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.     

Identification and partial characterization of a latent ATP,Mg-dependent protein phosphatase in rabbit skeletal muscle cytosol

Summary Fractionation of rabbit skeletal muscle cytosol on Aminohexyl-Sepharose has resulted in the identification of a latent ATP, Mg-dependent protein phosphatase whose catalytic subunit is in the active conformation, but is inhibited by the presence of more than one modulator unit. The partially purified enzyme is converted to an inactive, kinase F_A-dependent form upon incubation at 30°C unless modulator-specific polyclonal antibodies are added to the preparation. The immunoglobulins also relieve the inhibition which is responsible for the low basal phosphatase activity of the enzyme, and they counteract all of the heat-stable inhibitor activity present in the preparation. Addition of free catalytic subunit abolishes the inhibition of the latent enzyme in a dose-dependent way, but cannot prevent the inactivation process. The inactivated phosphatase and the original latent enzyme exhibit the same apparent M _r in sucrose density-gradient centrifugation (70 000) and in gel filtration (110 000).Abbreviations PMSF Phenylmethanesulphonyl Fluoride - TLCK L-l-chloro-3-(4-tosylamido)-7-amino2-heptanone-hydrochloride - TPCK L-l-chloro-3-(4-tosvlamido)-4-phenyl-2-butanone     

Value of a control decision rule for leek moth infestations in leek

Fourteen commercial leek fields with first and second generation Leek moth, Acrolepiopsis assectella Z., (LM) injury were sampled during 1986 in The Netherlands. For both generations, plant injury was more prevalent in the perimeter of the field than in interior portions. A sequential sampling program for use in making treatment decisions for LM was developed. An economic analysis of the value of sampling information derived from the sequential sampling program was performed. The parameters used for the analysis were crop yield and value, expected level of LM infestation, potential loss of value due to LM infestation, effectiveness of insecticide application, and cost of sampling. Due mainly to the high value of the crop and low cost of treatment, analysis indicates that there is little difference between a sampling-based management plan and prophylactic application of insecticides in terms of pest control costs. Additionally, such a sampling-based management plan is relatively insensitive to changes in the parameters used in the model. Thus, development of a threshold linked to a sampling procedure will not reduce pest control costs. Use of the sampling-based management plan will also not significantly increase pest control costs and will likely result in reduced insecticide use compared with a prophylactic treatment program.

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Zusammenfassung In den Niederlanden wurde 1986 der durch den Befall der ersten und zweiten Generation der Lauchmotte (Acrolepiosis assectella Z.) verursachte Schaden auf 14 kommerziell genutzten Porreefeldern ermittelt. Für beide Generationen wurde an den Feldrändern ein deutlich höherer Befall als in dem inneren Bereich eines Feldes festgestellt. Zur Bekämpfung der Lauchmotte wurde als Entscheidungsmodell ein sequentielles Probenahmeverfahren entwickelt. Der Informationsgehalt der sequentiellen Befallserhebung wurde einer ökonomischen Bewertung unterzogen. Hierbei wurden folgende Parameter zugrunde gelegt: Erntemenge und Ertrag, erwarteter Befallsgrad sowie hierdurch verursachter möglicher Ertragsverlust, Wirkungsgrad einer Insektizidbehandlung und Kosten der Stichprobennahme. Die Analyse der einzelnen Parameter ergab nur eine geringe Kostendifferenz zwischen einer gezielten Bekämpfung nach sequentieller Probenahme und prophylaktischen Insektizidspritzungen, bedingt durch den hohen Wert der Kultur und die niedrigen Kosten einer Bekämpfung. Darüber hinaus its das Verfahren einer gezielten Lauchmottenbekämpfung gegeüber Veränderungen der obengenannten Parameter relativ unempfindlich. Deshalb wird die Entwicklung eines Schwellenwertes der mit Probenahmeverfahren verbunden ist die Bekämpfungskosten nicht reduzieren. Die anwendung der Probenahmeplans würde Bekämpfungskosten auch nicht erhöhen und würde wahrscheinlich Insecktizidverbrauch reduzieren im Vergleich zu einen prophylaktischen Behandlungsprogramm.

     

The photosynthetic apparatus of C3 and CAM-induced Mesembryanthemum crystallinum L.

Accompanying the CAM induction of Mesembryanthemum crystallinum L. grown in high salinity there are changes in the enzymes of carbon metabolism. However, there are no changes in the electron transport activities, Chla/b ratios or in the distribution of chlorophyll amongst the various pigment-protein complexes of isolated thylakoids. Hence with CAM induction there are no changes in the photochemical apparatus of M. crystallinum thylakoids. Despite comparable amounts of chlorophylla/b-proteins of photosystem II to those found in typical C₃ sun plants, both the C₃ and CAM M. crystallinum chloroplasts have relatively more photosystem II, and, concommitantly, less photosystem I complex. This is consistent with greater fluorescence emission at 685 and 695 nm, and lower emission at 735 nm (measured at 77 K) than typically found for C₃ plants, whether sun or shade species. Photoinhibition of isolated C₃ and CAM thylakoids by white light led to comparable decreases in electron transport capacities and fluorescence emission at 77 K with photosystem II being more affected than PSI. We suggest however, that the presence of more core PSII complexes relative to PSI complexes in this CAM-inducible plant, may provide an additional strategy to mitigate photoinhibition in the short-term.     

