Differentiation of 23-S ribosomal RNA cistrons from 16-S ribosomal RNA cistrons in Escherichia coli by the sequence complementarity test.
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The diagnosis of polyarteritis nodosa. I. A literature-based decision analysis approach.
We investigated diagnostic testing in polyarteritis nodosa (PAN) by calculating, from published data, the sensitivity and specificity of visceral angiography and muscle, nerve, testicle, kidney, and liver biopsy. Test sequence strategies were constructed by Bayesian inference using a computer program written for this purpose. Test sequences were compared with an aggressive strategy consisting of repeated tests until there was a positive finding or until the available tests were exhausted, and a conservative strategy consisting of 1 biopsy procedure plus angiography. The Bayesian analysis agreed most closely with the conservative approach for most prior probabilities (degree of suspicion) that a patient had PAN. The aggressive strategy had an overall sensitivity of 90% and specificity of 91%, whereas the conservative strategy was 85% sensitive and 96% specific. Furthermore, the aggressive strategy was more costly ($2,986 versus $1,961) and had a higher rate of morbidity (3.8 versus 2.7 days of hospitalization per patient evaluated) than did the conservative strategy. The mortality rates of both strategies were equivalent (approximately 0.05 deaths per hundred patients evaluated). The per-case cost of diagnosis increased as prevalence decreased, and at 10% prevalence, the aggressive strategy cost more than $17,000 per case diagnosed. Sensitivity analysis revealed that the strategies were moderately affected by the test characteristics, within reasonable assumptions, but that the differences in conservative and aggressive approaches remained. Thus, our analysis based on available data and the assumption of test independence suggests that the preferred diagnostic evaluation of patients with symptoms suggestive of PAN consists, in most cases, of a single biopsy procedure, with angiographic evaluation if necessary.
Costs and Cost Analysis↗
Effects of intensity variations on auditory processing in aphasia. II. Different intensities at each ear.
A neurologic extinction model was applied to the auditory-processing disorders evidenced by 10 persons with aphasia. This model suggests that messages travel faster to the intact hemisphere, where they are more differentiated and articulated, than to the affected hemisphere. This leads to extinction and interference of the message. To overcome this extinction, the stimulus intensity was raised by 15 or 30 dB to one ear at a time. The stimuli were a cortical auditory-evoked response (AER) measure, a nonverbal intensity sequencing test (NVIST), a minimally varied phoneme-in-word discrimination and sequencing test (MVPT). and a semantic-syntactic level test (RTT). The results suggest that intensity can be traded for time in quantities large enough to overcome the extinction interference of auditory stimuli. Although some statistically significant results and meaningful trends toward improved performance were evident on the NVIST and the MVPT, a unilateral increase of stimulus intensity did not prove to be a potent mechanism for improving auditory comprehension. Sentence length material was not affected in either direction by selective amplification. The role of the left ear/right hemisphere as a facilitator of processing for linguistic and nonlinguistic material was suggested by the results of this study.
Adult↗
Deoxyribonucleic acid sequence homologies among bacterial insertion sequence elements and genomes of various organisms.
Plasmid and phage deoxyribonucleic acid (DNA) harboring bacterial insertion sequence (IS) elements IS1, IS2, and IS5 were characterized and used as probes to detect homologous sequences in various procaryotic and eucaryotic genomes. The hybridization method used permits the detection of sequences partially homologous to the elements. Hybridization of the IS-containing probes to each other revealed a region of limited homology between IS1 and IS2. Homologous sequences were then detected by computer analysis of the published IS1 and IS2 nucleotide sequences. The homologous sequence contains a tandemly repeated tetranucleotide sequence which resembles the repeated sequence at the hot spot for spontaneous mutations in the lacI gene (P. J. Farabaugh, U. Schmeissner, M. Hofer, and J. Miller, J. Mol. Biol. 126:847-863, 1978). Homology between the IS elements and various genomes was determined by hybridizing labeled DNA containing IS1, IS2, and IS5 sequences to Southern blots of chromosomal DNA cleaved with restriction endonucleases. IS1 and IS5 appear limited to the enteric bacteria, whereas IS2 sequences can also be detected in Pseudomonas putida, Pseudomonas aeruginosa, and Serratia marcescens. Bacteria which appear not to possess extrachromosomal elements, e.g., Caulobacter crescentus, did not show homology with any insertion sequences tested. In addition, sequences homologous to IS1, IS2, or IS5 were not detected in Saccharomyces cerevisiae, Dictyostelium discoideum, or calf thymus DNA.
