Can the acoustic adaptation hypothesis predict the structure of Australian birdsong?

The acoustic adaptation hypothesis (AAH) predicts that long-distance signals will be structured so as to maximize their transmission fidelity. Previous studies testing the hypothesis on birdsong have provided equivocal support. The best support comes from large-scale comparative studies and those studies where habitat is characterized as open versus densely vegetated. In the first case, sufficient statistical power is present to detect even small effects on song structure, whereas in the later case the effect size of the habitat may be sufficiently large. Most studies have focused on Holarctic or Neotropical species, which may ultimately share a common evolutionary history. In this study, Australian birds were chosen for a phylogenetically independent test of key predictions of the AAH. Specifically, birds in open habitats were predicted to sing songs with higher frequencies, greater bandwidth, have a greater probability of having overtones, and be emitted at a quicker rate than birds inhabiting densely forested habitats. Acoustic measurements were made on commercially available recordings of 121 species of Australian birds from 41 different families. Analyses controlled for variation explained by body mass (using ANCOVA), and phylogeny (using genus pairs analyses). We found only modest support for the AAH. Our finding that birds in open habitats produced higher frequency vocalizations and greater bandwidth vocalizations is also consistent with hypotheses about signal structure facilitating auditory distance assessment. Forest birds may therefore rely on cues other than frequency-dependent attenuation for ranging.     

How reliably can we predict the reliability of protein structure predictions?

Background  

Comparative methods have been the standard techniques for in silico protein structure prediction. The prediction is based on a multiple alignment that contains both reference sequences with known structures and the sequence whose unknown structure is predicted. Intensive research has been made to improve the quality of multiple alignments, since misaligned parts of the multiple alignment yield misleading predictions. However, sometimes all methods fail to predict the correct alignment, because the evolutionary signal is too weak to find the homologous parts due to the large number of mutations that separate the sequences.     

Can mosquitoes help to unravel the community structure of Plasmodium species?

There has been a recent revival in attempts to understand changes in patterns of abundance of Plasmodium spp. that infect humans. This has been driven by the purportedly beneficial effects of co-infection on clinical pathology and the recognition of Plasmodium vivax as a public health problem in its own right. In contrast to the attention given to mixed-species infections in humans, parasite infections and interactions within the mosquito vector remain poorly documented, even though the distribution of vector-borne parasites such as Plasmodium spp. depends on vector-vertebrate and, crucially, vector-parasite interactions. To understand malaria epidemiology and to design appropriate control measures, this gap must be re-addressed.     

Can the fluorescence of green fluorescent protein chromophore be related directly to the nativity of protein structure?

In studies of green fluorescence protein (GFP) or other proteins with the use of GFP as a marker, the fluorescence of GFP is for the most part related directly to the nativity of its structure. Naturally, such a relation does exist since the chromophore of this protein is formed autocatalytically only just after GFP acquires its native structure. However, the fluorescence method may not yield reliable information on protein structure when studying renaturation and denaturation of this protein (with the formed chromophore). Using proteolysis, denaturant gradient gel electrophoresis and circular dichroism, we demonstrate herein that at major disturbances of the native structure of protein GFP-cycle3 the intensity of fluorescence of its chromophore can change insignificantly. In other words, the chromophore fluorescence does not reliably mirror alterations in protein structure. Since the main conclusions of this study are especially qualitative, it can be suggested that during renaturation/denaturation of wild-type GFP and its “multicolored” mutants their fluorescence is also not always associated with the changes in the structure of these proteins.     

Can biological traits of stream invertebrates help disentangle the effects of multiple stressors in an agricultural catchment?

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Can morphological and behavioral traits predict the foraging and feeding dynamics of social arachnids?

Complex social insect species exhibit task specialization mediated by morphological and behavioral traits. However, evidence of such traits is scarce for other social arthropods. We investigated whether the social pseudoscorpion Paratemnoides nidificator exhibits morphologically and behaviorally specialized individuals in prey capture. We measured body and chela sizes of adult pseudoscorpions and analyzed predation processes. Larger individuals spent more time moving through the colony and foraging than smaller pseudoscorpions. Individuals that captured prey had increased body and absolute chelae sizes. Although larger individuals had relatively small chelae size, they showed a higher probability of prey capture. Larger individuals manipulated prey often, although they fed less than smaller pseudoscorpions. Individuals that initiated captures fed more frequently and for more time than the others. Natural selection might be favoring individuals specialized in foraging and colony protection, allowing smaller and less efficient adults to avoid contact with dangerous prey. To our knowledge, there is incipient information regarding specialized individuals in arachnids, and our results might indicate the emergence of a morphologically specialized group in this species.     

