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PubMed1994

Refining the locus for Best vitelliform macular dystrophy and mutation analysis of the candidate gene ROM1.

Vitelliform macular dystrophy (Best disease) is an autosomal dominant macular dystrophy which shares important clinical features with age-related macular degeneration, the most common cause of legal blindness in the elderly. Unfortunately, our understanding and treatment for this common age-related disorder is limited. Discovery of the gene which causes Best disease has the potential to increase our understanding of the pathogenesis of all types of macular degeneration, including the common age-related form. Best disease has recently been mapped to chromosome 11q13. The photoreceptor-specific protein ROM1 has also been recently mapped to this location, and the ROM1 gene is a candidate gene for Best disease. Using highly polymorphic markers, we have narrowed the genetic region which contains the Best disease gene to the 10-cM region between markers D11S871 and PYGM. Marker D11S956 demonstrated no recombinants with Best disease in three large families and resulted in a lod score of 18.2. In addition, a polymorphism within the ROM1 gene also demonstrated no recombinants and resulted in a lod score of 10.0 in these same three families. We used a combination of SSCP analysis, denaturing gradient gel electrophoresis, and DNA sequencing to screen the entire coding region of the ROM1 gene in 11 different unrelated patients affected with Best disease. No nucleotide changes were found in the coding sequence of any affected patient, indicating that mutations within the coding sequence are unlikely to cause Best disease.

Base Sequence↗
PubMed2000

Evolution of genetic codes through isologous diversification of cellular states.

Evolution of genetic codes is studied as change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states of a cell allows for a choice of enzymes, and this choice is later fixed genetically through evolution. To demonstrate this theory, a dynamical systems model consisting of the concentrations of metabolites, enzymes, amino acyl tRNA synthetase, and tRNA - amino acid complexes in a cell is introduced and studied numerically. It is shown that the biochemical states of cells are differentiated by cell-cell interactions, and each differentiated type starts to use a different synthetase. Through the mutation of genes, this difference in the genetic code is amplified and stabilized. The relevance of this theory to the evolution of non-universal genetic code in mitochondria is suggested. The present theory is based on our recent theory of isologous symbiotic speciation, which is briefly reviewed. According to the theory, phenotypes of organisms are first differentiated into distinct types through the interaction and developmental dynamics, even though they have identical genotypes; later, with mutation in the genotype, the genotype also differentiates into discrete types, while maintaining the "symbiotic" relationship between the types. Relevance of the theory to natural as well as artificial evolution is discussed.

Biological Clocks↗
PubMed1998

Changes in the pattern of twisted gastrulation gene expression among Drosophila species.

A long-standing hypothesis posits that morphological changes may be more likely to result from changes in regulation of gene expression than from changes in the protein coding sequences of genes. We have compared the expression pattern of the twisted gastrulation (tsg) gene among five Drosophila species: D. melanogaster, D. simulans, D. subobscura, D. mojavensis, and D. virilis. The tsg gene encodes a secreted protein that is required for the specification of dorsal midline fates in the Drosophila early embryo. TSG is unlike other secreted growth and differentiation factors in Drosophila in that its expression pattern can be experimentally varied and still result in normal development. Because of this, its regulatory region may be freer to diverge than that of other developmental genes whose misexpression may lead to lethal defects. Thus, the tsg gene may be a good indicator of the frequency and nature of evolutionary changes affecting patterns of gene expression. Over approximately 60 million years (Myr), the tsg gene has retained a dorsal-on/ventral-off pattern and a middorsal region of expression; but there have been marked changes in the middorsal domain of expression as well as the appearance/loss of other domains of expression along the anterior/posterior axis. Changes between closely related species (approximately 2-5 Myr since divergence) that are not reflected among more distantly related species suggest frequent changes in gene expression over evolutionary time. These changes in gene expression may serve as the raw material for eventual evolutionary changes in morphology.

Animals↗
PubMed1998

A novel toxinotyping scheme and correlation of toxinotypes with serogroups of Clostridium difficile isolates.

