Functional CD169 on Macrophages Mediates Interaction with Dendritic Cells for CD8+ T Cell Cross-Priming

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Unveiling network-based functional features through integration of gene expression into protein networks

Decoding health and disease phenotypes is one of the fundamental objectives in biomedicine. Whereas high-throughput omics approaches are available, it is evident that any single omics approach might not be adequate to capture the complexity of phenotypes. Therefore, integrated multi-omics approaches have been used to unravel genotype–phenotype relationships such as global regulatory mechanisms and complex metabolic networks in different eukaryotic organisms. Some of the progress and challenges associated with integrated omics studies have been reviewed previously in comprehensive studies. In this work, we highlight and review the progress, challenges and advantages associated with emerging approaches, integrating gene expression and protein-protein interaction networks to unravel network-based functional features. This includes identifying disease related genes, gene prioritization, clustering protein interactions, developing the modules, extract active subnetworks and static protein complexes or dynamic/temporal protein complexes. We also discuss how these approaches contribute to our understanding of the biology of complex traits and diseases. This article is part of a Special Issue entitled: Cardiac adaptations to obesity, diabetes and insulin resistance, edited by Professors Jan F.C. Glatz, Jason R.B. Dyck and Christine Des Rosiers.     

Construction of a potato YAC library and identification of clones linked to the disease resistance loci R1 and Gro1

 A yeast artificial chromosome (YAC) library was constructed from high-molecular-weight DNA of potato (Solanum tuberosum). Potato DNA fragments obtained after complete digestion with four different rare-cutter restriction enzymes were cloned using the pYAC-RC vector. The library consists of 21 408 YAC clones with an average insertion size of 140 kb. The frequency of YAC clones having insertions of chloroplast or mitochondrial DNA was estimated to be 0.5% and 0.3%, respectively. The YAC library was screened by PCR with 11 DNA markers detecting single genes or small gene families in the potato genome. YACs for 8 of the 11 markers were detected in the library. Using 2 markers that are linked to the resistance genes R1 and Gro1 of potato, we isolated two individual YAC clones. One of these YAC clones was found to harbour one member of a small family of candidate genes for the nematode resistance gene Gro1. Received : 5 May 1997 / Accepted : 20 May 1997     

First-Year Common Nightingales (Luscinia megarhynchos) Have Smaller Song-Type Repertoire Sizes Than Older Males

Based on the assumptions that birdsong indicates male quality and that quality is related to age, one might expect older birds to signal their age. That is, in addition to actual body condition, at least some song features should vary with age, presumably towards more complexity. We investigated this issue by comparing repertoire sizes of free‐ranging common nightingale males in their first breeding season with those of older males. Nightingales are a good model species as they are open‐ended learners, where song acquisition is not confined to an early sensitive period of learning. Moreover, nightingales develop an extraordinarily large song‐type repertoire (approx. 180 different song types per male), and differences in repertoire size among males are pronounced. We analysed repertoire characteristics of the nocturnal song of nine nightingales in their first breeding season and compared them with the songs of nine older males. The repertoire size of older males was on average 53% larger than that of yearlings. When analysing two song categories of nightingales, whistle and non‐whistle songs separately, we found similar results. Our findings show marked differences in repertoire size between age categories, suggesting that this song feature may reflect a male's age. We discuss those mechanisms that may constrain the development of larger repertoires in first‐year males. Whether repertoire sizes are crucial for female mate choice or in vocal interactions among conspecific males remains open to further investigations.     

Identification and Characterization of Di- and Tripeptide Transporter DtpT of Listeria monocytogenes EGD-e

Listeria monocytogenes is a gram-positive intracellular pathogen responsible for opportunistic infections in humans and animals. Here we identified and characterized the dtpT gene (lmo0555) of L. monocytogenes EGD-e, encoding the di- and tripeptide transporter, and assessed its role in growth under various environmental conditions as well as in the virulence of L. monocytogenes. Uptake of the dipeptide Pro-[¹⁴C]Ala was mediated by the DtpT transporter and was abrogated in a ΔdtpT isogenic deletion mutant. The DtpT transporter was shown to be required for growth when the essential amino acids leucine and valine were supplied as peptides. The protective effect of glycine- and proline-containing peptides during growth in defined medium containing 3% NaCl was noted only in L. monocytogenes EGD-e, not in the ΔdtpT mutant strain, indicating that the DtpT transporter is involved in salt stress protection. Infection studies showed that DtpT contributes to pathogenesis in a mouse infection model but has no role in bacterial growth following infection of J774 macrophages. These studies reveal that DptT may contribute to the virulence of L. monocytogenes.     

Discovery of novel hydroxy-thiazoles as HIF-alpha prolyl hydroxylase inhibitors: SAR, synthesis, and modeling evaluation

Inhibition of the PHD2 enzyme has been associated with increased red blood cell levels. From a screening hit, a series of novel hydroxyl-thiazoles were developed as potent PHD2 inhibitors.     

