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PubMed2003

Epigenetic phenomena and the evolution of plant allopolyploids.

Allopolyploid speciation is widespread in plants, yet the molecular requirements for successful orchestration of coordinated gene expression for two divergent and reunited genomes are poorly understood. Recent studies in several plant systems have revealed that allopolyploid genesis under both synthetic and natural conditions often is accompanied by rapid and sometimes evolutionarily conserved epigenetic changes, including alteration in cytosine methylation patterns, rapid silencing in ribosomal RNA and protein-coding genes, and de-repression of dormant transposable elements. These changes are inter-related and likely arise from chromatin remodeling and its effects on epigenetic codes during and subsequent to allopolyploid formation. Epigenetic modifications could produce adaptive epimutations and novel phenotypes, some of which may be evolutionarily stable for millions of years, thereby representing a vast reservoir of latent variation that may be episodically released and made visible to selection. This epigenetic variation may contribute to several important attributes of allopolyploidy, including functional diversification or subfunctionalization of duplicated genes, genetic and cytological diploidization, and quenching of incompatible inter-genomic interactions that are characteristic of allopolyploids. It is likely that the evolutionary success of allopolyploidy is in part attributable to epigenetic phenomena that we are only just beginning to understand.

Biological Evolution↗
PubMed1996

Batch-by-batch analysis of topographic changes induced by sutured and sutureless clear corneal incisions.

PURPOSE: To evaluate the effect of a suture on surgically induced corneal topographic changes in 5.0 mm clear corneal incisions. SETTING: University Eye Hospital, Vienna, Austria. METHODS: Thirty-seven eyes that had cataract surgery were included in the prospective study. A 5.0 mm long and 0.3 mm deep precut was followed by preparation of a corneal tunnel. After phacoemulsification and intraocular lens implantation, the self-sealing wound was left unsutured in 19 eyes; one radial 11-0 nylon suture was applied in 18 eyes. Using a TMS-1 videokeratoscope, corneal topography was measured preoperatively and at 1 week and 1 and 3 months postoperatively. The topographic data were evaluated by statistical batch-by-batch analysis. Each topographic image was cut into 178 fields in eight concentric rings. The refractive values of these fields were stored in a database. Differences between the four readings of each patient were calculated and the mean differences of the 178 fields in each group were transformed into color-coded maps. The significance of topographical changes and group comparisons of induced changes were computed by Wilcoxon tests. RESULTS: Both groups exhibited significant temporal flattening and vertical steepening. The unsutured eyes also displayed significant nasal flattening. Sutureless 5.0 mm clear corneal incisions induced significantly more vertical steepening and nasal flattening than sutured incisions. CONCLUSION: Application of one radial 11-0 nylon suture in 5.0 mm temporal clear corneal incisions significantly reduced shape changes in the nasal corneal region.

Aged↗
PubMedDate not supplied

Variants of the myocilin gene in Japanese patients with normal-tension glaucoma.

Myocilin (MYOC) mutations are associated with juvenile- and adult-onset primary open-angle glaucoma (POAG). The purpose of this study was to determine whether MYOC gene mutations are associated with normal-tension glaucoma (NTG). The prevalence of MYOC mutations was determined in 80 Japanese NTG patients and 100 control subjects. In addition, the expression of mutant MYOC was determined by transforming COS-1 cells with five myocilin variants (R158Q, D208E, I360N, A363T, and I477S) and examining whether myocilin was present in the cultured cells and/or the culture medium by western blotting. Six different nucleotide sequence variants, R46Stop, R76K, R158Q, D208E, A488A, and one in the 3' non-coding region, were identified in 80 NTG patients. Variants in codon 46 (R46Stop), codon 158 (R158Q), and codon 488 (A488A) were not found in the 100 normal controls. The frequency of other sequence changes (R76K, D208E, and 3' non-coding) in NTG patients did not differ significantly from the frequencies in the control subjects. COS-1 cells transfected with the wild type, R158Q, or D208E variants secreted myocilin into the culture medium. On the other hand, the detected myocilin was significantly reduced in the medium of cells transfected with the I360N, A363T, or I477S variants that were previously identified as mutations for POAG. Definitive evidence of MYOC variants associated with NTG was not found.

Animals↗
PubMed1994

Allelic polymorphism in the coding region of human TCR C alpha gene and characterization of structural variability in the alpha chain constant domain.

