High-throughput Protein Production for X-ray Crystallography and Use of Size Exclusion Chromatography to Validate or Refute Computational Biological Unit Predictions

The production of large numbers of highly purified proteins for X-ray crystallography is a significant bottleneck in structural genomics. At the Joint Center for Structural Genomics (JCSG; http://www.jcsg.org), specific automated protein expression, purification, and analytical methods are being utilized to study the proteome of Thermotoga maritima. Anion exchange and size exclusion chromatography (SEC), intended for the production of highly purified proteins, have been automated and the procedures are described here in detail. Analytical SEC has been included as a standard quality control test. A biological unit (BU) is the macromolecule that has been proven or is presumed to be functional. Correct assignment of BUs from protein structures can be difficult. BU predictions obtained via the Protein Quaternary Structure file server (PQS; http://pqs.ebi.ac.uk/) were compared to SEC data for 16 representative T. maritima proteins whose structures were solved at the JCSG, revealing an inconsistency in five cases. Herein, we report that SEC can be used to validate or disprove PQS-derived oligomeric models. A substantial amount of associated SEC and structural data should enable us to use certain PQS parameters to gauge the accuracy of these computational models and to generally improve their predictions.     

Where biology meets; or how science advances: Presidential Address to the Linnean Society delivered at the Anniversary Meeting, 24th May 1985

Major advances in 'unrestricted' sciences like biology commonly occur when individual scientists (or techniques) cross conventional discipline boundaries; intra-discipline studies are essential for the consolidation and progress of the science, but are less likely to produce significant insights. 'Restricted' (or exact) sciences ignore variation, and are probably less sensitive to warping from specialization. This generalization is illustrated by recent controversies in evolutionary biology, particularly the neutralism debates of the 1970s, where over-rigid adherence to theoretical models and unjustified assumptions about the effects of gene action were made. The consequence of some of these is shown by considering genetic changes in house mouse (Mus domesticus) populations which were used to demonstrate apparent drift operating on neutral traits, whereas longitudinal studies of closed populations proved that strong natural selection may operate; a proper understanding of genetical forces requires a knowledge both of the history of particular populations and of environmental pressures varying in time and space.     

Biological relativity to water–energy dynamics

Climate has long been related to geographical differences in the distribution and diversity of life. What has eluded explanation is why this should be so. One emerging possibility is biological relativity to water–energy dynamics: the relative nature of biotic dynamics to changes in energy/matter conditions caused by changes in water (all states) while doing work, especially liquid water. The dynamic parameters involved – liquid water and optimal energy conditions – are independent of life, and have been shown to provide a simple, globally predictive explanation for co‐variation between climate and the species richness of woody plants. Here I elaborate on what I mean by ‘biological relativity to water–energy dynamics’ and how it should relate to the geography and evolution of life in general (terrestrial, subterranean, marine/aquatic biota). Working through a natural hierarchy of physical, geographical, ecological and biological first principles, I outline the hierarchical, abiotic → biotic conceptual framework within which this idea operates. The implications of this idea include the following. First, the biosphere is better conceptualized as a ‘subsphere’ of the liquid hydrosphere – a system within a system, wherein ‘life’ has all the unique physical properties of liquid water, plus unique emergent properties of its own. Second, the fundamental capacity for life to exist and be dynamic in all biotic systems is determined by the abiotic capacity for liquid water to exist and be dynamic, which is always relative to the capacity for water–energy dynamics in general. Third, liquid water–energy dynamics acts as a fundamental mechanism of evolution, while being a constant mechanism of natural selection. Fourth, over space and time, there should be first‐order predictable and/or systematic differences in the capacity for, operation and outcomes of, biotic dynamics globally (e.g. species richness), that necessarily dissolve into apparent chaos locally. Fifth, biological relativity to water–energy dynamics provides a fundamental and natural framework for operationalizing hierarchy theory and developing trans‐scalar explanations for the geography and evolution of life's diversity.     

Genetic variation in Breviolum antillogorgium,a coral reef symbiont,in response to temperature and nutrients

Symbionts within the family Symbiodiniaceae are important on coral reefs because they provide significant amounts of carbon to many different reef species. The breakdown of this mutualism that occurs as a result of increasingly warmer ocean temperatures is a major threat to coral reef ecosystems globally. Recombination during sexual reproduction and high rates of somatic mutation can lead to increased genetic variation within symbiont species, which may provide the fuel for natural selection and adaptation. However, few studies have asked whether such variation in functional traits exists within these symbionts. We used several genotypes of two closely related species, Breviolum antillogorgium and B. minutum, to examine variation of traits related to symbiosis in response to increases in temperature or nitrogen availability in laboratory cultures. We found significant genetic variation within and among symbiont species in chlorophyll content, photosynthetic efficiency, and growth rate. Two genotypes showed decreases in traits in response to increased temperatures predicted by climate change, but one genotype responded positively. Similarly, some genotypes within a species responded positively to high‐nitrogen environments, such as those expected within hosts or eutrophication associated with global change, while other genotypes in the same species responded negatively, suggesting context‐dependency in the strength of mutualism. Such variation in traits implies that there is potential for natural selection on symbionts in response to temperature and nutrients, which could confer an adaptive advantage to the holobiont.     

