Biomedical subjects

L Hillier

Publications and source records attributed to L Hillier.

At least 37 records · Page 2Linked to original sources

PubMed1998

Expressed sequence tag analysis of the bradyzoite stage of Toxoplasma gondii: identification of developmentally regulated genes.

Toxoplasma gondii is a protozoan parasite responsible for widespread infections in humans and animals. Two major asexual forms are produced during the life cycle of this parasite: the rapidly dividing tachyzoite and the more slowly dividing, encysted bradyzoite. To further study the differentiation between these two forms, we have generated a large number of expressed sequence tags (ESTs) from both asexual stages. Previously, we obtained data on approximately 7,400 ESTs from tachyzoites (J. Ajioka et al., Genome Res. 8:18-28, 1998). Here, we report the results from analysis of approximately 2,500 ESTs from bradyzoites purified from the cysts of infected mice. We also report the results from analysis of 760 ESTs from parasites induced to differentiate from tachyzoites to bradyzoites in vitro. Comparison of the data sets from bradyzoites and tachyzoites reveals many previously uncharacterized sequence clusters which are largely or completely specific to one or other developmental stage. This class includes a bradyzoite-specific form of enolase. Combined with the previously identified bradyzoite-specific form of lactate dehydrogenase, this finding suggests significant differences in flux through the lower end of the glycolytic pathway in this stage. Thus, the generation of this data set provides valuable insights into the metabolism and growth of the parasite in the encysted form and represents a substantial body of information for further study of development in Toxoplasma.

Amino Acid Sequence↗

PubMed1997

The homozygous complete hydatidiform mole: a unique resource for genome studies.

The most frequent type of complete hydatidiform mole is a 46, XX homozygote formed by the fertilization of an empty ovum by a single haploid sperm that later duplicates its chromosomes to give a diploid tumor. The homozygous nature of these complete hydatidiform moles makes them unique resources for human genome studies. They can serve as homozygous controls in the development of single nucleotide polymorphism (SNP) markers and provide a way to obtain long-range haplotypes that are useful in population studies. The use of a homozygous control makes it possible to estimate the allele frequencies of the SNP markers in any population by sequencing pooled DNA samples. In this report, we present evidence of homozygosity of a complete hydatidiform mole using 20 diallelic markers distributed across the genome. Furthermore, its usefulness as a homozygous control in SNP development and as a resource for long-range haplotype determination is demonstrated using 11 newly discovered loci in the BRCA2 region on chromosome 13q12-q13.

BRCA2 Protein↗

PubMed1997

Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution.

Representation of subcloned Caenorhabditis elegans and human DNA sequences in both M13 and pUC sequencing vectors was determined in the context of large scale genomic sequencing. In many cases, regions of subclone under-representation correlated with the occurrence of repeat sequences, and in some cases the under-representation was orientation specific. Factors which affected subclone representation included the nature and complexity of the repeat sequence, as well as the length of the repeat region. In some but not all cases, notable differences between the M13 and pUC subclone distributions existed. However, in all regions lacking one type of subclone (either M13 or pUC), an alternate subclone was identified in at least one orientation. This suggests that complementary use of M13 and pUC subclones would provide the most comprehensive subclone coverage of a given genomic sequence.

Animals↗

PubMed1997

The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.

The yeast Saccharomyces cerevisiae is the pre-eminent organism for the study of basic functions of eukaryotic cells. All of the genes of this simple eukaryotic cell have recently been revealed by an international collaborative effort to determine the complete DNA sequence of its nuclear genome. Here we describe some of the features of chromosome XII.

Base Sequence↗

PubMed1997

'That's the problem with living in a small town': privacy and sexual health issues for young rural people.

