Transcriptomic response to differentiation induction

Background  

Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes.     

Targeted overexpression of sarcolipin in the mouse heart decreases sarcoplasmic reticulum calcium transport and cardiac contractility

The role of sarcolipin (SLN) in cardiac physiology was critically evaluated by generating a transgenic (TG) mouse model in which the SLN to sarco(endoplasmic)reticulum (SR) Ca(2+) ATPase (SERCA) ratio was increased in the ventricle. Overexpression of SLN decreases SR calcium transport function and results in decreased calcium transient amplitude and rate of relaxation. SLN TG hearts exhibit a significant decrease in rates of contraction and relaxation when assessed by ex vivo work-performing heart preparations. Similar results were also observed with muscle preparations and myocytes from SLN TG ventricles. Interestingly, the inhibitory effect of SLN was partially relieved upon high dose of isoproterenol treatment and stimulation at high frequency. Biochemical analyses show that an increase in SLN level does not affect PLB levels, monomer to pentamer ratio, or its phosphorylation status. No compensatory changes were seen in the expression of other calcium-handling proteins. These studies suggest that the SLN effect on SERCA pump is direct and is not mediated through increased monomerization of PLB or by a change in PLB phosphorylation status. We conclude that SLN is a novel regulator of SERCA pump activity, and its inhibitory effect can be reversed by beta-adrenergic agonists.     

Scorpion higher phylogeny and classification, taxonomic anarchy, and standards for peer review in online publishing

Soleglad and Fet's (2003a) attempt to reconstruct the phylogeny of Recent (including extant) scorpions, the revised classification derived from it, and recent emendations, mostly published in their self‐edited online journal, Euscorpius, are deficient. Separate analyses of three independent matrices (morphology, 16S rDNA, 18S rDNA) were presented. In the morphological matrix, 52 binary and 10 tristate trichobothrial characters were replaced with one character comprising six ordered states representing trichobothrial “types”. The remaining matrix of 105 characters was further reduced to 33 “fundamental” characters (20% of the morphological dataset), the analysis of which appears to be the basis for the revised classification presented. The taxon sample for the morphological analysis included 14 supraspecific terminal taxa representing genera, the monophyly of only 7 (12.5%) of which has been confirmed. A composite terminal, assembled from the fragments of fossils that may not be confamilial let alone monophyletic, was created for the Palaeopisthacanthidae, employed as the primary outgroup for the analysis. Other important outgroup taxa, notably eurypterids, xiphosurans and other arachnids, were omitted entirely. The morphological characters presented contained numerous unjustifiable assumptions of character polarity and phylogenetic relationship. An approach to character coding, deliberately adopted to reduce “homoplasy”, biased the analysis towards a preconceived result. Structurally and topographically similar features in different taxa were explicitly assigned separate (often autapomorphic) states according to presumed phylogenetic relationships among the taxa in which they were observed. Putative “reversals” were coded as separate characters or states. Character transformation was forced by ordering, additive coding or Sankoff optimization through allegedly intermediate states for which there is no empirical evidence. Many characters were defined in a manner that demonstrates either a lack of understanding of, or disregard for, established methods and standards of morphological character coding. Some states display overlapping variation whereas others subsume variation that is not structurally or topographically similar. Polymorphic “states” were created for terminals with interspecific variation and unknown “states” for terminals that should have been scored unknown. Many characters were not evaluated for particular terminal taxa, but merely scored inapplicable although the structures and, consequently, the characters in question are present and therefore applicable to them. In view of the significant theoretical and empirical problems with the approach to cladistics taken by Soleglad and Fet, we find no justification for accepting either the results of their analyses or the revised classification derived from them. Pending the outcome of a rigorous phylogenetic analysis, published according to acceptable standards of scholarship in a peer‐reviewed journal, we revert to the suprageneric classification of Scorpiones reflected by the most recent peer‐reviewed, published treatments and reject all changes to the classification proposed by Soleglad, Fet and colleagues since 2001. We argue that an analysis and revised classification of the kind presented in various papers by these authors could not survive the peer‐review process of a mainstream scientific journal. The poor scholarship exemplified by these and other papers published in Euscorpius emphasize the importance of quality control associated with the emergent infrastructure of online publishing. A centralized register of taxa may be the only solution for ensuring quality control in the taxonomy of the future. © The Willi Hennig Society 2005.     

Arabidopsis thaliana VTC4 encodes L-galactose-1-P phosphatase, a plant ascorbic acid biosynthetic enzyme