Can the meaning of multiple words be integrated unconsciously?

What are the limits of unconscious language processing? Can language circuits process simple grammatical constructions unconsciously and integrate the meaning of several unseen words? Using behavioural priming and electroencephalography (EEG), we studied a specific rule-based linguistic operation traditionally thought to require conscious cognitive control: the negation of valence. In a masked priming paradigm, two masked words were successively (Experiment 1) or simultaneously presented (Experiment 2), a modifier (‘not’/‘very’) and an adjective (e.g. ‘good’/‘bad’), followed by a visible target noun (e.g. ‘peace’/‘murder’). Subjects indicated whether the target noun had a positive or negative valence. The combination of these three words could either be contextually consistent (e.g. ‘very bad - murder’) or inconsistent (e.g. ‘not bad - murder’). EEG recordings revealed that grammatical negations could unfold partly unconsciously, as reflected in similar occipito-parietal N400 effects for conscious and unconscious three-word sequences forming inconsistent combinations. However, only conscious word sequences elicited P600 effects, later in time. Overall, these results suggest that multiple unconscious words can be rapidly integrated and that an unconscious negation can automatically ‘flip the sign’ of an unconscious adjective. These findings not only extend the limits of subliminal combinatorial language processes, but also highlight how consciousness modulates the grammatical integration of multiple words.     

Can the theory of critical distances predict the failure of shape memory alloys?

Components made from shape memory alloys (SMAs) such as nitinol often fail from stress concentrations and defects such as notches and cracks. It is shown here for the first time that these failures can be predicted using the theory of critical distances (TCDs), a method which has previously been used to study fracture and fatigue in other materials. The TCD uses the stress at a certain distance ahead of the notch to predict the failure of the material due to the stress concentration. The critical distance is believed to be a material property which is related to the microstructure of the material. The TCD is simply applied to a linear model of the material without the need to model the complication of its non-linear behaviour. The non-linear behaviour of the material at fracture is represented in the critical stress. The effect of notches and short cracks on the fracture of SMA NiTi was studied by analysing experimental data from the literature. Using a finite element model with elastic material behaviour, it is shown that the TCD can predict the effect of crack length and notch geometry on the critical stress and stress intensity for fracture, with prediction errors of less than 5%. The value of the critical distance obtained for this material was L?=?90?μm; this may be related to its grain size. The effects of short cracks on stress intensity were studied. It was shown that the same value of the critical distance (L?=?90?μm) could estimate the experimental data for both notches and short cracks.     

Can copper binding to the prion protein generate a misfolded form of the protein?

The native prion protein (PrP) has a two domain structure, with a globular folded α-helical C-terminal domain and a flexible extended N-terminal region. The latter can selectively bind Cu²⁺ via four His residues in the octarepeat (OR) region, as well as two sites (His96 and His111) outside this region. In the disease state, the folded C-terminal domain of PrP undergoes a conformational change, forming amorphous aggregates high in β-sheet content. Cu²⁺ bound to the ORs can be redox active and has been shown to induce cleavage within the OR region, a process requiring conserved Trp residues. Using computational modeling, we have observed that electron transfer from Trp residues to copper can be favorable. These models also reveal that an indole-based radical cation or Cu⁺ can initiate reactions leading to protein backbone cleavage. We have also demonstrated, by molecular dynamics simulations, that Cu²⁺ binding to the His96 and His111 residues in the remaining PrP N-terminal fragment can induce localized β-sheet structure, allowing us to suggest a potential mechanism for the initiation of β-sheet misfolding in the C-terminal domain by Cu²⁺.

Can the presence of structural phosphorus help to discriminate between abiogenic and biogenic magnetites?

The influence of phosphate on the competitive formation of magnetite and lepidocrocite and the properties of magnetite prepared from mixtures of Fe(II) and Fe(III) salts were studied. Products were prepared at 90 °C and pH 12.5 (series 1), 50 °C and pH 7 (series 2) and 20 °C and pH 8 (series 3). The P/Fe atomic ratio in the initial solution ranged from 0 to 3% and the pH was kept at the desired value with NaOH or KOH. Air was used as oxidant in series 2 and 3. All products, which were characterized by X-ray diffraction, transmission electron microscopy, chemical analysis and IR spectroscopy, contained a phase intermediate between magnetite and maghemite (referred to as magnetite in this paper). The products of series 1 consisted only of magnetite at all P/Fe ratios, whereas both magnetite and lepidocrocite formed in series 2 and 3 above a certain P/Fe ratio. On increasing the P/Fe ratio in the initial solution, the magnetite crystals became smaller and more oxidized (i.e. closer to maghemite) and the lepidocrocite/magnetite ratio increased. The P associated with magnetite was partly in the form of occluded P, i.e. non-surface-adsorbed phosphate. IR spectra suggested this P to be structural and occurring as low-symmetry PO₄ units. Because abiogenic magnetites produced in various environments incorporate structural P but some well-characterized biogenic magnetites seem to contain no P or be formed in P-poor environments, we hypothesize that natural magnetites containing occluded P are unlikely to be biogenic. However, more studies are needed to discard the presence of P in biogenic magnetites.     