Bacteria↗
Streptococcal throat infection: calculation of test standards and a comparison between an antigen detection test and culture.
The standard minimum sensitivity (94%) and minimum specificity (89%) of a group A streptococcus (GAS) test were calculated, assuming that no more than 10% false positive and no more than 2% false negative test results should be allowed. The clinical judgement of the need for immediate antibiotic treatment in tonsillitis/pharyngitis was an unreliable indicator of a GAS aetiology, 20-29% of the results being false positive and 2-10% false negative. The rapid antigen detection test Tandem Icon Strep A was not sensitive enough to be used as a single test, though it was specific enough. The sensitivity of culture almost reached the standard demand. Two combinations of rapid test and culture (sequence testing) were superior to the rapid test, but were not significantly better than culture.
Anti-Bacterial Agents↗
A parallel computing approach to genetic sequence comparison: the master-worker paradigm with interworker communication.
We have implemented a parallel version of a dynamic programming biological sequence comparison algorithm to study the potential applicability of using parallel computers for genetic sequence comparisons. Our parallel program is built using C-Linda, a machine-independent parallel programming language, and was tested on both a 10 CPU Sequent Symmetry and a 64 CPU Intel Hypercube. C-Linda implements a shared associative memory model, "tuple space," through which multiple processes can communicate and coordinate control. In our master-worker (MW) parallel implementation, a master process creates several worker processes, extracts a test sequence and multiple library sequences from a database and stores them in tuple space. Each worker reads the test sequence and then repeatedly extracts library strings from tuple space, performs pairwise sequence comparison using a local comparison algorithm to generate a similarity score, and returns the similarity scores to tuple space. The master collects the scores from tuple space and identifies the best match over all library sequences. We also implemented a method of global interworker communication to reduce the total search time by stopping those string comparisons that had no chance of improving on the current best match. Comparisons of the total run time, speedup, and efficiency were made for parallel and sequential versions of a basic MW implementation as well as versions with the global abort threshold.
Algorithms↗
Stiffness behaviour of trabecular bone specimens.
Trabecular bone specimens were tested by non-destructive technique with the purpose of investigating stiffness behaviour and optimizing stiffness determination. Cylindrical specimens (n = 25) were loaded repetitively (0.1 Hz, 30 cycles) by axial compression to 50% of predicted ultimate strength and finally compressed to failure. Analyses of single compression curves showed increasing stiffness (E') until a stress level about 50% of ultimate stress followed by decreasing stiffness. Curve fit analysis of the elastic part of the compression curve showed the best fit, when a second order polynomial was used (r = 0.94, p less than 0.001). The stiffness determined non-destructively at the 25% level of ultimate strength increased significantly to the tenth loading cycle followed by a steady state. The precision of stiffness determination as an average of five consecutive measurements at steady state was E' +/- less than 5% (95% confidence limits). A reproducibility test by repetition of the test sequence after 3 h rest showed qualitatively the same stiffness behaviour. The variation of stiffness determination between the two test sequences was +/- 27% at the first loading cycle falling to +/- 12% at steady state.
Bone and Bones↗
Opponent hues in visual masking.
Temporal interactions among opponent and non-opponent hues were investigated in a visual masking paradigm in which both backward and forward temporal sequences were employed. Subjective confidence ratings rather than identification thresholds alone served as response indicators for masking sequences. Results indicate that in the backward sequence (test stimulus followed by masking stimulus) a greater masking effect occurred when the stimuli were of non-opponent hue pairs (red-yellow, red-blue, green-yellow, green-blue) than when compared with opponent hue pairs (red-green, yellow-blue). For the forward sequence (test stimulus preceded by masking stimulus) the masking effect was reduced when compared with the backward sequence. These findings appear to reflect the presumed temporal and spatial antagonistic qualities of opponent hue processes as postulated in the Hering model of color vision.
Color↗
Interferon regulatory factor-1 (IRF-1) activates the synthetic IRF-1-responsive sequence (GAAAGT)4 in Saccharomyces cerevisiae.
