Main Menu (Mobile)- Block

Main Menu - Block

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


facetapi-Q2b17qCsTdECvJIqZJgYMaGsr8vANl1n | block

Associated Lab

facetapi-W9JlIB1X0bjs93n1Alu3wHJQTTgDCBGe | block
facetapi-PV5lg7xuz68EAY8eakJzrcmwtdGEnxR0 | block
facetapi-021SKYQnqXW6ODq5W5dPAFEDBaEJubhN | block

Type of Publication

general_search_page-panel_pane_1 | views_panes

1416 Publications

Showing 1321-1330 of 1416 results
Your Criteria:
    03/01/95 | Strain-dependent variation in carbon source regulation of nucleus-encoded mitochondrial proteins of Saccharomyces cerevisiae.
    Brown TA, Trumpower BL
    Journal of Bacteriology. 1995 Mar;177(5):1380-2

    Nuclear genes encoding mitochondrial proteins are regulated by carbon source with significant heterogeneity among four Saccharomyces cerevisiae strains. This strain-dependent variation is seen both in respiratory capacity of the cells and in the expression of beta-galactosidase reporter fusions to the promoters of CYB2, CYC1, CYC3, MnSOD, and RPO41.

    View Publication Page
    02/23/95 | Growth and differentiation in the Drosophila eye coordinated by hedgehog.
    Heberlein U, Singh CM, Luk AY, Donohoe TJ
    Nature. 1995 Feb 23;373(6516):709-11. doi: 10.1038/373709a0

    Differentiation of the Drosophila retina is asynchronous: it starts at the posterior margin of the eye imaginal disc and progresses anteriorly over two days. During this time the disc continues to grow, increasing in size by approximately eightfold. An indentation in the epithelium, the morphogenetic furrow, marks the front edge of the differentiation wave. Anterior progression of the furrow is thought to be driven by signals emanating from differentiating photoreceptor cells in the posterior eye disc. A good candidate for such a signal is the product of the hedgehog (hh) gene; it is expressed, and presumably secreted, by differentiating photoreceptors and its function is required for continued furrow movement. Here we show that ectopic expression of hedgehog sets in motion ectopic furrows in the anterior eye disc. In addition to changes in cell shape, these ectopic furrows are associated with a tightly orchestrated series of events, including proliferation, cell cycle synchronization and pattern formation, that parallel normal furrow progression. We propose that the morphogenetic furrow coincides with a transient boundary that coordinates growth and differentiation of the eye disc, and that hedgehog is necessary and sufficient to propagate this boundary across the epithelium.

    View Publication Page
    02/01/95 | Proposed method for molecular optical imaging. (With commentary)
    Betzig E
    Optics Letters. 1995 Feb 1;20:237-9

    We can resolve multiple discrete features within a focal region of m spatial dimensions by first isolating each on the basis of n >/= 1 unique optical characteristics and then measuring their relative spatial coordinates. The minimum acceptable separation between features depends on the point-spread function in the (m + n)d-dimensional space formed by the spatial coordinates and the optical parameters, whereas the absolute spatial resolution is determined by the accuracy to which the coordinates can be measured. Estimates of each suggest that near-field fluorescence excitation microscopy/spectroscopy with molecular sensitivity and spatial resolution is possible.

    Commentary: Inspired by my earlier work (see below) in single molecule imaging and the isolation of multiple exciton recombination sites within a single probe volume, here I proposed the principle which would eventually lead to PALM. Indeed, all methods of localization microscopy, including PALM, fPALM, PALMIRA, STORM, dSTORM, PAINT, GSDIM, etc. are specific embodiments of the general principle of single molecule isolation and localization I introduced here.

    View Publication Page

    We describe the life cycle and general biology of the tropical cerataphidine aphid Cerataphis fransseni. We demonstrate that this aphid migrates between trees of Styrax benzoin and various species of palms; palm-feeding populations have previously been known as C. variabilis and C. palmae, which now become synonyms of C. fransseni. On S. benzoin the fundatrix induces a relatively simple gall which can contain >6000 aphids at maturity with a large number of reproductively sterile soldiers that protect the gall from predators. These galls are apparently produced throughout the year. Colonies on the secondary host plants, palms, are apparently obligately tended by ants whereas colonies within galls on Styrax are never tended by ants. We discuss the life cycle of this tropical aphid with respect to hypotheses for the evolution and maintenance of host alternation.

