Individual growth rates do not predict aphid population densities under altered atmospheric conditions

• 1 Altered atmospheric composition, associated with climate change, can modify herbivore population dynamics through CO₂ and/or O₃‐mediated changes in plant quality.
• 2 Although pea aphid Acyrthosiphon pisum genotypes exhibit intraspecific variation in population growth in response to atmospheric composition, the proximate mechanisms underlying this variation are largely unknown.
• 3 By rearing single (green, pink) and mixed (green + pink) pea aphid genotypes on red clover Trifolium pratense at the Aspen Free Air CO₂ and O₃ Enrichment (Aspen FACE) site, we assessed whether: (i) elevated CO₂ and/or O₃ concentrations alter aphid growth and development and (ii) individual aphid growth rates predict aphid population densities.
• 4 We showed that growth and development of individual green and pink aphids were not influenced by CO₂ and/or O₃ concentrations when reared as individual or mixed genotypes. Individual growth rates, however, did not predict population densities.
• 5 Reared as a single genotype, green pea aphid populations decreased in response to elevated CO₂ concentrations, but not in response to elevated CO₂ + O₃ concentrations. Pink pea aphid populations reared as a single genotype were unaffected by augmented CO₂ or O₃. Populations of mixed genotypes, however, were reduced under elevated CO₂ concentrations, irrespective of O₃ concentrations.
• 6 Herbivore population sizes may not readily be predicted from growth rates of individual organisms under atmospheric conditions associated with global climate change.

     

How reliably do amino acid composition comparisons predict sequence similarities between proteins?

A method for comparing amino acid compositions of proteins (Cornish-Bowden, 1977) has been extended to allow proteins of unequal lengths to be compared. The method has been tested by applying it to proteins of known sequence. It tends to exaggerate the amount of difference between unrelated proteins. It is therefore a reliable guide to possible sequence similarities, in that it does not suggest that sequences are similar when they are not, though it sometimes fails to detect genuine similarities. When applied to related proteins the method gives results in good agreement with those predicted. A phylogenetic tree for 37 snake venom toxins has been constructed from their compositions and is similar in most important respects to one constructed from the corresponding sequences.     

Visual acuity measures do not reliably detect childhood refractive error--an epidemiological study

Purpose

To investigate the utility of uncorrected visual acuity measures in screening for refractive error in white school children aged 6-7-years and 12-13-years.

Methods

The Northern Ireland Childhood Errors of Refraction (NICER) study used a stratified random cluster design to recruit children from schools in Northern Ireland. Detailed eye examinations included assessment of logMAR visual acuity and cycloplegic autorefraction. Spherical equivalent refractive data from the right eye were used to classify significant refractive error as myopia of at least 1DS, hyperopia as greater than +3.50DS and astigmatism as greater than 1.50DC, whether it occurred in isolation or in association with myopia or hyperopia.

Results

Results are presented from 661 white 12-13-year-old and 392 white 6-7-year-old school-children. Using a cut-off of uncorrected visual acuity poorer than 0.20 logMAR to detect significant refractive error gave a sensitivity of 50% and specificity of 92% in 6-7-year-olds and 73% and 93% respectively in 12-13-year-olds. In 12-13-year-old children a cut-off of poorer than 0.20 logMAR had a sensitivity of 92% and a specificity of 91% in detecting myopia and a sensitivity of 41% and a specificity of 84% in detecting hyperopia.

Conclusions

Vision screening using logMAR acuity can reliably detect myopia, but not hyperopia or astigmatism in school-age children. Providers of vision screening programs should be cognisant that where detection of uncorrected hyperopic and/or astigmatic refractive error is an aspiration, current UK protocols will not effectively deliver.     

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.

