Ribozymes in wonderland.
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Biological Evolution↗
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Evolution of recommended dietary allowances--new directions?
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Diet↗
Evolution of a Progressive Self-Directed Diabetes Education Model.
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Diabetes Mellitus, Type 1↗
Future directions in residential services: reaction or evolution?
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Allied Health Personnel↗
Evolution of placentation among squamate reptiles: recent research and future directions.
Squamate reptiles are uniquely suited to study of evolution of reproductive mode and pattern of embryonic nutrition. Viviparous species have evolved from oviparous ancestors on numerous occasions, patterns of nutritional provision to embryos range widely from lecithotrophy, at one end of a continuum, to placentotrophy at the other, and structure and function of the maternal-embryonic relationship is highly constrained resulting in parallel evolutionary trajectories among taxa. Embryos of oviparous species primarily receive nourishment from yolk, but also mobilize a significant quantity of calcium from the eggshell. Most viviparous species also are predominantly lecithotrophic, yet all viviparous species are placentotrophic to some degree. Similarities in embryonic development and nutritional pattern between oviparous species and most viviparous species suggest that the pattern of nutrition of oviparous squamates is an exaptation for the evolution of viviparity and that placentotrophy and viviparity evolve concomitantly. The few species of squamates that rely substantially on placentotrophy have structural modifications of the interface between the embryo and mother that are interpreted as adaptations to enhance nutritional exchange. Recent studies have extended understanding of the diversity of embryonic nutrition and placental structure and have resulted in hypotheses for transitions in the evolution of placentotrophy, yet data are available for few species. Indirect tests of these hypotheses, by comparison of structural-functional relationships among clades in which viviparity has evolved, awaits further study of the reproductive biology of squamates.
Animals↗
Site-directed mutagenesis study on the roles of evolutionally conserved aspartic acid residues in human glutathione S-transferase P1-1.
The evolutionally conserved aspartyl residues (Asp57, Asp98 and Asp152) in human glutathione S-transferase P1-1 were replaced with alanine by site-directed mutagenesis to obtain the mutants (D57A, D98A and D152A). The replacement of Asp98 with alanine resulted in a decrease of the affinity for S-hexyl-GSH-agarose, a 5.5-fold increase of the KmGSH and a 2.9-fold increase of the I50 of S-hexyl-GSH for GSH-CDNB conjugation. Asp98 seems to participate in the binding of GSH through hydrogen bonding with the alpha-carboxylate of the gamma-glutamyl residue of GSH. The kcat of D98A was 2.6-fold smaller than that of the wild-type, and the pKa of the thiol group of GSH bound in D98A was approximately 0.8 pK units higher than those in the wild-type. Asp98 also seems to contribute to the activation of GSH to some extent. On the other hand, most of the kinetic parameters of D57A and D152A were similar to those of the wild-type. However, the thermostabilities of D57A and D152A were significantly lower than that of the wild-type. Asp57 and Asp152 seem to be important for maintaining the proper conformation of the enzyme.
Amino Acid Sequence↗
Is there conscious choice in directed mutation, phenocopies, and related phenomena? An answer based on quantum measurement theory.
In a previous article (Goswami, 1997), it was suggested that an application of quantum measurement theory under the auspices of a monistic idealist ontology (that consciousness is the ground of being) can solve many difficult problems of neo-Darwinism, e.g., alternating rapid creativity and homeostasis observed in evolution and the directionality, origin, and nature of life. In this article, we propose an epigenetic quantum mechanism to explain the connection of developmental processes and evolution, as has been evidenced in such controversial phenomena as directed mutation and phenocopies.
Animals↗
Using stories to assess values and establish medical directives.
While still developing in Germany, a consensus has emerged in the United States on the use of advance directives for guiding future medical decision making. This article outlines three phases in the evolution of advance directive forms--the legal phase, the checklist phase, and the story phase. The story-based approach is discussed as the best method for assessing patient values and incorporating them into advance directives, and a story-based advance directive form, which has been developed and tested during the past two years, is presented.
