Estimating dataset size requirements for classifying DNA microarray data.

A statistical methodology for estimating dataset size requirements for classifying microarray data using learning curves is introduced. The goal is to use existing classification results to estimate dataset size requirements for future classification experiments and to evaluate the gain in accuracy and significance of classifiers built with additional data. The method is based on fitting inverse power-law models to construct empirical learning curves. It also includes a permutation test procedure to assess the statistical significance of classification performance for a given dataset size. This procedure is applied to several molecular classification problems representing a broad spectrum of levels of complexity.     

Identification of a Novel Cryptosporidium Genotype in Pigs

Over a 3-year period, a total of 646 fecal samples from pigs in 22 indoor and outdoor herds from Western Australia were screened for Cryptosporidium spp. by microscopy. Results revealed that 39 of 646 samples (6.03%) were positive for Cryptosporidium. Cryptosporidium was much more common in outdoor herds (17.2%) than in indoor herds (0.5%) and was more common in animals between the ages of 5 and 8 weeks (69.2%) than in younger animals (P < 0.0001). Molecular characterization of the positive samples at the 18S ribosomal DNA locus identified two distinct genotypes of Cryptosporidium: the previously identified pig genotype I and a novel pig genotype (pig genotype II), both of which warrant species status.     

IN VIVO EFFECTS OF CARDIOTROPHIN-1

Cardiotrophin-1 (CT-1) is a recently discovered cytokine that was isolated based on its ability to induce cardiac myocyte hypertrophy in vitro. In this study, the effects of chronic administration of CT-1 to mice (0.5 or 2 μg by intraperitoneal injection, twice a day for 14 days) were determined. A dose-dependent increase in both the heart weight and ventricular weight to body ratios was observed in the treated groups. The body weights of the animals were unaffected. These results indicate that CT-1 can induce cardiac hypertrophy in vivo. CT-1 was not specific for the heart, however. It stimulated the growth of the liver, kidney, and spleen, and caused atrophy of the thymus. CT-1 administration also increased the platelet counts by 70%, with no change in mean platelet volume. Red blood cell counts were increased in the treated animals, and there was a concomitant increase in haemoglobin concentration. Thus, CT-1 has a broad spectrum of biological activities in vivo. This observation is consistent with previous in-vitro findings showing that the mRNA for CT-1 is expressed in several tissues, and that CT-1 can function through binding to the leukaemia inhibitory factor (LIF) receptor and signalling through the gp130 pathway.     

Crystal structure of the phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with myo-inositol.

Phosphatidylinositol (PI), once regarded as an obscure component of membranes, is now recognized as an important reservoir of second messenger precursors and as an anchor for membrane enzymes. PI-specific phospholipase C (PI-PLC) is the enzyme that cleaves PI, invoking numerous cellular responses. The crystal structure of PI-PLC from Bacillus cereus (EC 3.1.4.10) has been solved at 2.6 A resolution and refined to a crystallographic R factor of 18.7%. The structure consists of an imperfect (beta alpha)8-barrel similar to that first observed for triose phosphate isomerase and does not resemble any other known phospholipase structure. The active site of the enzyme has been identified by determining the structure of PI-PLC in complex with its inhibitor, myo-inositol, at 2.6 A resolution (R factor = 19.5%). This substrate-like inhibitor interacts with a number of residues highly conserved among prokaryotic PI-PLCs. Residues His32 and His82, which are also conserved between prokaryotic and eukaryotic PI-PLCs, most likely act as general base and acid respectively in a catalytic mechanism analogous to that observed for ribonucleases.     