In appropriate mammalian cells, interferon regulatory factor-1 (IRF-1) can activate the virus-responsive element of the IFN-beta promoter (VRE beta") or the synthetic oligonucleotide (GAAAGT)4. The latter contains two copies of the functional equivalent of PRDI, one of the regulatory domains of VRE beta". We prepared yeast strains containing an IRF-1 expression plasmid under the control of the galactose-inducible Gal1 promoter and a reporter plasmid with either (GAAAGT)4, VRE beta", or other test sequences placed upstream of a minimal promoter linked to the beta-galactosidase coding sequence. Upon induction of IRF-1 expression, the (GAAAGT)4-containing promoter was activated, but VRE beta" and all other sequences tested were inactive. Our results showed that IRF-1 belongs to a class of higher eukaryotic transcription factors that can interact with the yeast transcriptional machinery. Our findings also raised the question why the duplicate PRDI-like sequences in (GAAAGT)4 can be activated by IRF-1 synthesized in yeast, but not VRE beta", which also contains at least two PRDI-like sequences.
Base Sequence↗
Mutational analysis of the "slippery-sequence" component of a coronavirus ribosomal frameshifting signal.
The ribosomal frameshift signal in the genomic RNA of the coronavirus IBV is composed of two elements, a heptanucleotide "slippery-sequence" and a downstream RNA pseudoknot. We have investigated the kinds of slippery sequence that can function at the IBV frameshift site by analysing the frameshifting properties of a series of slippery-sequence mutants. We firstly confirmed that the site of frameshifting in IBV was at the heptanucleotide stretch UUUAAAC, and then used our knowledge of the pseudoknot structure and a suitable reporter gene to prepare an expression construct that allowed both the magnitude and direction of ribosomal frameshifting to be determined for candidate slippery sequences. Our results show that in almost all of the sequences tested, frameshifting is strictly into the -1 reading frame. Monotonous runs of nucleotides, however, gave detectable levels of a -2/+1 frameshift product, and U stretches in particular gave significant levels (2% to 21%). Preliminary evidence suggests that the RNA pseudoknot may play a role in influencing frameshift direction. The spectrum of slip-sequences tested in this analysis included all those known or suspected to be utilized in vivo. Our results indicate that triplets of A, C, G and U are functional when decoded in the ribosomal P-site following slippage (XXXYYYN) although C triplets were the least effective. In the A-site (XXYYYYN), triplets of C and G were non-functional. The identity of the nucleotide at position 7 of the slippery sequence (XXXYYYN) was found to be a critical determinant of frameshift efficiency and we show that a hierarchy of frameshifting exists for A-site codons. These observations lead us to suggest that ribosomal frameshifting at a particular site is determined, at least in part, by the strength of the interaction of normal cellular tRNAs with the A-site codon and does not necessarily involve specialized "shifty" tRNAs.
Base Sequence↗
Lesions of anterior thalamic nuclei impair acquisition of new and changing of preoperatively learnt active avoidance stereotypes.
Six-month-old male Long-Evans rats reproduced their preoperatively learnt active avoidance responses (CAR) in a Y-maze and in a jump test box after bilateral symmetric lesions of thalamic anterior ventral (AV) and anterior medial (AM) nuclei without significant changes. However, when the test sequence was changed in a way that transitions from high success probability (low error probability) to low success probability (high error probability) were taken into account, then problems with time limit and increased punishments were not overcome by lesioned rats. Transitions in the opposite direction were better mastered. All AV-AM rats were unable to acquire a new CAR stereotype in a W-like maze in which the first phase had a low success probability. Rats without lesions were rarely influenced by various test sequences. The lesioned rats showed purely arrest behaviour and did not develop learned helplessness in successless sessions and were transiently hyperactive in the open field test. The data support the hypothesis that the anterior thalamic nuclei as part of the Papez circuit participate in the analysis of success probability and preferent consolidation of correct responses, when stereotype behaviour has to be changed.
Animals↗
The effects of bradykinin and sequence-related analogs on the response properties of cutaneous nociceptors in monkeys.
