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1832 Janelia Publications

Showing 1741-1750 of 1832 results
06/01/09 | [Analysis on acupuncture literature in Science Citation Index (SCI) periodicals in 2007].
Gao L, Tian L, Guo Y
Zhongguo Zhen Jiu = Chinese Acupuncture & Moxibustion. 2009 Jun;29(6):504-7. doi: 10.1364/AO.50.001792

To grasp the international developing tendency of acupuncture research and provide some references for promoting acupuncture and moxibustion internationalization process, the articles about acupuncture in Science Citation Index (SCI) periodicals in 2007 were retrieved by adopting the retrieval tactics on line in combination with database searching. Results indicate that 257 articles about acupuncture had been retrived from the SCI Web databases. These articles were published in 125 journals respectively, most of which were Euramerican journals. Among these journals, the impact factor of the Journal of the American Medical Association (JAMA), 25. 547, is the highest one. It is shown that the impact factors of the SCI periodicals, in which acupuncture articles embodied are increased, the quality of these articles are improved obviously and the types of the articles are various in 2007, but there is obvious difference in the results of these studies due to the difference of experimental methods, the subjects of these experiments and acupuncture manipulations. Therefore, standardization of many problems arising from the researches on acupuncture is extremely imminent.

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06/01/09 | The ethomics era?
Reiser M
Nature Methods. 2009 Jun;6:413-4. doi: 10.1016/j.cub.2010.06.072

Applying modern machine-vision techniques to the study of animal behavior, two groups developed systems that quantify many aspects of the complex social behaviors of Drosophila melanogaster. These software tools will enable high-throughput screens that seek to uncover the cellular and molecular underpinnings of behavior.

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Eddy/Rivas Lab
05/15/09 | Infernal 1.0: inference of RNA alignments.
Nawrocki EP, Kolbe DL, Eddy SR
Bioinformatics. 2009 May 15;25:1335-7. doi: 10.1093/bioinformatics/btp157

SUMMARY: INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence alignments. AVAILABILITY: Source code, documentation and benchmark downloadable from http://infernal.janelia.org. INFERNAL is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.

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Eddy/Rivas Lab
05/15/09 | Local RNA structure alignment with incomplete sequence.
Kolbe DL, Eddy SR
Bioinformatics. 2009 May 15;25(10):1236-43. doi: 10.1093/bioinformatics/btp154

Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing.

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05/14/09 | Subcellular dynamics of type II PKA in neurons.
Zhong H, Sia G, Sato TR, Gray NW, Mao T, Khuchua Z, Huganir RL, Svoboda K
Neuron. 2009 May 14;62:363-74. doi: 10.1016/j.neuron.2009.03.013

Protein kinase A (PKA) plays multiple roles in neurons. The localization and specificity of PKA are largely controlled by A-kinase anchoring proteins (AKAPs). However, the dynamics of PKA in neurons and the roles of specific AKAPs are poorly understood. We imaged the distribution of type II PKA in hippocampal and cortical layer 2/3 pyramidal neurons in vitro and in vivo. PKA was concentrated in dendritic shafts compared to the soma, axons, and dendritic spines. This spatial distribution was imposed by the microtubule-binding protein MAP2, indicating that MAP2 is the dominant AKAP in neurons. Following cAMP elevation, catalytic subunits dissociated from the MAP2-tethered regulatory subunits and rapidly became enriched in nearby spines. The spatial gradient of type II PKA between dendritic shafts and spines was critical for the regulation of synaptic strength and long-term potentiation. Therefore, the localization and activity-dependent translocation of type II PKA are important determinants of PKA function.

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05/01/09 | Myosin-dependent targeting of transmembrane proteins to neuronal dendrites.
Lewis TL, Mao T, Svoboda K, Arnold DB
Nature Neuroscience. 2009 May;12(5):568-76. doi: 10.1038/nn.2318

The distinct electrical properties of axonal and dendritic membranes are largely a result of specific transport of vesicle-bound membrane proteins to each compartment. How this specificity arises is unclear because kinesin motors that transport vesicles cannot autonomously distinguish dendritically projecting microtubules from those projecting axonally. We hypothesized that interaction with a second motor might enable vesicles containing dendritic proteins to preferentially associate with dendritically projecting microtubules and avoid those that project to the axon. Here we show that in rat cortical neurons, localization of several distinct transmembrane proteins to dendrites is dependent on specific myosin motors and an intact actin network. Moreover, fusion with a myosin-binding domain from Melanophilin targeted Channelrhodopsin-2 specifically to the somatodendritic compartment of neurons in mice in vivo. Together, our results suggest that dendritic transmembrane proteins direct the vesicles in which they are transported to avoid the axonal compartment through interaction with myosin motors.

