Genome-Scale Validation of Deep-Sequencing Libraries

Chromatin immunoprecipitation followed by high-throughput (HTP) sequencing (ChIP-seq) is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers. Here we report a protocol, Mab-seq, that generates genome-scale quality evaluations for nucleic acid libraries intended for deep-sequencing. We show how commercially available genomic microarrays can be used to maximize the efficiency of library creation and quickly generate reliable preliminary data on a chromosomal scale in advance of deep sequencing. We also exploit this technique to compare enriched regions identified using microarrays with those identified by sequencing, demonstrating that they agree on a core set of clearly identified enriched regions, while characterizing the additional enriched regions identifiable using HTP sequencing.     

Indirect reciprocity and the evolution of “moral signals”

Signals regarding the behavior of others are an essential element of human moral systems and there are important evolutionary connections between language and large-scale cooperation. In particular, social communication may be required for the reputation tracking needed to stabilize indirect reciprocity. Additionally, scholars have suggested that the benefits of indirect reciprocity may have been important for the evolution of language and that social signals may have coevolved with large-scale cooperation. This paper investigates the possibility of such a coevolution. Using the tools of evolutionary game theory, we present a model that incorporates primitive “moral signaling” into a simple setting of indirect reciprocity. This model reveals some potential difficulties for the evolution of “moral signals.” We find that it is possible for “moral signals” to evolve alongside indirect reciprocity, but without some external pressure aiding the evolution of a signaling system, such a coevolution is unlikely.     

Measles Immune Suppression: Lessons from the Macaque Model

Measles remains a significant childhood disease, and is associated with a transient immune suppression. Paradoxically, measles virus (MV) infection also induces robust MV-specific immune responses. Current hypotheses for the mechanism underlying measles immune suppression focus on functional impairment of lymphocytes or antigen-presenting cells, caused by infection with or exposure to MV. We have generated stable recombinant MVs that express enhanced green fluorescent protein, and remain virulent in non-human primates. By performing a comprehensive study of virological, immunological, hematological and histopathological observations made in animals euthanized at different time points after MV infection, we developed a model explaining measles immune suppression which fits with the “measles paradox”. Here we show that MV preferentially infects CD45RA⁻ memory T-lymphocytes and follicular B-lymphocytes, resulting in high infection levels in these populations. After the peak of viremia MV-infected lymphocytes were cleared within days, followed by immune activation and lymph node enlargement. During this period tuberculin-specific T-lymphocyte responses disappeared, whilst strong MV-specific T-lymphocyte responses emerged. Histopathological analysis of lymphoid tissues showed lymphocyte depletion in the B- and T-cell areas in the absence of apoptotic cells, paralleled by infiltration of T-lymphocytes into B-cell follicles and reappearance of proliferating cells. Our findings indicate an immune-mediated clearance of MV-infected CD45RA⁻ memory T-lymphocytes and follicular B-lymphocytes, which causes temporary immunological amnesia. The rapid oligoclonal expansion of MV-specific lymphocytes and bystander cells masks this depletion, explaining the short duration of measles lymphopenia yet long duration of immune suppression.     

Effects of the North Atlantic Oscillation on growth and phenology of stream insects

Climatic variation associated with the North Atlantic Oscillation (NAO) influences terrestrial and marine ecosystems, but its effects on river and stream ecosystems are less well known. The influence of the NAO on the growth of stream insects was examined using long-term empirical data on the sizes of mayfly and stonefly nymphs and on water temperature data. Models of egg development and nymphal growth in relation to temperature were used to predict the effect of the NAO on phenology. The study was based in two upland streams in mid-Wales UK that varied in the extent of plantation forestry in their catchments. Winter stream temperatures at both sites were positively related to the winter NAO index, being warmer in positive phases and colder in negative phases. The observed mean size and the simulated developmental period of mayfly nymphs were significantly related to the winter NAO index, with nymphs growing faster in positive phases of the NAO, but the growth of stonefly nymphs was not related to the NAO. This may have been due to the semivoltine stonefly lifecycle, but stonefly nymph growth is also generally less dependent on temperature. There were significant differences in growth rates of both species between streams, with nymphs growing more slowly in the forested stream that was consistently cooler than the open stream. Predicted emergence dates for adult mayflies varied by nearly two months between years, depending on the phase of the NAO. Variation in growth and phenology of stream insects associated with the NAO may influence temporal fluctuations in the composition and dynamics of stream communities.