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

140 Publications

Showing 31-40 of 140 results
Your Criteria:
    Kainmueller Lab
    09/07/08 | Model-based autosegmentation of the central brain of the honeybee, Apis mellifera, using active statistical shape models.
    Singer J, Lienhard M, Seim H, Kainmueller D, Kuss A, Lamecker H, Zachow S, Menzel R, Rybak J
    Neuroinformatics 2008. 2008 Sep 07:. doi: 10.3389/conf.neuro.11.2008.01.064

    The Honeybee Brain Atlas serves as 3D database and communicative platform to accumulate structural data, i.e. reconstructed neurons, derived from confocal scans (Brandt et al., 2005) ( (1). Transforming neurons into the atlas requires manual segmentation of neuropils within confocal images, a time-consuming task requiring expertise in identifying biological structures which can result in different outcomes from various segmenters.

    View Publication Page
    09/06/08 | Automatic tracking of Escherichia coli bacteria.
    Xie J, Khan S, Shah M
    Medical Image Computing and Computer-Assisted Intervention: MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention. 2008 Sep 6;11:824-32

    In this paper, we present an automatic method for estimating the trajectories of Escherichia coli bacteria from in vivo phase-contrast microscopy videos. To address the low-contrast boundaries in cellular images, an adaptive kernel-based technique is applied to detect cells in sequence of frames. Then a novel matching gain measure is introduced to cope with the challenges such as dramatic changes of cells’ appearance and serious overlapping and occlusion. For multiple cell tracking, an optimal matching strategy is proposed to improve the handling of cell collision and broken trajectories. The results of successful tracking of Escherichia coli from various phase-contrast sequences are reported and compared with manually-determined trajectories, as well as those obtained from existing tracking methods. The stability of the algorithm with different parameter values is also analyzed and discussed.

    View Publication Page
    Pastalkova Lab
    09/05/08 | Internally generated cell assembly sequences in the rat hippocampus.
    Pastalkova E, Itskov V, Amarasingham A, Buzsáki G
    Science. 2008 Sep 5;321(5894):1322-7. doi: 10.1523/JNEUROSCI.3773-10.2011

    A long-standing conjecture in neuroscience is that aspects of cognition depend on the brain’s ability to self-generate sequential neuronal activity. We found that reliably and continually changing cell assemblies in the rat hippocampus appeared not only during spatial navigation but also in the absence of changing environmental or body-derived inputs. During the delay period of a memory task, each moment in time was characterized by the activity of a particular assembly of neurons. Identical initial conditions triggered a similar assembly sequence, whereas different conditions gave rise to different sequences, thereby predicting behavioral choices, including errors. Such sequences were not formed in control (nonmemory) tasks. We hypothesize that neuronal representations, evolved for encoding distance in spatial navigation, also support episodic recall and the planning of action sequences.

    View Publication Page
    09/01/08 | Bioimage informatics: a new area of engineering biology.
    Peng H
    Bioinformatics. 2008 Sep 1;24(17):1827-36. doi: 10.1007/s12021-010-9090-x

    In recent years, the deluge of complicated molecular and cellular microscopic images creates compelling challenges for the image computing community. There has been an increasing focus on developing novel image processing, data mining, database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problems. This emerging new area of bioinformatics can be called ’bioimage informatics’. This article reviews the advances of this field from several aspects, including applications, key techniques, available tools and resources. Application examples such as high-throughput/high-content phenotyping and atlas building for model organisms demonstrate the importance of bioimage informatics. The essential techniques to the success of these applications, such as bioimage feature identification, segmentation and tracking, registration, annotation, mining, image data management and visualization, are further summarized, along with a brief overview of the available bioimage databases, analysis tools and other resources.

    View Publication Page
    09/01/08 | Clonal analysis of Drosophila antennal lobe neurons: diverse neuronal architectures in the lateral neuroblast lineage.
    Lai S, Awasaki T, Ito K, Lee T
    Development. 2008 Sep;135(17):2883-93. doi: 10.1242/dev.024380

    The antennal lobe (AL) is the primary structure in the Drosophila brain that relays odor information from the antennae to higher brain centers. The characterization of uniglomerular projection neurons (PNs) and some local interneurons has facilitated our understanding of olfaction; however, many other AL neurons remain unidentified. Because neuron types are mostly specified by lineage and temporal origins, we use the MARCM techniques with a set of enhancer-trap GAL4 lines to perform systematical lineage analysis to characterize neuron morphologies, lineage origin and birth timing in the three AL neuron lineages that contain GAL4-GH146-positive PNs: anterodorsal, lateral and ventral lineages. The results show that the anterodorsal lineage is composed of pure uniglomerular PNs that project through the inner antennocerebral tract. The ventral lineage produces uniglomerular and multiglomerular PNs that project through the middle antennocerebral tract. The lateral lineage generates multiple types of neurons, including uniglomeurlar PNs, diverse atypical PNs, various types of AL local interneurons and the neurons that make no connection within the ALs. Specific neuron types in all three lineages are produced in specific time windows, although multiple neuron types in the lateral lineage are made simultaneously. These systematic cell lineage analyses have not only filled gaps in the olfactory map, but have also exemplified additional strategies used in the brain to increase neuronal diversity.