    View Publication Page
    01/15/95 | Dendritic glutamate receptor channels in rat hippocampal CA3 and CA1 pyramidal neurons.
    Spruston N, Jonas P, Sakmann B
    J Physiol. 1995 Jan 15;482 ( Pt 2):325-52

    1. Properties of dendritic glutamate receptor (GluR) channels were investigated using fast application of glutamate to outside-out membrane patches isolated from the apical dendrites of CA3 and CA1 pyramidal neurons in rat hippocampal slices. CA3 patches were formed (15-76 microns from the soma) in the region of mossy fibre (MF) synapses, and CA1 patches (25-174 microns from the soma) in the region of Schaffer collateral (SC) innervation. 2. Dual-component responses consisting of a rapidly rising and decaying component followed by a second, substantially slower, component were elicited by 1 ms pulses of 1 mM glutamate in the presence of 10 microM glycine and absence of external Mg2+. The fast component was selectively blocked by 2-5 microM 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) and the slow component by 30 microM D-2-amino-5-phosphonopentanoic acid (D-AP5), suggesting that the fast and slow components were mediated by the GluR channels of the L-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) and NMDA type, respectively. The peak amplitude ratio of the NMDA to AMPA receptor-mediated components varied between 0.03 and 0.62 in patches from both CA3 and CA1 dendrites. Patches lacking either component were rarely observed. 3. The peak current-voltage (I-V) relationship of the fast component was almost linear, whereas the I-V relationship of the slow component showed a region of negative slope in the presence of 1 mM external Mg2+. The reversal potential for both components was close to 0 mV. 4. Kainate-preferring GluR channels did not contribute appreciably to the response to glutamate. The responses to 100 ms pulses of 1 mM glutamate were mimicked by application of 1 mM AMPA, whereas 1 mM kainate produced much smaller, weakly desensitizing currents. This suggests that the fast component is primarily mediated by the action of glutamate on AMPA-preferring receptors. 5. The mean elementary conductance of AMPA receptor channels was about 10 pS, as estimated by non-stationary fluctuation analysis. The permeability of these channels to Ca2+ was low (approximately 5% of the permeability to Cs+). 6. The elementary conductance of NMDA receptor channels was larger, with a main conductance state of about 45 pS. These channels were 3.6 times more permeable to Ca2+ than to Cs+.(ABSTRACT TRUNCATED AT 400 WORDS)

    View Publication Page
    01/01/95 | A persistent RNA-DNA hybrid is formed during transcription at a phylogenetically conserved mitochondrial DNA sequence.
    Xu B, Clayton DA
    Molecular and Cellular Biology. 1995 Jan;15(1):580-9. doi: 10.1101/gad.1352105

    Critical features of the mitochondrial leading-strand DNA replication origin are conserved from Saccharomyces cerevisiae to humans. These include a promoter and a downstream GC-rich sequence block (CSBII) that encodes rGs within the primer RNA. During in vitro transcription at yeast mitochondrial replication origins, there is stable and persistent RNA-DNA hybrid formation that begins at the 5’ end of the rG region. The short rG-dC sequence is the necessary and sufficient nucleic acid element for establishing stable hybrids, and the presence of rGs within the RNA strand of the RNA-DNA hybrid is required. The efficiency of hybrid formation depends on the length of RNA synthesized 5’ to CSBII and the type of RNA polymerase employed. Once made, the RNA strand of an RNA-DNA hybrid can serve as an effective primer for mitochondrial DNA polymerase. These results reveal a new mechanism for persistent RNA-DNA hybrid formation and suggest a step in priming mitochondrial DNA replication that requires both mitochondrial RNA polymerase and an rG-dC sequence-specific event to form an extensive RNA-DNA hybrid.

