The nature of phonons and solitary waves in alpha-helical proteins.

A parametric study of the Davydov model of energy transduction in alpha-helical proteins is described. Previous investigations have shown that the Davydov model predicts that nonlinear interactions between phonons and amide-I excitations can stabilize the latter and produce a long-lived combined excitation (the so-called Davydov soliton), which propagates along the helix. The dynamics of this solitary wave are approximately those of solitons described using the nonlinear Schr?dinger equation. The present study extends these previous investigations by analyzing the effect of helix length and nonlinear coupling efficiency on the phonon spectrum in short and medium length alpha-helical segments. The phonon energy accompanying amide-I excitation shows periodic variation in time with fluctuations that follow three different time scales. The phonon spectrum is highly dependent upon chain length but a majority of the energy remains localized in normal mode vibrations even in the long chain alpha-helices. Variation of the phonon-exciton coupling coefficient changes the amplitudes but not the frequencies of the phonon spectrum. The computed spectra contain frequencies ranging from 200 GHz to 6 THz, and as the chain length is increased, the long period oscillations increase in amplitude. The most important prediction of this study, however, is that the dynamics predicted by the numerical calculations have more in common with dynamics described by using the Frohlich polaron model than by using the Davydov soliton. Accordingly, the relevance of the Davydov soliton model was applied to energy transduction in alpha-helical proteins is questionable.(ABSTRACT TRUNCATED AT 250 WORDS)     

Fluctuations in Adélie penguin prey size in the mid to late Holocene, northern Marguerite Bay, Antarctic Peninsula

We investigated temporal changes in Adélie penguin prey size in northern Marguerite Bay, Antarctic Peninsula, through excavations of three abandoned and one active colony at Lagoon (67°35'S, 68°16'W) and Ginger Islands (67°45'S, 68°41'W), respectively, in austral summer 1999/2000. Radiocarbon dates on penguin bones and eggshell fragments collected at each site indicate that Lagoon Island was first occupied after 6000 BP and Ginger Island near 2275 BP. Identifiable non-krill prey remains (otoliths and squid beaks) were recovered from ornithogenic soils at all sites, with Antarctic silverfish (Pleuragramma antarcticum) and squid (Psychroteuthis glacialis) being the most abundant species represented in the deposits. Estimated mean standard lengths and mantle lengths of these two prey taxa, based on regressions with otolith and beak measurements respectively, indicate that Adélie penguins primarily select these prey within a mean size range of 95-117 mm. Prey size also varied significantly across seven occupation periods from 6000 BP to the present, but did not correlate with climate change.     

Characterization of Streptococcus pneumoniae isolated from children with otitis media

Streptococcus pneumoniae is the main causative agent of acute otitis media in children. Serotype-based vaccines have provided some protection against otitis media, but not as much as anticipated, demonstrating the need for alternative vaccine options. Pneumococcal otitis media isolates were obtained from children 5 years old or younger from hospitals around Mississippi in the prevaccine era (1999-2000). These isolates were compared by capsular typing, pneumococcal surface protein A (PspA) family typing, antibiotic susceptibility, and DNA fingerprinting. Our study shows that there is great genetic variability among pneumococcal clinical isolates of otitis media, except with regard to PspA. Therefore, efforts focused on the development of a PspA-based pneumococcal vaccine would be well placed.     

Genetic construction and functional analysis of hybrid polyketide synthases containing heterologous acyl carrier proteins.

The gene that encodes the acyl carrier protein (ACP) of the actinorhodin polyketide synthase (PKS) of Streptomyces coelicolor A3(2) was replaced with homologs from the granaticin, oxytetracycline, tetracenomycin, and putative frenolicin polyketide synthase gene clusters. All of the replacements led to expression of functional synthases, and the recombinants synthesized aromatic polyketides similar in chromatographic properties to actinorhodin or to shunt products produced by mutants defective in the actinorhodin pathway. Some regions within the ACP were also shown to be interchangeable and allow production of a functional hybrid ACP. Structural analysis of the most abundant polyketide product of one of the recombinants by electrospray mass spectrometry suggested that it is identical to mutactin, a previously characterized shunt product of an actVII mutant (deficient in cyclase and dehydrase activities). Quantitative differences in the product profiles of strains that express the various hybrid synthases were observed. These can be explained, at least in part, by differences in ribosome-binding sites upstream of each ACP gene, implying either that the ACP concentration in some strains is rate limiting to overall PKS activity or that the level of ACP expression also influences the expression of another enzyme(s) encoded by a downstream gene(s) in the same operon as the actinorhodin ACP gene. These results reaffirm the idea that construction of hybrid polyketide synthases will be a useful approach for dissecting the molecular basis of the specificity of PKS-catalyzed reactions. However, they also point to the need for reducing the chemical complexity of the approach by minimizing the diversity of polyketide products synthesized in strains that produce recombinant polyketide synthases.     

