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At least 973 records · Page 54Linked to original sources
PubMed1995

Evolution of the intron-exon structure of eukaryotic genes.

The origin and evolution of intron-exon structures continue to be controversial topics. Two alternative theories, the 'exon theory of genes' and the 'insertional theory of introns', debate the presence or absence of introns in primordial genes. Both sides of the argument have focused on the positions of introns with respect to protein and gene structures. A new approach has emerged in the study of the evolution of intron-exon structures: a population analysis of genes. One example is the statistical analysis of intron phases--the position of introns within or between codons. This analysis detected a significant signal of exon shuffling in the DNA sequence database containing both ancient and modern exon sequences: intron phase correlations, that is, the association together within genes of introns of the same phase. The results of this analysis suggest that exon shuffling played an important role in the origin of both ancient and modern genes.

Animals↗
PubMed1982

Phylogenetic origins and adaptive evolution of avian and mammalian haemoglobin genes.

Recent years have seen rapid growth in amino acid sequence data on globins and nucleotide sequence data on haemoglobin genes and pseudogenes, and cladistic analysis of these data continues to reveal new facets of globin evolution. Our present findings demonstrate: (1) avian and mammalian embryonic alpha genes (pi and xi, respectively) had a monophyletic origin involving an alpha locus duplication about 400 Myr ago soon after the duplication which separated alpha and beta genes; (2) much later in phylogeny, independent beta-gene duplications produced the embryonic rho locus of birds and embryonic epsilon and fetal gamma loci of mammals. This parallels the earlier finding that myoglobins evolved more than once from generalized globin ancestors. Here we support the view that such globin evolution resulted from natural selection acting on mutations in duplicated genes. Thus, our evidence contradicts the neutralist view in which almost all amino acid substitutions in descent to extant globins evaded positive selection.

Amino Acid Sequence↗
PubMed2007

Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data.

Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by concerted evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of evolution, birth-and-death evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support concerted evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via concerted evolution. Comparisons with a repeat array undergoing birth-and-death evolution provide a clear contrast in the level of repeat array variation between these two forms of evolution, confirming that the rDNA indeed does evolve via concerted evolution. These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.

Aspergillus nidulans↗
PubMed2003

Coinfection and superinfection in RNA virus populations: a selection-mutation model.

In this paper, we present a general selection-mutation model of evolution on a one-dimensional continuous fitness space. The formulation of our model includes both the classical diffusion approach to mutation process as well as an alternative approach based on an integral operator with a mutation kernel. We show that both approaches produce fundamentally equivalent results. To illustrate the suitability of our model, we focus its analytical study into its application to recent experimental studies of in vitro viral evolution. More specifically, these experiments were designed to test previous theoretical predictions regarding the effects of multiple infection dynamics (i.e., coinfection and superinfection) on the virulence of evolving viral populations. The results of these experiments, however, did not match with previous theory. By contrast, the model we present here helps to understand the underlying viral dynamics on these experiments and makes new testable predictions about the role of parameters such the time between successive infections and the growth rates of resident and invading populations.

Evolution, Molecular↗
PubMed2026

Phylogeography and molecular evolution of Newcastle disease virus across a century of global surveillance.

Newcastle disease virus (NDV) remains one of the most economically important avian pathogens worldwide, causing recurrent outbreaks in poultry despite decades of vaccination and disease control efforts. Since the first reported outbreak of NDV a hundred years ago, numerous molecular epidemiological studies have been conducted globally across diverse geographic and production settings. Following a century of NDV circulation and evolution, the present study aimed to compile all publicly available NDV sequence data and perform a comprehensive global analysis of the genetic diversity, phylogenetic relationship, and global spatiotemporal distribution of NDV over a 100-year timescale. All publicly available NDV complete genome and full-length fusion (F) gene sequences were retrieved from GenBank up to February 2026. Following rigorous quality control, phylogenetic analyses were performed based on complete genomes and F gene datasets. Phylogenetic analysis identified two genotypes within Class I and 20 genotypes within Class II NDVs, with extensive diversification at the sub-genotype level. Genotype XIII exhibited the greatest sub-genotypic diversity, while genotype VII represented the most globally disseminated genotype, reported across 36 countries. Chronological assessment based on the earliest available reports indicated an increasing number of recognized genotypes from the 1930s to recently described sub-genotypes such as XIII.2.3 and XXII.2.2. Regional diversity analysis revealed the highest genotype diversity in Western Africa, Eastern Asia, and Southern Asia. Comparative residue analysis demonstrated substantial genotype-specific variation within critical functional domains of the fusion protein, including cleavage sites, neutralizing epitopes, and heptad repeat regions. Overall, this study provides the first comprehensive 100-year global overview of NDV evolution and phylogeography. The findings highlight continuous viral diversification, broad geographic dissemination of multiple genotypes, and ongoing molecular variation, emphasizing the need for sustained genomic surveillance and periodic evaluation of vaccine compatibility with emerging NDV genotypes.

