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An isolate of Aspergillus flavus used to reduce aflatoxin contamination in cottonseed has a defective polyketide synthase gene.

Contamination of certain foods and feeds with the highly toxic and carcinogenic family of Aspergillus mycotoxins, the aflatoxins, can place a severe economic burden on farmers. As one strategy to reduce aflatoxin contamination, the non-aflatoxin-producing A. flavus isolate AF36 is currently being applied to agricultural fields to competitively exclude aflatoxin-producing Aspergillus species. We now show that the polyketide synthase gene (pksA) required for aflatoxin biosynthesis in AF36, and in other members of the same vegetative compatibility group, possesses a nucleotide polymorphism near the beginning of the coding sequence. This nucleotide change introduces a premature stop codon into the coding sequence, thereby preventing enzyme production and aflatoxin accumulation.

Aflatoxins↗

Characterisation of the dihydrofolate reductase-thymidylate synthetase gene from human malaria parasites highly resistant to pyrimethamine.

To investigate the genetic basis of drug resistance in human malaria parasites, we have sequenced the entire dihydrofolate reductase thymidylate synthetase DHFR-TS bifunctional gene from the highly pyrimethamine-resistant K1 isolate of Plasmodium falciparum. The protein is predicted to consist of 607 amino acids (aa), (71,685 Da), with an N-terminal methionine encoded by the second start codon of the open reading frame. Compared to the sequence from drug-sensitive parasites, there are two nucleotide changes in the coding region which bring about a substitution of Arg for Cys at aa position 59 and Asn for Thr at aa position 108. Both changes occur in regions of the DHFR domain involved in inhibitor and cofactor binding and are hence strongly implicated in drug resistance. The gene is present as a single copy in both K1 and drug-sensitive FCR3 isolates, and is assigned to chromosome 4. Codon usage follows the pattern observed in that of malarial surface antigen genes, with the exception fo codons corresponding to Val and Pro. The Asn and Lys contents of the predicted protein are exceptionally high, these residues being particularly concentrated in the DHFR and junction domains.

Amino Acid Sequence↗

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

Comparative sequence analysis has facilitated the discovery of protein coding genes and important functional sequences within proteins, but has been less useful for identifying functional sequence elements in nonprotein-coding DNA because the relatively rapid rate of change of nonprotein-coding sequences and the relative simplicity of non-coding regulatory sequence elements necessitates the comparison of sequences of relatively closely related species. We tested the use of comparative DNA sequence analysis to aid identification of promoter regulatory elements, nonprotein-coding RNA genes, and small protein-coding genes by surveying random DNA sequences of several Saccharomyces yeast species, with the goal of learning which species are best suited for comparisons with S. cerevisiae. We also determined the DNA sequence of a few specific promoters and RNA genes of several Saccharomyces species to determine the degree of conservation of known functional elements within the genome. Our results lead us to conclude that comparative DNA sequence analysis will enable identification of functionally conserved elements within the yeast genome, and suggest a path for obtaining this information.

Base Sequence↗

The composition of coding joints formed in V(D)J recombination is strongly affected by the nucleotide sequence of the coding ends and their relationship to the recombination signal sequences.

V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of V(D)J recombination. In this study, we have tested the effect of small changes in coding-end nucleotide composition on the frequency of coding- and signal joint formation. Furthermore, we have determined the sequences of coding joints resulting from recombination of coding ends with different compositions. We found that the presence of two T nucleotides 5' of both RSSs, but not a single T, reduces the frequency of signal joint formation, i.e., interferes with the cleavage stage of V(D)J recombination. However, coding-joint processing is sensitive even to a single T. Both the sequence of the coding ends and the particular RSS (12-mer or 23-mer) with which the coding end is associated affect the final composition of the coding joints. Thus, the presence of P nucleotides, the conservation of one undeleted coding end, the formation of joints without any deletions, and the template-dependent insertion of nucleotides are strongly influenced by the coding-end nucleotide composition and/or RSS association. The implications of these results with respect to the processing of coding ends are discussed.

Animals↗

A mutation of the p63 gene in non-syndromic cleft lip.

Mutations in the p63 gene (TP63) underlie several monogenic malformation syndromes manifesting cleft lip with or without cleft palate (CL/P). We investigated whether p63 mutations also result in non-syndromic CL/P. Specifically, we performed mutation analysis of the 16 exons of the p63 gene for 100 Thai patients with non-syndromic CL/P. In total, 21 variant sites were identified. All were single nucleotide changes, with six in coding regions, including three novel non-synonymous changes: S90L, R313G, and D564H. The R313G was concluded to be pathogenic on the basis of its amino acid change, evolutionary conservation, its occurrence in a functionally important domain, its predicted damaging function, its de novo occurrence, and its absence in 500 control individuals. Our data strongly suggest, for the first time, a causative role of a heterozygous mutation in the p63 gene in non-syndromic CL/P, highlighting the wide phenotypic spectrum of p63 gene mutations.

