Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design

Finding the minimum energy amino acid side-chain conformation is a fundamental problem in both homology modeling and protein design. To address this issue, numerous computational algorithms have been proposed. However, there have been few quantitative comparisons between methods and there is very little general understanding of the types of problems that are appropriate for each algorithm. Here, we study four common search techniques: Monte Carlo (MC) and Monte Carlo plus quench (MCQ); genetic algorithms (GA); self-consistent mean field (SCMF); and dead-end elimination (DEE). Both SCMF and DEE are deterministic, and if DEE converges, it is guaranteed that its solution is the global minimum energy conformation (GMEC). This provides a means to compare the accuracy of SCMF and the stochastic methods. For the side-chain placement calculations, we find that DEE rapidly converges to the GMEC in all the test cases. The other algorithms converge on significantly incorrect solutions; the average fraction of incorrect rotamers for SCMF is 0.12, GA 0.09, and MCQ 0.05. For the protein design calculations, design positions are progressively added to the side-chain placement calculation until the time required for DEE diverges sharply. As the complexity of the problem increases, the accuracy of each method is determined so that the results can be extrapolated into the region where DEE is no longer tractable. We find that both SCMF and MCQ perform reasonably well on core calculations (fraction amino acids incorrect is SCMF 0.07, MCQ 0.04), but fail considerably on the boundary (SCMF 0.28, MCQ 0.32) and surface calculations (SCMF 0.37, MCQ 0.44).     

MHC class II DRB diversity, selection pattern and population structure in a neotropical bat species, Noctilio albiventris

Genes of the major histocompatibility complex (MHC) have a crucial role in the immune response of vertebrates, alter the individual odour and are involved in shaping mating preferences. Pathogen-mediated selection, sexual selection and maternal-fetal interactions have been proposed as the main drivers of frequently observed high levels of polymorphism in functionally important parts of the MHC. Bats constitute the second largest mammalian order and have recently emerged as important vectors of infectious diseases. In addition, Chiroptera are interesting study subjects in evolutionary ecology in the context of olfactory communication, mate choice and associated fitness benefits. Thus, it is surprising that they belong to the least studied mammalian taxa in terms of their MHC diversity. In this study, we investigated the variability in the functionally important MHC class II gene DRB, evidence for selection and population structure in the group-living lesser bulldog bat, Noctilio albiventris, in Panama. We found a single expressed, polymorphic Noal-DRB gene. The substitution pattern of the nucleotide sequences of the 18 detected alleles provided evidence for positive selection acting above the evolutionary history of the species in shaping MHC diversity. Roosting colonies were not genetically differentiated but females showed lower levels of heterozygosity than males, which might be a sign that the sexes differ in the selection pressures acting on the MHC. This study provides the prerequisites for further investigations of the role of the individual MHC constitution in parasite resistance, olfactory communication and mate choice in N. albiventris and other bats.     

Independent evolution of functional MHC class II DRB genes in New World bat species

Genes of the major histocompatibility complex (MHC) play a pivotal role in the vertebrate immune system and are attractive markers for functional, fitness-related, genetic variation. Although bats (Chiroptera) represent the second largest mammalian order and are prone to various emerging infectious diseases, little is known about MHC evolution in bats. In the present study, we examined expressed MHC class II DRB sequences (exons 1 to 4) of New World bat species, Saccopteryx bilineata, Carollia perspicillata, Noctilio albiventris and Noctilio leporinus (only exon 2). We found a wide range of copy number variation of DRB loci with one locus detected in the genus Noctilio and up to ten functional loci observed in S. bilineata. Sequence variation between alleles of the same taxa was high with evidence for positive selection. We found statistical support for recombination or gene conversion events among sequences within the same but not between bat species. Phylogenetic relationships among DRB alleles provided strong evidence for independent evolution of the functional MHC class II DRB genes in the three investigated species, either by recent gene duplication, or homogenization of duplicated loci by frequent gene conversion events. Phylogenetic analysis of all available chiropteran DRB exon 2 sequences confirmed their monophyletic origin within families, but revealed a possible trans-species mode of evolution pattern in congeneric bat species, e.g. within the genera Noctilio and Myotis. This is the first study investigating phylogenetic relationships of MHC genes within bats and therefore contributes to a better understanding of MHC evolution in one of the most dominant mammalian order.     

