Memory and cellular immunity induced by a DNA vaccine encoding self antigen TPD52 administered with soluble GM-CSF

Tumor protein D52 (TPD52) is involved in cellular transformation, proliferation and metastasis. TPD52 over expression has been demonstrated in several cancers including prostate, breast, and ovarian carcinomas. Murine TPD52 (mD52) has been shown to induce anchorage independent growth in vitro and metastasis in vivo, and mirrors the function and normal tissue expression patterns of the human orthologue of TPD52. We believe TPD52 represents a self, non-mutated tumor associated antigen (TAA) important for maintaining a transformed and metastatic cellular phenotype. The transgenic adeno-carcinoma of the mouse prostate (TRAMP) model was employed to study mD52 as a vaccine antigen. Naïve mice were immunized with either recombinant mD52 protein or plasmid DNA encoding the full-length cDNA of mD52. Following immunization, mice were challenged with a subcutaneous, tumorigenic dose of mD52 positive, autochthonous TRAMP-C1 tumor cells. Sixty percent of mice were tumor free 85 days post challenge with TRAMP-C1 when immunized with mD52 as a DNA-based vaccine admixed with soluble granulocyte-macrophage colony stimulating factor (GM-CSF). Survivors of the initial tumor challenge rejected a second tumor challenge given in the opposite flank approximately 150 days after the first challenge, and remained tumor free for more than an additional 100 days. The T cell cytokine secretion patterns from tumor challenge survivors indicated that a T_H1-type cellular immune response was involved in tumor protection. These data suggest that mD52 vaccination induced a memory, cellular immune response that resulted in protection from murine prostate tumors that naturally over express mD52 protein.     

Oligocene and Early Miocene gastropods from Kutch (NW India) document an early biogeographic switch from Western Tethys to Indo-Pacific

Shallow marine gastropod assemblages from Chattian, Aquitanian and Burdigalian sections in the Indian Kutch Basin are described. They provide insight into the composition and biogeographic relations of the gastropod assemblages at this junction between the Western Tethys and Proto-Indo-Pacific Ocean. For the first time, an improved biostratigraphy allows a clear separation of the assemblages, especially for the hitherto undifferentiated Early Miocene faunas. Throughout the Oligocene, about one-third of the species are also frequently found in the Western Tethys, documenting a passable Tethyan Seaway for nearshore molluscs. A considerable provincialism is evident as well. The expected turnover during the Early Miocene, due to the closing of the Tethyan Seaway, is reflected in the Miocene assemblages. Surprisingly, however, the cut appears very early, i.e. already during the Aquitanian, when the West–East interrelation drops to zero despite the passage having been open during this interval. In contrast, the Burdigalian assemblages witness a minor re-appearance of Western Tethys taxa, suggesting the re-establishment of rather ineffective migration pathways prior to the final closure of the Tethyan Seaway. Cerithium bermotiense and Lyria (Indolyria) maniyaraensis are introduced as new species.     

Does life originate from a single molecule?

Life did not emerge in a single step. In chemical evolution, the first formation of a self-replicating molecule was probably one of the most critical bottlenecks, which was overcome only with a very low probability. If only one such event was successful, present-day life originates from a single molecule. In this case, homochirality in DNA and RNA is explained almost without further assumptions. By contrast, the enantiomer excess, produced by the deterministic mechanisms suggested so far, is smaller than the statistical standard deviation, unless the postulated initial number of molecules is very--in some mechanisms unreasonably--large. A certain chiral nonuniformity of natural monosaccharides other than (deoxy)ribose supports the idea that homochirality originates not from such small molecules but from an early RNA-like oligomer. This nonuniformity seems also hard to explain by any deterministic mechanism.     

Origin and seasonality of subfossil caprine dung from the discovery site of the Iceman (Eastern Alps)

The discovery of a Neolithic glacier mummy (dated to 3300–3100 cal b.c.) on a remote site of an Alpine pass at 3,200 m in the Ötztal Mountains is still puzzling. In the initial phase of the Iceman research, four hypotheses were suggested to explain the find in its entirety. The speculations vary from a hunter or warrior to a shaman, a miner or a shepherd. None of these proposals is accepted or corroborated by archaeological findings, but on the basis of palynological investigations conducted in the vicinity of the discovery site the assumption that the Iceman was involved in an early form of transhumance has now gained general acceptance. Concerning this assumption we present in this paper a recent study conducted on about a hundred caprine (sheep/goat or ibex/chamois) dung pellets recovered from the find spot of the Iceman and which were dated from 5400 to 2000 cal b.c. The approach was to determine through plant remains from these faeces whether they were droppings derived from animals grazing in anthropogenic habitats at low altitudes or in alpine grasslands. The former case would suggest they were livestock, the latter game. The results showed that all droppings derive from animals grazing at high altitudes.     

