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PubMed2004

[New progresses on mitochondrial DNA in fish].

The study on mitochondrial DNA (mtDNA) is a hot field in recent molecular biology. With some special characteristics, mitochondrial DNA as an ideal genetic marker has been successfully applied to the research of population and evolutionary biology of fish. Many scientific achievements on mtDNA in fish have been made, however, a number of issues need to be further studied and explored. In the present paper, the research progresses on the complete mtDNA sequences, the structures and characteristics of mtDNA, the mtDNA control region structures, and mtDNA polymorphisms and detecting methods are introduced. Furthermore,we review the applications in the recent years in the fields of systematic evolution, hybridization and introgression, biogeography and population genetics of fish.

Animals↗
PubMed2005

A review of the history of U.S. radiation protection regulations, recommendations, and standards.

Shortly after the discovery of x rays by Wilhelm Konrad Roentgen in 1895, and the isolation of the element radium by Pierre and Marie Curie three years later, the fascination with and potential for an array of uses of ionizing radiation in medicine, science, and technology was born. As with any new technology, there was a need to balance both the beneficial and potential detrimental effects of uses of these new technologies for the advancement of humankind. In the early days, radiation hazards were not well understood. Over the decades increasing concerns in the scientific community and lay population demanded that standardized guidance and recommendations be developed for the use of ionizing radiation. Today, U.S. radiation protection standards and recommendations to protect the occupational worker, members of the general public, and the environment are numerous and complex. This review summarizes the history of the development and application of radiation protection standards and regulations to assure the safe use of radiation and radioactive materials. The evolution and roles of international and national scientific recommending and regulatory organizations that shape U.S. radiation protection policy are described and discussed.

Government Agencies↗
PubMed2005

A review of the history of U.S. radiation protection regulations, recommendations, and standards.

Shortly after the discovery of x rays by Wilhelm Konrad Roentgen in 1895, and the isolation of the element radium by Pierre and Marie Curie three years later, the fascination with and potential for an array of uses of ionizing radiation in medicine, science, and technology was born. As with any new technology, there was a need to balance both the beneficial and potential detrimental effects of uses of these new technologies for the advancement of humankind. In the early days, radiation hazards were not well understood. Over the decades increasing concerns in the scientific community and lay population demanded that standardized guidance and recommendations be developed for the use of ionizing radiation. Today, U.S. radiation protection standards and recommendations to protect the occupational worker, members of the general public, and the environment are numerous and complex. This review summarizes the history of the development and application of radiation protection standards and regulations to assure the safe use of radiation and radioactive materials. The evolution and roles of international and national scientific recommending and regulatory organizations that shape U.S. radiation protection policy are described and discussed.

Government Agencies↗
PubMed1980

A rationale for the treatment of dysmenorrhea.

Studies have elucidated the regulatory interplay between ovarian hormonal changes, prostaglandin levels and the evolution of intrauterine pressure that leads to dysmenorrhea. These studies substantiated the premise that primary dysmenorrhea is caused by endogenous prostaglandin excess and prompted clinical trials with naproxen sodium (Anaprox) in patients with primary dysmenorrhea. The primary action of prostaglandin is constriction of uterine blood vessels, with consequent anoxia and sustained myometrial contraction. Cyclic uterine contractions evolve later but gradually, with the progress of time. However, the cyclic contractions are not perceived as painful. It is important to realize that the source of uterine pain in dysmenorrhea is the high resting intrauterine pressure (tonus). Penetration of excess prostaglandins into general circulation fully accounts for the systemic symptoms of dysmenorrhea (nausea, vomiting, diarrhea, headache, etc). Rational treatment of dysmenorrhea should be directed at elimination of the excess prostaglandin action. Naproxen sodium and other prostaglandin synthesis inhibitors decrease intrauterine resting pressure as well as amplitude and frequency of uterine contractions and reduce the uterine concentrations of prostaglandins. These changes are associated with substantial pain relief. Thus, naproxen sodium and other prostaglandin synthesis inhibitors present a logical treatment modality to be used in dysmenorrhea.