100-years of data↗
PubMed2003

The role of vision on hand preshaping during reach to grasp.

During reaching to grasp objects with different shapes hand posture is molded gradually to the object's contours. The present study examined the extent to which the temporal evolution of hand posture depends on continuous visual feedback. We asked subjects to reach and grasp objects with different shapes under five vision conditions (VCs). Subjects wore liquid crystal spectacles that occluded vision at four different latencies from onset of the reach. As a control, full-vision trials (VC5) were interspersed among the blocked vision trials. Object shapes and all VCs were presented to the subjects in random order. Hand posture was measured by 15 sensors embedded in a glove. Linear regression analysis, discriminant analysis, and information theory were used to assess the effect of removing vision on the temporal evolution of hand shape. We found that reach duration increased when vision was occluded early in the reach. This was caused primarily by a slower approach of the hand toward the object near the end of the reach. However, vision condition did not have a significant effect on the covariation patterns of joint rotations, indicating that the gradual evolution of hand posture occurs in a similar fashion regardless of vision. Discriminant analysis further supported this interpretation, as the extent to which hand posture resembled object shape and the rate at which hand posture discrimination occurred throughout the movement were similar across vision conditions. These results extend previous observations on memory-guided reaches by showing that continuous visual feedback of the hand and/or object is not necessary to allow the hand to gradually conform to object contours.

Adult↗
PubMed2002

The decision to continue: the experiences and needs of parents who receive a prenatal diagnosis of holoprosencephaly.

Holoprosencephaly (HPE) is a condition characterized by a defect in the development of the midline embryonic forebrain. When detected prenatally, the diagnosis of HPE offers parents a poor but often uncertain prognosis. Since the majority of parents receiving a prenatal diagnosis of an abnormality terminate their pregnancies, few studies have examined parents' experiences and needs surrounding the decision to continue a pregnancy. We present a descriptive study of in-depth interviews with 24 parents who chose to continue their pregnancy after receiving a prenatal diagnosis of HPE. Parents were asked about their decision-making process to continue the pregnancy. Qualitative analysis was used to identify common themes that emerged from these parents' experiences. The results suggest that most parents did not make an active decision about continuing the pregnancy. Rather, they described a more subtle decision-making process that evolved over time and consisted of several factors. These factors included the parents' religious and personal beliefs, past experiences, and the uncertainty involved in the diagnosis of HPE. Throughout the decision-making process, they described informational, emotional, and supportive needs from family, friends, and health professionals. All of these factors contributed to the evolution of the parents' decision to continue the pregnancy and the acceptance of their decision. Results of this exploratory study suggest health care professionals need to work with parents as they make their decision to continue an affected pregnancy. The results also provide the groundwork for prospective investigation into parents' decision-making process as they receive and adjust to prenatal diagnoses of an abnormality.

Adult↗
PubMed2006

The next generation of microarray research: applications in evolutionary and ecological genomics.

Microarray technology is one of the key developments in recent years that has propelled biological research into the post-genomic era. With the ability to assay thousands to millions of features at the same time, microarray technology has fundamentally changed how biological questions are addressed, from examining one or a few genes to a collection of genes or the whole genome. This technology has much to offer in the study of genome evolution. After a brief introduction on the technology itself, we then focus on the use of microarrays to examine genome dynamics, to uncover novel functional elements in genomes, to unravel the evolution of regulatory networks, to identify genes important for behavioral and phenotypic plasticity, and to determine microbial community diversity in environmental samples. Although there are still practical issues in using microarrays, they will be alleviated by rapid advances in array technology and analysis methods, the availability of many genome sequences of closely related species and flexibility in array design. It is anticipated that the application of microarray technology will continue to better our understanding of evolution and ecology through the examination of individuals, populations, closely related species or whole microbial communities.

