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PubMed1995

Amino acid replacements and wavelength absorption of visual pigments in vertebrates.

An important unanswered question in phototransduction is how visual pigments (VPs) regulate their wavelength of maximal absorption (lambda max). By constructing the evolutionary tree for 28 opsins with known lambda max values, we can identify the times and directions of lambda max shift of different VPs. A total of 55 amino acid changes are shown to correlate with the directions of lambda max shift and might have been important in determining lambda max of a VP. Among these, three amino acid changes are already proven to be responsible in modifying the green-sensitive VP to the red-sensitive VP. The present evolutionary analysis opens a new direction in understanding the mechanism for the regulation of wavelength absorption by a VP and, more generally, in studying molecular mechanism involved in adaptive evolution.

Amino Acid Sequence↗
PubMed2002

A glutamate receptor subtype antagonist inhibits seizures in rat hippocampal slices.

2-Methyl-4-oxo-3H-quinazoline-3-acetyl piperidine (Q5), a selective inhibitor of the fast-desensitising component of transmembrane Ca2+ ion influx to (S)-alpha-amino-3-hydroxy-5-methyliso-xazole-4-propionate ((S)-AMPA) was tested for possible anticonvulsant effects in the low-[Mg2+] model of experimental epilepsy. Evolutionary analysis of burst parameters such as half-width, decay time constant, burst multiplicity, instantaneous frequency and amplitude disclosed an approximate doubling of half-width within periods of interictal activity, being predictive for the onset of seizure-like events (SLEs). We found that SLEs observed in the CA3 region of rat hippocampal slices were suppressed by the application of 50 microM Q5. These results suggest an AMPA receptor function shaping the dynamics of spontaneous epileptiform activity.

6-Cyano-7-nitroquinoxaline-2,3-dione↗
PubMed1979

An ethological view of human adolescence.

In modern times the essential "normality" of adolescence has been acknowledged. With its pan-cultural and functional perspective, ethology is in a position to elaborate a description of normal human adolescence. Ethologists attempt to elucidate four interrelated aspects of a given behavior: its survival function, evolution, development, and elicitation by internal and external factors. The basic research strategy is two-fold: to identify biologically based, or evolved, behaviors (chiefly by controlling for the effects of experience and seeing if a core of evolved behavior remains); and to discover their functions by isolating the necessary and sufficient ecological conditions for their evolution. Applying this evolutionary analysis to human adolescence, we find that two developments seem to be basic: reproductive maturation and gaining independence from parents. The remainder of the article is an interpretation of various behavioral, morphological, and cultural data in accordance with these two developmental functions. Puberty seems to be timed so as to promote these functions most effectively. Pubertal changes parallel somatic growth and are delayed by poor nutrition, disease, and psychological stress--patterns consistent with functional considerations. The influence of natural selection on the sequencing of pubertal events is also emphasized. The role of pubertal hormones in altering behavior as well as morphology is illustrated. The adolescent gains independence from his parents by means of maturation and sex differentiation. Males become specialized for vigorous exertion, and females for work near the settlement--although considerable overlap in morphological and behavioral tendencies exists between the sexes. Various examples of sex differentiation demonstrates how morphological, behavioral, and cultural factors complement each other. Adolescent initiation rites help channel boys and girls into appropriate adult roles, teach respect for one's culture, and favor the fittest individuals. Hopi rites of passage are described as an example. Reproductive maturation likewise involves adaptive morphological and behavioral changes that are reinforced by cultural mores. Males rely on intimidation more than females, in order to dominate other males and attract females; contrariwise, females employ an endearment strategy more than males do. Many sex differences in human reproductive behavior can be explained with reference to man's parental behavior pattern. These include the male's greater aggressiveness, the preponderance of polygyny over polyandry, and differences in the antecedents of jealousy. Lastly, the need for an ethological understanding of adolescence is underscored as promising to offer a useful perspective on the problems of U.S. youth.

Adolescent↗
PubMed1994

Molecular evolution of the family Camelidae: a mitochondrial DNA study.

