Arrayed primer extension in the "array of arrays" format: a rational approach for microarray-based SNP genotyping

This study provides a new version of the arrayed primer extension (APEX) protocol adapted to the 'array of arrays' platform using an instrumental setup for microarray processing not previously described. The primary aim of the study is to implement a system for rational cost-efficient genotyping where multiple singlenucleotide polymorphisms (SNPs) and individuals are genotyped on each microarray slide. Genotyping results are collected across 185 healthy Danish subjects and 76 SNPs on chromosome 3q13.31, because linkage to atopic disease phenotypes have been suggested in the Danish population. Linkage disequilibrium (LD) results from the experimental data are used in a novel comparison to baseline data defined by the international HapMap SNP database. Comparison on the LD results reveals a strong linear correlation irrespective of LD measure considered: R2 (D') = 0.73 and R2(r2) = 0.54. In conclusion, our results show that this setup is strong enough to support high-throughput genotyping, and these observations support that the HapMap genotype resource is important for defining SNP panels aimed at gene mapping in local subpopulations from Europe.     

Mesenchymal stem cells with high telomerase expression do not actively restore their chromosome arm specific telomere length pattern after exposure to ionizing radiation

Background  

Previous studies have demonstrated that telomeres in somatic cells are not randomly distributed at the end of the chromosomes. We hypothesize that these chromosome arm specific differences in telomere length (the telomere length pattern) may be actively maintained. In this study we investigate the existence and maintenance of the telomere length pattern in stem cells. For this aim we studied telomere length in primary human mesenchymal stem cells (hMSC) and their telomerase-immortalised counterpart (hMSC-telo1) during extended proliferation as well as after irradiation. Telomere lengths were measured using Fluorescence In Situ Hybridization (Q-FISH).     

In vitro and in silico assessment of the developability of a designed monoclonal antibody library

Despite major advances in antibody discovery technologies, the successful development of monoclonal antibodies (mAbs) into effective therapeutic and diagnostic agents can often be impeded by developability liabilities, such as poor expression, low solubility, high viscosity and aggregation. Therefore, strategies to predict at the early phases of antibody development the risk of late-stage failure of antibody candidates are highly valuable. In this work, we employ the in silico solubility predictor CamSol to design a library of 17 variants of a humanized mAb predicted to span a broad range of solubility values, and we examine their developability potential with a battery of commonly used in vitro and in silico assays. Our results demonstrate the ability of CamSol to rationally enhance mAb developability, and provide a quantitative comparison of in vitro developability measurements with each other and with more resource-intensive solubility measurements, as well as with in silico predictors that offer a potentially faster and cheaper alternative. We observed a strong correlation between predicted and experimentally determined solubility values, as well as with measurements obtained using a panel of in vitro developability assays that probe non-specific interactions. These results indicate that computational methods have the potential to reduce or eliminate the need of carrying out laborious in vitro quality controls for large numbers of lead candidates. Overall, our study provides support to the emerging view that the implementation of in silico tools in antibody discovery campaigns can ensure rapid and early selection of antibodies with optimal developability potential.     

Opposed latitudinal patterns of network‐derived and dietary specialization in avian plant–frugivore interaction systems

Latitudinal patterns of biodiversity have been studied for centuries, but it is only during the last decades that species interaction networks have been used to examine the proposed latitudinal gradient of biotic specialization. These studies have given idiosyncratic results, which may either be because of genuine biological differences between systems, different concepts and scales used to quantify biotic specialization or because the methodological approaches used to compare interaction networks were inappropriate. Here we carefully examine the latitudinal specialization gradient using a global dataset of avian plant–frugivore assemblages and interaction networks. In particular, we test whether network‐derived specialization patterns differ from patterns based on assemblage‐level information on avian dietary preferences on specific food types. We found that network‐derived measures of specialization (complementary specialization H₂′ and < d’>, modularity Q) increased with latitude, i.e. frugivorous birds divide the niche of fruiting plants most finely at high latitudes where they also formed more modular interaction networks than at tropical latitudes. However, the strength and significance of the relationship between specialization metrics and latitude was influenced by the methodological approach. On the other hand, assemblage‐level information on avian specialization on fruit diet (i.e. the proportion of obligate frugivorous bird species feeding primarily on fruit) revealed an opposed latitudinal pattern as more bird species were specialized on fruit diet in tropical than in temperate assemblages. This difference in the latitudinal specialization gradient reflects that obligate frugivores require a high diversity of fruit plants, as observed in tropical systems, and fulfil more generalized roles in plant–frugivore networks than bird species feeding on different food types. Future research should focus on revealing the underlying ecological, historical and evolutionary mechanisms shaping these patterns. Our results highlight the necessity of comparing different scales of biotic specialization for a better understanding of geographical patterns of specialization in resource–consumer interactions.     

