On the role of phylogeny in determining activity patterns of rodents

Evolutionary plasticity is limited, to a certain extent, by phylogenetic constraints. We asked whether the diel activity patterns of animals reflect their phylogenies by analyzing daily activity patterns in the order Rodentia. We carried out a literature survey of activity patterns of 700 species, placing each in an activity time category: diurnal, nocturnal, or active at both periods (a-rhythmic). The proportion of rodents active at these categories in the entire order, was compared to the activity patterns of species of different families for which we had data for over ten species each: Dipodidae, Echimyidae, Geomyidae, Heteromyidae, Muridae, and Sciuridae. Activity times of rodents from different habitat types were also compared to the ordinal activity time pattern. We also calculated the probability that two random species (from a particular subgroup: family, habitat, etc.) will be active in the same period of the day and compared it to this probability with species drawn from the entire order. Activity patterns at the family level were significantly different from the ordinal pattern, emphasizing the strong relationship between intra-family taxonomic affiliation and daily activity patterns. Large families (Muridae and Sciuridae) analyzed by subfamilies and tribes showed a similar but stronger pattern than that of the family level. Thus it is clear that phylogeny constrains the evolution of activity patterns in rodents, and may limit their ability to use the time niche axis for ecological separation. Rodents living in cold habitats differed significantly from the ordinal pattern, showing more diurnal and a-rhythmic activity patterns, possibly due to physiological constraints. Ground-dwelling rodents differed significantly, showing a high tendency towards a-rhythmic activity, perhaps reflecting their specialized habitat. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Isolation of a DNA Fragment Containing Replication Functions from IncP2 Megaplasmid pMG2

Replication functions with IncP2 specificity were identified on a 3-kilobase DNA fragment isolated from the 400-kilobase Pseudomonas megaplasmid pMG2.     

Chromatin Assembly Factor I Mutants Defective for PCNA Binding Require Asf1/Hir Proteins for Silencing

Chromatin assembly factor I (CAF-I) is a conserved histone H3/H4 deposition complex. Saccharomyces cerevisiae mutants lacking CAF-I subunit genes (CAC1 to CAC3) display reduced heterochromatic gene silencing. In a screen for silencing-impaired cac1 alleles, we isolated a mutation that reduced binding to the Cac3p subunit and another that impaired binding to the DNA replication protein PCNA. Surprisingly, mutations in Cac1p that abolished PCNA binding resulted in very minor telomeric silencing defects but caused silencing to be largely dependent on Hir proteins and Asf1p, which together comprise an alternative silencing pathway. Consistent with these phenotypes, mutant CAF-I complexes defective for PCNA binding displayed reduced nucleosome assembly activity in vitro but were stimulated by Asf1p-histone complexes. Furthermore, these mutant CAF-I complexes displayed a reduced preference for depositing histones onto newly replicated DNA. We also observed a weak interaction between Asf1p and Cac2p in vitro, and we hypothesize that this interaction underlies the functional synergy between these histone deposition proteins.     

Temperature dependence of the electric resistivity of the hornet cuticle

Resistance to electricity of the oriental hornet cuticle is temperature dependent. Evidence is provided to suggest that this electric resistance and its organic semiconductor-like behaviour are possibly interconnected with temperature detection by hornets.     

Variability in nectar production and standing crop, and their relation to pollinator visits in a Mediterranean shrub

Nectar standing crops in flowers within an individual plant are often highly variable. This variability may be a by-product of the foraging activity of insect pollinators. Alternatively, plants may be selected to produce highly variable rewards to reduce consecutive visitation by risk-averse pollinators, thus diminishing within-plant pollen transfer. This study evaluated the roles of pollinator control vs. plant control over nectar variability in the bee-pollinated shrub Rosmarinus officinalis L. (Lamiaceae). We sampled nectar production, standing crop and pollinator visits in three shrubs of one population over 17 days during one blooming season. Nectar production rates were highly variable (CV = 1.48), and increased after rainy days. Nectar standing crops were even more variable (CV = 2.16), decreased with increasing temperatures, and increased with time since the last rain. Pollinator visit rates decreased with variability in nectar standing crops, increased with flower number per shrub, and were unaffected by variability in nectar production rates. Repeated sampling of marked flowers revealed no correlation between their nectar standing crops and production rates. These findings support the role of reward variance in reducing pollinator visits, but suggest that plants are not in complete control of this variability. Rather, plant-generated variability can be modified by intensive foraging activity of pollinators. Such pollinator control over nectar variability is likely to reduce the selective advantage of plant-generated reward variation. Handling Editor: Neal Williams.     

