Inclusivity and decolonisation of the post-graduate public health curriculum: Reflections from a student-led approach.

The future of successful public health practice requires public health students to be educated within a decolonised curriculum that challenges the historical biases and inequalities that are deeply embedded within global public health and society. In this commentary, we reflect on what it can mean and why it's important to decolonise and diversify a public health curriculum. We describe how we used a student-led approach to begin this process, and share recommendations that are applicable to national and international curricula.

Exploring barriers to accessing mental health services within minoritised communities in Nottingham City, UK - a creative participatory approach to service improvement.

OBJECTIVES: We use an art-based approach to engage and involve members of African, African Caribbean and Muslim communities' in exploring barriers to accessing and using mental health services in the co creation and co-production of mental health communication material. STUDY DESIGN: A creative practice approach underpinned by the principles of participatory action research was used. METHODS: Seven community-based interactive workshops were held between February and June 2022 at three community centres in Nottingham, UK Attendees were invited to take part in open discussions around the conceptualisations of mental health, well-being and emotional health and to draw or describe their experiences of accessing mental health services. RESULTS: Attendance was higher than anticipated, with 72 individuals from African, African Caribbean and Pakistan communities taking part in the workshops. What emerged was the low level of understanding of the services available in addressing mental health. In addition, it was felt that health professionals in the National Health Service (NHS) do not sufficiently acknowledge or consider the ethnic, social, cultural and economic factors influencing the mental health and emotional well-being of minoritised communities. Attendees critiqued and provided feedback on service providers' posters and leaflets. They commented on the lack of key information provided, the inclusion of what was viewed as irrelevant content and the use of unfamiliar terminology. Some attendees created mock-ups of what they believed a good poster should look like. CONCLUSION: A creative practice approach that follows the principles of participatory action research can play an important role in engaging members of minoritised communities in the co-production and co-design of services. This approach highlighted the need to establish trust and shared ownership among marginalized communities affected by inequities of mental health service provision.

Disease profiling arrays: reverse format cDNA arrays complimentary to microarrays.

The identification of differentially expressed genes enables us to understand the molecular mechanisms associated with disease, conditions of stress, drug treatments and developmental processes. Microarrays provide a powerful tool for studying these complex phenomena. Verification of differentially expressed genes and correlation with biological function, which is usually done by northern blot analysis, RNase protection assay or RT-PCR, is the bottleneck in all these protocols. We developed a new type of cDNA array for high-throughput expression profiling of multiple tissues and blood samples (i) for confirmation analysis of statistically significant number of clinical samples (ii) from limited amount of starting material, and (iii) with detailed clinical data from each individual. In contrast to traditional cDNA arrays, these arrays are spotted with a complex cDNA representing the entire mRNA message expressed in a given tissue or blood sample. cDNAs for these arrays were generated using SMART technology and accurately represent the original mRNA population, producing specific and quantitative signals during hybridization. cDNAs on Disease Profiling Arrays were derived from total RNAs of diseased and normal tissues or different blood fractions of patients. These cDNAs were spotted onto nylon membranes along with positive and negative controls. The arrays were then hybridized with gene-specific probes. Hybridization results revealed disease-related as well as patient-specific gene expression patterns between different disease types for these genes. These studies demonstrate that Disease Profiling Arrays are suitable for high-throughput studies comparing the relative abundance of a target gene, for simultaneously detecting differentially expressed genes in a wide variety of tissues and blood samples, and can be used down-stream from cDNA microarrays for confirmation analysis.

Assessment of the accuracy of a three-dimensional imaging system for archiving dental study models.

OBJECTIVE: The use of stone and plaster study models is an integral part of any dental practice and is required for research. Storage of study models is problematic in terms of space and cost. Ayoub et al.(1) introduced a new technique based on the recent advances in stereophotogrammetry for archiving dental study models in a digital format. However, assessment of the accuracy of the generated three-dimensional (3D) models has not been carried out yet. It was the aim of this study to evaluate the accuracy of this technique. DESIGN: A comparative assessment between direct measurements of dental study models and measurements of computer generated 3D images of the same study models was performed. MATERIALS AND METHODS: Twenty-two dental study models stored at Glasgow Dental Hospital and School for the purposes of research were used in the study. The models were captured in three dimensions using a photostereometric technique and stored in digital format. MAIN OUTCOME MEASURES: Measurements were conducted directly on dental study models and on the computer generated 3D images using Euclidean Distance Matrix Analysis.(2) The difference between the two sets of measurements was statistically analysed using a two-sample t-test. RESULTS: The average difference between measurements of dental casts and 3D images was 0.27 mm. This difference was within the range of operator errors (0.10-0.48 mm) and was not statistically significant (P < 0.05). CONCLUSION: This study shows that it is possible to use 3D imaging to store dental study models for treatment monitoring and research with a satisfactory degree of accuracy.

