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PubMed1973

Genetic analysis of bacteriophage Mu-induced flagellar mutants in Escherichia coli.

In previous work, at least 10 discrete cistrons involved in the synthesis of flagella in Escherichia coli were described. Six cistrons were located between his and uvrC on the genetic map. These were referred to as hag, flaA, flaB, flaC, flaD, and flaE. Four cistrons referred to as mot, flaG, flaH, and flaI were located between uvrC and aroD. In order to determine whether these genes are organized into transcriptional units, a series of Mu phage-induced flagellar mutants was studied. The mutant strains behaved as if they were carrying strong polar mutations. Of 228 independent Mu-induced mutants, 114 with mutations in the his-aroD region of the genetic map were tested by preparing partial diploid strains with episomes carrying a variety of previously defined mutations. The pattern of complementation that emerged indicated that cistrons flaB, flaC, and flaE form a transcriptional unit. Cistron flaO, defined in the course of this study, is also a member of this transcriptional unit. The order of transcription is B-C-O-E. flaA was found to be complex, and it included four cistrons, flaA, flaP, flaQ, and flaR, with the transcriptional order A-P-Q-R. Cistrons flaG and flaH are cotranscribed with the transcriptional order G-H. The remaining genes, flaD, flaI, hag, and mot do not belong to multicistronic transcriptional units. Complementation analysis suggested that the cheC locus is the same as cistron flaA.

Chromosome Mapping↗
PubMed1990

Mean arterial blood pressure changes in premature infants and those at risk for intraventricular hemorrhage.

Bedside microcomputer-derived, minute-to-minute mean arterial pressure (MAP) values during the first 48 hours of life were studied in 100 preterm babies with birth weight less than or equal to 1500 gm. In those babies (n = 72) with no periventricular-intraventricular hemorrhage (PV-IVH) or with grade 1 PV-IVH, the MAP values increased during the study period, with minute-to-minute variation and interval undulation. The MAP values in those with birth weight greater than 1000 gm were higher than in those of lower birth weight. Infants in whom grades 2 to 4 PV-IVH developed (n = 28) had consistently lower MAP values during the study period. Minute-to-minute variability, expressed as the average of the coefficients of variation at 15-minute intervals, did not differ between birth weight groups, nor did they differ between the PV-IVH group and their matched control subjects. However, those with PV-IVH spent a greater percentage of time, with a coefficient of variation greater than or equal to 13% or less than 3%, than their matched control subjects spent (p less than 0.005). This study provides reference data for MAP changes in premature babies. The observed MAP changes in those with PV-IVH lend support to a significant role for MAP alterations in the pathogenesis of PV-IVH.

Blood Pressure↗
PubMed2026

Development and evaluation of a one-pot RPA-Cas12a assay based on a primer-driven reverse screening strategy for preliminary screening of megalocytivirus-related viruses.

A primer-driven reverse-screening strategy was used to identify an RPA-Cas12a target suitable for the rapid preliminary screening of megalocytivirus-related viruses. The ISKNV reference genome NC_003494.1 was used as the initial template, and candidate amplification units were designed according to RPA primer-design requirements, primer physicochemical properties, and the availability of Cas12a protospacer-adjacent motif (PAM) sites and crRNA target sequences. Following preliminary amplification assessment, the retained candidate primers were aligned individually against 75 complete genome sequences of megalocytivirus-related viruses. Of these, 67 sequences met the predefined criteria for target-region integrity, primer-binding-site compatibility, and Cas12a recognition. Retrospective mapping to the reference genome located the candidate amplification region within ORF057L. Based on the resulting candidate detection unit, a one-pot RPA-Cas12a assay incorporating a commercially available lyophilized RPA amplification module was developed. Optimization showed that 400 nM reporter and 80 nM crRNA-1 provided relatively stable fluorescence output. A cut-off value of 1281.6 relative fluorescence units (RFU) was established as the mean plus three standard deviations of the endpoint fluorescence values obtained from 20 qPCR-negative samples. In analytical sensitivity testing, the assay generated fluorescence signals above the negative control at low plasmid copy numbers. However, because only a limited number of replicates were tested at these low template concentrations, these findings were not used to define a formal limit of detection. ISKNV, RSIV, and TRBIV samples tested positive, whereas the MRV sample produced an endpoint fluorescence value below the cut-off. Repeatability analysis of the same sample in six independent reactions yielded a coefficient of variation of 8.03%. Among the 39 samples examined, no discordant qualitative results were observed between the RPA-Cas12a assay and qPCR. These findings support the use of the ORF057L-targeted one-pot RPA-Cas12a assay as a rapid preliminary screening tool for megalocytivirus-related viruses. Nevertheless, its formal limit of detection, inter-batch stability, cross-reactivity with additional non-target pathogens, and clinical diagnostic performance require further evaluation.

