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PubMed1988

The human somatic cytochrome c gene: two classes of processed pseudogenes demarcate a period of rapid molecular evolution.

We have isolated and determined the DNA sequences of the human somatic cytochrome c gene (HCS) and 11 processed pseudogenes. HCS is the functional homologue to the previously characterized rat somatic gene because it correctly encodes the human heart protein, is present in single copy in the human genome, is nearly identical in both size and intron/exon structure to rodent somatic genes, and shares a high degree of sequence homology with its rat counterpart including a well-conserved promoter region (77% over 250 nucleotides). In contrast to the rodent system, however, where the known pseudogenes all originated from a locus encoding the present day cytochrome c, the human pseudogenes are of two types. A predominant class of older pseudogenes came from a progenitor of HCS that encoded an ancestral form of the protein, while a second group of only a few young pseudogenes originated from a recent parent of HCS that encoded the current cytochrome c polypeptide. These two distinct classes of human pseudogenes provide a molecular record of the history of cytochrome c evolution in primates and demarcate a short period of rapid evolution of the functional gene.

Animals↗
PubMed1989

Protein evolution on rugged landscapes.

We analyze a mathematical model of protein evolution in which the evolutionary process is viewed as hill-climbing on a random fitness landscape. In studying the structure of such landscapes, we note that a large number of local optima exist, and we calculate the time and number of mutational changes until a protein gets trapped at a local optimum. Such a hill-climbing process may underlie the evolution of antibody molecules by somatic hypermutation.

Biological Evolution↗
PubMed1991

Psychological factors related to prehospital delay during acute myocardial infarction.

BACKGROUND: Prior studies have had difficulty identifying factors that significantly explain patients' delay in responding to symptoms of acute myocardial infarction (AMI). METHODS AND RESULTS: We therefore examined factors affecting the time between symptom onset and hospital arrival for 103 AMI patients admitted to a Detroit metropolitan hospital between October 1989 and January 1990. Variables evaluated included demographic and medical history factors, psychological characteristics of somatic and emotional awareness, and type A behavior. The mean prehospital delay time was 9.0 +/- 10.8 hours (median, 5.0 hours; range, 0.25-62.0 hours). Delay time was not significantly associated with demographic or medical history categories or with type A behavior. Of study variables that can be identified prior to evolution of an AMI, somatic and emotional awareness were the only factors significantly predictive of delay time. Patients who were more capable of identifying inner experiences of emotions and/or bodily sensations sought treatment significantly earlier than patients with low emotional or somatic awareness (low emotional awareness median delay, 12.8 hours; high emotional awareness median delay, 3.8 hours; low somatic awareness median delay, 7 hours; high somatic awareness median delay, 4 hours). CONCLUSIONS: Variations in sensitivity to bodily sensations and emotions appear to play an important role in treatment seeking and thus potentially in treatment outcome for AMI patients. Assessment of these characteristics in patients with coronary risk factors could allow early identification of persons at risk of excessive delay in responding to symptoms of AMI.

Attitude to Health↗
PubMed1982

Changes in gene order and gene expression.

Studies on changes in gene position in germ line and somatic cell chromosomes during evolution and differentiation have led biologists to abandon the static view of chromosomes as invariant linear arrays of hereditary information. Prokaryotic cells contain several classes of DNA insertion elements which move from place to place in the genome and mediate chromosome rearrangements. Similar elements exist in a wide variety of eukaryotic organisms (yeasts, insects, plants, and vertebrates). In addition, both reversible and irreversible changes of chromosome primary structure provide developmental controls on gene activity in bacteria, bacteriophages, yeasts, trypanosomes, and mammalian lymphocytes. At least five recombination mechanisms are known to catalyze chromosome changes: 1) general homologous, 2) site-specific reciprocal, 3) illegitimate, 4) DNA splicing, and 5) replicative. Various combinations of these mechanisms can explain many different chromosome rearrangements and changes in gene dosage. Changes in gene position can alter gene expression in many ways, some of which we understand (such as insertional mutation and inversion of coding and regulatory sequences) and some of which are still unexplained. The activities of DNA insertion elements and somatic rearrangement systems are subjects to controls at several levels by specific regulatory systems, natural selection, and connection to cell lineage. Despite the recent increase in knowledge about the biological importance of changes in gene order on chromosomes, there are far more questions than answers, particularly about the mechanisms that coordinate recombination events and cell division in higher organisms.

