Flutter discrimination: neural codes,perception, memory and decision making

Recent studies combining psychophysical and neurophysiological experiments in behaving monkeys have provided new insights into how several cortical areas integrate efforts to solve a vibrotactile discrimination task. In particular, these studies have addressed how neural codes are related to perception, working memory and decision making in this model. The primary somatosensory cortex drives higher cortical areas where past and current sensory information are combined, such that a comparison of the two evolves into a behavioural decision. These and other observations in visual tasks indicate that decisions emerge from highly-distributed processes in which the details of a scheduled motor plan are gradually specified by sensory information.     

HIV-1 protease inhibitors with picomolar potency against PI-resistant HIV-1 by modification of the P1' substituent

Transposition of the pyridyl nitrogen from the P(3) substituent to the P(1)' substituent in HIV-1 protease inhibitors (PI) affords compounds such as 3 with an improved inhibitory profile against multiple P450 isoforms. These compounds also displayed increased potency, with 3 inhibiting viral spread (CIC(95)) at <8 nM for every strain of PI-resistant HIV-1 tested. The poor to modest bioavailability of these compounds may correlate in part to their aqueous solubility.     

Laying date and clutch size of Great Tits(Parus major) in the Mediterranean region: a comparison of four habitat types

Summary Laying data and clutch size of Great Tits were studied in four different habitats in eastern Spain: two holm oak(Quercus ilex) forests, at 500 and 900–950 m a.s.l., a zeen oak(Quercus faginea) forest, at 900–1100 m a.s.l., a pine(Pinus sylvestris) forest, at 1000–1050 m a.s.l., and orange(Citrus aurantium) plantations, at 30 m a.s.l. All sites were placed at about the same latitude (39–41°N), and all were studied during the same years (1992–95). Our results show that (1) laying date did not differ between the natural habitats at the same altitude (range of the means of yearly means 4–8 May); (2) within the same habitat type (holm oak forest) laying date was earlier at low altitude (30 Aprilvs. 8 May); (3) laying date was earlier in the orange plantations (21 April) than in natural habitats; (4) among natural habitats at the same altitude, clutch size decreased from zeen oak (mean of yearly means 7.3 eggs) to holm oak (7.0 eggs) to pine forests (6.4 eggs), though only the difference between zeen oak and pine forests was significant; (5) within the same habitat type (holm oak forest), the clutch size tended to be larger at high altitude (7.0vs. 5.9 eggs); and (6) clutch size in orange plantations (7.7 eggs) did not differ significantly from that of the zeen oak forest, but was larger than in the holm oak and pine forests. We discuss the effect of the habitat type on laying date and clutch size of Great Tits.

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Legedatum und Gelegegröße der Kohlmeise(Parus major) in mediterranen Gebieten: Ein Vergleich zwischen vier verschiedenen Biotopen

Zusammenfassung Legedatum und Gelegegröße der Kohlmeise wurden in vier unterschiedlichen Biotopen in Ostspanien untersucht: zwei Steineichenwälder(Quercus ilex) in 500 m und 900–950 mNN, ein Bergeichenwald(Quercus faginea) in 900–1100 mNN, ein Kiefernwald(Pinus sylvestris) in 1000–1050 mNN und eine Orangenpflanzung(Citrus aurantium) in 30 mNN. Alle fünf Gebiete lagen auf etwa demselben Breitengrad (39–41°N) und wurden 1992–1995 parallel untersucht.(1) Auf gleicher Meereshöhe unterscheidet sich der Legebeginn nicht zwischen den verschiedenen Waldbiotopen (im Mittel 4.–8. Mai). (2) Innerhalb desselben Biotoptyps (Steineichenwald) war der Legebeginn auf niedrigerer Meereshöhe früher als in höheren Lagen (30. April vs. 8. Mai). (3) Im Orangenhain wurde früher mit der Eiablage begonnen (21. April) als in den Waldbiotopen. (4) Auf gleicher Meereshöhe nahm die Gelegegröße vom Bergeichenwald (Mittelwert 7.3 Eier) über die Steineichenwälder (7,0 Eier) zum Kiefernwald hin ab (6.4 Eier), jedoch ist nur der Unterschied zwischen Bergeichenwald und Kiefernwald signifikant. (5) Innerhalb der Steineichenwälder besteht die Tendenz zu größerer Gelegegröße in den höheren Lagen (7.0 vs. 5.9 Eier). (6) Im Orangenhain war die Gelegegröße mit durchschnittlich 7.7 Eier ähnlich der im Bergeichenwald, aber größer als in den Steineichen- und Kiefernwälder.