Can climate matching predict the current and future climatic suitability of the UK for the establishment of non-native birds?

Capsule: Current UK distributions of non-native birds poorly match areas identified as being climatically suitable.

Aims: Non-native species are spreading at unprecedented rates and though invasions are expected to increase under climate change, evidence for this is mixed. We assess climatic suitability throughout the UK based on the apparent match to the climate in species’ native ranges and investigate potential climatic limitation within the non-native range.

Methods: Climate was characterized within polygons representing the native ranges of 167 potentially invasive species. Parts of the UK with current and future climate similar to that in the native range were deemed climatically suitable. The incidence of recent observations inside and outside suitable areas was used to test hypotheses about climatic limitation of non-native ranges.

Results: Climate matching suggests that 69 of 167 non-native bird species could currently find climatically suitable areas for establishment in the UK. Future climate change would see this number increase by 14% by 2080. However, observed occurrences of non-native species in the UK were not significantly correlated to climatic suitability. Only 44 of the 69 species with suitable climate in the UK were present. Moreover, 85% of species observed in the UK had some UK occurrences in climatically unsuitable areas and for 57 species their entire UK range was in climatically unsuitable areas. Similar results were apparent for the subset of 12 species with established UK populations.

Conclusions: Climate matching provides a relatively poor indication of the extent of current and future suitable areas because species can adapt to new climates or other factors constrain the native range and many climatically suitable areas are currently unoccupied. Improvements to climate matching techniques and ongoing surveillance are required to refine predictions to support effective management policies.     

Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins

The packing of α-helices and β-sheets in six $\text{α}\text{β}$ proteins (e.g. flavodoxin) has been analysed. The results provide the basis for a computer algorithm to predict the tertiary structure of an $\text{α}\text{β}$ protein from its amino acid sequence and actual assignment of secondary structure.The packing of an individual α-helix against a β-sheet generally involves two adjacent ± 4 rows of non-polar residues on the α-helix at the positions i, i + 4, i + 8, i + 1, i + 5, i + 9. The pattern of interacting β-sheet residues results from the twisted nature of the sheet surface and the attendant rotation of the side-chains. At a more detailed level, four of the α-helical residues (i + 1, i + 4, i + 5 and i + 8) form a diamond that surrounds one particular β-sheet residue, generally isoleucine, leucine or valine. In general, the α-helix sits 10 Å above the sheet and lies parallel to the strand direction.The prediction follows a combinational approach. First, a list of possible β-sheet structures (10⁶ to 10¹⁴) is constructed by the generation of all β-sheet topologies and β-strand alignments. This list is reduced by constraints on topology and the location of non-polar residues to mediate the sheet/helix packing, and then rank-ordered on the extent of hydrogen bonding. This algorithm was uniformly applied to 16 $\text{α}\text{β}$ domains in 13 proteins. For every structure, one member of the reduced list was close to the crystal structure; the root-mean-square deviation between equivalenced C^α atoms averaged 5.6 Å for 100 residues. For the $\text{α}\text{β}$ proteins with pure parallel β-sheets, the total number of structures comparable to or better than the native in terms of hydrogen bonds was between 1 and 148. For proteins with mixed β-sheets, the worst case is glyceraldehyde-3-phosphate dehydrogenase, where as many as 3800 structures would have to be sampled. The evolutionary significance of these results as well as the potential use of a combinatorial approach to the protein folding problem are discussed.     

Can Gas-Exchange Characteristics help Explain the Invasive Success of Lythrum salicaria?

