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At least 109 records · Page 6Linked to original sources
PubMed1986

A model for DNA sequence evolution within transposable element families.

A quantitative model is proposed for the expected degree of relationship between copies of a family of transposable elements in a finite population of hosts. Special cases of the model (in which the process of homogenization of element copies either is or is not limited by transposition rate) are presented and illustrated, using data on mobile sequences from different species. It is shown that transposition will be expected, in large populations, to result in only a rather distant relationship between transposable elements at different genomic sites. Possible inadequacies of the model are suggested and quantified.

Animals↗
PubMed1987

Selection by differential molecular survival: a possible mechanism of early chemical evolution.

A model is proposed to account for selective chemical evolution, progressing from a relatively simple initial set of abiotic synthetic phenomena up to the elaborately sophisticated processes that are almost certainly required to produce the complex molecules, such as replicatable RNA-like oligonucleotides, needed for a Darwinian form of selection to start operating. The model makes the following assumptions: (i) that a small number of micromolecular substances were present at high concentration; (ii) that a random assembly mechanism combined these molecules into a variety of multimeric compounds comprising a wide repertoire of rudimentary catalytic activities; and (iii) that a lytic system capable of breaking down the assembled products existed. The model assumes further that catalysts supplied with substrates were significantly protected against breakdown. It is shown that, by granting these assumptions, an increasingly complex network of metabolic pathways would progressively be established. At the same time, the catalysts concerned would accumulate selectively to become choice substrates for elongation and other modifications that could enhance their efficiency, as well as their survival. Chemical evolution would thus proceed by a dual process of metabolic extension and catalytic innovation. Such a process should be largely deterministic and predictable from initial conditions.

Biochemical Phenomena↗
PubMed1984

Composite human VK genes and a model of their evolution.

A phage library and two cosmid libraries were screened for human VK genes. Two recombinant phage and four cosmid clones were analysed in detail by restriction mapping and sequencing. Each one contained a single VKI sequence. Two of these six sequences are potentially functional VK genes and four are pseudogenes. Two pseudogenes derived from different genomic DNAs are highly homologous and are therefore either allelic variants or the products of a recent duplication event. Comparisons of our sequences with all fully determined human VKI amino acid and DNA sequences reveal identical segments which at first sight appear like minigenes. But these segments do not coincide with the subregions and some of the segments include both, framework and complementarity determining regions (FR, CDR, ref. 2). The findings may be explained by an evolutionary model generating composite genes by gene conversion and selection.

Alleles↗
PubMed1987

Nucleotide sequence and organization of the human S-protein gene: repeating peptide motifs in the "pexin" family and a model for their evolution.

The S-protein/vitronectin gene was isolated from a human genomic DNA library, and its sequence of about 5.3 kilobases including the adjacent 5' and 3' flanking regions was established. Alignment of the genomic DNA nucleotide sequence and the cDNA sequence indicated that the gene consisted of eight exons and seven introns. The intron positions in the S-protein gene and their phase type were compared to those in the hemopexin gene which shares amino acid sequence homologies with transin and the S-protein. Three introns have been found at equivalent positions; two other introns are very close to these positions and are interpreted as cases of intron sliding. Introns 3-7 occur at a conserved glycine residue within repeating peptide segments, whereas introns 1 and 2 are at the boundaries of the Somatomedin B domain of S-protein. The analysis of the exon structure in relation to repeating peptide motifs within the S-protein strongly suggests that it contains only seven repeats, one less than the hemopexin molecule. A very similar repeat pattern like that in hemopexin is shown to be present also in two other related proteins, transin and interstitial collagenase. An evolutionary model for the generation of the repeat pattern in the S-protein and the other members of this novel "pexin" gene family is proposed, and the sequence modifications for some of the repeats during divergent evolution are discussed in relation to known unique functional properties of hemopexin and S-protein.

Amino Acid Sequence↗
PubMed1990

Gene structure of nuclear lamin LIII of Xenopus laevis; a model for the evolution of IF proteins from a lamin-like ancestor.