Lyophilized RPA↗
PubMed1992

Waardenburg syndrome (WS) type I is caused by defects at multiple loci, one of which is near ALPP on chromosome 2: first report of the WS consortium.

Previous studies have localized the gene for Waardenburg syndrome (WS) type I to the distal portion of chromosome 2q, near the ALPP locus. We pooled linkage data obtained from 41 WS type I and 3 WS type II families which were typed for six polymorphic loci on chromosome 2q in order to refine the location of the WS locus (WS1) and evaluate the extent of genetic heterogeneity. In the course of this work, we developed diagnostic criteria for genetic and phenotypic studies. Our findings, based on two-locus and multilocus analysis using a linkage map established from reference pedigrees, suggest that there are two or more mutations causing WS, one of which (i.e., WS1) is located on chromosome 2q, between the ALPP and FN1 loci, at distances of 7.8 cM and 11.2 cM for each marker, respectively. The results also indicate that WS1 is responsible for the illness in approximately 45% of all families in this sample. However, the odds favoring this position over a location between ALPP and SAG are only 2:1 when alternate assumptions about the proportion of linked families are considered. We conclude that a more saturated map of this region of chromosome 2q, including highly polymorphic markers, will be needed to accurately distinguish linked families and, ultimately, isolate the mutant gene.

Alkaline Phosphatase↗
PubMed1988

Partial linkage map of chromosome 13q in the region of the Wilson disease and retinoblastoma genes.

Genetic linkage maps are useful tools for defining the location of disease genes. Previously published maps of human chromosome 13 have been incomplete and have had ambiguities of order in the vicinity of the Wilson disease (WND) and retinoblastoma (RB1) genes. We have defined a six-locus map of this region using a large reference pedigree from Venezuela. Our map provides landmarks which will aid in the localization of WND, in determining the extent of deletions in retinoblastoma, and in the mapping of other marker loci.

Chromosome Mapping↗
PubMed1988

Chromosomal location and structure of the operon encoding peptide-chain-release factor 2 of Escherichia coli.

The prfB gene encodes peptide-chain-release factor 2 of Escherichia coli, which catalyzes translation termination at UGA and UAA codons. The gene, identified by sequencing, is located at the 62-min region of the E. coli chromosome. The prfB gene is followed by an open reading frame encoding a 57,603-Da protein. This downstream open reading frame was identified as herC, a gene defined by a suppressor mutation that restores replication of a ColE1 plasmid mutant. RNA blot hybridization and S1 nuclease protection analyses of in vivo transcripts showed that prfB and herC are cotranscribed into a 2800-base transcript in the counterclockwise direction with respect to the E. coli genetic map. Thus, we refer to the two genes as the prfB-herC operon. Data are presented that suggest that supK, a mutation in Salmonella typhimurium that suppresses UGA termination, is the structural gene for Salmonella release factor 2. Translation control within the prfB-herC operon and the relationship of these genes to a tRNA methyltransferase are discussed.

Amino Acid Sequence↗
PubMedDate not supplied

Inter- and intra-individual probability maps in EEG cartography by use of nonparametric Fisher tests.

The three types of non-parametric permutation Fisher tests have been applied to inter-individual group studies and further to intra-individual multiple EEG recording sequences, providing computations of EEG probability maps testing two ordinal hypotheses. Two examples of previous group studies with "EEG local cerebral activation" are given: mental computation in a group of 20 controls and caffeine effects versus placebo in a group of 10 controls. For the intra-individual study, two successive recordings of 2.3 min eyes closed (EC1 and EC2), obtained at 50 min intervals, were compared by paired exact permutation Fisher tests (over 15 or 42 synchronous EEG sequences). These tests were applied to descriptive spectral parameters: RMS and % amplitudes, mean frequencies, resonance coefficient, for raw unfiltered EEG and delta, theta, alpha, alpha 1, alpha 2, beta 1, beta 2 frequency bands. Two hypotheses were tested for each of the computed 31 parameters, providing two probability maps indicating if the parameter was greater or lower in the first EEG recording or in the second. The second EEG sequence, EC2, was "EEG activated" compared to the first sequence EC1 if the following were present: decreased amplitudes mainly in raw EEG, low activity and alpha bands; increased frequencies mainly, in raw EEG, delta and beta 1 fast activities; increased fast activity percentages; decreased coefficient of resonance. The effect of choice of reference was also evaluated: probability maps for a frontal reference were different than other probability maps obtained after computation of average reference or source derivation.(ABSTRACT TRUNCATED AT 250 WORDS)

Brain Mapping↗
PubMed1991

Predictive testing for Wilson's disease using tightly linked and flanking DNA markers.