Energetic cost of hovering flight in nectar-feeding bats (Phyllostomidae: Glossophaginae) and its scaling in moths, birds and bats

Three groups of specialist nectar-feeders covering a continuous size range from insects, birds and bats have evolved the ability for hovering flight. Among birds and bats these groups generally comprise small species, suggesting a relationship between hovering ability and size. In this study we established the scaling relationship of hovering power with body mass for nectar-feeding glossophagine bats (Phyllostomidae). Employing both standard and fast-response respirometry, we determined rates of gas exchange in Hylonycteris underwoodi (7 g) and Choeronycteris mexicana (13–18 g) during hover-feeding flights at an artificial flower that served as a respirometric mask to estimate metabolic power input. The O₂ uptake rate (V˙ _o2) in ml g⁻¹ h⁻¹ (and derived power input) was 27.3 (1.12 W or 160 W kg⁻¹) in 7-g Hylonycteris and 27.3 (2.63 W or 160 W kg⁻¹) in 16.5-g Choeronycteris and thus consistent with measurements in 11.9-g Glossophagasoricina (158 W kg⁻¹, Winter 1998). V˙ _o2 at the onset of hovering was also used to estimate power during forward flight, because after a transition from level forward to hovering flight gas exchange rates initially still reflect forward flight rates. V˙ _o2 during short hovering events (<1.5 s) was 19.0 ml g⁻¹ h⁻¹ (1.8 W) in 16-g Choeronycteris, which was not significantly different from a previous, indirect estimate of the cost of level forward flight (2.1 W, Winter and von Helversen 1998). Our estimates suggest that power input during hovering flight P _h (W) increased with body mass M (kg) within 13–18-g Choeronycteris (n = 4) as P _h  = 3544 (±2057 SE) M ^{1.76 (±0.21 SE)} and between different glossophagine bat species (n = 3) as P _h  = 128 (±2.4 SE) M ^{0.95 (±0.034 SE)}. The slopes of three scaling functions for flight power (hovering, level forward flight at intermediate speed and submaximal flight power) indicate that: 1. The relationship between flight power to flight speed may change with body mass in the 6–30-g bats from a J- towards a U-shaped curve. 2. A metabolic constraint (hovering flight power equal maximal flight power) may influence the upper size limit of 30–35 g for this group of flower specialists. Mass-specific power input (W kg⁻¹) during hovering flight appeared constant with regard to body size (for the mass ranges considered), but differed significantly (P < 0.001) between groups. Group means were 393 W kg⁻¹ (sphingid moths), 261 W kg⁻¹ (hummingbirds) and 159 W kg⁻¹ (glossophagine bats). Thus, glossophagine bats expend the least metabolic power per unit of body mass supported during hovering flight. At a metabolic power input of 1.1 W a glossophagine bat can generate the lift forces necessary for balancing 7 g against gravitation, whereas a hummingbird can support 4 g and a sphingid moth only 3 g of body mass with the same amount of metabolic energy. These differences in power input were not fully explained by differences in induced power output estimated from Rankine-Froude momentum-jet theory. Accepted: 10 November 1998     

Organization of Ca2+ release units in excitable smooth muscle of the guinea-pig urinary bladder

Ca(2+) release from internal stores (sarcoplasmic reticulum or SR) in smooth muscles is initiated either via pharmaco-mechanical coupling due to the action of an agonist and involving IP3 receptors, or via excitation-contraction coupling, mostly involving L-type calcium channels in the plasmalemma (DHPRs), and ryanodine receptors (RyRs), or Ca(2+) release channels of the SR. This work focuses attention on the structural basis for the coupling between DHPRs and RyRs in phasic smooth muscle cells of the guinea-pig urinary bladder. Immunolabeling shows that two proteins of the SR: calsequestrin and the RyR, and one protein the plasmalemma, the L-type channel or DHPR, are colocalized with each other within numerous, peripherally located sites located within the caveolar domains. Electron microscopy images from thin sections and freeze-fracture replicas identify feet in small peripherally located SR vesicles containing calsequestrin and distinctive large particles clustered within small membrane areas. Both feet and particle clusters are located within caveolar domains. Correspondence between the location of feet and particle clusters and of RyR- and DHPR-positive foci allows the conclusion that calsequestrin, RyRs, and L-type Ca(2+) channels are associated with peripheral couplings, or Ca(2+) release units, constituting the key machinery involved in excitation-contraction coupling. Structural analogies between smooth and cardiac muscle excitation-contraction coupling complexes suggest a common basic mechanism of action.     