Two hundred nineteen Clostridium difficile isolates from 22 serogroups were screened for changes in the genes coding for toxin B (tcdB) and toxin A (tcdA). Parts of the toxin genes were amplified, and the PCR fragments were checked for length polymorphisms and cut with several restriction enzymes to monitor restriction fragment length polymorphisms (RFLPs). For 47 strains (21%), differences in the toxin genes were found compared to the toxin genes of reference strain VPI 10,463. Polymorphisms were usually observed in both toxin genes. RFLPs were more commonly found in the tcdB gene, in which a single restriction enzyme could give up to five different patterns. Restriction sites seemed to be less heterogeneous in the tcdA gene, in which for most enzymes only two different RFLPs were recognized. However, deletions were observed in tcdA, and four new types of shortened tcdA genes are described. According to the changes in their toxin genes, variant strains could be divided into 10 groups (toxinotypes I to X). A toxinotype was characterized by similar patterns of changes in the toxin genes and in other regions of the pathogenicity locus and also similar pulsed-field gel electrophoresis patterns. Variant toxinotypes were found in 9 of the 22 serogroups studied, and some toxinotypes were clearly associated with specific serogroups. Toxinotype VIII is characteristic for all strains of serogroup F. Other serogroups in which variant toxinotypes were commonly found are A1, A15, E, and X. Testing of variability in C. difficile toxin genes not only might be useful as a molecular typing system but also could have implications in diagnostics and pathogenesis.

Bacterial Proteins↗
PubMed1993

Dysregulated surface gene expression from disrupted hepatitis B virus genomes.

During chronic infection by hepatitis B virus, the viral genome frequently integrates into the host chromosome, causing gross disruption and rearrangement of the viral DNA. We have obtained data showing that viral genomic disruptions which delete the enhancers from the transcribed region of the viral surface gene can lead to dysregulation of surface gene expression at the transcriptional level. Specifically, in cells transfected with such disrupted genomes, there is a decreased amount of transcripts coding for the major form of the surface protein but little change in the amount of transcripts coding for the large surface protein. In these cells, secretion of the surface proteins is blocked in the endoplasmic reticulum-Golgi intermediate compartment, consistent with previous work from other groups showing that relative overexpression of the large surface protein can block secretion of all forms of the surface protein. Our findings suggest that viral genomic rearrangements during integration may be a contributing factor in the pathogenesis of ground-glass hepatocytes, which contain large amounts of intracellular surface proteins as a result of a block in secretion and are frequently seen in the livers of patients with chronic hepatitis B.

Base Sequence↗
PubMed2002

Kjellin's syndrome: fundus autofluorescence, angiographic, and electrophysiologic findings.

OBJECTIVE: Syndromes with genetically determined retinal diseases and concurrent multiple neurologic abnormalities are rare. Kjellin described an autosomal recessive entity with spastic paraplegia, mental retardation, amyotrophia, and macular dystrophy. We sought to further characterize the retinal phenotype and to contrast fundus changes and the genotype to Stargardt's disease in a young patient with progressive Kjellin's syndrome. DESIGN: Observational case report and family genetic study. PATIENTS: One affected and 11 unaffected members of a family with Kjellin's syndrome were investigated. METHODS: Complete ophthalmologic and neurologic examinations were performed, including electrophysiologic evaluation, color vision assessment, fundus autofluorescence, and fluorescence angiography. To investigate a possible role of the ABCA4 gene in the etiology of the macular changes, the entire 50 coding exons, including flanking intronic sequences of the patient, were analyzed by direct sequencing. MAIN OUTCOME MEASURES: The patient was evaluated for her symptoms, retinal function, fundus autofluorescence, angiography, and mutations in the ABCA4 gene. RESULTS: A 27-year-old female patient initially was seen with trembling of her right hand. Subsequently, progressive paraspasticity occurred, and a diagnostic workup revealed mild mental retardation. Biomicroscopy disclosed symmetric multiple round yellowish flecks at the level of the retinal pigment epithelium scattered at the posterior pole, which showed increased intrinsic fluorescence in the center, with a halo of reduced autofluorescence. Multifocal electroretinography elicited abnormal responses in the macular area in the presence of normal Ganzfeld electroretinography recordings. In gene mapping, several common variants were identified, although none seem to be associated with the disease features. CONCLUSIONS: Macular changes in Kjellin's syndrome share phenotypic characteristics with Stargardt's disease, although there are differences with regard to appearance, distribution, angiographic, and autofluorescence behavior of the retinal flecks. Ophthalmologic examination is prudent in patients with similar neurologic deficits, because it is essential for the diagnosis and because visual symptoms may be absent even in the presence of obvious and widespread retinal manifestations. The abnormal gene product in Kjellin's syndrome seems to cause progressive dysfunction in various neuronal tissues but seems to be distinct from the major defect underlying the Stargardt's disease phenotype.