We studied DNA polymorphisms for five new chromosome 13 markers in 52 Wilson's disease (WD) families from Europe, North America, and the Middle East. There was significant evidence for linkage between the Wilson's disease locus (WND) and all the marker loci. Multilocus linkage analysis, using a genetic linkage map established from reference pedigrees, suggested that WND is most likely between D13S31 and D13S59, at distances of 0.4 and 1.2 centimorgans, respectively. Our results suggest that the chromosomal location of the Wilson's disease gene is the same in all families from the populations studied. This evidence and the availability of many close, flanking, and polymorphic DNA markers make possible accurate and informative testing of potential carriers and WD homozygotes in families with at least one previously affected child. An advantage of a genetic linkage test over other laboratory methods for prediction of genotype in WD is that a reliable diagnosis can be made at a much earlier stage in life, including prenatally. In addition, DNA testing can be used in place of an invasive liver biopsy procedure to confirm a diagnosis in patients with borderline serum ceruloplasmin levels. Presymptomatic identification will also allow therapeutic intervention to prevent symptoms before irreparable liver or neurologic damage occurs. We describe the implementation of prenatal and preclinical diagnosis for two families with WD.

Chromosome Mapping↗
PubMed1990

Afferent and efferent connections of the oculomotor region of the fastigial nucleus in the macaque monkey.

Afferent and efferent connections of the fastigial oculomotor region (FOR) were studied in macaque monkeys by using axonal transport of wheat germ agglutinin conjugated horseradish peroxidase (WGA-HRP). When injected HRP is confined to the FOR, retrogradely labeled cells appear in lobules VIc and VII of the ipsilateral vermis and in group b of the contralateral medial accessory olive (MAO). In reference to the maps of topographical organization, the extent of the effective site in the fastigial nucleus (FN) could be assessed from the distributions of labeled Purkinje cells (P cells) in the vermis and labeled olivary neurons in the MAO. In contrast to the unilateral nature of the P-cell and climbing-fiber projections, those from the other brainstem regions to the FOR were bilateral. Following the injection of HRP into the FOR, the largest number of retrogradely labeled cells appeared in the pontine nuclei. Although the number of labeled cells was greater on the contralateral side in both the peduncular and dorsomedial pontine nuclei (DMPN), the number of each side was virtually identical in the dorsolateral pontine nucleus (DLPN). In the nucleus reticularis tegmenti pontis (NRTP), labeled cells were located only in its medial and dorsolateral portions bilaterally. In the vestibular complex, labeled cells appeared in the superior (SVN), medial (MVN), and inferior vestibular nuclei (IVN) bilaterally. The lateral vestibular nucleus (LVN), including y group and the ventrolateral vestibular nucleus, were free of labeled cells. Labeled cells appeared also in the perihypoglossal nucleus (PHN) bilaterally. In the pontine raphe (PR) and paramedian pontine reticular formation (PPRF), labeled cells appeared bilaterally in the caudal third of the area between the oculomotor and abducens nuclei. Labeled cells appeared also in the mesencephalic and medullary reticular formation. Tracing of anterogradely labeled axons demonstrated that most fibers from the FOR decussated within the cerebellum and entered the brainstem via the contralateral uncinate fasciculus. Some crossed fibers ascended with the contralateral brachium conjunctivum and terminated in the midbrain tegmentum. A small contingent of fibers advanced further to the thalamus. In the mesodiencephalic junction, labeled terminals were found contralaterally in the rostral interstitial nucleus of medial longitudinal fasciculus (riMLF) and a medial portion of FOrel's H Field. They appeared also in the central mesencephalic reticular formation (cMRF), the periaqueductal gray (PAG), the posterior commissure nucleus, and the superior colliculus. The oculomotor and trochlear nuclei, the red nucleus, and the interstitial nucleus of Cajal were free of labeled terminals.(ABSTRACT TRUNCATED AT 400 WORDS)

Afferent Pathways↗
PubMed1990

The decomposition of the middle latency auditory evoked potential (MLAEP) Pa component into superficial and deep source contributions.

