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PubMed2001

Earth--moon evolution: implications for the mechanism of the biological clock?

The geophysical characteristics of the planet Earth dictate the physiological traits of living organisms. Changes in the geophysical conditions over the course of geological time are responsible for major evolutionary changes in life emergence and evolvement. Calendar day length is one of earth's geophysical characteristics which is under a constant, if extremely small, progressive change. This enforces an adjustment of circadian rhythmicity throughout geological time. The calendar day has extended approximately 9 hours in the last 3.5 billion years. Two mechanisms for circadian-rhythm adjustment are suggested: a directional selection mechanism -- an endogenous -- oriented explanation regarding a genetic drift in the population's endogenous oscillation toward a lengthened daily cycle; and an exogenous calibration mechanism - a hypothesis on the existence of a geophysical responsive element which senses a geophysical stimuli and calibrates the inner cellular oscillation in accordance with the length of the calendar day. A distinguishing experiment between the two explanations is suggested and discussed. Circadian rhythm mechanism and the evolution of circadian rhythmicity are tightly connected. Circadian rhythms' evolutionary theories are discussed in light of their contribution to our understanding of the selective pressures being applied throughout geological time and of how, once the clock has been established, it maintains an ongoing adjustment to a continuous change in the length of day.I argue that the exogenous calibration mechanism combines with the endosymbiont coordination theory, together, present an explanation to the path by which the calendar day adjustment was acquired and maintained. This hypothesis suggests a role for gravity cyclic force and for cytoskeleton's components in calendar day adjustment mechanism and circadian rhythm entrainment.

Animals↗
PubMed2005

The modeled structure of the RNA dependent RNA polymerase of GBV-C virus suggests a role for motif E in Flaviviridae RNA polymerases.

BACKGROUND: The Flaviviridae virus family includes major human and animal pathogens. The RNA dependent RNA polymerase (RdRp) plays a central role in the replication process, and thus is a validated target for antiviral drugs. Despite the increasing structural and enzymatic characterization of viral RdRps, detailed molecular replication mechanisms remain unclear. The hepatitis C virus (HCV) is a major human pathogen difficult to study in cultured cells. The bovine viral diarrhea virus (BVDV) is often used as a surrogate model to screen antiviral drugs against HCV. The structure of BVDV RdRp has been recently published. It presents several differences relative to HCV RdRp. These differences raise questions about the relevance of BVDV as a surrogate model, and cast novel interest on the "GB" virus C (GBV-C). Indeed, GBV-C is genetically closer to HCV than BVDV, and can lead to productive infection of cultured cells. There is no structural data for the GBV-C RdRp yet. RESULTS: We show in this study that the GBV-C RdRp is closest to the HCV RdRp. We report a 3D model of the GBV-C RdRp, developed using sequence-to-structure threading and comparative modeling based on the atomic coordinates of the HCV RdRp structure. Analysis of the predicted structural features in the phylogenetic context of the RNA polymerase family allows rationalizing most of the experimental data available. Both available structures and our model are explored to examine the catalytic cleft, allosteric and substrate binding sites. CONCLUSION: Computational methods were used to infer evolutionary relationships and to predict the structure of a viral RNA polymerase. Docking a GTP molecule into the structure allows defining a GTP binding pocket in the GBV-C RdRp, such as that of BVDV. The resulting model suggests a new proposition for the mechanism of RNA synthesis, and may prove useful to design new experiments to implement our knowledge on the initiation mechanism of RNA polymerases.

Binding Sites↗
PubMedDate not supplied

The metamorphosis of health planning in the Netherlands and the USA.

