High-throughput gene discovery in the rat

The rat is an important animal model for human diseases and is widely used in physiology. In this article we present a new strategy for gene discovery based on the production of ESTs from serially subtracted and normalized cDNA libraries, and we describe its application for the development of a comprehensive nonredundant collection of rat ESTs. Our new strategy appears to yield substantially more EST clusters per ESTs sequenced than do previous approaches that did not use serial subtraction. However, multiple rounds of library subtraction resulted in high frequencies of otherwise rare internally primed cDNAs, defining the limits of this powerful approach. To date, we have generated >200,000 3′ ESTs from >100 cDNA libraries representing a wide range of tissues and developmental stages of the laboratory rat. Most importantly, we have contributed to ∼50,000 rat UniGene clusters. We have identified, arrayed, and derived 5′ ESTs from >30,000 unique rat cDNA clones. Complete information, including radiation hybrid mapping data, is also maintained locally at http://genome.uiowa.edu/clcg.html. All of the sequences described in this article have been submitted to the dbEST division of the NCBI

Internal wave-driven transport of fluid away from the boundary of a lake

A field experiment was conducted to study transport of fluid from the boundary to the interior of a lake. Tracking of a tracer injected into the metalimnion was combined with measurements of meteorological forcing, internal waves, and temperature microstructure. Seiches of vertical mode 2 and horizontal modes 1 and 2 were initiated after a wind event, and the tracer moved 950 m into the interior after 29.2 h. Four potential mechanisms for spreading of the tracer from the boundary to the interior were considered: intrusions from boundary mixing, horizontal dispersion, advection by seiches, and advection and dispersion driven by internal waves. Some evidence of boundary mixing was observed 0.5 h before the dye injection, when the speed of seiche-driven currents was large, but a model of an intrusion driven by steady input overpredicted the propagation distance by a factor of about two. A one-dimensional model with only dispersion yielded a dispersion coefficient of 0.8 m(2) s(-1), and a one-dimensional model with only advection caused by internal waves predicted the position of the peak concentration and a change in longitudinal variance that was 60% of the measured change. Estimates of dispersion caused by the interaction of vertical diffusion with velocity gradients in the internal wave field are large enough to explain the rest of the spreading and suggest that the transport can be modeled as wave-driven advection and dispersion

Internal wave-driven transport of fluid away from the boundary of a lake

A field experiment was conducted to study transport of fluid from the boundary to the interior of a lake. Tracking of a tracer injected into the metalimnion was combined with measurements of meteorological forcing, internal waves, and temperature microstructure. Seiches of vertical mode 2 and horizontal modes 1 and 2 were initiated after a wind event, and the tracer moved 950 m into the interior after 29.2 h. Four potential mechanisms for spreading of the tracer from the boundary to the interior were considered: intrusions from boundary mixing, horizontal dispersion, advection by seiches, and advection and dispersion driven by internal waves. Some evidence of boundary mixing was observed 0.5 h before the dye injection, when the speed of seiche-driven currents was large, but a model of an intrusion driven by steady input overpredicted the propagation distance by a factor of about two. A one-dimensional model with only dispersion yielded a dispersion coefficient of 0.8 m2 s−1, and a one-dimensional model with only advection caused by internal waves predicted the position of the peak concentration and a change in longitudinal variance that was 60% of the measured change. Estimates of dispersion caused by the interaction of vertical diffusion with velocity gradients in the internal wave field are large enough to explain the rest of the spreading and suggest that the transport can be modeled as wave-driven advection and dispersion.This article is from Limnology and Oceanography 58 (2013): 429–442, doi:10.4319/lo.2013.58.2.0429. Posted with permission.</p

Internal wave-driven transport of fluid away from the boundary of a lake

A field experiment was conducted to study transport of fluid from the boundary to the interior of a lake. Tracking of a tracer injected into the metalimnion was combined with measurements of meteorological forcing, internal waves, and temperature microstructure. Seiches of vertical mode 2 and horizontal modes 1 and 2 were initiated after a wind event, and the tracer moved 950 m into the interior after 29.2 h. Four potential mechanisms for spreading of the tracer from the boundary to the interior were considered: intrusions from boundary mixing, horizontal dispersion, advection by seiches, and advection and dispersion driven by internal waves. Some evidence of boundary mixing was observed 0.5 h before the dye injection, when the speed of seiche-driven currents was large, but a model of an intrusion driven by steady input overpredicted the propagation distance by a factor of about two. A one-dimensional model with only dispersion yielded a dispersion coefficient of 0.8 m(2) s(-1), and a one-dimensional model with only advection caused by internal waves predicted the position of the peak concentration and a change in longitudinal variance that was 60% of the measured change. Estimates of dispersion caused by the interaction of vertical diffusion with velocity gradients in the internal wave field are large enough to explain the rest of the spreading and suggest that the transport can be modeled as wave-driven advection and dispersion

1274 Full-Open Reading Frames of Transcripts Expressed in the Developing Mouse Nervous System

As part of the trans-National Institutes of Health (NIH) Mouse Brain Molecular Anatomy Project (BMAP), and in close coordination with the NIH Mammalian Gene Collection Program (MGC), we initiated a large-scale project to clone, identify, and sequence the complete open reading frame (ORF) of transcripts expressed in the developing mouse nervous system. Here we report the analysis of the ORF sequence of 1274 cDNAs, obtained from 47 full-length-enriched cDNA libraries, constructed by using a novel approach, herein described. cDNA libraries were derived from size-fractionated cytoplasmic mRNA isolated from brain and eye tissues obtained at several embryonic stages and postnatal days. Altogether, including the full-ORF MGC sequences derived from these libraries by the MGC sequencing team, NIH_BMAP full-ORF sequences correspond to ∼20% of all transcripts currently represented in mouse MGC. We show that NIH_BMAP clones comprise 68% of mouse MGC cDNAs ≥5 kb, and 54% of those ≥4 kb, as of March 15, 2004. Importantly, we identified transcripts, among the 1274 full-ORF sequences, that are exclusively or predominantly expressed in brain and eye tissues, many of which encode yet uncharacterized proteins