Flux balance models of metabolism use stoichiometry of metabolic pathways, metabolic demands of growth, and optimality principles to predict metabolic flux distribution and cellular growth under specified environmental conditions. These models have provided a mechanistic interpretation of systemic metabolic physiology, and they are also useful as a quantitative tool for metabolic pathway design. Quantitative predictions of cell growth and metabolic by-product secretion that are experimentally testable can be obtained from these models. In the present report, we used independent measurements to determine the model parameters for the wild-type Escherichia coli strain W3110. We experimentally determined the maximum oxygen utilization rate (15 mmol of O2 per g [dry weight] per h), the maximum aerobic glucose utilization rate (10.5 mmol of Glc per g [dry weight] per h), the maximum anaerobic glucose utilization rate (18.5 mmol of Glc per g [dry weight] per h), the non-growth-associated maintenance requirements (7.6 mmol of ATP per g [dry weight] per h), and the growth-associated maintenance requirements (13 mmol of ATP per g of biomass). The flux balance model specified by these parameters was found to quantitatively predict glucose and oxygen uptake rates as well as acetate secretion rates observed in chemostat experiments. We have formulated a predictive algorithm in order to apply the flux balance model to describe unsteady-state growth and by-product secretion in aerobic batch, fed-batch, and anaerobic batch cultures. In aerobic experiments we observed acetate secretion, accumulation in the culture medium, and reutilization from the culture medium. In fed-batch cultures acetate is cometabolized with glucose during the later part of the culture period.(ABSTRACT TRUNCATED AT 250 WORDS)     

A killer appetite: metabolic consequences of carnivory in marine mammals

Among terrestrial mammals, the morphology of the gastrointestinal tract reflects the metabolic demands of the animal and individual requirements for processing, distributing, and absorbing nutrients. To determine if gastrointestinal tract morphology is similarly correlated with metabolic requirements in marine mammals, we examined the relationship between basal metabolic rate (BMR) and small intestinal length in pinnipeds and cetaceans. Oxygen consumption was measured for resting bottlenose dolphins and Weddell seals, and the results combined with data for four additional species of carnivorous marine mammal. Data for small intestinal length were obtained from previously published reports. Similar analyses were conducted for five species of carnivorous terrestrial mammal, for which BMR and intestinal length were known. The results indicate that the BMRs of Weddell seals and dolphins resting on the water surface are 1.6 and 2.3 times the predicted levels for similarly sized domestic terrestrial mammals, respectively. Small intestinal lengths for carnivorous marine mammals depend on body size and are comparatively longer than those of terrestrial carnivores. The relationship between basal metabolic rate (kcal day(-1)) and small intestinal length (m) for both marine and terrestrial carnivores was, BMR=142.5 intestinal length(1.20) (r(2)=0.83). We suggest that elevated metabolic rates among marine mammal carnivores are associated with comparatively large alimentary tracts that are presumably required for supporting the energetic demands of an aquatic lifestyle and for feeding on vertebrate and invertebrate prey.     

Evolutionary rates do not drive latitudinal diversity gradients

Among the several hypotheses invoked for explaining latitudinal diversity gradients (LDGs), some models classified within the 'evolutionary hypothesis' family assume that LDGs are the direct consequence of latitudinal variations in the speciation and/or extinctions rates. Spatially structured simulations of the biogeographical dispersal of a randomly generated clade refute the central tenet of these explanatory models and indicate that global diversity patterns are combined outcomes of geographic and thermal mid-domain effects under a phylogenetically controlled niche conservatism constraint. The positive correlation observed in several higher taxa between speciation rate and diversity does not involve any causal relationship between these two parameters but is most likely the first order by-product of a positive correlation between temperature and per capita speciation rate.     

Interspecific patterns of phenotypic selection do not predict intraspecific patterns

We estimated linear (β) and nonlinear (γ) selection gradients to quantify host plant‐mediated selection on the trait gall size in each of 22 unequally sampled subpopulations of the cynipid gall wasp Belonocnema treatae. We characterized the relationship between variation in subpopulation sample size and the magnitude of and the variance among selection gradients. We then tested the hypothesis that the intraspecific patterns we observed would follow two patterns that have emerged from published estimates of linear and nonlinear selection gradients compiled across species, namely that the average magnitude of β and γ and the variance among estimated β and γ decrease with increasing sample size. For both β and γ, intraspecific patterns of phenotypic selection in relation to sample size were not predicted by interspecific patterns. Thus, our results suggest that when selection is heterogeneous among subpopulations, variation in the biological basis for selection is more important in influencing estimates of selection than is variation in study size. Our study highlights the value of inspecting selection in relation to sampling effort at the level at which understanding the sources of variation in selection is most important, among populations within species.     