We report the first molecular evolutionary analysis of the family Camelidae by analysing the full DNA sequence of the mitochondrial cytochrome b gene. Estimates for the time of divergence of the Old World (Camelini) and New World (Lamini) tribes obtained from sequence data are in agreement with those derived from the fossil record. The DNA sequence data were also used to test current hypotheses concerning the ancestors of the domesticated llama and alpaca. The results show that hybridization has occurred in the ancestry of both domesticated camelids, obscuring the origin of the domestic species.

Animals↗
PubMed2005

Local phylogenetic divergence and global evolutionary convergence of skull function in reef fishes of the family Labridae.

The Labridae is one of the most structurally and functionally diversified fish families on coral and rocky reefs around the world, providing a compelling system for examination of evolutionary patterns of functional change. Labrid fishes have evolved a diverse array of skull forms for feeding on prey ranging from molluscs, crustaceans, plankton, detritus, algae, coral and other fishes. The species richness and diversity of feeding ecology in the Labridae make this group a marine analogue to the cichlid fishes. Despite the importance of labrids to coastal reef ecology, we lack evolutionary analysis of feeding biomechanics among labrids. Here, we combine a molecular phylogeny of the Labridae with the biomechanics of skull function to reveal a broad pattern of repeated convergence in labrid feeding systems. Mechanically fast jaw systems have evolved independently at least 14 times from ancestors with forceful jaws. A repeated phylogenetic pattern of functional divergence in local regions of the labrid tree produces an emergent family-wide pattern of global convergence in jaw function. Divergence of close relatives, convergence among higher clades and several unusual 'breakthroughs' in skull function characterize the evolution of functional complexity in one of the most diverse groups of reef fishes.

Animals↗
PubMed2006

Handling time promotes the coevolution of aggregation in predator-prey systems.

Predators often have type II functional responses and live in environments where their life history traits as well as those of their prey vary from patch to patch. To understand how spatial heterogeneity and predator handling times influence the coevolution of patch preferences and ecological stability, we perform an ecological and evolutionary analysis of a Nicholson-Bailey type model. We prove that coevolutionarily stable prey and searching predators prefer patches that in isolation support higher prey and searching predator densities, respectively. Using this fact, we determine how environmental variation and predator handling times influence the spatial patterns of patch preferences, population abundances and per-capita predation rates. In particular, long predator handling times are shown to result in the coevolution of predator and prey aggregation. An analytic expression characterizing ecological stability of the coevolved populations is derived. This expression implies that contrary to traditional theoretical expectations, predator handling time can stabilize predator-prey interactions through its coevolutionary influence on patch preferences. These results are shown to have important implications for classical biological control.

Animals↗
PubMed2005

TaxI: a software tool for DNA barcoding using distance methods.

DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding.

Animals↗
PubMed2002

'Candidatus mycoplasma haemodidelphidis' sp. nov., 'Candidatus mycoplasma haemolamae' sp. nov. and Mycoplasma haemocanis comb. nov., haemotrophic parasites from a naturally infected opossum (Didelphis virginiana), alpaca (Lama pacos) and dog (Canis familiaris): phylogenetic and secondary structural relatedness of their 16S rRNA genes to other mycoplasmas.

The 16S rRNA sequence of newly characterized haemotrophic bacteria in an opossum (Didelphis virginiana) and alpaca (Lama pacos) was determined. In addition, the 16S rRNA sequence of a haemotrophic parasite in the dog (Canis familiaris) was determined. Sequence alignment and evolutionary analysis as well as secondary structural similarity and signature nucleotide sequence motifs of their 16S rRNA genes, positioned these organisms in the genus Mycoplasma. The highest scoring sequence similarities were 16S rRNA genes from haemotrophic mycoplasma species (Haemobartonella and Eperythrozoon spp.). However, the lack of several higher-order structural idiosyncrasies used to define the pneumoniae group, suggests that these organisms and related haemotrophic mycoplasmas represent a new group of mycoplasmas. It is recommended that the organisms be named 'Candidatus Mycoplasma haemodidelphidis', 'Candidatus Mycoplasma haemolamae' and Mycoplasma haemocanis comb. nov., to provide some indication of the target cell and host species of these parasites, and to reflect their phylogenetic affiliation.

