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S J Jones

Publications and source records attributed to S J Jones.

At least 55 records · Page 3Linked to original sources
PubMed2000

Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.

Genome sequencing projects generate a wealth of information; however, the ultimate goal of such projects is to accelerate the identification of the biological function of genes. This creates a need for comprehensive studies to fill the gap between sequence and function. Here we report the results of a functional genomic screen to identify genes required for cell division in Caenorhabditis elegans. We inhibited the expression of approximately 96% of the approximately 2,300 predicted open reading frames on chromosome III using RNA-mediated interference (RNAi). By using an in vivo time-lapse differential interference contrast microscopy assay, we identified 133 genes (approximately 6%) necessary for distinct cellular processes in early embryos. Our results indicate that these genes represent most of the genes on chromosome III that are required for proper cell division in C. elegans embryos. The complete data set, including sample time-lapse recordings, has been deposited in an open access database. We found that approximately 47% of the genes associated with a differential interference contrast phenotype have clear orthologues in other eukaryotes, indicating that this screen provides putative gene functions for other species as well.

Animals↗
PubMed2000

QTc-interval abnormalities and psychotropic drug therapy in psychiatric patients.

BACKGROUND: Sudden unexplained death in psychiatric patients may be due to drug-induced arrhythmia, of which lengthening of the rate-corrected QT interval (QTc) on the electrocardiogram is a predictive marker. We estimated the point prevalence of QTc lengthening in psychiatric patients and the effects of various psychotropic drugs. METHODS: Electrocardiograms were obtained from 101 healthy reference individuals and 495 psychiatric patients in various inpatient and community settings and were analysed with a previously validated digitiser technique. Patients with and without QTc lengthening, QTc dispersion, and T-wave abnormality were compared by logistic regression to calculate odds ratios for predictive variables. FINDINGS: Abnormal QTc was defined from the healthy reference group as more than 456 ms and was present in 8% (40 of 495) of patients. Age over 65 years (odds ratio 3.0 [95% CI 1.1-8.3]), use of tricyclic antidepressants (4.4 [1.6-12.1]), thioridazine (5.4 [2.0-13.7]), and droperidol (6.7 [1.8-24.8]) were robust predictors of QTc lengthening, as was antipsychotic dose (high dose 5.3 [1.2-24.4]; very high dose 8.2 [1.5-43.6]). Abnormal QT dispersion or T-wave abnormalities were not significantly associated with antipsychotic treatment, but were associated with lithium therapy. INTERPRETATION: Antipsychotic drugs cause QTc lengthening in a dose-related manner. Risks are substantially higher for thioridazine and droperidol. These drugs may therefore confer an increased risk of drug-induced arrhythmia.

Adolescent↗
PubMed2000

Comparative genomics of the eukaryotes.

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

Animals↗
PubMed2000

Antibacterial proteins in rainbow trout, Oncorhynchus mykiss.

Antibacterial proteins are an important part of the innate immune system for all animals. They have been extensively studied in mammals, amphibians and invertebrates, but have received only scant attention in fish. Their expression and processing, however, provide a way of monitoring defence vigour during development or with seasonal changes in physiology. The aim of the present work was to identify and characterise antibacterial proteins in rainbow trout. In vitro analyses of extracts of the peripheral blood leucocytes, head kidney leucocytes and mucus from adult unstimulated (non-immune) fish showed marked antibacterial activity against Gram positive bacteria. Fractionation by ion exchange chromatography and RP-HPLC of head kidney extracts showed the presence of two forms of lysozyme but no constitutively expressed antimicrobial proteins of < 10 kDa. By contrast, chromatographic analyses of mucus revealed at least four antibacterial proteins. Two are conventional lysozymes, a third is an unusual lysozyme-like protein with a low isoelectric point, and the fourth is a highly hydrophobic, cationic peptide of c. 3 kDa.

