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At least 775 records · Page 43Linked to original sources
PubMed1996

The targeting of somatic hypermutation.

Somatic hypermutation does not occur randomly within immunoglobulin V genes but, rather, is preferentially targeted to certain nucleotide positions (hot spots) and away from others (cold spots). Cold spots often coincide with residues essential for V gene folding. Hotspots, which appear to be strategically located to favour affinity maturation, are most frequently located in the CDRs (particularly CDR1) though conserved hotspots are also found at the base of FR3. Hotspots are in part created by local DNA sequence and the strong biases of codon usage in V genes indicate that the genes have evolved such that somatic hypermutation is targeted to those parts of the V where it is likely to prove most useful. These features of mutational hotspots and biased codon usage are also evident in V genes of lower animals suggesting that diversification by strategic targeting of non-templated mutation may have evolved early in antigen receptor evolution.

Animals↗
PubMed2000

Evolutionary relationships among the soybean bradyrhizobia reconstructed from 16S rRNA gene and internally transcribed spacer region sequence divergence.

From sequence divergence of 16S rRNA genes and the internally transcribed spacer (ITS) region it is reported that variation in phylogenetic placement exists among the 17 different serotype strains of Bradyrhizobium that have been isolated from nodules of soybean. Evolutionary relationships among the bradyrhizobia were more resolved using reconstructions derived from ITS than from 16S rRNA gene sequence divergence. Strain USDA 129 was placed together with USDA 62, 110, 122 and 126, but did not cluster with USDA 123 and 127, with which it shares antigenic determinants. The results from the phylogenetic analysis were supported with data from determinations of genetic diversity among additional strains within each of these serogroups using amplified fragment length polymorphism analysis. From these results it was concluded that strains of serogroup 129 were more similar to strains of serogroups 62, 110 and 122 than they were to strains of serogroups 123 and 127. The serotype strain of Bradyrhizobiumjaponicum USDA 135 and the type strain for Bradyrhizobium liaoningense possessed identical 16S rRNA gene and ITS region sequences. Also, the type strain for B. liaoningense cross-reacted with antisera prepared against somatic antigens of USDA 135. Therefore, it was not possible to distinguish B. liaoningense from serogroup 135 in our analysis of B. japonicum and Bradyrhizobium elkanii.

Bradyrhizobium↗
PubMed1998

The signature of somatic hypermutation appears to be written into the germline IgV segment repertoire.

We present here a unifying hypothesis for the molecular mechanism of somatic hypermutation and somatic gene conversion in IgV genes involving reverse transcription using RNA templates from the V-gene loci to produce cDNA which undergoes homologous recombination with chromosomal V(D)J DNA. Experimental evidence produced over the last 20 years is essentially consistent with this hypothesis. We also review evidence suggesting that somatically generated IgV sequences from B lymphocytes have been fed back to germline DNA over evolutionary time.

Animals↗
PubMed1997

Genomic imprinting in mammals.

A handful of autosomal genes in the mammalian genome are inherited in a silent state from one of the two parents, and in a fully active form from the other, thereby rendering the organism functionally hemizygous for imprinted genes. To date 19 imprinted genes have been identified; 5 are expressed from the maternal chromosome while the rest are expressed from the paternal chromosome. Allele-specific methylation of CpG residues, established in one of the germlines and maintained throughout embryogenesis, has been clearly implicated in the maintenance of imprinting in somatic cells. Although the function of imprinting remains a subject of some debate, the process is thought to have an important role in regulating the rate of fetal growth.

Animals↗
PubMed2002

Principles guiding implementation of the Operation Solace plan: "Pieces of PIES," therapy by walking around, and care management.

Operation Solace is the name given to a post-September 11, 2002 plan directed by the Army Surgeon General to proactively address the predictable behavioral health distress/disorders and related somatic phenomenon expected to occur among the Pentagon employees, family members, and Department of Defense beneficiaries located in the National Capitol Region affected by the terrorist attack. Using well-known and also relatively novel preventive population-based methodologies for minimizing the post-attack behavioral health-related morbidity resulted in the evolution of simplified principles ("Pieces of PIES") and methods (Therapy by Walking around and Care Management), which are briefly elaborated in this article.

Aircraft↗
PubMedDate not supplied

[The molecular diagnosis of cancer].