Abortion, Induced↗
PubMed2000

Evolution of serpin specificity: cooperative interactions in the reactive-site loop sequence of antithrombin specifically restrict the inhibition of activated protein C.

Protease cascades and their inhibitors are a common feature of many biological regulatory systems, and the various components of such cascades have been subjected to a long and concerted evolution. We present here evidence that in the coagulation cascade, the sequence of the protease-binding reactive-site loop of antithrombin has evolved such that the majority of its residues has been acquired not for the efficient inhibition of its target proteases, thrombin and factor Xa, but to avoid the inhibition of activated protein C (APC). We substituted residues of the reactive-site loop of antithrombin into alpha(1)-antitrypsin and tested the chimeras against thrombin, factor Xa, and APC. With respect to factor Xa and thrombin, the difference in association rate between the fastest and the slowest inhibitors was 5.5- and 88-fold, respectively. However, with respect to APC the difference was 12,500-fold. While most of the variation in the inhibition rates of thrombin could be accounted for by P2 Gly-to-Pro substitutions, for APC almost every residue had an effect on inhibition. In 22 of 25 direct comparisons of antitrypsin residues with antithrombin residues, either singly or in blocs, the antithrombin residues caused a decrease in the rate of inhibition of APC. The antithrombin residue Asn393, at position P'3, emerged as particularly important for avoiding the inhibition of APC, however, its 190-fold effect was seen only when in conjunction with antithrombin P7 to P'2 residues. Cooperative effects among residues of the reactive-site loop thus emerged as critical for restricting the activity of this sequence against APC.

Amino Acid Substitution↗
PubMed2024

Genome evolution of the ancient hexaploid Platanus × acerifolia (London planetree).

Whole-genome duplication (WGD; i.e., polyploidy) and chromosomal rearrangement (i.e., genome shuffling) significantly influence genome structure and organization. Many polyploids show extensive genome shuffling relative to their pre-WGD ancestors. No reference genome is currently available for Platanaceae (Proteales), one of the sister groups to the core eudicots. Moreover, Platanus × acerifolia (London planetree; Platanaceae) is a widely used street tree. Given the pivotal phylogenetic position of Platanus and its 2-y flowering transition, understanding its flowering-time regulatory mechanism has significant evolutionary implications; however, the impact of Platanus genome evolution on flowering-time genes remains unknown. Here, we assembled a high-quality, chromosome-level reference genome for P. × acerifolia using a phylogeny-based subgenome phasing method. Comparative genomic analyses revealed that P. × acerifolia (2n = 42) is an ancient hexaploid with three subgenomes resulting from two sequential WGD events; Platanus does not seem to share any WGD with other Proteales or with core eudicots. Each P. × acerifolia subgenome is highly similar in structure and content to the reconstructed pre-WGD ancestral eudicot genome without chromosomal rearrangements. The P. × acerifolia genome exhibits karyotypic stasis and gene sub-/neo-functionalization and lacks subgenome dominance. The copy number of flowering-time genes in P. × acerifolia has undergone an expansion compared to other noncore eudicots, mainly via the WGD events. Sub-/neo-functionalization of duplicated genes provided the genetic basis underlying the unique flowering-time regulation in P. × acerifolia. The P. × acerifolia reference genome will greatly expand understanding of the evolution of genome organization, genetic diversity, and flowering-time regulation in angiosperms.

Polyploidy↗
PubMed2002

Selenoprotein R is a zinc-containing stereo-specific methionine sulfoxide reductase.

