A web server to locate periodicities in a sequence

Summary : FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db. uoa.gr/FT Contact : shamodr@atlas.uoa.gr      

Effects of predation danger on migration strategies of sandpipers

We examine the potential selective importance of predation danger on the evolution of migration strategies of arctic‐breeding calidrid sandpipers. Adult calidrids truncate parental care for reasons not obviously related to levels of food abundance on the breeding areas or at migratory stopover sites, suggesting that a different trade‐off occurs between providing additional care and adult survivorship. The southward migrations of adult western sandpipers precede those of migratory peregrine falcons by almost a month. By moving early and quickly, adults remain ahead of migrant falcons all the way to their non‐breeding areas, where they rapidly moult flight feathers. They complete the moult just as falcons arrive in late September–October. By migrating early, they avoid exposure to falcons when they are unusually vulnerable, due to the requirements for fuelling migratory flight and of wing feather moult. Juvenile western sandpipers migrate south just as falcon numbers start to increase, but do not moult flight feathers in their first winter. Pacific dunlin use an alternative strategy of remaining and moulting in Alaska after falcons depart, and migrating to their overwintering sites after migrants have passed. East of the Rocky Mountains, the southbound migration of falcons begins 4–6 weeks later. Southbound semipalmated sandpipers make extended migratory stopovers, but their lengths of stay shorten prior to falcon migration to the sites in September. Predation danger also may affect the evolution of migration routes. Southbound western sandpipers fly directly from Alaska to southern British Columbia, in contrast to the multi‐stage journey northward along the Alaska panhandle. We estimate that a direct flight would be more economical on northward migration, but may be avoided because it would expose sandpipers to higher mass‐dependent predation danger from migratory falcons, which travel north with sandpipers. By contrast, few raptors are present in Alaska during preparation for the southward flight. A temporal and spatial window of safety may also permit semipalmated sandpipers to become extremely vulnerable while preparing for trans‐Atlantic southward flights. Danger management may account for the these previously enigmatic features of calidrid migration strategies, and aspects of those of other birds.     

Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses

Cassava is infected by numerous geminiviruses in Africa and India that cause devastating losses to poor farmers. We here describe the molecular diversity of seven representative cassava mosaic geminiviruses (CMGs) infecting cassava from multiple locations in Tanzania. We report for the first time the presence of two isolates in East Africa: (EACMCV-[TZ1] and EACMCV-[TZ7]) of the species East African cassava mosaic Cameroon virus, originally described in West Africa. The complete nucleotide sequence of EACMCV-[TZ1] DNA-A and DNA-B components shared a high overall sequence identity to EACMCV-[CM] components (92% and 84%). The EACMCV-[TZ1] and -[TZ7] genomic components have recombinations in the same genome regions reported in EACMCV-[CM], but they also have additional recombinations in both components. Evidence from sequence analysis suggests that the two strains have the same ancient origin and are not recent introductions. EACMCV-[TZ1] occurred widely in the southern part of the country. Four other CMG isolates were identified: two were close to the EACMV-Kenya strain (named EACMV-[KE/TZT] and EACMV-[KE/TZM] with 96% sequence identity); one isolate, TZ10, had 98% homology to EACMV-UG2Svr and was named EACMV-UG2 [TZ10]; and finally one isolate was 95% identical to EACMV-[TZ] and named EACMV-[TZ/YV]. One isolate of African cassava mosaic virus with 97% sequence identity with other isolates of ACMV was named ACMV-[TZ]. It represents the first ACMV isolate from Tanzania to be sequenced. The molecular variability of CMGs was also evaluated using partial B component nucleotide sequences of 13 EACMV isolates from Tanzania. Using the sequences of all CMGs currently available, we have shown the presence of a number of putative recombination fragments that are more prominent in all components of EACMV than in ACMV. This new knowledge about the molecular CMG diversity in East Africa, and in Tanzania in particular, has led us to hypothesize about the probable importance of this part of Africa as a source of diversity and evolutionary change both during the early stages of the relationship between CMGs and cassava and in more recent times. The existence of multiple CMG isolates with high DNA genome diversity in Tanzania and the molecular forces behind this diversity pose a threat to cassava production throughout the African continent.     

Life-history evolution in guppies. VII. The comparative ecology of high- and low-predation environments

Prior research has demonstrated a strong association between the species of predators that co-occur with guppies and the evolution of guppy life histories. The evolution of these differences in life histories has been attributed to the higher mortality rates experienced by guppies in high-predation environments. Here, we evaluate whether there might be indirect effects of predation on the evolution of life-history patterns and whether there are environmental differences that are correlated with predation. To do so, we quantified features of the physical and chemical environment and the population biology of guppies from seven high- and low-predation localities. We found that high-predation environments tend to be larger streams with higher light levels and higher primary productivity, which should enhance food availability for guppies. We also found that guppy populations from high-predation environments have many more small individuals and fewer large individuals than those from low-predation environments, which is caused by their higher birth rates and death rates. Because of these differences in size distribution, guppies from high-predation environments have only one-fourth of the biomass per unit area, which should also enhance food availability for guppies in these localities. Guppies from high-predation sites allocate more resources to reproduction, grow faster, and attain larger asymptotic sizes, all of which are consistent with higher levels of resource availability. We conclude that guppies from high-predation environments experience higher levels of resource availability in part because of correlated differences in the environment (light levels, primary productivity) and in part as an indirect consequence of predation (death rates and biomass density). These differences in resource availability can, in turn, augment the effect of predator-induced mortality as factors that shape the evolution of guppy life-history patterns. We found no differences in the invertebrate communities from high- and low-predation localities, so we conclude that there do not appear to be multitrophic, indirect effects associated with these differences in predation.     

