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Biomedical subjects

Steven Russell

Publications and source records attributed to Steven Russell.

17 recordsLinked to original sources
PubMed2006

SimArray: a user-friendly and user-configurable microarray design tool.

BACKGROUND: Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic. RESULTS: We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation. CONCLUSION: SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from http://www.flychip.org.uk/SimArray/.

Documentation↗
PubMed2005

Spotted-dick, a zinc-finger protein of Drosophila required for expression of Orc4 and S phase.

The highly condensed chromosomes and chromosome breaks in mitotic cells of a Drosophila mutant, spotted-dick/pita, are the consequence of defects in DNA replication. Reduction of levels of Spotted-dick protein, by either RNAi or mutation, leads to the accumulation of cells that have DNA content intermediate to 2N and 4N in proliferating tissues and also compromises endoreduplication in larval salivary glands. The Spotted-dick Zinc-finger protein is present in the nuclei of cells committed to proliferation but necessary in cells undertaking S phase. We show that Spotted-dick/Pita functions as a transcription factor and that, in cultured S2 cells, it is an activator of expression of some 30 genes that include the Orc4 gene, required for initiation of DNA replication. Chromatin immunoprecipitation indicates that it associates with the genes that it activates in S2 cells together with other sites that could represent genes activated in other tissues. We discuss the role of Spotted-dick in the coordination of cellular growth and DNA replication.

Animals↗
PubMed2005

Sexually transmitted diseases and HIV/AIDS in Vanuatu: a cause for concern and action.

AIMS: This article argues that sexually transmitted infections (STIs) and HIV/AIDS in Vanuatu are a cause for concern and that a strong response is needed to stem an epidemic. METHODS: Three sources of data are used: studies and policy documents on STIs and HIV/AIDS in Vanuatu; analysis of reported STI cases from public health facilities; and key informant interviews with 14 policy stakeholders. RESULTS: In Port Vila (capital of Vanuatu), more than a quarter of the women attending antenatal clinics were positive for at least one STI. Although Vanuatu Ministry of Health (MoH) case records for gonorrhoea, genital ulceration, and syphilis show national prevalence rates have remained relatively constant between 1.2% and 2%, there is probably gross under-reporting because MoH data exclude trichomoniasis and chlamydiasis cases; surveillance systems are poor; and patient access to services is limited. High STI prevalence and several socioeconomic factors create a high-risk environment for the rapid spread of HIV/AIDS. DISCUSSION: The need for a strategic response in Vanuatu is pressing. Priorities for action include the scaling up of awareness programmes for young people, particularly girls, and the development of surveillance systems. Government capacity weaknesses mean the MoH should explore possible partnerships with the non-government organisation (NGO) sector and point to the need for international support to implement a new government Strategic Plan.

Adolescent↗
PubMed2005

Illuminating cases: understanding the economic burden of illness through case study household research.

Understanding the economic burden of illness for households can inform pro-poor health and social protection policy, yet research is in its infancy and appropriate methods require further debate. Quantitative studies are powerful when applied to the right health policy questions, including the measurement of illness cost burden indicators. However, this paper argues that not all dimensions of economic burden can be measured easily, some dimensions relevant to policy, such as social actors' responses to illness and their strategies to cope with illness costs, cannot be reduced to quantitative indicators at all, and large-scale surveys may overlook context-specific processes operating at household level that influence people's paths in and out of poverty as a result of illness. This leaves scope for longitudinal case-study household research to enhance understanding of economic burden and provide additional policy insights on how to better protect households from cost burdens and improve resilience. Drawing on the experience of research in urban Sri Lanka, the paper sets out several comparative advantages of case study research in this area. First, it complemented household survey data by revealing the complex and dynamic nature of illness costs and how these cost patterns (for example, sudden cost peaks) influenced household ability to manage costs. Secondly, it improved understanding of vulnerability or resilience to illness costs by capturing the diverse resources, within and outside the household, used by people to cope with illness costs, and the social institutions and decision-making processes that influenced access to them. Thirdly, the cases enabled the research to develop a picture of the inter-connected factors mediating the impact of illness on livelihood outcomes.

Adaptation, Psychological↗
PubMed2005

Genomic analysis of heat-shock factor targets in Drosophila.

We have used a chromatin immunoprecipitation-microarray (ChIP-array) approach to investigate the in vivo targets of heat-shock factor (Hsf) in Drosophila embryos. We show that this method identifies Hsf target sites with high fidelity and resolution. Using cDNA arrays in a genomic search for Hsf targets, we identified 141 genes with highly significant ChIP enrichment. This study firmly establishes the potential of ChIP-array for whole-genome transcription factor target mapping in vivo using intact whole organisms.