Analysis of Orthologous Retrovirus-Like Elements in the White-Footed Mouse,Peromyscus leucopus

Three loci in the genome of the white-footed mouse, Peromyscus leucopus, were examined for the presence or absence of orthologous copies of the retrovirus-like element mys using polymerase chain reaction. We examined these loci in 28 mice collected throughout the P. leucopus species range. Mys insertions were present in only one of the individuals examined at the mys-1 and mys-7 loci. Conversely, the mys-6 element was found in several individuals, but the presence of this element was limited to northern latitudes. Because the long terminal repeats (LTRs) of a given element are expected to be identical at the time of retrotransposition into the genome, and to accumulate changes over evolutionary time, within-element LTR sequence comparisons can be used to estimate the relative age of insertions. Within-element LTR differences are greater in mys-6 than in mys-1 or mys-7. The LTRs from orthologous mys-6 elements of six mice were sequenced. The alignment revealed 13 of the 22 differences between the right and left LTRs that were shared by all orthologous mys-6 sites, suggesting that relative to its time of insertion into the genome, mys-6 has only recently spread across the northern part of the species range. Received: 23 January 1996 / Accepted: 24 April 1996     

A test for preference of association in a color polymorphic poeciliid fish: laboratory study

Synopsis The ecological and evolutionary forces maintaining genetic polymorphism within populations is of continuing interest to evolutionary biologists. Male pygmy swordtails,Xiphophorus pygmaeus, are polymorphic at a Y-linked locus controlling body color. Fish with the + and cp alleles have blue bodies; those with the con allele have bright gold bodies. Male and female fish were tested in the laboratory to determine if there were any preferences for association with groups of male fish based on color. Single test fish were presented with two groups of males of different phenotypes, and times in which the test fish spent in proximity to each group were recorded. Males of different phenotypes showed no differences in preference, nor did phenotype of the males in the groups affect the behavior of the test fish. Females also showed no preference for males of a particular phenotype. Finally, female test fish showed no preference for groups containing a male with the rare phenotype compared to a group containing all males of the same phenotype.     

Postcranial paleoneurology of the Diapsida

The relationships between the size of the spinal cord and the size of the neural canal, and between gross spinal cord anatomy and locomotor style, were documented in a wide range of living diapsids. Observed relationships were used to make predictions about spinal cord anatomy and about limb use and position in related fossil taxa. In particular, the data suggest that the brachial plexus, and therefore the cervical/dorsal vertebral transition, of the theropod dinosaurs studied was located considerably posterior to its presently accepted location, and that the forelimbs of the giant carnosaurs Tyrannosaurus rex and Carnotaurus sastrei were of biologically insignificant use. Neural canal measurements support previous interpretations of locomotor style in extinct crocodilians, and can be used to predict limb placement in plesiosaurs.     

The ultrastructural basis of endothelial cell surface functions

Several enzymes, enzyme inhibitors, receptors and transport structures are situated on the luminal surface of endothelium. Some enzymes and transport systems are continuously active and, in effect, regulate the composition of blood moving downstream. Other components are latent. Their activities are not expressed in the absence of stimulus. Thus, endothelial cells injured by granulocytes or viral infection possess receptors for the Fc segment of IgG and for C3b, whereas normal endothelial cells do not. Both normal and injured endothelial cells express receptors for Clq. To visualize surface enzymes, inhibitors, receptors and transport structures, we have prepared surface replicas suitable for high resolution EM. The surface replication technique, coupled with immunocytochemical procedures, facilitates studies of the topographies of surface enzymes such as angiotensin converting enzyme (ACE) and carboxypeptidase N (CPN). In addition, the replicas provide unique views of the glycocalyx, a cell coating previously believed to be amorphous but now seen to be a highly organized carpet-work under which surface enzymes, receptors, etc are embedded. Given its content of fibronectin, the glycocalyx may be the Clq receptor. Cells treated with antibodies to ACE or CPN show disarrayed glycocalyces and bind Fc and C3b. Latency of the Fc and C3b receptors may be owing to the physical barrier provided by the glycocalyx. Apparently, damage to the glycocalyx creates conditions favoring binding of immune complexes, complement activation and intravascular coagulation with loss of gradients between blood and parenchyma. Whether some non-thrombogenic properties of endothelium require an intact glycocalyx deserves consideration as does the role of the glycocalyx in regulating microvascular permeability.     