Biophysical properties of cadherin bonds do not predict cell sorting

Differential binding between cadherin subtypes is widely believed to mediate cell sorting during embryogenesis. However, a fundamental unanswered question is whether cell sorting is dictated by the biophysical properties of cadherin bonds, or by broader, cadherin-dependent differences in intercellular adhesion or membrane tension. This report describes atomic force microscope measurements of the strengths and dissociation rates of homophilic and heterophilic cadherin (CAD) bonds. Measurements conducted with chicken N-CAD, canine E-CAD, and Xenopus C-CAD demonstrated that all three cadherins cross-react and form multiple, intermolecular bonds. The mechanical and kinetic properties of the heterophilic bonds are similar to the homophilic interactions. The thus quantified bond parameters, together with previously reported adhesion energies were further compared with in vitro cell aggregation and sorting assays, which are thought to mimic in vivo cell sorting. Trends in quantified biophysical properties of the different cadherin bonds do not correlate with sorting outcomes. These results suggest that cell sorting in vivo and in vitro is not governed solely by biophysical differences between cadherin subtypes.     

Increasing metabolic pathway flux by using machine learning models

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Effective population size does not predict codon usage bias in mammals

Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (N_e), with selection on CUB operating less efficiently in species with small N_e. Here, we specifically ask whether variation in N_e predicts differences in CUB in mammals and report two main findings. First, across 41 mammalian genomes, CUB was not correlated with two indirect proxies of N_e (body mass and generation time), even though there was statistically significant evidence of selection shaping CUB across all species. Interestingly, autosomal genes showed higher codon usage bias compared to X‐linked genes, and high‐recombination genes showed higher codon usage bias compared to low recombination genes, suggesting intraspecific variation in N_e predicts variation in CUB. Second, across six mammalian species with genetic estimates of N_e (human, chimpanzee, rabbit, and three mouse species: Mus musculus, M. domesticus, and M. castaneus), N_e and CUB were weakly and inconsistently correlated. At least in mammals, interspecific divergence in N_e does not strongly predict variation in CUB. One hypothesis is that each species responds to a unique distribution of selection coefficients, confounding any straightforward link between N_e and CUB.     

Herbarium records do not predict rediscovery of presumed nationally extinct species

Rediscoveries of species previously thought to be extinct present a dilemma to conservation biology. On one hand, such instances offer the chance to change the course of events away from one that would have led to extinctions. On the other hand, public support for conservation may wane if scientists are frequently seen to overstate and prematurely declare extinctions. Recent studies have adopted a probabilistic approach to infer extinction, using sightings or collections and statistical models to calculate the chance that a species may still be extant. We conduct the first broad-scale test of such models using a recently compiled national red list and national herbarium collection records, including collections of presumed nationally extinct species made after the red list publication, which constitute “rediscoveries”. There was little evidence that the probabilities calculated by these models were associated with rediscoveries over a 3.5-year period. Current probabilistic models of extinction using sighting records could hence be inadequate for use with most natural history collection data.     

Zoo‐housed mammals do not avoid giving birth on weekends

There is evidence that zoo visitor presence can influence the behaviour and, in some cases, adrenal response of zoo animals, and can sometimes compromise animal welfare. In some laboratory studies, significantly more primate births have been reported on weekends, when fewer people are working there, compared with weekdays when staffing levels are at their highest. Here, we investigate whether there is evidence of a “weekend effect” on births in zoo animals as a result of visitor numbers. Unlike laboratories, zoos are typically busier with visitors on weekends than on weekdays, although staffing levels remain fairly consistent across days of the week. If zoo animal parturition is sensitive to human presence, then fewer births would be expected on weekends compared with weekdays. We tested this using birth data and visitor numbers on the entrance gate from zoo records across 16 species representing artiodactyls, perissodactyls, carnivores and primates at four British zoos, to see whether there is an association between mean daily birth rates and average visitor numbers. We predict that, if there is a visitor effect, daily births should be lower on weekends than weekdays and should correlate with mean daily visitor numbers. Results showed that births for all 16 species were randomly distributed through the week, and there was no significant decline in births on weekends. We conclude that the “weekend effect”, if such a thing exists, does not appear to be a feature of zoo births, suggesting that elevated weekend visitor numbers are not sufficiently stressful to trigger delayed parturition.     

