Functional integration for enrolment constrains evolutionary variation of phacopid trilobites despite developmental modularity

Modularity and integration are variational properties expressed at various levels of the biological hierarchy. Mismatches among these levels, for example developmental modules that are integrated in a functional unit, could be informative of how evolutionary processes and trade‐offs have shaped organismal morphologies as well as clade diversification. In the present study, we explored the full, integrated and modular spaces of two developmental modules in phacopid trilobites, the cephalon and the pygidium, and highlight some differences among them. Such contrasts reveal firstly that evolutionary processes operating in the modular spaces are stronger in the cephalon, probably due to a complex regime of selection related to the numerous functions ensured by this module. Secondly, we demonstrate that the same pattern of covariation is shared among species, which also differentiate along this common functional integration. This common pattern might be the result of stabilizing selection acting on the enrolment and implying a coordinate variation between the cephalon and the pygidium in a certain direction of the morphospace. Finally, we noticed that Austerops legrandi differs slightly from other species in that its integration is partly restructured in the way the two modules interact. Such a divergence can result from the involvement of the cephalon in several vital functions that may have constrained the response of the features involved in enrolment and reorganized the covariation of the pygidium with the cephalon. Therefore, it is possible that important evolutionary trade‐offs between enrolment and other functions on the cephalon might have partly shaped the diversification of trilobites.     

Length–weight relationships of six elasmobranch species captured at the artisanal fishery of Margarita Island,Venezuela

This study reports the length – weight relationship (LWR) for five batoid and one shark species, all frequently captured by the artisanal commercial fishery on Margarita Island (10º44’ – 11º10’N and 63º46’ – 64º13’W), Venezuela. In 2013, elasmobranchs captured by the artisanal fleet (using bottom gillnets 200–400 m in length with 5–8 inch mesh size) were identified, sized, weighed and sexed. The value of a ranged from 0.0006 to 0.0351, meanwhile the b value ranged from 2.84 (for pooled Myliobatis freminvillei) to 3.39 (male Mustelus higmani), with r² ranging from 0.920 to 0.991. Differences in LWR due to sex were observed for three elasmobranch species. This study offers LWRs separate for males and females, also for species for which LWRs already exist and thus new knowledge is gained through the estimate presented here.     

Synthesis,resolution, and chiroptical properties of hemicryptophane cage controlling the chirality of propeller arrangement of a C3 triamide unit

The five‐steps synthesis of a hemicryptophane cage combining a benzene‐1,3,5‐tricarboxamide unit and a cyclotriveratrylene (CTV) moiety is described. Chiral high‐performance liquid chromatography (HPLC) was used to resolve the racemic mixture. The absolute configuration of the isolated enantiomers was assigned by comparison of the experimental electronic circular dichroism (ECD) spectra with the calculated ones. X‐ray molecular structures reveal that the capped benzene‐1,3,5‐tricarboxamide unit adopts a structurally chiral conformation in solid state: the chirality of CTV moiety controls the Λ or Δ orientation of the three amides.     

Dynamics of Fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants

In characterizing mutants and covalently inhibited complexes of Fusarium solani cutinase, which is a 197-residue lipolytic enzyme, 34 variant structures, crystallizing in 8 different crystal forms, have been determined, mostly at high resolution. Taking advantage of this considerable body of information, a structural comparative analysis was carried out to investigate the dynamics of cutinase. Surface loops were identified as the major flexible protein regions, particularly those forming the active-site groove, whereas the elements constituting the protein scaffold were found to retain the same conformation in all the cutinase variants studied. Flexibility turned out to be correlated with thermal motion. With a given crystal packing environment, a high flexibility turned out to be correlated with a low involvement in crystal packing contacts. The high degree of crystal polymorphism, which allowed different conformations with similar energy to be detected, made it possible to identify motions which would have remained unidentified if only a single crystal form had been available. Fairly good agreement was found to exist between the data obtained from the structural comparison and those from a molecular dynamics (MD) simulation carried out on the native enzyme. The crystallographic approach used in this study turned out to be a suitable tool for investigating cutinase dynamics. Because of the availability of a set of closely related proteins in different crystal environments, the intrinsic drawback of a crystallographic approach was bypassed. By combining several static pictures, the dynamics of the protein could be monitored much more realistically than what can be achieved on the basis of static pictures alone. Proteins 26:442–458 © 1996 Wiley-Liss, Inc.     