Multiple transcription factor profiling by enzyme-linked immunoassay.

Transcription factor-DNA interactions have been widely studied in the regulation of gene expression. We have established an enzyme-linked immunoassay platform to quantify specific transcriptionfactor-DNA interactions. In our assay, dsDNA immobilized on a 96-well plate captures the transcriptionfactor from the nuclear extract of mammalian cells. The DNA-bound transcription factor is detected and quantified by enzyme-linked immunoassay using a transcription factor-specific antibody. We have profiled multiple transcription factors involved in inflammation including NFkappaB p50, NFkappaB p65, c-Rel, c-Fos, CREB-1, and ATF-2. When compared with the traditional electrophoretic mobility shift assay, the enzyme-linked immunoassay shows a 10-fold higher sensitivity, eliminates the use of radioactivity, allows for a high-throughput format, and is faster.

Caveolin-1 is down-regulated in human ovarian carcinoma and acts as a candidate tumor suppressor gene.

To identify novel markers differentially expressed in ovarian cancer versus normal ovary, we hybridized microarrays with cDNAs derived from normal human ovaries and advanced stage ovarian carcinomas. This analysis revealed down-regulation of the caveolin-1 gene (CAV1) in ovarian carcinoma samples. Suppression of CAV1 in ovarian carcinomas was confirmed using a tumor tissue array consisting of 68 cDNA pools from different matched human tumor and normal tissues. Immunohistochemistry demonstrated expression of caveolin-1 in normal and benign ovarian epithelial cells, but loss of expression in serous ovarian carcinomas. In low-grade carcinomas, redistribution of caveolin-1 from a membrane-associated pattern observed in normal epithelium to a cytoplasmic localization pattern was observed. No expression of caveolin-1 was detectable in four of six ovarian carcinoma cell lines investigated. In SKOV-3 and ES-2 carcinoma cells, which express high levels of the caveolin-1 protein, phosphorylation of the 22-kd caveolin-1 isoform was detected. Inhibition of both DNA methylation and histone deacetylation using 5-aza-2'deoxycytidine and Trichostatin A, respectively, relieves down-regulation of caveolin-1 in OAW42 and OVCAR-3 cells which is in part mediated by direct regulation at the mRNA level. Expression of CAV1 in the ovarian carcinoma cell line OVCAR-3, resulted in suppression of tumor cell survival in vitro, suggesting that the CAV1 gene is likely to act as a tumor suppressor gene in human ovarian epithelium.

Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction.

Here, we describe a fast, simple method for constructing full-length cDNA libraries using SMART technology. This novel procedure uses the template-switching activity of Moloney murine leukemia virus (MMLV) reverse transcriptase to synthesize and anchor first-strand cDNA in one step. Following reverse transcription, three cycles of PCR are performed using a modified oligo(dT) primer and an anchor primer to enrich the cDNA population for full-length sequences. Starting with 1 microgram human skeletal muscle poly(A)+ RNA, a cDNA library was constructed that contained 3 x 10(6) independent clones with an average insert size of 2 kb. Sequence analysis of 172 randomly selected clones showed that 77% of cDNA clones corresponding to known genes contained intact open reading frames. The average length of complete open reading frames was 2.4 kb. Furthermore, 86% of the full-length clones retained longer 5' UTR sequences than the longest 5' end deposited in the GenBank database. cDNA libraries generated using this method will be useful for accelerating the collection of mRNA 5' end sequence information, which is currently very limited in GenBank.

Generation of full-length cDNA libraries enriched for differentially expressed genes for functional genomics.

Here, we describe the application of a RecA-based cloning technology to generate full-length cDNA libraries enriched for genes that are differentially expressed between tumor and normal tissue samples. First, we show that the RecA-based method can be used to enrich cDNA libraries for several target genes in a single reaction. Then, we demonstrate that this method can be extended to enrich a cDNA library for many full-length cDNA clones using fragments derived from a subtracted cDNA population. The results of these studies show that this RecA-mediated cloning technology can be used to convert subtracted cDNAs or a mixture of several cDNA fragments corresponding to differentially expressed genes into a full-length library in a single reaction. This procedure yields a population of expression-ready clones that can be used for further high-throughput functional screening.

Use of SMART-generated cDNA for gene expression studies in multiple human tumors.

We demonstrate here that SMART PCR-amplified cDNAs arrayed on a nylon membrane are suitable for high-throughput tissue expression profiling when starting biological materials are limited. We show that SMART cDNA accurately reflects gene expression patterns found in total RNA by comparing the expression level of several target genes in SMART PCR-amplified cDNAs and their corresponding total RNAs. We also arrayed cDNAs from 68 matched tumor and normal samples on a nylon membrane to determine whether SMART PCR-amplified cDNA could be used for detecting differentially expressed genes in these tissues. These arrays containing normalized tumor and normal cDNAs were hybridized with probes for glutathione peroxidase and gelsolin. The hybridization results revealed cancer-related and patient-specific gene expression differences between tumor and normal tissues for these genes. These studies show that SMART PCR-amplified cDNAs maintain the complexity of the original mRNA population and are thus suitable for high-throughput studies to compare the relative abundance of target genes and to detect differentially expressed genes in a wide variety of tissues simultaneously.