An allelic variant of the human TCR C alpha gene, designated C alpha AL, which encodes a structurally different protein product has been characterized. C alpha AL was independently sequenced using polymerase chain reaction (PCR)-amplified TCR C alpha cDNA from various T cell clones derived from a same individual. It differed from the most usual C alpha sequence by two non-synonymous base changes at codons 4 (AAC-->AAG) and 84 (GAA-->GCA) of the C alpha coding region. These changes imply amino acid substitutions Asn-->Lys and Glu-->Ala respectively. An oligotyping method, based on hybridization of allele-specific oligonucleotides to PCR-amplified C alpha DNA, is also described. It was used for differential typing of the two C alpha forms in family and population studies. In each of three T cell clones analyzed from the same donor having two rearranged TCR alpha chain transcripts, C alpha AL was found in only one of the transcripts. In addition, C alpha AL segregated as a co-dominant mendelian allele within the family of this donor. Population analysis was carried out in 73 spanish individuals. Twelve donors (16.4%) were heterozygous, implying that C alpha AL was present in this population sample with an allelic frequency of 0.08. The observed frequencies of C alpha genotypes were those expected for the two alleles being in Hardy-Weinberg equilibrium. This demonstration of structural polymorphism in the constant region of TCR alpha chains provides a useful genetic marker for TCR and disease association studies due to its precise mapping within the C alpha coding region, and its significant frequency in the analyzed population.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed1987

Directional fixation of mutations in vertebrate evolution.

We have made pairwise comparisons between the coding sequences of 21 genes from cold-blooded vertebrates and 41 homologous sequences from warm-blooded vertebrates. In the case of 12 genes, GC levels were higher, especially in third codon positions, in warm-blooded vertebrates compared to cold-blooded vertebrates. Six genes showed no remarkable difference in GC level and three showed a lower level. In the first case, higher GC levels appear to be due to a directional fixation of mutations, presumably under the influence of body temperature (see Bernardi and Bernardi 1986b). These GC-richer genes of warm-blooded vertebrates were located, in all cases studied, in isochores higher in GC than those comprising the homologous genes of cold-blooded vertebrates. In the third case, increases appear to be due to a limited formation of GC-rich isochores which took place in some cold-blooded vertebrates after the divergence of warm-blooded vertebrates. The directional changes in the GC content of coding sequences and the evolutionary conservation of both increased and unchanged GC levels are in keeping with the existence of compositional constraints on the genome.

Animals↗
PubMed2006

Trauma surgeons practice what they preach: The NTDB story on solid organ injury management.

BACKGROUND: Recent studies advocate a nonoperative approach for hepatic and splenic trauma. The purpose of this study was to determine whether the literature has impacted surgical practice and, if so, whether or not the overall mortality of these injuries had changed. METHODS: The American College of Surgeons' National Trauma Data Bank (NTDB 4.0) was analyzed using trauma admission dates ranging from 1994 to 2003. All hepatic and splenic injuries were identified by ICD-9 codes. As renal trauma management has not changed during the study period, renal injuries were included as a control. Nonoperative management (NOM) rates and overall mortality were determined for each organ. Proportions were compared using chi analysis with significance set at p < 0.05. RESULTS: There were 87,237 solid abdominal organ injuries reported and included: 35,767 splenic, 35,510 hepatic, 15,960 renal injuries. There was a significant (p < 0.00000000005) increase in percentage of NOM for hepatic and splenic trauma whereas renal NOM remained stable for the study period. Despite an increase in NOM for splenic and hepatic injuries, mortality has remained unchanged. CONCLUSIONS: This study demonstrates that the management of hepatic and splenic injuries has significantly changed in the past 10 years with no appreciable effect on mortality. NOM has become the standard of care for the management of hepatic and splenic trauma. The NTDB can be used to monitor changes in trauma care in response to new knowledge regarding improved outcomes.

Adolescent↗
PubMed1988

Interferons.

Interferon (IFN)-alpha and -beta are produced by virus-infected cells; IFN-gamma is produced as a primary response of T lymphocytes to mitogenic stimulation, IFN-gamma gene activation being brought about by changes in Ca2+ and phosphatidyl inositol metabolism. IFNs act by binding to cell surface receptors and triggering activation of IFN-responsive genes, probably via specific base sequences located in the 5' non-coding region of such genes, resulting in changes in cell function. Important genes activated in this way are the MHC antigen genes; class I induced by all IFNs, class II by IFN-gamma only. This MHC activation may have important consequences for lymphocyte function.

Animals↗
PubMed1982

An unusual evolutionary behaviour of a sea urchin histone gene cluster.