Animals↗
PubMed1987

Germ cell-somatic cell relationships: a comparative study of intercellular junctions during spermatogenesis in selected non-mammalian vertebrates.

Specialized germ cell-somatic cell relationships were surveyed in the testis of species representative of four classes of non-mammalian vertebrates. Desmosome-like junctions were present in all classes studied. In the teleost fish studied (bluegill; Lepomis macrochirus), small, infrequent desmosomes, seen between the spherical cyst cells and spermatocytes, were characterized by poorly represented subsurface densities. In the bullfrog (Rana catesbeiana), similar desmosome-like junctions were found between cyst cell processes and spermatocytes. Reptilian (turtle; Pseudameys scripta) desmosome-like junctions between Sertoli cells and germ cells were heterogeneous and more numerous than those junctions found in fish and amphibians. In general, the reptilian desmosome-like junctions were extensive structures displaying 10 nm filaments associated with the Sertoli cell component of the junctions. Regions within the desmosome where the two plasma membranes converged suggested that gap junctions were a component of the desmosome-like junctions. "Desmosome-gap" junctions persisted in turtle spermatids for sometime after nuclear elongation had commenced. In birds (chicken; Gallus domesticus), "desmosome-gap" junctions, similar to those seen in turtles were described between both spermatocytes and Sertoli cells, and spermatids and Sertoli cells. These junctions were frequently lined by saccules of endoplasmic reticulum. The presence of gap junctions suggest the evolution of mechanisms for somatic cell-germ cell communication although more species should be examined to confirm this hypothesis.

Animals↗
PubMed1997

Integration of foreign DNA and its consequences in mammalian systems.

The insertion of foreign DNA into the genomes of established cells and organisms and the consequences of this integration event are of significance for viral oncology, reverse genetics, transgenic organisms, human somatic gene therapy and evolution. This review summarizes recent experimental findings and focuses on the alteration of cellular DNA methylation at regions remote from the site of insertion. We also discuss experimental data demonstrating that foreign DNA ingested by mice is not completely degraded in their gastrointestinal tracts; fragments of this DNA have been found to be covalently linked to DNA with 70% homology to the mouse IgE receptor gene.

Animals↗
PubMed1988

Conserved organization of the human and murine T-cell receptor beta-gene families.

Generation of an immune response depends on the interaction of haematopoietic cell types, among which T cells and their receptors are of central importance. The T-cell receptor is a heterodimer consisting of disulphide-linked alpha and beta-chains, each chain divided into variable (V) and constant (C) regions. The beta-chain is encoded by the rearrangement of separate variable (V beta), diversity (D beta) and joining (J beta) gene segments during T-cell differentiation. To examine the mechanisms of somatic DNA rearrangement and evolution of the beta-gene segments, we have constructed a physical map of the human T-cell receptor beta-chain family containing 40 V beta gene segments as well as both C beta gene clusters. A comparison of the published nucleotide sequences of human and murine V beta gene segments reveals 12 examples of gene segments sharing 65% or more interspecies homology. The relative order of these human and murine V beta gene segment homologues is also conserved along the chromosome, apart from more extensive human gene duplication, presumably as a consequence of constraints imposed on evolutionary mechanisms operating to diversify these gene families or of selective pressures operating to maintain order.

Animals↗
PubMed1996

Molecular cloning of mouse somatic and testis-specific H2B histone genes containing a methylated CpG island.