The endogenous peptide bradykinin is found in plasma and inflammatory exudates and has been implicated as a chemical mediator of inflammatory pain and hyperalgesia. Two subtypes of bradykinin receptors, B1 and B2, have been described, and antagonists for the receptor subtypes have been synthesized. The bradykinin analogs [desArg9,Leu8]BK and DArg[Hyp3,DPhe7]BK have been reported to have antagonist activity at the B1 and B2 bradykinin receptors in smooth muscle, respectively. Behavioral studies in rats indicate that the bradykinin analogs can block the algesic effects of bradykinin. We wished to determine the effects of bradykinin and the bradykinin analogs (B1 and B2 analogs, respectively) on cutaneous nociceptors in the monkey. In addition, we wished to determine the type of bradykinin receptor that mediates the sensitizing effects of bradykinin. Recordings were made from single C-fiber and A-fiber nociceptive afferents (CMHs and AMHs) that innervated hairy skin. Heat sensitivity before and after the injections was determined with a heat test sequence consisting of stimuli that ranged, in 1 degree C increments, from 41 degrees to 49 degrees C. Intradermal injections of vehicle (neutral normal saline) failed to alter the heat response of CMHs. Bradykinin (10 nmol in 10 microliters) evoked activity in 6 of 10 CMHs and sensitized all the fibers to heat stimuli. After the bradykinin injection, the mean heat threshold of the CMHs decreased from 44 +/- 0.5 degrees to 42.7 +/- 0.5 degrees C (mean +/- SEM, p less than 0.02), and the total response to the heat test sequence increased by 87% (p less than 0.002). In a related psychophysical study in human volunteers, the same dose of bradykinin resulted in a comparable (115%) increase in ratings of pain (Manning et al., 1991). Bradykinin also evoked activity in 10 of 17 AMHs and sensitized 8 AMHs to heat stimuli. Bradykinin failed to alter the threshold for activation of CMHs to mechanical stimuli as measured by application of von Frey hairs to the receptive field. In contrast to bradykinin, intradermal injection of the B1 and B2 analogs (10 nmol in 10 microliters) evoked activity in 2 of 6 and 0 of 5 CMHs, respectively. A noteworthy finding was that both analogs enhanced the response of CMHs to heat stimuli by 50% (B1 analog, 1.5 +/- 0.1; B2 analog, 1.5 +/- 0.2). The B1 (n = 10) and B2 (n = 5) analogs did not evoke activity in any of the 15 AMHs tested.(ABSTRACT TRUNCATED AT 400 WORDS)
Afferent Pathways↗
Evaluation of orthogonal mechanical properties and density of human trabecular bone from the major metaphyseal regions with materials testing and computed tomography.
We evaluated the orthogonal mechanical properties of human trabecular bone from the major metaphyseal regions with materials testing and quantitative computed tomography (CT). The proximal tibia, distal femur, proximal femur, distal radius, and proximal humerus from fresh cadaver specimens between the ages of 55 and 70 years were excised and prepared for experimentation. The bones were embedded and scanned at 1 or 1.5 mm intervals on a Technicare HPS 1440 and GE 9800 CT scanner. After scanning, the bones were sectioned, producing 8-mm cubes of trabecular bone which were mechanically tested in uniaxial compression at a strain rate of 1%. The testing sequence consisted of preyield tests in two of the three orthogonal directions and failure in the third. After testing, the cubes were evaluated for apparent density and ash weight. The results of the study show that the strength and stiffness of trabecular bone varies significantly within metaphyseal regions and from metaphysis to metaphysis. The power and significance of relationships between density and modulus varied as a function of metaphyseal location. Both linear and nonlinear models were significant, suggesting that trabecular deformation occurs in response to both axial and bending loads. Finally, the need for architectural measures of trabecular bone to predict mechanical properties is emphasized.
Aged↗
A sequence of tests of minute human blood stains for human origin identification and ABO blood grouping.
A series of examinations is presented for human origin identification and ABO blood grouping of doubtful minute human blood stains. A blood-stained thread (0.5 cm in length) was first tested to identify human origin by microprecipitation method and then the ABO blood type was determined by both a modified absorption-elution test and a modified mixed agglutination. In the continuous tests, the maximum limits of positive reactions of the microprecipitation method, the modified absorption-elution test, and the modified mixed agglutination were 1:640, 1:160, and 1:2,560 diluted blood, respectively. A and B agglutinogens were more sensitively determined than H agglutinogen. Hemagglutinogens of blood stains on cotton threads were more easily detected than those of polyester ones.
ABO Blood-Group System↗
Sequence ability in parkinsonians, patients with frontal lobe lesions and patients who have undergone unilateral temporal lobectomies.
Patients in the early stages of Parkinson's disease were compared with patients who had sustained damage specific to either the frontal or temporal lobes and normal controls on a number of sequencing tests. These tests involved the reproduction of sequences of hand gestures, sequences tapped out on blocks, and sequences of digits. Only the groups with frontal lobe lesions or right temporal lobectomies were impaired on any of these tasks, though no group was impaired on all of the sequencing tasks.
