PhysioSpace: Relating Gene Expression Experiments from Heterogeneous Sources Using Shared Physiological Processes

Relating expression signatures from different sources such as cell lines, in vitro cultures from primary cells and biopsy material is an important task in drug development and translational medicine as well as for tracking of cell fate and disease progression. Especially the comparison of large scale gene expression changes to tissue or cell type specific signatures is of high interest for the tracking of cell fate in (trans-) differentiation experiments and for cancer research, which increasingly focuses on shared processes and the involvement of the microenvironment. These signature relation approaches require robust statistical methods to account for the high biological heterogeneity in clinical data and must cope with small sample sizes in lab experiments and common patterns of co-expression in ubiquitous cellular processes. We describe a novel method, called PhysioSpace, to position dynamics of time series data derived from cellular differentiation and disease progression in a genome-wide expression space. The PhysioSpace is defined by a compendium of publicly available gene expression signatures representing a large set of biological phenotypes. The mapping of gene expression changes onto the PhysioSpace leads to a robust ranking of physiologically relevant signatures, as rigorously evaluated via sample-label permutations. A spherical transformation of the data improves the performance, leading to stable results even in case of small sample sizes. Using PhysioSpace with clinical cancer datasets reveals that such data exhibits large heterogeneity in the number of significant signature associations. This behavior was closely associated with the classification endpoint and cancer type under consideration, indicating shared biological functionalities in disease associated processes. Even though the time series data of cell line differentiation exhibited responses in larger clusters covering several biologically related patterns, top scoring patterns were highly consistent with a priory known biological information and separated from the rest of response patterns.     

Der neuholl?ndische Fl?tenvogel(Gymnorhina leuconota) in der Gefangenschaft

Ohne Zusammenfassung     

Reactivation of human immunodeficiency virus type 2 in macaques after simian immunodeficiency virus SIVmac superinfection.

By superinfection of human immunodeficiency virus type 2 (HIV-2) strain HIV-2ben-infected macaques with simian immunodeficiency virus (SIV) strain SIVmac, we investigated the mutual influences of an apathogenic and a pathogenic virus in vivo. Four rhesus and two cynomolgus monkeys were infected with HIV-2ben in 1988 and 1989, respectively. Virus could be reisolated from five of six animals 6 weeks after infection. The monkeys remained healthy over the next 2 to 3 years. PCR for viral RNA became negative, and virus could no longer be reisolated by coculture. All six macaques were superinfected with the pathogenic SIVmac251/32H. Subsequently, five monkeys became persistently viremic, while one animal was protected against the SIVmac infection. In the peripheral blood mononuclear cells and cocultures of the five viremic animals, DNA from both HIV-2 and SIVmac was present. The plasma contained RNA from both viruses. Thus, superinfection with SIVmac activated HIV-2. A proliferative T-cell response against both HIV-2 and SIVmac was measured in all animals after superinfection. Such a response was regularly seen after infection with the apathogenic HIV-2 but never when the pathogenic SIVmac alone was administered. While naive control monkeys inoculated with SIVmac251/32H regularly develop AIDS-like symptoms soon after infection and have to be killed, none of the preinfected animals has developed AIDS-like symptoms, but two of six animals developed tumors. After the SIVmac challenge, however, apoptotic lymphocytes were detected in the peripheral blood mononuclear cells of all animals. Thus, the presence of an apathogenic viral variant seems to retard the disease occurring after infection with a pathogenic virus rather than to confirm total protection. This partial protection appears to depend on a specific proliferative T-cell response early after infection.     

Thermococcus alcaliphilus sp. nov., a new hyperthermophilic archaeum growing on polysulfide at alkaline pH

A novel coccoid-shaped, hyperthermophilic, heterotrophic member of the archaea was isolated from a shallow marine hydrothermal system at Vulcano Island, Italy. The isolate grew between 56 and 90° C with an optimum around 85° C. The pH range for growth was 6.5 to 10.5, with an optimum around 9.0. Polysulfide and elemental sulfur were reduced to H₂S. Sulfur stimulated the growth rate. The isolate fermented yeast extract, peptone, meat extract, tryptone, and casein. Isovalerate, isobutyrate, propionate, acetate, CO₂, NH₃, and H₂S (in the presence of S°) were detected as end products. Growth was not inhibited by H₂. Based on DNA-DNA hybridization and 16S rRNA partial sequences, the new isolate represents a new species of Thermococcus, which we named Thermococcus alcaliphilus. The type strain is isolate AEDII12 (DSM 10322) Received: 7 July 1995 / Accepted: 25 August 1995     

Elektronenmikroskopische Untersuchung der Zwittergonadenacini von Planorbarius corneus L. (Basommatophora)