Animals↗
PubMed2000

Mutational accessibility of essential genes on chromosome I(left) in Caenorhabditis elegans.

We have analyzed a region of approximately 5.4 million base pairs for mutations, which under standard laboratory conditions result in developmental arrest, sterility, or maternal-effect lethality in Caenorhabditis elegans. Lethal mutations were isolated, maintained, and genetically manipulated as homozygotes using sDp2--a duplication of the left half of chromosome I. All of the lethals and rearrangements used in this analysis were balanced by sDp2. Relatively low doses of mutagen, (approximately 15 mM ethylmethane sulfate; EMS), were used so as to limit the occurrence of second-site mutations, thus increasing the probability of recovering single nucleotide substitutions. Treatment of over 32,400 marked chromosomes resulted in 486 analyzed mutations. In this paper, we add 133 previously unidentified let genes, isolated in the EMS screens, and one let gene identified by a gamma-ray induced mutation, to our collection of 103 essential genes. We also recovered lethal alleles of genes for which visible mutants already existed. In total, eight deficiencies and alleles of 237 essential genes were identified. Eighty-nine of the previously unidentified let genes are represented by more than one lethal allele. Statistical analysis indicates a minimum estimate of 400 essential genes in the region of chromosome I balanced by sDp2. This region occupies approximately half of chromosome I, and contains over 1135 protein-coding genes predicted from the genomic sequence data. Thus, approximately one-third of the predicted genes are estimated to be essential. Of these approximately 60% are represented by lethal alleles. Less than 2% of the lethal-bearing strains recovered in our analysis, including the eight genetically definable deficiencies, carried more than one lethal mutation. Several screens were used to recover mutations for this analysis. Because all the mutations were isolated using the same balancer, under similar screening conditions, it was possible to compare intervals within the sDp2 region with each other. The fraction of essential genes that present relatively large targets for EMS was highest within the central cluster (dpy-5 to unc-13).

Animals↗
PubMed2000

A global profile of germline gene expression in C. elegans.

We used DNA microarrays to profile gene expression patterns in the C. elegans germline and identified 1416 germline-enriched transcripts that define three groups. The sperm-enriched group contains an unusually large number of protein kinases and phosphatases. The oocyte-enriched group includes potentially new components of embryonic signaling pathways. The germline-intrinsic group, defined as genes expressed similarly in germlines making only sperm or only oocytes, contains a family of piwi-related genes that may be important for stem cell proliferation. Finally, examination of the chromosomal location of germline transcripts revealed that sperm-enriched and germline-intrinsic genes are nearly absent from the X chromosome, but oocyte-enriched genes are not.

Animals↗
PubMed2000

Spectro-temporal analysis of complex tones: two cortical processes dependent on retention of sounds in the long auditory store.

OBJECTIVES: To examine whether two cortical processes concerned with spectro-temporal analysis of complex tones, a 'C-process' generating CN1 and CP2 potentials at cf. 100 and 180 ms after sudden change of pitch or timbre, and an 'M-process' generating MN1 and MP2 potentials of similar latency at the sudden cessation of repeated changes, are dependent on accumulation of a sound image in the long auditory store. METHODS: The durations of steady (440 Hz) and rapidly oscillating (440-494 Hz, 16 changes/s) pitch of a synthesized 'clarinet' tone were reciprocally varied between 0.5 and 4.5 s within a duty cycle of 5 s. Potentials were recorded at the beginning and end of the period of oscillation in 10 non-attending normal subjects. RESULTS: The CN1 at the beginning of pitch oscillation and the MN1 at the end were both strongly influenced by the duration of the immediately preceding stimulus pattern, mean amplitudes being 3-4 times larger after 4.5 s as compared with 0.5 s. CONCLUSIONS: The processes responsible for both CN1 and MN1 are influenced by the duration of the preceding sound pattern over a period comparable to that of the 'echoic memory' or long auditory store. The store therefore appears to occupy a key position in spectro-temporal sound analysis. The C-process is concerned with the spectral structure of complex sounds, and may therefore reflect the 'grouping' of frequency components underlying auditory stream segregation. The M-process (mismatch negativity) is concerned with the temporal sound structure, and may play an important role in the extraction of information from sequential sounds.

