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Sequences of six genes and several open reading frames in the kinetoplast maxicircle DNA of Leishmania tarentolae.

The DNA sequence of approximately 80% of the transcribed region of the kinetoplast maxicircle DNA of Leishmania tarentolae was obtained, and structural genes were localized by comparison of the translated amino acid sequences with those of known mitochondrial genes from other organisms. By this method, the genes for cytochrome oxidase subunits I, II, and III, cytochrome b, and human mitochondrial unidentified reading frames 4 and 5 were identified. By comparing the amino acid sequences of the putative L. tarentolae genes with those of known genes, we conclude that TGA codes for tryptophan, as in most other mitochondrial systems. This is the only apparent change from the universal genetic code. The six identified structural genes show various degrees of divergence from the homologous genes in other species, with cytochrome oxidase subunit I being the most conserved and cytochrome oxidase subunit III being the least conserved. A comparison of the cytochrome b genes from L. tarentolae and Trypanosoma brucei showed that the ratio of transversions to transitions is 1:1, suggesting that these species diverged from each other more than 80 X 10(6) years ago. Several as yet unidentified open reading frames were also present in the maxicircle sequence. These data confirm that maxicircle DNA has a coding potential which typifies other mitochondrial systems.

Amino Acid Sequence↗

Mutation of the phospholamban promoter associated with hypertrophic cardiomyopathy.

Phospholamban is an endogenous inhibitor of sarcoplasmic reticulum calcium ATPase and plays a prime role in cardiac contractility and relaxation. Phospholamban may be a candidate gene responsible for cardiomyopathy. We investigated genome sequence of phospholamban in patients with cardiomyopathy. PCR-based direct sequence was performed for the promoter region and the whole coding region of phospholamban in 87 hypertrophic, 10 dilated, and 2 restricted cardiomyopathic patients. We found a heterozygous single nucleotide transition from A to G at -77-bp upstream of the transcription start site in the phospholamban promoter region of one patient with familial hypertrophic cardiomyopathy. This nucleotide change was not found in 296 control subjects. Using neonatal rat cardiomyocytes, the mutation, -77A-->G, increased the phospholamban promoter activity. No nucleotide change in the phospholamban coding region was found in 99 patients with cardiomyopathy. We suspect that the mutation plays an important role in the development of hypertrophic cardiomyopathy.

Animals↗

Epigenetic information in chromatin: the code of entry for DNA repair.

Epigenetic changes are important etiological factors of human cancer. Epigenetic information in chromatin (known as 'histone code') is a fascinating feature used by cells to extend and modulate the genetic (DNA) code. The histone code is thus proposed to be 'read' by cells to regulate accessibility to, and functions of, chromatin DNA. While the role of the epigenetic code involving chromatin modifying/remodeling complexes in transcriptional regulation is well established, it is only recently that these mechanisms have been implicated in DNA damage detection and DNA repair. However, how the components of the DNA damage sensing and repair machinery gain access to broken DNA in compacted chromatin remains a mystery. Recent studies provide important insights into DNA damage- and repair-specific modifications to histones and shed light on how the epigenetic code controls DNA repair.

Animals↗

Assessment of middle cerebral artery diameter after aneurysmal subarachnoid hemorrhage by transcranial color-coded duplex sonography.

This study examined if vasospasm after aneurysmal subarachnoid hemorrhage could be visualized by middle cerebral artery (MCA) diameter changes in transcranial color-coded duplex sonography (TCCS). Comparative measurements between mean blood velocity (MBV) and MCA diameter were carried out in 17 patients in 76 instances. At two depth ranges (proximal, 60 55 mm: distal, 50-45 mm) two observers assessed the MCA diameter as indicated by the visualized blood flow column. At both points of measurement, the diameter differences between the two observers were within the ¿ 2 S.D. range of the mean difference indicating interobserver agreement. In 17 instances, MBV was > 120 cm/s indicating vasospasm but MBV did not correlate with absolute or relative diameter changes. MCA diameter assessment in TCCS seems reproducible. Because TCCS imaging is influenced by several factors comparative angiographic studies are necessary to clarify the TCCS findings.

Female↗

Correct coding for the orthopedic surgeon.