Zusammenfassung In den Spitzenbereichen der Zwittergonadenacini fertiler Tiere der Pulmonatenspezies Planorbarius corneus sind drei Zelltypen stets gleichzeitig anzutreffen: Oocyten, Spermatiden und Begleitzellen. Die Abgrenzung der Acinusspitze gegen das interacinäre Gewebe hin bildet die Basalmembran des wandständigen Begleitzellepithels. Die Oocyten werden follikelartig von den ineinander verzahnten und durch Desmosomen verknüpften Begleitzellen umgeben. Nur in der Acinuskuppe liegen sie der hier stark verdickten Basalmembran unmittelbar auf. Die Spermatiden sitzen nur mit ihrem anterioren Zellpol den Begleitzellen apikal auf und sind durch Desmosomen mit ihnen verknüpft. Veränderungen der Ultrastruktur der Spermatiden während der Spermiohistogenese werden an drei gegeneinander abgrenzbaren Spermiohistogenesestadien aufgezeigt. Dabei finden die Kernstruktur, das Auftreten von Tubulikörpern und das Abstreifen des Restplasmas vom Mittelstück besondere Beachtung. Den recht uneinheitlich strukturierten Begleitzellen kommen für Oocyten und Spermatiden Ernährungs- und Transportfunktionen zu. Sie phagocytieren überfällige Geschlechtszellen. Es können jedoch trotz ihrer heteromorphen Struktur keine prinzipiell verschiedenen Begleitzelltypen mit jeweils nur einer spezifischen Funktion unterschieden werden. Das in früheren lichtmikroskopischen Arbeiten als Begleitzellprodukt beschriebene Kinoplasma erweist sich als kernwärts wanderndes Restplasma der Spermatiden.

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Electron microscopy of hermaphroditic gonad-acini of Planorbarius corneus L. (Basommatophora)

Summary Three species of cells always coexist in the tips of hermaphroditic gonad-acini of fertile Planorbarius corneus: oocytes, spermatids and auxiliary cells. The basement membrane of the auxiliary cell epithelium separates the acinus tips from the interacinary tissue. Like follicles the oocytes are enclosed by interlocked and desmosomically attached auxiliary cells. Only in the utmost tips of the acinus the oocytes are in direct contact with the here dilated basement membrane. The spermatids are attached to the auxiliary cells only with their anterior cell-pole and connected with these by desmosomes. Alterations of the spermatid-ultrastructure during the spermiohistogenesis can be studied in three separate stages of the spermiohistogenesis. Particular attention is given to the nuclear structure, the tubular bodies and the shedding of residual plasma from the middle-piece. The rather irregularly structured cells serve oocytes and spermatids as mediators for nutrition and transport. Occasionally occurs phagocytosis of germ-cells. Basically, even though their structures vary, auxiliary cells are not restricted to one specific function. The Kinoplasma-described in previous light microscopic studies as a product of the auxiliary cells, proves to be spermatidic residual plasma moving towards the nucleus.

Frau Prof. Dr. A. Nolte danke ich für Anregungen und ihr stetes Interesse am Fortschreiten dieser Untersuchung. Frau R. Dingerdissen, Abteilung für Elektronenmikroskopie des Physikalischen Instituts, gilt mein Dank für technische Assistenz am Elmiskop.     

In vivo labeling with stable isotopes as a tool for the identification of unidentified peaks in the metabolome analysis of Corynebacterium glutamicum by GC/MS

Of the hyphenated techniques used for metabolic profiling of cell and tissue extracts, GC/MS is in some ways advantageous as it allows the simultaneous fingerprinting of chemically very different metabolites, and the electron impact mass spectra recorded in many cases lead to unambiguous identification of the compounds. However, prior to chromatography, the hydrophilic substances of the cell extracts have to be converted to vaporizable derivatives, the mass spectra of which often are not known or not listed in the available spectral libraries, even if they are derived from simple biochemicals. Thus, numerous chromatographic peaks remain as yet unidentified. Attempts to identify these peaks afford the acquisition of more data on these compounds. The value of in vivo labeling of metabolites with (13)C and (15)N for this purpose is described.     

Improving d-mannitol productivity of Escherichia coli: Impact of NAD,CO2 and expression of a putative sugar permease from Leuconostoc pseudomesenteroides

The highly productive whole-cell biotransformation of d-fructose to d-mannitol with recombinant, resting cells of Escherichia coli BL21(DE3) requires the combined expression of mdh, fdh and glf which encode mannitol and formate dehydrogenases and a sugar facilitator, respectively. However, long-term stability of the system was restricted, possibly due to loss of the cofactor NAD, high concentrations of formate, formation of CO₂ affecting the internal pH of the cells, accumulation of high intracellular concentrations of d-mannitol, and export of d-mannitol. Downstream of the mdh gene of Leuconostoc pseudomesenteroides, we identified an open reading frame encoding for a putative mannitol permease. The gene was cloned and expressed in E. coli. Biochemical analyses revealed an activity as secondary carrier for d-fructose. Therefore, the carrier was named FupL and participation in d-mannitol transport was excluded. In biotransformation experiments, the productivity of d-mannitol formation obtained with the strain expressing the additional fupL gene was enhanced by 20%.