Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes

Background  

With the growing number of public repositories for high-throughput genomic data, it is of great interest to combine the results produced by independent research groups. Such a combination allows the identification of common genomic factors across multiple cancer types and provides new insights into the disease process. In the framework of the proportional hazards model, classical procedures, which consist of ranking genes according to the estimated hazard ratio or the p-value obtained from a test statistic of no association between survival and gene expression level, are not suitable for gene selection across multiple genomic datasets with different sample sizes. We propose a novel index for identifying genes with a common effect across heterogeneous genomic studies designed to remain stable whatever the sample size and which has a straightforward interpretation in terms of the percentage of separability between patients according to their survival times and gene expression measurements.     

Development of gastric sensitivity to histamine in the rat

Sensitivity of the developing rat stomach to histamine (HA) was examined on isolated gastric mucosae of rats of various ages from the fetal to adult periods. Spontaneous acid secretion in mu eq/h.cm2 occurred at all the ages studied, at a basal rate of 0.45 +/- 0.07 in fetuses to 0.22 +/- 0.03 (day 5), 0.11 +/- 0.04 (day 10), 0.12 +/- 0.04 (day 12), 0.22 +/- 0.08 (day 16) and 0.33 +/- 0.04 (adults). In the fetal rats as in the adults, marked responses to respectively 10(-5) and 10(-4) M HA were demonstrated. The H2-receptor antagonist cimetidine diminished HA-induced secretion by 66 and 57% in fetuses and adults respectively. Between these two stages (from days 5 to 12), basal secretion and the response to HA dropped significantly. On day 21 of gestation, as well as on the critical days 5 and 12 after parturition, db-cAMP (10(-4) M) caused maximal stimulation of acid secretion. These results indicate that the development of responsiveness to HA in the rat is biphasic. They suggest that after birth, the H2-receptor adenylate cyclase system undergoes major modifications which might lead to the complete lack of responsiveness to HA by day 12.     

About the specificity of photoinduced affinity labeling of Escherichia coli ribosomes by dihydrorosaramicin, a macrolide related to erythromycin

Photoactivation of the [3H]dihydrorosaramicin chromophore at a wavelength above 300 nm allows the covalent attachment of the macrolide antibiotic to the bacterial ribosome. Bidimensional electrophoresis shows that the radioactivity is mainly associated with proteins L1, L5, L6, L15, L18, L19, S1, S3, S4, S5 and S9. When photoincorporation of the drug is conducted in the presence of puromycin as effector of [3H]dihydrorosaramicin-binding sites, a decrease in the labeling of most proteins is observed, except for L18 and L19, which are radiolabeled to a larger extent. These results allow us to speculate that L18 and L19 belong to the high-affinity binding site of rosaramicin antibiotic.     

Orthologs of key vertebrate neural genes are expressed during neurogenesis in the annelid Platynereis dumerilii

SUMMARY The molecular mechanisms underlying the formation and patterning of the nervous system are relatively poorly understood for lophotrochozoans (like annelids) as compared with ecdysozoans (especially Drosophila ) and deuterostomes (especially vertebrates). Therefore, we have undertaken a candidate gene approach to study aspects of neurogenesis in a polychaete annelid Platynereis dumerilii . We determined the spatiotemporal expression for Platynereis orthologs of four genes ( SoxB, Churchill, prospero / Prox , and SoxC) known to play key roles in vertebrate neurogenesis. During Platynereis development, SoxB is expressed in the neuroectoderm and its expression switches off when committed neural precursors are formed. Subsequently, Prox is expressed in all differentiating neural precursors in the central and peripheral nervous systems. Finally, SoxC and Churchill are transcribed in patterns consistent with their involvement in neural differentiation. The expression patterns of Platynereis SoxB and Prox closely resemble those in Drosophila and vertebrates—this suggests that orthologs of these genes play similar neurogenic roles in all bilaterians. Whereas Platynereis SoxC , like its vertebrate orthologs, plays a role in neural cell differentiation, related genes in Drosophila do not appear to be involved in neurogenesis. Finally, conversely to Churchill in Platynereis , vertebrate orthologs of this gene are expressed during neuroectoderm formation, but not later during nerve cell differentiation; in the insect lineage, homologs of these genes have been secondarily lost. In spite of such instances of functional divergence or loss, the present study shows conspicuous similarities in the genetic control of neurogenesis among bilaterians. These commonalities suggest that key features of the genetic program for neurogenesis are ancestral to bilaterians.     

Multiple molecular forms of rat superior cervical ganglion acetylcholinesterase: Developmental aspects in primary cell culture and during postnatal maturation in vivo

Four main molecular forms of acetylcholinesterase (AChE) can be solubilized from newborn rat superior cervical ganglia (SCG), homogenized in the presence of a high-ionic-strength, detergent-containing medium. These forms, respectively referred to as 16, 10, 6.5, and 4 S, are characterized by their sedimentation coefficients. Their relative proportions in SCG are notably different in vivo during postnatal maturation, and in culture. The 16-S AChE appears to be mainly neuronal in origin, is maintained in culture independently of original presynaptic in vivo elements, and its cellular pool is not depleted in the presence of tetrodotoxin (TTX).     