     

Structural Organization of Virulence-Associated Plasmids of Yersinia pestis

The complete nucleotide sequence and gene organization of the three virulence plasmids from Yersinia pestis KIM5 were determined. Plasmid pPCP1 (9,610 bp) has a GC content of 45.3% and encodes two previously known virulence factors, an associated protein, and a single copy of IS100. Plasmid pCD1 (70,504 bp) has a GC content of 44.8%. It is known to encode a number of essential virulence determinants, regulatory functions, and a multiprotein secretory system comprising the low-calcium response stimulation that is shared with the other two Yersinia species pathogenic for humans (Y. pseudotuberculosis and Y. enterocolitica). A new pseudogene, which occurs as an intact gene in the Y. enterocolitica and Y. pseudotuberculosis-derived analogues, was found in pCD1. It corresponds to that encoding the lipoprotein YlpA. Several intact and partial insertion sequences and/or transposons were also found in pCD1, as well as six putative structural genes with high homology to proteins of unknown function in other yersiniae. The sequences of the genes involved in the replication of pCD1 are highly homologous to those of the cognate plasmids in Y. pseudotuberculosis and Y. enterocolitica, but their localization within the plasmid differs markedly from those of the latter. Plasmid pMT1 (100,984 bp) has a GC content of 50.2%. It possesses two copies of IS100, which are located 25 kb apart and in opposite orientations. Adjacent to one of these IS100 inserts is a partial copy of IS285. A single copy of an IS200-like element (recently named IS1541) was also located in pMT1. In addition to 5 previously described genes, such as murine toxin, capsule antigen, capsule anchoring protein, etc., 30 homologues to genes of several bacterial species were found in this plasmid, and another 44 open reading frames without homology to any known or hypothetical protein in the databases were predicted.     

Localisation of Ig heavy chain mRNA positive cells in Atlantic cod (Gadus morhuaL.) tissues; identified byin situhybridisation

Localisation of immunoglobulin heavy chain (IgH) producing cells was determined in sections from head kidney, spleen, thymus, gills, gut, skin, heart and liver from the Atlantic cod. In general, IgH mRNA positive cells were detected in all organs examined and were mainly located to the connective tissue surrounding the vascular system in these organs. In the head kidney and spleen, IgH mRNA positive cells appeared as single distributed cells or as dense clusters, whereas in the thymus only single distributed positive cells were observed. The percentage of Ig heavy chain mRNA positive (plasma) cells in the head kidney, spleen and thymus was estimated at about 1% of the total cell mass. The number of IgH mRNA positive cells was lower than this in all the other organs examined.     

Influence of Edaphic,Climatic, and Agronomic Factors on the Composition and Abundance of Nitrifying Microorganisms in the Rhizosphere of Commercial Olive Crops

The microbial ecology of the nitrogen cycle in agricultural soils is an issue of major interest. We hypothesized a major effect by farm management systems (mineral versus organic fertilizers) and a minor influence of soil texture and plant variety on the composition and abundance of microbial nitrifiers. We explored changes in composition (16S rRNA gene) of ammonia-oxidizing archaea (AOA), bacteria (AOB), and nitrite-oxidizing bacteria (NOB), and in abundance of AOA and AOB (qPCR of amoA genes) in the rhizosphere of 96 olive orchards differing in climatic conditions, agricultural practices, soil properties, and olive variety. Majority of archaea were 1.1b thaumarchaeota (soil crenarchaeotic group, SCG) closely related to the AOA genus Nitrososphaera. Most AOB (97%) were identical to Nitrosospira tenuis and most NOB (76%) were closely related to Nitrospira sp. Common factors shaping nitrifiers assemblage composition were pH, soil texture, and olive variety. AOB abundance was positively correlated with altitude, pH, and clay content, whereas AOA abundances showed significant relationships with organic nitrogen content and exchangeable K. The abundances of AOA differed significantly among soil textures and olive varieties, and those of AOB among soil management systems and olive varieties. Overall, we observed minor effects by orchard management system, soil cover crop practices, plantation age, or soil organic matter content, and major influence of soil texture, pH, and olive tree variety.     