Animals↗
PubMed2005

Conserved genomic organisation of Group B Sox genes in insects.

BACKGROUND: Sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. The vertebrate B subgroup contains the Sox1, Sox2 and Sox3 genes that have early functions in neural development. Previous studies show that Drosophila Group B genes have been functionally conserved since they play essential roles in early neural specification and mutations in the Drosophila Dichaete and SoxN genes can be rescued with mammalian Sox genes. Despite their importance, the extent and organisation of the Group B family in Drosophila has not been fully characterised, an important step in using Drosophila to examine conserved aspects of Group B Sox gene function. RESULTS: We have used the directed cDNA sequencing along with the output from the publicly-available genome sequencing projects to examine the structure of Group B Sox domain genes in Drosophila melanogaster, Drosophila pseudoobscura, Anopheles gambiae and Apis mellifora. All of the insect genomes contain four genes encoding Group B proteins, two of which are intronless, as is the case with vertebrate group B genes. As has been previously reported and unusually for Group B genes, two of the insect group B genes, Sox21a and Sox21b, contain introns within their DNA-binding domains. We find that the highly unusual multi-exon structure of the Sox21b gene is common to the insects. In addition, we find that three of the group B Sox genes are organised in a linked cluster in the insect genomes. By in situ hybridisation we show that the pattern of expression of each of the four group B genes during embryogenesis is conserved between D. melanogaster and D. pseudoobscura. CONCLUSION: The DNA-binding domain sequences and genomic organisation of the group B genes have been conserved over 300 My of evolution since the last common ancestor of the Hymenoptera and the Diptera. Our analysis suggests insects have two Group B1 genes, SoxN and Dichaete, and two Group B2 genes. The genomic organisation of Dichaete and another two Group B genes in a cluster, suggests they may be under concerted regulatory control. Our analysis suggests a simple model for the evolution of group B Sox genes in insects that differs from the proposed evolution of vertebrate Group B genes.

Animals↗
PubMed2005

Treatment-seeking behaviour in urban Sri Lanka: trusting the state, trusting private providers.

Trust is central to good relationships between patients and health-care providers because, firstly, patient uncertainty about health conditions requires them to have confidence in a doctor's motives and decisions, and secondly, trust facilitates communication and patient focus which encourages people to utilise health services. This paper focuses on patient trust because of its effect on treatment-seeking behaviour and the treatment costs incurred by poor households. Drawing from other studies the paper distinguishes between trust based on the perceived technical competence of the provider, and on inter-personal dimensions of quality of care. Trust is also analysed at two inter-related levels: personal trust that is built through face-to-face encounters with providers; and more abstract institution-level trust. The paper applies these notions of trust to examine treatment-seeking behaviour in two poor urban communities in Colombo, Sri Lanka. Household survey data and qualitative data show that people from a range of income groups preferred to use public providers for more serious illnesses because public services were free and they trusted the technical competence of public providers at both a personal and institutional level. The data also show, however, that inter-personal quality of care was lacking in the public sector and that residents from the two communities, including a considerable minority of the poorest, preferred to use private providers for moderate acute illnesses. People were willing to pay for private services because it saved time, doctors listened and they could build better relationships with private doctors. Despite the strengths of Sri Lanka's public health sector, poor relationships act as an access barrier and push a range of income groups to the private sector. The threat to access and affordability posed by these poor relationships should be the focus of current reform debates.

Delivery of Health Care↗
PubMed2005

Robotic spotting of cDNA and oligonucleotide microarrays.

DNA microarrays are a uniquely efficient method for simultaneously assessing the expression levels of thousands of genes. Owing to their flexibility and value, mechanically spotted microarrays remain the most popular platform. Here, we review recent technological advances with a focus on spotted arrays. Robotic spotting still poses numerous technical challenges. To reduce artefacts, many laboratories have recently investigated ways of improving the spotting process. We compare alternative options and discuss implications for next-generation systems. Together with modern approaches to data analysis, such developments bring greatly improved reliability to individual microarray experiments. Advancing towards the ultimate goal of delivering calibrated, truly quantitative gene-expression measurements on a genomic scale, microarray technology remains at the forefront of post-genomic systems biology.

DNA Probes↗
PubMed2004

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics.