    View Publication Page
    12/01/94 | A test of geometric hypotheses for soldier investment patterns in the gall producing tropical aphidCerataphis fransseni (Homoptera, Hormaphididae)
    D. L. Stern , S. Aoki , U. Kurosu
    Insectes sociaux;41(4):457-460. doi: 10.1007/BF01240648

    The gall-forming aphidCerataphis fransseni produces soldiers that defend against predators. Soldiers are produced soon after colony foundation and the number of soldiers increases nonlinearly during colony growth. The number of soldiers scales to the square-root of the number of non-soldiers and linearly to the surface area of the gall. This suggests that soldiers are produced to defend an area, for example the perimeter of the colony or the surface of the gall, rather than individual aphids.

    View Publication Page
    12/01/94 | Neuropeptide induction of cyclic GMP increases in the insect CNS: resolution at the level of single identifiable neurons.
    Ewer J, de Vente J, Truman JW
    The Journal of Neuroscience: The Official Journal of the Society for Neuroscience. 1994 Dec;14(12):7704-12

    In insects, the neuropeptide eclosion hormone (EH) acts on the CNS to evoke the stereotyped behaviors that cause ecdysis, the shedding of the cuticle at the end of each molt. Concomitantly, EH induces an increase in cyclic GMP (cGMP). Using antibodies against this second messenger, we show that this increase is confined to a network of 50 peptidergic neurons distributed throughout the CNS. Increases appeared 30 min after EH treatment, spread rapidly throughout these neurons, and were extremely long lived. We show that this response is synaptically driven, and does not involve the soluble, nitric oxide (NO)-activated, guanylate cyclase. Stereotyped variations in the duration of the cGMP response among neurons suggest a role in coordinating responses having different latencies and durations.

    View Publication Page
    11/01/94 | A sublinear algorithm for approximate keyword matching.
    Myers E
    Algorithmica. 1994 Nov;12(4-5):345-74

    Given a relatively short query stringW of lengthP, a long subject stringA of lengthN, and a thresholdD, theapproximate keyword search problem is to find all substrings ofA that align withW with not more than D insertions, deletions, and mismatches. In typical applications, such as searching a DNA sequence database, the size of the “database”A is much larger than that of the queryW, e.g.,N is on the order of millions or billions andP is a hundred to a thousand. In this paper we present an algorithm that given a precomputedindex of the databaseA, finds rare matches in time that issublinear inN, i.e.,N c for somec<1. The sequenceA must be overa. finite alphabet σ. More precisely, our algorithm requires 0(DN pow(ɛ)  logN) expected-time where ɛ=D/P is the maximum number of differences as a percentage of query length, and pow(ɛ) is an increasing and concave function that is 0 when ɛ=0. Thus the algorithm is superior to current O(DN) algorithms when ɛ is small enough to guarantee that pow(ɛ) < 1. As seen in the paper, this is true for a wide range of ɛ, e.g., ɛ. up to 33% for DNA sequences (¦⌆¦=4) and 56% for proteins sequences (¦⌆¦=20). In preliminary practical experiments, the approach gives a 50-to 500-fold improvement over previous algorithms for prolems of interest in molecular biology.

    View Publication Page
    Tjian LabRubin Lab
    07/15/94 | The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway.
    O’Neill EM, Rebay I, Tjian R, Rubin GM
    Cell. 1994 Jul 15;78(1):137-47. doi: 10.1186/gb-2007-8-7-r145

    We show that the activities of two Ets-related transcription factors required for normal eye development in Drosophila, pointed and yan, are regulated by the Ras1/MAPK pathway. The pointed gene codes for two related proteins, and we show that one form is a constitutive activator of transcription, while the activity of the other form is stimulated by the Ras1/MAPK pathway. Mutation of the single consensus MAPK phosphorylation site in the second form abrogates this responsiveness. yan is a negative regulator of photoreceptor determination, and genetic data suggest that it acts as an antagonist of Ras1. We demonstrate that yan can repress transcription and that this repression activity is negatively regulated by the Ras1/MAPK signal, most likely through direct phosphorylation of yan by MAPK.

    View Publication Page