Ecology↗
PubMed1984

Evidence that phosphorylation and dephosphorylation regulate the distribution of excitation energy between the two photosystems of photosynthesis in vivo: Photoacoustic and fluorimetric study of an intact leaf.

State 1-state 2 transitions in an intact tobacco leaf were monitored by the photoacoustic method. Modulated oxygen evolution yield and its enhancement by continuous far-red light ("Emerson enhancement") were used to characterize the balance of light distribution between the two photosystems. These measurements were additionally supported by fluorimetry. Adaptation of the leaf to far-red light (lambda [unk] 700 nm), mainly absorbed in photosystem I (light 1), results in state 1, where short-wavelength light (light 2) is distributed in favor of photosystem II. This is shown by a low yield of oxygen evolution, a high extent of Emerson enhancement, a concomitantly high extent of fluorescence quenching by far-red light, and a low ratio of the 77 K emission peaks at 730 and 695 nm. The magnitudes of these parameters were reversed when the leaf was adapted to light 2 (state 2), indicating a change towards a more equal distribution of the excitation between the two photosystems. Preincubation of an intact leaf with NaF, a specific phosphatase inhibitor, stimulated the extent of adaptation to light 2, shown by all the above criteria, and completely abolished adaptation to light 1. Light 1 preillumination prior to NaF treatment resulted initially in state 1, but then a transition to state 2 was irreversibly induced by any light. The NaF effect was specific because NaCl did not affect the state 1-state 2 transitions. Leaching out the NaF restored the original physiological transitions of the leaf. NaF presumably acts here in the same way as it acts in isolated thylakoids-by blocking the dephosphorylation of membranal proteins (particularly the chlorophyll a/b-protein complex) phosphorylated by a light 2-activated kinase. Our results give direct support to the suggestion [Allen, J. F., Bennett, J., Steinback, K. E. & Arntzen, C. J. (1981) Nature (London) 291, 25-29] that it is the phosphorylation level of thylakoid proteins that controls the light distribution between the two photosystems in vivo, shown previously in isolated thylakoids.

Journal Article↗
PubMed2003

Homeosis and atavistic regeneration: the 'biogenetic law' in Entwicklungsmechanik.

Homeosis is a developmental abnormality corresponding to the transformation of a part of the body into another one. This term was introduced in 1894 by William Bateson, who aimed to make an inventory of all kinds of biological variation in order to understand how evolution proceeds. But, immediately afterwards experimental embryology, or Entwicklungsmechanik in Germany, adopted and redefined this term to refer to abnormal regenerations in which the newly developed organ was not identical to the initial one but rather resembled another part of the body. At that time, many experimental embryologists, such as Wilhelm Roux, were calling for the elimination of any phylogenetic explanation of development and were attempting to promote more mechanistic, proximate explanations. Despite these recommendations, several biologists continued to account for developmental processes by turning to phylogeny instead of mechanical forces. The case of homeosis is representative. Indeed, abnormal regenerations were often seen as examples of atavisms, or recurrence of ancestral characteristics, and many embryologists appealed to Ernst Haeckel's 'fundamental biogenetic law' to explain these strange phenomena. The break between Haeckelian tradition and Entwicklungsmechanik is thus less radical than often assumed, and the homeosis concept represents one of the factors of this continuity.

Biological Evolution↗
PubMed2006

Biliary strictures in living donor liver transplantation: incidence, management, and technical evolution.

Biliary complications, biliary strictures (BS) in particular, continue to be a significant cause of morbidity after LDLT despite technical refinement. In this study, we assessed the incidence of BS and their management in living donor liver transplantation (LDLT) with special reference to the type of biliary reconstruction. A total of 182 LDLTs performed at our institution for either adult (n = 157) or pediatric (n = 25) patients were included in the study. The duct-to-duct (DD) biliary reconstruction was performed for 106 cases, while the conventional Roux-en-Y hepaticojejunostomy (HJ) was utilized for the remaining 76 cases. Overall, BS developed in 46/182 (25.3%) of the cases (DD, 26.4%; HJ, 25.0%). The 1- and 3-year cumulative incidences of BS were 22.9% and 31.9%, respectively, in the DD group, and 15.2% and 29.1%, respectively, in the HJ group (P= not significant). The left-lobe LDLT was more prone to develop BS. Continuous anastomosis tended to be associated with the high incidence of BS in the DD group. The incidence of anastomotic leak was significantly lower in the DD group. Intervention via either pre-cutaneous or endoscopic approach was successful in the majority of cases, although recurrence could occur in some patients. In conclusion, BS was not associated with the type of reconstruction in LDLT. The primary radiological or endoscopic interventions were satisfactory treatments of choice. Technical refinement is an important factor to reduce the incidence of BS.