DNA sequences of cloned histone coding sequences and spacers of sea urchin species that diverged long ago in evolution were compared. The highly repeated H4 and H3 genes active during early embryogenesis had evolved (in their silent sites) at a rate (0.5-0.6% base changes/Myr) similar to single-copy protein-coding genes and nearly as fast as spacer DNA (0.7% base changes/Myr) and unique DNA. Thus, evolution in the major histone genes conforms to a universal evolutionary clock based on the rate of base sequence change. By contrast, the H4 and H3 coding sequences and a non-transcribed spacer of the DNA clone h19 of Psammechinus miliaris show an exceptionally low rate of sequence evolution only 1/100 to 1/200 that predicted from the clock hypothesis. According to the classical model of gene inheritance, the h19 DNA sequences in the Psammechinus genome require unusual conservation mechanisms by selection at the level of the gene and spacer sequences. An alternative explanation could be recent horizontal gene transfer of a histone gene cluster from the very distantly related Strongylocentrotus dröbachiensis to the P. miliaris genome.

Journal Article↗
PubMed1994

Polymorphisms of the prion protein gene in Italian patients with Creutzfeldt-Jakob disease.

Creutzfeldt-Jakob disease (CJD) is a transmissible neurodegenerative disorder characterized by the accumulation of the amyloid protein PrP in the CNS. Two coding polymorphisms of the PrP gene (PRNP) are a methionine (Met) to valine (Val) change at codon 129, and a deletion in the octapeptide coding region. In the United Kingdom, homozygosity at codon 129 appears to be associated with a predisposition to develop CJD. However, in Japan, where allelic frequencies and genotype distribution are significantly different, such an association has not been demonstrated. To determine whether such deletion(s) or codon 129 polymorphisms of PRNP predispose to the development of CJD in Italian patients, 31 sporadic CJD patients with no known PRNP mutations, and 186 unrelated control subjects were studied. Genotypic frequencies at codon 129 in these Italian CJD patients revealed a significant excess of methionine alleles, and a different genotype distribution in comparison with the normal Italian population. Deletions of a 24-bp segment located in the PrP octapeptide coding region were found in two control subjects, but in none of the sporadic CJD patients. These data suggest that Met homozygosity at codon 129 may contribute, with other environmental or endogenous factors, to CJD development.

Adult↗
PubMed2001

The low-incidence MNS antigens M(v), s(D), and Mit arise from single amino acid substitutions on GPB.

BACKGROUND: GPB carries 'N' at its N:-terminus and S and s, determined by a polymorphism at amino acid position 29 (Met29Thr). The low-incidence antigens M(v), s(D), and Mit are associated with weakened expression of S and/or s, and the purpose of this study was to define their molecular bases. METHODS: The GPB gene (GYPB) was sequenced after RT-PCR of RNA from four samples: two M(v)+, one s(D)+, and one Mit+. The point mutations observed were confirmed by sequencing of genomic DNA from these and other examples of s(D)+ and Mit+ samples. RESULTS: A point mutation of 65C>G observed in the M(v)+ samples predicted a change of Thr3Ser. A mutation of C>G at nucleotide 173 of the GYPB coding sequence, observed in two s(D)+ samples, predicted a change of Pro39Arg. Three Mit+ samples showed a nucleotide substitution of 161G>A, which predicted a change of Arg35His. Altered expression of S or s was confirmed by serologic tests. CONCLUSION: These results confirm that Arg35 is important for full expression of S. Pro39 and, surprisingly, Thr3 are also important for full expression of s. Furthermore, Thr3 must be essential for expression of 'N,' as M(v)+ RBCs lack 'N.'

Amino Acid Substitution↗
PubMed2004

Prognostic stratification of Dukes B colon cancer by a neoglycoprotein.

Disease progression of tumors is accompanied by structural changes of the glycan chains of cellular glycoconjugates. Within the concept of the sugar code the presence of complementary receptors such as lectins translates changes in ligand presentation into biological effects, for example in growth regulation and adhesion. By introducing neoglycoproteins to histopathological colon cancer analysis the questions are addressed as to whether specific binding sites for main N- and O-glycan components are present and whether they harbor potential for prognostic predictions. Synthetic conjugation of fucose, lactose, and mannose derivatives to a carrier protein yielded neoglycoproteins for glycohistochemical analysis. The tumor panel included routinely fixed tissue sections from 67 cancer cases (15 Dukes A, 20 Dukes B, 15 Dukes C, and 17 metastatic tumors) and 6 hepatic metastases as well as 20 normal biopsy specimens as control. Quantitative image analysis determined the labeling index and the mean optical density in each case, separating tumor and peritumoral connective tissue. Specific carbohydrate-dependent binding with inter-individual heterogeneity was observed. The distinct staining profiles were not associated with disease stage or metastasis formation. Strong expression of lactose-binding sites in the peritumoral connective tissue especially in terms of the labeling index was significantly correlated with reduced survival in Dukes B patients (p=0.02). A similar tendency was observed in the Dukes C group. In conclusion, the application of the synthetic markers aimed at lectin detection defines lactose binding as new prognostic marker. It has potential relevance for improving the benefit from adjuvant therapy in Dukes B colorectal cancer patients. Technically, chemical ligand immobilization to an inert carrier can find useful application beyond glycosciences in the quest to extend the panel of tumor markers.