Child, Preschool↗

Towards standardized measurement of adverse events in spine surgery: conceptual model and pilot evaluation.

BACKGROUND: Independent of efficacy, information on safety of surgical procedures is essential for informed choices. We seek to develop standardized methodology for describing the safety of spinal operations and apply these methods to study lumbar surgery. We present a conceptual model for evaluating the safety of spine surgery and describe development of tools to measure principal components of this model: (1) specifying outcome by explicit criteria for adverse event definition, mode of ascertainment, cause, severity, or preventability, and (2) quantitatively measuring predictors such as patient factors, comorbidity, severity of degenerative spine disease, and invasiveness of spine surgery. METHODS: We created operational definitions for 176 adverse occurrences and established multiple mechanisms for reporting them. We developed new methods to quantify the severity of adverse occurrences, degeneration of lumbar spine, and invasiveness of spinal procedures. Using kappa statistics and intra-class correlation coefficients, we assessed agreement for the following: four reviewers independently coding etiology, preventability, and severity for 141 adverse occurrences, two observers coding lumbar spine degenerative changes in 10 selected cases, and two researchers coding invasiveness of surgery for 50 initial cases. RESULTS: During the first six months of prospective surveillance, rigorous daily medical record reviews identified 92.6% of the adverse occurrences we recorded, and voluntary reports by providers identified 38.5% (surgeons reported 18.3%, inpatient rounding team reported 23.1%, and conferences discussed 6.1%). Trained observers had fair agreement in classifying etiology of 141 adverse occurrences into 18 categories (kappa = 0.35), but agreement was substantial (kappa > or = 0.61) for 4 specific categories: technical error, failure in communication, systems failure, and no error. Preventability assessment had moderate agreement (mean weighted kappa = 0.44). Adverse occurrence severity rating had fair agreement (mean weighted kappa = 0.33) when using a scale based on the JCAHO Sentinel Event Policy, but agreement was substantial for severity ratings on a new 11-point numerical severity scale (ICC = 0.74). There was excellent inter-rater agreement for a lumbar degenerative disease severity score (ICC = 0.98) and an index of surgery invasiveness (ICC = 0.99). CONCLUSION: Composite measures of disease severity and surgery invasiveness may allow development of risk-adjusted predictive models for adverse events in spine surgery. Standard measures of adverse events and risk adjustment may also facilitate post-marketing surveillance of spinal devices, effectiveness research, and quality improvement.

Humans↗

Increase in hospitalisation for childhood asthma.

Asthma admissions among children under 15 years of age have increased nearly three-fold over the period 1959-73. The possible reasons for this increase have been examined using available data supplemented by the results of a special study of hospital disease indexes and case notes. Changes in diagnostic coding and trends in diagnostic fashion do not appear to be important. Part of the increase may be due to an increase in readmission rates. Changes in admission criteria resulting from changes in therapy, organisation of care, and illness behaviour have been considered. However, on present evidence an increase in morbidity cannot be excluded, and this could be investigated by repeat prevalence surveys of schoolchildren. If morbidity remains unchanged, admission policies for children with asthma should be reviewed.

Adolescent↗

Asthma mortality: another opinion--is it a matter of life and ... bread?

There is a general consensus that the mortality rates for asthma in much of the developed world have been increasing for the past 10-15 years. This has occurred despite an improved information base regarding diagnosis and management as well as the development of novel and more effective therapeutic modalities. Several explanations have been proposed for this increase, including a statistical artifact based on a change in the coding criteria for asthma from the International Classification of Diseases Version 8 (ICD-8) to ICD-9, worsened pollution, delays in seeking medical help, behavioral changes, deficits in asthma education of both patients and primary care providers, toxicity of beta agonists, and noncompliance with medications. We suggest that although all of these are potential etiological factors, there may exist still another major etiological risk. There have been dramatic changes in our eating habits and food preparation. In general, we eat less total calories, more meals outside the home, and more refined or prepared foods. With the emphasis on reducing the intake of saturated fats and cholesterol, we eat more polyunsaturated fats both by choice and secondary to manufacturers' attempts to improve the appeal of foods to health-conscious government and the public. The drive to remove animal fats and cholesterol from our diet has resulted in the replacement of animal fats with vegetable oil in food manufacture, fast-food frying, and even home preparation. One result of these dietary habits has been a doubling from 8 to 15% of the percentage of the polyunsaturated linoleic acid in body fat. We postulate that this, and other nutritional changes, will render asthma a more difficult syndrome to manage and will contribute adversely to the inflammatory abnormalities in airways.