Protein lipoylation in mitochondria requires Fe–S cluster assembly factors NFU4 and NFU5

Plants have evolutionarily conserved NifU (NFU)-domain proteins that are targeted to plastids or mitochondria. “Plastid-type” NFU1, NFU2, and NFU3 in Arabidopsis (Arabidopsis thaliana) play a role in iron–sulfur (Fe–S) cluster assembly in this organelle, whereas the type-II NFU4 and NFU5 proteins have not been subjected to mutant studies in any plant species to determine their biological role. Here, we confirmed that NFU4 and NFU5 are targeted to the mitochondria. The proteins were constitutively produced in all parts of the plant, suggesting a housekeeping function. Double nfu4 nfu5 knockout mutants were embryonic lethal, and depletion of NFU4 and NFU5 proteins led to growth arrest of young seedlings. Biochemical analyses revealed that NFU4 and NFU5 are required for lipoylation of the H proteins of the glycine decarboxylase complex and the E2 subunits of other mitochondrial dehydrogenases, with little impact on Fe–S cluster-containing respiratory complexes or aconitase. Consequently, the Gly-to-Ser ratio was increased in mutant seedlings and early growth improved with elevated CO₂ treatment. In addition, pyruvate, 2-oxoglutarate, and branched-chain amino acids accumulated in nfu4 nfu5 mutants, further supporting defects in the other three mitochondrial lipoate-dependent enzyme complexes. NFU4 and NFU5 interacted with mitochondrial lipoyl synthase (LIP1) in yeast 2-hybrid and bimolecular fluorescence complementation assays. These data indicate that NFU4 and NFU5 have a more specific function than previously thought, most likely providing Fe–S clusters to lipoyl synthase.

A pair of evolutionarily conserved proteins involved in iron–sulfur cofactor assembly have a specific role in lipoate biosynthesis for mitochondrial dehydrogenases.     

Host in reserve: The role of common shrews (Sorex araneus) as a supplementary source of tick hosts in small mammal communities influenced by rodent population cycles

Rodents often act as important hosts for ticks and as pathogen reservoirs. At northern latitudes, rodents often undergo multi‐annual population cycles, and the periodic absence of certain hosts may inhibit the survival and recruitment of ticks. We investigated the potential role of common shrews (Sorex araneus) to serve as a supplementary host source to immature life stages (larvae and nymphs) of a generalist tick Ixodes ricinus and a small mammal specialist tick I. trianguliceps, during decreasing abundances of bank voles (Myodes glareolus). We used generalized mixed models to test whether ticks would have a propensity to parasitize a certain host species dependent on host population size and host population composition across two high‐latitude gradients in southern Norway, by comparing tick burdens on trapped animals. Host population size was defined as the total number of captured animals and host population composition as the proportion of voles to shrews. We found that a larger proportion of voles in the host population favored the parasitism of voles by I. ricinus larvae (estimate = −1.923, p = .039) but not by nymphs (estimate = −0.307, p = .772). I. trianguliceps larvae did not show a lower propensity to parasitize voles, regardless of host population composition (estimate = 0.875, p = .180), while nymphs parasitized shrews significantly more as vole abundance increased (estimate = 2.106, p = .002). These results indicate that common shrews may have the potential to act as a replacement host during periods of low rodent availability, but long‐term observations encompassing complete rodent cycles may determine whether shrews are able to maintain tick range expansion despite low rodent availability.     

Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors

Accurate measurements of metabolic fluxes in living cells are central to metabolism research and metabolic engineering. The gold standard method is model-based metabolic flux analysis (MFA), where fluxes are estimated indirectly from mass isotopomer data with the use of a mathematical model of the metabolic network. A critical step in MFA is model selection: choosing what compartments, metabolites, and reactions to include in the metabolic network model. Model selection is often done informally during the modelling process, based on the same data that is used for model fitting (estimation data). This can lead to either overly complex models (overfitting) or too simple ones (underfitting), in both cases resulting in poor flux estimates. Here, we propose a method for model selection based on independent validation data. We demonstrate in simulation studies that this method consistently chooses the correct model in a way that is independent on errors in measurement uncertainty. This independence is beneficial, since estimating the true magnitude of these errors can be difficult. In contrast, commonly used model selection methods based on the χ²-test choose different model structures depending on the believed measurement uncertainty; this can lead to errors in flux estimates, especially when the magnitude of the error is substantially off. We present a new approach for quantification of prediction uncertainty of mass isotopomer distributions in other labelling experiments, to check for problems with too much or too little novelty in the validation data. Finally, in an isotope tracing study on human mammary epithelial cells, the validation-based model selection method identified pyruvate carboxylase as a key model component. Our results argue that validation-based model selection should be an integral part of MFA model development.