Selenoprotein R (SelR) is a mammalian selenocysteine-containing protein with no known function. Here we report that cysteine homologs of SelR are present in all organisms except certain parasites and hyperthermophiles, and this pattern of occurrence closely matches that of only one protein, peptide methionine sulfoxide reductase (MsrA). Moreover, in several genomes, SelR and MsrA genes are fused or clustered, and their expression patterns suggest a role of both proteins in protection against oxidative stress. Consistent with these computational screens, growth of Saccharomyces cerevisiae SelR and MsrA mutant strains was inhibited, and the strain lacking both genes could not grow, in the presence of H2O2 and methionine sulfoxide. We found that the cysteine mutant of mouse SelR, as well as the Drosophila SelR homolog, contained zinc and reduced methionine-R-sulfoxide, but not methionine-S-sulfoxide, in in vitro assays, a function that is both distinct and complementary to the stereo-specific activity of MsrA. These findings identify a function of the conserved SelR enzyme family, define a pathway of methionine sulfoxide reduction, reveal a case of convergent evolution of similar function in structurally distinct enzymes, and suggest a previously uncharacterized redox regulatory role of selenium in mammals.

Amino Acid Sequence↗
PubMed2003

Evolution of cis-regulation of the proneural genes.

The current state of knowledge concerning cis-regulatory sequences of the proneural genes of vertebrates and Drosophila is discussed. Many proneural genes have a complex modular arrangement of discrete enhancer elements. One unusual feature of these genes is that many distant enhancer elements, regulating expression in specific spatial locations, require input from previously synthesized protein from the proneural gene itself, in addition to other transcriptional activators. This is distinct from the auto-regulation, via E boxes in the promoter, that takes place in neural precursors. The selection of neural precursors from a field of cells expressing a proneural gene, is mediated by Notch signalling and requires up-regulation of proneural gene expression in the precursor concurrently with down-regulation in the surrounding cells. Although the way in which a single cell is selected remains unclear, a number of feedback loops have been uncovered that reinforce the choice. These are briefly surveyed. A specific regulatory element, the Sensory Organ Precursor element, that mediates selection of the precursors of the large sensory bristles, has been described in Drosophila. We report the conservation of this sequence in Calliphora vicina, a higher fly. In contrast, no such sequence is seen in the achaete-scute complex of Anopheles gambiae, a basal Dipteran species. We suggest that this enhancer may have arisen during the evolution of the cyclorraphous flies and present a hypothesis for its possible function.

Animals↗
PubMed2006

Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks.

Numerous studies in both prokaryotes and eukaryotes have shown that, under standard growth conditions, less than 20% of the protein-coding genes are essential for survival. This suggests that biological systems have evolved to have a high degree of robustness to mutational disruptions that can affect the majority of their genes. This mutational robustness could arise either due to redundancy, i.e. direct backup, or due to distributed architecture, i.e. indirect backup where multiple genes contribute to the functioning of a process in the system. Despite clear evidence for direct backup, the prevalence of indirect backup is poorly understood. In this study, we reveal the existence of a hidden distributed architecture behind the scale-free transcriptional regulatory network of yeast by applying a unique network transformation procedure and show that the network is tolerant even to mutations that disrupt regulatory hubs. Contrary to what is generally accepted, our observation that hubs can be lost or replaced in evolution suggests that this hidden distributed architecture behind scale-free networks protects the overall transcriptional program of the organism from mutations affecting major regulatory hubs. We show that the distributed architecture has been provided by an unexpectedly large number of coordinating partners for any regulatory protein. On the basis of these findings, we propose that the existence of such architecture can allow organisms to explore the adaptive landscape in changing environments by providing the plasticity required to reprogram levels of expression of specific genes that may enhance survival. Thus, an "over-engineered" backup system in the form of distributed architecture is likely to be a major determinant of the "evolvability" of the gene expression in organisms faced with environmental diversity.

Algorithms↗
PubMedDate not supplied

A simulation study of the genetic regulatory hierarchy for butterfly eyespot focus determination.

