Rejoinder to Use of Principal Component Analysis and the GE -Biplot for the Graphical Exploration of Gene Expression Data

Summary This note is in response to Wouters et al. (2003, Biometrics 59, 1131–1139) who compared three methods for exploring gene expression data. Contrary to their summary that principal component analysis is not very informative, we show that it is possible to determine principal component analyses that are useful for exploratory analysis of microarray data. We also present another biplot representation, the GE‐biplot (Gene Expression biplot), that is a useful method for exploring gene expression data with the major advantage of being able to aid interpretation of both the samples and the genes relative to each other.     

Vergleichende histophysiologische Tracer-Untersuchungen an verschiedenen Organsystemen von Branchiostoma lanceolatum (Cephalochordata) und Brachydanio rerio (Teleostei)

Zusammenfassung In vergleichend autoradiographischen Untersuchungen wurde der Einbau von percutan applizierten 3H-Uridin, 3H-Histidin und 3H-Glucose in die wichtigsten Organsysteme (Epidermis, ZNS, Muskeln, Chorda, Leber, Kiemendarm, Darm) von Branchiostoma lanceolatum (Acranier) und Brachydanio rerio (Teleosteer) nach Inkorporationszeiten von 11 min bis zu 7 Tagen verfolgt. Der Stoffwechsel der markierten Substanzen in den einzelnen morphologisch miteinander zu homologisierenden Organen war bei den beiden Spezies sehr ähnlich, bei Branchiostoma allerdings (mit Ausnahme des ZNS) 4–5mal stärker als bei Brachydanio. Bei dem letzteren wurde außerdem eine zeitliche Verzögerung in der Tracer-Aufnahme (lag-Phase) beobachtet. Insbesondere der ZNS-Stoffwechsel von Acraniern zeigte ähnliche Charakteristika wie der von Vertebraten: Verbleib des Hauptanteils der neusynthetisierten RNS im Perikaryon, axonalen Protein-Transport, Vorwiegen der Glykogensynthese in den Nervenfaserendformationen. Allerdings fanden sich im ZNS von Branchiostoma niedrigere Stoffwechselraten als im ZNS von Brachydanio.

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Comparative histophysiological investigations of different organs in Branchiostoma lanceolatum (Cephalochordata) and Brachydanio rerio (Teleostei)

Summary Incorporation of 3H-uridine, 3H-histidine and 3H-glucose into some organs (epidermis, CNS, muscles, spinal cord, notochord, liver, gills, intestine) of Branchiostoma lanceolatum (Acrania) and Brachydanio rerio (Teleostei) was investigated by means of comparative autoradiograms following incorporation periods of 11 min to 7 days. The metabolism of the labeled substances in the various homologous organs examined was quite similar, although it was 4 to 5 times higher in Branchiostoma than in Brachydanio; in the latter there was also a delay of tracer incorporation of about 3 hrs, a so-called lag-phase. In particular the metabolism of the CNS of Branchiostoma showed the same characteristics as the CNS of vertebrates, e. g. storage of neuronally synthesized RNA in the neuronal perikarya, axonal flow of proteins, glycogen synthesis in nerve endings. However, metabolic activity of the CNS was lower in Branchiostoma.

Mit dankenswerter Unterstützung durch die Deutsche Forschungsgemeinschaft.     

The complex role of B7 molecules in tumor immunology

T-cell activation requires the interaction of the T-cell receptor with a cognate major histocompatibility complex (MHC)-peptide complex. Initiated by antigen engagement, the adaptive immune response is orchestrated by a complex balance between stimulatory and inhibitory signals that are predominantly controlled by members of the B7 family. Here, we review the current knowledge on B7 family members concerning their constitutive and regulated expression, modulation of the immune response and their role in the evasion of host immune surveillance. We also discuss recent therapeutic strategies that aim to improve immune-cell recognition of tumors and induce tolerance to autoreactive immune responses in normal tissues by manipulating B7 functions.     