Animals↗
PubMed1997

Evolution of European bat lyssaviruses.

Forty-seven European bat lyssaviruses (EBL) and two African insectivorous bat lyssaviruses (Duvenhage viruses) were selected for a comparison to be made of their evolutionary relationships. Studies were based on direct sequencing of the PCR-amplified products of the 400 nucleotides coding for the amino terminus of the nucleoprotein. Phylogenetic relationships were analysed after bootstrap resampling using the maximum parsimony and the neighbour-joining methods. Analyses of both the nucleotide and amino acid sequences placed these viruses in three separate clusters, namely genotype 4 (Duvenhage), genotype 5 (EBL1) and genotype 6 (EBL2). Evolutionary analysis of the nucleoprotein gene of EBL1 and EBL2 indicated low intrinsic heterogeneity mainly due to synonymous substitutions. In addition, both EBL1 and EBL2 evolved into at least two genetically distinguishable lineages (a and b) following geographical drifting. We can speculate that subsequently the lineages EBL1a and EBL1b were introduced into parts of northern Europe from two different geographical directions; EBL1b was probably introduced most recently and was from North Africa. Eptesicus serotinus appears to be the principal reservoir for EBL1 and Myotis dasycneme and M. daubentonii the reservoirs for EBL2.

Amino Acid Sequence↗
PubMed2025

The landscape of structural variation in pediatric cancer.

Structural variants (SVs) account for over 60% of the driver variants in pediatric cancer, and in many cases act as the cancer initiating event. To study SVs from a pan-cancer perspective, we analyzed 1,616 pediatric cancer genomes in 16 major cancer types of hematological malignancies (n = 908), brain tumors (n = 183), and solid tumors (n = 525) and compared their profiles to those of 2,203 adult cancers. The SV burden varied ~100-fold across pediatric cancer types and demonstrated an 8- to 16-fold reduction compared to adult brain and solid tumors but was comparable in pediatric versus adult hematological malignancies. Recurrent SV hotspots occurred uniquely in pediatric acute lymphoblastic leukemias (ALLs) in proximity to RAG-mediated recombination signal sequences (RSS) and disrupted multiple immune-related loci as well as 69 genes, which often involved cryptic RSS sites. By contrast, such hotspots affected only immune-related loci but not driver genes in adult lymphoid cancers. Eight SV signatures extracted from the cohort had varying distributions across cancer types, with clustered translocations reflecting templated insertions in osteosarcoma, and medium-sized deletions (10 kb to 1 Mb) enriched in cancers with RAG-mediated deletions. Intra-patient evolutionary analysis in 13 patients with multiple spatiotemporally distinct samples revealed that RAG-mediated recombination in leukemia and complex rearrangements in solid tumors occurred both early in disease initiation and continuously during later diversification, contributing to clonal heterogeneity. Finally, we found that both driver genes and fragile sites were the two genomic regions most frequently disrupted by SVs. The unique and diverse SV landscapes that emerged from this comprehensive analysis expand the scope of RSS-mediated mutagenesis in pediatric ALL and will be a valuable resource for guiding future functional studies and the design of clinical genomic testing in pediatric cancer.

Journal Article↗
PubMed2003

Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization.

Large-scale genomic rearrangements are a major force of evolutionary change and the ascertainment of such events between the human and great ape genomes is fundamental to a complete understanding of the genetic history and evolution of our species. Here, we present the results of an evolutionary analysis utilizing array comparative genomic hybridization (array CGH), measuring copy-number gains and losses among these species. Using an array of 2460 human bacterial artificial chromosomes (BACs) (12% of the genome), we identified a total of 63 sites of putative DNA copy-number variation between humans and the great apes (chimpanzee, bonobo, gorilla, and orangutan). Detailed molecular characterization of a subset of these sites confirmed rearrangements ranging from 40 to at least 175 kb in size. Surprisingly, the majority of variant sites differentiating great ape and human genomes were found within interstitial euchromatin. These data suggest that such large-scale events are not restricted solely to subtelomeric or pericentromeric regions, but also occur within genic regions. In addition, 5/9 of the verified variant sites localized to areas of intrachromosomal segmental duplication within the human genome. On the basis of the frequency of duplication in humans, this represents a 14-fold positional bias. In contrast to previous cytogenetic and comparative mapping studies, these results indicate extensive local repatterning of hominoid chromosomes in euchromatic regions through a duplication-driven mechanism of genome evolution.