    View Publication Page
    09/01/08 | Shape registration by optimally coding shapes.
    Jiang Y, Xie J, Tsui H
    IEEE Transactions on Information Technology in Biomedicine : A Publication of the IEEE Engineering in Medicine and Biology Society. 2008 Sep;12(5):627-35. doi: 10.1109/TITB.2008.920798

    This paper formulates shape registration as an optimal coding problem. It employs a set of landmarks to establish the correspondence between shapes, and assumes that the best correspondence can be achieved when the polygons formed by the landmarks optimally code all the shape contours, i.e., obtain their minimum description length (MDL). This is different from previous MDL-based shape registration methods, which code the landmark locations. In this paper, each contour is discretized to be a set of points to make the coding feasible, and a number of strategies are adopted to tackle the difficult optimization problem involved. The resulting algorithm, called CAP, is able to yield statistical shape model with better quality in terms of model generalization error, which is demonstrated on both synthetic and biomedical shapes.

    View Publication Page
    Tjian Lab
    09/01/08 | TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription.
    Hsu J, Juven-Gershon T, Marr MT, Wright KJ, Tjian R, Kadonaga JT
    Genes & Development. 2008 Sep 1;22(17):2353-8. doi: 10.1073/pnas.1100640108

    The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional module. RNAi depletion and overexpression experiments revealed a genetic circuit that controls the balance of transcription from two core promoter motifs, the TATA box and the downstream core promoter element (DPE). In this circuit, TBP activates TATA-dependent transcription and represses DPE-dependent transcription, whereas Mot1 and NC2 block TBP function and thus repress TATA-dependent transcription and activate DPE-dependent transcription. This regulatory circuit is likely to be one means by which biological networks can transmit transcriptional signals, such as those from DPE-specific and TATA-specific enhancers, via distinct pathways.

    View Publication Page
    09/01/08 | The loci of evolution: how predictable is genetic evolution?
    Stern DL, Orgogozo V
    Evolution. 2008 Sep;62(9):2155-77. doi: 10.1111/j.1558-5646.2008.00450.x

    Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis-regulatory, rather than the coding, regions of developmental genes. This "cis-regulatory hypothesis" has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis-regulatory hypothesis. We then test the empirical support for the cis-regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis-regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis-regulatory changes published annually is rapidly increasing. Above the species level, cis-regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis-regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question "Do coding or cis-regulatory mutations cause more phenotypic evolution?" hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.

    View Publication Page
    Truman LabRiddiford Lab
    08/22/08 | Developmental model of static allometry in holometabolous insects.
    Shingleton AW, Mirth CK, Bates PW
    Proceedings of the Royal Society B: Biological Sciences. 2008 Aug 22;275(1645):1875-85. doi: 10.1098/rspb.2008.0227

    The regulation of static allometry is a fundamental developmental process, yet little is understood of the mechanisms that ensure organs scale correctly across a range of body sizes. Recent studies have revealed the physiological and genetic mechanisms that control nutritional variation in the final body and organ size in holometabolous insects. The implications these mechanisms have for the regulation of static allometry is, however, unknown. Here, we formulate a mathematical description of the nutritional control of body and organ size in Drosophila melanogaster and use it to explore how the developmental regulators of size influence static allometry. The model suggests that the slope of nutritional static allometries, the ’allometric coefficient’, is controlled by the relative sensitivity of an organ’s growth rate to changes in nutrition, and the relative duration of development when nutrition affects an organ’s final size. The model also predicts that, in order to maintain correct scaling, sensitivity to changes in nutrition varies among organs, and within organs through time. We present experimental data that support these predictions. By revealing how specific physiological and genetic regulators of size influence allometry, the model serves to identify developmental processes upon which evolution may act to alter scaling relationships.

    View Publication Page
    Magee Lab
    08/15/08 | Altered synaptic and non-synaptic properties of CA1 pyramidal neurons in Kv4.2 knockout mice.
    Andrásfalvy BK, Makara JK, Johnston D, J.C. Magee
    The Journal of Physiology. 2008 Aug 15;586(16):3881-92. doi: 10.1113/jphysiol.2008.154336

    Back-propagating action potentials (bAPs) travelling from the soma to the dendrites of neurons are involved in various aspects of synaptic plasticity. The distance-dependent increase in Kv4.2-mediated A-type K(+) current along the apical dendrites of CA1 pyramidal cells (CA1 PCs) is responsible for the attenuation of bAP amplitude with distance from the soma. Genetic deletion of Kv4.2 reduced dendritic A-type K(+) current and increased the bAP amplitude in distal dendrites. Our previous studies revealed that the amplitude of unitary Schaffer collateral inputs increases with distance from the soma along the apical dendrites of CA1 PCs. We tested the hypothesis that the weight of distal synapses is dependent on dendritic Kv4.2 channels. We compared the amplitude and kinetics of mEPSCs at different locations on the main apical trunk of CA1 PCs from wild-type (WT) and Kv4.2 knockout (KO) mice. While wild-type mice showed normal distance-dependent scaling, it was missing in the Kv4.2 KO mice. We also tested whether there was an increase in inhibition in the Kv4.2 knockout, induced in an attempt to compensate for a non-specific increase in neuronal excitability (after-polarization duration and burst firing probability were increased in KO). Indeed, we found that the magnitude of the tonic GABA current increased in Kv4.2 KO mice by 53% and the amplitude of mIPSCs increased by 25%, as recorded at the soma. Our results suggest important roles for the dendritic K(+) channels in distance-dependent adjustment of synaptic strength as well as a primary role for tonic inhibition in the regulation of global synaptic strength and membrane excitability.

    View Publication Page