The results of recent investigations have suggested that the Middle Latency Auditory Evoked Potential (MLAEP) Pa component derives its physiological origins from both cortical and subcortical sources. The purpose of the present investigation was to determine if support for this hypothesis could be obtained from the off-line manipulation of the topographically recorded Pa component. The multichannel MLAEP from 15 normal hearing, neurologically intact subjects was collected following monaural left and right ear click stimulation. Data was originally collected using the linked ear reference and was subsequently re-referenced using the common average reference (CAR). These mapped data were converted off-line to source current density using the source derivation (SD) technique described by Hjorth (1975, 1980). This technique is sensitive to current activity that is generated in the superficial cerebral cortex. These SD maps of the MLAEP were subsequently subtracted from the CAR maps of the MLAEP. The derived CAR-SD maps are believed to represent that activity that is generated deep to the cerebral cortex (Hjorth and Rodin 1988). Interpretation of the mapped data have demonstrated support for the hypothesis that Pa is generated by a minimum of two systems including: 1) bilateral sources located in the posterior temporal lobes, and 2) a deeper midline generator system.

Acoustic Stimulation↗
PubMed1985

Variation among hepatitis A virus strains. I. Genomic variation detected by T1 oligonucleotide mapping.

The genomes of eight hepatitis A virus (HAV) strains originating from far distant geographic regions such as Europe, North Africa, Middle and North America, Australia and The People's Republic of China were compared by RNase T1 oligonucleotide mapping. For this purpose, the viruses were propagated in cell cultures and viral RNA was isolated from highly purified mature virions. It could be shown that variation in nucleotide sequence is common among HAV isolates, but is in the order of magnitude reported for other picornaviruses. For viruses isolated in cell culture directly from stool samples of diseased individuals, changes usually amounted to 1-4% of RNA genome sites. Genomic differences between two virus strains derived from one fecal sample but replicating at either 32 or 37 degrees C were in the same order of magnitude. Thereby, the number of consecutive in vitro passages proved to have only limited influence on the development of genetic variation. For two HAV strains, however, adaptation to and passage in marmosets evidently had imposed highly selective conditions which had favored the appearance of viral genomes differing in up to 75% of their large oligonucleotides (about 10% in sequence) from the oligonucleotide map of a reference HAV strain.

Animals↗
PubMed2026

A genome-wide coverage-based pipeline for the identification of host-derived candidate DNA biomarkers from cell-free blood.

We have created a new data-analysis pipeline for the discovery of host-specific candidate DNA biomarkers derived from sequencing data of cell-free blood. Unlike approaches that rely on specific molecular or genetic signatures, our method leverages the coverage distribution of cell-free DNA sequences mapped to a reference genome, applying statistical analyses to identify informative short genomic regions for biomarker discovery. The pipeline is applicable to diverse diseases and can be used to analyze cell-free DNA sequences from plasma or serum to identify candidate biomarkers that are characteristic of disease states in mammals. Core functionalities were developed in Java and integrated with open-source software tools for the preprocessing of raw sequencing data, complemented by Python scripts for the machine-learning analysis and statistical validation. The pipeline is designed for HPC use and users can access the pipeline through a Galaxy workflow, which offers a user-friendly web interface for input selection prior to execution and analysis progress monitoring. Performance tests, carried out using duplicate sets of COVID-19 samples and controls, showed linear scalability of execution time with an increasing dataset size, as well as a substantial reduction in execution time through parallelized computation, whereby each HPC node is used to process the data of one chromosome. Further statistical tests confirmed the quality of the pipeline's results by showing that the set of identified candidate biomarkers remained stable across varying dataset sizes.

Biomarkers↗
PubMed1986

Correspondence analysis applied to steroid receptor binding.

The relative binding affinities of 48 steroids for four classes of hormone receptor (progestin, PR; androgen, AR; glucocorticoid, GR; mineralocorticoid, MR) have been analyzed by correspondence analysis. The steroids were, for the most part, derivatives of nortestosterone, differing by their degree of unsaturation, by the presence or absence of a 17 alpha-ethynyl group, and by the length of the C-13 alkyl substituent. Derivatives of norprogesterone were included as reference compounds. Distribution maps visualizing the results of the mathematical analysis revealed that the majority of the test steroids were within the zone of influence of AR and PR and had limited affinity for GR and MR. Overall lack of specificity and enhanced affinity for GR and MR were induced by increasing unsaturation and by the presence of a C-13 ethyl group. The general and specific conclusions of the analysis confirm and extend previous intuitive and partial interpretations of the data. Correspondence analysis, however, has the advantage of taking into account the sum total of the available information, without any preconceived notion of the relative importance of a specific structural feature or biological parameter and, furthermore, enables simultaneous representation on a single graph of the receptor and steroid fields. The present example demonstrates the use of this type of methodology in processing routine screening data involving multiple parameters.

Chemical Phenomena↗
PubMed1985

Chromosomal location of the gene encoding the neural cell adhesion molecule (N-CAM) in the mouse.