Coding accurately is one of the main principles of a successful practice. Some changes that we will see shortly include deletion of the term "separate procedure," deletion of the term "with and/or without," deletion of the term "any method," revision of the criteria for choosing E/M levels, and 52 new and revised Hand Surgery codes. Some other changes to come will be category II and category III codes. More changes are occurring as this is written, and the best advice is to stay tuned. It is obvious to the authors that coding is mainly for reimbursement purposes. The orthopedic surgeon must remain vigilant and must not pass this task on to someone else. Ignorance of coding methods is not an excuse [2]. We must all watch carefully and speak up when necessary. In this day of decreasing reimbursement, we can all increase our revenue stream without working any harder if we code our work properly, completely, and promptly.

American Medical Association↗

Receptive field organization of bipolar and amacrine cells in the goldfish retina.

1. Intracellular recordings were made from bipolar and amacrine cells in the isolated goldfish retina. Cells were identified mainly from their response patterns to a spot and an annulus in reference to the knowledge obtained from the previous work of intracellular Procion Yellow injection. Using white light and monochromatic lights receptive field organization of recorded cells were analysed.2. All bipolar cells had a centre-surround organization in their receptive fields. The field centre was estimated to be 100-200 mum in diameter, and the surround 1-1.5 mm.3. Bipolar cells were classified into two types according to the response properties to monochromatic lights. Opponent colour cells received inputs from red and green cones, responding with red on-centre, red and green off-surround or vice versa. Cells without colour coding received input from red cones both in the field centre and the surround. In these cells the centre and the surround were well balanced.4. Amacrine cells were also classified into two types, a sustained type and a transient type. The sustained type amacrine cells responded with a steady potential change and were colour coded. They were hyperpolarized by red and depolarized by green light. The transient type amacrine cells responded with transient depolarization at on and off of light flashes. They received input chiefly from red cones and were not colour coded. Both types of amacrine cells showed a large spatial summation in an area over 2.5 mm; centre-surround antagonism was not seen.5. Comparing the size of the receptive field with anatomy, especially with the size of dendritic spread, the field centre of bipolar cells agreed in size with their dendritic spread. Bipolar cell surround clearly exceeded its dendritic field. Since the response properties of the bipolar cell surround was mimicked most closely by the receptive field of external horizontal cells, the input to the bipolar cell surround is thought to be mediated by external horizontal cells.6. By comparing receptive field properties of various retinal cells it is suggested that both the opponent colour bipolar cells and the colour coded amacrine cells converge on to the double opponent ganglion cells.

Animals↗

Anatomical correlates of the passive properties underlying the developmental shift in the frequency map of the mammalian cochlea.

As the cochlea develops, the cells in the basal cochlea become sensitive to progressively higher frequencies. To identify features of cochlear morphology that may underlie the place code shift, measurements of infant and adult gerbil cochleas were made at both the light and electron microscopic levels. The measurements included areas of the cochlear duct, basilar membrane, and organ of Corti, height and width of the basilar membrane, thickness of the tympanic cover layer, thickness of the upper and lower basilar membrane fiber bands, and optical density of the basilar membrane. The results indicated that basilar membrane dimensions do not change as the place code shifts and that regions that code for the roughly the same frequency (e.g., approximately 11.2 kHz) at different ages can have basilar membranes of very different dimensions. In contrast, the size of the organ of Corti and the thickness of fiber bands inside the basilar membrane do change in ways consistent with the shift in the frequency map.

Acoustic Stimulation↗

[Hereditary changes in gene activity as 1 of the causes of phenotypic heterogeneity in 8-azaguanine-resistant Chinese hamster cells (CHO-K1)].

Eight Chinese hamster clones (CHO-K1) growing at the 30 mg/ml concentration of 8-azaguanine (AG) were studied. Clones were differentiated by their resistance to AG and to 6-thioguanine, by their plating efficiency on HAT medium, and by the level of hypoxantine incorporation in cells. The differences in phenotypic properties were shown to be associated with variability in hypoxanthine-guanine phosphoribosyltransferase (HPRT) activity. HPRT Michaelis constant (KM) for hypoxanthine and phosphoribosylpyrophosphate, and maximal reaction rate (Vm) offered considerable differences between all the resistant clones and sensitive cells. The only possible reason of these differences is a change in the HPRT coding locus. According to the results of the analysis of B15-4b-4 subclones, phenotypic and HPRT activity differences are also connected with each other; however, all subclones have the same KM of HPRT as that of the parental clone. So, differences in HPRT activity (and in Vm) may reflect changes in the HPRT content in cells of subclones. Hence, phenotypic heterogeneity of AG-resistant clones is determined by the interaction of mutational changes in the HPRT locus, and hereditable changes of genetic activity, responsible for variation of HPRT quantity in cells.