ATP-Binding Cassette Transporters↗
PubMed2002

Epigenetics in colorectal cancer.

Malignant transformation is now known to require a series of molecular alterations that disrupt a limited number of pathways including autocrine and paracrine responses to growth factors, cell-cycle control, senescence, motility, and invasion. Studies on hereditary cancers have established genetic changes as the primary driving force for these molecular alterations. Recently, however, it has been recognized that epigenetic changes, defined as clonal changes in gene expression without accompanying changes in primary DNA coding sequence, can also be a driving force in neoplastic transformation, for selected genes, and in specific tumors. DNA methylation within gene promoters and associated alterations in histone acetylation appear primary mediators of epigenetic inheritance in cancer cells. In the large intestine, aberrant DNA methylation arises very early, initially in normal-appearing mucosa, and may be part of the age-related field defect observed in sporadic colorectal neoplasia. Aberrant methylation also contributes to later stages of colon cancer formation and progression through a hypermethylator phenotype termed cytosine phosphoguanosine (CpG) island methylator phenotype (CIMP), which appears to be a defining event in approximately half of all sporadic tumors. In sporadic colon cancer, CIMP has distinct epidemiologic and clinical features and is responsible for most cases of microsatellite instability related to hMLH1 inactivation. The recognition of epigenetic changes as a driving force in colorectal neoplasia opens new areas of research in disease epidemiology, risk assessment, screening, and treatment.

Journal Article↗
PubMed2006

Amino acid change 335 E to K affects the sialic-acid-binding and neuraminidase activities of Urabe AM9 mumps virus hemagglutinin-neuraminidase glycoprotein.

A mutation coding for the amino acid change E335 to K is frequently found in the hemagglutinin-neuraminidase (HN) gene of Urabe AM9 mumps viruses isolated during post-vaccination meningitis cases. To identify if this mutation modifies the biological activities of the HN glycoprotein, two variants of Urabe AM9 vaccine differing at amino acid 335 (HN-E335 and HN-K335) were isolated and their receptor-binding specificity was determined by means of competence assays. Pre-incubation of the viruses with sialic acids inhibited both syncytia formation in Vero cells and replication in SH-SY5Y cells. Thus, HN-K335 showed higher affinity towards sialylalpha2,6lactose, whereas HN-G335 preferred sialylalpha2,3lactose. These results are relevant because a high expression of sialylalpha2,6lactose in nerve cells was confirmed by means of Sambucus nigra lectin-cytochemistry. In addition, kinetics assays showed that HN-K335 and HN-E335 also differ in their hydrolysis rate (Vmax values of 37.5 vs. 3.5 nmol min-1mg-1, respectively). Therefore, HN-K335 variant presented a neuraminidase activity level 11-fold higher than that of HN-E335 variant. In conclusion, the mutation affects the receptor-binding and neuraminidase activities of Urabe AM9 mumps virus variants.

Amino Acid Substitution↗
PubMed1988

The compositional distribution of coding sequences and DNA molecules in humans and murids.

The compositional distributions of coding sequences and DNA molecules (in the 50-100-kb range) are remarkably narrower in murids (rat and mouse) compared to humans (as well as to all other mammals explored so far). In murids, both distributions begin at higher and end at lower GC values. A comparison of homologous coding sequences from murids and humans revealed that their different compositional distributions are due to differences in GC levels in all three codon positions, particularly of genes located at both ends of the distribution. In turn, these differences are responsible for differences in both codon usage and amino acids. When GC levels at first + second codon positions and third codon positions, respectively, of murid genes are plotted against corresponding GC levels of homologous human genes, linear relationships (with very high correlation coefficients and slopes of about 0.78 and 0.60, respectively) are found. This indicates a conservation of the order of GC levels in homologous genes from humans and murids. (The same comparison for mouse and rat genes indicates a conservation of GC levels of homologous genes.) A similar linear relationship was observed when plotting GC levels of corresponding DNA fractions (as obtained by density gradient centrifugation in the presence of a sequence-specific ligand) from mouse and human. These findings indicate that orderly compositional changes affecting not only coding sequences but also noncoding sequences took place since the divergence of murids. Such directional fixations of mutations point to the existence of selective pressures affecting the genome as a whole.

