IL2RA/CD25 Gene Polymorphisms: Uneven Association with Multiple Sclerosis (MS) and Type 1 Diabetes (T1D)

Background

IL-2 receptor (IL2R) alpha is the specific component of the high affinity IL2R system involved in the immune response and in the control of autoimmunity.

Methods and Results

Here we perform a replication and fine mapping of the IL2RA gene region analyzing 3 SNPs previously associated with multiple sclerosis (MS) and 5 SNPs associated with type 1 diabetes (T1D) in a collection of 798 MS patients and 927 matched Caucasian controls from the south of Spain. We observed association with MS in 6 of 8 SNPs. The rs1570538, at the 3′- UTR extreme of the gene, previously reported to have a weak association with MS, is replicated here (P = 0.032). The most associated T1D SNP (rs41295061) was not associated with MS in the present study. However, the rs35285258, belonging to another independent group of SNPs associated with T1D, showed the maximal association in this study but different risk allele. We replicated the association of only one (rs2104286) of the two IL2RA SNPs identified in the recently performed genome-wide association study of MS.

Conclusions

These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.     

Paleogenomics in a Temperate Environment: Shotgun Sequencing from an Extinct Mediterranean Caprine

Background

Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations.

Methodology/Principals Findings

A DNA extraction of a ∼6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.

Conclusions

A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.     

The Influence of Clinical Information in the Histopathologic Diagnosis of Melanocytic Skin Neoplasms

Background

We tested the relevance of clinical information in the histopathologic evaluation of melanocytic skin neoplasm (MSN).

Methods

Histopathologic specimens from 99 clinically atypical MSN were circulated among ten histopathologists; each case had clinical information available in a database with a five-step procedure (no information; age/sex/location; clinical diagnosis; clinical image; dermoscopic image); each step had a histopathologic diagnosis (D1 through D5); each diagnostic step had a level of diagnostic confidence (LDC) ranging from 1 (no diagnostic certainty) to 5 (absolute diagnostic certainty). The comparison of the LDC was employed with an analysis of variance (ANOVA) for repeated measures.

Findings

In D1 (no information), 36/99 cases (36.3%) had unanimous diagnosis; in D5 (full information available), 51/99 cases (51.5%) had unanimous diagnosis (p for difference between proportions <0.001). The observer agreement expressed as kappa increased significantly from D1 to D5. The mean LDC linearly increased for each observer from D1 through D5 (p for linear trend <0.001). On average, each histopathologist changed his initial diagnosis in 7 cases (range: 2–23). Most diagnostic changes were in D2 (age/sex/location).

Interpretation

The histopathologic criteria for the diagnosis of MSN can work as such, but the final histopathologic diagnosis is a clinically-aided interpretation. Clinical data sometimes reverse the initial histopathologic evaluation.     

Electron microscopy of Xrcc4 and the DNA ligase IV–Xrcc4 DNA repair complex

The DNA ligase IV–Xrcc4 complex is responsible for the ligation of broken DNA ends in the non-homologous end-joining (NHEJ) pathway of DNA double strand break repair in mammals. Mutations in DNA ligase IV (Lig4) lead to immunodeficiency and radiosensitivity in humans. Only partial structural information for Lig4 and Xrcc4 is available, while the structure of the full-length proteins and their arrangement within the Lig4–Xrcc4 complex is unknown. The C-terminal domain of Xrcc4, whose structure has not been solved, contains phosphorylation sites for DNA-PKcs and is phylogenetically conserved, indicative of a regulatory role in NHEJ. Here, we have purified full length Xrcc4 and the Lig4–Xrcc4 complex, and analysed their structure by single-particle electron microscopy. The three-dimensional structure of Xrcc4 at a resolution of ～37 Å reveals that the C-terminus of Xrcc4 forms a dimeric globular domain connected to the N-terminus by a coiled-coil. The N- and C-terminal domains of Xrcc4 locate at opposite ends of an elongated molecule. The electron microscopy images of the Lig4–Xrcc4 complex were examined by two-dimensional image processing and a double-labelling strategy, identifying the site of the C-terminus of Xrcc4 and the catalytic core of Lig4 within the complex. The catalytic domains of Lig4 were found to be in the vicinity of the N-terminus of Xrcc4. We provide a first sight of the structural organization of the Lig4–Xrcc4 complex, which suggests that the BRCT domains could provide the link of the ligase to Xrcc4 while permitting some movements of the catalytic domains of Lig4. This arrangement may facilitate the ligation of diverse configurations of damaged DNA.     

Quantitative and qualitative analysis of cellular prion protein (PrPC) expression in bovine somatic tissues

The host encoded cellular prion protein (PrP^C) is an N-linked glycoprotein tethered to the cell membrane by a glycophosphatidylinositol (GPI) anchor. Under certain conditions, PrP^C can undergo conversion into a conformationally-altered isoform (PrP^Sc) widely believed to be the pathogenic agent of transmissible spongiform encephalopathies (TSEs). Understanding the tissue-specific expression of PrP^C is crucial considering that cells expressing high levels of PrP^C bear a risk for conversion and accumulation of PrP^Sc. In the present study, fifteen bovine somatic tissues were analyzed for PrP^C expression by quantitative western blot and immunohistochemistry. Quantitative western blot analysis revealed highest expression of PrP^C in cerebellum, obex and spinal cord. Intermediate levels were detected in thymus, intestine, nerve, heart and spleen, and lower levels in lung, muscle, kidney, lymph node, skin, pancreas and liver. Immunohistochemical analysis detected intense cellular-specific PrP^C staining in neurons, thymocytes and lymphocytes. PrP^C was also detected in the enteric wall, pancreatic islets of langerhans, myocardium, pulmonary alveolar sacs, renal glomeruli and dermal epithelial cells. This study demonstrated the quantitatively varied, wide-spread, tissue- and cell-specific expression pattern of PrP^C in bovine somatic tissues. The importance of this study is to lay the foundation for understanding the tissue-specific expression of PrP^C and to consider the potential participation of more bovine tissues in the transmission of BSE infection.Key words: cellular prion protein (PrP^C), protein expression, bovine somatic tissues, BSE, western blot, immunohistochemistry     