Acoustic Stimulation↗
PubMed2000

Auditory evoked potentials to spectro-temporal modulation of complex tones in normal subjects and patients with severe brain injury.

In order to assess higher auditory processing capabilities, long-latency auditory evoked potentials (AEPs) were recorded to synthesized musical instrument tones in 22 post-comatose patients with severe brain injury causing variably attenuated behavioural responsiveness. On the basis of normative studies, three different types of spectro-temporal modulation were employed. When a continuous 'clarinet' tone changes pitch once every few seconds, N1/P2 potentials are evoked at latencies of approximately 90 and 180 ms, respectively. Their distribution in the fronto-central region is consistent with generators in the supratemporal cortex of both hemispheres. When the pitch is modulated at a much faster rate ( approximately 16 changes/s), responses to each change are virtually abolished but potentials with similar distribution are still elicited by changing the timbre (e.g. 'clarinet' to 'oboe') every few seconds. These responses appear to represent the cortical processes concerned with spectral pattern analysis and the grouping of frequency components to form sound 'objects'. Following a period of 16/s oscillation between two pitches, a more anteriorly distributed negativity is evoked on resumption of a steady pitch. Various lines of evidence suggest that this is probably equivalent to the 'mismatch negativity' (MMN), reflecting a pre-perceptual, memory-based process for detection of change in spectro-temporal sound patterns. This method requires no off-line subtraction of AEPs evoked by the onset of a tone, and the MMN is produced rapidly and robustly with considerably larger amplitude (usually >5 microV) than that to discontinuous pure tones. In the brain-injured patients, the presence of AEPs to two or more complex tone stimuli (in the combined assessment of two authors who were 'blind' to the clinical and behavioural data) was significantly associated with the demonstrable possession of discriminative hearing (the ability to respond differentially to verbal commands, in the assessment of a further author who was blind to the AEP findings). Behavioural and electrophysiological findings were in accordance in 18/22 patients, but no AEPs could be recorded in two patients who had clear behavioural evidence of discriminative hearing. The absence of long-latency AEPs should not, therefore, be considered indicative of complete functional deafness. Conversely, AEPs were substantially preserved in two patients without behavioural evidence of discriminative hearing. Although not necessarily indicative of conscious 'awareness', such AEP preservation might help to identify sentient patients who are prevented by severe motor disability from communicating their perception.

Acoustic Stimulation↗
PubMed1999

Nonmethylated transposable elements and methylated genes in a chordate genome.

The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of methylated and nonmethylated domains. Multiple copies of an apparently active long terminal repeat retrotransposon and a long interspersed element are nonmethylated and a large fraction of abundant short interspersed elements are also methylation free. Genes, by contrast, are predominantly methylated. These data are incompatible with the genome defense model, which proposes that DNA methylation in animals is primarily targeted to endogenous transposable elements. Cytosine methylation in this urochordate may be preferentially directed to genes.

Animals↗
PubMed1999

TNF recruits TRADD to the plasma membrane but not the trans-Golgi network, the principal subcellular location of TNF-R1.