The lamin LIII gene of Xenopus laevis has been characterized. The gene is duplicated in the Xenopus genome. The transcribed region spreads over 22 kb of genomic DNA encoding 12 exons. Two alternatively spliced mRNAs are observed which encode LIII isoforms that differ only by the 12 C-terminal amino acids which, however, both contain the CaaX motif known to be the target of post-translational modifications. The intron pattern of the lamin LIII gene is strikingly similar to that of an invertebrate intermediate filament (IF) gene over the entire protein coding sequence. The similarity in gene structure is restricted to the rod domain when compared with vertebrate types I-III IF genes. Our data suggest a model of how IF proteins evolved from a lamin-like ancestor by deletion of two signal sequences; the nuclear localization signal and the C-terminal ras-related CaaX motif. The data rule out the previously proposed hypothesis that IF proteins evolved from an intronless ancestor with an early divergence of neuronal and non-neuronal IF proteins. Together with the data presented in the accompanying paper by Dodemond et al. it can be concluded that the tail domains of lamins and invertebrate IF proteins, but not those of vertebrate IF proteins, are homologous. Thus, the different vertebrate IF proteins probably evolved by combination of the central rod domain with different tail domains by exon shuffling.

Amino Acid Sequence↗
PubMed2025

Multi-scale phylodynamic modelling of rapid punctuated pathogen evolution.

Computational multi-scale pandemic modelling remains a major and timely challenge. Here we identify specific requirements for a new class of models simulating pandemics across three scales: (1) pathogen evolution, often punctuated by the rapid emergence of new variants, (2) human interactions within a heterogeneous population, and (3) public health responses which constrain individual actions to control the disease transmission. We then present a pandemic modelling framework satisfying these requirements and capable of simulating feedback loops between dynamics unfolding at these different scales. The developed framework comprises a stochastic agent-based model of pandemic spread, coupled with a phylodynamic model that incorporates within-host pathogen evolution. It is validated with a case study, modelling the punctuated evolution of SARS-CoV-2, based on global and contemporary genomic surveillance data, which captures a large heterogeneous population. We demonstrate that the model replicates the essential features of the COVID-19 pandemic and virus evolution, while retaining computational tractability and scalability.

SARS-CoV-2↗
PubMed1985

Structural organization of the human kininogen gene and a model for its evolution.

The entire human kininogen gene has been isolated as a set of overlapping genomic DNA fragments, and the 11 exons encompassing approximately 27 kilobase pairs have been mapped by restriction enzyme analysis and nucleotide sequence determination. The nine 5'-terminal exons encode the 5'-untranslated region and the protein-coding region for the signal peptide and the heavy chain, which are common for high molecular weight (HMW) and low molecular weight (LMW) prekininogen mRNAs. Exon 10 consists of the common sequence for bradykinin and the immediately following unique sequence for HMW prekininogen mRNA. Exon 11 is then located following a 90-nucleotide sequence downstream from exon 10 and precisely specifies the sequence unique to LMW prekininogen mRNA. This, together with the hybridization analysis of total human cellular DNA, leads us to conclude that human HMW and LMW prekininogen mRNAs are produced from a single gene as a consequence of alternative RNA processing events. The structural analysis of the kininogen gene also shows that each of the nine 5'-terminal exons discretely specifies the nine protein domains observed in the amino-terminal portion of the kininogens. Furthermore, these nine genetic domains can be characterized by a thrice repeated pattern of three genetic segments, and two sets of these three domains, encompassing exons 3-5 and exons 6-8, are most closely related to each other. Therefore, we have proposed two successive duplication mechanisms as a model for the generation of the structure of the kininogen gene.

Base Sequence↗
PubMed1985

Models of molecular evolution. 2. Stereospecificity of dipeptide syntheses by means of cyanamides and carbodiimides.

Acetyl, benzyloxycarbonyl and tosyl protected DL-alanine, DL-leucine, DL-methionine, DL-phenylalanine, and DL-valine were condensed with DL-amino acid methyl esters. Cyanamide, diethylcyanamide, diisopropyl carbodiimide, dicyclohexyl carbodiimide, and N-cyclohexyl-N'-(2-morpholino ethyl) carbodiimide-N''-methotosylate served as condensing reagents. Water, methanol, and dimethylformamide were used as reaction media. The stereochemical course of these dipeptide syntheses was elucidated by means of 13C-n.m.r. spectroscopy. The formation of L-L and D-D bonds (isotactic sequences) was favoured in ca. 80% of all condensations. L-L/L-D (D-D/D-L) ratios of up to 6:1 were found.

