MicroRNA regulation of molecular networks mapped by global microRNA, mRNA, and protein expression in activated T lymphocytes

MicroRNAs (miRNAs) regulate specific immune mechanisms, but their genome-wide regulation of T lymphocyte activation is largely unknown. We performed a multidimensional functional genomics analysis to integrate genome-wide differential mRNA, miRNA, and protein expression as a function of human T lymphocyte activation and time. We surveyed expression of 420 human miRNAs in parallel with genome-wide mRNA expression. We identified a unique signature of 71 differentially expressed miRNAs, 57 of which were previously not known as regulators of immune activation. The majority of miRNAs are upregulated, mRNA expression of these target genes is downregulated, and this is a function of binding multiple miRNAs (combinatorial targeting). Our data reveal that consideration of this complex signature, rather than single miRNAs, is necessary to construct a full picture of miRNA-mediated regulation. Molecular network mapping of miRNA targets revealed the regulation of activation-induced immune signaling. In contrast, pathways populated by genes that are not miRNA targets are enriched for metabolism and biosynthesis. Finally, we specifically validated miR-155 (known) and miR-221 (novel in T lymphocytes) using locked nucleic acid inhibitors. Inhibition of these two highly upregulated miRNAs in CD4(+) T cells was shown to increase proliferation by removing suppression of four target genes linked to proliferation and survival. Thus, multiple lines of evidence link top functional networks directly to T lymphocyte immunity, underlining the value of mapping global gene, protein, and miRNA expression.     

The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus

Xenopus NO38 is an abundant nucleolar chaperone and a member of the nucleoplasmin (Np) family. Here, we report high-resolution crystal structures of the N-terminal domain of NO38, as a pentamer and a decamer. As expected, NO38 shares the Np family fold. In addition, NO38- and Np-core pentamers each use highly conserved residues and numerous waters to form their respective decamers. Further studies show that NO38 and Np each bind equal amounts of the four core histones. However, NO38 prefers the (H3-H4)(2) tetramer, while Np probably prefers H2A-H2B dimers. We also show that NO38 and Np will each bind noncognate histones when the preferred partner is absent. We suggest that these chaperones must form decamers in order to bind histones and differentiate between histone tetramers and dimers. When taken together, these data imply that NO38 may function as a histone chaperone in the nucleolus.     

Causes of male sexual trait divergence in introduced populations of guppies

Males from different populations of the same species often differ in their sexually selected traits. Variation in sexually selected traits can be attributed to sexual selection if phenotypic divergence matches the direction of sexual selection gradients among populations. However, phenotypic divergence of sexually selected traits may also be influenced by other factors, such as natural selection and genetic constraints. Here, we document differences in male sexual traits among six introduced Australian populations of guppies and untangle the forces driving divergence in these sexually selected traits. Using an experimental approach, we found that male size, area of orange coloration, number of sperm per ejaculate and linear sexual selection gradients for male traits differed among populations. Within populations, a large mismatch between the direction of selection and male traits suggests that constraints may be important in preventing male traits from evolving in the direction of selection. Among populations, however, variation in sexual selection explained more than half of the differences in trait variation, suggesting that, despite within‐population constraints, sexual selection has contributed to population divergence of male traits. Differences in sexual traits were also associated with predation risk and neutral genetic distance. Our study highlights the importance of sexual selection in trait divergence in introduced populations, despite the presence of constraining factors such as predation risk and evolutionary history.     

Variant CJD

It is now 18 years since the first identification of a case of vCJD in the UK. Since that time, there has been much speculation over how vCJD might impact human health. To date there have been 177 case reports in the UK and a further 51 cases worldwide in 11 different countries. Since establishing that BSE and vCJD are of the same strain of agent, we have also shown that there is broad similarity between UK and non-UK vCJD cases on first passage to mice. Transgenic mouse studies have indicated that all codon 129 genotypes are susceptible to vCJD and that genotype may influence whether disease appears in a clinical or asymptomatic form, supported by the appearance of the first case of potential asymptomatic vCJD infection in a PRNP 129MV patient. Following evidence of blood transfusion as a route of transmission, we have ascertained that all blood components and leucoreduced blood in a sheep model of vCJD have the ability to transmit disease. Importantly, we recently established that a PRNP 129MV patient blood recipient with an asymptomatic infection and limited PrP^Sc deposition in the spleen could readily transmit disease into mice, demonstrating the potential for peripheral infection in the absence of clinical disease. This, along with the recent appendix survey which identified 16 positive appendices in a study of 32 441 cases, underlines the importance of continued CJD surveillance and maintaining control measures already in place to protect human health.     

