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PubMed1998

Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences.

We recently reported that formation of allopolyploid wheat was accompanied by rapid nonrandom changes in low-copy noncoding DNA sequences. In this report we show that following allopolyploidization, changes also occurred in coding sequences. Genomic DNA of nine different newly synthesized amphiploids of different ploidy levels and their parental lines was digested with five restriction enzymes and probed with 43 coding sequences. The sequences, 19 genomic and 24 cDNA sequences, are group (homoelogous) specific and represent the proximal and distal regions of the short and long arms of the seven homoeologous groups of the Triticeae. We revealed three types of changes: disappearance of a parental hybridization fragment(s), appearance of a novel fragment(s), and simultaneous disappearance of a parental fragment(s) and appearance of a novel fragment(s). No elimination of sequences took place, since in every sequence studied the parental hybridization fragments were present in at least one of the enzyme digests. Variations in pattern among individual plants of the same amphiploid, as well as a between several synthetic and natural amphiploids, indicated that at least some of the genomic changes occurred at random. Intergenomic recombination was not the cause of the observed changes. Evidence was obtained, however, that changes were also brought about by DNA methylation. Methylation may cause inactivation of genes or modify their expression levels in some of the newly synthesized amphiploid plants, leading to genetic diploidization and gene-dosage compensation and thus increasing variation among individuals.

Avena↗
PubMed1992

Six new mutations in the ornithine transcarbamylase gene detected by single-strand conformational polymorphism.

We describe six new mutations in the ornithine transcarbamylase (OTC) gene found in patients with OTC deficiency. These mutations were detected by single-strand conformational polymorphism analysis of amplified genomic DNA and characterized by direct sequencing of double-stranded DNA. Three of the mutations were found in males who had neonatal onset of hyperammonemia. The mutations are a single base deletion (guanine) in exon 5 at nucleotide 403 causing a frame-shift error, a guanine to adenine substitution at the 3' end of intron 2 nucleotide 217 (-1) causing an acceptor splicing site error, and a guanine to adenine substitution at base 236 changing the code from glycine to glutamic acid at position 47 of the mature enzyme. Two different mutations were found in two males whose onset of clinical problems occurred after the neonatal period. One patient had a guanine to cytosine transversion in the sense strand of exon 3 at nucleotide 281 resulting in a substitution of threonine for arginine in position 62 of the mature OTC protein. This substitution changes the composition of the putative active site for carbamyl phosphate from Ser-Thr-Arg-Thr-Arg to Ser-Thr-Arg-Thr-Thr. The second patient has a guanine to thymine substitution at nucleotide 912 of the sense strand of exon 9, changing the code for leucine to phenylalanine in position 272 of the mature OTC protein. This changes a conserved domain of the gene likely to be the ornithine binding site from Phe-Leu-His-Cys-Leu-Pro to Phe-Leu-His-Cys-Phe-Pro.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Metabolism, Inborn Errors↗
PubMed2025

Single-Cell Splicing Isoform Atlas of the Adult Human Heart and Heart Failure.

BACKGROUND: Alternative splicing plays crucial roles in normal heart development and cardiac disease by influencing protein-coding sequences, functional domains, and molecular networks. However, a detailed characterization of the human heart isoform landscape remains incomplete. METHODS: Leveraging long-read single-nucleus RNA sequencing and computational analysis, we dissected full-length isoform heterogeneities, expression patterns, and usage shifts across cell types, cell states, and cardiac conditions of the adult left ventricle. We applied in silico approaches to assess the functional relevance of identified isoforms; validated isoform compositions of representative cardiac genes using reverse transcription quantitative polymerase chain reaction and targeted amplicon sequencing; and developed a web server for interactive navigation of our results. RESULTS: The data revealed that isoform heterogeneity is widespread in the cardiac cellular system, serving as a posttranscriptional buffer mechanism that calibrates the molecule reservoirs in human hearts. In healthy left ventricles, ≈30% of cell type-specific genes were polyform, using multiple isoforms tailored to cell type-specific programs. Among ubiquitously expressed genes, >300 showed differential isoform usage with cell type specificity in normal hearts. Comparisons of cardiomyocytes across conditions uncovered 379 genes with marked isoform usage shifts, most of which are predicted to change protein coding outcomes through direct changes in protein coding sequences and switches between intron retention and non-protein-coding biotypes. In contrast, cell state-specific programs tend to operate on monoform genes associated with changes among cell states. In addition, our data revealed heart failure-associated differential isoform usage events in stromal and immune cell types in the cardiac microenvironment. CONCLUSIONS: We present a comprehensive atlas of splicing isoforms in the normal adult heart and heart failure through long-read single-nucleus RNA sequencing and computational analyses. The results suggest crucial roles of isoforms in buffering core cellular programs and contributing to disease-associated cell states. The full-length details of these cell-specific isoforms serve as an important reference for downstream translational and mechanistic studies and are available on our online data portal at https://github.com/gaolabtools/heart-isoform-atlas.

