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Cold Spring Harbor, NY, United States

Agency: GTR | Branch: MRC | Program: | Phase: Intramural | Award Amount: 4.37M | Year: 2009

The brain has evolved to detect and process sensory information to produce appropriate behavioural outputs. To achieve this, the incoming sensory information must be placed in context. For example, the location of a sound or odor source can only be ascertained if the brain has an internal representation of the direction of the head in space, a process that relies on the coding properties of individual neurons and neuronal circuits. We are therefore investigating several aspects of the cellular and network mechanisms underlying sensory computation. In the olfactory bulb, a region of brain that processes odor information, we will determine whether the transmission of signals between specific subsets of connected cells influences a neurons intrinsic physiological and coding properties. Secondly, by recording large-scale network activity in the intact animal during rotation we are investigating how large populations of interconnected neurons use information from the vestibular system to encode the velocity and the direction of body motion.

Kawahara Y.,Japan National Institute of Agrobiological Science | de la Bastide M.,Cold Spring Harbor Laboratory CSHL | Hamilton J.P.,Michigan State University | Kanamori H.,Japan National Institute of Agrobiological Science | And 20 more authors.

Background: Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results: The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/ deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions: A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. Source

Baslan T.,State University of New York at Stony Brook | Baslan T.,Cold Spring Harbor Laboratory CSHL | Hicks J.,Cold Spring Harbor Laboratory CSHL
Current Opinion in Genetics and Development

Biological phenotype is the output of complex interactions between heterogeneous cells within a specified niche. These interactions are tightly governed and regulated by the genetic, epigenetic, and transcriptional states of single cells, with deregulation of these states resulting in disease. As such, genome wide single cell investigations are bound to enhance our knowledge of the underlying principles that govern biological systems. Recent technological advances have enabled such investigations in the form of single-cell sequencing. Here, we review the most recent developments in genome wide profiling of single cells, discuss some of the novel biological observations gleaned by such investigations, and touch upon the promise of single cell sequencing in unraveling biological systems. © 2014 Elsevier Ltd. Source

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