Nucleotide sequence, genomic organization and cell-cycle-dependent expression of a Chlamydomonas 14-3-3 gene

Members of the 14-3-3 protein family have been identified as regulatory elements in intracellular signalling pathways and cell cycle control. Previously we reported the nucleotide sequence of a 14-3-3 cDNA cloned from the unicellular green alga Chlamydomonas reinhardtii. In this communication, we describe the nucleotide sequence, the genomic organization and the cell-cycle-dependent expression of the corresponding gene. The coding sequence of this gene was found to be interrupted by four introns of 124, 116, 81, and 659 bp, respectively. Introns 2-4 were found in conserved positions as compared to the Arabidopsis 14-3-3 genes. A counterpart to intron 1 absent in the Arabidopsis 14-3-3 genes was found in the human 14-3-3 epsilon gene.     

Linkage mapping in prairie cordgrass (<Emphasis Type="Italic">Spartina pectinata</Emphasis> Link) using genotyping-by-sequencing

Prairie cordgrass (Spartina pectinata Link) is a polyploid Chloridoid grass with tetraploid (2n = 40), hexaploid (2n = 60), and octoploid (2n = 80) cytotypes and is a potential dedicated energy crop with promising yields in marginal environments. Efforts to breed prairie cordgrass are currently hampered by the lack of a linkage map, the lack of a Chloridoid reference genome, and the lack of information on inheritance patterns (disomic versus polysomic). Genotyping-by-sequencing (GBS) was applied to a population of 85 progenies from a reciprocal cross of heterozygous tetraploid parents. A total of 26,418 SNPs were discovered, with a distribution of allele frequencies suggesting disomic inheritance. A filtered set of 3034 single-dose, high-coverage SNPs was used for pseudo-testcross mapping with 63 progenies, resulting in two parental maps of 20 linkage groups containing 1522 and 1016 SNPs and a nearly 1:1 ratio of coupling to repulsion phase linkages, again suggesting disomic inheritance. Genomic contigs from tef, another Chloridoid grass, were used as a bridge to associate genetic markers in prairie cordgrass with unique positions in the sorghum genome, providing a glimpse into synteny between Chloridoids and other grasses. GBS enabled rapid generation of a linkage map that will aid in future breeding and genomics efforts in prairie cordgrass.     

Plasticity in foraging behaviour and diet buffers effects of inter-annual environmental differences on chick growth and survival in southern rockhopper penguins <Emphasis Type="Italic">Eudyptes chrysocome chrysocome</Emphasis>

In marine ecosystems, primary productivity and consequently food availability for higher trophic levels are often strongly affected by the water temperature. Thus, differences in sea surface temperatures (SST) may lead to differences in the diet composition of predators, but this link is still unknown in many species. By combining GPS tracking and dive analyses on chick-rearing southern rockhopper penguins (Eudyptes chrysocome chrysocome) with stable isotope analyses and monitoring of chick growth rates and chick survival, we here attempted a comprehensive assessment of the effects of inter-annual environmental variability as indicated by SST and chlorophyll a (reflecting primary productivity) data. Inter-annual differences in environmental variables around our study colony on New Island, Falkland/Malvinas Islands, contradicted the general expectation, with higher chlorophyll a concentrations coinciding with higher spring SST in 2010/2011 compared to 2009/2010. Penguins foraged further away from the colony during guard and crèche in 2010/2011 compared to 2009/2010, while performing deeper dives in 2009/2010. Stable isotope mixing models suggested a crustacean-dominated chick diet in 2009/2010, compared to a mixture of squid and fish in 2010/2011. These differences in foraging behaviour and diet, however, had no consequences for chick growth rates or chick survival and thus had no apparent effect on population trajectories. Potentially, environmental conditions in both years could still be seen as favourable compared to other years and breeding sites, enabling the parental birds to buffer the environmental differences by plastic foraging behaviour.