Amino Acid Sequence↗
PubMed2000

In vitro and in vivo extrapolations of genotoxin exposures: consideration of factors which influence dose-response thresholds.

The concept of a threshold of activity of a genotoxic agent is primarily based upon considerations of protective mechanisms and multiple cellular targets, which require inactivation before a toxic response is produced. In this paper, we have considered and evaluated the influences of compound metabolism, DNA lesion formation, mutation induction and sequence content, aneuploidy induction and the influence of repair enzymes upon genetic endpoints produced by both DNA reactive chemicals and by those chemicals which modify non-DNA cellular targets. Thresholds of activity have been evaluated by critical analysis of the published literature and original data analysing both the role of sequence context upon point mutation induction and DNA repair mechanisms upon the sensitivity of cultured cells to the induction of aneuploidy. In the case of DNA reactive chemicals, the presence of a threshold of chemical activity will be dependent upon cellular activities such as those of the Phase II enzymes reducing the activity of chemicals before lesion formation takes place and/or those of the DNA repair enzymes which reduce the proportion of DNA lesions which are processed into DNA sequence changes. Under such conditions, a given exposure of a DNA reactive chemical does not produce a linear or semi-linear increase in DNA lesions or in mutation frequency. However, even when these protective mechanisms are overwhelmed by the high exposures of genotoxic chemicals the biological effects of a genotoxin may be influenced by the sequence context of the gene under consideration. Here, we demonstrate that point mutations are detected at relatively higher frequencies in the non-coding introns compared with the coding exons. Many of the base changes detected in the exons do not produce amino acid changes in the proteins coded for by the genes being monitored for mutation induction. Both sequence context and the types of base changes induced may provide a "buffering" effect reducing the biological consequences of mutation induction. Spindle damaging chemicals, such as colcemid and vinblastine, induce aneuploidy by modifying the numbers of spindle fibres which regulate the segregation of chromosomes during mitosis and meiosis. The redundancy of spindle fibres in the dividing mammalian cell leads to the prediction that only chemical exposures which damage most, if not all, of the fibres will lead to the induction of polyploidy and/or aneuploidy. Such predicted thresholds of chemical activity can be observed when both chromosome loss and non-disjunction are measured in wild type cultures. However, we observed a substantial increase in sensitivity to aneugenic chemicals when measurements were made in primary cell cultures derived from xerodoma pigmentosum and trichothiodystrophy patients. Further studies are necessary to evaluate the consequences of the genetic background of tester strains upon the nature of the dose-response curve of aneugenic chemicals.

1,2-Dimethylhydrazine↗
PubMed2005

Adaptive evolution of non-coding DNA in Drosophila.

A large fraction of eukaryotic genomes consists of DNA that is not translated into protein sequence, and little is known about its functional significance. Here I show that several classes of non-coding DNA in Drosophila are evolving considerably slower than synonymous sites, and yet show an excess of between-species divergence relative to polymorphism when compared with synonymous sites. The former is a hallmark of selective constraint, but the latter is a signature of adaptive evolution, resembling general patterns of protein evolution in Drosophila. I estimate that about 40-70% of nucleotides in intergenic regions, untranslated portions of mature mRNAs (UTRs) and most intronic DNA are evolutionarily constrained relative to synonymous sites. However, I also use an extension to the McDonald-Kreitman test to show that a substantial fraction of the nucleotide divergence in these regions was driven to fixation by positive selection (about 20% for most intronic and intergenic DNA, and 60% for UTRs). On the basis of these observations, I suggest that a large fraction of the non-translated genome is functionally important and subject to both purifying selection and adaptive evolution. These results imply that, although positive selection is clearly an important facet of protein evolution, adaptive changes to non-coding DNA might have been considerably more common in the evolution of D. melanogaster.