"Fluorescent timer": protein that changes color with time.

We generated a mutant of the red fluorescent protein drFP583. The mutant (E5) changes its fluorescence from green to red over time. The rate of color conversion is independent of protein concentration and therefore can be used to trace time-dependent expression. We used in vivo labeling with E5 to measure expression from the heat shock-dependent promoter in Caenorhabditis elegans and from the Otx-2 promoter in developing Xenopus embryos. Thus, E5 is a "fluorescent timer" that can be used to monitor both activation and down-regulation of target promoters on the whole-organism scale.

Detection of differentially expressed genes in lymphomas using cDNA arrays: identification of clusterin as a new diagnostic marker for anaplastic large-cell lymphomas.

This study reports the first use of gene array technology for the identification of a tumor-specific marker in lymphoid neoplasms. The differential gene expression of 31 hematopoietic cell lines, representing most major lymphoma subgroups of B- and T-cell origin, was assessed by hybridizing labeled complementary DNA to Atlas human expression arrays containing 588 genes. Genes known to be specific for B, T, or myelomonocytic lineages were appropriately identified in the arrays, validating the general utility of this approach. One gene, clusterin, not previously known to be expressed in lymphoid neoplasms, was specifically found in all 4 anaplastic large-cell lymphoma (ALCL) cell lines, but not in any of the 27 remaining tumor lines. Using a monoclonal antibody against clusterin, its differential expression was confirmed by Western blotting and immunohistochemistry. A total of 198 primary lymphomas (representing most major lymphoma subtypes), including 36 cases of systemic ALCL, were surveyed for clusterin expression by immunohistochemistry and Western blotting. All of the 36 ALCL cases marked for clusterin, with most cases showing moderate to strong staining in the majority of neoplastic cells. Clusterin expression was not related to expression of anaplastic lymphoma kinase-1. With 2 exceptions, none of the remaining 162 non-ALCL cases marked with the clusterin antibody, including Hodgkin disease and primary cutaneous ALCL. In reactive lymphoid tissues, only follicular dendritic cells and fibroblastic reticular cells exhibited staining. Clusterin is a highly conserved glycoprotein implicated in intercellular and cell matrix interactions, regulation of the complement system, lipid transport, stress responses, and apoptosis. Although its function in ALCL is unknown, the unique expression of clusterin within this category of lymphoma provides an additional marker for the diagnosis of ALCL. This study illustrates the enormous potential of gene array technologies for diagnostic marker discovery. (Blood. 2000;96:398-404)

RecA-mediated affinity capture: a method for full-length cDNA cloning.

We describe an improved method for rapid cloning of full-length cDNA from cDNA libraries. This approach is based on the ability of Escherichia coli RecA protein to form a stable nucleoprotein complex with a linear single-stranded DNA probe and homologous sequences in circular double-stranded DNA. Hybridization of RecA-coated biotinylated DNA probes to homologous plasmid DNA creates triple-stranded complexes, which are then captured on streptavidin-coated magnetic beads. Following magnetic separation of the hybrid molecules, the enriched plasmid population is recovered by alkaline treatment, precipitated, resuspended and used to transform bacteria. Typically, many clones can then be recovered by colony hybridization screening of a single plate of the enriched library. We have used this technology to clone full-length and alternatively spliced forms of the human bcl-xL cDNA from a human liver cDNA library.

Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes.

A new and highly effective method, termed suppression subtractive hybridization (SSH), has been developed for the generation of subtracted cDNA libraries. It is based primarily on a technique called suppression PCR, and combines normalization and subtraction in a single procedure. The normalization step equalizes the abundance of cDNAs within the target population and the subtraction step excludes the common sequences between the target and driver populations. As a result only one round of subtractive hybridization is needed and the subtracted library is normalized in terms of abundance of different cDNAs. It dramatically increases the probability of obtaining low-abundance differentially expressed cDNA and simplifies analysis of the subtracted library. The SSH technique is applicable to many molecular genetic and positional cloning studies for the identification of disease, developmental, tissue-specific, or other differentially expressed genes. This chapter provides detailed protocols for the generation of subtracted cDNA and differential screening of subtracted cDNA libraries. As a representative example we demonstrate the usefulness of the method by constructing a testis-specific cDNA library as well as using the subtracted cDNA mixture as a hybridization probe. Finally, we discuss the characteristics of subtracted libraries, the nature and level of background nondifferentially expressed clones in the libraries, as well as a procedure for the rapid identification of truly differentially expressed cDNA clones.