Cellular and molecular markers of anteroposterior and dorsoventral organisation in the vitellogenic follicles of adult Sarcophaga bullata (Diptera) and dorsoventral orientation of follicles in the ovary

Summary Polar organisation in the follicles of adult Sarcophaga bullata is reflected in the nurse cell-oocyte axis and in the orientation of the two polar cell pairs in the follicular epithelium. The internal organisation of the nurse cell chamber contributes to polarity but not to dorsoventral asymmetry. Dorsoventral asymmetry is correlated with the eccentric position of the germinal vesicle and the orientation of the polar cell pairs; no other follicle cell specialisations are seen. In an ovary, follicles are preferentially orientated with the dorsal side to the centre of the ovary. Cytoskeletal and some haemolymph proteins are molecular markers of polarity. Thus, in pre-vitellogenic stages, tubulin immunoreactivity is higher in the oocyte than in the nurse cells, actin immunoreactivity is the same over the cystocytes and larval serum proteins are restricted to the poles. During vitellogenesis, both actin and tubulin become more concentrated in the nurse cells and larval serum protein 1 accumulated in the polar cells during border cell migration when yolk polypeptides also accumulate in the oocyte. At the end of vitellogenesis a lipophorin is taken up by the oocyte. No molecular marker of dorsoventral asymmetry was identified.     

Was “Lucy” more human than her “child”? Observations on early hominid postcranial skeletons

Fully adult partial skeletons attributed to Australopithecus afarensis (AL 288-1, “Lucy”) and to Homo habilis (OH 62, “Lucy's child”), respectively, both include remains from upper and lower limbs. Relationships between various limb bone dimensions of these skeletons are compared to those of modern African apes and humans. Surprisingly, it emerges that OH 62 displays closer similarities to African apes than does AL 288-1. Yet A. afarensis, whose skeleton is dated more than 1 million years earlier, is commonly supposed to be the ancestor of Homo habilis. If OH 62, classified as Homo habilis by its discoverers, does indeed represent a stage intermediate between A. afarensis and later Homo, a revised interpretation of the course of human evolution would be necessary.     

Choline acetyltransferase-like immunoreactivity in the brain of Drosophila melanogaster

Summary Using a monoclonal antibody selective for the acetylcholine (ACh)-synthesizing enzyme choline acetyltransferase (ChAT) of Drosophila melanogaster we find ChAT-like immunoreactivity in specific synaptic regions throughout the brain of Drosophila melanogaster apart from the lobes and the peduncle of the mushroom body and most of the first visual neuropile (lamina). Several anatomically well-defined central brain structures exhibit particularly strong binding. Characteristic differential staining patterns are observed for each of the four neuromeres of the optic lobes. Cell bodies appear not to bind this antibody. The prominent features of the distribution of ChAT-like immunoreactivity are paralleled by the distribution of acetylcholine hydrolyzing enzymatic activity as revealed by histochemical staining for acetylcholine esterase (AChE). These results are discussed in comparison with published data on enzyme distribution, choline uptake and ACh receptor binding in the nervous system of Drosophila melanogaster.     

Abortive Infection of F-Plasmid-Containing Escherichia coli Cells by Bacterial Virus T7 Is Determined by the Right End of T7 Gene 1

Phage T7 infects male (F-plasmid-carrying) Escherichia coli cells abortively, whereas the closely related phage T3 grows normally. The inability or ability of phage to replicate in male host cells depends on whether the right end of gene 1 (coding for the phage-specific RNA polymerase) consists of T7 or T3 DNA base sequences.     

Fatty Acid Composition of the Peribacteroid Membrane and the ER in Nodules of Glycine max Varies after Infection by Different Strains of the Microsymbiont Bradyrhizobiumjaponicum

The fatty acid composition of ER, Golgi and peribacteroid membrane (PBM) from root nodules formed on Glycine max after infection with different strains of Bradyrhizobium japonicum has been analysed by gas chromatography. In each plant-microsymbiont combination the fatty acid composition (FAC) of the PBM is distinct from ER and Golgi. The similarity between ER and PBM fatty acid composition is significantly stronger than between Golgi and PBM. In addition the fatty acid composition of all membrane systems in nodules is affected by the microsymbiont strain. A comparison of four strains of Bradyrhizobium japonicum grown in agar surface culture and isolated as the symbiotic bacteroids reveals a decrease in oleic acid during bacteroid differentiation.