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PubMed2001

Differential evolution of eastern equine encephalitis virus populations in response to host cell type.

Arthropod-borne viruses (arboviruses) cycle between hosts in two widely separated taxonomic groups, vertebrate amplifying hosts and invertebrate vectors, both of which may separately or in concert shape the course of arbovirus evolution. To elucidate the selective pressures associated with virus replication within each portion of this two-host life cycle, the effects of host type on the growth characteristics of the New World alphavirus, eastern equine encephalitis (EEE) virus, were investigated. Multiple lineages of an ancestral EEE virus stock were repeatedly transferred through either mosquito or avian cells or in alternating passages between these two cell types. When assayed in both cell types, derived single host lineages exhibited significant differences in infectivity, growth pattern, plaque morphology, and total virus yield, demonstrating that this virus is capable of host-specific evolution. Virus lineages grown in alternation between the two cell types expressed intermediate phenotypes consistent with dual adaptation to both cellular environments. Both insect-adapted and alternated lineages greatly increased in their ability to infect insect cells. These results indicate that different selective pressures exist for virus replication within each portion of the two-host life cycle, and that alternation of hosts selects for virus populations well adapted for replication in both host systems.

Animals↗

PubMed1993

Comparison of the sequence of fibrinopeptide A cleavage from fibrinogen fragment E by thrombin, atroxin, or batroxobin.

In order to investigate the sequence of fibrinopeptide release from the amino terminal end of a dimeric fibrinogen-derived substrate by thrombin or batroxobins, we studied their effects on plasmic fragment E1, a core fragment from the central domain of fibrinogen containing both A alpha chain fibrinopeptide A (FPA) sequences. Isoelectric focussing (IEF) was employed as a means of resolving des A-fragment E1, from which one FPA had been cleaved, from des AA-fragment E1 resulting from the loss of both FPA's. Using densitometric gel scanning for quantification of the levels of intact fragment E1, des A-fragment E1, and des AA-fragment E1, in mixtures incubated with enzyme for various periods of time, we found similar catalytic rate constants (k1, k2) for release of the first fibrinopeptide A, (FPA1) or the second, (FPA2) from fragment E1, with either thrombin or batroxobin (k2:k1 ratios of 1.10 +/- 0.42, 1.34 +/- 0.26 respectively). Atroxin released FPA2 more slowly than FPA1 with a k2:k1 ratio of 0.34 +/- 0.1. Th finding that the cleavage of FPA2 by Atroxin is three-fold slower than thrombin and almost four-fold slower than batroxobin, suggest that batroxobin and thrombin cleavage of FPA2 may be cooperative in nature. However, the cooperativity in the cleavage sequence is insufficient to markedly suppress the evolution of intermediate des A fragment E species during early and intermediate phases of FPA cleavage from fragment E.

Amino Acid Sequence↗

PubMed2004

Vicious circles: positive feedback in major evolutionary and ecological transitions.

Evolutionary biologists and ecologists often focus on equilibrium states that are subject to forms of negative feedback, such as optima for phenotypic traits or regulation of population sizes. However, recent theoretical and empirical studies show how positive feedback can be instrumental in driving many of the most important and spectacular processes in evolutionary ecology, including the evolution of sex and genetic systems, mating systems, life histories, complex cooperation in insects and humans, ecological specialization, species diversity, species ranges, speciation and extinction. Taken together, this work suggests that positive feedback is more common than is generally appreciated, and that its self-reinforcing dynamics generate the conditions for changes that might otherwise be difficult or impossible for selection or other mechanisms to achieve. Testing for positive feedback requires analysing each causal link in feedback loops, tracking genetic, character and population-dynamic changes across generations, and elucidating the conditions that can result in self-reinforcing change.

Journal Article↗

PubMed2003

Identification of operator sites of the CI repressor of phage TP901-1: evolutionary link to other phages.