The United States and the Netherlands are the focus for this comparative analysis of the evolutionary interaction between health planning and the political system, seen in the context of change in social and economic ideologies. While health planning in the USA started in 1946, it was the comprehensive health planning program in 1966 that created the form to be followed by Health Systems Agency effort in 1974: local, voluntary planning, coordinated by state agencies, supported by federal funding. Health planning in the Netherlands has moved through four distinct periods: a hospital construction period starting during the post-war recovery; a hospital regionalization period, from 1971 through the late 1970s; a transition period from the late 1970s to 1982, during which several planning approaches were considered; and, the current comprehensive health and social services planning period. Today, federal support for health planning in the US has been eliminated as part of the current de-regulatory, competitive health care strategy. Health planning in the US is now an institutional activity, with less focus on community needs. Advocated changes in the Dutch planning approach incorporate ideas similar to past approaches in the US; but, a failed approach in one nation may work in another, if the underlying cultural and organizational characteristics are sufficiently different.

Delivery of Health Care↗
PubMedDate not supplied

Evolution and revolution as organizations grow. 1972.

The influence of history on an organization is a powerful but often overlooked force. Managers, in their haste to build companies, frequently fail to ask such critical developmental questions as, Where has our organization been? Where is it now? and What do the answers to these questions mean for where it is going? Instead, when confronted with problems, managers fix their gaze outward on the environment and toward the future, as if more precise market projections will provide the organization with a new identity. In this HBR Classic, Larry Greiner identifies a series of developmental phases that companies tend to pass through as they grow. He distinguishes the phases by their dominant themes: creativity, direction, delegation, coordination, and collaboration. Each phase begins with a period of evolution, steady growth, and stability, and ends with a revolutionary period of organizational turmoil and change. The critical task for management in each revolutionary period is to find a new set of organizational practices that will become the basis for managing the next period of evolutionary growth. Those new practices eventually outlast their usefulness and lead to another period of revolution. Managers therefore experience the irony of seeing a major solution in one period become a major problem in a later period. Originally published in 1972, the article's argument and insights remain relevant to managers today. Accompanying the original article is a commentary by the author updating his earlier observations.

Administrative Personnel↗
PubMed2006

Testing hypotheses of convergence with multivariate data: morphological and functional convergence among herbivorous lizards.

Despite its importance to evolutionary theory, convergence remains an understudied phenomenon and is usually investigated using qualitative data. This paper advances a new, multidimensional view of convergence. Three patterns indicative of convergence are discussed, and techniques to discover and test convergent patterns in a quantitative framework are developed. These concepts and methods are applied to a dataset of digitized coordinates on 1554 lizard skulls and 1292 lower jaws to test hypotheses of convergence among herbivorous lizards. Encompassing seven independent acquisitions of herbivory, this lizard sample provides an ideal natural experiment for exploring ideas of convergence among different systems (here, morphological and functional). Three related questions are addressed: (1) Do herbivorous lizards show evidence of convergence in skull and lower jaw morphology? (2) What, if any, is the morphospace pattern associated with this convergence? (3) Is it possible to predict the direction of convergence using functional models? Relative warp analysis and permutation tests reveal that the skulls and lower jaws of herbivorous lizards do show evidence of convergence. Herbivore skulls deviate from their carnivorous or omnivorous sister groups toward the same area of morphospace. Without a phylogenetic perspective, this pattern would not be recognizable. Lower jaws of herbivores are not convergent in morphology but are convergent in function: herbivores deviate away from their carnivorous sister groups toward higher values of mechanical advantage. These results illustrate the desirability of quantitative methods, informed by phylogenetic information, in the study of convergence.

Adaptation, Biological↗
PubMed1996

Crystal structure of the 2[4Fe-4S] ferredoxin from Chromatium vinosum: evolutionary and mechanistic inferences for [3/4Fe-4S] ferredoxins.