Advance Directives↗
[Reverse transcriptase and its biological role].
Elements with open-reading translation frames homologous to retroviral RNA-dependent DNA polymerases (reverse transcriptases) were found in eukaryotic cell genomes. Expression of endogenous reverse transcriptases in prokaryotic and eukaryotic cells is confirmed directly and indirectly. Evolution and function of reverse transcriptases are analyzed, and their phylogenetic and ontogenetic role is evaluated.
Biological Evolution↗
Evolution of major histocompatibility complex class II allelic diversity: direct descent in mice and humans.
The high degree of polymorphism seen at major histocompatibility complex (MHC) class II loci is a feature unique to the MHC. Most of the beta-chain polymorphism is localized in "hypervariable" regions (HVRs). HVR amino acid sequence similarity between distantly related species has recently been found. We have employed a Monte-Carlo statistic to show that shared HVR polymorphism between beta-chain genes of humans and mice represents direct descent of ancestral sequences rather than convergent evolution. Furthermore, half the sequence polymorphism seen in class II beta-chain genes of mice persists in evolution and is encoded by the same DNA sequence in humans. No evidence for increased mutation rate within the HVR was found. We postulate that the HVR can be considered the genetic unit of recombination, with selection for HVR sequences and combinations of HVRs constrained by functional considerations.
Alleles↗
Comparative genomics of mitochondrial DNA in Drosophila simulans.
The current study compares the nucleotide variation among 22 complete mitochondrial genomes of the three distinct Drosophila simulans haplotypes with intron 1 of the alcohol dehydrogenase-related locus. This is the first study to investigate the sequence variation of multiple complete mitochondrial genomes within distinct mitochondrial haplotypes of a single species. Patterns of variation suggest distinct forces are influencing the evolution of mitochondrial DNA (mtDNA) and autosomal DNA in D. simulans. First, there is little variation within each mtDNA haplotype but strong differentiation among them. In contrast, there is no support for differentiation of the mitochondrial haplotypes at the autosomal locus. Second, there is a significant deficiency of mitochondrial variation in each haplotype relative to the autosomal locus. Third, the ratio of nonsynonymous to synonymous substitutions is not equal in all branches of the well-resolved phylogeny. There is an excess of nonsynonymous substitutions relative to synonymous substitutions within each D. simulans haplotype. This result is similar to that previously observed within the mtDNA of distinct species. A single evolutionary force may be causally linked to the observed patterns of mtDNA variation-a rickettsia-like microorganism, Wolbachia pipientis, which is known to directly influence mitochondrial evolution but have a less direct influence on autosomal loci.
Alcohol Dehydrogenase↗
A ribozyme for the aldol reaction.
Directed in vitro evolution can create RNA catalysts for a variety of organic reactions, supporting the "RNA world" hypothesis, which proposes that metabolic transformations in early life were catalyzed by RNA molecules rather than proteins. Among the most fundamental carbon-carbon bond-forming reactions in nature is the aldol reaction, mainly catalyzed by aldolases that utilize either an enamine mechanism (class I) or a Zn(2+) cofactor (class II). We report on isolation of a Zn(2+)-dependent ribozyme that catalyzes an aldol reaction at its own modified 5' end with a 4300-fold rate enhancement over the uncatalyzed background reaction. The ribozyme can also act as an intermolecular catalyst that transfers a biotinylated benzaldehyde derivative to the aldol donor substrate, coupled to an external hexameric RNA oligonucleotide, supporting the existence of RNA-originated biosynthetic pathways for metabolic sugar precursors and other biomolecules.
Aldehydes↗
Structural evolution of colloidal crystals with increasing ionic strength.