Late Holocene landscape development around a Roman Iron Age mass grave,Alken Enge,Denmark

Sediments from the small lake Ilsø situated in the Illerup/Alken Enge Valley were studied in order to investigate past landscape development at the time of a probably ritual human mass burial following battle during the Roman Iron Age (ad 1–400). A pollen record from Ilsø and a number of other records from Jutland were combined using the Landscape Reconstruction Algorithm to reconstruct local vegetation changes through the last 2,800 years. These methods were supplemented by studies of catchment-related geochemistry of the Ilsø lake sediments. The results show a marked reforestation event associated with a strong decrease in erosion levels at the very beginning of the first century ad, contemporaneous with the finds of human remains at Alken Enge. Comparison with a pollen record 10 km away and with those from other sites, reveals that this reforestation occurs unusually early and rapidly, and is an unparalleled development in a Danish context. We suggest that the major landscape changes at the beginning of the Roman Iron Age and forest cover for the next few centuries comprise a possible example of ritual control of local land-use.     

Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance

The effective population size (N_e) is a central factor in determining maintenance of genetic variation. The neutral theory predicts that loss of variation depends on N_e, with less genetic drift in larger populations. We monitored genetic drift in 42 Drosophila melanogaster populations of different adult census population sizes (10, 50 or 500) using pooled RAD sequencing. In small populations, variation was lost at a substantially lower rate than expected. This observation was consistent across two ecological relevant thermal regimes, one stable and one with a stressful increase in temperature across generations. Estimated ratios between N_e and adult census size were consistently higher in small than in larger populations. The finding provides evidence for a slower than expected loss of genetic diversity and consequently a higher than expected long‐term evolutionary potential in small fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent with this hypothesis, the X‐chromosome, which is largely free of recessive deleterious alleles due to hemizygosity in males, fits neutral expectations even in small populations. Our experiments provide experimental answers to a range of unexpected patterns in natural populations, ranging from variable diversity on X‐chromosomes and autosomes to surprisingly high levels of nucleotide diversity in small populations.     

Integrated Inflammatory Stress (ITIS) Model

During the last decade, there has been an increasing interest in the coupling between the acute inflammatory response and the Hypothalamic–Pituitary–Adrenal (HPA) axis. The inflammatory response is activated acutely by pathogen- or damage-related molecular patterns, whereas the HPA axis maintains a long-term level of the stress hormone cortisol which is also anti-inflammatory. A new integrated model of the interaction between these two subsystems of the inflammatory system is proposed and coined the integrated inflammatory stress (ITIS) model. The coupling mechanisms describing the interactions between the subsystems in the ITIS model are formulated based on biological reasoning and its ability to describe clinical data. The ITIS model is calibrated and validated by simulating various scenarios related to endotoxin (LPS) exposure. The model is capable of reproducing human data of tumor necrosis factor alpha, adrenocorticotropic hormone (ACTH) and cortisol and suggests that repeated LPS injections lead to a deficient response. The ITIS model predicts that the most extensive response to an LPS injection in ACTH and cortisol concentrations is observed in the early hours of the day. A constant activation results in elevated levels of the variables in the model while a prolonged change of the oscillations in ACTH and cortisol concentrations is the most pronounced result of different LPS doses predicted by the model.     