Impacts of the emerald ash borer (EAB) eradication and tree mortality: potential for a secondary spread of invasive plant species

Since the discovery of the emerald ash borer in 2002, eradication efforts have been implemented in an attempt to eliminate or contain the spread of this invasive beetle. The eradication protocol called for the removal of every ash tree within a 0.8 km radius around an infested tree. In 2005 this study was established to identify environmental changes attributed to the eradication program and measure subsequent shifts in forest community composition and structure. We conducted this study in Ohio and compared areas that received the eradication treatment (ash trees cut down), to areas that were left uncut, (ash still standing). The goal of this project was to identify how the plant community is responding in these two areas. The eradication protocol accelerated the formation and size of gaps within the forest and thus increased the duration and intensity of light penetrating through to the forest floor. In addition, the use of track vehicles for removal of cut trees resulted in significant soil compaction. The resultant plant community had greater species diversity (H′). When specific species composition differences were compared, an increase in the establishment of invasive plant species was detected in areas that received eradication efforts compared to those that did not. Invasive species accounted for 18.7% of the total herbaceous cover in this highly disturbed environment which included Cirsium arvense, Rhamnus cathartica and 2 species of Lonicera. In contrast, invasive species accounted for <1% of the total herbaceous cover in the undisturbed uncut areas.     

A new herrerasaurid (Dinosauria, Saurischia) from the Upper Triassic Ischigualasto Formation of northwestern Argentina

Herrerasauridae comprises a basal clade of dinosaurs best known from the Upper Triassic of Argentina and Brazil, which have yielded remains of Herrerasaurus ischigualastensis and Staurikosaurus pricei, respectively. Systematic opinion regarding the position of Herrerasauridae at the base of Dinosauria has varied. Here we describe a new herrerasaurid, Sanjuansaurus gordilloi gen. n., sp. n., based on a partial skeleton from Carnian-age strata of the the Upper Triassic Ischigualasto Formation of northwestern Argentina. The new taxon is diagnosed by numerous features, including long, band-shaped and posterolaterally oriented transverse process on the posterior cervical vertebrae; neural spines of the sixth to eighth dorsal vertebrae, at least, bearing acute anterior and posterior processes; scapula and coracoid with everted lateral margins of the glenoid; and short pubis (63% of the femoral length). Phylogenetic analysis placed Sanjuansaurus within a monophyletic Herrerasauridae, at the base of Theropoda and including Herrerasaurus and Staurikosaurus. The presence of Sanjuansaurus at the base of the Ischigualasto Formation, along with other dinosaurs such as Herrerasaurus, Eoraptor, Panphagia, and Chromogisaurus suggests that saurischian dinosaurs in southwestern Pangea were already widely diversified by the late Carnian rather than increasing in diversity across the Carnian-Norian boundary.     

Papillomavirus particles assembled in 293TT cells are infectious in vivo

Papillomaviruses (PVs) demonstrate both tissue and species tropisms. Because PVs replicate only in terminally differentiating epithelium, the recent production of infectious PV particles in 293 cells marks an important breakthrough. In this article, we demonstrate that infectious PV particles produced in 293TT cells can cause papillomatous growths in the natural host animal. Moreover, we show that species-matched PV genomes can be successfully delivered in vivo by a heterologous, species-mismatched PV capsid. Additionally, our results indicate that the addition of the simian virus 40 origin of replication to the papillomavirus genome increases the production of infectious papillomavirus particles by increasing genome amplification in the transfected 293TT cells.     

N-glycans on Nipah virus fusion protein protect against neutralization but reduce membrane fusion and viral entry

Nipah virus (NiV) is a deadly emerging paramyxovirus. The NiV attachment (NiV-G) and fusion (NiV-F) envelope glycoproteins mediate both syncytium formation and viral entry. Specific N-glycans on paramyxovirus fusion proteins are generally required for proper conformational integrity and biological function. However, removal of individual N-glycans on NiV-F had little negative effect on processing or fusogenicity and has even resulted in slightly increased fusogenicity. Here, we report that in both syncytium formation and viral entry assays, removal of multiple N-glycans on NiV-F resulted in marked increases in fusogenicity (>5-fold) but also resulted in increased sensitivity to neutralization by NiV-F-specific antisera. The mechanism underlying the hyperfusogenicity of these NiV-F N-glycan mutants is likely due to more-robust six-helix bundle formation, as these mutants showed increased fusion kinetics and were more resistant to neutralization by a fusion-inhibitory reagent based on the C-terminal heptad repeat region of NiV-F. Finally, we demonstrate that the fusogenicities of the NiV-F N-glycan mutants were inversely correlated with the relative avidities of NiV-F's interactions with NiV-G, providing support for the attachment protein "displacement" model of paramyxovirus fusion. Our results indicate that N-glycans on NiV-F protect NiV from antibody neutralization, suggest that this "shielding" role comes together with limiting cell-cell fusion and viral entry efficiencies, and point to the mechanisms underlying the hyperfusogenicity of these N-glycan mutants. These features underscore the varied roles that N-glycans on NiV-F play in the pathobiology of NiV entry but also shed light on the general mechanisms of paramyxovirus fusion with host cells.