Dissecting direct and indirect genetic effects on chronic obstructive pulmonary disease (COPD) susceptibility

Cigarette smoking is the major environmental risk factor for chronic obstructive pulmonary disease (COPD). Genome-wide association studies have provided compelling associations for three loci with COPD. In this study, we aimed to estimate direct, i.e., independent from smoking, and indirect effects of those loci on COPD development using mediation analysis. We included a total of 3,424 COPD cases and 1,872 unaffected controls with data on two smoking-related phenotypes: lifetime average smoking intensity and cumulative exposure to tobacco smoke (pack years). Our analysis revealed that effects of two linked variants (rs1051730 and rs8034191) in the AGPHD1/CHRNA3 cluster on COPD development are significantly, yet not entirely, mediated by the smoking-related phenotypes. Approximately 30 % of the total effect of variants in the AGPHD1/CHRNA3 cluster on COPD development was mediated by pack years. Simultaneous analysis of modestly (r ² = 0.21) linked markers in CHRNA3 and IREB2 revealed that an even larger (~42 %) proportion of the total effect of the CHRNA3 locus on COPD was mediated by pack years after adjustment for an IREB2 single nucleotide polymorphism. This study confirms the existence of direct effects of the AGPHD1/CHRNA3, IREB2, FAM13A and HHIP loci on COPD development. While the association of the AGPHD1/CHRNA3 locus with COPD is significantly mediated by smoking-related phenotypes, IREB2 appears to affect COPD independently of smoking.     

Nominal species of the genus Gyrodactylus von Nordmann 1832 (Monogenea: Gyrodactylidae), with a list of principal host species

The total diversity of the monogenean genus Gyrodactylus is evaluated. There are 409 potentially valid species names within the genus, recorded from c. 400 host species. Five species have been placed within Fundulotrema and an additional 51 Gyrodactylus species names represent synonyms, nomina nuda or have been reassigned to other non-viviparous monogenean genera. While the majority of Gyrodactylus species (59%) are recorded from single hosts, some have a much broader broad range.     

The MHC class II-associated chicken invariant chain shares functional properties with its mammalian homologs

The nucleotide sequence of chicken invariant chain (Ii) was determined, and the amino acid sequence similarity with human Ii is 61%. Certain regions important for the biological function of human Ii are highly conserved between chicken and mammals. The cytoplasmic tail of chicken Ii fused to the plasma membrane reporter molecule neuraminidase relocated the protein to endosomes. Moreover, like the mammalian orthologs, the cytoplasmic tail was found to contain two independent leucine-based endosomal sorting signals. Chicken Ii was found to interact with human Ii and crosslinking studies also indicate that chicken Ii assembles as a trimer. The chicken Ii can furthermore bind the human MHC class II (HLA-DR1). Many of the functional properties between the chicken Ii and its mammalian orthologs are thus maintained in spite of their sequence differences.     

Evaluation of the impact of shielding materials in radiation protection in transgenic animals