Cancer is considered a genetic disease, being classified as an accumulative somatic disorder aside of the Mendelian diseases, the chromosomopaties and the multifactorial diseases. It has been demonstrated in several human cancers that specific mutations in some genes are related to hystopathologic features and tumor progression. Thereby, mutations represent potentially valuable markers in disease-stage detection and evaluation. Mutations associated with neoplasia development and evolution are very valuable, and the related genes are classified as: oncogenes, tumor suppressing genes, DNA repairing genes and cell cycle regulator genes. The factability to determine and characterize these genes and relate them with one or several steps of tumorogenesis, makes them molecular markers that let us predict risk, make an early diagnosis, confirm a diagnosis, establish prognosis, guide the therapy and determine resistance to treatments. Molecular methods used today for analysis of this markers offer great advantages: they are vary sensitive, use a small sample, are fast, can be easily automated, are easily interpreted, allows quantitations and, very importantly, they become cheaper when a large quantity of samples are handled. In this review we mention some types of cancers and molecular methods that can be used to take advantage of their biomarkers.

Biomarkers, Tumor↗
PubMed1998

Somatic hypermutation, clonal diversity, and preferential expression of the VH 51p1/VL kv325 immunoglobulin gene combination in hepatitis C virus-associated immunocytomas.

A high prevalence of chronic hepatitis C virus (HCV) infection has recently been shown in a subset of B-cell non-Hodgkin's lymphomas, most of which belong to the lymphoplasmacytoid lymphoma/immunocytoma subtype and are characterized by the production of a monoclonal IgM cryoglobulin with rheumatoid factor activity. To better define the stage of differentiation of the malignant B cell and to investigate the role of chronic antigen stimulation in the pathogenesis of the HCV-associated immunocytomas, we analyzed the variable (V) region gene repertoire in 16 cases with this type of tumor. The lymphoma-derived V gene sequences were successfully determined in 8 cases; 5 of them expressed the 51p1 VH gene in combination with the kv325 VL gene. Moreover, a monoclonal 51p1-expressing B-cell population was detected in 4 of the remaining immunocytomas by an allele-specific Ig gene fingerprinting assay, indicating that HCV-associated immunocytomas represent clonal proliferations of a highly selected B-cell population. Somatic mutations and intraclonal diversity were observed in all of the lymphoma V genes, and clonally related IgM and IgG VH transcripts indicative of isotype switching were present in one case. These findings are consistent with an antigen-driven process and support a role for chronic antigen stimulation in the growth and clonal evolution of HCV-associated immunocytomas.

Adult↗
PubMed2006

Dynamics, stability and inheritance of somatic DNA methylation imprints.

Recent research highlights the role of CpG methylation in genomic imprinting, histone and chromatin modification, transcriptional regulation, and 'gene silencing' in cancer development. An unresolved issue, however, is the role of stable inheritance of factors that manage epigenetic imprints in renewing or expanding cell populations in soma. Here we propose a mathematical model of CpG methylation that is consistent with the cooperative roles of de novo and maintenance methylation. This model describes (1) the evolution of methylation imprints toward stable, yet noisy equilibria, (2) bifurcations in methylation levels, thus the dual stability of both hypo- and hypermethylated genomic regions, and (3) sporadic transitions from hypo- to hypermethylated equilibria as a result of methylation noise in a finite system of CpG sites. Our model not only affords an explanation of the persistent coexistence of these two equilibria, but also of sporadic changes of site-specific methylation levels that may alter preset epigenetic imprints in a renewing cell population.

Animals↗
PubMed2005

Visualizing the onset and evolution of an autoantibody response in systemic autoimmunity.

The onset of systemic autoimmunity is variable, making it difficult to identify early events. In this study, we show in rheumatoid factor (RF) Ig-transgenic autoimmune-prone mice that the appearance of RF B cells in blood signifies the onset of RF B cell activation in spleen, providing a novel window into the initiation of an autoantibody response. This allowed us to study the early and late phases of spontaneous induction of the B cell autoimmune response. Using this approach we showed that extensive Ab-forming cell generation in spleen, accompanied by somatic hypermutation, occurred despite the lack of an early germinal center response. The onset of the RF response correlated with the levels of IgG2a-containing immune complexes but not total IgG2a. By identifying the time of onset in individual mice, we were able to track progression of disease. We found remissions of RF Ab-forming cell production in some mice, suggesting that at the clonal level, chronic autoantibody responses are dynamic and episodic, much like acute pathogen responses. Surprisingly, there was little accumulation of long-lived plasma cells in bone marrow of mice with long-standing RF responses in spleen. These studies are among the first to define the early events of a spontaneous B cell autoimmune response.

Animals↗
PubMed2005

Molecular evolution of herbicide resistance to phytoene desaturase inhibitors in Hydrilla verticillata and its potential use to generate herbicide-resistant crops.

