an inhibitory phosphorylation mechanism, suggesting that a signal transduction pathway that regulates Shaggy is engaged during habituation. Although shaggy mutations also affected circadian rhythm period, this requirement was genetically separable from its role in habituation. Thus, shaggy functions in different neuronal circuits to regulate behavioral plasticity to an olfactory startle and circadian rhythmicity.

    View Publication Page
    03/01/07 | Automatic recognition and annotation of gene expression patterns of fly embryos.
    Zhou J, Peng H
    Bioinformatics. 2007 Mar 1;23(5):589-96. doi: 10.1007/s12021-010-9090-x

    Gene expression patterns obtained by in situ mRNA hybridization provide important information about different genes during Drosophila embryogenesis. So far, annotations of these images are done by manually assigning a subset of anatomy ontology terms to an image. This time-consuming process depends heavily on the consistency of experts.

    View Publication Page
    03/01/07 | Drosophila melanogaster Methoprene-tolerant (Met) gene homologs from three mosquito species: members of PAS transcriptional factor family.
    Wang S, Baumann A, Wilson TG
    Journal of Insect Physiology. 2007 Mar;53:246-53. doi: 10.1016/j.jinsphys.2006.07.011

    The Methoprene-tolerant (Met) gene in Drosophila melanogaster has been shown to function in juvenile hormone (JH) action. Met homologs were isolated from three mosquito species, Culex pipiens, Aedes aegypti and Anopheles gambiae. Sequence similarity was found to be high in bHLH and PAS conserved domains, and the majority of the 7-9 introns in AaMet and AgMet are located in either identical or similar positions, indicating evolutionary relatedness. Sequence comparison with Met and the similar germ-cell expressed (gce) gene in D. melanogaster showed that the mosquito genes are more similar to gce than to Met. Moreover, the multiple introns in AgMet and AaMet are more similar in number with the 7 introns in Dmgce than to the single intron in DmMet; in fact, six intron positions in AaMet and AgMet are similar to those in Dmgce. Efforts to identify a second homologous gene in mosquitoes were unsuccessful, suggesting a single gene in lower Diptera, consistent with the single gene uncovered in genomic sequencing of Ae. aegypti and An. gambiae. These results suggest that a gene duplication occurred during the evolution of higher Diptera, resulting in Met and gce.

    View Publication Page
    03/01/07 | Purification, crystallization and preliminary crystallographic analysis of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus.
    Wu H, Sun L, Brouns SJ, Fu S, Akerboom J, Li X, van der Oost J
    Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 2007 Mar 1;63:239-41. doi: 10.1107/S1744309107008500

    A predicted GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus, termed SsGBP, has been cloned and overexpressed in Escherichia coli. The purified protein was crystallized using the hanging-drop vapour-diffusion technique in the presence of 0.05 M cadmium sulfate and 0.8 M sodium acetate pH 7.5. A single-wavelength anomalous dispersion data set was collected to a maximum resolution of 2.0 A using a single cadmium-incorporated crystal. The crystal form belongs to space group P2(1)2(1)2(1), with approximate unit-cell parameters a = 65.0

    View Publication Page