We have isolated a mouse testis-specific H2B histone gene based on the unusual methylation of the CpG island of rat testis-specific H2B gene in somatic tissues. After digestion of genomic DNA with the methylation-sensitive restriction enzyme Hha I, we found that, among 10-20 copies of mouse H2B histone genes, at least three copies are methylated in somatic tissues, but not in testis. Cloning and sequence analysis of two methylated H2B genes revealed that one gene, MTH2B, is strikingly similar to the testis-specific histone H2B (TH2B) gene of rat and the other, psH2B, is a pseudogene of the somatic-type H2B gene. Northern blot analysis revealed that the expression of the MTH2B gene is testis-specific. During spermatogenesis, the MTH2B gene is expressed predominantly in pachytene spermatocytes, as observed in the expression of rat TH2B gene. Interestingly, the MTH2B gene is largely unmethylated in embryonic stem cells, but methylated in F9 embryonal carcinoma cells. The psH2B pseudogene is methylated in somatic tissues and F9 cells, but only partially methylated in embryonic stem cells. Methylation of the psH2B pseudogene seems to be attributed to its location within the context of repetitive sequences including the B1 element. The unmethylation of both H2B histone genes in the testis explains how CpG islands of those histone genes can be maintained during evolution despite heavy methylation in somatic tissues.

Amino Acid Sequence↗
PubMed1994

Mitochondrial DNA sequence variation in human evolution and disease.

Germ-line and somatic mtDNA mutations are hypothesized to act together to shape our history and our health. Germ-line mtDNA mutations, both ancient and recent, have been associated with a variety of degenerative diseases. Mildly to moderately deleterious germ-line mutations, like neutral polymorphisms, have become established in the distant past through genetic drift but now may predispose certain individuals to late-onset degenerative diseases. As an example, a homoplasmic, Caucasian, tRNA(Gln) mutation at nucleotide pair (np) 4336 has been observed in 5% of Alzheimer disease and Parkinson disease patients and may contribute to the multifactorial etiology of these diseases. Moderately to severely deleterious germ-line mutations, on the other hand, appear repeatedly but are eliminated by selection. Hence, all extant mutations of this class are recent and associated with more devastating diseases of young adults and children. Representative of these mutations is a heteroplasmic mutation in MTND6 at np 14459 whose clinical presentations range from adult-onset blindness to pediatric dystonia and basal ganglial degeneration. To the inherited mutations are added somatic mtDNA mutations which accumulate in random arrays within stable tissues. These mutations provide a molecular clock that measures our age and may cause a progressive decline in tissue energy output that could precipitate the onset of degenerative diseases in individuals harboring inherited deleterious mutations.

Amino Acid Sequence↗
PubMed1986

Differentiation of oocyte- and somatic-type 5S rRNAs in animals.

In some amphibians and bony fishes, oocyte- and somatic-type 5S rRNA genes are expressed differently in oocytes and somatic cells. In order to determine at what stage of animal evolution this differential expression system appeared and how it is regulated, the sequences of oocyte and somatic 5S rRNAs from three invertebrates (sea urchin, sea hare, and silkworm) and two vertebrates (lamprey and chick) were analyzed. It was found that the oocyte 5S rRNA from lamprey consists of two components, while its somatic 5S rRNA consists of only one. In other animals, such differential expression of 5S rRNA in oocytes and somatic cells was not seen. A phylogenetic tree of 63 animal 5S rRNAs was constructed by means of the parsimony method, and the evolution of oocyte and somatic-type 5S rRNAs was discussed.

Animals↗
PubMed1993

Somatic variation precedes extensive diversification of germline sequences and combinatorial joining in the evolution of immunoglobulin heavy chain diversity.

In Heterodontus, a phylogenetically primitive shark species, the variable (VH), diversity (DH), joining (JH) segments, and constant (CH) exons are organized in individual approximately 18-20-kb "clusters." A single large VH family with > 90% nucleic acid homology and a monotypic second gene family are identified by extensive screening of a genomic DNA library. Little variation in the nucleotide sequences of DH segments from different germline gene clusters is evident, suggesting that the early role for DH was in promoting junctional diversity rather than contributing unique coding specificities. A gene-specific oligodeoxynucleotide screening method was used to relate specific transcription products (cDNAs) to individual gene clusters and showed that gene rearrangements are intra- rather than intercluster. This provides further evidence for restricted diversity in the immunoglobulin heavy chain of Heterodontus, from which it is inferred that combinatorial diversity is a more recently acquired means for generating diversity. The observed differences between cDNA sequences selected and the sequences of segmental elements derived from conventional genomic libraries as well as from VH segment-specific libraries generated by direct PCR amplification of genomic DNA indicate that the VH repertoire is diversified by both junctional diversity and somatic mutation. Taken together, these findings suggest a heretofore unrecognized contribution of somatic variation that preceded both extensive diversification of the germline repertoire and the combinatorial joining process in the evolution of humoral immunity.