We are using a plasmid-based transgenic mouse mutation model system to evaluate the effectiveness of aluminum or low-density polyethylene (LDPE) shielding after 250 MeV/u protons or 1 GeV/u iron ion irradiation. Transgenic mice, with multiple copies of the plasmid pUR288 lacZ transgene integrated into the genome of every cell of the animal, were either irradiated or sham-treated. Multiple endpoints, including early cytogenetic damage in erythrocytes at 48 h after exposure, chromosome aberrations in bone marrow lymphocytes, and lacZ mutant frequencies (MF) in brain and spleen tissues were measured in the same animals. The frequency of total circulating reticulocytes (fRET) dropped precipitously at 48 h after 2 Gy of proton irradiation. The average level of micronucleated reticulocytes (fMN–RET) was fivefold higher in the irradiated samples relative to the controls at the same time point. There was an increase in total chromosome aberrations in bone marrow lymphocytes at 8 weeks after proton irradiation but this increase was not statistically significant relative to the controls. Evaluation of the lacZ MF in the brain and spleen tissues showed that proton irradiation induced a twofold increase in MF in each tissue. Similar samples were collected from animals that were shielded from the proton beam by aluminum. Compared to the unshielded treatment group, we noted no difference in fRET, fMN–RET, chromosome aberrations in lymphocytes and lacZ MF in brain and spleen tissues obtained from these animals. In a separate study, animals were exposed to high-energy iron ions with or without 10 or 15 cm LDPE. Using the same approach, we noted a precipitous drop in fRET, and an elevation in fMN–RET within 48 h after 1 Gy of iron ions. Total chromosome aberrations in bone marrow lymphocytes were slightly elevated but not significant at 8 weeks after iron ion exposure. Shielding animals with 10 or 15 cm of polyethylene appeared to have no effect on the level of RET, MN–RET or chromosome aberrations in these animals. LacZ MF in brain and spleen tissues increased 1.5–2-fold above control levels after 1 Gy iron ions at 8 weeks after treatment. On the other hand, MF in tissues harvested from shielded animals appeared to be lower than their unshielded litermates, suggesting the polyethylene shielding was effective in reducing the iron-induced genomic damage in tissues. Although shielding may be effective, in some cases, in reducing the physical dose of particle radiation, our cytogenetic results showed that the biological impact of the particle beam remain unchanged. On the other hand, reduction in transgene MF in tissues from LDPE-shielded animals but not in the aluminum-shielded animals strongly suggests that careful consideration of the biological endpoints used is necessary in the evaluation of the efficacy of the selected shielding material.     

Invariant chain increases the half-life of MHC II by delaying endosomal maturation

Mounting adaptive immune responses requires the cell surface expression of major histocompatibility class II molecules (MHC II) loaded with antigenic peptide. However, in the absence of antigenic stimuli, the surface population of MHC II is highly dynamic and exhibits a high turnover. Several studies have focused on the regulation of MHC II, and it is now recognized that ubiquitination is one key mechanism operating in the turnover of MHC II in B cells and dendritic cells. Here, we describe how the invariant chain (Ii) can prolong the half-life of MHC II through its action on the endocytic pathway. We find that in cells expressing intermediate-to-high levels of Ii, the half-life of MHC II is increased, with MHC II accumulating in slowly-maturing endosomes. The accumulation in endosomes is not due to retention of new MHC II directed from the endoplasmatic reticulum, as also mature, not Ii associated, MHC II is preserved. We suggest that this alternative endocytic pathway induced by Ii would serve to enhance the rate, quantity and diversity of MHC II antigen presentation by concentrating MHC II into specialized compartments and reducing the need for new MHC II synthesis upon antigen encounter.     

Towards a systems understanding of MHC class I and MHC class II antigen presentation

The molecular details of antigen processing and presentation by MHC class I and class II molecules have been studied extensively for almost three decades. Although the basic principles of these processes were laid out approximately 10 years ago, the recent years have revealed many details and provided new insights into their control and specificity. MHC molecules use various biochemical reactions to achieve successful presentation of antigenic fragments to the immune system. Here we present a timely evaluation of the biology of antigen presentation and a survey of issues that are considered unresolved. The continuing flow of new details into our understanding of the biology of MHC class I and class II antigen presentation builds a system involving several cell biological processes, which is discussed in this Review.     

Trans-Atlantic genetic uniformity in the rare snowbed sedge <Emphasis Type="Italic">Carex rufina</Emphasis>

The red-listed, amphi-Atlantic sedge Carex rufina is highly specialized to certain alpine snowbeds, and threatened by current changes in snow cover duration and moisture conditions. Here we address its range-wide genetic diversity, history, and conservation using amplified fragment length polymorphisms (AFLPs). Despite extensive primer testing, we detected very low overall diversity (4.1% polymorphic markers). Only a single AFLP phenotype was found throughout Norway and across the Atlantic to Iceland and Greenland, while another was found in Canada, suggesting glacial survival in one East and one West Atlantic refugium. East Atlantic C. rufina has probably been heavily bottlenecked in a small refugium, possibly situated within the maximum limits of the ice sheets. Its lack of diversity is likely maintained through local clonal growth causing longevity of genotypes. Habitat availability appears as the main limiting factor for C. rufina, and its currently occupied habitats need to be preserved to ensure its long-time survival.