New retinoid chemotypes: 9-cis-retinoic acid analogs with hydrophobic rings derived from terpenes as selective RAR agonists

A series of 9-cis-retinoic acid analogs modified at the hydrophobic ring with a (bi)cyclohexenyl moiety derived from natural terpenes has been stereoselectively prepared using a Suzuki cross-coupling as key step. Transient transactivation studies indicate that modification of the hydrophobic ring impacts dramatically on RXR-binding and transactivation, with most retinoids being inactive on RXRbeta, while preserving their RAR pan-agonist profile. Furthermore, only the RARgamma subtype was capable of enantiomeric discrimination with some pairs of enantiomeric terpene-retinoids.     

Leukemia: beneficial actions of retinoids and rexinoids

Acute promyelocytic leukemia (APL), a subtype of acute myeloid leukemia, is the prototype of a cancer that can be cured by differentiation therapy using combined retinoic acid (RA) and chemotherapy. Acute promyelocytic leukemia is caused by chromosomal translocations, which in the large majority of cases generate the prototypic promyelocytic leukemia-retinoic-acid receptor alpha (PML-RARalpha) an oncogenic fusion protein formed from the retinoic-acid receptor alpha and the so-called PML protein. The fusion protein leads to the deregulation of wild type PML and RARalpha function, thus inducing the differentiation block and an altered survival capacity of promyelocytes of affected patients. A plethora of studies have revealed molecular details that account for the oncogenic properties of acute promyelocytic leukemia fusion proteins and the events that contribute to the therapy-induced differentiation and apoptosis of patients' blasts. Illustrating the beneficial mechanisms of action of retinoids for acute promyelocytic leukemia patients this review goes on to discuss a plethora of recently recognized molecular paradigms by which retinoids and rexinoids, alone or in combination with other compounds, regulate growth, differentiation and apoptosis also in non-acute promyelocytic leukemia cells, highlighting their potential as drugs for cancer therapy and prevention.     

B7/CD28 costimulation of T cells induces a distinct proteome pattern

Effective immune strategies for the eradication of human tumors require a detailed understanding of the interaction of tumor cells with the immune system, which might lead to an optimization of T cell responses. To understand the impact of B7-mediated costimulation on T cell activation comprehensive proteome analysis of B7-primed T cell populations were performed. Using this approach we identified different classes of proteins in T cells whose expression is either elevated or reduced upon B7-1- or B7-2-mediated CD28 costimulation. The altered proteins include regulators of the cell cycle and cell proliferation, signal transducers, components of the antigen processing machinery, transporters, cytoskeletal proteins, and metabolic enzymes. A number of differentially expressed proteins are further modified by phosphorylation. Our results provide novel insights into the complexity of the CD28 costimulatory pathway of T cells and will help to identify potential targets of therapeutic interventions for modulating anti-tumor T cell activation.     

Cellular substructures in the optic tectum of Antarctic and temperate fish

The brain of Antarctic fish of the perciform suborder Notothenioidea was analysed with lightand electronmicroscopical methods. The overall organization and ultrastructure of the optic tectum is very similar to that of fish from temperate climates. However, unusual structures were observed in neurons and glial cells, sometimes in high frequencies. The structures are ovoid or elongated, about 200-600 nm in diameter and surrounded by two layers of membranes in a uniform distance of about 30 nm. The enclosed inter-membrane space is similar to extracellular space, both in size and in cytochemical calcium precipitation, while the interior of the structures resembles cytoplasm. These structures are sometimes connected to neuronal processes, so that they seem to originate by a sort of budding process, but most of them are isolated as can be concluded from thick sections of up to 800 nm thickness, analysed with energy-filtering transmission electron microscopy (EFTEM). These unusual objects are present in high abundance in members of the white-blooded Antarctic fish family Channichthyidae. These so-called icefish lack haemoglobin and exhibit the highest degree of cold adaptation. The red-blooded notothenoid fish had smaller amounts of these structures and they were observed even in fish from temperate climates (trout, carp, cichlid fish). In fish from temperate climates the unusual substructures were more abundant during adaptation to cold water temperatures (winter) than to warm conditions (summer). Therefore, the findings may indicate a general phenomenon of cold adaptation with unusual interactions of neurons and glial cells, but the precise function is not yet understood.