Hydrilla [Hydrilla verticillata (Lf) Royle] is one of the most serious invasive aquatic weed problems in the USA. This plant possesses numerous mechanisms of vegetative reproduction that enable it to spread very rapidly. Management of this weed has been achieved by the systemic treatment of water bodies with the herbicide fluridone. At least three dioecious fluridone-resistant biotypes of hydrilla with two- to fivefold higher resistance to the herbicide than the wild-type have been identified. Resistance is the result of one of three independent somatic mutations at the arginine 304 codon of the gene encoding phytoene desaturase, the molecular target site of fluridone. The specific activities of the three purified phytoene desaturase variants are similar to the wild-type enzyme. The appearance of these herbicide-resistant biotypes may jeopardize the ability to control the spread of this non-indigenous species to other water bodies in the southern USA. The objective of this paper is to provide general information about the biology and physiology of this aquatic weed in relation to its recent development of resistance to the herbicide fluridone, and to discuss how this discovery might lead to a new generation of herbicide-resistant crops.

Crops, Agricultural↗
PubMed1992

Localization of the human CYP17 gene (cytochrome P450(17 alpha)) to 10q24.3 by fluorescence in situ hybridization and simultaneous chromosome banding.

The gene for human P450(17 alpha) (CYP17) was previously mapped to chromosome 10 through analysis of somatic cell hybrids. Using a modified procedure of fluorescence in situ hybridization, this gene has now been visualized on simultaneously banded chromosomes and localized to a specific subband of chromosome 10 at q24.3. This precise assignment may facilitate the understanding of the molecular basis of 17 alpha-hydroxylase/17,20-lyase deficiency and the evolution of the CYP superfamily of genes.

Chromosome Banding↗
PubMed1996

Structural instability of a transgene locus in tobacco is associated with aneuploidy.

This paper describes molecular and cytogenetic evidence for the stability of a transgene locus that is present on the triplicated chromosome in an aneuploid tobacco line. This instability was manifested in several ways in trisomics including a major chromosome rearrangement that was detectable cytogenetically, smaller scale DNA rearrangements that occurred both germinally and somatically, and methylation/epigenetic silencing. In a deletion derivative of the locus, DNA breakpoints were found in AT-rich regions. One of these regions binds to nuclear scaffolds in vitro, suggesting a possible role for aberrant topoisomerase II cleavage in destabilization of the locus. The implications of increased chromosome instability in aneuploids for plant karyotype evolution and human carcinogenesis are discussed.

Aneuploidy↗
PubMed1988

Chromosome assignment of the gene loci ETS1 and THY1 in the owl monkey.

Our previous assignment of the gene loci HBB, HRAS1, INS, PTH, LDHA, and CAT to owl monkey chromosome 19 of karyotype VI (K-VI) indicated a putative homology of this owl monkey chromosome with the short arm of human chromosome 11 (HSA 11p). To investigate further the extent of shared homology, we localized in the owl monkey complement two genes known to be on HSA 11q. Segregation analysis of ETS1 and THY1 homologous DNA in three karyotypically different panels of rodent x owl monkey somatic cell hybrids provided evidence for the syntenic assignment of these loci to homologous chromosomes of three owl monkey karyotypes, namely, chromosomes 4 (K-VI), 3 (K-II), and 5 (K-V). The results indicate a disruption of syntenic gene loci on the distal portion of HSA 11q from 11p during primate evolution.

Animals↗
PubMed2003

Positive Darwinian selection operating on the immunoglobulin heavy chain of Antarctic fishes.

The cooling of the Southern Ocean to the freezing point of seawater (-1.9 degrees C) over the past 25 million years played a dominant selective role in the evolution of the Antarctic fish fauna. During this period, the perciform suborder Notothenioidei, which is largely endemic to the Antarctic, diversified and developed numerous cold-adapted characters. In this report, we provide compelling evidence that the immunoglobulin heavy chain (IgH) of the notothenioid fishes has undergone adaptive selection. Two and four IgH clones were isolated, respectively, from spleen cDNA libraries prepared from the Antarctic icefish Chaenocephalus aceratus and the yellowbelly rockcod Notothenia coriiceps. The transmembrane region of the membrane form of the rockcod IgM heavy chain was located at the end of the second constant (C(H)) domain, in contrast to other teleost IgMs in which the transmembrane region is located at the end of the third constant domain. Phylogenetic analyses of C(H) regions revealed that rates of nonsynonymous nucleotide substitution were higher than rates of synonymous nucleotide substitution. Many of the nonsynonymous substitutions introduced charge changes, consistent with positive Darwinian selection acting to adapt the structure of the notothenioid immunoglobulins. The rates of nonsynonymous nucleotide substitutions were higher than the rates of synonymous nucleotide substitutions in complementarity determining regions of variable regions, suggesting that diversity at antigen binding sites is enhanced by genomic and/or somatic selection. Results of Southern blot hybridization experiments were consistent with a translocon type of IgH gene organization reminiscent of bony fishes and tetrapods.