The subcellular localization of TNF-R1 to the Golgi apparatus, initially observed in endothelial cells, has been confirmed using transfection of bovine aortic endothelial cells with a human TNF-R1 expression plasmid. The subcellular interactions of TNF-R1 and the TRADD (TNFR-associated death domain protein) adaptor protein have been analyzed in the human monocyte cell line U937 and the human endothelial cell line ECV304 by confocal immunofluorescence microscopy and by Western blot analysis of fractionated cell extracts. In untreated cells, in which TNF-R1 is found on the cell surface but principally localizes to the trans-Golgi network, TRADD is concentrated in the cis- or medial-Golgi region, but separates from the Golgi during cell fractionation. Coimmunoprecipitation studies have shown that TRADD binds to TNF-R1 within 1 min of TNF treatment in a cell fraction-containing plasma membrane. This association is followed by a gradual dissociation, which is prevented if receptor-mediated endocytosis is inhibited by hypertonic medium. In contrast, no association is detected between TRADD and TNF-R1 in the Golgi in response to exogenous TNF at any time examined. These results suggest that although TNF-R1 is predominantly a Golgi-associated protein and TRADD also localizes to the Golgi region, exogenous TNF causes TRADD to bind to TNF-R1 only at the plasma membrane.

Animals↗
PubMed1999

The microscopic structure of bone in normal children and patients with osteogenesis imperfecta: a survey using backscattered electron imaging.

The microstructure of iliac crest biopsies from normal children or from those afflicted with osteogenesis imperfecta (OI) has not previously been studied to determine the tissue histology in the context of the degree of mineralization. The material in this study comprised 112 iliac crest biopsies from children aged 1.9-22.9 years. Fifty-eight were reference biopsies taken from children with no bone disease and the remainder were biopsies from children diagnosed as having OI (23 were Type I, 8 Type III, 18 Type IV, and 5 Type V). The specimens, which had been embedded in polymethylmethacrylate (PMMA), were micromilled and carbon coated to permit backscattered electron imaging. Reference biopsies from very young children often contained densely mineralized cartilage, and evidence of rapid cortical drift. Circumferential lamellae became a prominent feature after the toddler stage, and active remodeling and slower cortical drift continued through childhood. The biopsies from older teenagers and young adults were indistinguishable. Occasional mineralized osteocyte lacunae were detected in even the youngest children. Bone from children with OI Type I often appeared normal in microstructure and amount, but in some there was a dearth of bone and an abundance of osteocytes. Compared with age-matched controls, cortical and trabecular bone from children with OI Types III and IV were markedly sparse and very cellular, and primary osteonal systems continued to be formed later than expected. A distinguishing feature of the bone from OI Type V patients was the failure of patches of bone to mineralize, especially adjoining a reversal line. Packets of bone tissue exhibiting either considerably higher than normal or deficient mineralization would contribute to the characteristic trait of mechanical weakness.

Adolescent↗
PubMed1999

The mineralization density of iliac crest bone from children with osteogenesis imperfecta.

We studied iliac crest biopsy cores taken from young individuals with osteogenesis imperfecta of several types, and from age-matched normals; the same samples had been used in prior studies using conventional light microscopic histomorphometric procedures. The PMMA blocks were micro-milled to a fine finish, carbon coated, and imaged using backscattered electrons (BSE) in an automated digital scanning electron microscope (SEM). For comparison of BSE signal levels between samples, microscope operation parameters were standardized by reference to halogenated dimethacrylate standards, and recording data from stereological arrays of 512*512 nonoverlapping pixels at 3.5 micrometer separation. All OI types showed higher average mineralization densities than age- and site-matched normals. This is interpreted as the result of the failure in matrix assembly, such that it has a higher water volume fraction available for mineral deposition. Added to the net deficit in bone quantity, the predicted higher stiffness of the more mineralized bone will account for much of the observed 'brittleness' that characterizes this class of genetic disease. The mean mineralization density, which was higher in types III, IV, and V than in type I, appears to be correlated with disease severity.

Adolescent↗
PubMed1999

The resorption of vital and devitalized bone in vitro: significance for bone grafts.