Humans↗
PubMedDate not supplied

[Analysis of selected changes in project the penal code].

In this paper the authors have analysed selected proposals of changes in the project of amendments in the penal code. Special attention has been placed on problem of the legality of the "comma" in art. 156 of the penal code. In this matter also a review of court jurisdiction has been made.

Crime↗
PubMed2006

Specific changes in hippocampal spatial codes predict spatial working memory performance.

This study examined the relationship between hippocampal place fields and spatial working memory. Place cells were recorded while rats solved a spatial working memory task in light and dark testing conditions. Rats made significantly more errors when tested in darkness, and although place fields changed in multiple ways in darkness, only changes in place field specificity predicted the degree of impaired spatial memory. This finding suggests that more spatially distinct place fields may contribute to hippocampal-dependent mnemonic functions.

Animals↗
PubMed1996

Formal descriptions and adaptive mechanisms for changes in controlled medical vocabularies.

Standard controlled medical vocabularies are typically based on a coding scheme, while medical informatics applications tend to have a more formal conceptual foundation. When such applications attempt to use data coded with standard vocabularies, problems can arise when the standard vocabulary changes over time. A formal taxonomy is presented for describing the semantic changes which can occur in a vocabulary, such as simple addition, refinement, precoordination, disambiguation, redundancy, obsolescence, discovered redundancy, major name changes, minor name changes, code reuse, and changed codes. The taxonomy is described that used to effect change in one concept-based vocabulary (the Medical Entities Dictionary), and the utility of the approach is demonstrated by applying it to the changes appearing in the 1994 release of the International Classification of Diseases, Ninth Edition, with Clinical Modifications (ICD-9-CM).

Classification↗
PubMed1980

[Interpretation of the ECG changes using the Minnesota code in the presence of right-ventricular (high-altitude) cardiac hypertrophy].

The research showed a high incidence of electrocardiographic signs of hypertrophy of the right ventricle of the heart under high-altitude conditions. Code 2-3 was found in 49.2% of highlanders examined, code 2-4 in 1.5%, code 3-2 in 17.0%, and code 9-4-2 in 54.4%. Some cases of hypertrophy of the right ventricle of the heart (code 3-2, approximately 4-5%) are attended by disturbances in the repolarization processes in the right chest electrocardiographic leads (code 5-1 or 5-2). According to the interpretations of the Minnesota code, these shifts should be considered ischemic. But information yielded by the Rouz questionnaire, the results of clinical examination, and tests with maximum physical load in 8 persons who had such shifts on the ECG did not confirm the presence of symptoms of ischemic heart disease. That is why changes in T wave detected in highland aborigenes with marked right-ventricular hypertrophy but no clinical symptoms of ischemic heart disease should be accepted as evidence of ischemia. Otherwise, if the disturbances in the repolarization processes are interpreted as signs of myocardial ischemia, the prevalence of ischemic heart disease among the population of the highlands may be overestimated. The introductin of restriction in relation to code 3-2 when it is combined with code 5-1 or 5-2 will make it possible to study more exactly the true prevalence of ischemic heart disease in the presence of hypertrophy of the right ventricle of the heart.

Adult↗
PubMed2004

The BRCA1-associated protein BACH1 is a DNA helicase targeted by clinically relevant inactivating mutations.

BACH1 is a nuclear protein that directly interacts with the highly conserved, C-terminal BRCT repeats of the tumor suppressor, BRCA1. Mutations within the BRCT repeats disrupt the interaction between BRCA1 and BACH1, lead to defects in DNA repair, and result in breast and ovarian cancer. BACH1 is necessary for efficient double-strand break repair in a manner that depends on its association with BRCA1. Moreover, some women with early-onset breast cancer and no abnormalities in either BRCA1 or BRCA2 carry germline BACH1 coding sequence changes, suggesting that abnormal BACH1 function contributes to tumor induction. Here, we show that BACH1 is both a DNA-dependent ATPase and a 5'-to-3' DNA helicase. In two patients with early-onset breast cancer who carry distinct germline BACH1 coding sequence changes, the resulting proteins are defective in helicase activity, indicating that these sequence changes disrupt protein function. These results reinforce the notion that mutant BACH1 participates in breast cancer development.