Computational generation and screening of RNA motifs in large nucleotide sequence pools

Although identification of active motifs in large random sequence pools is central to RNA in vitro selection, no systematic computational equivalent of this process has yet been developed. We develop a computational approach that combines target pool generation, motif scanning and motif screening using secondary structure analysis for applications to 10¹²–10¹⁴-sequence pools; large pool sizes are made possible using program redesign and supercomputing resources. We use the new protocol to search for aptamer and ribozyme motifs in pools up to experimental pool size (10¹⁴ sequences). We show that motif scanning, structure matching and flanking sequence analysis, respectively, reduce the initial sequence pool by 6–8, 1–2 and 1 orders of magnitude, consistent with the rare occurrence of active motifs in random pools. The final yields match the theoretical yields from probability theory for simple motifs and overestimate experimental yields, which constitute lower bounds, for aptamers because screening analyses beyond secondary structure information are not considered systematically. We also show that designed pools using our nucleotide transition probability matrices can produce higher yields for RNA ligase motifs than random pools. Our methods for generating, analyzing and designing large pools can help improve RNA design via simulation of aspects of in vitro selection.     

A comparison of photographic analyses used to quantify zooxanthella density and pigment concentrations in Cnidarians

Many cnidarians exist in an obligatory mutualism with dinoflagellates commonly called zooxanthellae. When these symbioses are stressed, zooxanthella densities often decrease (i.e., bleaching), resulting in reduced host fitness or mortality. Because zooxanthellae play a prominent role in the coloration of hosts, several analyses of reflected spectra from photographic images have been developed to quantify zooxanthella densities and serve as a proxy for invasive sampling methods. To date these techniques have not been compared. In this study, global information system (GIS) tools, commonly used with aerial and satellite images, and photographs of healthy and bleached sea anemones, Aiptasia pallida (Verrill), were used to compare these image analysis methods. Zooxanthella densities and chlorophyll-a concentrations were correlated with image brightness (i.e., digital number) in: the red, green, and blue bands (RGB); the average of the three RGB bands (RGB/3); intensity and saturation bands (IHS); and using a principal components analysis (PCA) of the RGB bands. RGB brightness correlations with zooxanthella densities and chlorophyll-a concentrations were highest using the blue band, followed by green, then red. Using any one band within RGB, however, restricts comparisons to similar color morphs. RGB/3, IHS or PCA transformations enable intra and inter-specific comparisons where colors may vary. Among these transformations, PCA and intensity had higher correlations, followed by RGB/3, then saturation. RGB/3 and IHS, unlike PCA, ignore the correlations between the three RGB bands, treating each pixel independently. PCA uses these correlations, and in doing so lessens the effects of heteroscedasticity in the data. In addition, the observed reciprocal relationship of intensity and saturation may serve as a standardized criterion for bleaching. Finally, this study demonstrates that GIS has broad interdisciplinary applications for spatial and spectral analyses from the individual colony to reef scale assessments.     

Solar Disinfection of Viruses in Polyethylene Terephthalate Bottles

Solar disinfection (SODIS) of drinking water in polyethylene terephthalate (PET) bottles is a simple, efficient point-of-use technique for the inactivation of many bacterial pathogens. In contrast, the efficiency of SODIS against viruses is not well known. In this work, we studied the inactivation of bacteriophages (MS2 and ϕX174) and human viruses (echovirus 11 and adenovirus type 2) by SODIS. We conducted experiments in PET bottles exposed to (simulated) sunlight at different temperatures (15, 22, 26, and 40°C) and in water sources of diverse compositions and origins (India and Switzerland). Good inactivation of MS2 (>6-log inactivation after exposure to a total fluence of 1.34 kJ/cm²) was achieved in Swiss tap water at 22°C, while less-efficient inactivation was observed in Indian waters and for echovirus (1.5-log inactivation at the same fluence). The DNA viruses studied, ϕX174 and adenovirus, were resistant to SODIS, and the inactivation observed was equivalent to that occurring in the dark. High temperatures enhanced MS2 inactivation substantially; at 40°C, 3-log inactivation was achieved in Swiss tap water after exposure to a fluence of only 0.18 kJ/cm². Overall, our findings demonstrate that SODIS may reduce the load of single-stranded RNA (ssRNA) viruses, such as echoviruses, particularly at high temperatures and in photoreactive matrices. In contrast, complementary measures may be needed to ensure efficient inactivation during SODIS of DNA viruses resistant to oxidation.     

Proteogenomics of glioblastoma associates molecular patterns with survival

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