Quantitative rt-PCR.

Although reverse transcriptase polymerase chain reaction (RT-PCR) is an extremely sensitive method of mRNA analysis, obtaining quantitative information with this technique can be difficult. This is caused primarily by the fact that there are two sequential enzymatic steps involved: the synthesis of DNA from the RNA template and PCR. In practice, the exponential nature of PCR and the practical aspects of performing PCR pose the most serious obstacles to obtaining quantitative information. With some adaptations, however, RT-PCR can yield accurate quantitative results.

A vision-based three-dimensional capture system for maxillofacial assessment and surgical planning.

We describe a vision-based three-dimensional facial data capture system designed for the planning of maxillofacial operations. We describe the system requirements and outline the methods used to develop a complete three-dimensional facial capture system. Our approach is based upon imaging the face using two stereo-pair sets of cameras. Scale-space-based stereo-matching is then used to recover correspondences between each of the captured stereo-pairs. Photogrammetric routines based on adjustment of bundles are used off-line to calibrate the system by imaging a single object that references all cameras to the same co-ordinate frame. This calibration scheme allows us to convert stereo correspondences to world points for each pair of cameras without the need for any subsequent fusion of data. Initial results show that we are able to capture key facial landmarks to within 0.5 mm.

PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori.

Genes that are characteristic of only certain strains of a bacterial species can be of great biologic interest. Here we describe a PCR-based subtractive hybridization method for efficiently detecting such DNAs and apply it to the gastric pathogen Helicobacter pylori. Eighteen DNAs specific to a monkey-colonizing strain (J166) were obtained by subtractive hybridization against an unrelated strain whose genome has been fully sequenced (26695). Seven J166-specific clones had no DNA sequence match to the 26695 genome, and 11 other clones were mixed, with adjacent patches that did and did not match any sequences in 26695. At the protein level, seven clones had homology to putative DNA restriction-modification enzymes, and two had homology to putative metabolic enzymes. Nine others had no database match with proteins of assigned function. PCR tests of 13 unrelated H. pylori strains by using primers specific for 12 subtracted clones and complementary Southern blot hybridizations indicated that these DNAs are highly polymorphic in the H. pylori population, with each strain yielding a different pattern of gene-specific PCR amplification. The search for polymorphic DNAs, as described here, should help identify previously unknown virulence genes in pathogens and provide new insights into microbial genetic diversity and evolution.

Rt-PCR methods and applications.

Control of gene transcription, the process in which a gene's DNA sequence serves as a template for mRNA synthesis, plays a critical role in the multistep process that regulates gene expression. Gene transcrtption levels within a cell change in response to a wide variety of signals that occur during cell development, differentiation, and normal physiological function. Changes in transcrip tion levels also occur in response to disease and other factors. In turn, these changes in transcription levels cause variations in the steady-state levels of indivtdual mRNAs. Thus, analysis of specific mRNA levels 1s vital in a broad range of research areas.

Quantitative rt-PCR.

Although reverse transcriptase polymerase chain reaction (RT-PCR) is an extremely sensitive method of mRNA analysis, obtaining quantitative information with this technique can be difficult. This is caused primarily by the fact that there are two sequential enzymatic steps involved: the synthesis of DNA from the RNA template and PCR. In practice, the exponential nature of PCR and the practical aspects of performing PCR pose the most serious obstacles to obtaining quantitative information. With some adaptations, however, RT-PCR can yield accurate quantitative results.

Identification of an alternative form of human lactoferrin mRNA that is expressed differentially in normal tissues and tumor-derived cell lines.

Lactoferrin (LF), traditionally known as an iron-binding protein present in high concentrations in milk and various secretions, has emerged as a multifunctional protein involved in many aspects of the host defense against infection. Recently, LF has been shown to inhibit the growth of solid tumors and reduce experimental metastasis in mice, suggesting that LF also may play a role in the defense against tumorigenesis. Here we provide the sequence of the cDNA and promoter region, the chromosome assignment, and tissue expression pattern of a novel form of LF mRNA (delta LF). The sequence of delta LF mRNA is nearly identical to that of LF mRNA; however, at the 5' end, we find a novel sequence that replaces the N-terminal signal peptide sequence of LF mRNA. We map the delta LF mRNA to human chromosome 3 and find that both delta LF and LF sequences colocalize to the same cloned 90- to 150-kb genomic DNA fragment. We further show that the delta LF mRNA is the product of alternative splicing of the LF gene and likely is specified by use of an alternative promoter. Although we find delta LF mRNA at various levels in 20 of 20 adult and fetal human tissues, we do not find delta LF mRNA in any of 14 diverse tumor-derived cell lines.