The color patterns on the wings of butterflies have been an important model system in evolutionary developmental biology. Two types of models have been used to study these patterns. The first type of model employs computational techniques and generalized mechanisms of pattern formation to make predictions about how color patterns will vary as parameters of the model are changed. These generalized mechanisms include diffusion gradient, reaction-diffusion, lateral inhibition, and threshold responses. The second type of model uses known genetic interactions from Drosophila melanogaster and patterns of candidate gene expression in one of several butterfly species (most often Junonia (Precis) coenia or Bicyclus anynana) to propose specific genetic regulatory hierarchies that appear to be involved in color pattern formation. This study combines these two approaches using computational techniques to test proposed genetic regulatory hierarchies for the determination of butterfly eyespot foci (also known as border ocelli foci). Two computer programs, STELLA 8.1 and Delphi 2.0, were used to simulate the determination of eyespot foci. Both programs revealed weaknesses in a genetic model previously proposed for eyespot focus determination. On the basis of these simulations, we propose two revised models for eyespot focus determination and identify components of the genetic regulatory hierarchy that are particularly sensitive to changes in model parameter values. These components may play a key role in the evolution of butterfly eyespots. Simulations like these may be useful tools for the study of other evolutionary developmental model systems and reveal similar sensitive components of the relevant genetic regulatory hierarchies.

Animals↗
PubMed1999

Molecular evolution of immunoglobulin and fibronectin domains in titin and related muscle proteins.

The family of regulatory and structural muscle proteins, which includes the giant kinases titin, twitchin and projectin, has sequences composed predominantly of serially linked immunoglobulin I set (Ig) and fibronectin type III (FN3) domains. This paper explores the evolutionary relationships between 16 members of this family. In titin, groups of Ig and FN3 domains are arranged in a regularly repeating pattern of seven and 11 domains. The 11-domain super-repeat has its origins in the seven-domain super-repeat and a model for the duplications which gave rise to this super-repeat is proposed. A super-repeat composed solely of immunoglobulin domains is found in the skeletal muscle isoform of titin. Twitchin and projectin, which are presumed to be orthologs, have undergone significant insertion/deletion of domains since their divergence. The common ancestry of myomesin, skelemin and M-protein is shown. The relationship between myosin binding proteins (MyBPs) C and H is confirmed, and MyBP-H is proposed to have given rise to MyBP-C by the acquisition of some titin domains.

Amino Acid Sequence↗
PubMed1986

The evolution of self-regulated transposition of transposable elements.

This paper examines the conditions under which self-regulated rates of transposition can evolve in populations of transposable elements infecting sexually reproducing hosts. Models of the evolution of both cis-acting regulation (transposition immunity) and trans-acting regulation (transposition repression) are analyzed. The potential selective advantage to regulation is assumed to be derived from the deleterious effects of mutations associated with the insertion of newly replicated elements. It is shown that both types of regulation can easily evolve in hosts with low rates of genetic recombination per generation, such as bacteria or bacterial plasmids. Conditions are much more restrictive in organisms with relatively free recombination. In haploids, the main selective force promoting regulation is the induction of lethal or sterile mutations by transposition; in diploids, a sufficiently high frequency of dominant lethal or sterile mutations associated with transpositions is required. Data from Drosophila and maize suggest that this requirement can sometimes be met. Coupling of regulatory effects across different families of elements would also aid the evolution of regulation. The selective advantages of restricting transposition to the germ line and of excising elements from somatic cells are discussed.

Animals↗
PubMed1978

Gene dosage compensation and the evolution of sex chromosomes.

Dosage compensation is a mechanism by means of which the activity of X-linked or Z-linked genes is made equal in the two sexes of organisms with an XX compared to XY or ZZ compared to ZW basis of sex determination. In mammals, compensation is achieved by the inactivation of one X chromosome in somatic cells of females. In Drosophila, compensation does not involve inactivation. The two X chromosomes in females as well as the single X in males are regulated, and individual genes are thought to respond independently to the regulatory mechanism. It is proposed that in both groups of organisms the evolution of heteromorphic sex chromosomes was gradual and occurred as the direct result of the evolution of dosage compensation rather than the reverse.

Alleles↗
PubMed2005

Evidence for widespread degradation of gene control regions in hominid genomes.