Adaptation, Physiological↗
PubMed1997

The natural selection of the chemical elements.

Evolution is treated here in a novel way. DNA or any other code is considered to be conservative and therefore, once life began, it would prevent change. Change was imposed upon the DNA code as a stress resulting in vulnerability to "advantageous" DNA damage and mutation. In this respect it is the stress, the changing environment, that opened up a possibility of evolution once an early life form had optimised itself in primitive circumstances. Here I examine the initial slow-coming-to-terms with the environment of primitive life, and then its evolution as the environment forced the DNA into novel development by introducing chemical elements in new forms. The situation today is no different. Environmental change is hostile to present day life and will lead to further evolution.

Biological Evolution↗
PubMed1985

The primate as a model for the human temperature-sensing system: 1. Adapting temperature and intensity of thermal stimuli.

The thermal sensitivity of three humans and two rhesus monkeys was measured behaviorally, using the "yes-no" paradigm of the Theory of Signal Detection. The aim was to evaluate the monkey's thermal-sensing system as a model for that of humans. Three of the principal variables of human thermal sensations--rate of the temperature change, area of stimulation, and site of stimulation--were held constant. The other three variables--adapting skin temperature (AT), intensity, and direction of the temperature change--were varied systematically. Systematic differences between species were not evident for warming or cooling stimuli. Isodetectability curves (d'e = 1) for small cooling stimuli plotted as a function of the AT were isomorphic, and the points for the human and monkey subjects were frequently superimposed. Isodetectability curves for warming stimuli, on the other hand, had similar shapes for ATs between 33 degrees and 40 degrees C, but the points for the different subjects were not superimposed. At ATs below 30 degrees C, one of the two humans in the warming series and the two monkeys continued to show similarly shaped curves, but the other human was markedly different. Qualitative descriptions of the thermal sensations obtained during threshold measurements of human subjects, reported previously, suggest that this unusual subject probably adopted a criterion qualitatively different from that used by the other subjects. The data presented here and in combination with previously published work from this laboratory (Kenshalo, 1970) suggest that thermal stimuli produce similar sensations in rhesus monkeys and humans, and that the neural systems responsible for coding AT and temperature change in the two species are fundamentally similar.

Adaptation, Physiological↗
PubMed1992

NOVACODE serial ECG classification system for clinical trials and epidemiologic studies.

Traditional serial electrocardiogram (ECG) change classification schemes used in clinical trials such as the Minnesota Code rely on independent classification of the baseline and each follow-up or acute event ECG, whereby graded changes in the hierarchic severity level of the code signify new events such as myocardial infarction (MI). This approach suffers from classification errors caused by repeated instability at decision boundaries at each step when the baseline and each acute event ECG is classified, and various "verification rules" must be used at the end of the coding process to prevent trivial serial changes from causing large transitions in coded events. The NOVACODE algorithms for visual and computer coding of serial ECGs were designed to alleviate some of these instability problems by quantifying changes in critical waveform patterns on a continuous scale. This is achieved by determining, for each ECG coded, a Q-QS Score, ST Depression Score, ST Elevation Score and T-Wave Score, each ranging from 0 to 50. In the next step, a score is derived for ST-T evolution and this ST-T Evolution Score together with changes in Q-QS Score define criteria for a hierarchic mutually exclusive serial ECG change classification scheme that includes coding categories for Q-wave and non-Q wave MIs, equivocal Q wave evolution, evolving ischemic ST-T abnormalities, and various combinations of nonevolving Q-QS wave, and ST-T abnormalities.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed1984

Quality coding of a complex odorant in an invertebrate.

