Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data

Background  

Using DNA microarrays, we have developed two novel models for tumor classification and target gene prediction. First, gene expression profiles are summarized by optimally selected Self-Organizing Maps (SOMs), followed by tumor sample classification by Fuzzy C-means clustering. Then, the prediction of marker genes is accomplished by either manual feature selection (visualizing the weighted/mean SOM component plane) or automatic feature selection (by pair-wise Fisher's linear discriminant).     

Spooneromyces, a new genus to accommodate Peziza laeticolor and the new species S. helveticus

A new genus Spooneromyces is proposed for Peziza laeticolor (syn. Melastiza asperula ). A second species of the genus is described here as S. helveticus sp. nov. Spooneromyces has the following combination of distinctive generic marks: superficial, stiff, brownish hairs; orange to reddish carotenoid-containing hymenium, and heavily sculptured ascospore walls. It is referred to tribe Scutellinieae of the Pyrone-metaceae.     

Phylogenetic and structural studies in the thelebolaceae (Ascomycota)

Several minute dung-inhabiting discomycetes have been classified in the family Thelebolaceae, which has traditionally been included in the order Pezizales. The non-operculate type-genusThelebolus has recently been excluded from the Pezizales. The phylogenetic distribution of other genera associated with Thelebolaceae is still obscure. We have analysed ca. 580 bp from a variable part of the nuclear SSU rRNA gene fromAscozonus, Caccobius, Lasiobolus andThecotheus, and compared these with ca. 1700 bp sequences fromThelebolus, Pleospora, Pezizales, leotiales and Leotiales-related taxa. In the resulting tree,Ascozonus andCaccobius group withThelebolus and the inoperculate discomycetes;Lasiobolus groups withAscodesmis, andThecotheus withAscobolus within Pezizales. SEM pictures of fruit-bodies and ascus apices ofAscozonus, and ascospores fromThecotheus are presented to illustrate characteristic features of these taxa. Submitting author: FAX: +47-22 85 46 64, TEL: +47-22 85 46 61.     

Monensin inhibits receptor-mediated endocytosis of asialoglycoproteins in rat hepatocytes

Isolated rat liver parenchymal cells incubated in the presence of monensin exhibited a reduced uptake of ¹²⁵I-asialofetuin (¹²⁵I-AF). Binding studies indicated that the effect was due to a rapid reduction in the number of active surface receptors for the asialoglycoprotein. Monensin had no effect on receptor internalization, but apparently interrupted the recycling of receptors back to the cell surface. Monensin also inhibited the degradation of ¹²⁵I-AF previously bound to the cells; this inhibition was probably not due to a direct effect on intralysosomal proteolysis, as no lysosomal accumulation of undegraded ligand could be demonstrated in subcellular fractionation studies by means of sucrose gradients. It is more likely that monensin inhibits transfer of the labelled ligand from endocytic vesicles to lysosomes, as indicated by the accumulation of radioactivity in the former and by the ability of monensin to prevent the normally observed time-dependent increase in the buoyant density of endocytic vesicles. Whereas the effect of monensin on binding and uptake of asialofetuin was reversible, the effect on asialofetuin degradation could not be reversed.     

Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography

In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a ‘digital twin’ software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.     

Effect of extrusion on trypsin inhibitor activity and nutrient digestibility of diets based on fish meal, soybean meal and white flakes

The effects of moist extrusion processing of diets containing fish meal (FM) and conventional defatted soybean meal (SBM) or untoasted defatted soybean meal (white flakes [WF]) on amino acid composition, trypsin inhibitor activity (TIA), and apparent total tract digestibility of nutrients were studied. Three diets with the nutritional characteristics of feeds for salmonid fish were formulated: one control based on FM as protein source and two others where 40% of total amino acids from FM were substituted by either SBM or WF. Each diet was fed to mink either as an unextruded mixture of the ingredients or as extruded pellets in order to determine the effect of extrusion processing. Extrusion did not change the amino acid composition of the diets significantly, but reduced the TIA of both diets containing soy products by approximately 76%. Intake of the unextruded WF diet was only one-third compared with the other diets. The dry matter concentration in faeces from mink fed diets containing soy products was significantly lower than in mink fed the FM diet. Digestibility of crude protein, all amino acids and fat was lower, but starch higher, in the unextruded WF diet than in the FM and SBM diets, whereas no significant differences were found among the extruded diets. Extrusion of the WF diet increased digestibility of protein and all amino acids. The greatest increase in digestibility after extrusion of the WF diet was observed for cysteine followed by tryptophan. Extrusion of the FM and SBM diets had no significant effect on amino acid digestibility. Digestibility of starch was, in general, increased by extrusion. It is concluded that the heat treatment involved in typical moist extrusion processing used for fish feed may be sufficient to inactivate most of the TIA in unheated soybean meal, and to increase digestibility of the protein in WF to approximately the same level as found for SBM and FM. Still, extrusion is a lenient process with minor effects on nutrient digestibility of diets containing fish meal or toasted soybean meal as major protein sources.     

Molecular phylogenetics suggest a North American link between the anthropogenic dry rot fungus Serpula lacrymans and its wild relative S. himantioides

The dry rot fungus Serpula lacrymans causes damages in wooden buildings and constructions in temperate regions worldwide. In this study, the global phylogeography of S. lacrymans and its wild relative S. himantioides has been investigated to clarify genealogical relationships and determine the origin and spread of the building strains. Internal transcribed spacer (ITS) nrDNA and parts of the beta-tubulin (tub) and the translation elongation factor (efa) 1a genes were sequenced, and phylogenetic relationships inferred. Some analyses suggest that S. lacrymans may have originated from an ancient S. himantioides lineage, but most results support that S. lacrymans and S. himantioides are monophyletic sister species. Phylogenetic analysis of the ITS data revealed two subgroups within S. lacrymans corresponding to two earlier described varieties; one group occurring frequently in houses worldwide ('Domesticus'), and one group represented by individuals from forests in Northern California ('Shastensis'). A few collections from nature were included in the Domesticus group as well, among other specimens from two newly discovered localities in Far East Russia and Siberia. In the Domesticus group little sequence variation occurs, suggesting a recent worldwide dispersal, possibly linked to human activity. Phylogenetic analyses indicate that the Domesticus group may have originated from an ancient lineage related closely to the Shastensis group. A remarkable shift in morphology and habitat preferences has occurred during the evolution of the Domesticus lineage, linked to the transition from nature to human-made habitats.     

Can sunspot activity and ultraviolet-B radiation explain cyclic outbreaks of forest moth pest species?

Cyclic outbreaks of forest moth pest species have long remained a puzzle for foresters and ecologists. This paper presents time-series exhibiting a strong negative relationship between sunspot numbers and population indices of autumnal and winter moths, both in a mountain birch forest in central Norway and in a mixed lowland forest in southern Norway. In the latter area, also the population level of a moth species feeding entirely on lichens was negatively related to sunspot numbers. Low sunspot activity leads to a thinner ozone layer and thus higher surface ultraviolet (UV)-B radiation. As winter moth larvae prefer leaves subjected to enhanced UV-B radiation, we suggest that the causal relationship between sunspots and moths is that the metabolic costs of producing UV-B-protective pigments during periods of low sunspot activity reduce trees' and lichens' resistance to herbivores, and thus increase the survival of moth larvae. Higher peak densities of moth cycles in mountain forests could be explained by the general higher UV-B radiation at higher altitudes.