The crystal structure of the 2[4Fe-4S] ferredoxin from Chromatium vinosum has been solved by molecular replacement using data recorded with synchrotron radiation. The crystals were hexagonal prisms that showed a strong tendency to develop into long tubes. The hexagonal prisms diffracted to 2.1 A resolution at best, and a structural model for C. vinosum ferredoxin has been built with a final R of 19.2%. The N-terminal domain coordinates the two [4Fe-4S] clusters in a fold that is almost identical to that of other known ferredoxins. However, the structure has two unique features. One is a six-residue insertion between two ligands of one cluster forming a two-turn external loop; this short loop changes the conformation of the Cys 40 ligand compared to other ferredoxins and hampers the building of one NH...S H-bond to one of the inorganic sulfurs. The other remarkable structural element is a 3.5-turn alpha-helix at the C-terminus that covers one side of the same cluster and is linked to the cluster-binding domain by a six-residue external chain segment. The charge distribution is highly asymmetric over the molecule. The structure of C. vinosum ferredoxin strongly suggests divergent evolution for bacterial [3/4Fe-4S] ferredoxins from a common ancestral cluster-binding core. The unexpected slow intramolecular electron transfer rate between the clusters in C. vinosum ferredoxin, compared to other similar proteins, may be attributed to the unusual electronic properties of one of the clusters arising from localized changes in its vicinity rather than to a global structural rearrangement.

Amino Acid Sequence↗
PubMed2000

Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey.

BACKGROUND: Proteins from thermophilic organisms usually show high intrinsic thermal stability but have structures that are very similar to their mesophilic homologues. From prevous studies it is difficult to draw general conclusions about the structural features underlying the increased thermal stability of thermophilic proteins. RESULTS: In order to reveal the general evolutionary strategy for changing the heat stability of proteins, a non-redundant data set was compiled comprising all high-quality structures of thermophilic proteins and their mesophilic homologues from the Protein Data Bank. The selection (quality) criteria were met by 64 mesophilic and 29 thermophilic protein subunits, representing 25 protein families. From the atomic coordinates, 13 structural parameters were calculated, compared and evaluated using statistical methods. This study is distinguished from earlier ones by the strict quality control of the structures used and the size of the data set. CONCLUSIONS: Different protein families adapt to higher temperatures by different sets of structural devices. Regarding the structural parameters, the only generally observed rule is an increase in the number of ion pairs with increasing growth temperature. Other parameters show just a trend, whereas the number of hydrogen bonds and the polarity of buried surfaces exhibit no clear-cut tendency to change with growth temperature. Proteins from extreme thermophiles are stabilized in different ways to moderately thermophilic ones. The preferences of these two groups are different with regards to the number of ion pairs, the number of cavities, the polarity of exposed surface and the secondary structural composition.

Amino Acids↗
PubMed2000

Evolution of two-component signal transduction.

Two-component signal transduction (TCST) systems are the principal means for coordinating responses to environmental changes in bacteria as well as some plants, fungi, protozoa, and archaea. These systems typically consist of a receptor histidine kinase, which reacts to an extracellular signal by phosphorylating a cytoplasmic response regulator, causing a change in cellular behavior. Although several model systems, including sporulation and chemotaxis, have been extensively studied, the evolutionary relationships between specific TCST systems are not well understood, and the ancestry of the signal transduction components is unclear. Phylogenetic trees of TCST components from 14 complete and 6 partial genomes, containing 183 histidine kinases and 220 response regulators, were constructed using distance methods. The trees showed extensive congruence in the positions of 11 recognizable phylogenetic clusters. Eukaryotic sequences were found almost exclusively in one cluster, which also showed the greatest extent of domain variability in its component proteins, and archaeal sequences mainly formed species-specific clusters. Three clusters in different parts of the kinase tree contained proteins with serine-phosphorylating activity. All kinases were found to be monophyletic with respect to other members of their superfamily, such as type II topoisomerases and Hsp90. Structural analysis further revealed significant similarity to the ATP-binding domain of eukaryotic protein kinases. TCST systems are of bacterial origin and radiated into archaea and eukaryotes by lateral gene transfer. Their components show extensive coevolution, suggesting that recombination has not been a major factor in their differentiation. Although histidine kinase activity is prevalent, serine kinases have evolved multiple times independently within this family, accompanied by a loss of the cognate response regulator(s). The structural and functional similarity between TCST kinases and eukaryotic protein kinases raises the possibility of a distant evolutionary relationship.