Survey and focus group discussions examining sexual health issues for young people were conducted with 1168 year 8 and year 10 secondary school students living in small rural communities across Australia. Growing up in the country was generally perceived as a positive experience; however, many young people felt that they had little privacy. Two main areas of concern emerged in relation to sexual health issues: worries about being recognised in public venues such as doctor's surgeries and chemists, and the informal mechanisms among peer groups that appraised and regulated sexual behaviour and attitudes. There were some significant gender differences evident in the expectations and experiences attached to these concerns, with girls expressing more awareness of and concern towards their public reputations when accessing sexual health services. They also felt that their sexual reputations among peers were closely monitored by way of their behaviour and appearance. This can militate against confident and assertive safer sex strategies such as condom use, when initiating or insisting upon condom use is construed as evidence of promiscuity or a preparedness to engage in sex. Concerns around privacy may be acutely experienced by young rural women, and health services providers need to be aware of these issues and efforts need to be made to address and allay the apprehensions of young people in this sensitive area.

Adolescent↗

PubMed1996

Lane tracking software for four-color fluorescence-based electrophoretic gel images.

Software to track sample lanes automatically in four-color, fluorescence-based, electrophoretic gel images has been developed for application in large-scale DNA sequencing projects. Lanes and lane boundaries are tracked by analyzing a first difference approximation to the gradient of a vertically integrated and processed "brightness" profile. Initially lanes are located in a region of the gel image selected for good horizontal lane spacing and signal strength. The software uses models of expected lane and interlane spacing and lateral lane behavior to maintain accurate tracking on imperfect gels. In areas where intensity-based tracking is difficult, interpixel column correlation is also used to locate and define lane features. Summary statistics and compressed-in-time images are generated for user evaluation of tracking performance. The software developed has been tested successfully on gel images with degradations including significant horizontal lane motion (curving) and image artifacts, and is now in full-scale use in our sequencing projects.

Algorithms↗

PubMed1995

The construction and analysis of M13 libraries prepared from YAC DNA.

Yeast artificial chromosomes (YACs) provide a powerful way to isolate and map large regions of genomic DNA and their use in genome analysis is now extensive. We modified a series of procedures to produce high quality shotgun libraries from small amounts of YAC DNA. Clones from several different libraries have been sequenced and analyzed for distribution, sequence integrity and degree of contamination from yeast DNA. We describe these procedures and analyses and show that sequencing at about 1-fold coverage, followed by database comparison (survey sequencing) offers a relatively quick method to determine the nature of previously uncharacterized cosmid or YAC clones.

Bacteriophage M13↗

PubMed1995

Genomic DNA sequencing methods.

Sequence analysis of cosmids from C. elegans and other organisms currently is best done using the random or "shotgun" strategy (Wilson et al., 1994). After shearing by sonication, DNA is used to prepare M13 subclone libraries which provide good coverage and high-quality sequence data. The subclones are assembled and the data edited using software tools developed especially for C. elegans genomic sequencing. These same tools facilitate much of the subsequent work to complete both strands of the sequence and resolve any remaining ambiguities. Analysis of the finished sequence is then accomplished using several additional computer tools including Genefinder and ACeDB. Taken together, these methods and tools provide a powerful means for genome analysis in the nematode.

Animals↗

PubMed1995

'What I said' versus 'what you heard': a comparison of physicians' and parents' reporting of anticipatory guidance on child safety issues.

OBJECTIVE: Unintentional injuries are the number one cause of death for infants. Many of these injuries could be prevented if parents took additional safety precautions. In this study physicians' and parents' perspectives regarding the part that physicians play in educating first time parents about child safety issues were compared. METHODS: All pediatricians and family physicians in London, Ontario were surveyed by mail (68% return rate) regarding their practices, attitudes, and beliefs related to parent education about child safety issues. A sample of 114 first time mothers, including 38 each with 6, 12, and 18 month old infants, completed a telephone interview. All parents had physicians who had returned questionnaires. RESULTS: There was good correspondence between parents' and physicians' judgments about the safety issues most often covered, and what role physicians should adopt regarding parent education about child safety issues. In addition, they both agreed that parents seldom seek out safety information by asking questions. Relative to parent reports, however, physicians significantly overestimated the time they spent on safety issues and the degree of their direct involvement in communicating this information. The best predictor of time spent by physicians on safety issues was their rating of the importance of assuming the role of parent educator. The best predictor of parents asking questions about child safety was their rating of the adequacy of physicians' responses to previously asked questions. CONCLUSIONS: The results suggest that both physicians and parents contribute to undermine communication about child safety during well-baby visits.