Identifying proteins in cell extracts by shotgun proteomics involves digesting the proteins, sequencing the resulting peptides by data-dependent mass spectrometry (MS/MS), and searching protein databases to identify the proteins from which the peptides are derived. Manual analysis and direct spectral comparison reveal that scores from two commonly used search programs (Sequest and Mascot) validate less than half of potentially identifiable MS/MS spectra (class positive) from shotgun analyses of the human erythroleukemia K562 cell line. Here we demonstrate increased sensitivity and accuracy using a focused search strategy along with a peptide sequence validation script that does not rely exclusively on XCorr or Mowse scores generated by Sequest or Mascot, but uses consensus between the search programs, along with chemical properties and scores describing the nature of the fragmentation spectrum (ion score and RSP). The approach yielded 4.2% false positive and 8% false negative frequencies in peptide assignments. The protein profile is then assembled from peptide assignments using a novel peptide-centric protein nomenclature that more accurately reports protein variants that contain identical peptide sequences. An Isoform Resolver algorithm ensures that the protein count is not inflated by variants in the protein database, eliminating approximately 25% of redundant proteins. Analysis of soluble proteins from a human K562 cells identified 5130 unique proteins, with approximately 100 false positive protein assignments.

Cell Line, Tumor↗
PubMed2004

The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster.

We describe a collection of P-element insertions that have considerable utility for generating custom chromosomal aberrations in Drosophila melanogaster. We have mobilized a pair of engineered P elements, p[RS3] and p[RS5], to collect 3243 lines unambiguously mapped to the Drosophila genome sequence. The collection contains, on average, an element every 35 kb. We demonstrate the utility of the collection for generating custom chromosomal deletions that have their end points mapped, with base-pair resolution, to the genome sequence. The collection was generated in an isogenic strain, thus affording a uniform background for screens where sensitivity to genetic background is high. The entire collection, along with a computational and genetic toolbox for designing and generating custom deletions, is publicly available. Using the collection it is theoretically possible to generate >12,000 deletions between 1 bp and 1 Mb in size by simple eye color selection. In addition, a further 37,000 deletions, selectable by molecular screening, may be generated. We are now using the collection to generate a second-generation deficiency kit that is precisely mapped to the genome sequence.

Animals↗
PubMed2004

The economic burden of illness for households in developing countries: a review of studies focusing on malaria, tuberculosis, and human immunodeficiency virus/acquired immunodeficiency syndrome.

Ill-health contributes to impoverishment, a process brought into sharper focus by the impact of the human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) epidemic. This paper reviews studies that have measured the economic costs and consequences of illness for households, focusing on malaria, tuberculosis (TB), and HIV/AIDS. It finds that in resource-poor settings illness imposed high and regressive cost burdens on patients and their families. Direct and indirect costs of illness for malaria were less than 10% of the household income, but still significant when combined with the costs of other illnesses. The costs of TB and HIV/AIDS were catastrophic for households (more than 10% of the income). Health service weaknesses in many countries, including low coverage, user charges, and poor quality of care, contributed to high costs. Poor households in developing countries with a member with TB or HIV/AIDS struggled to cope, highlighting the urgent need for a substantial increase in health sector investment to expand access to preventive and curative health services. Government and non-governmental interventions should also be broadened to encompass measures that reduce the substantial indirect costs associated with diseases such as malaria, TB, and HIV/AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed2003

Temporally dynamic response to Wingless directs the sequential elaboration of the proximodistal axis of the Drosophila wing.

The Drosophila wing imaginal disc gives rise to three main regions along the proximodistal axis of the dorsal mesothoracic segment: the notum, proximal wing, and wing blade. Development of the wing blade requires the Notch and wingless signalling pathways to activate vestigial at the dorsoventral boundary. However, in the proximal wing, Wingless activates a different subset of genes, e.g., homothorax. This raises the question of how the downstream response to Wingless signalling differentiates between proximal and distal fate specification. Here, we show that a temporally dynamic response to Wingless signalling sequentially elaborates the proximodistal axis. In the second instar, Wingless activates genes involved in proximal wing development; later in the third instar, Wingless acts to direct the differentiation of the distal wing blade. The expression of a novel marker for proximal wing fate, zfh-2, is initially activated by Wingless throughout the "wing primordium," but later is repressed by the activity of Vestigial and Nubbin, which together define a more distal domain. Thus, activation of a distal developmental program is antagonistic to previously established proximal fate. In addition, Wingless is required early to establish proximal fate, but later when Wingless activates distal differentiation, development of proximal fate becomes independent of Wingless signalling. Since P-element insertions in the zfh-2 gene result in a revertable proximal wing deletion phenotype, it appears that zfh-2 activity is required for correct proximal wing development. Our data are consistent with a model in which Wingless first establishes a proximal appendage fate over notum, then the downstream response changes to direct the differentiation of a more distal fate over proximal. Thus, the proximodistal domains are patterned in sequence and show a distal dominance.