Biomarkers, Tumor↗
PubMed1997

Processing of color- and noncolor-coded signals in the gourami retina. III. Ganglion cells.

The dynamics of intracellular responses from ganglion cells, as well as that of spike discharges, were studied with the stimulus regimens and analytic procedures identical to those used to study the dynamics of the responses from horizontal and amacrine cells (,). The stimuli used were large fields of red and green light given as a pulsatile input or modulation about a mean luminance by a white-noise signal. Spike discharges evoked by a white-noise stimulus were analyzed in exactly the same manner as that used for analysis of analog responses. The canonical nature of kernels allowed us to correlate the first- and second-order components in a spike train with those of the intracellular responses from horizontal, amacrine, and ganglion cells. Both red and green stimuli given alone in darkness produced noncolor-coded responses from all ganglion cells. In the case of some cells, steady red illumination changed the polarity or waveform of the response to green light. Color-coded ganglions responded only to simultaneous color contrast. Nonlinearities recovered from intracellular responses, and spike discharges were similar to those found in responses from amacrine cells and were of two types, one characteristic of the C amacrine cells and the other characteristic of the N amacrine cells. The first-order kernels of most ganglion cells could be divided into two basic types, biphasic and triphasic. The combination of kernels of these two basic types with different polarities can produce a wide range of responses. Addition of two types of second-order nonlinearity could render color coding in this relatively simple retina as an extremely complex process. Color information appeared to be represented by the polarity, as well as the waveform, of the first-order kernel. The response dynamics is a means of transmission of color-coded information. Second-order components carry information about changes around a mean luminance regardless of the color of an input. Some spike discharges produced a well-defined cross-kernel between red and green inputs to show that a particular time sequence of red and green stimuli was detected by the retinal neuron network. The similarity between signatures of second-order kernels for both amacrine and ganglion cells indicates that signals undergo a minimal transformation in the temporal domain when they are transmitted from amacrine to ganglion cells and then transformed into a spike train. Under our experimental conditions, a single spike train carried simultaneously information about red and green inputs, as well as about linear and nonlinear components. In addition, the spike train also carries a cross-talk component. A spike train is a carrier of multiple signals. Conversely, many types of information in a stimulus are independently encoded into a spike train.

Animals↗
PubMed1991

Effects of parathyroid hormone on ornithine decarboxylase activity in human osteosarcoma cells.

Ornithine decarboxylase (ODC) is a rate-limiting enzyme of the biosynthesis of polyamines, which are important in cell growth and differentiation. Here, we studied whether parathyroid hormone (PTH) affects the induction of ODC and the proliferation of the human osteoblast-like cell line SaOS2, which is sensitive to PTH. In confluent cells, ODC activity was not detected, but activity was significantly induced by fresh medium, with maximum activity 6 h after the change. PTH potentiated this enzyme induction in a dose-dependent manner at 10(-9) and 10(-8) M at which range the intracellular cAMP level also rose. Dibutyryl cAMP, cholera toxin, and 3-isobutyl-1-methylxanthine each caused an increase in ODC activity similar to that with PTH. The half-life of enzyme activity was about 30 min and was not changed by the addition of PTH. mRNA coding for ODC was detected in the confluent cells and its concentration was increased two- to threefold by the fresh medium. No further increase in mRNA occurred when PTH was added. At 48 h after the change of medium, PTH inhibited the DNA synthesis induced by fresh medium. These results suggest that the increase in ODC activity caused by PTH was caused by enhancement of cAMP synthesis, and that this augmentation involves post-transcriptional regulation.

Bucladesine↗
PubMed1982

Five nucleotide changes in the large intervening sequence of a beta globin gene in a beta+ thalassemia patient.