Gamma-lactams—A novel scaffold for highly potent and selective α7 nicotinic acetylcholine receptor agonists

A novel class of α7 nicotinic acetylcholine receptor (nAChR) agonists has been discovered through high-throughput screening. The cis γ-lactam scaffold has been optimized to reveal highly potent and selective α7 nAChR agonists with in vitro activity and selectivity and with good brain penetration in mice.     

Discovering the Molecular Components of Intercellular Junctions��A Historical View

The organization of metazoa is based on the formation of tissues and on tissue-typical functions and these in turn are based on cell–cell connecting structures. In vertebrates, four major forms of cell junctions have been classified and the molecular composition of which has been elucidated in the past three decades: Desmosomes, which connect epithelial and some other cell types, and the almost ubiquitous adherens junctions are based on closely cis-packed glycoproteins, cadherins, which are associated head-to-head with those of the hemi-junction domain of an adjacent cell, whereas their cytoplasmic regions assemble sizable plaques of special proteins anchoring cytoskeletal filaments. In contrast, the tight junctions (TJs) and gap junctions (GJs) are formed by tetraspan proteins (claudins and occludins, or connexins) arranged head-to-head as TJ seal bands or as paracrystalline connexin channels, allowing intercellular exchange of small molecules. The by and large parallel discoveries of the junction protein families are reported.In the year of the bicenturial jubilee of Charles Darwin (born 1809) and his 1859 publication of the concept of natural selection as the decisive driving force of evolution, it is perhaps appropriate to begin this review with the notion that the four major kinds of cell–cell junctions are among the oldest and most important structures contributing to the formation and functional diversification of multilayered metazoan organisms. From mere associations of individual cells, whether protozoan or parazoan, it was the cooperation of the molecular ensembles of these junctions to provide the basis for eumetazoan life. Note, however, that some protocadherin glycoproteins and armadillo-type proteins already occur in certain nonmetazoa (e.g., King et al. 2003; Nichols et al. 2006; for refs. Halbleib and Nelson 2006). In particular, diverse cell–cell junction molecules were—and are—needed to assemble and organize metazoan architecture, notably that of the Bilateria, to allow the formation of the epithelial layers of ectoderm and endoderm, mesoderm-derived tissues, and the segregation of diverse kinds of interstitial cells and the organs derived therefrom. So, it is not so surprising that major kinds of cell junctional structures already exist in the lowest divisions of eumetazoa (e.g., Hobmayer et al. 1996, 2000).In general, metazoan animals possess three intercellular junction systems of the adhering type formed by characteristic transmembrane molecules and proteins that assemble into specific submembranous plaques (

Desmosomes (maculae adherentes) are by far the most abundant junctions in stratified epithelia and have been studied with special impetus by researchers analyzing the cytoskeleton and tissue architecture, and by dermatologists.

Adherens junctions, including the zonulae and fasciae adherentes, have first attracted the special interest of developmental biologists because of their importance in mammalian embryogenesis.

Tight junctions (zonulae occludentes), and in particular the transmembrane molecules involved, had long been sought as this structure was important in controlling the paracellular transport of molecules and particles. Finally, the centrally important tetraspan proteins, desired by a generation of physiologists and membranologists, have been found as the result of careful cell particle fractionation work and immunoelectron microscopy.

Gap junctions (nexus) had always fascinated electron microscopists and crystallographers because of their esthetic paracrystalline substructural order, as well as physiologists studying lateral direct molecule exchange from cell to cell. Here, the stability of the structure itself helped in its isolation and reconstitution in vitro.

Table 1.