In plants, a proposed ascorbate (vitamin C) biosynthesis pathway occurs via GDP-D-mannose (GDP-D-Man), GDP-L-galactose (GDP-L-Gal), and L-galactose. However, the steps involved in the synthesis of L-Gal from GDP-L-Gal in planta are not fully characterized. Here we present evidence for an in vivo role for L-Gal-1-P phosphatase in plant ascorbate biosynthesis. We have characterized a low ascorbate mutant (vtc4-1) of Arabidopsis thaliana, which exhibits decreased ascorbate biosynthesis. Genetic mapping and sequencing of the VTC4 locus identified a mutation (P92L) in a gene with predicted L-Gal-1-P phosphatase activity (At3g02870). Pro-92 is within a beta-bulge that is conserved in related myo-inositol monophosphatases. The mutation is predicted to disrupt the positioning of catalytic amino acid residues within the active site. Accordingly, L-Gal-1-P phosphatase activity in vtc4-1 was approximately 50% of wild-type plants. In addition, vtc4-1 plants incorporate significantly more radiolabel from [2-(3)H]Man into L-galactosyl residues suggesting that the mutation increases the availability of GDP-L-Gal for polysaccharide synthesis. Finally, a homozygous T-DNA insertion line, which lacks a functional At3g02870 gene product, is also ascorbate-deficient (50% of wild type) and deficient in L-Gal-1-P phosphatase activity. Genetic complementation tests revealed that the insertion mutant and VTC4-1 are alleles of the same genetic locus. The significantly lower ascorbate and perturbed L-Gal metabolism in vtc4-1 and the T-DNA insertion mutant indicate that L-Gal-1-P phosphatase plays a role in plant ascorbate biosynthesis. The presence of ascorbate in the T-DNA insertion mutant suggests there is a bypass to this enzyme or that other pathways also contribute to ascorbate biosynthesis.     

Brightness induction: rate enhancement and neuronal synchronization as complementary codes

In cat visual cortex, we investigated with parallel recordings from multiple units the neuronal correlates of perceived brightness. The perceived brightness of a center grating was changed by varying the orientation or the relative spatial phase of a surrounding grating. Brightness enhancement by orientation contrast is associated with an increase of discharge rates of responses to the center grating but not with changes in spike synchronization. In contrast, if brightness enhancement is induced by phase offset, discharge rates are unchanged but synchronization increases between neurons responding to the center grating. The changes in synchronization correlate well with changes in perceived brightness that were assessed in parallel in human subjects using the same stimuli. These results indicate that in cerebral cortex the modulation of synchronicity of responses is used as a mechanism complementary to rate changes to enhance the saliency of neuronal responses.     

Detection of Suppressiveness against Rotylenchulus reniformis in Soil from Cotton (Gossypium hirsutum) Fields in Texas and Louisiana

Rotylenchulus reniformis is a major problem confronting cotton production in the central part of the cotton belt of the United States of America. In this study, the hypothesis that natural antagonists in some cases are responsible for unusually low densities of the nematode in certain fields was tested by assaying soils from 22 selected fields for the presence of transferable agents in pots containing cotton plants. In one field, soil from four different depth ranges was tested. In the first of two types of assays, 1 part nematode infested soil was added to 9 parts test soil that was left untreated or autoclaved before mixing; this mixture was used to fill pots. In the second type of assay, 1 part test soil was added to 9 or 19 parts pasteurized fine sand, and nematodes were introduced in aqueous suspension. In three experiments representing both types of assay, transferable or autoclavable agent(s) from four fields in South Texas suppressed nematode populations by 48, 78, 90 and 95%. In one experiment, transferable agents in five fields in Louisiana suppressed populations from 37 to 66%. Identification and evaluation of these agents for biological control of R. reniformis merits further study.     

Culture, embodiment and genes: unravelling the triple helix

Much recent work stresses the role of embodiment and action in thought and reason, and celebrates the power of transmitted cultural and environmental structures to transform the problem-solving activity required of individual brains. By apparent contrast, much work in evolutionary psychology has stressed the selective fit of the biological brain to an ancestral environment of evolutionary adaptedness, with an attendant stress upon the limitations and cognitive biases that result. On the face of it, this suggests either a tension or, at least, a mismatch, with the symbiotic dyad of cultural evolution and embodied cognition. In what follows, we explore this mismatch by focusing on three key ideas: cognitive niche construction; cognitive modularity; and the existence (or otherwise) of an evolved universal human nature. An appreciation of the power and scope of the first, combined with consequently more nuanced visions of the latter two, allow us to begin to glimpse a much richer vision of the combined interactive potency of biological and cultural evolution for active, embodied agents.     

Phylogenetic analysis of the endemic New Caledonian cockroach Lauraesilpha. Testing competing hypotheses of diversification

New Caledonia is a tropical hotspot of biodiversity with high rates of regional and local endemism. Despite offering an ideal setting to study the evolution of endemism, New Caledonia has received little attention compared with the other nearby hotspots, particularly New Zealand. Most studies of the Neocaledonian endemism have been carried out at the regional level, comparing the various groups and species present in New Caledonia but absent in neighboring territories. In addition, remarkably high short‐range endemism has been documented among plants, lizard and invertebrates, although these have usually been done, lacking a phylogenetic perspective. Most studies of Neocaledonian endemism have referred to the geological Gondwanan antiquity of the island and its metalliferous soils derived from ultramafic rocks. Very old clades are thought to have been maintained in refugia and diversified on the metalliferous soils. The present study documents the pattern of diversification and establishment of short‐range endemism in a phylogenetic context using the Neocaledonian cockroach genus Lauraesilpha. Mitochondrial and nuclear genes were sequenced to reconstruct phylogenetic relationships among the species of this genus. These relationships, in the light of the species distribution, do not support the hypothesis that species diversified via an adaptive radiation on metalliferous soils and are not consistent with areas of highest rainfall. Species of Lauraesilpha have similar altitudinal ranges and ecological habits and are short‐range endemics on mountains. What our analysis did reveal was that closely related species are found on nearby or contiguous mountains, and thus these formations probably played the key role establishing short‐range endemism (in association with recent climatic changes). © The Willi Hennig Society 2008.