Adrenergic beta-Agonists↗

Heterogeneous expression of glycoprotein Ib, IX and V in platelets from two patients with Bernard-Soulier syndrome caused by different genetic abnormalities.

Bernard-Soulier syndrome (BSS) is a rare inherited bleeding disorder, which is caused by deficiency or decrease of the platelet GPIb/IX/V complex. Analysis of two patients with BSS by flow cytometry of the blood revealed different expression patterns of the components of the GPIb/IX/V complex. In case 1, GPIX was completely absent but residual amounts of GPIb alpha and GPV were detectable; in case 2, GPIb alpha was completely absent. We amplified the coding regions of GPIb alpha, GPIb beta, GPV, and GPIX from the patients' genomic DNA with the polymerase chain reaction (PCR) and sequenced the PCR products. in case 1, we identified a point mutation in the GPIX coding region that changes the codon for tryptophan-126 (TGG) to a nonsense codon (TGA). In case 2, we found a deletion of nucleotide within seven adenine repeats at the position of 1932 to 1938 in the coding region of GPIb alpha, which causes a frame shift that results in 58 altered amino acids and a premature stop codon. These genetic changes alter the transmembrane domain of GPIX or GPIb alpha and, therefore, would prevent proper insertion of the proteins in the plasma membrane. Thus, abnormality of a single component protein (GPIX or GPIb alpha) alters the assembly of the GPIb/IX/V complex and causes heterogeneous surface expression of GPIb alpha, GPV and GPIX.

Adult↗

Changes in steady-state levels of mRNAs coding for type IV collagen, laminin and fibronectin following capillary basement membrane thickening in human adult onset diabetes.

The development of capillary basement membrane thickening has been linked to microvascular changes known to occur in tissues of patients with type II diabetes. Previous evidence has suggested that capillary basement membrane thickening is due to increased basement membrane synthesis. In this study, skin samples from 8 diabetic patients with confirmed capillary basement membrane thickening and 7 non-diabetic controls were used to assess steady state levels of mRNAs coding for several basement components including pro alpha 1(IV) collagen, laminin and fibronectin. Total RNA was extracted from abdominal skin samples and levels of mRNAs coding for the basement membrane components laminin, fibronectin and pro alpha 1(IV) collagen, a fibrillar collagenous protein, pro alpha 1(I) collagen and an intracellular polypeptide, gamma-actin, were determined by dot blot hybridization analysis. While there were no changes of steady state levels of pro alpha 1(I) collagen mRNA and laminin mRNA, a significant reduction was noted in the quantitative recovery of mRNA levels for pro alpha 1(IV) collagen, gamma-actin and fibronectin in total RNA isolated from the skin of diabetic patients. This reduction in levels of mRNAs coding for basement membrane components contrasts with pathological confirmation of an accumulation of endothelial capillary basement membrane in skin from diabetic patients and suggests that basement membrane thickening arises more as a consequence of reduced basement membrane degradation than elevated synthesis of basement membrane components.

Aged↗

Age-related loss of the GABA synthetic enzyme glutamic acid decarboxylase in rat primary auditory cortex.

Age-related changes within the auditory brainstem typically include alterations in inhibitory neurotransmission and coding mediated by GABA and glycinergic circuits. As part of an effort to evaluate the impact of aging on neurotransmission in the higher auditory centers, the present study examined age-related changes in the GABA synthetic enzyme, glutamic acid decarboxylase (GAD), in rat primary auditory cortex (AI), which contains a vast network of intrinsic and extrinsic GABAergic circuits throughout its layers. Message levels of the two GAD isoforms found in brain, GAD(65) and GAD(67), and GAD(67) protein levels were compared in young adult, middle-aged and aged rats using in situ hybridization and quantitative immunocytochemistry, respectively. For comparison, age-related GAD changes were also assessed in the parietal cortex and hippocampus. Significant age-related decreases in GAD(65&67) messages were observed in AI layers II-VI of aged rats relative to their young adult cohorts. The largest changes were identified in layer II (GAD(65): -26.6% and GAD(67): -40.1%). GAD(67) protein expression decreased significantly in parallel with mRNA decreases in all layers of AI. Adjacent regions of parietal cortex showed no significant GAD(67) protein changes among the age groups, except in layer IV. As previously described, GAD(67) message and protein levels in selected hippocampal regions were significantly reduced in aged rats. Age-related GAD reductions likely reflect decreases in both metabolic and pre-synaptic GABA levels suggesting a plastic down-regulation of normal adult inhibitory GABA neurotransmission. Consistent with the present findings, functional studies in primate visual cortex and preliminary studies in AI find coding changes suggestive of altered inhibitory processing in aged animals. An age-related loss of normal adult GABA neurotransmission in AI would likely alter temporal coding properties and could contribute to the loss in speech understanding observed in the elderly.