Animals↗

Fifth mutation in human immunodeficiency virus type 1 reverse transcriptase contributes to the development of high-level resistance to zidovudine.

It is recognized that high-level resistance to 3'-azido-3'-deoxythymidine (AZT, zidovudine, or Retrovir) is conferred by the presence of four mutations in the human immunodeficiency virus (HIV) reverse transcriptase [RT; deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed), EC 2.7.7.49] coding sequence. However, a number of clinical isolates have been observed that exhibit high-level resistance but contain only three of the four identified mutations (Asn-67, Arg-70, and Tyr-215). Construction of a molecular clone with this genotype gave rise to only a partially resistant virus, raising the possibility that an additional mutation existed in some clinical isolates. Using an HIV marker rescue system, we have mapped and identified a fifth mutation conferring resistance to zidovudine, namely, methionine to leucine at codon 41 of HIV RT. An infectious molecular clone containing this mutation together with three previously identified mutations in the RT coding sequence yielded highly resistant HIV after transfection of T cells. Direct detection of the fifth mutation in DNA samples from cocultured peripheral blood lymphocytes by the PCR revealed that it occurred relatively early in the development of zidovudine resistance. However, this mutation was only detected after the appearance of the codon 215 change in the RT coding sequence. Identification of this mutation in addition to the other known mutations conferring resistance enables rapid and direct correlation between an RT genotype and sensitivity of the virus.

Amino Acid Sequence↗

[The patient record form in psychiatry: nomenclature of the types of management].

The patient form (PF) is a data carrier in mental health, established by the French General Department of Health to improve the annual report of each psychiatric sector, the assessment of the care given and the patients involved. We suppose that despite of national efforts to standardize the use of the PF, in practice are noticed: 1) different operative senses given to the codes of care; 2) a hierarchical system of treatments and a counting far from being unequivocal. This study undertaken in Centre Hospitalier Spécialisé de Maison Blanche investigates and compares: 1) the different operative senses given to the codes of care; 2) the use of these codes to transcribe and to count psychiatric treatments. These goals were fulfilled by a strictly anonymous questionnaire survey that ensures an analysis of the replies individually, in relation to occupational groups and to psychiatric sectors. In particular, all the psychiatrists, the nurse supervisors and the medical secretaries who worked in the hospital for at least 9 months, including 6 months at least in their current sector at the time of the survey, in the previous calendar year were concerned. Altogether that comes to 207 subjects. The administrative staff and the employees of the Medical Information Department were not involved. Upon 207 questionnaires, 58 replies were sent back i.e. a general reply rate of 28.02 +/- 6.12%. The secretaries took a more active part in the survey: 43.06 +/- 11.44% (31/72) significantly higher than the general rate (p = 0.03). The results show that regardless of the occupational groups neither the coding of treatments nor their counting are carried out the same way in different sectors respectively 70.69 +/- 11.71% and 77.59 +/- 10.73%. The operative senses of some codes like CO, AT, AP, AJ vary a lot. Sometimes the multiplicity of treatments coming under a code lead to these changes. At other times local initiatives explain the divergences. When senses are unequivocal, the hierarchical system of treatments is rather a problem. So, in case of several treatments the same day, the study makes obvious: 1) a giving up of the hierarchical system and as a result, the one of the incompatibility between some codes; 2) the coding and the count of as many as possible services the same day. The outpatient care is the 3rd of the three kinds of treatment according to the hierarchical system. It is the one for which codings and counts vary the most. It is essentially without hotel element. On the other hand accommodation twenty-four hours a day characterizes the full-time (inpatient) care. The part-time care, between both previous is a patchwork where predominates sometimes a mode of accommodation and sometimes a place for care. It is less accurate than the full-time care. The PF serves many purposes among which some are irreconcilable. It certainly allows a more accurate count of the patients who refer to a sector during a year period; but the various care and treatments are less assessed. The main subdivisions of the nomenclature of patient care maintain the dichotomy inpatient care/outpatient care. The links between the PF and the Information System Medicalization Program (ISMP) can no longer be concealed. Unfortunately, even the analysis of the data collected by the PF, for a financial assessment of the sectors, leads to very biased outcomes because of the qualitative and quantitative underestimation of care, treatments and all the necessary activities. The patient form looks like a multipurpose tool serving the minimum requirements for either descriptive, analytic or evaluative epidemiology; hospital management; planning; etc. Even though this multipurpose vocation could be a weakness, advantage could be also be taken of it to make a more efficient instrument, hence the need for some suggestions.