We have directly observed the structural evolution of colloidal crystals as a function of increasing ionic strength using confocal scanning laser microscopy. Silica colloids were sedimented onto a glass substrate in deionized water to create large, single domain crystals. The solution ionic strength was then increased by one of three methods of controlled electrolyte addition: (1) direct injection of electrolyte solutions, (2) single step diffusion of electrolyte solutions through a dialysis membrane, and (3) multiple step diffusion of electrolyte solutions of increasing ionic strength through a dialysis membrane. During direct injection of electrolyte solutions, initially large, single domain colloidal crystals were shear melted and then evolved into polycrystalline structures at low ionic strengths and gels at higher ionic strengths. Diffusion of electrolyte solutions though dialysis membranes in a single step produced gradient-driven transport that also melted initial single domain crystals to yield polycrystalline and gel structures similar to the injection approach. Interestingly, the multistep diffusion of several electrolyte solutions through dialysis membranes facilitated retention of large, single domain crystals even as particles came into adhesive contact. This was achieved by reducing the contraction rate of the crystalline lattice to allow sufficient time for diffusion-limited configurational rearrangements to occur within the evolving structure. These mechanically robust, single domain colloidal crystals may find important applications as templates for photonic materials and sensors.
Journal Article↗
Evolutionary basis of parallelism in North American scincid lizards.
This study uses a phylogenetic framework to explore the causes of parallelism in two North American scincid lizard assemblages: the skiltonianus and fasciatus species groups of the genus Plestiodon. Each group consists of several closely related species with conserved neonate morphology; features that distinguish species become accentuated during ontogeny, and these differences often resemble different endpoints along a developmental continuum. This continuum is believed to be an expression of the ancestral ontogeny, and has led to the hypothesis that evolutionary change in development has generated much of the observed morphological diversity. However, progress on understanding these mechanisms is limited by a lack of well-supported phylogenetic data for the fasciatus group, and for Plestiodon in general. Recent phylogenetic studies on the skiltonianus group have revealed previously undetected cases of parallelism, and raise the possibility that similar cases have yet to be discovered in the fasciatus group. Here, I estimate a phylogeny to test the monophyly of the fasciatus group and infer its relationship with other North American Plestiodon using 2537 bp from six mtDNA genes. I use the phylogeny to reconstruct the mode (graduated vs. punctuated) and direction of body size evolution, to map the evolution of two predominant color morphs, and to test whether size and color pattern evolve concertedly. The results show that the morphotypes of the traditional fasciatus group constitute good species, but that the species group is rendered paraphyletic by several geographically overlapping species that deviate from the fasciatus-like ontogeny. Body size evolution has occurred gradually and bi-directionally, and shifts to large body size have been consistently associated with the loss of the striped color pattern during ontogeny. I show that parallelism, a lack of rigorous phylogenetic analysis, and a reliance on shared ontogenetic features for predicting phylogenetic relatedness, has misled the traditional systematics of these lizards, but that general ideas concerning the role of development in their morphological evolution remain supported. I close by proposing that the processes influencing repeated phyletic patterns in the skiltonianus and fasciatus groups represent adherence to an ancestral ground state, and discuss the importance of using phylogenies for the initial characterization of evolutionary changes in development.
Animals↗
Morphological evolution, ecological diversification and climate change in rodents.
Among rodents, the lineage from Progonomys hispanicus to Stephanomys documents a case of increasing size and dental specialization during an approximately 9 Myr time-interval. On the contrary, some contemporaneous generalist lineages like Apodemus show a limited morphological evolution. Dental shape can be related to diet and can be used to assess the ecological changes along the lineages. Consequently, size and shape of the first upper molar were measured in order to quantify the patterns of morphological evolution along both lineages and compare them to environmental trends. Climatic changes do not have a direct influence on evolution, but they open new ecological opportunities by changing vegetation and allow the evolution of a specialist like Stephanomys. On the other hand, environmental changes are not dramatic enough to destroy the habitat of a long-term generalist like Apodemus. Hence, our results exemplify a case of an influence of climate on the evolution of specialist species, although a generalist species may persist without change.
Analysis of Variance↗
Evolutionary convergence in Otx expression in the pentameral adult rudiment in direct-developing sea urchins.