Animals↗
PubMed2003

Sex-specific apoptosis regulates sexual dimorphism in the Drosophila embryonic gonad.

Sexually dimorphic development of the gonad is essential for germ cell development and sexual reproduction. We have found that the Drosophila embryonic gonad is already sexually dimorphic at the time of initial gonad formation. Male-specific somatic gonadal precursors (msSGPs) contribute only to the testis and express a Drosophila homolog of Sox9 (Sox100B), a gene essential for testis formation in humans. The msSGPs are specified in both males and females, but are only recruited into the developing testis. In females, these cells are eliminated via programmed cell death dependent on the sex determination regulatory gene doublesex. Our work furthers the hypotheses that a conserved pathway controls gonad sexual dimorphism in diverse species and that sex-specific cell recruitment and programmed cell death are common mechanisms for creating sexual dimorphism.

Animals↗
PubMed2003

Transposable elements as tools for genomics and genetics in Drosophila.

The P-element has been the workhorse of Drosophila genetics since it was developed as a tool for transgenesis in 1982; the subsequent development of a variety of systems based on the transposon have provided a range of powerful and flexible tools for genetics and genomics applications. P-element insertions are frequently used as starting-points for generating chromosomal deletions to remove flanking genes, either by screening for imprecise excision events or by selecting for male recombination events. Elements that utilise the yeast FLP/FLP recombination target (FRT) site-specific recombination system have been widely used to generate molecularly marked mitotic clones for mosaic analysis, extending the reach of this powerful genetic tool to virtually all areas of developmental biology. P-elements are still widely used as traditional mutagenesis reagents and form the backbone of projects aimed at generating insertions in every predicted gene in the fly genome. In addition, vectors based on the FLP/FRT system are being used for genome-wide applications, including the development of molecularly-mapped deletion and duplication kits. In addition to these 'traditional' genetic approaches, a variety of engineered elements have been developed for a wide range of transgenic applications, including enhancer trapping, gene-tagging, targeted misexpression, RNA interference (RNAi) delivery and homologous recombination/gene replacement. To complement the use of P-elements, alternative transposon vectors have been developed. The most widely used of these are the lepidopteran element piggyBac and a Drosophila hydei transposon, Minos. In total, a range of transposon vectors offers the Drosophila biologist considerable flexibility and sophistication in manipulating the genome of the fly and has allowed rapid advances in all areas of developmental biology and genome science.

Animals↗
PubMed2002

Drosophila melanogaster as a model system for drug discovery and pathway screening.

Although the freakish nightmare world of Mr Samsa may seem completely divorced from our view of the real world, the comparisons between the Drosophila and human genomes indicate that we are a lot closer to insects than we like to think. The use of sophisticated genetic approaches combined with emerging genomics technologies suggest that the fly has much to offer as a tool for understanding basic cellular processes and provides an attractive and complex model system for exploring the molecular basis of human diseases such as cancer, Alzheimer's disease and Huntington's disease.

Animals↗
PubMed2002

Evidence for differential and redundant function of the Sox genes Dichaete and SoxN during CNS development in Drosophila.

Group B Sox-domain proteins encompass a class of conserved DNA-binding proteins expressed from the earliest stages of metazoan CNS development. In all higher organisms studied to date, related Group B Sox proteins are co-expressed in the developing CNS; in vertebrates there are three (Sox1, Sox2 and Sox3) and in Drosophila there are two (SoxNeuro and Dichaete). It has been suggested there may be a degree of functional redundancy in Sox function during CNS development. We describe the CNS phenotype of a null mutation in the Drosophila SoxNeuro gene and provide the first direct evidence for both redundant and differential Sox function during CNS development in Drosophila. In the lateral neuroectoderm, where SoxNeuro is uniquely expressed, SoxNeuro mutants show a loss or reduction of achaete expression as well as a loss of many correctly specified lateral neuroblasts. By contrast, in the medial neuroectoderm, where the expression of SoxNeuro and Dichaete overlaps, the phenotypes of both single mutants are mild. In accordance with an at least partially redundant function in that region, SoxNeuro/Dichaete double mutant embryos show a severe neural hypoplasia throughout the central nervous system, as well as a dramatic loss of achaete expressing proneural clusters and medially derived neuroblasts. However, the finding that Dichaete and SoxN exhibit opposite effects on achaete expression within the intermediate neuroectoderm demonstrates that each protein also has region-specific unique functions during early CNS development in the Drosophila embryo.

Animals↗