Accident Prevention↗

PubMed1994

Sound localization in newborn human infants.

Newborns' localization of sounds was examined in two experiments that utilized different psychophysical procedures and imposed different task demands. The results of both experiments were consistent in indicating that neonates not only differentiate the hemifield of a sound source but have some capacity to localize a sound within the hemifields. Adjustment of their initial head turn angle following a within-hemifield shift in location of an ongoing sound indicated that head orientation in neonates is elicited not only by sound onset but also by changes in location of an ongoing sound. Thus, multiple stimulus parameters impact on this neonatal response. Results are related to research on sound localization in older infants, and discussed in light of early development of the central auditory system.

Arousal↗

PubMed1993

Ancient conserved regions in new gene sequences and the protein databases.

Sets of new gene sequences from human, nematode, and yeast were compared with each other and with a set of Escherichia coli genes in order to detect ancient evolutionarily conserved regions (ACRs) in the encoded proteins. Nearly all of the ACRs so identified were found to be homologous to sequences in the protein databases. This suggests that currently known proteins may already include representatives of most ACRs and that new sequences not similar to any database sequence are unlikely to contain ACRs. Preliminary analyses indicate that moderately expressed genes may be more likely to contain ACRs than rarely expressed genes. It is estimated that there are fewer than 900 ACRs in all.

Amino Acid Sequence↗

PubMed1993

Alu and L1 sequence distributions in Xq24-q28 and their comparative utility in YAC contig assembly and verification.

The contents of Alu- and L1-containing TaqI restriction fragments were assessed by Southern blot analyses across YAC contigs already assembled by other means and localized within Xq24-q28. Fingerprinting patterns of YACs in contigs were concordant, and using software based on that of M. V. Olson et al. (1986, Proc. Natl. Acad. Sci. USA 83: 7826) to analyze digitized data on fragment sizes, fingerprinting itself could establish matches among about 40% of a test group of 435 YACs. At 100-kb resolution, both repetitive elements were found throughout the region, with no apparent enrichment of Alu or L1 in DNA of G compared to that found in R bands. However, consistent with a random overall distribution, delimited regions of up to 100 kb contained clusters of repetitive elements. The local concentrations may help to account for the reported differential hybridization of Alu and L1 probes to segments of metaphase chromosomes.

Chromosome Mapping↗

PubMed1992

The C. elegans genome sequencing project: a beginning.

The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues.

Animals↗

PubMed1992

Infants' perception of illusions in sound localization: reaching to sounds in the dark.

Sixteen infants each at 4, 6, and 8 months of age were tested for reaching to sounding toys in the dark under two auditory illusion conditions: the Haas-effect, which creates the illusion of a single lateralized sound based on an interaural intensity difference (the toy was visible and invisible under some test conditions); and the midline illusion, which creates the illusion of a single sound at midline due to an absence of any interaural time or intensity differences (invisible toy condition only). No-sound control trials indicated the level of spontaneous reaching in the dark. Results indicate that by 4 months infants perceive both the Haas-effect and midline illusions. The ability to reach both for invisible and visible sounding objects in the dark was well developed by 4 months of age, although developmental changes in aspects of reaching behavior were observed and, at all ages, object contact was most frequent when visual localization cues accompanied sound localization cues. The incidence of spontaneous reaching in the dark was low and did not vary with age. Theoretical and methodological implications of this research are discussed.