Palaeo‐ecology of the Gap and Coturaundee Ranges,western New South Wales,using stick‐nest rat (Leporillus spp.) (Muridae) middens

Pollen, plant and animal macrofossils recovered from nine Leporillus spp. (Muridae) middens found in the Gap and Coturaundee Ranges, western New South Wales were examined. By comparing current vegetation, pollen from modern surface samples and pollen from midden samples, general vegetation characteristics over the last 6500 years BP were reconstructed. Evidence shows that a greater shrub cover was apparent between 6500 and 5200 BP , while other aspects of the vegetation cover were similar to present. An increase in tree pollen, possibly indicating greater tree cover, occurred around 3400–2600 BP , while vegetation in the last 1300 years was similar to present. These interpretations, particularly from the older samples, are tentative due to spatial and temporal limitations. Animal macrofossils from the middens indicate that several mammal species now extinct or uncommon in western New South Wales have occurred in the area in the past 3000 years. This study also confirms that reconstruction of vegetation from Leporillus spp. midden evidence should be seen as separate ‘snapshots’, rather than continuous records over a stratigraphically defined timescale.     

Robust Hydrocarbon Degradation and Dynamics of Bacterial Communities during Nutrient-Enhanced Oil Spill Bioremediation

Degradation of oil on beaches is, in general, limited by the supply of inorganic nutrients. In order to obtain a more systematic understanding of the effects of nutrient addition on oil spill bioremediation, beach sediment microcosms contaminated with oil were treated with different levels of inorganic nutrients. Oil biodegradation was assessed respirometrically and on the basis of changes in oil composition. Bacterial communities were compared by numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Nutrient amendment over a wide range of concentrations significantly improved oil degradation, confirming that N and P limited degradation over the concentration range tested. However, the extent and rate of oil degradation were similar for all microcosms, indicating that, in this experiment, it was the addition of inorganic nutrients rather than the precise amount that was most important operationally. Very different microbial communities were selected in all of the microcosms. Similarities between DGGE profiles of replicate samples from a single microcosm were high (95% ± 5%), but similarities between DGGE profiles from replicate microcosms receiving the same level of inorganic nutrients (68% ± 5%) were not significantly higher than those between microcosms subjected to different nutrient amendments (63% ± 7%). Therefore, it is apparent that the different communities selected cannot be attributed to the level of inorganic nutrients present in different microcosms. Bioremediation treatments dramatically reduced the diversity of the bacterial community. The decrease in diversity could be accounted for by a strong selection for bacteria belonging to the alkane-degrading Alcanivorax/Fundibacter group. On the basis of Shannon-Weaver indices, rapid recovery of the bacterial community diversity to preoiling levels of diversity occurred. However, although the overall diversity was similar, there were considerable qualitative differences in the community structure before and after the bioremediation treatments.     

Formal language theory and DNA: An analysis of the generative capacity of specific recombinant behaviors

A new manner of relating formal language theory to the study of informational macromolecules is initiated. A language is associated with each pair of sets where the first set consists of double-stranded DNA molecules and the second set consists of the recombinational behaviors allowed by specified classes of enzymatic activities. The associated language consists of strings of symbols that represent the primary structures of the DNA molecules that may potentially arise from the original set of DNA molecules under the given enzymatic activities. Attention is focused on the potential effect of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and reassociated to produce further molecules. The associated languages are analysed by means of a new generative formalism called a splicing system. A significant subclass of these languages, which we call the persistent splicing languages, is shown to coincide with a class of regular languages which have been previously studied in other contexts: the strictly locally testable languages. This study initiates the formal analysis of the generative power of recombinational behaviors in general. The splicing system formalism allows observations to be made concerning the generative power of general recombination and also of sets of enzymatic activities that include general recombination.     

An assessment of the influence of recruitment from the sediment on the development of planktonic populations of cyanobacteria in a temperate mesotrophic lake

1. A number of planktonic cyanobacteria species form resting stages that survive in the sediments of lakes. The significance of this life history strategy to the ecology of new planktonic populations was investigated in Esthwaite Water, a mesotrophic lake in the English Lake District.
2. A simple trapping technique was used to quantify vertical movements of five species of buoyant gas-vacuolate cyanobacteria from close to the sediments, along a depth transect.
3. 'Recruitment' from the sediments was found to be widespread amongst the cyanobacteria species associated with the summer phytoplankton community.
4. Estimates of the vertical upward fluxes of cyanobacteria based upon trap catches could not account for observed increases in the planktonic populations suggesting that 'recruitment' was not a significant source of biomass.
5. Vertical upward movements of Anabaena solitaria were recorded prior to this species becoming established in the plankton suggesting that benthic populations might be a source of cells for initial pelagic growth of populations of this species.
6. Low numbers of vegetative filaments of Anabaena flos-aquae , Aphanizomenon flos-aquae and Oscillatoria agardhii were observed in the plankton through the winter. These small overwintering populations appeared to be the primary source of inocula for the large summer populations of these species.