Aging↗

A proposed revision of current ICD-9-CM malnutrition code definitions.

Protein-energy malnutrition (PEM) is as common today in adult medical and surgical patients as it was when it was first identified more than 25 years ago. Under the current diagnosis-related group (DRG) payment system, malnutrition is considered a comorbidity or complicating condition. Thus, the identification and coding of malnutrition through the use of the International Classification of Diseases, ninth edition, Clinical Modification (ICD-9-CM) malnutrition codes can potentially change a patient's DRG and subsequently increase the amount of reimbursement a hospital receives. Unfortunately, the definitions for the current ICD-9-CM malnutrition diagnosis codes were developed principally in relation to clinical syndromes of primary PEM seen in pediatric age groups in less developed countries, rather than in relation to syndromes seen in hospitalized adult patients in industrialized societies. This discrepancy often leads to confusion and inconsistency when institutions attempt to code adult patients for malnutrition. Furthermore, inaccurate coding can result in inadequate reimbursement or rejection of a claim. Clearly, a separate description of the different forms of PEM seen in adults is needed not only for optimal application of nutrition support therapies but also for accurate medical records, quality assurance procedures, and reimbursement purposes. On the basis of 20 years of experience providing nutrition support to hospitalized adult patients, this article presents a schema developed at the Deaconess Hospital (Boston,Mass) that attempts to better define adult PEM using the ICD-9-CM malnutrition codes. The purpose of this article is to foster discussion and ultimately promote general agreement about a definition of adult PEM.

Aged↗

Genes involved in cell cycle G1 checkpoint control are frequently mutated in human melanoma metastases.

A common characteristic of cancer cells is unrestrained cell division. This may be caused by mutational changes in genes coding for components of cell cycle-controlling networks. Alterations in genes involved in G1 checkpoint control have been registered in many human tumours, and investigations from several laboratories show that such alterations, taken together, are the most frequent changes detected in cancer cells. The present paper describes mutational analysis by polymerase chain reaction-single-strand conformation polymorphism (PCR/SSCP) and nucleotide sequence analysis of the genes coding for the p15, p53 and N-ras proteins in 26 metastases from 25 melanoma patients. The registered mutation frequencies add together with previously registered mutations in p16 in the same patient samples to a substantial total frequency of 44% of patients with mutation in at least one of the investigated genes. These results show the occurrence of heterogeneous defects among components of the cell cycle controlling machinery in a human melanoma tumour sample collection and demonstrate that the total frequency of detected alterations increases with the number of cell cycle controlling genes included in the screening panel.

Carrier Proteins↗

Genetic code 1990. Outlook.

The genetic code is evolving as shown by 9 departures from the universal code: 6 of them are in mitochondria and 3 are in nuclear codes. We propose that these changes are preceded by disappearance of a codon from coding sequences in mRNA of an organism or organelle. The function of the codon that disappears is taken by other, synonymous codons, so that there is no change in amino acid sequences of proteins. The deleted codon then reappears with a new function. Wobble pairing between anticodons and codons has evolved, starting with a single UNN anticodon pairing with 4 codons. Directional mutation pressure affects codon usage and may produce codon reassignments, especially of stop codons. Selenocysteine is coded by UGA, which is also a stop codon, and this anomaly is discussed. The outlook for discovery of more changes in the code is favorable, and open reading frames should be compared with actual sequential analyses of protein molecules in this search.

Anaerobiosis↗

Parallelizing a molecular dynamics algorithm on a multiprocessor workstation using OpenMP.

The atomistic molecular dynamics program YASP has been parallelized for shared-memory computer architectures. Parallelization was restricted to the most CPU-time-consuming parts: neighbor-list construction, calculation of nonbonded, angle and dihedral forces, and constraints. Most of the sequential FORTRAN code was kept; parallel constructs were inserted as compiler directives using the OpenMP standard. Only in the case of the neighbor list did the data structure have to be changed. The parallel code achieves a useful speedup over the sequential version for systems of several thousand atoms and above. On an IBM Regatta p690+, the throughput increases with the number of processors up to a maximum of 12-16 processors depending on the characteristics of the simulated systems. On dual-processor Xeon systems, the speedup is about 1.7.

