Cloning and expression pattern of vat-1 homolog gene in zebrafish

The VAT-1 protein is present in the electric organ of marine rays where it is suggested to play a central role in nerve signal transmission. VAT-1 homolog protein was also identified in mouse and human but its function remains to be determined. We have investigated VAT-1 homolog in zebrafish Danio rerio since it is an excellent model amenable to the combination of genetic, molecular and embryological studies. Amino acid sequence analysis shows that the zebrafish VAT-1 homolog shares approximately 51-61% identity with the electric ray, mouse, and human counterparts. By in situ hybridization, vat-1 homolog mRNA is first observed in the trigeminal nuclei at the 8-somite stage. At 20-somite stage, vat-1 homolog is detected in the brain, namely in primary clusters of neurons, in the epiphysis and in the hindbrain. vat-1 homolog is also present in the neural tube but this expression disappears after 72 h post-fertilization. At 24 h post-fertilization, vat-1 homolog starts to be expressed in the developing gut. At later stages, vat-1 homolog is present throughout the brain, appears in the maturing retina and the pharyngeal cavity.     

Cerebral metabolism during upper and lower body exercise.

When continuation of exercise calls for a "will," the cerebral metabolic ratio of O2 to (glucose + lactate) decreases, with the largest reduction (30-50%) at exhaustion. Because a larger effort is required to exercise with the arms than with the legs, we tested the hypothesis that the reduction in the cerebral metabolic ratio would become more pronounced during arm cranking than during leg exercise. The cerebral arterial-venous differences for blood-gas variables, glucose, and lactate were evaluated in two groups of eight subjects during exhaustive arm cranking and leg exercise. During leg exercise, exhaustion was elicited after 25 +/- 6 (SE) min, and the cerebral metabolic ratio was reduced from 5.6 +/- 0.2 to 3.5 +/- 0.2 after 10 min and to 3.3 +/- 0.3 at exhaustion (P < 0.05). Arm cranking lasted for 35 +/- 4 min and likewise decreased the cerebral metabolic ratio after 10 min (from 6.7 +/- 0.4 to 5.0 +/- 0.3), but the nadir at exhaustion was only 4.7 +/- 0.4, i.e., higher than during leg exercise (P < 0.05). The results demonstrate that exercise decreases the cerebral metabolic ratio when a conscious effort is required, irrespective of the muscle groups engaged. However, the comparatively small reduction in the cerebral metabolic ratio during arm cranking suggests that it is influenced by the exercise paradigm.     

Array-A-Lizer: A serial DNA microarray quality analyzer

Background  

The proliferate nature of DNA microarray results have made it necessary to implement a uniform and quick quality control of experimental results to ensure the consistency of data across multiple experiments prior to actual data analysis.     

Association with membrane protrusions makes ErbB2 an internalization-resistant receptor

In contrast to the epidermal growth factor (EGF) receptor, ErbB2 is known to remain at the plasma membrane after ligand binding and dimerization. However, why ErbB2 is not efficiently down-regulated has remained elusive. Basically, two possibilities exist: ErbB2 is internalization resistant or it is efficiently recycled after internalization. By a combination of confocal microscopy, immunogold labeling electron microscopy, and biochemical techniques we show that ErbB2 is preferentially associated with membrane protrusions. Moreover, it is efficiently excluded from clathrin-coated pits and is not seen in transferrin receptor-containing endosomes. This pattern is not changed after binding of EGF, heregulin, or herceptin. The exclusion from coated pits is so pronounced that it cannot just be explained by lack of an internalization signal. Although ErbB2 is a raft-associated protein, the localization of ErbB2 to protrusions is not a result of raft binding. Also, an intact actin cytoskeleton is not required for keeping ErbB2 away from coated pits. However, after efficient cross-linking, ErbB2 is removed from protrusions to occur on the bulk membrane, in coated pits, and in endosomes. These data show that ErbB2 is a remarkably internalization-resistant receptor and suggest that the mechanism underlying the firm association of ErbB2 with protrusions also is the reason for this resistance.     

Functional consequences of alterations to Ile279, Ile283, Glu284, His285, Phe286, and His288 in the NH2-terminal part of transmembrane helix M3 of the Na+,K(+)-ATPase