The repressor encoded by the cI gene of the temperate Lactococcus lactis subsp. cremoris bacteriophage TP901-1 has been purified. Gel-retardation and footprinting analyses identified three palindromic operator sites (O(R), O(L), and O(D)). The operator site O(R) is located between the two divergent early promoters P(R) and P(L), O(L) overlaps the transcriptional start of the lytic P(L) promoter, and O(D) is located downstream of the mor gene, the first gene in the lytic gene cluster. The function of O(L) was verified by mutational analysis. Binding was found to be specific and cooperative. Multimeric forms of the repressor were observed, thus indicating that the repressor may bind simultaneously to all three operator sites. Inverted repeats with homology to the operator sites of TP901-1 were identified in phage genomes encoding repressors homologous to CI of TP901-1. Interestingly, the locations of these repeats on the phage genomes correspond to those found in TP901-1, indicating that the same system of cooperative repression of early phage promoters has been inherited by modular evolution.

Amino Acid Sequence↗

PubMed2005

Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach.

Understanding and ultimately predicting protein associations is immensely important for functional genomics and drug design. Here, we propose that binding sites have preferred organizations. First, the hot spots cluster within densely packed 'hot regions'. Within these regions, they form networks of interactions. Thus, hot spots located within a hot region contribute cooperatively to the stability of the complex. However, the contributions of separate, independent hot regions are additive. Moreover, hot spots are often already pre-organized in the unbound (free) protein states. Describing a binding site through independent local hot regions has implications for binding site definition, design and parametrization for prediction. The compactness and cooperativity emphasize the similarity between binding and folding. This proposition is grounded in computation and experiment. It explains why summation of the interactions may over-estimate the stability of the complex. Furthermore, statistically, charge-charge coupling of the hot spots is disfavored. However, since within the highly packed regions the solvent is screened, the electrostatic contributions are strengthened. Thus, we propose a new description of protein binding sites: a site consists of (one or a few) self-contained cooperative regions. Since the residue hot spots are those conserved by evolution, proteins binding multiple partners at the same sites are expected to use all or some combination of these regions.

Binding Sites↗

PubMed1997

Ontogenetic variation in small-bodied New World primates: implications for patterns of reproduction and infant care.

This paper explores relations of ontogeny, life history strategies and patterns of infant care in 11 species of small-bodied New World monkeys. Analysis of these data suggests that differences in the social systems of Aotus, Callicebus, Saimiri, Callimico, Saguinus, Leontopithecus, Cebuella and Callithrix are closely tied to both the costs of reproduction and to the ontogenetic requirements of maturing young. In Saimiri, both rapid prenatal body weight and perinatal brain growth result in relatively high metabolic costs to breeding females. These costs, coupled with minimal nonmaternal assistance in caregiving, appear to favor a reproductive strategy that limits offspring production to a single birth at 2-year intervals. In contrast, tamarins and marmosets are capable of producing twins twice in the same year. Prenatal investment in each offspring is relatively low, and the potentially high postnatal costs of nursing 2 infants are minimized by the evolution of a social system involving extensive extramaternal care-giving. Cooperative infant care in callitrichins (tamarins and marmosets) serves to distribute the metabolic costs of infant ontogeny among several group members. Callimico is also characterized by a high reproductive output, with females capable of producing a single infant twice during the year. Infants continue to grow rapidly after weaning. Patterns of infant development in Callimico are similar to those found in tamarins and marmosets and support a close phylogenetic relationship among these taxa. Aotus and Callicebus are characterized by an alternative strategy. In these taxa, a monogamous mating system is associated with paternal certainty, male parental care, and provisioning of the young. The transfer of male energetic resources to a single offspring allows night and titi monkeys to maintain a comparatively short interbirth interval (1 year). Ecological and social factors, such as predation and feeding competition, do not appear to adequately explain much of the observed variation in infant development and preadult growth rates in these platyrrhines. Instead, reproductive strategies are strongly linked to ontogenetic patterns and life histories.

Aging↗

PubMed2001

Modeling two-state cooperativity in protein folding.

A protein model with the pairwise interaction energies varying as the local environment changes, i.e., including some kind of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical characteristics and free energy profile show a well-defined two-state behavior and cooperativity of folding for such a model. As a comparison, related simulations for the usual G&o model, where the interaction energies are independent of the local conformation, are also made. Our results indicate that the evolution of interactions during the folding process plays an important role in the two-state cooperativity in protein folding.

Biophysics↗

PubMed2001

Directed evolution of polymerase function by compartmentalized self-replication.