Ambulatory Care↗

Structure of the HLA-A*0204 antigen, found in South American Indians. Spatial clustering of HLA-A2 subtype polymorphism.

The primary structure of the HLA-A2 subtype A*0204 (isoelectric focusing variant A2.4) has been determined. cDNA encoding this subtype was amplified by the polymerase chain reaction. Four independent full-length cDNA clones encoding A*0204 were analyzed to obtain a consensus sequence for this subtype. A*0204 differs from A*0201 by a single nucleotide change of G to T through the coding regions, resulting in an Arg to Met change at position 97. This substitution accounts for the isoelectric focusing pattern of the subtype. The same change occurs in other HLA-A specificities in association with other changes in its vicinity. The absence of additional substitutions in A*0204 suggests that it could have arisen from A*0201 by point mutation, and that recurrent mutations may take place during HLA diversification. The spatial location of this change implies that A*0204 must be a functional variant. Comparison of its sequence with other HLA-A2 subtypes reveals that much of the HLA-A2 subtype polymorphism is generated by variations in four neighboring positions, including position 97, which are located in two adjacent beta-strands on the floor of the peptide binding site of the molecule.

Amino Acid Sequence↗

Detection of a point mutation in sphingolipid activator protein-1 mRNA in patients with a variant form of metachromatic leukodystrophy.

The lysosomal degradation of sulfatide requires the specific enzyme, arylsulfatase A, as well as a heat stable protein called sphingolipid activator protein-1 (SAP-1). While most patients with metachromatic leukodystrophy have defects in arylsulfatase A, some patients have defects in SAP-1. SAP-1 is coded for by a gene on human chromosome 10 that also codes for three other proposed SAP. Examination of the cDNA from two siblings with SAP-1 deficiency revealed a point mutation of nucleotide #650 (counting from the initiation ATG) which is in the SAP-1 coding domain. This C to T transition changed the codon from threonine (ACC) to one coding for isoleucine (ATC). This eliminated the only glycosylation site in mature SAP-1 and could explain the findings made at the protein level.

Base Sequence↗

Polymorphisms in the human homologue of the drosophila Indy (I'm not dead yet) gene.

Insertion of a P element in one copy of the Drosophila Indy gene results in a significant increase in Drosophila lifespan. In order to examine whether mutations or polymorphisms in the human Indy gene promoted human longevity, the Indy gene was sequenced in 13 subjects of age 90-99, 12 subjects between age 38-49 and 18 subjects <age 23. Three coding region polymorphisms resulting in an amino acid change, F62L, V80L and I550V, two silent coding region polymorphisms, A99A and I551I, and three intron polymorphisms, IVS2+10 C deletion, IVS9+40T/A and IVS10+38C/T were identified. The I550V polymorphism occurred in whites, Hispanics, Asians and African-Americans at allele frequencies of 0.3514, 0.5104, 0.4274 and 0.5375, respectively. The I550V polymorphism was genotyped in 2366 subjects and examined for its association with age and weight.

Adult↗

Three novel mutations in exon 21 encoding beta-cardiac myosin heavy chain.

Familial hypertrophic cardiomyopathy has a complex multigenic background. Previous work allowed to determine one of the gene loci responsible for this disease on chromosome 14 band q11-q12, and linked it to the alpha and beta-cardiac myosin heavy chains. In this study we demonstrate changes in exon 21, coding for beta-myosin heavy chain. We described 4 patients from different families with an unequivocal diagnosis of hypertrophic cardiomyopathy based on the clinical picture. Direct sequencing of exon 21 revealed the presence of 5 novel mutations. Two of the mutations in codons 771 and 781 revealed in our study did not result in any changes in amino acid sequence. The next three were as follows: in codon 782 (AGC > GAC) transition responsible for Ser-->Asp substitution; in codon 779 (GAG > TAG) mutation that results in replacement of Glu-->Stop; in codon 774 (GAG > GTG) which is expressed as substitution of Glu-->Val. These mutations are located close to mutations identified and described in the literature, so they are likely to cause similar symptoms.