Adaptation, Physiological↗
PubMed1990

Localization of the gene for interphotoreceptor retinoid-binding protein to mouse chromosome 14 near Np-1.

Interphotoreceptor retinoid-binding protein (IRBP) is a large glycoprotein known to bind retinoids and found primarily in the interphotoreceptor matrix of the retina between the retinal pigment epithelium and the photoreceptor cells. It is thought to transport retinoids between the retinal pigment epithelium and the photoreceptors, a critical role in the visual process. We have used a 900-bp bovine IRBP cDNA fragment to map the corresponding gene, Rbp-3, to mouse chromosome 14 with somatic cell hybrids and have positioned the gene near Np-1 (nucleoside phosphorylase-1) by analysis of the progeny of an intersubspecific backcross. In the human genome, NP maps to human chromosome 14 and RBP3 to human chromosome 10. Thus, these two genes span the putative site of a chromosomal translocation which contributed to divergent karyotype evolution of man and mouse.

Animals↗
PubMed1991

Molecular cloning, chromosomal assignment, and nucleotide sequence of the feline homeobox HOX3A.

The feline homolog to the mammalian homeobox locus, HOX3A, was isolated by screening a domestic cat genomic library with the murine Hox-3.1 probe. The nucleotide sequence similarity of the feline homeobox was 96% to human HOX3A, 94% to mouse Hox-3.1, and 94% to rat R4. The deduced amino acid sequence (homeodomain) of this feline homeobox was identical to all homeodomains of these cognate genes. Using a panel of feline x rodent somatic cell hybrids, the HOX3A locus was assigned to feline chromosome B4. Human HOX3A and mouse Hox-3.1 have been mapped previously to human chromosome 12 and mouse chromosome 15, respectively, both of which share syntenic homology to feline chromosome B4. These data demonstrate evolutionary conservation of both HOX3A gene sequences and chromosomal location during mammalian evolution.

Amino Acid Sequence↗
PubMed2006

Structural phylogenetic analysis of activation-induced deaminase function.

In mammals, activation-induced deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of Ig genes. SHM and CSR activities require separate regions within AID. A chromosome region maintenance 1 (CRM1)-dependent nuclear export signal (NES) at the AID C terminus is necessary for CSR, and has been suggested to associate with CSR-specific cofactors. CSR appeared late in AID evolution, during the emergence of land vertebrates from bony fish, which only display SHM. Here, we show that AID from African clawed frog (Xenopus laevis), but not pufferfish (Takifugu rubripes), can induce CSR in AID-deficient mouse B cells, although both are catalytically active in bacteria and mammalian cell systems, albeit at decreased level. Like mammalian AID, Takifugu AID is actively exported from the cell nucleus by CRM1, and the Takifugu NES can substitute for the equivalent region in human AID, indicating that all the CSR-essential NES motif functions evolutionarily predated CSR activity. We also show that fusion of the Takifugu AID catalytic domain to the entire human noncatalytic domain restores activity in mammalian cells, suggesting that AID features mapping within the noncatalytic domain, but outside the NES, influence its function.

Amino Acid Sequence↗
PubMed2003

Reconstructing life history of hominids and humans.

Aspects of life history, such as processes and timing of development, age at maturation, and life span are consistently associated with one another across the animal kingdom. Species that develop rapidly tend to mature and reproduce early, have many offspring, and exhibit shorter life spans (r-selection) than those that develop slowly, have extended periods of premature growth, mature later in life, reproduce later and less frequently, have few offspring and/or single births, and exhibit extended life spans (K-selection). In general, primates are among the most K-selected of species. A suite of highly derived life history traits characterizes humans. Among these are physically immature neonates, slowed somatic development both in utero and post-natally, late attainment of reproductive maturity and first birth, and extended post-mature survival. Exactly when, why, and through what types of evolutionary interactions this suite arose is currently the subject of much conjecture and debate. Humankind's biocultural adaptations have helped to structure human life history evolution in unique ways not seen in other animal species. Among all species, life history traits may respond rapidly to alterations in selective pressures through hormonal processes. Selective pressures on life history likely varied widely among hominids and humans over their evolutionary history. This suggests that current patterns of human growth, development, maturation, reproduction, and post-mature survival may be of recent genesis, rather then long-standing adaptations. Thus, life history patterns observed among contemporary human and chimpanzee populations may provide little insight to those that existed earlier in hominid/human evolution.

Adaptation, Physiological↗