Amino Acid Sequence↗
PubMed2006

How flies get their size: genetics meets physiology.

Body size affects important fitness variables such as mate selection, predation and tolerance to heat, cold and starvation. It is therefore subject to intense evolutionary selection. Recent genetic and physiological studies in insects are providing predictions as to which gene systems are likely to be targeted in selecting for changes in body size. These studies highlight genes and pathways that also control size in mammals: insects use insulin-like growth factor (IGF) and Target of rapamycin (TOR) kinase signalling to coordinate nutrition with cell growth, and steroid and neuropeptide hormones to terminate feeding after a genetically encoded target weight is achieved. However, we still understand little about how size is actually sensed, or how organ-intrinsic size controls interface with whole-body physiology.

Animals↗
PubMed2001

Genetic characterization of hybridization and introgression between anadromous rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki).

Interspecific hybridization represents a dynamic evolutionary phenomenon and major conservation problem in salmonid fishes. In this study we used amplified fragment length polymorphisms (AFLP) and mitochondrial DNA (mtDNA) markers to describe the extent and characterize the pattern of hybridization and introgression between coastal rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Hybrid individuals were initially identified using principle coordinate analysis of 133 polymorphic AFLP markers. Subsequent analysis using 23 diagnostic AFLP markers revealed the presence of F1, rainbow trout backcross, cutthroat trout backcross and later-generation hybrids. mtDNA analysis demonstrated equal numbers of F1 hybrids with rainbow and cutthroat trout mtDNA indicating reciprocal mating of the parental types. In contrast, rainbow and cutthroat trout backcross hybrids always exhibited the mtDNA from the recurrent parent, indicating a male hybrid mating with a pure female. This study illustrates the usefulness of the AFLP technique for generating large numbers of species diagnostic markers. The pattern of hybridization raises many questions concerning the existence and action of reproductive isolating mechanisms between these two species. Our findings are consistent with the hypothesis that introgression between anadromous populations of coastal rainbow and coastal cutthroat trout is limited by an environment-dependent reduction in hybrid fitness.

Animals↗
PubMed2003

Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers.

Cucurbita pepo is a highly polymorphic species. The cultivars can be grouped into eight morphotypes in two subspecies, ssp. pepo and ssp. ovifera. A collection of 69 accessions representative of the morphotypes and some unclassified types was used for analysing the morphological and molecular diversity of this species. This collection includes commercial cultivars and Spanish landraces, which represent the great diversification of types that have arisen in Europe after this species arrived from America. For the molecular variability studies, two PCR-based systems were employed, AFLP and SRAP, which preferentially amplify ORFs. Principal coordinates analysis and cluster analysis using the UPGMA method clearly separate the accessions into the two subspecies through the use of both markers. However, the gene diversity and the genetic identity values among morphotypes and subspecies varied between the two marker systems. The information given by SRAP markers was more concordant to the morphological variability and to the evolutionary history of the morphotypes than that of AFLP markers. In ssp. ovifera, the accessions of the different morphotypes were basically grouped according to the fruit colour. This may indicate different times of development and also the extent of breeding in the accessions used. This study has allowed identification of new types that can be employed for the development of new cultivars. The landraces of the spp. ovifera, used as ornamental in Europe, have proved to be of great interest for preserving the diversity of C. pepo.

Cluster Analysis↗
PubMed1998

Comparative molecular analysis of Na+/H+ exchangers: a unified model for Na+/H+ antiport?

