Metabolic scaling: a many-splendoured thing

Animals at rest and during exercise display rates of aerobic metabolism, VO2, that represent mainly the sum of mitochondrial respiration rates in various organs. The relative contributions of these organs change with physiological state such that internal organs such as liver, kidney and brain account for most of the whole-body VO2 at rest, while locomotory muscles account for >90% of the maximum rate, VO2max, during maximal aerobic exercise. Mechanisms that regulate VO2 are complex and the relative importance of each step in a series, estimated by metabolic control analysis, depends upon the level of biological organization under consideration as well as physiological state. Despite this complexity, prominent single-cause models propose that metabolic rates are supply-limited and that the scaling of supply systems provides a sufficient explanation for the allometric scaling of metabolism. We argue that some assumptions, as well as current interpretations of the meaning (or consequences) of these constraints are flawed, i.e., elephants do not have lower mass-specific basal or maximal rates of aerobic metabolism because their mitochondria are more supply-limited than those of shrews. Animals do not violate the laws of physics, and the allometric scaling of supply systems would be expected, to some extent, to be matched by capacities for (and rates of) energy expenditure. But life is not so simple. Animals are so diverse that to do justice to metabolic scaling, it is also necessary to consider the scaling of energy expenditure. It is by doing so that models of metabolic scaling can be consistent with current paradigms in metabolic regulation and accommodate the range of inter- and intraspecific exponents found in nature. The "allometric cascade," a first attempt at such an accounting, was a source of great satisfaction to Peter Hochachka. It was the last door that he helped open to comparative physiologists before he said goodbye.     

Mutational analysis of the 5'' non-coding region of human immunodeficiency virus type 1: effects of secondary structure on translation.

The first 111 nt from the 5' end of human immunodeficiency virus type 1 (HIV-1) mRNAs are shown to have a strong inhibitory effect on the translation of mRNA in in vitro translation extracts as well as in Xenopus oocytes. Mutations in the sequence of the 5' untranslated region (UTR) designed to disrupt predicted secondary structure of this region relieve the inhibition. Inhibition is restored by mutations that reconstruct the predicted secondary structure. The accessibility of the 5'-terminal cap structure was also found to be increased by some of these mutations. We conclude that secondary structure in the 5' UTR of HIV-1 mRNAs and resultant inaccessibility of the cap structure is responsible for the inhibition of translation. The implications of these findings for the understanding of the life cycle of HIV-1 are discussed.     

Bacterial aspects associated with the expression of a single-chain antibody fragment in Escherichia coli

The bacterial expression of a single-chain antibody fragment, designated L6 sFv, was examined. Periplasmic targeting resulted in the production of a correctly folded protein that bound tumor antigen. However, immediately after induction at either 30°C or 37°C there was a significant loss in bacterial viability, which was followed by a loss in absorbance. The loss in absorbance correlated with cell lysis and release of the L6 sFv into the culture supernatant. The kinetics of appearance of L6 sFv in the supernatant paralleled that of periplasmic \-lactamase and confirmed an initial loss of cell-wall integrity prior to cell lysis. Bacteria incubated at 30°C produced approximately threefold more correctly folded antibody fragment because of an increase in the number of cells/A ₆₆₀ at the lower incubation temperature. More than 95% of the L6 sFv, made at either incubation temperature, was incorrectly folded. Osmotic-shock procedures did not release L6 sFv. However, in situ subtilisin susceptibility experiments with bacterial spheroplasts confirmed a periplasmic location. French press disruption resulted in the release of correctly but not incorrectly folded material. Membrane fractionation revealed that the incorrectly folded L6 sFv remained associated with both the inner and outer membrane. These results demonstrate that, in this system, antibody fragment expression resulted initially in cell death, which was followed by release of protein into the culture supernatant and eventually cell lysis. It is also suggested that membrane association in the periplasmic space may impede proper folding.     

Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

Abstract Two chronosequences of unsaturated, buried loess sediments, ranging in age from <10,000 years to >1 million years, were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession was inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Core samples were collected at two sites 40 km apart in the Palouse region of eastern Washington State, near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the Winona site elevation is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was approximately 250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: approximately 1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Same-age sediments had equal quantities of microorganisms, but different community types. Differences in community makeup between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the microbial community age can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be considerably older than the porewater ages, since microbial transport is severely restricted in unsaturated sediments. This is particularly true at the Winona site, which was never flooded.     