Three-Dimensional Structure of Aleutian Mink Disease Parvovirus: Implications for Disease Pathogenicity

The three-dimensional structure of expressed VP2 capsids of Aleutian mink disease parvovirus strain G (ADVG-VP2) has been determined to 22 A resolution by cryo-electron microscopy and image reconstruction techniques. A structure-based sequence alignment of the VP2 capsid protein of canine parvovirus (CPV) provided a means to construct an atomic model of the ADVG-VP2 capsid. The ADVG-VP2 reconstruction reveals a capsid structure with a mean external radius of 128 A and several surface features similar to those found in human parvovirus B19 (B19), CPV, feline panleukopenia virus (FPV), and minute virus of mice (MVM). Dimple-like depressions occur at the icosahedral twofold axes, canyon-like regions encircle the fivefold axes, and spike-like protrusions decorate the threefold axes. These spikes are not present in B19, and they are more prominent in ADV compared to the other parvoviruses owing to the presence of loop insertions which create mounds near the threefold axes. Cylindrical channels along the fivefold axes of CPV, FPV, and MVM, which are surrounded by five symmetry-related beta-ribbons, are closed in ADVG-VP2 and B19. Immunoreactive peptides made from segments of the ADVG-VP2 capsid protein map to residues in the mound structures. In vitro tissue tropism and in vivo pathogenic properties of ADV map to residues at the threefold axes and to the wall of the dimples.     

In situ T cells in melanoma

During the past decade new insights have been gained into the role of T lymphocytes in the host's immune response to cancer in general and to melanoma in particular. Several melanoma-associated antigens (MAA) recognized by T cells have been characterized, and a number of HLA class I- and class II-restricted peptides have been identified. These antigens can be divided into three different groups: tumor-associated testis-specific antigens, melanocyte differentiation antigens, and mutated or aberrantly expressed antigens. These proteins give rise to several antigenic peptides. The number of known melanoma-associated peptides that can induce killing by cytotoxic T-lymphocytes (CTL) exceeds 30 and is still increasing. In line with these findings, clinical data indicate that the immune system is essential in the control of tumor growth. A brisk infiltration of lymphocytes is associated with a favorable prognosis, and complete or partial regression of primary melanoma occurs quite frequently. Furthermore, immunomodulatory therapies have accomplished complete or partial tumor regression in a number of patients. However, the immune response is in most cases inadequate to control tumor growth as tumor progression often occurs. Hence, the coexistence of a cellular immune response in melanoma lesions, demonstrated by the presence of clonally expanded T cells, remains a major paradox of tumor immunology. In the present paper we review current knowledge regarding tumor infiltrating lymphocytes (TIL) in melanoma and discuss possible mechanisms of escape from immune surveillance. Received: 20 March 1999 / Accepted: 3 March 1999     

Mutation of fungal endoglucanases into glycosynthases and characterization of their acceptor substrate specificity

Humicola insolens mutant Cel7B E197A is a powerful endo-glycosynthase displaying an acceptor substrate specificity restricted to β-d-glucosyl, β-d-xylosyl, β-d-mannosyl and β-d-glucosaminyl in +1 subsite. Our aim was to extend this substrate specificity to β-d-N-acetylglucosaminyl, in order to get access to a wider array of oligosaccharidic structures obtained through glycosynthase assisted synthesis. In a first approach a trisaccharide bearing a β-d-N-acetylglucosaminyl residue was docked at the +1 subsite of H. insolens Cel7B, indicating that the mutation of only one residue, His209, could lead to the expected wider acceptor specificity. Three H. insolens Cel7B glycosynthase mutants (H209A, H209G and H209A/A211T) were produced and expressed in Aspergillus oryzae. In parallel, sequence alignment investigations showed that several cellulases from family GH7 display an alanine residue instead of histidine at position 209. Amongst them, Trichoderma reesei Cel7B, an endoglucanase sharing the highest degree of sequence identity with Humicola Cel7B, was found to naturally accept a β-d-N-acetylglucosaminyl residue at +1 subsite. The T. reesei Cel7B mutant nucleophile E196A was produced and expressed in Saccharomyces cerevisiae, and its activity as glycosynthase, together with the H. insolens glycosynthase mutants, was evaluated toward various glycosidic acceptors.