Despite 30 years of study on Na+/H+ exchange, the molecular mechanisms of antiport remain obscure. Most challenging, the identity of amino acids involved in binding transported cations is still unknown. We review data examining the identity of residues that are involved in cation binding and translocation of prokaryotic and eukaryotic Na+/H+ antiporters. Several polar residues specifically distributed within or immediately adjacent to membrane spanning regions are implicated as being important. These key amino acids are conserved in prokaryotes and in some lower eukaryotic forms of the Na+/ H+ antiporter, despite their being dispersed throughout the protein and despite an overall low similarity in the linear sequence of these Na+/H+ antiporters. We suggest that this conservation of isolated residues (together with distances between them) reflects a general physicochemical mechanism of cation binding by exchangers. The binding could be based on coordination of the substrate cation by a crown ether-like cluster of polar atomic groups amino acids, as has been hypothesized by Boyer. Traditional screening for the extended, highly conserved linear protein sequences might not be applicable when searching for functional domains of ion transporters. Three-dimensional constellations of polar residues (3D-motifs) may be evolutionary conserved rather than linear primary sequence.

Amino Acid Sequence↗
PubMed1976

The quarterly review of biology.

In recent years, the evidence suggesting that honey bees communicate with a "dance language" has been stronly attached on both theoretical and experimental grounds. An alternative theory has been proposed by which bees are supposed to use only odors to locate sources of food. A review of the evolution of the controversy isolates and analyzes the main issues. Early experiments which she fundamental problem in this important dispute has been that dancing bees advertise a food location with site-specific odoer information as well as symbolic distance and direction coordinates. A new technique has overcome this problem and demonstrated that von Frisch's dance language theory is, on the whole, correct. The apparently contradictory results of Wenner and his colleagues are shown to be due to their techniques for training bees. The dance-language controversy raises issues beyond how bees communicate. These include whether and when "evolutionary" arguments are useful, and to what extent Kuhn's scientific revolution paradign fits the dispute.

Animal Communication↗
PubMed2006

Polo-like kinase 1: target and regulator of transcriptional control.

Deregulated cell cycle control is a hallmark of cancer cells. Developmental or other mitogenic stimuli activate the proliferation of normal cells in response to the requirements of growing tissues. In contrast, cancer cells liberate from proliferative restrictions exerted by anti-proliferative signals arising from the stroma and by endogenous genetic programs that correlate to the terminal differentiation of cells. The study of cyclin-dependent kinases (Cdks) and polo-like kinases (Plks) as evolutionary conserved regulators of the cell cycle has contributed significantly to our current understanding of the mechanisms that underlie the proliferation of mammalian cells. Given the importance of Plk1 for mitotic progression the temporal expression of Plk1 is crucial and has to be tightly regulated. It is known that steady-state Plk1 mRNA and protein levels are coordinately regulated during cell cycle progression, being low during interphase but high in mitosis. This review will summarize the current knowledge on how cell cycle-dependent transcriptional regulation of the Plk1 gene is achieved. While binding sites for various transcriptional activators are dispersed throughout the entire Plk1 promoter region, the cell cycle-dependent regulation of the Plk1 gene expression seems to be regulated by G1-specific repression rather than by G2/M-specific activation of the Plk1 transcriptional unit. The tumor suppressor gene p53 was identified as a key player in the precise restriction of Plk1 gene expression to the G2/M phase. The activity of p53 is in turn controlled by Plk1 itself indicating the existence of an auto-regulatory mechanism involved in the cell cycle-dependent regulation of the Plk1 gene. Furthermore, transcription factors regulated by Plk1 will also be subject of discussion.

Animals↗
PubMed1992

Subcellular fractionation of the two organelle DNAs of malaria parasites.

Malaria parasites contain two extrachromosomal DNAs, a 6 kb repetitive linear molecule which is assigned on the basis of its genetic content to the mitochondria, and a 35 kb transcriptionally active circular molecule whose intracellular location is not known. We used the polymerase chain reaction to detect and estimate the numbers of both molecules in sub-cellular fractions derived from the rodent parasite Plasmodium yoelii. The two DNA molecules were not coordinately partitioned by the fractionation process, the 6 kb molecule being more abundant, relative to the 35 kb circle, in a fraction enriched for mitochondria, the converse being true for a less dense fraction of unknown identity. This implies that the two molecules are located in different cellular compartments, and is consistent with other evidence suggesting they have different evolutionary origins.

Animals↗
PubMed2006

Primary body axes of vertebrates: generation of a near-Cartesian coordinate system and the role of Spemann-type organizer.