Relationship between root volatiles of some carrot cultivars and their resistance to the carrot fly, Psila rosae

Field experiments investigated the resistance of some carrot cultivars to Psila rosae. In addition, headspace vapour and steam distillate from the roots of resistant and susceptible varieties were compared by gas-liquid chromatography. The field data confirmed that resistance may operate by decreasing the numbers of eggs laid indicating a nonpreference by the female Psila. Root resistance to the larva was also confirmed but the mechanism was unclear. A new finding was that root resistance is independent of the effect of egg laying, some cultivars evincing one or the other effect and some such as Regulus Imperial displaying both. It was clear that root resistance to the larva is the crucial prerequisite in breeding resistant varieties.One consistent difference was detected by the chemical comparisons: intact roots of resistant varieties released substantially less volatiles. Specifically, Regulus released almost five times less of the volatiles already shown to positively influence host-finding behaviour by the larva.

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Résumé La résistance à P. rosae de quelques cultivars de carotte a été étudiée en plein champ. Parallèlement, les substances volatiles diffusées et celles extraites par la vapeur des racines de variétés résistantes et sensibles, ont été comparées en chromatographie gaz-liquide (GLC). Les résultats en champ ont confirmé que la résistance peut être due à une diminution du nombre d'oeufs pondus, révélant une absence d'attractivité pour les femelles de P. rosae. La résistance des racines aux larves a été aussi confirmée, mais les raisons n'en étaient pas claires. Un aspect nouveau est que la résistance des racines est indépendante de l'effet de la ponte, quelques cultivars présentant l'un ou l'autreeffet et certains, comme Regulus Imperial, manifestant les deux. Il est net que la résistance racinaire aux larves est la condition essentielle pour la sélection de variétés résistantes. Une différence importante a été mise en évidence par les comparaisons chimiques: les racines intactes de variétés résistantes libèrent nettement moins de substances volatiles. Précisément, Regulus a libéré 5 fois moins de substances volatiles déjà connues comme influençant positivement le comportement de découverte de l'hôte par la larve.

     

Use of monoclonal antibody probes against rat hepatic cytochromes P-450c and P-450d to detect immunochemically related isozymes in liver microsomes from different species

Nine distinct monoclonal antibodies raised against purified rat liver cytochrome P-450c react with six different epitopes on the antigen, and one of these epitopes is shared by cytochrome P-450d. None of these monoclonal antibodies recognize seven other purified rat liver isozymes (cytochromes P-450a, b, and e-i) or other proteins in the cytochrome P-450 region of "Western blots" of liver microsomes. Each of the monoclonal antibodies was used to probe "Western blots" of liver microsomes from untreated, or 3-methylcholanthrene-, or isosafrole-treated animals to determine if laboratory animals other than rats possess isozymes immunochemically related to cytochromes P-450c and P-450d. Two protein-staining bands immunorelated to cytochromes P-450c and P-450d were observed in all animals treated with 3-methylcholanthrene (rabbit, hamster, guinea pig, and C57BL/6J mouse) except the DBA/2J mouse, where no polypeptide immunorelated to cytochrome P-450c was detected. The conservation of the number of rat cytochrome P-450c epitopes among these species varied from as few as two (guinea pig) to as many as five epitopes (C57BL/6J mouse and rabbit). The relative mobility in sodium dodecyl sulfate-gels of polypeptides immunorelated to cytochromes P-450c and P-450d was similar in all species examined except the guinea pig, where the polypeptide related to cytochrome P-450c had a smaller Mr than cytochrome P-450d. With the use of both monoclonal and polyclonal antibodies, we were able to establish that purified rabbit cytochromes P-450 LM4 and P-450 LM6 are immunorelated to rat cytochromes P-450d and P-450c, respectively.