Adenosine Triphosphatases↗
PubMed1995

The effect of changes in nucleotide sequence coding for the N-terminus on expression levels of ovine growth hormone variants in Escherichia coli.

The expression levels of coding sequences for pituitary growth hormone, introduced into Escherichia coli by genetic manipulation techniques, vary markedly according to the precise sequence introduced. In order to understand the basis of this variation more fully, we have studied the relationship between the level of expression in E. coli of a series of ovine growth hormone variants and the nucleotide sequences coding for their N-terminal regions. Sequence variation resulted from the introduction of deletions, or site-directed mutations, into a plasmid containing the coding sequence for ovine growth hormone preceded by the initiation codon and 25 bases derived from beta-galactosidase or linker regions of plasmid pUC8. The expression levels of the variants varied from less than 0.01% to over 34% of the total cell protein, indicating that changes in the nucleotide sequence close to the initiation codon had a marked effect on expression level. The results of a comparison of closely related sequences in pairs of plasmids giving poor or good expression are consistent with the hypothesis that poor translation of growth hormone mRNAs is caused by the presence of secondary structures close to the initiation codon. Secondary structures are identified that appear to explain the variation in expression levels.

Animals↗
PubMedDate not supplied

[The molecular mechanism of evolution of changes in the genetic code].

Alterations to the standard genetic code have been found in both prokaryotes and eukaryotes. This finding demolished the central dogma of molecular biology, postulated by Crick in 1968, of an immutable and universal genetic code and raised the question of how organisms survive genetic code alterations? Recent studies suggest that genetic code alterations are driven by selection using a mechanism that requires translational ambiguity. In C. albicans, the leucine CUG codon is decoded as serine through structural alterations of the translational machinery, in particular, of a Ser-tRNACAG which has dual identity and novel decoding properties. Here, we review the molecular mechanism of CUG reassignment focusing on the structural change of the translational machinery and on the impact that such alteration had on the evolution of the Candida albicans genome.

Base Sequence↗
PubMed1980

Human and murine tumours: changes in cell surface structures coded by the major histocompatibility complex region.

Serological and structural changes of surface markers involved in immune reactions may occur in human and murine tumour systems. Thus nine out of twenty-one human tumour cell lines and SV40-transformed fibroblasts differed from autologous lymphoblastoid cells or fibroblasts in their reactivity with HLA alloantisera. H-2 antigens isolated from the murine tumour cells 6C3HED and TP1422, undergo structural changes. An alien HLA-B7 was detected in sera from two melanoma patients. The serologic activity of H-2 antigens was significantly increased in the serum and ascites fluid of tumour bearing mice. Additionally, human SV40-transformed fibroblasts acquire receptors for monkey red blood cells and the murine lymphosarcoma cells 6C3HED express receptors for sheep red blood cells.

Animals↗
PubMed1986

Medicare case-mix index increase.

Medicare paid hospitals a higher amount per admission in 1984 than had been planned because the case-mix index (CMI), which reflects the proportion of patients in high-weighted DRG's versus low-weighted ones, increased more than had been projected. This study estimated the degree to which the increase in the CMI from 1981 reflected medical practice changes, the aging of the Medicare inpatient population, changes in coding practices of physicians and hospitals, and changes in the way that the Health Care Financing Administration collects the data on case-mix. All of the above, except for aging, contributed to the increase in the CMI.

Abstracting and Indexing↗
PubMedDate not supplied

The effect of income projection on resident charges for services.

This study examined how family practice residents coded their patient care services, and whether feedback on coding patterns together with income projections would alter coding behavior. Current and future income projections were calculated using assumptions about the practice setting. The collected and calculated data were presented to the residents after the study period, together with a discussion of coding of patient care services and fees. The same data were collected three months and nine months later. There was no significant difference in coding patterns when comparing first- to second- to third-year residents. Six months after the information was presented to the residents, the percentage of brief visits coded decreased significantly, and the percentages of intermediate and comprehensive visits coded increased significantly. Twelve months later, the changes in coding patterns had reverted to the initial findings. This appears to be an effective approach that could be used elsewhere to teach coding of patient care services as part of a practice management curriculum.

Curriculum↗
PubMed2006

Outcome and code status of lung cancer patients admitted to the medical ICU.