Constitutive molecular components of the major types of symmetrical (homotypic) junctions

	Occurrence	Associated filaments	Transmembrane proteins and glycoproteins	Specific plaque proteins
DesmosomesMaculae adherentes	Epithelial cells, various types of cardiomyocytes, meningothelial cells, dendritic reticulum cells of the thymus and lymph follicles	Intermediate-sized filaments (keratins, vimentin, desmin)	Desmogleins 1–4a desmocollins 1–3a	Plakoglobinb desmoplakin I/II plakophilins 1–3a
Adherens junctionsZonulae adherentes Fasciae adherentes Puncta adhaerentia	Epithelial cells, endothelial cells, various types of cardiomyocytes, mesenchymal and neural cells	Microfilaments (actin)	Typical cadherinsa (e.g., E-cadherin, N-cadherin, P-cadherin, VE-cadherin, cadherin-11)	α- and β-Catenin, plakoglobin, protein p120, protein ARVCF, protein p0071, neurojungin (δ-catenin)a, (plakophilin-2c) proteins ZO-1, ZO-2, ZO-3
Tight junctionsZonulae occludentes Fasciae occludentes Puncta adhaerentia	Epithelial cells, endothelial cells	–d	Occludin, claudins 1–24a tricellulin(s)e proteins of the JAMA-group, CARa, ESAMa	Proteins ZO-1, ZO-2, ZO-3, cingulin
Gap junctions (nexus)	All kinds of tissue-forming cells	–	Connexins 1–21a	Proteins ZO-1, ZO-2, ZO-3

Open in a separate windowOnly established, i.e., repeatedly confirmed, constituent structural molecules are mentioned here; some further regulatory or peripherally associated molecules are not listed here but are discussed in the text.^aOne or combinations of a few representatives, with cell type and cell layer specificities.^bProteins of the so-called armadillo family are in italics.^cOnly in specific proliferatively active cells (Rickelt et al. 2009).^dActin microfilaments are seen near some tight junctions but their specific association is not clear.^eThere are at least two mRNA splice products but only one protein has so far been localized.Thus, at about the same time in the late 1970s, when the ultrastructural organization and specificities of the diverse kinds of these junctions had been well determined (for reviews, see Farquhar and Palade 1963; Staehelin 1974), the race by cell biologists to elucidate the molecular compositions of these junctions began. Although this analytical research period is not quite over and a few new junction diamonds may still just lie around the corner, the prime interest of the community of cell biological researchers has already moved on to the next research arena, studying the mechanisms of junction formation and the functions of the junctions. Over the last two decades, these major structural elements of our bodies have also become objects of intense medical research, already with some startling results.In the following, the by and large parallel searches for constituent molecules of the four major categories of cell–cell junctions in vertebrate cells is described. However, only constituents localized and confirmed by different groups and with various methods are mentioned as generally accepted components. This, of course, does not exclude the presence of others for which the available evidence does not yet seem sufficient. Furthermore, certain special types of junctions that do not fit one of the four major categories will be reviewed elsewhere (Franke et al. 2009).     

Sequential estimation for prescribed statistical accuracy in stochastic simulation of biological systems

Stochastic simulation of biological systems proceeds by repeatedly generating sample paths or trajectories of the underlying stochastic process, from which many relevant and important system properties can be obtained. While a great deal of research is targeted towards accelerated trajectory generation, issues concerned with the variability across trajectories are often neglected. Advanced methods for properly quantifying the statistical accuracy and determining a reasonable number of trajectories are hardly addressed formally in the context of biological system simulation, though mathematical statistics provides a large body of powerful theory. We invoke this theory and show how mathematically well-founded sequential estimation approaches serve for systematically generating enough but not too many trajectories for achieving a certain prescribed accuracy. The practical applicability is demonstrated and illustrated by numerical examples through simulation studies of an immigration-death process and a gene regulatory network.     

Chromosomal evolution of the PKD1 gene family in primates

Correction to Kirsch S, Pasantes J, Wolf A, Bogdanova N, Münch C, Pennekamp P, Krawczak M, Dworniczak B, Schempp W: Chromosomal evolution of the PKD1 gene family in primates. BMC Evolutionary Biology 2008, 8 :263 (doi:10.1186/1471-2148-8-263)     

Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers

Background

Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies.

Results

We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae.

Conclusion

Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL analyses.

     

Pathogenesis of tendinopathies: inflammation or degeneration?

The intrinsic pathogenetic mechanisms of tendinopathies are largely unknown and whether inflammation or degeneration has the prominent role is still a matter of debate. Assuming that there is a continuum from physiology to pathology, overuse may be considered as the initial disease factor; in this context, microruptures of tendon fibers occur and several molecules are expressed, some of which promote the healing process, while others, including inflammatory cytokines, act as disease mediators. Neural in-growth that accompanies the neovessels explains the occurrence of pain and triggers neurogenic-mediated inflammation. It is conceivable that inflammation and degeneration are not mutually exclusive, but work together in the pathogenesis of tendinopathies.