The gene encoding the neural cell adhesion molecule, N-CAM, has been localized on mouse chromosome 9. A BALB/cJ mouse genomic library prepared in lambda bacteriophage EMBL4 was screened by using a cDNA probe, pEC204, that corresponds to the coding region of the chicken N-CAM gene. Four weakly reactive and one strongly reactive recombinant phage were isolated. A region of the latter that was strongly homologous to pEC204 was subcloned to yield a new probe, pEC501. RNA transfer blots and nucleotide sequencing indicated that pEC501 encoded part of the mouse N-CAM gene. This probe defined a unique genetic locus, Ncam, associated with a restriction fragment length polymorphism that allowed the definition of two alleles. The locus could be provisionally assigned either to chromosome 9 or to chromosome 10 by correlating the presence or absence of mouse-specific DNA fragments reactive with the probe in a panel of somatic hybrid cell lines with the presence or absence of the various mouse chromosomes. Analysis of the inheritance of the Ncam-associated DNA polymorphism in recombinant inbred strains of mice revealed close linkage between Ncam and the Lap-1, Sep-1, and Thy-1 loci on chromosome 9. This result suggests an additional linkage between Ncam and the locus for the cerebellar mutation staggerer (sg). The Ncam locus provides an important reference point for mapping the genes for additional cell adhesion molecules as well as genes for other molecules involved in neural development and function.

Animals↗
PubMed1986

Words created by children versus aphasic adults: an analysis of their form and communicative effectiveness.

The creation of words through the novel combination of English morphemes (e.g., "map ball" to refer to a globe) was studied in 40 preschool children, 40 grade school children, and 40 adults. These lexical innovations were collected while subjects named pictured objects, and were evaluated in terms of incidence, communicative effectiveness, novelty, semantic accuracy, and certain linguistic characteristics. Preschool children's innovations were as communicatively effective as those of grade school children and adults and contained the highest proportion of innovations with redundant elements. Grade school children produced the highest proportion with semantic inaccuracies. This suggests that preschoolers invent words from a limited set of highly familiar terms, whereas grade schoolers rely more on partially known terms. In addition, the children's innovations differed significantly from those previously collected from aphasic adults. This demonstrates that aphasia does not cause a regression to an early level of linguistic sophistication.

Anomia↗
PubMed1991

Enzymatic cleavage of a bacterial chromosome at a transposon-inserted rare site.

The sequential use of the methylase M.Xbal (5'.TCTAGm6A) and the methylation-dependent endonuclease Dpnl (5'-Gm6A decreases TC) results in cleavage at 5'.TCTAGA decreases TCTAGA. This recognition sequence was introduced into a transposon derived from the Mu bacteriophage and transposed into the genome of the bacterium Salmonella typhimurium. M.Xbal methylation was provided in vivo by a plasmid containing the M.Xbal gene and the S. typhimurium genome was cleaved to completion by Dpnl at one or more sites, depending on the number of transposon insertions. The resulting genomic fragments were resolved by pulsed-field electrophoresis. The potential use of single M.Xbal/Dpnl cleavage sites as reference positions to map rare restriction sites is discussed.

Base Sequence↗
PubMed1978

The vestibular nuclei in the domestic hen (Gallus domesticus). IV. The projection to the spinal cord.

Horseradish peroxidase was injected at various levels of the spinal cord of the hen and the cells in the brain stem, labeled due to retrograde transport of the tracer enzyme, were mapped with particular reference to the vestibular nuclear complex. The Deiters' nuclei project ipsilaterally to the spinal cord. The projection from the nucleus Deiters ventralis reaches down to the lumbosacral spinal cord. The spinal projection from the nucleus Deiters dorsalis is somatotopically organized. Cells localized rostrally within the nucleus project to upper parts of the spinal cord cells localized caudally project to the lumbosacral spinal cord. The medial and the descending nucleus contain labeled cells in two compartments of the nuclei. In each of them a rostral one projects to the upper cervical cord, a caudal one projects to the thoracical spinal cord. In addition, labeled cells are observed in the reticular formation, mainly in the pons and the medulla oblongata, in the red nucleus, in the raphe nuclei and in the periaqueductal grey. Very few labeled cells are observed in the locus ceruleus, the nucleus intercalatus and in the nucleus of the solitary tract. In some cases, the number of labeled cells in the various nuclei in the brain stem projecting to the spinal cord was counted to get an impression of the quantitative importance of the vestibulospinal projection relative to afferents to the spinal cord from the other nuclei. The findings are discussed in the light of what is known of the vestibulospinal projection in mammals.

Animals↗