A beta globin gene from a patient with homozygous beta+ thalassemia has been cloned and completely sequenced. No changes from normal are found in the 200 nucleotides 5' to the cap site, in the 3' untranslated region up to the poly A addition site, in the small intervening sequence (IVS 1), or in the coding sequence except for a third base change in codon 2. The only other differences are in the large intervening sequence (IVS 2). One of these, at a position 16 nucleotides from the 5' end of IVS 2, has been reported previously in normal individuals, and is probably a polymorphism. Four other changes, at positions 74, 81, 666, and 705 are also seen in IVS 2. Abnormal beta globin mRNA precursors detected in the bone marrow cells of this patient, and abnormal beta globin RNA splicing observed when this gene is transcribed in a tissue culture system taken together with these IVS 2 changes, suggest that the beta+ thalassemia phenotype is produced by a decrease in normal beta globin mRNA processing.

Base Sequence↗
PubMed2001

Bar code, good for industry and trade--how does it benefit the dentist?

Every dentist who attentively follows the change in product labelling can easily see that the HIBC bar code is on the increase. In fact, according to information from FIDE/VDDI and ADE/BVD, the dental industry and trade are firmly resolved to apply the HIBC bar code to all products used internationally in dental practices. Why? Indeed, at first it looks like extra expense to additionally print a bar code on the packages. Good reasons can only lie in advantages which manufacturers and the trade expect from the HIBC bar code, Indications in dental technician circles are that the HIBC bar code is coming. If there are advantages, what are these, and can the dentist also profit from them? What does HIBC bar code mean and what items of interest does it include? What does bar code cost and does only one code exist? This is explained briefly, concentrating on the benefits bar code can bring for different users.

Dental Equipment↗
PubMedDate not supplied

mRNA expression induced by cell-substrate interaction. A two-dimensional tissue formation process.

This study aimed to develop a quantitative assay method of determining cellular events at the mRNA level during tissue formation. Quantitative assessment of mRNAs coding specific proteins (beta-actin, fibronectin, laminin) during tissue formation on tissue culture dishes was attained using a Northern blot technique with autoradiography. The amount of beta-actin mRNA, the expression of which is initiated shortly after adhesion, greatly increased with incubation time and reached maximal levels near the confluent state, followed by a reduced expression at a later stage of tissue formation. The time course of beta-actin mRNA expression, which reflects cytoskeletal organization, corresponded well to morphologic changes in adherent cells. Expression of mRNAs coding the extracellular matrix proteins, fibronectin and laminin, was initiated at the proliferation stage. After maximum expression levels were observed at the confluent stage, a gradual decrease in the expression of both mRNAs was seen after longer culture periods. Expression patterns of mRNAs coding cytoskeletal and extracellular matrix proteins greatly depended upon the type of artificial substrates. Thus, the dynamic changes in tissue formation were quantified to elucidate the significance of artificial substrates in tissue formation at the mRNA level.

Actins↗
PubMed1990

Bioethics in Chile: present and future status.

Chile's health system has been evolving rapidly in recent years. Among other things, profit-making enterprises have assumed a growing role, medical care has become increasingly technical, and the importance of less highly trained health workers has grown. Also, the assigned role of the Chilean Medical Association in deciding matters of medical misconduct has diminished, while that of the courts has grown; the nature of the doctor-patient relationship has changed; and clear divergences between medical ethics codes, laws, and prevailing social practices have emerged. Within this context, bioethics has come to be regarded as a necessary element in the teaching and practice of medicine. So while this discipline has not yet become fully institutionalized in Chile, it seems likely to play a growing role in dealing with the aforementioned changes and could make a substantial contribution toward solution of associated problems in the future.

Bioethical Issues↗
PubMed1981

Synthesis of Chloroplast Proteins during Germination and Early Development of Cucumber.

Cell-free protein synthesizing systems have been used to study the developmental changes in the synthesis of chloroplast proteins in the cotyledons of cucumber seedlings grown in the light or in the dark. Escherichia coli and wheat germ in vitro protein synthesizing systems have been used to assay the changes in the levels of the mRNA's coding for ribulose 1,5-bisphosphate carboxylase (RuBPCase). The large subunit of cucumber RuBPCase has been identified among the translation products of the E. coli system. The wheat germ system translates the cucumber mRNA coding for the small subunit of RuBPCase to produce a 25,000 molecular weight precursor polypeptide. Plastids isolated from light-grown cotyledons were used to study developmental changes in their capacity to synthesize protein. The data obtained indicate that in the light there is an initial 48-hour period of accumulation of the mRNA's coding for the large and small subunits of RuBPCase, coupled with an increase in the capacity of the isolated plastids to synthesize protein. This is followed by a decline. This decline is not reflected in the accumulation of RuBPCase in the cotyledons which remains constant over the period of study.

Journal Article↗