Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.     

Evolutionary origins of members of a superfamily of integral membrane cytochrome c biogenesis proteins

We have analyzed the relationships of homologues of the Escherichia coli CcmC protein for probable topological features and evolutionary relationships. We present bioinformatic evidence suggesting that the integral membrane proteins CcmC (E. coli; cytochrome c biogenesis System I), CcmF (E. coli; cytochrome c biogenesis System I) and ResC (Bacillus subtilis; cytochrome c biogenesis System II) are all related. Though the molecular functions of these proteins have not been fully described, they appear to be involved in the provision of heme to c-type cytochromes, and so we have named them the putative Heme Handling Protein (HHP) family (TC #9.B.14). Members of this family exhibit 6, 8, 10, 11, 13 or 15 putative transmembrane segments (TMSs). We show that intragenic triplication of a 2 TMS element gave rise to a protein with a 6 TMS topology, exemplified by CcmC. This basic 6 TMS unit then gave rise to two distinct types of proteins with 8 TMSs, exemplified by ResC and the archaeal CcmC, and these further underwent fusional or insertional events yielding proteins with 10, 11 and 13 TMSs (ResC homologues) as well as 15 TMSs (CcmF homologues). Specific evolutionary pathways taken are proposed. This work provides the first evidence for the pathway of appearance of distantly related proteins required for post-translational maturation of c-type cytochromes in bacteria, plants, protozoans and archaea.     

Reinstatement of short-latency responses after asymptotic Pavlovian conditioning training by the presentation of an extraneous stimulus

The purpose of this study was to examine whether the progressive disappearance of short-latency conditioned responses, or inhibition of delay, observed in Pavlovian conditioning with long inter-stimulus intervals, could be reverted by the presentation of a novel stimulus. In one experiment, two groups of rabbits received extensive training with a short (250 ms) or a long (1500 ms) tone that overlapped and terminated with a periorbital shock unconditioned stimulus. After training, the presentation of an extraneous stimulus prior to tone onset produced a reinstatement of short latency CRs in the group trained with the long CS, but did not affect CR latency in the group trained with the short CS. This finding is consistent with Pavlov's (1927) view that conditioning with long conditioned stimuli involves the acquisition of response tendencies in the early portion of the stimulus that are subsequently suppressed by the development of an inhibitory process.     

Canopy height variation and environmental heterogeneity in the tropical dry forests of coastal Oaxaca,Mexico

Despite its importance for carbon storage and other ecosystem functions, the variation in vegetation canopy height is not yet well understood. We examined the relationship between this community attribute and environmental heterogeneity in a tropical dry forest of southern Mexico. We sampled vegetation in 15 sites along a 100‐km coastal stretch of Oaxaca State, and measured the heights of all woody plants (excluding lianas). The majority of the ca. 4000 individuals recorded concentrated in the 4–8 m height range. We defined three plant sets to describe overall community canopy height at each site: a set including all plants, a set made up by the tallest plants representing 10 percent of all individuals, and a set comprising the 10 tallest plants. For each site we computed maximum height and the mean and median heights of the three sets. Significant collinearity was observed between the seven resulting height variables, but null distributions constructed through bootstrap revealed their different behaviors as functions of species richness and density of individuals. Through linear modeling and a model selection procedure, we identified 21 models that best described the variation in canopy height variables. These models pointed out to soil (measured as PC1 of a principal component analysis performed on 10 soil variables), water stress, and elevation as the main drivers of canopy height variation in the region. In the event of increasing water stress resulting from global climate change, the studied tropical dry forests could become shorter and thus decrease their carbon storage potential.     

Derivatives of characiol,macrocyclic diterpene esters of the jatrophane type from Euphorbia characias

Eight non-irritant macrocyclic diterpene esters of the jatrophane type were obtained from an irritant acetone extract of latex and from an irritant methanol extract of roots of Euphorbia characias. They were shown to be diesters of the new parent alcohols characiol, characiol-5β,6β-oxide and 5β-hydroxyisocharaciol and pentaesters of 2,5β,8-trihydroxyisocharaciol.     

Stimulus representation in SOP: II. An application to inhibition of delay

The componential extension of SOP accounts for conditioned response (CR) timing in Pavlovian conditioning by assuming that learning accrues with relative independence to stimulus elements that are differentially occasioned during the duration of the conditioned stimulus (CS). SOP, using a competitive learning rule and the assumption that temporal learning emerges via resolution of what is equivalent to an "AX+BX-" discrimination, predicts a progressive increase in the latency of the CR over training, or what Pavlov refer to as "inhibition of delay." Other componential models, which use noncompetitive learning rules, do not predict inhibition of delay. Either type of model makes the prediction indicated, independently of the length of the CS-unconditioned stimulus (US) interval. We report two experiments that demonstrated inhibition of delay when rabbits were trained with relatively long, but not with short, CS-US intervals. To account for this divergence, we assumed that the SOP stimulus trace involves two kinds of elements, some with a temporally distributed pattern of activity over the duration of the CS duration, and some with a randomly distributed pattern. This stimulus representation, not only allows for inhibition of delay with long but not short CS-US intervals, but in combination with SOP's performance rule deduces CR's with "Weber variability."