Mechanisms whereby the olfactory system of the spiny lobster codes food odors were quantitatively analyzed. A 23-component chemical mixture, with a composition based on a tissue extract from a known food of lobsters, and 8 of the mixture's components were used to describe responses of single cells at two neural levels: a) olfactory receptor cells and b) low-order interneurons projecting from the main olfactory center of the brain. Cluster analysis identified six classes of narrowly tuned receptor cells. Interneurons, on the other hand, were significantly more broadly tuned than receptor cells and could not be grouped into a small number of discrete, highly correlated cell types. Nonetheless, some chemosensory interneurons (unimodal interneurons) had specificities as narrow as receptor cells. Across-neuron correlations between stimuli showed that the increase in neuronal breadth of responsiveness from the level of receptors to the level of interneurons was paralleled by an increase in similarity in across-neuron patterns and, therefore, a decline in ability to discriminate between any two compounds. Across-neuron correlations between concentrations of a given compound showed that stimulus quality had a much stronger effect on across-neuron patterns than did stimulus quantity and, hence, stimulus qualities could be distinguished in spite of concurrent changes in stimulus quantity. Coding of odor quality could be accomplished at the receptor level by a labeled-lines code. At the interneuronal level, odor quality appears to be coded by across-fiber patterns. However, the finding that unimodal interneurons were as narrowly tuned as receptor cells indicates that specific channels for some food-odor components (e.g., taurine and glycine) are conserved even at higher neuronal levels. These narrow-spectrum interneurons may have a special function in quality coding either by dominating the interneuronal across-fiber pattern for that stimulus or by being processed independently of the broad-spectrum interneurons and thereby transferring information about certain components by way of specific channels to even higher neuronal levels.

Animals↗
PubMed1993

Acorn barnacle Megabalanus rosa lectin (BRA-3): cDNA cloning, gene structure and seasonal changes of mRNA and protein levels.

We have isolated cDNA clones coding for a lectin (BRA-3) from the acorn barnacle, Megabalanus rosa. Sequence comparison of the cDNA clones has revealed polymorphism in the BRA-3 mRNA, which results from single-nucleotide (nt) differences at three positions. All three differences are within the coding region and cause conservative amino acid (aa) changes. The BRA-3 gene is composed of four exons, and the three single-nt differences are located on different exons. In addition, the BRA-3 mRNA and BRA-3 protein levels increased during early summer in a similar fashion, indicating that BRA-3 production is regulated mainly at the level of transcription.

Amino Acid Sequence↗
PubMed2004

Association between bone mineral density and LDL receptor-related protein 5 gene polymorphisms in young Korean men.

Recently, It has been reported that the LDL receptor-related protein 5 (LRP5) regulates bone formation, and that mutations of the gene cause osteoporosis-pseudoglioma syndrome or high bone mass phenotypes. However, the mutations cannot explain a genetic trait for osteoporosis in the general population because of their rarity. From 219 Korean men aged 20-34 yr, we looked for six known polymorphisms causing amino acid changes in the LRP5 coding region, and investigated their association with bone mineral density (BMD) at the following anatomical sites: lumbar spine (L2-L4) and the left proximal femur (femoral neck, Ward's triangle, trochanter and shaft). We found that the Q89R polymorphism was significantly associated with BMD at the femoral neck and Ward's triangle (p=0.004 and <0.001, respectively). However, after adjusting for age, weight and height, a statistically significant association only occurred at the Ward's triangle (p=0.043), and a marginal association was observed at the femoral neck (p=0.098). No A400V, V667M, R1036Q and A1525V polymorphisms were found, and no statistically significant association was found between the A1330V polymorphism and BMD at any sites. Although we failed to demonstrate a clear association between the LRP5 polymorphism and peak bone mass in young men, the present study suggests that larger-scale studies on the Q89R polymorphism need to be performed.

Adult↗
PubMed2025

Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.

Genetic variants (both coding and noncoding) can impact gene function and expression, driving disease mechanisms such as cancer progression. The systematic study of endogenous genetic variants is hindered by inefficient precision editing tools, combined with technical limitations in confidently linking genotypes to gene expression at single-cell resolution. We developed single-cell DNA-RNA sequencing (SDR-seq) to simultaneously profile up to 480 genomic DNA loci and genes in thousands of single cells, enabling accurate determination of coding and noncoding variant zygosity alongside associated gene expression changes. Using SDR-seq, we associate coding and noncoding variants with distinct gene expression in human induced pluripotent stem cells. Furthermore, we demonstrate that in primary B cell lymphoma samples, cells with a higher mutational burden exhibit elevated B cell receptor signaling and tumorigenic gene expression. SDR-seq provides a powerful platform to dissect regulatory mechanisms encoded by genetic variants, advancing our understanding of gene expression regulation and its implications for disease.

Humans↗