Since its introduction to North America, Lythrum salicaria (L.) (purple loosestrife) has become invasive in marshy and riparian habitats. We compared gas-exchange responses to external CO₂ partial pressure and light, as well as related leaf structural and biochemical characteristics, of L. salicaria with those of co-occurring native Asclepias syriaca (common milkweed) and Solidago graminifolia (lance-leaved goldenrod) along a pond bank in the Black Rock Forest, Cornwall, New York, USA to examine if the invasive success of L. salicaria may be influenced by robust leaf gas-exchange characteristics, including relatively high rates of photosynthesis and low rates of respiration, compared with those of less successful co-occurring native plant species. Neither the mean rate of net photosynthesis measured at ambient CO₂ and saturating photon flux density (A) nor the mean dark respiration rate (R_D) differed significantly between L. salicaria and either of the native species, while both the mean maximum rate of photosynthesis at saturating CO₂ concentration and photon flux density (A _max) and the mean rate of respiration measured in light (R_L) were significantly higher in L. salicaria than A. syriaca, but no different between L. salicaria and S. graminifolia. Likewise, photosynthetic nitrogen-use efficiency was greater in L. salicaria than A. syriaca only, while photosynthetic water-use efficiency was significantly less in both L. salicaria and S. graminifolia than in A. syriaca. Despite limited interspecific differences in leaf photosynthesis, respiration, and resource-use efficiency, particularly between L. salicaria and S. graminifolia, we found that L. salicaria assimilated 208% more carbon per unit of energy invested in leaf biomass than either of the co-occurring native species, suggesting that increased photosynthetic energy-use efficiency may influence its observed invasive success. This revised version was published online in July 2006 with corrections to the Cover Date.     

Can molecular dynamics simulations provide high‐resolution refinement of protein structure?

Recent advances in efficient and accurate treatment of solvent with the generalized Born approximation (GB) have made it possible to substantially refine the protein structures generated by various prediction tools through detailed molecular dynamics simulations. As demonstrated in a recent CASPR experiment, improvement can be quite reliably achieved when the initial models are sufficiently close to the native basin (e.g., 3-4 A C(alpha) RMSD). A key element to effective refinement is to incorporate reliable structural information into the simulation protocol. Without intimate knowledge of the target and prediction protocol used to generate the initial structural models, it can be assumed that the regular secondary structure elements (helices and strands) and overall fold topology are largely correct to start with, such that the protocol limits itself to the scope of refinement and focuses the sampling in vicinity of the initial structure. The secondary structures can be enforced by dihedral restraints and the topology through structural contacts, implemented as either multiple pair-wise C(alpha) distance restraints or a single sidechain distance matrix restraint. The restraints are weakly imposed with flat-bottom potentials to allow sufficient flexibility for structural rearrangement. Refinement is further facilitated by enhanced sampling of advanced techniques such as the replica exchange method (REX). In general, for single domain proteins of small to medium sizes, 3-5 nanoseconds of REX/GB refinement simulations appear to be sufficient for reasonable convergence. Clustering of the resulting structural ensembles can yield refined models over 1.0 A closer to the native structure in C(alpha) RMSD. Substantial improvement of sidechain contacts and rotamer states can also be achieved in most cases. Additional improvement is possible with longer sampling and knowledge of the robust structural features in the initial models for a given prediction protocol. Nevertheless, limitations still exist in sampling as well as force field accuracy, manifested as difficulty in refinement of long and flexible loops.     

ROOTMAP—a model in three-dimensional coordinates of the growth and structure of fibrous root systems

A model is described which simulates the growth of fibrous root systems. The root growth is specified in terms of growing time, numbers of axes, initiation times of axes, growth rates and branching characteristics of the roots, and characteristics governing the direction of root growth. The model generates a representation of the root system in which the locations of all branches and root tips are recorded in three-dimensional coordinates, and updates this representation in discrete time steps until the specified growing time is reached. Data are presented from a simulation of wheat root growth by the model. The simulated root system is represented pictorially and also graphically in the form of root length and root tip number profiles which are stratified by branching order class. The pictorial representations produced by the model are much more realistic than any which have been produced by past root growth models, and the graphical representations show trends in root length and root tip numbers which are the same as those commonly observed in real roots.     

Can life history predict the effect of demographic stochasticity on extinction risk?

Demographic stochasticity is important in determining extinction risks of small populations, but it is largely unknown how its effect depends on the life histories of species. We modeled effects of demographic stochasticity on extinction risk in a broad range of generalized life histories, using matrix models and branching processes. Extinction risks of life histories varied greatly in their sensitivity to demographic stochasticity. Comparing life histories, extinction risk generally increased with increasing fecundity and decreased with higher ages of maturation. Effects of adult survival depended on age of maturation. At lower ages of maturation, extinction risk peaked at intermediate levels of adult survival, but it increased along with adult survival at higher ages of maturation. These differences were largely explained by differences in sensitivities of population growth to perturbations of life-history traits. Juvenile survival rate contributed most to total demographic variance in the majority of life histories. Our general results confirmed earlier findings, suggesting that empirical patterns can be explained by a relatively simple model. Thus, basic life-history information can be used to assign life-history-specific sensitivity to demographic stochasticity. This is of great value when assessing the vulnerability of small populations.