Assessing the application of a geographic presence-only model for land suitability mapping

Recent advances in ecological modeling have focused on novel methods for characterizing the environment that use presence-only data and machine-learning algorithms to predict the likelihood of species occurrence. These novel methods may have great potential for land suitability applications in the developing world where detailed land cover information is often unavailable or incomplete. This paper assesses the adaptation and application of the presence-only geographic species distribution model, MaxEnt, for agricultural crop suitability mapping in a rural Thailand where lowland paddy rice and upland field crops predominant. To assess this modeling approach, three independent crop presence datasets were used including a social-demographic survey of farm households, a remote sensing classification of land use/land cover, and ground control points, used for geodetic and thematic reference that vary in their geographic distribution and sample size. Disparate environmental data were integrated to characterize environmental settings across Nang Rong District, a region of approximately 1300 sq. km in size. Results indicate that the MaxEnt model is capable of modeling crop suitability for upland and lowland crops, including rice varieties, although model results varied between datasets due to the high sensitivity of the model to the distribution of observed crop locations in geographic and environmental space. Accuracy assessments indicate that model outcomes were influenced by the sample size and the distribution of sample points in geographic and environmental space. The need for further research into accuracy assessments of presence-only models lacking true absence data is discussed. We conclude that the MaxEnt model can provide good estimates of crop suitability, but many areas need to be carefully scrutinized including geographic distribution of input data and assessment methods to ensure realistic modeling results.     

Cell-lineage patterns in the shoot apical meristem of the germinating maize embryo

A fate map for the shoot apical meristem of Zea mays L. at the time of germination was constructed by examining somatic sectors (clones) induced by -rays. The shoot apical meristem produced stem, leaves, and reproductive structures above leaf 6 after germination and the analysis here concerns their formation. On 160 adult plants which had produced 17 or 18 leaves, 277 anthocyanin-deficient sectors were scored for size and position. Sectors found on the ear shoot or in the tassel most often extended into the vegetative part of the plant. Sectors ranged from one to six internodes in length and some sectors of more than one internode were observed at all positions on the plant. Single-internode sectors predominated in the basal internodes (7,8,9) while longer sectors were common in the middle and upper internodes. The apparent number of cells which gave rise to a particular internode was variable and sectors were not restricted to the lineage unit: a leaf, the internode below it, and the axillary bud and prophyll at the base of the internode. These observations established two major features of meristem activity: 1) at the time of germination the developmental fate of any cell or group of cells was not fixed, and 2) at the time of germination cells at the same location in a meristem could produce greatly different amounts of tissue in the adult plant. Consequently, the developmental fate of specific cells in the germinating meristem could only be assigned in a general way.Abbreviations ACN apparent cell number - LI, LII, LI-LII sectors restricted to the epidermis, the subepidermis, or encompassing epidermis and subepidermis - PCN progenitor cell     

Do “hot moments” become hotter under climate change? Soil nitrogen dynamics from a climate manipulation experiment in a post-harvest forest

Whole-tree forest harvest can increase soil nitrous oxide (N₂O) effluxes and leaching of nitrogen (N) from soils. These altered N dynamics are often linked to harvesting effects on microclimate, suggesting that this “hot moment” for N cycling may become hotter with climate change. We hypothesized that increases in temperature and precipitation during this post-harvest period would increase availability of soil mineral N and soil-atmosphere N₂O efflux. To test this hypothesis we implemented a climate manipulation experiment after a forest harvest, and measured soil N₂O fluxes and inorganic N accumulating on ion exchange resins. Climate treatments were: control (A, ambient), heated (H, +2.5 °C), wetted (W, +23 % precipitation), and a two-factor treatment (H+W). For all treatments, the first year after harvest had highest N₂O efflux and resin N. Wetting significantly increased cumulative soil N₂O fluxes, but only when soils were not heated too. The cumulative soil-to-atmosphere N₂O efflux from W (5.8 mg N₂O–N m^?2) was significantly higher than A (?1.9 mg N₂O–N m^?2), but H+W (~0 mg N₂O–N m^?2) was similar to A. Regardless of wetting, heating increased resin N, but only on certain dates. Cumulative resin N was on average 125 % greater in the H plots than non-heated plots. Thus, changes in temperature and precipitation each impart distinct changes to the soil N cycle. Heating increased resin N regardless of water inputs, while wetting increasing N₂O but not when combined with heating. Our results suggest that climate change may exacerbate soil N losses from whole-tree harvest in the future, but the form and quantity of N loss will depend on how the future climate changes.