Inferring Cetacean Population Densities from the Absolute Dynamic Topography of the Ocean in a Hierarchical Bayesian Framework

We inferred the population densities of blue whales (Balaenoptera musculus) and short-beaked common dolphins (Delphinus delphis) in the Northeast Pacific Ocean as functions of the water-column’s physical structure by implementing hierarchical models in a Bayesian framework. This approach allowed us to propagate the uncertainty of the field observations into the inference of species-habitat relationships and to generate spatially explicit population density predictions with reduced effects of sampling heterogeneity. Our hypothesis was that the large-scale spatial distributions of these two cetacean species respond primarily to ecological processes resulting from shoaling and outcropping of the pycnocline in regions of wind-forced upwelling and eddy-like circulation. Physically, these processes affect the thermodynamic balance of the water column, decreasing its volume and thus the height of the absolute dynamic topography (ADT). Biologically, they lead to elevated primary productivity and persistent aggregation of low-trophic-level prey. Unlike other remotely sensed variables, ADT provides information about the structure of the entire water column and it is also routinely measured at high spatial-temporal resolution by satellite altimeters with uniform global coverage. Our models provide spatially explicit population density predictions for both species, even in areas where the pycnocline shoals but does not outcrop (e.g. the Costa Rica Dome and the North Equatorial Countercurrent thermocline ridge). Interannual variations in distribution during El Niño anomalies suggest that the population density of both species decreases dramatically in the Equatorial Cold Tongue and the Costa Rica Dome, and that their distributions retract to particular areas that remain productive, such as the more oceanic waters in the central California Current System, the northern Gulf of California, the North Equatorial Countercurrent thermocline ridge, and the more southern portion of the Humboldt Current System. We posit that such reductions in available foraging habitats during climatic disturbances could incur high energetic costs on these populations, ultimately affecting individual fitness and survival.     

LUMOS - A Sensitive and Reliable Optode System for Measuring Dissolved Oxygen in the Nanomolar Range

Most commercially available optical oxygen sensors target the measuring range of 300 to 2 μmol L^-1. However these are not suitable for investigating the nanomolar range which is relevant for many important environmental situations. We therefore developed a miniaturized phase fluorimeter based measurement system called the LUMOS (Luminescence Measuring Oxygen Sensor). It consists of a readout device and specialized “sensing chemistry” that relies on commercially available components. The sensor material is based on palladium(II)-5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorphenyl)-porphyrin embedded in a Hyflon AD 60 polymer matrix and has a K_SV of 6.25 x 10^-3 ppmv^-1. The applicable measurement range is from 1000 nM down to a detection limit of 0.5 nM. A second sensor material based on the platinum(II) analogue of the porphyrin is spectrally compatible with the readout device and has a measurement range of 20 μM down to 10 nM. The LUMOS device is a dedicated system optimized for a high signal to noise ratio, but in principle any phase flourimeter can be adapted to act as a readout device for the highly sensitive and robust sensing chemistry. Vise versa, the LUMOS fluorimeter can be used for read out of less sensitive optical oxygen sensors based on the same or similar indicator dyes, for example for monitoring oxygen at physiological conditions. The presented sensor system exhibits lower noise, higher resolution and higher sensitivity than the electrochemical STOX sensor previously used to measure nanomolar oxygen concentrations. Oxygen contamination in common sample containers has been investigated and microbial or enzymatic oxygen consumption at nanomolar concentrations is presented.