We describe compartmentalized self-replication (CSR), a strategy for the directed evolution of enzymes, especially polymerases. CSR is based on a simple feedback loop consisting of a polymerase that replicates only its own encoding gene. Compartmentalization serves to isolate individual self-replication reactions from each other. In such a system, adaptive gains directly (and proportionally) translate into genetic amplification of the encoding gene. CSR has applications in the evolution of polymerases with novel and useful properties. By using three cycles of CSR, we obtained variants of Taq DNA polymerase with 11-fold higher thermostability than the wild-type enzyme or with a >130-fold increased resistance to the potent inhibitor heparin. Insertion of an extra stage into the CSR cycle before the polymerase reaction allows its application to enzymes other than polymerases. We show that nucleoside diphosphate kinase and Taq polymerase can form such a cooperative CSR cycle based on reciprocal catalysis, whereby nucleoside diphosphate kinase produces the substrates required for the replication of its own gene. We also find that in CSR the polymerase genes themselves evolve toward more efficient replication. Thus, polymerase genes and their encoded polypeptides cooperate to maximize postselection copy number. CSR should prove useful for the directed evolution of enzymes, particularly DNA or RNA polymerases, as well as for the design and study of in vitro self-replicating systems mimicking prebiotic evolution and viral replication.

DNA-Directed DNA Polymerase↗

PubMed2004

[Evolution of a quality assurance programme for physiotherapy schools - results of the first quality inspections].

In cooperation with the Hochrhein-Institute for Research in Rehabilitation (HRI), the Association for Assuring the Quality of Education in Physiotherapy Schools in Germany (ISQ) has developed a quality assurance programme for physiotherapy schools. It aims at assessing the quality of physiotherapy schools in Germany, and to award a quality seal based on compliance with defined criteria. First, a catalogue of quality features and criteria relevant for education in physiotherapy was developed. It is based on the analysis of questionnaires that had been sent to all German physiotherapy schools, to selected physiotherapists and leading physiotherapists in hospitals, to competent federal authorities, and to three school-classes with group discussions. The persons addressed named 360 different quality features. They were collected in a catalogue, revised in a multi-stage Delphi procedure, and approved consensually. The final criteria were transformed into basic quality requirements, and formulated as a check-list. Assessment of the quality features is carried out by trained visitors. In addition, the satisfaction of students is assessed with a questionnaire. The results of the interviews and the questionnaires are fed back to the schools in a quality report. Schools meeting all basic quality requirements are awarded the seal of quality. The seal is valid for three years. Since January 2003, this procedure is available for all schools in Germany. Until September 2002, a pretest of visitations and student questionnaires had been carried out with 31 member schools of the ISQ; according to the resulting quality reports, none of these schools would instantly be awarded the quality seal. In all, more than half of the schools do not meet 10 of the 42 basic criteria. Fundamental deficiencies have been found in the documentation pertaining to supervision of practical training. In terms of training, further training and professional development of their teachers and associated professors, needs for improvement could be shown in more than 66 % of all visited schools. Only 9 of 31 schools could produce a written syllabus. Additionally, the requirements of teachers conferences and equipment of libraries were not met by the majority. A general problem among the schools is inadequate documentation in many fields.

Clinical Competence↗

PubMed1996

Origin and evolution of circular waves and spirals in Dictyostelium discoideum territories.

Randomly distributed Dictyostelium discoideum cells form cooperative territories by signaling to each other with cAMP. Cells initiate the process by sending out pulsatile signals, which propagate as waves. With time, circular and spiral patterns form. We show that by adding spatial and temporal noise to the levels of an important regulator of external cAMP levels, the cAMP phosphodiesterase inhibitor, we can explain the natural progression of the system from randomly firing cells to circular waves whose symmetries break to form double- and single- or multi-armed spirals. When phosphodiesterase inhibitor is increased with time, mimicking experimental data, the wavelength of the spirals shortens, and a proportion of them evolve into pairs of connected spirals. We compare these results to recent experiments, finding that the temporal and spatial correspondence between experiment and model is very close.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed2005

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.

As whole-genome sequencing efforts extend beyond more traditional model organisms to include a deep diversity of species, comparative genomic analyses will be further empowered to reveal insights into the human genome and its evolution. The discovery and annotation of functional genomic elements is a necessary step toward a detailed understanding of our biology, and sequence comparisons have proven to be an integral tool for that task. This review is structured to broadly reflect the statistical challenges in discriminating these functional elements from the bulk of the genome that has evolved neutrally. Specifically, we review the comparative genomics literature in terms of specificity, sensitivity, and phylogenetic scope, as well as the trade-offs that relate these factors in standard analyses. We consider the impact of an expanding diversity of orthologous sequences on our ability to resolve functional elements. This impact is assessed through both recent comparative analyses of deep alignments and mathematical modeling.