Animals↗
PubMed2025

Defining the genome-wide mutagenic impact of APOBEC3 enzymes.

Somatic mutations drive cancer initiation and tumor evolution. Therefore, the etiology of mutagenesis in cancer is important to preventative and treatment strategies. Somatic mutagenesis in cancer is a multifactorial process and includes both endogenous and exogenous sources of mutations. One recently recognized source of mutagenesis in cancer is the innate immune APOBEC3 family of enzymes, which catalyze cytosine deamination to restrict viral infection but can aberrantly act on the cellular genome, resulting in mutations. Single base substitution (SBS) signatures, or mutational patterns, identified in cancer genomes have demonstrated widespread mutagenesis caused by APOBEC3 enzymes throughout human tumors. To comprehensively define the consequences of APOBEC3 mutagenesis, we developed an experimental pipeline for prospective analysis of genome-wide mutations caused by APOBEC3 activity. This pipeline can be adapted to analyze additional sources of mutagenesis across a spectrum of cells.

Humans↗
PubMed1983

Sequential generation of antibody diversity during B-cell development.

It has become increasingly apparent that generation of and variation in antigen-combining sites of antibodies occurs sequentially during B-cell development. Allelic and isotypic exclusion mechanisms ensure that a B cell produces antibody molecules having a single kind of combining site. A major reason for evolution of mechanisms which result in asynchronous formation of functional H and L chain genes may be the need for allelic and isotypic exclusion; but this may not be the only advantage of asynchronous formation of H and L chain genes. The evolution of mechanisms causing nonjunctional somatic mutation late in B cell development - only after antigen exposure apparently - may result from the biological advantages of: (1) 'fine tuning' of the combining site; (2) a response to an anti-idiotype regulatory network, or (3) expanded memory.

Alleles↗
PubMed2026

Integrative quantum and systems biology of cancer: From molecular fluctuations to ecological outcomes.

This review treats cancer as a multiscale adaptive system, asks what the framework must predict to be worth adopting, and separates at each scale what the evidence establishes from what is proposed. It is an expert narrative synthesis, not a systematic review, and states the limits of that design. Proton transfer and tautomeric shifts contribute to spontaneous mispairing but do not license claims of directed or non-random mutation: replication timing, three-dimensional chromatin organization, sequence context and known mutagenic processes explain most mutational heterogeneity, leaving any quantum contribution as a residual against that baseline. The Waddington quasi-potential is bounded: outside detailed balance the dynamics are not gradient-derivable and require a probability-flux term. Hysteresis, rate-limited bimodality and return to state after perturbation distinguish an attractor from a transcriptomic cluster. Single-cell karyotype and live-imaging evidence supports whole-genome doubling as an unstable intermediate of heterogeneous origin and context-dependent consequence, not a uniform adaptive strategy. Systems and synthetic biology, virtual cells and digital twins are assessed against benchmarks, not promise. Tissue-scale ecology is reported with the spatial measurements now quantifying it, including evidence that stromal niche construction is not uniformly tumor-supporting. RNA modification is a layer in its own right, showing that the interpretation of a regulatory signal, not its magnitude, is biologically decisive. A dedicated section states the framework's commitments, the observable and evidence at each scale, and what would falsify them, asking what this adds to somatic mutation theory with clonal evolution and plasticity.

Neoplasms↗
PubMed1983

Complete nucleotide sequence of an immunoglobulin VH gene homologue from Caiman, a phylogenetically ancient reptile.