Phenotypic plasticity is not affected by experimental evolution in constant,predictable or unpredictable fluctuating thermal environments

The selective past of populations is presumed to affect the levels of phenotypic plasticity. Experimental evolution at constant temperatures is generally expected to lead to a decreased level of plasticity due to presumed costs associated with phenotypic plasticity when not needed. In this study, we investigated the effect of experimental evolution in constant, predictable and unpredictable daily fluctuating temperature regimes on the levels of phenotype plasticity in several life history and stress resistance traits in Drosophila simulans. Contrary to the expectation, evolution in the different regimes did not affect the levels of plasticity in any of the traits investigated even though the populations from the different thermal regimes had evolved different stress resistance and fitness trait means. Although costs associated with phenotypic plasticity are known, our results suggest that the maintenance of phenotypic plasticity might come at low and negligible costs, and thus, the potential of phenotypic plasticity to evolve in populations exposed to different environmental conditions might be limited.     

Diffusion approximations for one-locus multi-allele kin selection,mutation and random drift in group-structured populations: a unifying approach to selection models in population genetics

Diffusion approximations are ascertained from a two-time-scale argument in the case of a group-structured diploid population with scaled viability parameters depending on the individual genotype and the group type at a single multi-allelic locus under recurrent mutation, and applied to the case of random pairwise interactions within groups. The main step consists in proving global and uniform convergence of the distribution of the group types in an infinite population in the absence of selection and mutation, using a coalescent approach. An inclusive fitness formulation with coefficient of relatedness between a focal individual J affecting the reproductive success of an individual I, defined as the expected fraction of genes in I that are identical by descent to one or more genes in J in a neutral infinite population, given that J is allozygous or autozygous, yields the correct selection drift functions. These are analogous to the selection drift functions obtained with pure viability selection in a population with inbreeding. They give the changes of the allele frequencies in an infinite population without mutation that correspond to the replicator equation with fitness matrix expressed as a linear combination of a symmetric matrix for allozygous individuals and a rank-one matrix for autozygous individuals. In the case of no inbreeding, the mean inclusive fitness is a strict Lyapunov function with respect to this deterministic dynamics. Connections are made between dispersal with exact replacement (proportional dispersal), uniform dispersal, and local extinction and recolonization. The timing of dispersal (before or after selection, before or after mating) is shown to have an effect on group competition and the effective population size. In memory of Sam Karlin.     

To Rink or Not to Rink Amide Link, that is the Question to Address for More Economical and Environmentally Sound Solid-Phase Peptide Synthesis

A comparative study is presented on the solid-phase peptide synthesis (SPPS) of the acyl carrier protein (ACP 65–74) sequence on a series of Rink amide resins possessing different matrix structures: poly(vinyl alcohol)-graft-poly(ethylene glycol) (PVA-g-PEG, 4), Tentagel-S-RAM (TG, 5), NovaGel (NG, 6), ChemMatrix (CM, 7) and polystyrene-divinylbenzene (PS-DVB, 8). In this comparison, the PEG-containing resins proved significantly better suited for the synthesis of pure ACP target sequence than the conventional PS-DVB solid supports (75–90% versus 52% crude purity). Amongst themselves, the PEG resins 4-7 exhibited similar capacity for providing pure peptide. Selecting PVA-g-PEG resin for a comparison of Rink amide linker versus no linker, the ACP (65–74) sequence was synthesized directly on the PVA-g-PEG resin 1, under identical conditions as employed in the synthesis on resin 4 bearing the Fmoc Rink linker, except for the final cleavage step, which was performed under more environmentally sound conditions using ester displacement with aqueous ammonia. Relative to its Rink amide counterpart 4, PVA-g-PEG resin 1 was cheaper to produce and possessed twice as much loading capacity (0.48 vs. 0.81 mmol/g). Moreover, Rink-less resin 1 gave higher yields of isolated pure peptide (61 vs. 45%) relative to its Fmoc Rink linker counterpart 4. In light of these results, the importance of the linker has been brought into question. As the need for large scale solid-phase peptide synthesis grows with greater demand for peptide products, ideal resins should be inexpensive to produce and employable under environmentally sound conditions to provide pure products. In this light, PVA-g-PEG resin 1 has demonstrated significant promise for economic and “green” SPPS.     