Animals↗
PubMed2006

Extensive low-affinity transcriptional interactions in the yeast genome.

Major experimental and computational efforts are targeted at the characterization of transcriptional networks on a genomic scale. The ultimate goal of many of these studies is to construct networks associating transcription factors with genes via well-defined binding sites. Weaker regulatory interactions other than those occurring at high-affinity binding sites are largely ignored and are not well understood. Here I show that low-affinity interactions are abundant in vivo and quantifiable from current high-throughput ChIP experiments. I develop algorithms that predict DNA-binding energies from sequences and ChIP data across a wide dynamic range of affinities and use them to reveal widespread functionality of low-affinity transcription factor binding. Evolutionary analysis suggests that binding energies of many transcription factors are conserved even in promoters lacking classical binding sites. Gene expression analysis shows that such promoters can generate significant expression. I estimate that while only a small percentage of the genome is strongly regulated by a typical transcription factor, up to an order of magnitude more may be involved in weaker interactions. Low-affinity transcription factor-DNA interaction may therefore be important both evolutionarily and functionally.

Algorithms↗
PubMed2003

Genome-wide characterization of the lignification toolbox in Arabidopsis.

Lignin, one of the most abundant terrestrial biopolymers, is indispensable for plant structure and defense. With the availability of the full genome sequence, large collections of insertion mutants, and functional genomics tools, Arabidopsis constitutes an excellent model system to profoundly unravel the monolignol biosynthetic pathway. In a genome-wide bioinformatics survey of the Arabidopsis genome, 34 candidate genes were annotated that encode genes homologous to the 10 presently known enzymes of the monolignol biosynthesis pathway, nine of which have not been described before. By combining evolutionary analysis of these 10 gene families with in silico promoter analysis and expression data (from a reverse transcription-polymerase chain reaction analysis on an extensive tissue panel, mining of expressed sequence tags from publicly available resources, and assembling expression data from literature), 12 genes could be pinpointed as the most likely candidates for a role in vascular lignification. Furthermore, a possible novel link was detected between the presence of the AC regulatory promoter element and the biosynthesis of G lignin during vascular development. Together, these data describe the full complement of monolignol biosynthesis genes in Arabidopsis, provide a unified nomenclature, and serve as a basis for further functional studies.

Alcohol Oxidoreductases↗
PubMed1999

The alpha-subunit of protein prenyltransferases is a member of the tetratricopeptide repeat family.

Lipidation catalyzed by protein prenyltransferases is essential for the biological function of a number of eukaryotic proteins, many of which are involved in signal transduction and vesicular traffic regulation. Sequence similarity searches reveal that the alpha-subunit of protein prenyltransferases (PTalpha) is a member of the tetratricopeptide repeat (TPR) superfamily. This finding makes the three-dimensional structure of the rat protein farnesyltransferase the first structural model of a TPR protein interacting with its protein partner. Structural comparison of the two TPR domains in protein farnesyltransferase and protein phosphatase 5 indicates that variation in TPR consensus residues may affect protein binding specificity through altering the overall shape of the TPR superhelix. A general approach to evolutionary analysis of proteins with repetitive sequence motifs has been developed and applied to the protein prenyltransferases and other TPR proteins. The results suggest that all members in PTalpha family originated from a common multirepeat ancestor, while the common ancestor of PTalpha and other members of TPR superfamily is likely to be a single repeat protein.

Alkyl and Aryl Transferases↗
PubMed2003

Initial stages of reproductive isolation in two species of the endangered Sonoran topminnow.