Adolescent↗
Understanding recurrence in Mycobacterium avium complex pulmonary disease: genotypic strategies to support clinical decision-making.
Pulmonary disease caused by Mycobacterium avium complex (MAC-PD) is a chronic, recurrent disease, and its high recurrence rate after treatment makes clinical management difficult. Distinguishing whether recurrence is due to persistence of existing strains or reinfection with new strains is essential for establishing treatment strategies, preventing overuse of antimicrobials, and establishing infection control measures. According to reports, 54%-74% of MAC-PD recurrence is due to reinfection, which may be mainly related to environmental reservoirs such as household water supply. In this review, we present various clinical scenarios in which MAC-PD recurrence may occur and examine genotyping techniques as a strategy to distinguish and respond to them. From traditional methods such as IS1245-based restriction fragment length polymorphism, pulsed-field gel electrophoresis, and hsp65 and rpoB gene sequencing to high-resolution analysis techniques such as multilocus sequence testing and whole-genome sequencing, the latest molecular typing methods are comprehensively summarized. Integrating these genotype data into clinical settings, standardizing single-nucleotide polymorphism-based interpretation thresholds, and promoting the establishment of a global MAC strain database will make a substantial contribution to more accurately distinguishing the recurrence mechanisms of MAC-PD and establishing personalized treatment strategies.IMPORTANCEThe global burden of nontuberculous mycobacterial pulmonary disease (PD) is increasing, with Mycobacterium avium (MAC)-PD being the most prevalent and clinically challenging form. Its low treatment success rates, high frequency of recurrence, and persistent environmental exposure complicate both diagnosis and management. A critical clinical issue is determining whether recurrence represents true relapse, due to persistence of the original strain, or reinfection with a new strain, as this guides treatment and prevents overtreatment. Genotypic strategies capable of resolving strain-level differences can improve diagnostic accuracy, prevent misclassification, and ultimately support more informed treatment decisions. Therefore, integrating genotyping data into clinical workflows, standardizing single-nucleotide polymorphism thresholds, and establishing a global MAC strain database will not only support personalized treatment but also enhance the broader public health response to this disease.
Humans↗
Characterization of bacteriophage P1 library containing inserts of Drosophila DNA of 75-100 kilobase pairs.
A multiple-hit bacteriophage P1 library containing DNA fragments from Drosophila melanogaster in the size range 75-100 kb was created and subjected to a preliminary evaluation for completeness, randomness, fidelity, and clone stability. This P1 library presently contains 3840 individual clones, or approximately two genome equivalents. The library was screened with a small set of unique-sequence test probes, and clones containing the sequences have been recovered. In situ hybridization with salivary gland chromosomes indicates that the clones originate from the site of the probe sequences in the genome, and filter hybridization of restriction digests suggests that the clones are not rearranged in comparison with the genomic sequences. Approximately 1.7% of the clones contain sequences that hybridize with ribosomal DNA. A small subset of these clones was tested for stability by examination of restriction fragments produced after repeated subculturing, and no evidence for instability was found. The P1 cloning system has general utility in molecular genetics and may provide an important intermediate level of resolution in physical mapping of the Drosophila genome.
Animals↗
DNA-sequence and metal-ion specificity of the formation of *H-DNA.
The homopyrimidine-homopurine sequence d(CT/GA)22 undergoes, in the presence of zinc ions, transition to an altered DNA conformation (*H-DNA) which is neither H-DNA nor B-DNA. *H-DNA is characterized by a peculiar chemical reactivity pattern in which most of the polypyrimidine strand is hyperreactive to osmium tetroxide and the central part of the polypurine strand is sensitive to diethylpyrocarbonate. Formation of *H-DNA is specific of metal-ion. *H-DNA is detected in the presence of Zn++, Cd++ and Mn++. The efficiency on promoting the transition is in the order of Zn++ greater than Cd++ much greater than Mn++. Formation of *H-DNA is also specific of nucleotide sequence. From all the different homopolymeric sequences tested only the d(CT/GA)22 sequence showed the zinc-induced transition to *H-DNA. These results suggest that stabilization of *H-DNA involves the formation of a specific complex between the metal-ion and the nucleotide sequence. The biological relevance of these results is discussed in view of the important role that zinc ions play on many nucleic acids processes.
Base Sequence↗