Biological Role of Tyrosinase Related Protein and its Biosynthesis and Transport From TGN to Stage I Melanosome,Late Endosome,Through Gene Transfection Study

Tyrosinase-related protein (TRP)-1 is one of the most abundant melanosomal glycoproteins involved in melanogenesis. This report summarizes our recent research efforts related to the biological role and biosynthesis of TRP-1 and its transport from TGN (trans-Golgi network) to the stage I melanosome. Our UV irradiation and tyrosinase and TRP-1 cDNA co-transfection studies indicated that human TRP-1 is involved in not only melanogenesis but also prevention of melanocyte death, which may occur during biosynthesis of melanin pigment in the presence of tyrosinase. Furthermore, a coordinated gene interaction was indicated between tyrosinase and TRP-1, resulting in upregulation of mRNA and protein expression of LAMP (lysosome-associated membrane protein)-1 that would directly prevent the tyrosinase-mediated programmed cell death of melanocytes. Similar to tyrosinase, however, TRP-1 appears to require a molecular chaperone, calnexin, which we have cloned recently. Our cDNA transfection study of tyrosinase with calnexin showed clearly the necessity of calnexin in order to have efficient, functional activity of melanosomal glycoprotein, especially tyrosinase. Once glycosylation is completed, TRP-1 will be transported from TGN to the stage I melanosome. At this stage, TRP-1 will have its own target signal, in particular, tyrosine-rich leucine residues in cytoplasmic tail. Our TRP-1 cDNA transfection and immunoelectron microscopy study shows that TRP-1 will be transported through small vesicles, probably non-clathrin-coated type, to large vacuoles, identical to the MPR (mannose-6-phosphate receptor)-positive, late endosomes. In this transport process, a low molecular weight G-protein, rab-7, was isolated from the purified melanosomal protein on 2D-PAGE and identified by subsequent sequencing and PCR amplification. Confocal microscopy with double immunostaining and immunoelectron microscopy confirmed the co-localization of rab-7 and TRP-1 in the melanosomes with early stages of maturation (I-III). Furthermore, this process will also be regulated by phosphatidylinositol 3-kinase (PI-3 kinase).     

Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long‐lived tree endemic to Hainan Island,China

Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long‐lived trees. Dracaena cambodiana is an endangered, long‐lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter‐simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat‐private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments.     

From Augmentation to Conservation of Entomopathogenic Nematodes: Trophic Cascades, Habitat Manipulation and Enhanced Biological Control of Diaprepes abbreviatus Root Weevils in Florida Citrus Groves

The use of entomopathogenic nematodes (EPN) for management of the root weevil, Diaprepes abbreviatus, in Florida citrus groves is considered a biological control success story and typically involves augmentation in which EPN are applied inundatively as biopesticides to quickly kill the pest. However, recent evidence indicates that efficacy of EPN applications in Florida citrus depends on soil type. They are very effective in the well drained coarse sands of the Central Ridge but often less so in poorly drained fine-textured soils of the Flatwoods. Moreover, groves on the Central Ridge can harbor rich communities of endemic EPN that might often suppress weevil populations below economic thresholds, whereas Flatwoods groves tend to have few endemic EPN and frequent weevil problems. Current research is examining the ecological dynamics of EPN in Florida citrus groves, the potential impact of EPN augmentation on soil food webs, especially endemic EPN, and whether habitat manipulation and inoculation strategies might be effective for conserving and enhancing EPN communities to achieve long-term control in problem areas. Conservation biological control could extend the usefulness of EPN in Florida citrus and be especially appropriate for groves with persistent weevil problems.     

How to avoid becoming a prey: Predatory encounters between an orb-weaving spider,Araneus pinguis (Karsch) (Araneae: Araneidae) and flying insects

Insects flying into the web of an orb-weaving spiderAraneus pinguis (Karsch) and their avoidance of (pre-hitting process) and escapes from (post-hitting process) the web were examined by direct observation under natural and semi-natural conditions. In the pre-hitting process, mobile insects such as Brachycera, Lepidoptera and Hymenoptera showed a low hitting ratio (number of insects hitting/number of insects flying within 1 m³ space around the web-site) because of active web avoidance and flying activity in layers lower or higher than those in which the webs are usually laid. In contrast, less mobile insects like Heteroptera, Coleoptera and Homoptera showed a high hitting ratio. In the post-hitting process, Brachycera, Lepidoptera and some Nematocera frequently escaped without being detained by the web. Many Orthoptera and Hymenoptera escaped without any sign of detection by the spider. Coleoptera frequently escaped during the spider's attack. Small insects from the Homoptera, Nematocera and Hymenoptera rarely escaped from the web, but were not immediately attacked. Mean escape time of insects was correlated significantly with capture success of the spider. Overall most of the escapes occurred in the early phases of the predation process. This indicates that escapes are unlikely to result in heavy loss of time and energy expenditure due to unsuccessful predation. Escape patterns of insects seem to be related to their mobility.     

Attraction of red turpentine beetle and other Scolytinae to ethanol, 3‐carene or ethanol + 3‐carene in an Oregon pine forest

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