Crystal structure of the EndoG/EndoGI complex: mechanism of EndoG inhibition

EndoG is a ubiquitous nuclease that is translocated into the nucleus during apoptosis to participate in DNA degradation. The enzyme cleaves double- and single-stranded DNA and RNA. Related nucleases are found in eukaryotes and prokaryotes, which have evolved sophisticated mechanisms for genome protection against self-antagonizing nuclease activity. Common mechanisms of inhibition are secretion, sequestration into a separate cellular compartment or by binding to protein inhibitors. Although EndoG is silenced by compartmentalization into the mitochondrial intermembrane space, a nucleus-localized protein inhibitor protects cellular polynucleotides from degradation by stray EndoG under non-apoptotic conditions in Drosophila. Here, we report the first three-dimensional structure of EndoG in complex with its inhibitor EndoGI. Although the mechanism of inhibition is reminiscent of bacterial protein inhibitors, EndoGI has evolved independently from a generic protein-protein interaction module. EndoGI is a two-domain protein that binds the active sites of two monomers of EndoG, with EndoG being sandwiched between EndoGI. Since the amino acid sequences of eukaryotic EndoG homologues are highly conserved, this model is valid for eukaryotic dimeric EndoG in general. The structure indicates that the two active sites of EndoG occupy the most remote spatial position possible at the molecular surface and a concerted substrate processing is unlikely.     

Molecular Identification and Hidden Diversity of Novel Daphnia Parasites from European Lakes

Parasites play important roles in local population dynamics and genetic structure. However, due to insufficient diagnostic tools, detailed host-parasite interactions may remain concealed by hidden parasite diversity in natural systems. Microscopic examination of 19 European lake Daphnia populations revealed the presence of three groups of parasites: fungi, microsporidia, and oomycetes. For most of these parasites no genetic markers have been described so far. Based on sequence similarities of the nuclear small-subunit and internal transcribed spacer (ITS) rRNA gene regions, one fungus, four microsporidian, and nine oomycete taxa were discovered in 147 infected Daphnia (and/or three other zooplankton crustaceans). Additionally, cloning of rRNA gene regions revealed parasite sequence variation within host individuals. This was most pronounced in the ITS region of one microsporidian taxon, where the within-host sequence variation ranged from 1.7% to 5.3% polymorphic sites for parasite isolates from 14 different geographical locations. Interestingly, the parasite isolates from close locations grouped together based on sequence similarities, suggesting that there was parasite dispersal. Taken together, the data obtained in this study revealed hidden diversity of parasite communities in Daphnia lake populations. Moreover, a higher level of resolution for identifying parasite strains makes it possible to test new hypotheses with respect to parasite dispersal, transmission routes, and coinfection.During the last decade, microparasites of Daphnia species, which are small zooplankton crustaceans, have become a popular study system in ecological and evolutionary research (for a review, see reference 15). It has been shown both in the field and under controlled laboratory conditions that parasites have a substantial impact on Daphnia fitness (7, 21, 52). Parasite-induced reductions in Daphnia population density (11, 12) or even population crashes (17) might result in disruptions of aquatic food webs, as daphnids play important roles as main phytoplankton grazers and as a major food of planktivorous fish (27). Moreover, as infections are often genotype specific (6, 8), they can lead to changes in the gene pool of a Daphnia population (7, 14), sometimes significantly increasing the genetic diversity of the host population (12, 54). Thus, Daphnia parasites cause not only ecological but also evolutionary changes in aquatic systems.Conclusions regarding the importance of parasites in natural systems require powerful tools to detect and properly identify parasite taxa. Thus far, few species-specific molecular markers have been developed for Daphnia parasites (33, 38, 39, 41) and then used in experimental studies (3). In surveys of natural Daphnia populations, parasite identification has been based primarily on microscopic examination (4, 5, 29, 52), with only one exception (32). The parasites recorded in natural populations of Daphnia are thus considered members of certain taxa, or even species, without genetic confirmation. The fact that molecular markers are not used to characterize Daphnia infections makes it difficult to compare epidemic patterns across different habitats and/or various field surveys, as parasites cannot be unambiguously identified by microscopic examination alone. Even if microscopic identification is theoretically possible (for example, by examining ultrastructural morphology by electron microscopy [37]), this approach is not feasible for routine analysis. Consequently, classification of parasites that actually belong to different taxa in the same group might introduce noise into field surveys, as parasite taxa differ widely in virulence and host range (for a review, see reference 15).Most of the known Daphnia parasites that have been described were obtained from small temporary ponds and rock pools (4, 16, 43). In permanent lakes, lower parasite diversity was assumed, mainly because increased fish predation reduces the population density of potential hosts (18), whereas high host density is a crucial determinant of epidemic spread (1, 2, 45). In addition, infected Daphnia spp. are more vulnerable to fish that hunt visually due to loss of their transparent appearance (11, 13). On the other hand, it was recently shown that even if Daphnia host density was reduced by selective fish predation, the prevalence of infection did not decline, probably due to the very high rates of transmission of the parasite that was observed (11). In contrast, we expected that the highly heterogeneous biotic and abiotic conditions in permanent lakes (27) would provide a variety of niches (for a review, see reference 47), which also favor a high level of parasite diversity. Therefore, Czech canyon-shaped reservoirs were chosen as our main study systems, because in these lakes environmental gradients are particularly pronounced in both the horizontal and vertical dimensions (42). Moreover, the Daphnia communities of these reservoirs are dominated by members of the Daphnia longispina complex (35), taxa which have previously been shown to be infected by a variety of parasites (52).The results of our study revealed a high level of diversity of Daphnia parasites in permanent lakes. Fourteen different parasite taxa were detected using nuclear small-subunit (SSU) and internal transcribed spacer (ITS) rRNA gene sequence information. In addition, a high level of sequence variation was observed in the ITS region of one microsporidian taxon. Thus, molecular markers are now available which allow discrimination with high resolution among and within parasite taxa and provide tools to address more detailed questions concerning lake Daphnia-microparasite systems.