Dipeptides↗
PubMed1986

Satellite DNA in the three C-bands of an unusual mouse marker chromosome. A model of chromosomal evolution.

A marker chromosome in the stemline of a new murine cell line is described on the basis of different stainings and in situ hybridization. The marker was characterized originally by three C-bands, one from each centromeric region of the three chromosomes constituting the marker. In the course of stemline evolution, two of the C-bands have been lost and the marker has developed into a monocentric chromosome, phenotypically and functionally normal.

Animals↗
PubMedDate not supplied

Review of cefotaxime sodium for surgical prophylaxis. A model for the evolution toward single-dose or short-course cost-effective regimens.

Cefotaxime is a parenteral broad-spectrum cephalosporin, used extensively worldwide for chemotherapy of serious infections. Since its release in 1979, cefotaxime has also been studied to minimize surgery-related infections and, more than any other new compound, has been used in a volume of evaluable cases. Because of the current cost-containment medical practice environment, most cefotaxime prophylaxis studies have established single-dose or short-course regimens. Over 9000 published cefotaxime prophylaxis cases were reviewed, and 81 references were cited. Single-dose cefotaxime was clearly indicated for a wide variety of operations, including hysterectomy, cesarean sections, bone and joint procedures, upper gastrointestinal cases, biliary tract procedures, transurethral resections, open urologic procedures, and some vascular cases. Approximately 24 hr of prophylaxis (cefotaxime X 4 doses) may be required for colorectal resections, cardiac surgery, head and neck surgery, transplants, and some pediatric surgical cases. Although contaminated abdominal cases and trauma surgery were not a true prophylaxis use, cefotaxime regimens have reduced wound morbidity to less than or equal to 10%. Changing to one- to four-dose schedules will have very favorable clinical impact by reducing prophylaxis cost, pharmacy preparation time, adverse reactions, and antimicrobic-resistance pressures. Surgeons should not hesitate to employ new cephalosporins (cefotaxime and others) with proved limited dose indications that would greatly benefit their patients and the hospital environment.

Bacterial Infections↗
PubMed1990

Group selection among alternative evolutionarily stable strategies.

Many important models of the evolution of social behavior have more than one evolutionarily stable strategy (ESS). Examples include co-ordination games, contests, mutualism, reciprocity, and sexual selection. Here we show that when there are multiple evolutionarily stable strategies, selection among groups can cause the spread of the strategy that has the lowest extinction rate or highest probability of contributing to the colonization of empty habitats, and that this may occur even when groups are usually very large, migration rates are substantial, and "extinction" entails only the disruption of the group and the dispersal of its members. The main requirements are: (1) individuals drawn from a single surviving group make up a sufficiently large fraction newly formed groups, and (2) the processes increasing the frequency of successful strategies within groups are strong compared to rate of migration among groups. The latter condition suggests that this form of group selection will be particularly important when behavioral variation is culturally acquired.

Animals↗
PubMed1988

Gene encoding capsid protein VP1 of foot-and-mouth disease virus: a quasispecies model of molecular evolution.

A phylogenetic tree relating the VP1 gene of 15 isolates of foot-and-mouth disease virus (FMDV) of serotypes A, C, and O has been constructed. The most parsimonious tree shows that FMDV subtypes and isolates within subtypes constitute sets of related, nonidentical genomes, in agreement with a quasispecies mode of evolution of this virus. The average number of nucleotide replacements per site for all possible pairs of VP1 coding segments is higher among representatives of serotype A than serotype C or O. In comparing amino acid sequences, the values of dispersion index (variance/mean value) are greater than 1, with the highest values scored when all sequences are considered. This indicates an accumulation of mutations at a limited number of residues, suggesting that distributions of sequences fluctuate around points of high stability. Evolution of FMDV follows a path very distant from that of a star phylogeny, and it has not been possible to derive conclusions on constancy of evolutionary rates with the test applied to the analysis. FMDVs, as other RNA viruses, are of limited genetic complexity and their population sizes are extremely large. Their evolution concerns complex, indeterminate mixtures of genomes rather than a single, determinate species.

Amino Acids↗