Long-term geographic isolation can result in reproductive incompatibilities due to forces such as mutation, genetic drift, and differential selection. In the Sonoran topminnow, molecular genetic studies of mtDNA, microsatellites, and MHC genes have shown that the endangered Gila and Yaqui topminnows are substantially different, suggesting that divergence took place approximately two million years ago. Here we examined hybrid crosses and backcrosses between these two allopatric taxa to evaluate the accumulation of postmating barriers to reproduction. These results are then compared with results from a previous study where male topminnows were shown to mate assortatively with conspecific females. Despite their preference for conspecific mates, both types of interspecific crosses successfully produced offspring. There was evidence of reduced hybrid fitness, including smaller mean brood size and male-biased sex ratio, for some classes of backcrosses. Brood sizes and interbrood intervals varied significantly when hybrids were subdivided into different cross categories. Our results illustrate the importance of distinctly defining hybrid classes in studies of reproductive isolation. To our knowledge, this is the first such detailed evolutionary analysis in endangered fish taxa.

Animals↗
PubMed1999

Cloning, sequencing, and functional expression in Escherichia coli of chaperonin (groESL) genes from Vibrio cholerae.

Using a series of oligonucleotides synthesized on the basis of conserved nucleotide motifs in heat-shock genes, the groESL heat-shock operon from a Vibrio cholerae TSI-4 strain has been cloned and sequenced, revealing that the presence of two open reading frames (ORFs) of 291 nucleotides and 1,632 nucleotides separated by 54 nucleotides. The first ORF encoded a polypeptide of 97 amino acids, GroES homologue, and the second ORF encoded a polypeptide of 544 amino acids, GroEL homologue. A comparison of the deduced amino acid sequences revealed that the primary structures of the V. cholerae GroES and GroEL proteins showed significant homology with those of the GroES and GroEL proteins of other bacteria. Complementation experiments were performed using Escherichia coli groE mutants which have the temperature-sensitive growth phenotype. The results showed that the groES and groEL from V. cholerae were expressed in E. coli, and groE mutants harboring V. cholerae groESL genes regained growth ability at high temperature. The evolutionary analysis indicates a closer relationship between V. cholerae chaperonins and those of the Haemophilus and Yersinia species.

Amino Acid Sequence↗
PubMedDate not supplied

Beyond knowledge deficit to a proposal for information-seeking behaviors.

TOPIC: Nursing assessment of knowledge of informational needs. PURPOSE: To present of a brief evolutionary analysis of knowledge deficit in terms of its significance, application, and use, and to present a proposal diagnosis, "information-seeking behaviors." SOURCES: Literature review of knowledge deficit and "information-seeking behaviors." CONCLUSIONS: Knowledge deficit is a nursing diagnosis that is significant for identifying a patient's need for education or knowledge. Its application has revealed limitations to validity and subsequent use. "Information-seeking behaviors" is proposed as an alternative diagnosis. Antecedents and defining characteristics are presented and areas for future research proposed.

Humans↗
PubMed2025

Comparative Genomics of Sex-Determination-Related Genes Reveals Shared Evolutionary Patterns Between Bivalves and Mammals, but Not Fruit Flies.

The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood in many animal groups. Bivalves, a diverse class of molluscs with a variety of reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution of sexual systems. However, the absence of a comprehensive framework has limited progress in this field, particularly regarding the study of sex-determination-related genes (SRGs). In this study, we performed a genome-wide sequence evolutionary analysis of the Dmrt, Sox and Fox gene families in more than 40 bivalve species. For the first time, we provide an extensive and phylogenetically aware dataset of these SRGs, and we find support for the hypothesis that Dmrt-1L and Sox-H may act as primary sex-determining genes by showing their high levels of sequence diversity within the bivalve genomic context. To validate our findings, we studied the same gene families in two well-characterised systems, mammals and fruit flies (genus Drosophila). In the former, we found that the male sex-determining gene Sry exhibits a pattern of amino acid sequence diversity similar to that of Dmrt-1L and Sox-H in bivalves, consistent with its role as master SD regulator. In contrast, no such pattern was observed among genes of the fruit fly SD cascade, which is controlled by a chromosomic mechanism. Overall, our findings highlight similarities in the sequence evolution of some mammal and bivalve SRGs, possibly driven by a comparable architecture of SD cascades. This work underscores once again the importance of employing a comparative approach when investigating understudied and non-model systems.

Animals↗