Although sequences containing regulatory elements located close to protein-coding genes are often only weakly conserved during evolution, comparisons of rodent genomes have implied that these sequences are subject to some selective constraints. Evolutionary conservation is particularly apparent upstream of coding sequences and in first introns, regions that are enriched for regulatory elements. By comparing the human and chimpanzee genomes, we show here that there is almost no evidence for conservation in these regions in hominids. Furthermore, we show that gene expression is diverging more rapidly in hominids than in murids per unit of neutral sequence divergence. By combining data on polymorphism levels in human noncoding DNA and the corresponding human-chimpanzee divergence, we show that the proportion of adaptive substitutions in these regions in hominids is very low. It therefore seems likely that the lack of conservation and increased rate of gene expression divergence are caused by a reduction in the effectiveness of natural selection against deleterious mutations because of the low effective population sizes of hominids. This has resulted in the accumulation of a large number of deleterious mutations in sequences containing gene control elements and hence a widespread degradation of the genome during the evolution of humans and chimpanzees.

Animals↗
PubMed1993

Origin of JC polyomavirus variants associated with progressive multifocal leukoencephalopathy.

JC polyomavirus (JCV) DNAs from the urine of nonimmunocompromised individuals (designated archetypal isolates) regularly contain a regulatory sequence that may have generated various regulatory sequences of JCV isolates derived from the brain of patients with progressive multifocal leukoencephalopathy (PML). In this report, we constructed a phylogenetic tree for 14 isolates (7 archetypes and 7 PML types) from DNA sequence data on the VP1 (major capsid protein) gene. According to the phylogenetic tree, the 14 isolates diverged into types A and B, each of which contained archetypal and PML-type isolates. Each type further diverged into several groups containing archetypal and PML-type isolates. We conclude that PML-type isolates are polyphyletic in their origin and do not constitute a unique lineage. This conclusion suggests that PML-type JCV isolates are generated from archetypal strains during persistence in the hosts. Furthermore, the present phylogenetic analysis indicates that an ancestral JCV carried the archetypal regulatory sequence and that this structure has been conserved in the course of JCV evolution.

Base Sequence↗
PubMed2005

From phenotypic to molecular polymorphisms involved in naturally occurring variation of plant development.

An enormous amount of naturally occurring genetic variation affecting development is found within wild and domesticated plant species. This diversity is presumably involved in plant adaptation to different natural environments or in human preferences. In addition, such intraspecific variation provides the basis for the evolution of plant development at larger evolutionary scales. Natural phenotypic differences are now amenable to genetic dissection up to the identification of causal DNA polymorphisms. Here we describe 30 genes and their functional nucleotide polymorphisms currently found as underlying allelic variation accounting for plant intraspecific developmental diversity. These studies provide molecular and cellular mechanisms that determine natural variation for quantitative and qualitative traits such as: fruit and seed morphology, colour and composition; flowering time; seedling emergence; plant architecture and inflorescence or flower morphology. Besides, analyses of flowering time variation within several distant species allow molecular comparisons between species, which are detecting homologous genes with partly different functions and unrelated genes with analogous functions. Thus, considerable gene function differences are being revealed also among species. Inspection of a catalogue of intraspecific nucleotide functional polymorphisms shows that transcriptional regulators are the main class of genes involved. Furthermore, barely more than half of the polymorphisms described are located in coding regions and affect protein structure, while the rest are regulatory changes altering gene expression. These limited analyses of intraspecific developmental variation support Doebley and Lukens's proposition (1998) that modifications in cis -regulatory regions of transcriptional regulators represent a predominant mode for the evolution of novel forms, but await more detailed studies in wild plant species.

Adaptation, Physiological↗
PubMed1993

[The genetic language: grammar, semantics, evolution].

The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics. There is a review of these general attributes of genetic language, including also the problems of synonymy and evolution. The main directions of theoretical investigations of genetic language and neighbouring questions are formulated: (1) cryptographic problems, (2) analysis of genetic texts, (3) theoretical-linguistic problems, (4) evolutionary linguistic questions. The problem of genetic language becomes one of the key ones of molecular genetics, molecular biology and gene engineering.

Codon↗