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Magee Lab
04/16/09 | Pathway interactions and synaptic plasticity in the dendritic tuft regions of CA1 pyramidal neurons.
Takahashi H, Magee JC
Neuron. 2009 Apr 16;62(1):102-11. doi: 10.1016/j.neuron.2009.03.007

Input comparison is thought to occur in many neuronal circuits, including the hippocampus, where functionally important interactions between the Schaffer collateral and perforant pathways have been hypothesized. We investigated this idea using multisite, whole-cell recordings and Ca2+ imaging and found that properly timed, repetitive stimulation of both pathways results in the generation of large plateau potentials in distal dendrites of CA1 pyramidal neurons. These dendritic plateau potentials produce widespread Ca2+ influx, large after-depolarizations, burst firing output, and long-term potentiation of perforant path synapses. Plateau duration is directly related to the strength and temporal overlap of pathway activation and involves back-propagating action potentials and both NMDA receptors and voltage-gated Ca2+ channels. Thus, the occurrence of highly correlated SC and PP input to CA1 is signaled by a dramatic change in output mode and an increase in input efficacy, all induced by a large plateau potential in the distal dendrites of CA1 pyramidal neurons.

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Riddiford Lab
04/01/09 | The molecular mechanisms of cuticular melanization: the ecdysone cascade leading to dopa decarboxylase expression in Manduca sexta.
Hiruma K, Riddiford LM
Insect Biochemistry and Molecular Biology. 2009 Apr;39(4):245-53. doi: 10.1016/j.ibmb.2009.01.008

Many insect developmental color changes are known to be regulated by both ecdysone and juvenile hormone. Yet the molecular mechanisms underlying this regulation have not been well understood. This review highlights the hormonal mechanisms involved in the regulation of two key enzymes [dopa decarboxylase (DDC) and phenoloxidase] necessary for insect cuticular melanization, and the molecular action of 20-hydroxyecdysone on various transcription factors leading to DDC expression at the end of a larval molt in Manduca sexta. In addition, the ecdysone cascade found in M. sexta is compared with that of other organisms.

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03/11/09 | Loss of sensitivity in an analog neural circuit.
Borghuis BG, Sterling P, Smith RG
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience. 2009 Mar 11;29:3045-58. doi: 10.1523/JNEUROSCI.5071-08.2009

A low-contrast spot that activates just one ganglion cell in the retina is detected in the spike train of the cell with about the same sensitivity as it is detected behaviorally. This is consistent with Barlow’s proposal that the ganglion cell and later stages of spiking neurons transfer information essentially without loss. Yet, when losses of sensitivity by all preneural factors are accounted for, predicted sensitivity near threshold is considerably greater than behavioral sensitivity, implying that somewhere in the brain information is lost. We hypothesized that the losses occur mainly in the retina, where graded signals are processed by analog circuits that transfer information at high rates and low metabolic cost. To test this, we constructed a model that included all preneural losses for an in vitro mammalian retina, and evaluated the model to predict sensitivity at the cone output. Recording graded responses postsynaptic to the cones (from the type A horizontal cell) and comparing to predicted preneural sensitivity, we found substantial loss of sensitivity (4.2-fold) across the first visual synapse. Recording spike responses from brisk-transient ganglion cells stimulated with the same spot, we found a similar loss (3.5-fold) across the second synapse. The total retinal loss approximated the known overall loss, supporting the hypothesis that from stimulus to perception, most loss near threshold is retinal.

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03/06/09 | Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.
Akerboom J, Rivera JD, Guilbe MM, Malavé EC, Hernandez HH, Tian L, Hires SA, Marvin JS, Looger LL, Schreiter ER
The Journal of Biological Chemistry. 2009 Mar 6;284:6455-64. doi: 10.1074/jbc.M807657200

The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca2+-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.

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