Cardiomyopathy, Hypertrophic, Familial↗

[Signs of change in the affective context of dreams and the psychoanalytic process].

The author inquires whether dreams related in psychoanalysis can be indicator of curative change, and if so what affective conditions go to making this possible. To answer this question convincingly, he puts forward a new model of dream generation. It proceeds from the relation between cognitive elements, regulatory affective processes and species of interaction represented in individual dream situations. Such a model requires a new theory of mental representation, affective processes and memory. For precise analysis of change processes, Moser has recourse to a coding system for dream content. Finally he compares change processes in dreams with those in the psychoanalytic situation and suggests hypotheses on the extent to which changes in dreams can be indicators of changes in the psychoanalytic process.

Affect↗

Development and verification of a "virtual" cohort using the National VA Health Information System.

BACKGROUND: The VA's integrated electronic medical record makes it possible to create a "virtual" cohort of veterans with and without HIV infection to monitor trends in utilization, toxicity, and outcomes. OBJECTIVES: We sought to develop a virtual cohort of HIV-infected veterans by adapting an existing algorithm, verifying this algorithm against independent clinical data, and finally identifying demographically-similar HIV-uninfected comparators. RESEARCH DESIGN: Subjects were identified from VA administrative data in fiscal years 1998-2003 using a modified existing algorithm, then linked with Immunology Case Registry (ICR, the VA's HIV registry) and Pharmacy Benefits Management (centralized database of outpatient prescriptions) to verify accuracy of identification. The algorithm was modified to maximize positive predictive value (PPV) against ICR. Finally, 2 HIV-uninfected comparators were matched to each HIV-infected subject. RESULTS: Using a single HIV code, 30,564 subjects were identified (positive predictive value 69%). Modification to require >1 outpatient or 1 inpatient code improved the positive predictive value to 88%. The lack of confirmatory laboratory and pharmacy data for the majority of subjects with a single outpatient code also supported this change. Of subjects identified with the modified algorithm, 89% had confirmatory evidence. When the modified algorithm was applied to fiscal years 1997-2004, 33,420 HIV-infected subjects were identified. Two HIV-uninfected comparators were matched to each subject for an overall cohort sample of 100,260. CONCLUSIONS: In the HAART era, HIV-related codes are sufficient for identifying HIV-infected subjects from administrative data when patients with a single outpatient code are excluded. A large cohort of HIV-infected subjects and matched comparators can be identified from existing VA administrative datasets.

Adult↗

Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes.

Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes.

Databases, Genetic↗

Cortical FMRI activation to sequences of tones alternating in frequency: relationship to perceived rate and streaming.

Human listeners were functionally imaged while reporting their perception of sequences of alternating-frequency tone bursts separated by 0, 1/8, 1, or 20 semitones. Our goal was to determine whether functional magnetic resonance imaging (fMRI) activation of auditory cortex changes with frequency separation in a manner predictable from the perceived rate of the stimulus. At the null and small separations, the tones were generally heard as a single stream with a perceived rate equal to the physical tone presentation rate. fMRI activation in auditory cortex was appreciably phasic, showing prominent peaks at the sequence onset and offset. At larger-frequency separations, the higher- and lower-frequency tones perceptually separated into two streams, each with a rate equal to half the overall tone presentation rate. Under those conditions, fMRI activation in auditory cortex was more sustained throughout the sequence duration and was larger in magnitude and extent. Phasic to sustained changes in fMRI activation with changes in frequency separation and perceived rate are comparable to, and consistent with, those produced by changes in the physical rate of a sequence and are far greater than the effects produced by changing other physical stimulus variables, such as sound level or bandwidth. We suggest that the neural activity underlying the changes in fMRI activation with frequency separation contribute to the coding of the co-occurring changes in perceived rate and perceptual organization of the sound sequences into auditory streams.

Acoustic Stimulation↗