Adult↗
PubMed1994

Health care reform. The 1993-1994 evolution.

Health care costs in the United States continue to increase, as does the number of individuals who lack health care coverage. The magnitude of these critical problems assures that health reform of the health care system will continue to be debated over the next decade. Increasing health care costs are associated with increased complexity of services and a greater number of health care providers. As health costs increase and the number of individuals covered by private insurance decreases, states will face increasing pressure to develop effective methods of providing coverage for those without health insurance. Employer mandates will be viewed as one method of extending health coverage. Psychologists must be involved in policy issues so as to ensure the utilization of psychological knowledge and attention to psychological and behavioral health needs.

Health Care Costs↗
PubMed1999

Novelty effects in a multimodal warning signal.

The warning signals of toxic insects are often 'multimodal', combining bright coloration with sounds or odours (or both). Pyrazine (a common insect warning odour) can elicit an intrinsic avoidance in domestic chicks Gallus gallus domesticus, both against novel coloured food, and also against food colours that are specifically associated with aposematism, namely yellow and red. In three experiments, we investigated the role of novelty in this innate bias against yellow coloured food in the presence of pyrazine. Naive chicks were familiarized either to pyrazine odour or to coloured food before being tested for a bias against yellow (warningly coloured) food as opposed to green (nonwarningly coloured) food. In experiment 1, pyrazine novelty was shown to be vital for eliciting a bias against yellow food. However, experiment 2 suggested that colour novelty was not important: chicks familiarized with coloured crumbs still avoided yellow crumbs when pyrazine was presented. In a third experiment that gave chicks an even greater degree of pre-exposure to coloured crumbs, the bias against yellow food eventually waned, although pyrazine continued to elicit an aversion to yellow even after birds had had experience of up to 24 palatable yellow crumbs. Pyrazine novelty has been an important pressure in the evolution of multimodal warning signals, and can continue to promote the avoidance of warningly coloured food, even when it is relatively familiar. The implications for warning signals are discussed. Copyright 1999 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1976

Model consideration for the origin of life. Environmental structure as stimulus for the evolution of chemical systems.

In an attempt to understand the origin of living systems we encounter the following problems: How can we conceive the origin of the first self-reproducing forms, and by means of what stimuli could a constant increase in the complexity of such forms commence? How can a translation apparatus for genetic information develop? One cannot imagine that such an apparatus for the synthesis of enzymes can function alone without the interference of enzymes themselves, which, however, could only become available after the construction of the apparatus itself. What stimulus mechanism is conceivable that leads to the division of the genetic apparatus into a replication system, and an enzyme-synthesis system? The main problem therefore, is not the search for basic theoretical concepts. It is not a question which can be answered by means of specific experiments. One should rather explore the principal possibilities of how molecules combine to produce more and more complicated functional units. We look for the fundamental structural changes in the organizational systems and the driving forces initiating these developments. Questions concerning the detailed chemical realization are of secondary importance. In trying to solve the puzzle of how the genetic apparatus is gradually built up as complex aggregates of molecules, we consider a consistent causal chain of simple and transparent physiochemical model steps. The driving force for the self-organization of matter is seen in a specific environmental structure to be found on the surface of the earth. By this structure, which is periodic in time and heterogeneous in space, evolution is initiated and driven towards a continuously increasing degree of complexity correlated with a continuous expansion of the accessible living space. This process is a necessity under proper environmental conditions. Accidental events initiate each step but do not determine the general course of evolution which is determined by the selection mechanism.

Adenosine Monophosphate↗
PubMed2005

Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus.