Animals↗

PubMed2006

Long homopurine*homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region.

Homo(purine*pyrimidine) sequences (R*Y tracts) with mirror repeat symmetries form stable triplexes that block replication and transcription and promote genetic rearrangements. A systematic search was conducted to map the location of the longest R*Y tracts in the human genome in order to assess their potential function(s). The 814 R*Y tracts with > or =250 uninterrupted base pairs were preferentially clustered in the pseudoautosomal region of the sex chromosomes and located in the introns of 228 annotated genes whose protein products were associated with functions at the cell membrane. These genes were highly expressed in the brain and particularly in genes associated with susceptibility to mental disorders, such as schizophrenia. The set of 1957 genes harboring the 2886 R*Y tracts with > or =100 uninterrupted base pairs was additionally enriched in proteins associated with phosphorylation, signal transduction, development and morphogenesis. Comparisons of the > or =250 bp R*Y tracts in the mouse and chimpanzee genomes indicated that these sequences have mutated faster than the surrounding regions and are longer in humans than in chimpanzees. These results support a role for long R*Y tracts in promoting recombination and genome diversity during evolution through destabilization of chromosomal DNA, thereby inducing repair and mutation.

Animals↗

PubMed2004

Adaptation and enslavement in endosymbiont-host associations.

The evolutionary persistence of symbiotic associations is a puzzle. Adaptation should eliminate cooperative traits if it is possible to enjoy the advantages of cooperation without reciprocating-a facet of cooperation known in game theory as the Prisoner's Dilemma. Despite this barrier, symbioses are widespread and may have been necessary for the evolution of complex life. The discovery of strategies such as tit-for-tat has been presented as a general solution to the problem of cooperation. However, this only holds for within-species cooperation, where a single strategy will come to dominate the population. In a symbiotic association each species may have a different strategy, and the theoretical analysis of the single-species problem is no guide to the outcome. We present basic analysis of two-species cooperation and show that a species with a fast adaptation rate is enslaved by a slowly evolving one. Paradoxically, the rapidly evolving species becomes highly cooperative, whereas the slowly evolving one gives little in return. This helps understand the occurrence of endosymbioses where the host benefits, but the symbionts appear to gain little from the association.

Animals↗

PubMed1983

X-chromosome inactivation and evolution in marsupials and other mammals.

Sex chromosome dosage compensation in Australian marsupials exhibits several characteristics not ordinarily manifested in eutherian mammals. They are: 1) preferential inactivation of the paternally derived X-chromosome in somatic tissues; 2) a state of partial inactivity at some paternally derived X-linked gene loci in some cells; 3) absence of dosage compensation in some cell types; 4) absence of nuclear sex dimorphism at interphase; 5) discordance between late DNA replication and gene inactivation in some cell types; 6) failure of the X-chromosome to behave as a single unit. Despite these seemingly major differences between the dosage compensation systems of Australian marsupials and eutherians, there are also many underlying similarities. We propose that the two systems arose from a common ancestral mechanism in which the X-chromosome was regulated in a piecemeal fashion, rather than as a whole. To determine more precisely the sequence and timing of evolutionary events, we have initiated an investigation of dosage compensation in American marsupials, which diverged from Australian marsupials soon after the divergence of marsupials from eutherian mammals.

Animals↗

PubMed2004

Construction and characterization of chimeric proteins composed of type-1 and type-2 periplasmic binding proteins MglB and ArgT.

The respective type-1 and type-2 periplasmic binding proteins (PBPs) MglB and ArgT are believed to have evolved from a common ancestor into siblings showing topological differences in their main chain connectivity. At first glance, they show similar structure. But, more detailed examination reveals that the chain connectivity of ArgT is more convoluted than that of MglB. Reflecting that complexity, the folding of ArgT is complicated and involves intermediate folds. On the other hand, the folding of MglB is a simple two-state transition. In the present study, we constructed and characterized several chimeras made up of various subdomains of MglB and ArgT with the aim of gaining insight into the evolution of protein folding and protein structure. Although these chimeras did not fold as compactly as their parental proteins, some did exhibit cooperative folding, which suggests that novel proteins with new connectivity and new folding pathways could have emerged at a fairly high rate throughout the evolution of proteins.