A rationale for the complex-appearing generation of the primary body axes in vertebrates can be obtained if this process is divided into two parts. First, an ancestral system is responsible for the anteroposterior (AP) patterning of the brain and the positioning of the heart. The blastopore (marginal zone) acts as a source region that generates primary AP-positional information for the brain, a process that is largely independent of the organizer. This evolutionary old system was once organizing the single axis of radial-symmetric ancestors. Second, the trunk is assumed to be an evolutionary later addition. The AP organization of the trunk depends on a time-controlled posterior transformation in which an oscillation plays a crucial role. This oscillation also leads to the repetitive nature of the trunk pattern as seen in somites or segments. The function of the Spemann-type organizer is not to specify the dorsoventral (DV) positional information directly but to initiate the formation of a stripe-shaped midline organizer, realized with different structures in the brain and in the trunk (prechordal plate vs. notochord). The distance of the cells to this midline (rather than to the organizer) is crucial for the DV specification. The basically different modes of axes formation in vertebrates and insects is proposed to have their origin in the initial positioning of the mesoderm. Only in vertebrates the mesoderm is initiated in a ring at a posterior position. Thus, only in vertebrates complex tissue movements are required to transform the ring-shaped posterior mesoderm into the rod-shaped axial structures.

Animals↗
PubMed2004

Coevolution of gene expression among interacting proteins.

Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well documented and has been used to predict interacting proteins, domains, and amino acids. Interacting proteins are also often precisely coexpressed with one another, presumably to maintain proper stoichiometry among interacting components. Here, we show that the expression levels of physically interacting proteins coevolve. We estimate average expression levels of genes from four closely related fungi of the genus Saccharomyces using the codon adaptation index and show that expression levels of interacting proteins exhibit coordinated changes in these different species. We find that this coevolution of expression is a more powerful predictor of physical interaction than is coevolution of amino acid sequence. These results demonstrate that gene expression levels can coevolve, adding another dimension to the study of the coevolution of interacting proteins and underscoring the importance of maintaining coexpression of interacting proteins over evolutionary time. Our results also suggest that expression coevolution can be used for computational prediction of protein-protein interactions.

Amino Acid Sequence↗
PubMed2003

A hyaluronan binding link protein gene family whose members are physically linked adjacent to chondroitin sulfate proteoglycan core protein genes: the missing links.

We describe a vertebrate hyaluronan and proteoglycan binding link protein gene family (HAPLN), consisting of four members including cartilage link protein. The encoded proteins share 45-52% overall amino acid identity. In contrast to the average sequence identity between family members, the sequence conservation between vertebrate species was very high. Human and mouse link proteins share 81-96% amino acid sequence identity. Two of the four link protein genes (HAPLN2 and HAPLN4) were restricted in expression to the brain/central nervous system, while one of the four genes (HAPLN3) was widely expressed. Genomic structures revealed that all four HAPLN genes were similar in exon-intron organization and were also similar in genomic organization to the 5' exons for the CSPG core protein genes. Strikingly, all four HAPLN genes were located immediately adjacent to the four CSPG core protein genes creating four pairs of CSPG-HAPLN genes within the mammalian genome. Furthermore, the two brain-specific HAPLN genes (HAPLN2 and HAPLN4) were physically linked to the brain-specific CSPG genes encoding brevican and neurocan, respectively. The tight physical association of the HAPLN and CSPG genes supports a hypothesis that the first HAPLN gene arose as a partial gene duplication event from an ancestral CSPG gene. There is some degree of coordinated expression of each gene pair. Collectively, the four HAPLN genes are expressed by most tissue types, reflecting the fundamental importance of the hyaluronan-dependent extracellular matrix to tissue architecture and function in vertebrate species. Comparison of the genomic structures for the HAPLN, CSPG genes and other members of the link module superfamily provide strong support for a common evolutionary origin from an ancestral gene containing one link module encoding exon.

Animals↗