Mutations Ile279 --> Ala, Ile283 --> Ala, Glu284 --> Ala, His285 --> Ala, His285 --> Lys, His285 --> Glu, Phe286 --> Ala, and His288 --> Ala in transmembrane helix M3 of the Na+,K(+)-ATPase were studied. Except for His285 --> Ala, these mutations were compatible with cell viability, permitting analysis of their effects on the overall and partial reactions of the Na+,K(+)-transport cycle. In Ile279 --> Ala and Ile283 --> Ala, the E1 form accumulated, whereas in His285 --> Lys and His285 --> Glu, E1P accumulated. Phe286 --> Ala displaced the conformational equilibria of dephosphoenzyme and phosphoenzyme in parallel in favor of E2 and E2P, respectively, and showed a unique enhancement of the E1P --> E2P transition rate. These effects suggest that M3 undergoes significant rearrangements in relation to E1-E2 and E1P-E2P conformational changes. Because the E1-E2 and E1P-E2P conformational equilibria were differentially affected by some of the mutations, the phosphorylated conformations seem to differ significantly from the dephospho forms in the M3 region. Mutation of His285 furthermore increased the Na(+)-activated ATPase activity in the absence of K+ ("Na(+)-ATPase activity"). Ile279 --> Ala, Ile283 --> Ala, and His288 --> Ala showed reduced Na+ affinity of the E1 form. The rate of Na(+)-activated phosphorylation from ATP was reduced in Ile279 --> Ala and Ile283 --> Ala, and these mutants showed evidence similar to Glu329 --> Gln of destabilization of the Na(+)-occluded state.     

Microbial diversity in ikaite tufa columns: an alkaline,cold ecological niche in Greenland

Ikaite tufa columns from the Ikka Fjord in south-western Greenland constitute a natural, stable environment at low temperature and with a pH ranging from neutral at the exterior to very alkaline (pH 10.4) at the interior of the column. Phylogenetic analysis of culturable organisms revealed ten different isolates representing three of the major bacterial divisions. Nine of the isolates showed 94-99% similarity to known sequences, whereas one isolate displayed a low degree of similarity (less than 90%) to a Cyclobacterium species. Seven of the isolates were shown to be cold active alkaliphiles, whereas three isolates showed optimal growth at neutral pH. Phylogenetic analysis of DNA isolated directly from the ikaite material demonstrated the presence of a microbial flora more diverse than the culturable isolates. Whereas approximately half of the phylotypes showed 90-99% similarity to known meso- or thermophilic alkaliphiles, the rest of the sequences displayed less than 90% similarity when compared to known 16S rRNA gene sequences in databases. Thus, in the present paper, we demonstrate that ikaite columns that host a specialized macroscopic flora and fauna also contain a unique, cold active, alkaliphilic microflora.     

EVIDENCE FOR IMPACTS OF NONINDIGENOUS MACROALGAE: A META‐ANALYSIS OF EXPERIMENTAL FIELD STUDIES1

Invasions by nonindigenous macroalgal species (NIMS) potentially cause severe impacts on native species. We conducted a meta‐analysis of 18 field‐based manipulative experiments to quantify the direction and magnitude of impacts (Hedges effect size d, hereafter ES). We found significant small‐to‐medium negative effects on “macrophyte abundance” (cover, biomass of native taxa; ES_cumulative = ?0.30) and medium‐to‐large negative effects on “macrophyte assemblages” (richness, diversity, total abundance; ES_cumulative = ?0.70). In contrast, ES_cumulative were not significant for “macrophyte processes” (growth, mortality; ES_cumulative = ?0.39), “animal abundance” (densities; ES_cumulative = ?0.13), or “animal assemblages” (richness, diversity; ES_cumulative = 0.75). The nonsignificant effect sizes were characterized by low sample sizes and should be interpreted with caution. Three study‐specific effect sizes were particularly large (cumulative are likely biased toward larger effects because only the most conspicuous NIMS have been tested and because nonsignificant results are less likely to be published. To better understand the impacts of NIMS, more manipulative experiments are needed, testing more species and under contrasting environmental conditions. Future studies should include procedural control treatments and report the abundance of the NIMS to avoid ambiguous interpretations. In conclusion, current experimental evidence shows that NIMS have, on average, small‐to‐large negative impacts on native plant species and assemblages. It is possible that these effects can result in severe consequences when accumulated over long time periods and large spatial scales.     

Evidence Accumulation and Choice Maintenance Are Dissociated in Human Perceptual Decision Making

Perceptual decision making in monkeys relies on decision neurons, which accumulate evidence and maintain choices until a response is given. In humans, several brain regions have been proposed to accumulate evidence, but it is unknown if these regions also maintain choices. To test if accumulator regions in humans also maintain decisions we compared delayed and self-paced responses during a face/house discrimination decision making task. Computational modeling and fMRI results revealed dissociated processes of evidence accumulation and decision maintenance, with potential accumulator activations found in the dorsomedial prefrontal cortex, right inferior frontal gyrus and bilateral insula. Potential maintenance activation spanned the frontal pole, temporal gyri, precuneus and the lateral occipital and frontal orbital cortices. Results of a quantitative reverse inference meta-analysis performed to differentiate the functions associated with the identified regions did not narrow down potential accumulation regions, but suggested that response-maintenance might rely on a verbalization of the response.