Circular Dichroism↗

PubMed2003

Dissecting cooperative and additive binding energetics in the affinity maturation pathway of a protein-protein interface.

When two proteins associate they form a molecular interface that is a structural and energetic mosaic. Within such interfaces, individual amino acid residues contribute distinct binding energies to the complex. In combination, these energies are not necessarily additive, and significant positive or negative cooperative effects often exist. The basis of reliable algorithms to predict the specificities and energies of protein-protein interactions depends critically on a quantitative understanding of this cooperativity. We have used a model protein-protein system defined by an affinity maturation pathway, comprising variants of a T cell receptor Vbeta domain that exhibit an overall affinity range of approximately 1500-fold for binding to the superantigen staphylococcal enterotoxin C3, in order to dissect the cooperative and additive energetic contributions of residues within an interface. This molecular interaction has been well characterized previously both structurally, by x-ray crystallographic analysis, and energetically, by scanning alanine mutagenesis. Through analysis of group and individual maturation and reversion mutations using surface plasmon resonance spectroscopy, we have identified energetically important interfacial residues, determined their cooperative and additive energetic properties, and elucidated the kinetic and thermodynamic bases for molecular evolution in this system. The summation of the binding free energy changes associated with the individual mutations that define this affinity maturation pathway is greater than that of the fully matured variant, even though the affinity gap between the end point variants is relatively large. Two mutations in particular, both located in the complementarity determining region 2 loop of the Vbeta domain, exhibit negative cooperativity.

Algorithms↗

PubMed1999

Evolution and molecular characterization of a beta-globin gene from the Australian Echidna Tachyglossus aculeatus (Monotremata).

Coinciding with a period in evolution when monotremes, marsupials, and eutherians diverged from a common ancestor, a proto-beta-globin gene duplicated, producing the progenitors of mammalian embryonic and adult beta-like globin genes. To determine whether monotremes contain orthologues of these genes and to further investigate the evolutionary relationships of monotremes, marsupials, and eutherians, we have determined the complete DNA sequence of an echidna (Tachyglossus aculeatus) beta-like globin gene. Conceptual translation of the gene and sequence comparisons with eutherian and marsupial beta-like globin genes and echidna adult beta-globin indicate that the gene is adult expressed. Phylogenetic analyses do not clearly resolve the branching pattern of mammalian beta-like globin gene lineages and it is therefore uncertain whether monotremes have orthologues of the embryonic beta-like globin genes of marsupials and eutherians. Four models are proposed that provide a framework for interpreting further studies on the evolution of beta-like globin genes in the context of the evolution of monotremes, marsupials, and eutherians.

Amino Acid Sequence↗

PubMed2004

Adaptive evolution of the histone fold domain in centromeric histones.

Centromeric DNA, being highly repetitive, has been refractory to molecular analysis. However, centromeric structural proteins are encoded by single-copy genes, and these can be analyzed by using standard phylogenetic tools. The centromere-specific histone, CenH3, replaces histone H3 in centromeric nucleosomes, and is required for the proper distribution of chromosomes during cell division. Whereas histone H3s are nearly identical between species, CenH3s are divergent, with an N-terminal tail that is highly variable in length and sequence. Both the N-terminal tail and histone fold domain (HFD) are subject to adaptive evolution in Drosophila. Similarly, comparisons between Arabidopsis thaliana and Arabidopsis arenosa detected adaptive evolution, but only in the N-terminal tail. We have extended our evolutionary analyses of CenH3s to other members of the Brassicaceae, which allowed the detection of positive selection in both the N-terminal tail and in the HFD. We find that adaptively evolving sites in the HFD can potentially interact with DNA, including sites in the loop 1 region of the HFD that are required for centromeric targeting in Drosophila. Other adaptively evolving sites in the HFD can be localized on the structure of the nucleosome core particle, revealing an extended surface in addition to loop 1 in which conformational changes might alter histone-DNA contacts or water bridges. The identification of adaptively evolving sites provides a structural basis for the interaction between centromeric DNA and the protein that is thought to underlie the evolution of centromeres and the accumulation of pericentric heterochromatin.

Amino Acid Sequence↗