Acoustic Stimulation↗

PubMed1992

A survey of expressed genes in Caenorhabditis elegans.

As an adjunct to the genomic sequencing of Caenorhabditis elegans, we have investigated a representative cDNA library of 1,517 clones. A single sequence read has been obtained from the 5' end of each clone, allowing its characterization with respect to the public databases, and the clones are being localized on the genome map. The result is the identification of about 1,200 of the estimated 15,000 genes of C. elegans. More than 30% of the inferred protein sequences have significant similarity to existing sequences in the databases, providing a route towards in vivo analysis of known genes in the nematode. These clones also provide material for assessing the accuracy of predicted exons and splicing patterns and will lead to a more accurate estimate of the total number of genes in the organism than has hitherto been available.

Animals↗

PubMed1991

A trace display and editing program for data from fluorescence based sequencing machines.

'Ted' (Trace editor) is a graphical editor for sequence and trace data from automated fluorescence sequencing machines. It provides facilities for viewing sequence and trace data (in top or bottom strand orientation), for editing the base sequence, for automated or manual trimming of the head (vector) and tail (uncertain data) from the sequence, for vertical and horizontal trace scaling, for keeping a history of sequence editing, and for output of the edited sequence. Ted has been used extensively in the C.elegans genome sequencing project, both as a stand-alone program and integrated into the Staden sequence assembly package, and has greatly aided in the efficiency and accuracy of sequence editing. It runs in the X windows environment on Sun workstations and is available from the authors. Ted currently supports sequence and trace data from the ABI 373A and Pharmacia A.L.F. sequencers.

Animals↗

PubMed1991

Sequence of human glucose-6-phosphate dehydrogenase cloned in plasmids and a yeast artificial chromosome.

The sequence of 20,114 bp of DNA including the human glucose-6-phosphate dehydrogenase (G6PD) gene was determined. The region included a prominent CpG island, starting about 680 nucleotides upstream of the transcription start site, extending about 1050 nucleotides downstream of the start site, and ending just at the start of the first intron. The transcribed region from the start site to the poly(A) addition site covers 15,860 bp. The sequence of the 13 exons agreed with published cDNA sequence and for the 11 exons tested, with the corresponding sequence in a yeast artificial chromosome (YAC). The latter confirms YAC cloning fidelity at the DNA sequence level. Sixteen Alu sequences constitute 24% of the total sequence tract. Four were outside the borders of the mRNA transcript of the gene; all the others were found in a large (9858 bp) intron between exons 2 and 3. Two Alu clusters each contain Alus lying between the monomers of another.

Amino Acid Sequence↗

PubMed1991

OSP: a computer program for choosing PCR and DNA sequencing primers.

OSP (Oligonucleotide Selection Program) selects oligonucleotide primers for DNA sequencing and the polymerase chain reaction (PCR). The user can specify (or use default) constraints for primer and amplified product lengths, %(G+C), (absolute or relative) melting temperatures, and primer 3' nucleotides. To help minimize nonspecific priming and primer secondary structure, OSP screens candidate primer sequences, using user-specifiable cutoffs, against potential base-pairing with a variety of sequences present in the reaction, including the primer itself, the other primer (for PCR), the amplified product, and any other sequences desired (e.g., repetitive element sequences in genomic templates, vector sequence in cloned templates, or other primer pair sequences in multiplexed PCR reactions). Base-pairing involving the primer 3' end is considered separately from base-pairing involving internal sequences. Primers meeting all constraints are ranked by a "combined score," a user-definable weighted sum of any of the above parameters. OSP is being routinely and extensively used to select sequencing primers for the Caenorhabditis elegans genome sequencing project and human genomic PCR primer pairs for the Washington University Genome Center mapping project, with success rates exceeding 96% and 81%, respectively. It is available for research purposes from the authors, at no cost, in both text output and interactive graphics (X windows) versions.

Animals↗