Acyl chain specificity of the acyltransferases LpxA and LpxD and substrate availability contribute to lipid A fatty acid heterogeneity in Porphyromonas gingivalis

Porphyromonas gingivalis lipid A is heterogeneous with regard to the number, type, and placement of fatty acids. Analysis of lipid A by matrix-assisted laser desorption ionization-time of flight mass spectrometry reveals clusters of peaks differing by 14 mass units indicative of an altered distribution of the fatty acids generating different lipid A structures. To examine whether the transfer of hydroxy fatty acids with different chain lengths could account for the clustering of lipid A structures, P. gingivalis lpxA (lpxA(Pg)) and lpxD(Pg) were cloned and expressed in Escherichia coli strains in which the homologous gene was mutated. Lipid A from strains expressing either of the P. gingivalis transferases was found to contain 16-carbon hydroxy fatty acids in addition to the normal E. coli 14-carbon hydroxy fatty acids, demonstrating that these acyltransferases display a relaxed acyl chain length specificity. Both LpxA and LpxD, from either E. coli or P. gingivalis, were also able to incorporate odd-chain fatty acids into lipid A when grown in the presence of 1% propionic acid. This indicates that E. coli lipid A acyltransferases do not have an absolute specificity for 14-carbon hydroxy fatty acids but can transfer fatty acids differing by one carbon unit if the fatty acid substrates are available. We conclude that the relaxed specificity of the P. gingivalis lipid A acyltransferases and the substrate availability account for the lipid A structural clusters that differ by 14 mass units observed in P. gingivalis lipopolysaccharide preparations.     

Breeding expansion of sandhill cranes in Quebec

Sandhill cranes (Antigone canadensis) were broadly extirpated from much of their historical range in North America at the beginning of the twentieth century. Various conservation-related legislation, such as the United States Migratory Bird Treaty Act, have assisted with population recovery. The eastern population of sandhill cranes has been growing rapidly since the 1980s and is thought to have expanded its geographic range to Quebec, Canada. Understanding the colonization and habitat use by the species in previously unoccupied breeding areas is necessary to develop and apply management measures. Using a dynamic occupancy modeling approach, we investigated the recent colonization and extirpation patterns of sandhill cranes in Quebec from 2004–2019. We combined data from 3 data sets (helicopter surveys, breeding bird atlas surveys, and eBird) to increase the spatial coverage and the number of species occurrence records while accounting for imperfect detection probability. Detection probability was highest for the helicopter survey (0.70), whereas the 2 other data sets had relatively low detection levels (0.10–0.26). Based on a simulation study, we found that excluding the eBird data from the analysis produced more biased estimates than excluding the atlas and helicopter survey data sets. Throughout the study, sandhill cranes seemed to have completed their colonization of western Quebec and only recently started to nest in eastern areas. Initial occupancy increased with wetland cover and colonization probability increased weakly with the cover of agricultural areas, suggesting that in our study area sandhill cranes rely essentially on natural wetlands during the breeding season.     

Flight muscle enzyme activities do not differ between pelagic and near-shore foraging seabird species

Common terns (Sterna hirundo), sooty terns (S. fuscata) and brown noddies (Anous stolidus) are phylogenetically related seabirds that differ in field activity levels and daily energy expenditure. To test whether muscle metabolic capacities co-evolve with activity levels and energy expenditure, we collected pectoral muscle biopsies from members of each species, and measured the activities of key enzymes in oxidative metabolism (citrate synthase, CS), anaerobic metabolism (lactate dehydrogenase, LDH), glycolysis (pyruvate kinase, PK), fatty acid oxidation (3-hydroxyacyl CoA dehydrogenase) and phosphocreatine hydrolysis (creatine phosphokinase, CPK). We hypothesized that temperate-breeding common terns would have higher enzyme activities than the two tropical species (sooty terns and brown noddies); consistent with the higher activity level of common terns. There were no differences in enzyme activities among adults of the three species. Common tern chicks within 2-3 days of flight had two-fold higher pyruvate kinase activity than adults, suggesting an increased glycolytic capacity in the chicks. Given the lack of difference among species at the enzymatic level, our results support the notion that behavior and whole organism performance can evolve considerably before there are detectable changes in underlying lower-level physiological/biochemical traits.     

Multiscale assessment of the influence of habitat structure and composition on bird assemblages in boreal forest

The relative contributions of habitat structure and composition to biodiversity are often scale-dependent. Although bird communities in boreal forest have been largely altered and threatened by forest harvesting, bird habitat selection in this ecosystem has not been fully understood. Our study aimed to assess the relative contributions of habitat structure and composition on the assemblages of boreal birds at multiple spatial scales characterized by radii ranging from 100 to 1,000?m. We recorded bird species occurrence at 96 stations located in an old-growth forest in the C?te-Nord region of Québec, Canada. We characterized habitat structure using the proportion of dense, open, and sparse stands, and habitat composition using the proportions of coniferous, mixedwood, and deciduous stands. We used partial canonical correspondence analyses and hierarchical variance partitioning to assess the relative contribution of habitat structure and composition on bird assemblage, and logistic regression to model the probability of occurrence for individual species in response to habitat variables. Our results revealed that habitat structure and composition explained similar proportions of the variance in bird assemblage (21.7 vs. 21.6?%), regardless of spatial scale. Whilst logistic regression yielded fair predictions in the occurrence of individual species (i.e., area under the receiver-operating characteristic curve >0.70 for 90?% of the species), it further confirmed our findings in community level analysis. Our study indicates that habitat structure and composition are both important in shaping bird assemblages, but spatial scale draws little influence on their relative contributions.