Fine‐scale Population Genetic Structure of Two Dioecious Indian Keystone Species,Ficus hispida and Ficus exasperata (Moraceae)

Although Ficus (Moraceae) is a keystone plant genus in the tropics, providing resources to many frugivorous vertebrates, its population genetic structure, which is an important determinant of its long‐term survival, has rarely been investigated. We examined the population genetic structure of two dioecious fig species (Ficus hispida and Ficus exasperata) in the Indian Western Ghats using co‐dominant nuclear microsatellite markers. We found high levels of microsatellite genetic diversity in both species. The regression slopes between genetic relationship coefficients (f_ij) and spatial distances were significantly negative in both species indicating that, on average, individuals in close spatial proximity were more likely to be related than individuals further apart. Mean parent–offspring distance (σ) calculated using these slopes was about 200 m in both species. This should be contrasted with the very long pollen dispersal distances documented for monoecious Ficus species. Nevertheless, overall population genetic diversity remained large suggesting immigrant gene flow. Further studies will be required to analyze broader scale patterns.     

Murine monoclonal antibody against aldosterone: production, characterization and use for enzymoimmunoassay

Hybridomas secreting monoclonal antibodies to aldosterone were obtained by fusion of myeloma cells and spleen cells from Balb/c mice immunized with aldosterone-3-carboxylmethyloxime-bovine serum albumin. A monoclonal antibody was purified from ascites fluid and characterized. An affinity constant of 1.61 x 10(9) M-1 has been measured and no cross-reactivity with tetrahydroaldosterone (THA), cortisol, cortisone, corticosterone, deoxycorticosterone (DOC), dehydroepiandrosterone (DHA), progesterone and estrone, could be detected. A peroxidase conjugated-antibody (1.5 mole of enzyme per mole of antibody) was obtained and used for microwell enzyme immunoassay and Immun-Blot assay. The high affinity and specificity of this antibody should make the direct determination of aldosterone in biological fluids possible at concentrations as low as 5 x 10(-10) M.     

Effects of experimental acidification on a lotic macroinvertebrate community

A three month experimental acidification was carried out on lotic bottom communities. Experiments were conducted under semi-natural conditions in plasticized wooden channels. Acidified communities (pH 4.0), with or without added aluminum, were compared with a reference community (pH 6.3–6.9). Added aluminum concentrations were respectively 0.2 and 0.4 mg 1^–1 in experiments performed in 1982 and 1983. Water chemistry and taxonomic composition of the macroinvertebrate communities were monitored. Under acidified conditions, results were similar, with or without added aluminum. Mean abundances of all groups of organisms were lowered. Mayflies nearly completely disappeared from the acidified channels. The only organism not affected by the acidification was Microtendipes sp. Differences in the organism response were observed: Orthocladiinae (Rheocricotopus, Parametriocnemus, Corynoneura, Thienemanniella, Nanocladius, Cricotopus) and Ephemeroptera (Baetis, Habrophlebia, Habrophlebiodes, Paraleptophlebia, Ephemerella), especially early instars, were very sensitive to low pH, Chironomini and Tanypodinae were much less sensitive, while Tanytarsini were intermediate; Oligochaeta and Nematoda were difficult to classify, their response being different from one year to another. Organisms inhabiting the surface of artificial substrates disappeared very rapidly from the system, while those buried inside had a delayed reaction to acidification. Aluminum which was mainly in the monomeric form was not responsible for community modifications. Direct action of hydrogen ions through a physiological stress seems a more credible explanation. These results, induced by a continuous experimental acidification, suggest that if this small headwater stream undergoes acidification, the resulting invertebrate community will be very simplified, with only resistant species able to cope with the acid conditions.     

Evidence for negative regulation of T cell growth by low affinity interleukin 2 receptors

Two experimental situations have been studied, and the results provide evidence for a negative regulatory role for the low affinity interleukin 2 receptor (LA-IL 2R). The IL 2-dependent T helper cell line L-14, deprived of IL 2, becomes quiescent and expresses comparable numbers of high affinity IL 2R (HA-IL 2R) and LA-IL 2R. After activation by recombinant IL 2, this cell line preferentially expresses LA-IL 2R. The IL 2 responsiveness of the L-14 cell line was found to vary according to the ratio of LA-IL 2R to HA-IL 2R: the relative predominance of the LA-IL 2R coincides with a hyporeactivity of cells to IL 2. In contrast, a predominance of HA-IL 2R is accompanied by an increase in cellular IL 2 reactivity. Treatment of three IL 2-dependent T cell lines (L-14, HT-2, and C30.1) with limited amounts of recombinant IL 2 and moderate concentrations of anti-IL 2R monoclonal antibodies stimulates T cell growth. This treatment was shown to selectively diminish the expression of membrane LA-IL 2R. The stimulation was attributed to the decrease of expression of LA-IL 2R.     

KIN, a mammalian nuclear protein immunologically related to E. coli RecA protein

A polypeptide of about 120 kDa, called KIN, has been identified in rat FR 3T3 cells by immunoblotting using affinity-purified antibodies against the RecA protein of Escherichia coli (38 kDa). The KIN protein as shown by fluorescent light microscopy and electron microscopy is essentially concentrated in the nucleus. Its level is higher in proliferating than in quiescent cells. Cell treatment with mitomycin C increases the level of the KIN protein. We sought similar proteins in other mammalian cells. Proteins with the same electrophoretic mobility were detected in mouse, monkey and human cell lines as well as in rat and mouse embryos.