Journal Article↗

Bone mass effects of a BMP4 gene polymorphism in postmenopausal women.

The pathogenesis of osteoporosis involves both genetic and environmental factors. On the basis of linkage data suggesting gene effects on bone density at chromosome 14q and data locating the BMP4 gene to 14q, we performed a positional candidate study to examine a possible association of BMP4 gene polymorphisms, hip bone density (n = 1012) and fracture rates (n = 1232) in postmenopausal women (mean age 75). On genotype analysis of the three selected single nucleotide polymorphisms (SNP), the 6007C > T polymorphism was associated with total and intertrochanteric hip BMD and BMD was lower in the 32% of subjects homozygous for the C allele. This polymorphism codes for a nonsynonymous amino acid change with the T allele coding for valine, while the C allele codes for alanine. The difference in BMD was 3.1% (TT vs. CC) and 2.3% (CT versus CC) for the total hip (P = 0.023), and 3.7% (TT vs. CC) and 2.8% (CT versus CC) for the intertrochanter site (P = 0.012). Haplotype analysis demonstrated 6 haplotypes of frequency greater than 2%. A major haplotype defined by G-C-T alleles in SNPs -5826G > A, 3564C > T and 6007C > T respectively, showed association with high bone mass. No SNP showed association with fracture rates. We conclude that a polymorphism found in the BMP4 gene, affecting amino acid sequence, is associated with hip bone density in postmenopausal women, presumably via regulation of anabolic effects on the skeleton.

Aged↗

Dolichol phosphate mannose synthase (DPM1) mutations define congenital disorder of glycosylation Ie (CDG-Ie)

Congenital disorders of glycosylation (CDGs) are metabolic deficiencies in glycoprotein biosynthesis that usually cause severe mental and psychomotor retardation. Different forms of CDGs can be recognized by altered isoelectric focusing (IEF) patterns of serum transferrin (Tf). Two patients with these symptoms and similar abnormal Tf IEF patterns were analyzed by metabolic labeling of fibroblasts with ¿2-(3)Hmannose. The patients produced a truncated dolichol-linked precursor oligosaccharide with 5 mannose residues, instead of the normal precursor with 9 mannose residues. Addition of 250 microM mannose to the culture medium corrected the size of the truncated oligosaccharide. Microsomes from fibroblasts of these patients were approximately 95% deficient in dolichol-phosphate-mannose (Dol-P-Man) synthase activity, with an apparent K(m) for GDP-Man approximately 6-fold higher than normal. DPM1, the gene coding for the catalytic subunit of Dol-P-Man synthase, was altered in both patients. One patient had a point mutation, C(274)G, causing an R(92)G change in the coding sequence. The other patient also had the C(274)G mutation and a 13-bp deletion that presumably resulted in an unstable transcript. Defects in DPM1 define a new glycosylation disorder, CDG-Ie.

Brain Diseases, Metabolic, Inborn↗

Interventional pain management: evolving issues for 2003.

The new millennium has seen the introduction of an array of new Current Procedural Terminology(R) (CPT) codes and the expansion of interventional techniques. Among the many issues of interest to physicians practicing interventional pain management in 2003 are CPT coding, correct coding issues, and utilization. The CPT developed and updated by the American Medical Association, is the most important and commonly used coding system for interventional pain physicians in the United States. A recent development in the CPT system has been to include Category I, Category II, and Category III CPT codes. Inclusion of a code in Category I is generally based on the procedure being consistent with contemporary medical practice and being performed by many physicians in clinical practice in multiple locations. In contrast, CPT Category III, also known as emerging technology codes, is a set of temporary codes for emerging technology, services, and procedures. There have been many new codes since 2000, along with changes in the definitions of the codes and vignettes. In order for the correct coding initiative to be effective, it is essential that the coding describes what actually transpires at each patient encounter. When multiple procedures are performed at the same session, the procedure and post-procedure work do not have to be repeated for each procedure, and, therefore, a comprehensive code describing the multiple services commonly performed together can be used. Thus, many activities which are integral to a procedure are considered as generic activities and are assumed to be included as acceptable medical/surgical practice and, while they couldn't be performed separately, they should not be considered as such when a code narrative is defined. Under this initiative, almost all interventional techniques are affected. The utilization of interventional techniques in the modern era is the final issue. Utilization has been increasing gradually. Thus, it is important for interventional pain physicians to understand the utilization patterns across the nation and for various techniques. This review will discuss the issues of CPT coding, correct coding, and utilization as they pertain to interventional techniques.

Journal Article↗