Identification of genome-scale metabolic network models using experimentally measured flux profiles

Genome-scale metabolic network models can be reconstructed for well-characterized organisms using genomic annotation and literature information. However, there are many instances in which model predictions of metabolic fluxes are not entirely consistent with experimental data, indicating that the reactions in the model do not match the active reactions in the in vivo system. We introduce a method for determining the active reactions in a genome-scale metabolic network based on a limited number of experimentally measured fluxes. This method, called optimal metabolic network identification (OMNI), allows efficient identification of the set of reactions that results in the best agreement between in silico predicted and experimentally measured flux distributions. We applied the method to intracellular flux data for evolved Escherichia coli mutant strains with lower than predicted growth rates in order to identify reactions that act as flux bottlenecks in these strains. The expression of the genes corresponding to these bottleneck reactions was often found to be downregulated in the evolved strains relative to the wild-type strain. We also demonstrate the ability of the OMNI method to diagnose problems in E. coli strains engineered for metabolite overproduction that have not reached their predicted production potential. The OMNI method applied to flux data for evolved strains can be used to provide insights into mechanisms that limit the ability of microbial strains to evolve towards their predicted optimal growth phenotypes. When applied to industrial production strains, the OMNI method can also be used to suggest metabolic engineering strategies to improve byproduct secretion. In addition to these applications, the method should prove to be useful in general for reconstructing metabolic networks of ill-characterized microbial organisms based on limited amounts of experimental data.     

Antarctic marine molluscs do have an HSP70 heat shock response

The success of any organism depends not only on niche adaptation but also the ability to survive environmental perturbation from homeostasis, a situation generically described as stress. Although species-specific mechanisms to combat “stress” have been described, the production of heat shock proteins (HSPs), such as HSP70, is universally described across all taxa. Members of the HSP70 gene family comprising the constitutive (HSC70) and inducible (HSP70) members, plus GRP78 (glucose-regulated protein, 78 kDa), a related HSP70 family member, were cloned using degenerate polymerase chain reaction (PCR) from two evolutionary divergent Antarctic marine molluscs (Laternula elliptica and Nacella concinna), a bivalve and a gastropod, respectively. The expression of the HSP70 family members was surveyed via quantitative PCR after an acute 2-h heat shock experiment. Both species demonstrated significant up-regulation of HSP70 gene expression in response to increased temperatures. However, the temperature level at which these responses were induced varied with the species (+6–8°C for L. elliptica and +8–10°C for N. concinna) compared to their natural environmental temperature). L. elliptica also showed tissue-specific expression of the genes under study. Previous work on Antarctic fish has shown that they lack the classical heat shock response, with the inducible form of HSP70 being permanently expressed with an expression not further induced under higher temperature regimes. This study shows that this is not the case for other Antarctic animals, with the two molluscs showing an inducible heat shock response, at a level probably set during their temperate evolutionary past.     

Human immunodeficiency virus-specific CD8(+) T-cell responses do not predict viral growth and clearance rates during structured intermittent antiretroviral therapy

There is a continuing search for better ways to use existing drugs against human immunodeficiency virus (HIV). One idea is to use short therapy interruptions to "autovaccinate" HIV-infected patients. A group of 13 chronically HIV-infected patients enrolled in a trial of such so-called structured treatment interruptions (STIs) were intensively studied with respect to their viral load (VL) and HIV-specific CD8+ T-cell (cytotoxic T-lymphocyte [CTL]) responses. We found that 10 of the 13 patients had plateau VLs after STIs that were lower than their pretreatment VLs. While viral rebound rates became lower over STIs, there were no changes in clearance rates. Although numbers of CTLs did increase over the same time that viral rebounds decreased, there was no correlation between CTL count and either viral rebound rates or clearance rates. Finally, we asked whether absolute numbers of or changes in numbers of CTLs predict plateau VLs after STIs. No measure of CTLs was able to predict plateau VLs. Thus, there was no signature in these data of an important contribution to virological control from HIV-specific CD8+ T lymphocytes.