Several studies have suggested that devitalized bone is less satisfactory than live tissue for surgical grafting purposes because an initial resorption step, prior to new formation, is lacking. We have compared the osteoclastic resorption of cultured bone containing living osteocytes with that of similar bone in which the osteocytes were dead. In experiment I, transverse slices cut from freshly harvested adult rabbit femora were either placed in phosphate buffered saline (Set 1) or subjected to freezing and thawing (Set 2). In experiment II, a heated set (Set 3) was prepared in addition. All slices were cultured with osteoclasts for 24 hours, eight slices per set being seeded with bone cells in experiment I and three per set in experiment II. The areas and volumes of resorption pits formed during the culture period were measured using reflection confocal microscopy. In both experiments, the mean values for the areas of the pits were smaller in the bone containing live osteocytes (P < 0.03, Mann Whitney test), and in experiment II the volumes of the pits in Set 1 were smaller than those in Set 3 (P < 0. 0001, Mann Whitney test). However, in neither experiment was there a significant difference between the Sets in the volume:area ratios (mean depths) of the pits. The findings show that devitalized bone is resorbed by osteoclasts at least as readily as bone containing vital osteocytes in vitro, and indicate that if grafted devitalized bone resorbs less well in vivo it is not because the bone tissue is intrinsically resistant to osteoclastic resorption.

Animals↗
PubMed1999

Long-term recovery and fellow eye deterioration after optic neuritis, determined by serial visual evoked potentials.

Twelve optic neuritis patients (part of a larger group in whom the effects of intravenous methylprednisolone treatment were previously reported), were followed-up 3 years from the onset of symptoms with visual evoked potentials (VEPs), contrast sensitivity and visual field examination. Findings from the previously "unaffected" eyes, none of which had had symptomatic optic neuritis, were also assessed. Between 6 months and 3 years after the onset of symptoms the VEPs of the affected eyes showed a significant shortening of mean latency (whole field, 131-123 ms; central field, 136-125 ms). Conversely, the responses of the previously unaffected eyes showed a contemporaneous latency prolongation (significant for the whole field, 110-113 ms) which exceeded the expected effect of aging. Contrast sensitivity tests showed no significant change in the affected eyes but a mild deterioration in the unaffected eyes, while the visual fields showed no overall pattern of improvement or deterioration. If the strong tendency for VEP latencies to shorten is due to ongoing remyelination, the lack of significant improvement in visual function may be because the visual deficit at 6 months is due to irreversible axonal loss rather than demyelination. The absence of functional deterioration in the affected eye, while VEPs and contrast sensitivity deteriorated in the unaffected eye, suggests that long-term remyelination may for a while counteract the effects of insidious demyelination and axonal degeneration which affect the visual pathway during clinical remission.

Adult↗
PubMed1999

Cortical processing of complex tone stimuli: mismatch negativity at the end of a period of rapid pitch modulation.

In this study, synthesised instrumental tones were used to examine human auditory cortical processes engaged at the end of a period of rapid pitch modulation. It was previously [S.J. Jones, O. Longe, M. Vaz Pato, Auditory evoked potentials to abrupt pitch and timbre change of complex tones: electrophysiological evidence of 'streaming'?, Electroencephalogr. Clin. Neurophysiol., 108 (1998) 131-142] suggested that the 'change-N1' produced by infrequent changes in pitch or timbre of a continuous complex tone represents the activity of a neuronal population topographically distinct from that responsible for the 'onset-N1' at the beginning of the tone. In the present study a superficially similar negativity was produced when the tone came to rest on a steady pitch after a period of rapid (8-16 changes/s) modulation; its scalp maximum was anterior to that of the two previously identified potentials but similar to that of the mismatch negativity elicited by discontinuous tones. By varying the modulation rate the latency was shown to be relatively constant with respect to the time the next pitch change was expected but failed to occur. The largest responses averaging c. 7 microV were evoked at the end of modulation sequences which were both rhythmic and repetitive, but a potential was still produced when there was no rhythmic pattern or repetition of individual notes. This response to non-occurrence of an expected but not necessarily specified change implies an automatic process for comparing the incoming sound with an extrapolated template of the preceding pattern in which timing as well as pitch information is accurately represented. We suggest this technique offers a robust method for eliciting the mismatch negativity, which may extend the opportunities for electrophysiological investigation of higher auditory processes.