Non-LTR retrotransposons R1 and R2 have persisted in rRNA gene loci (rDNA) since the origin of arthropods despite their continued elimination by the recombinational mechanisms of concerted evolution. This study evaluated the short-term evolutionary dynamics of the rDNA locus by measuring the divergence among replicate Drosophila melanogaster lines after 400 generations. The total number of rDNA units on the X chromosome of each line varied from 140 to 310, while the fraction of units inserted with R1 and R2 retrotransposons ranged from 37 to 65%. This level of variation is comparable to that found in natural population surveys. Variation in locus size and retrotransposon load was correlated with large changes in the number of uninserted and R1-inserted units, yet the numbers of R2-inserted units were relatively unchanged. Intergenic spacer (IGS) region length variants were also used to evaluate changes in the rDNA loci. All IGS length variants present in the lines showed significant increases and decreases of copy number. These studies, combined with previous data following specific R1 and R2 insertions in these lines, help to define the type and distribution, both within the locus and within the individual units, of recombinational events that give rise to the concerted evolution of the rDNA locus.

Animals↗
PubMed2002

Hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprinting.

Genome sequencing projects produce large amounts of information that could be translated into potential protein sequences. Such amounts of material continuously increase protein database sizes. At present, 22 times more protein sequences are available in the SWISS-PROT and TrEMBL databases than 8 years ago in SWISS-PROT. One of the methods of choice for protein identification makes use of specific endoproteolytic cleavage followed by matrix-assisted laser desorption/ionisation mass spectrometric (MALDI-MS) analysis of the digested product. Since 1993, when this technique was first demonstrated, the conditions required for a correct identification have changed dramatically. Whilst 4-5 peptides with an uncertainty of 2-3 Da were sufficient for a correct identification in 1993, 10-13 peptides with less than 60 ppm mass error are now required for human and E. coli proteins. This evolution is directly related to the continuous increase in protein database sizes, which causes an increase in the number of false positive matches in identification results. Use of an information complement deduced from the primary protein sequence, in the process of identification by peptide mass fingerprints, can help to increase confidence in the identification results. In this article, we propose the exchange of labile hydrogen atoms with deuterium atoms to provide an alternative information complement. The exchange reaction with optimised techniques has shown an average 95% of hydrogen/deuterium (H/D) exchange on tryptic peptides. This level of exchange was sufficient to single out one or more peptides from a list of potential candidate proteins due to the dependence of H/D exchange on the peptide primary structure. This technique also has clear advantages in the identification of small proteins where direct protein identification is impaired by the limited number of endoproteolytic peptides. Then, information related to primary sequence obtained with this technique could help to identify proteins with high confidence without any expensive tandem mass spectrometry instruments.

Amino Acid Sequence↗
PubMed2006

Interaction of MEQ protein and C-terminal-binding protein is critical for induction of lymphomas by Marek's disease virus.

Marek's disease virus (MDV) is an oncogenic herpesvirus that induces fatal T cell lymphomas in chickens. With more than 20 billion doses of vaccine used annually, vaccination constitutes the cornerstone of Marek's disease control. Despite the success of vaccination, evolution of virulence among MDV strains continues to threaten the effectiveness of the current Marek's disease vaccines. MDV-encoded protein MEQ (MDV EcoRI Q) probably acts as a transcription factor and is considered to be the major MDV oncoprotein. MEQ sequence shows a Pro-Leu-Asp-Leu-Ser (PLDLS) motif known to bind C-terminal-binding protein (CtBP), a highly conserved cellular transcriptional corepressor with roles in the regulation of development, proliferation, and apoptosis. Here we show that MEQ can physically and functionally interact with CtBP through this motif and that this interaction is critical for oncogenesis because mutations in the CtBP-interaction domain completely abolished oncogenicity. This direct role for MEQ-CtBP interaction in MDV oncogenicity highlights the convergent evolution of molecular mechanisms of neoplastic transformation by herpesviruses because Epstein-Barr virus oncoproteins EBNA 3A and 3C also interact with CtBP. We also demonstrate that the nononcogenic MDV generated by mutagenesis of the CtBP-interaction domain of MEQ has the potential to be an improved vaccine against virulent MDV infection. Engineering MDV with precisely defined attenuating mutations, therefore, represents an effective strategy for generating new vaccines against this major poultry disease.

Alcohol Oxidoreductases↗