Convergence is a significant evolutionary phenomenon. Arrival at similar morphologies from different starting points indicates a strong role for natural selection in shaping morphological phenotypes. There is no evidence yet of convergence in the developmental mechanisms that underlie the evolution of convergent developmental phenotypes. Here we report the expression domains in sea urchins of two important developmental regulatory genes ( Orthodenticle and Runt), and show evidence of molecular convergence in the evolution of direct-developing sea urchins. Indirect development is ancestral in sea urchins. Evolutionary loss of the feeding pluteus stage and precocious formation of the radially symmetric juvenile has evolved independently in numerous sea urchin lineages, thus direct development is an evolutionary convergence. Indirect-developing species do not express Otx during the formation of their five primordial tube feet, the ancestral condition. However, each direct-developing urchin examined does express Otx in the tube feet. Otx expression in the radial arms of direct-developing sea urchins is thus convergent, and may indicate a specific need for Otx use in direct development, a constraint that would make direct development less able to evolve than if there were multiple molecular means for it to evolve. In contrast, Runt is expressed in tube feet in both direct- and indirect-developing species. Because echinoderms are closely related to chordates and postdate the protostome/deuterostome divergence, they must have evolved from bilaterally symmetrical ancestors. Arthropods and chordates use Otx in patterning their anterior axis, and Runt has multiple roles including embryonic patterning in arthropods, and blood and bone cell differentiation in vertebrates. Runt has apparently been co-opted in echinoderms for patterning of pentamery, and Otx in pentameral patterning among direct-developing echinoids. The surprisingly dynamic nature of Otx evolution reinvigorates debate on the role of natural selection vs shared ancestry in the evolution of novel features.
Animals↗
From epithelial dysplasia to squamous carcinoma in the head and neck region: an epidemiological assessment.
The evolution of 97 cases of epithelial dysplasia in the head and neck region was retrospectively controlled, with a mean follow-up of 30 months. Dysplastic mucosal areas were observed in the oral cavity in 11 cases, in the pharynx (oro- and hypopharynx) in 39 cases and in the larynx (supraglottic and glottic regions) in 47 cases. According to the criteria defined by the WHO the dysplasia was classified as mild, moderate and severe. Fifty out of the 97 patients developed a squamous carcinoma in the same area, demonstrating a significant direct correlation between age and neoplastic evolution. A direct correlation was also observed between severity of dysplasia and carcinomatous evolution. Further direct correlations were observed between degree of dysplasia, carcinomatous evolution and amount of exposure to cigarette smoke and alcohol.
Aged↗
Mechanistic basis of life history evolution in anuran amphibians: thyroid gland development in the direct-developing frog, Eleutherodactylus coqui.
Direct development is a widespread, alternative life history in Recent amphibians. There is no free-living, aquatic larva; adult features form in the embryo and are present at hatching. The mechanistic bases of direct development remain relatively unexplored. The current study describes the embryonic ontogeny of the thyroid gland in the direct-developing frog Eleutherodactylus coqui (Leptodactylidae) and quantifies histological changes that occur in the gland after its initial appearance. The thyroid gland of E. coqui is first apparent at Townsend-Stewart stage 10, approximately two-thirds of the way through embryogenesis. Soon after this the thyroid begins to accumulate follicular colloid. Quantitative analyses of thyroid histology reveal embryonic peaks in two measures, follicle number and follicle volume, which are followed by declines in these measures prior to hatching. These peaks in thyroid activity in E. coqui are correlated with morphological changes that are directly comparable to metamorphic changes in frogs that retain the ancestral, biphasic life history. In metamorphic taxa, a histologically identifiable thyroid gland does not form until the larval period, well after hatching. Nevertheless, measures of thyroid histology observed in E. coqui follow the pattern reported for metamorphosing amphibians. The present results support the hypothesis that the evolution of direct development in anurans is associated with precocious development and activity of the thyroid axis.
Animals↗