Antimicrobial metabolites produced by an intertidal Acremonium furcatum

In a screening for antimicrobial metabolites, amides of D-allo- and L-isoleucine derivatives were isolated from the culture of a marine strain of Acremonium furcatum. Structural elucidation of these compounds was performed by analysis of spectroscopic data and confirmed by synthesis. All of the compounds, natural and synthetic intermediates, were bioassayed against bacteria and phytopathogenic fungi, with many showing remarkable antifungal activities.     

Structure of Hepatitis B Surface Antigen from Subviral Tubes Determined by Electron Cryomicroscopy

Hepatitis B virus consists of an icosahedral core containing the double-stranded DNA genome, enveloped by a membrane with embedded surface proteins. The crystal structure of the core protein has been solved but little information about the structure of the surface proteins has so far been available. There are three sizes of surface protein, small (S), medium (M) and large (L), which form disulfide-bonded homo- and heterodimers. The three proteins, expressed from different start sites in the coding sequence, share the common C-terminal S region; the M protein contains an additional preS2 sequence N-terminal to S, and the L protein a further preS1 sequence N-terminal to M. In infected individuals, the surface proteins are produced in huge excess over the amount needed for viral envelopment and are secreted as a heterogeneous mixture of isometric and tubular subviral particles. We have used electron cryomicroscopy to study tubular particles extracted from human serum. Helical Fourier-Bessel analysis was used to calculate a low-resolution map, although it showed that the tubes were quite disordered. From the symmetry derived from this analysis, we used single-particle methods to improve the resolution. We found that the tubes had a diameter of approximately 250 Å, with spike-like features projecting from the membrane. In the plane of the membrane the proteins appear to be close packed. We propose a model for the packing arrangement of surface protein dimers in the tubes.     

Curcumin nanofibers for the purpose of wound healing

Poor wound healing is a highly prevalent clinical problem with, as yet, no entirely satisfactory solution. A new technique, termed electrospinning, may provide a solution to improve wound healing. Due to their large surface area to volume ratio and porosity, the nanofibers created by electrospinning are able to deliver sustained drug release and oxygen to the wound. Using different types of polymers with varying properties helps strengthening nanofiber and exudates absorption. The nanofibers appear to have an ideal structure applicable for wound healing and, in combination with curcumin, can blend the anti-inflammatory and antioxidant properties of curcumin into a highly effective wound dressing. The use of suitable curcumin solvents and the slow release of curcumin from the nanofiber help in overcoming the known limitations of curcumin, specifically its low stability and limited bioavailability. Here, we review the studies which have been done on synthesized nanofibers containing curcumin, produced by the electrospinning technique, for the purpose of wound healing.     

A suite of citrate-derived siderophores from a marine Vibrio species isolated following the Deepwater Horizon oil spill

Nearly all microbes require iron for growth. The low concentration of iron found in the ocean makes iron acquisition a particularly difficult task. In response to these low iron conditions, many bacteria produce low-molecular-weight iron-binding molecules called siderophores to aid in iron uptake. We report herein the isolation and structural characterization of a suite of amphiphilic siderophores called the ochrobactins-OH, which are produced by a Vibrio species isolated from the Gulf of Mexico after the 2010 Deepwater Horizon oil spill. The citrate-based ochrobactins-OH are derivatives of aerobactin, replacing the acetyl groups with fatty acid appendages ranging in size from C8 to C12, and are distinctly different from the ochrobactins in that the fatty acid appendages are hydroxylated rather than unsaturated. The discovery of the marine amphiphilic ochrobactin-OH suite of siderophores increases the geographic and phylogenetic diversity of siderophore-producing bacteria.     

Testing Three Species Distribution Modelling Strategies to Define Fish Assemblage Reference Conditions for Stream Bioassessment and Related Applications

Species distribution models are widely used for stream bioassessment, estimating changes in habitat suitability and identifying conservation priorities. We tested the accuracy of three modelling strategies (single species ensemble, multi-species response and community classification models) to predict fish assemblages at reference stream segments in coastal subtropical Australia. We aimed to evaluate each modelling strategy for consistency of predictor variable selection; determine which strategy is most suitable for stream bioassessment using fish indicators; and appraise which strategies best match other stream management applications. Five models, one single species ensemble, two multi-species response and two community classification models, were calibrated using fish species presence-absence data from 103 reference sites. Models were evaluated for generality and transferability through space and time using four external reference site datasets. Elevation and catchment slope were consistently identified as key correlates of fish assemblage composition among models. The community classification models had high omission error rates and contributed fewer taxa to the ‘expected’ component of the taxonomic completeness (O/E₅₀) index than the other strategies. This potentially decreases the model sensitivity for site impact assessment. The ensemble model accurately and precisely modelled O/E₅₀ for the training data, but produced biased predictions for the external datasets. The multi-species response models afforded relatively high accuracy and precision coupled with low bias across external datasets and had lower taxa omission rates than the community classification models. They inherently included rare, but predictable species while excluding species that were poorly modelled among all strategies. We suggest that the multi-species response modelling strategy is most suited to bioassessment using freshwater fish assemblages in our study area. At the species level, the ensemble model exhibited high sensitivity without reductions in specificity, relative to the other models. We suggest that this strategy is well suited to other non-bioassessment stream management applications, e.g., identifying priority areas for species conservation.