OBJECTIVES: To determine the outcome of lung cancer patients admitted to the medical ICU (MICU), to examine their code status at MICU admission and prior to death, and to determine which subspecialty physician was responsible for the change in code status. DESIGN: Retrospective chart review study. SETTING: A 19-bed MICU in a tertiary-care university hospital. PATIENTS: Consecutive patients with a diagnosis of lung cancer admitted to the MICU from July 2002 to June 2004. MEASUREMENTS AND MAIN RESULTS: Forty-seven patients with a diagnosis of lung cancer accounted for 53 MICU admissions. Mean (+/- SD) age at MICU admission was 65 +/- 10 years. Sixty-six percent were male. Eighty-three percent had non-small cell lung cancer (NSCLC); 64% of these were stage IV NSCLC. The most common organ system implicated on MICU admission was pulmonary, with 38% of patients presenting with pneumonia. Overall MICU mortality was 43%, and in-hospital mortality was 60%. Patients who required mechanical ventilation or had more advanced lung cancer stage had the worst prognosis, with mortality rates of 74% and 68%, respectively. Seventy-four percent of patients were "full code" at MICU admission. Subsequently, the code status was changed to "do not resuscitate" in 49% of these cases. The pulmonary/critical care physician was involved in this change 96% of the time and was the sole physician in 65% of cases. CONCLUSIONS: This study confirms that patients with lung cancer admitted to the MICU have a high mortality. Despite this, the majority of patients are full code on MICU admission. Pulmonary/critical care physicians play an important role in the end-of-life decision making of lung cancer patients admitted to the MICU, perhaps because of their availability in the MICU and also because of their sense of responsibility in maintaining and withdrawing life support.

Aged↗
PubMed1993

The evolutionary change of the genetic code as restricted by the anticodon and identity of transfer RNA.

The discovery of non-universal genetic codes in several mitochondria and nuclear systems during the part ten years has necessitated a reconsideration of the concept that the genetic code is universal and frozen, as was once believed. Here, the flexibility of the relationship between codons and amino acids is discussed on the basis of the distribution of non-universal genetic codes in various organisms insofar as has been observed to date. Judging from the result of recent investigations into tRNA identity, it would appear that the non-participation of the anticodon in recognition by aminoacyl-tRNA synthetase has significantly influenced the variability of codons.

Animals↗
PubMed1990

Changes in messenger RNAs coding for neurotransmitter receptors and voltage-operated channels in the developing rat cerebral cortex.

The ontogenetic development of poly(A)+ mRNAs coding for receptors to several neurotransmitters (kainate, glutamate, acetylcholine, and serotonin) and voltage-operated channels (sodium and calcium) was studied by isolating total poly(A)+ mRNA from the brains of rats at various developmental stages and injecting it into Xenopus oocytes. The oocytes translated the foreign mRNA and incorporated functional receptor/ion channel complexes into the cell membrane. Thus, recording of induced membrane currents in voltage-clamped oocytes gave a measure of the relative amounts of the different messengers. Responses induced by kainate, glutamate, acetylcholine, and serotonin all increased with age and reached a maximum in oocytes injected with mRNA from adult cortex. Messenger RNAs for the earliest ages examined, Embryonic Days 15 and 18, expressed little or no response to kainate, glutamate, or acetylcholine, while 50-70% of the adult response was reached by Postnatal Day 10. In contrast, the serotonin-induced response was already comparatively large (16% of the adult level) in oocytes injected with mRNA from Embryonic Day 15 brain and increased postnatally to adult levels. The expression of voltage-dependent sodium and calcium channels was small in oocytes injected with mRNA from embryonic animals and increased postnatally to reach a maximum in oocytes injected with mRNA from adult animals.

Aging↗
PubMed1984

Transformation-associated changes in nuclear-coded mitochondrial proteins in 3T3 cells and SV40-transformed 3T3 cells.

Comparative two-dimensional gel electrophoretic studies were performed on mitochondrial proteins in nontransformed mouse 3T3 cells and in SV40-transformed 3T3 cells, SV-T2. Two polypeptides, of 58 and 40 kDa, were present in increased amounts in SV40-transformed cells. These polypeptides were demonstrated to be nuclear-coded mitochondrial proteins by their absence in mitochondrial preparations, when labeling was performed in the presence of a mitochondrial-specific inhibitor, Rhodamine 6G. Temperature-sensitive mutants for transformation were derived from 3T3 cells by transfection with cloned SV40 DNA containing the ts A58 mutation. Increased amounts of the 58 kDa protein were apparent in these cells at the permissive temperature (33 degrees C) compared to the restrictive temperature (39.5 degrees C).

Animals↗