Immunoglobulin variable (V) gene regions typify extensive multigenic families in terms of overall size, chromosomal arrangement and presence of large numbers of apparent pseudogenes. A unique mechanism of somatic reorganization involving recombination of VH, D and JH or VL and JL segments accompanies the differentiation of lymphoid cells and together with somatic mutation and other types of recombination accounts for V-region diversity. Although these processes have been well characterized in higher mammals, little is known concerning their origin and diversification during phylogenetic time. Previously, we described the blot-hybridization characteristics of murine VHIII probes with restriction enzyme-digested genomic DNA isolated from several phylogenetically critical species, including Caiman crocodylus, a modern representative of an ancient reptilian subclass. Here we have used a murine probe, S107V, to select homologous clones from a library of Caiman genomic DNA constructed in a lambda bacteriophage. The complete nucleotide sequence of a Caiman gene homologous to the murine VH gene and its adjacent 5' and 3' region is described. Comparison of the sequence with mammalian prototypes shows evidence of considerable organizational and structural homology extending outside the presumed VH-coding region and including elements believed to be involved in somatic recombination. Inferences about the evolution of this multigenic family can now be extended to the level of phylogenetic class.

Alligators and Crocodiles↗
PubMed1996

Genetic pathways in colorectal cancer.

The model of colorectal tumorigenesis put forward by Fearon and Vogelstein has had great influence on molecular oncology. They proposed that a series of mutations occur in the progression from normal cells to colorectal cancer and that these mutations are associated with the histological features of such tumours. Several postulates of the model appear to be correct, particularly its emphasis on the stepwise accumulation of genetic changes and the inclusion of mutations at the adenomatous polyposis coli (APC) and TP53 loci. Since the publication of the original model, however, mutations at other loci have been identified which may be alternatives or additions. There is also evidence to suggest that some colorectal cancers develop along a different genetic pathway. In this review, we discuss how tumour development can occur as Darwinian evolution through selection of advantageous somatic mutations. The non-random nature of mutation selection gives rise to genetic pathways of tumorigenesis. In addition, we consider the Fearon and Vogelstein model, its shortcomings and possible additions to it. The evidence suggests that not all colorectal cancers follow the same genetic pathway during carcinogenesis.

Carcinoma↗
PubMed1990

Genomic organization of the mouse pore-forming protein (perforin) gene and localization to chromosome 10. Similarities to and differences from C9.

Genomic clones encompassing the entire coding region of the mouse lymphocyte pore-forming protein gene (Pfp) have been isolated and used to determine its intron-exon organization. In contrast to C9, Pfp has a simple structure, consisting of only three exons (two of which encode polypeptide), a large 5' intron, and a single, smaller intron that is situated approximately one-third of the way through the protein-coding portions of the gene. The regions encoding the homologous domains of PFP and C9 are encoded on exons 7, 8, 9, and 10 of C9, but form only approximately half of the open reading frame of exon III in Pfp. Although encoding polypeptides with related functions, the two genes possess such sharply contrasting structures as to suggest that their analogous regions may have risen independently, by a process of convergent evolution. Using a panel of somatic cell hybrid cell lines, Pfp has been mapped to chromosome 10.

Amino Acid Sequence↗
PubMed1994

The axio-somatic model in embryonic and tumoral development.

The growth and evolution of human tissues observed in embryogenesis and neoplasia are both reduced to a cellular theoretical axio-somatic model. The unlimited expansion and phenotype change of the model, are assured by the continuous generation of new cellular mitotic phenotypes which are grafted in a sequential order. Neogeneration results from the interaction between two cells of specific origins and situations: (a) axial cells of actual germ cell origin, generators and vectors of mitotic potential, (b) mitotically exhausted somatic cells of distal phenotypes, involved in meiotic recombinations, generating potential of neodifferentiation. The potentialities of both, axis and soma, are transformed by 'fertilization' in effectively growing new mitotic phenotypes. Bi-potent differentiation of germ line derived cells in gametopoiesis and haematopoiesis, is the source of the axial phenotype, identified in tissues as specific acid fast 'lymphoid' cells and/or vectors, formed by highly condensed hyperchromatinic nuclei and/or micronuclei endowed with DNAs of centromeric and kinetochoric types, wrapped in ceramide rich photo-affinity biomembranes.

Cell Differentiation↗