Acoustic Stimulation↗
PubMed1999

Effects of IGF-I, IGF-II, bFGF and PDGF on the initiation of mRNA translation in C2C12 myoblasts and differentiating myoblasts.

In order to study the mechanisms by which growth factors stimulate protein synthesis, C2C12 myogenic cells were treated with a variety of growth factors and the recruitment of free ribosomes to polysomes was quantified. All experiments were conducted on C2C12 myoblasts (24 h prior to induction of fusion) and differentiating myoblasts (24 h after induction of fusion). After the 2 h incubation, cells were rinsed with phosphate buffered saline and quickly frozen at -80 degrees C. Cell lysates were fractionated on 15-60% sucrose gradients by centrifugation at 200,000 x g for 1 h. Absorbance at 254 nm was recorded continuously across the gradient. The response to each of the four growth factors, IGF-I and-II, basic fibroblast growth factor (FGF), and platelet-derived growth factor was a decrease (P < 0.05) in monosome peak height and a increase (P < 0.05) in polysome percentage (P < 0.05). All responses were linear, except IGF-I, and the monosome peak height response to FGF which were quadratic (P < 0.05). None of the growth factors had a significant effect (P > 0.05) on RNA concentrations over the 2-h incubation. Protein content did not vary due to growth factor or level of treatment. This corroborates the hypothesis that the acute increase of protein synthesis exhibited by growth factor treated cells is due to an increase in the activity of existing ribosomes rather than an increase in ribosome synthesis. These results suggest that we can study the mechanisms regulating protein synthesis in muscle cells effectively by studying shifts in ribosomal activity. This method gave more consistent results than the H3-tyrosine incorporation and has the added benefit of not requiring the use of radioactivity. The strong correlation between monosome peak heights and percentage polysomes will allow researchers to measure total protein synthetic activity in a culture from the free or cytoplasmic fraction and to reserve the polysomes for other uses. The similarity of response among the various growth factors may indicate a common mechanism for increasing the initiation of protein synthesis.

Animals↗
PubMed1999

Effects of serum deprivation, insulin and dexamethasone on polysome percentages in C2C12 myoblasts and differentiating myoblasts.

An increase in the rate of protein synthesis in living cells can be achieved by regulating the quantity of mRNA, ribosomes, and enzymes available for translation or by regulating the efficiency at which existing components are used. Efficiency can be measured by comparing the number of ribosomes actively engaged in the synthesis of protein (polysomes) to the pool of free ribosomes. The objective of this study was to determine the percentage of ribosomes found as polysomes in C2C12 cells deprived of serum or exposed to insulin or dexamethasone 24 h before and after being stimulated to differentiate. Individual 60 mm culture dishes were exposed to serum-free control medium, medium containing serum, insulin, or dexamethasone for a period of 1 h or 2 h and then quickly frozen. The ribosomes and polysomes from these cells were separated by ultracentrifugation on 15 to 60% sucrose gradients and the absorbance across the gradient at 254 nm was recorded. Polysome percentages were determined as the area under the polysome peak divided by the total area under the curve. Serum deprivation caused a 12% decline in the percentage of ribosomes found as polysomes (P < 0.01). Dexamethasone caused a quadratic decline (P < 0.05) in polysome percentage, while insulin yielded a quadratic increase (P < 0.05). Protein synthesis assays measuring 3H-tyrosine uptake showed similar responses. These changes occurred in the absence of any differences in total RNA concentration. It was concluded that differentiation and the absence of serum in the media reduced the rate of recruitment of ribosomes for protein synthesis. Insulin increased ribosome recruitment which was also observed by a similar increase in incorporation of radio-labeled tyrosine.

Animals↗