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Biomedical subjects

A J Simpson

Publications and source records attributed to A J Simpson.

At least 19 recordsLinked to original sources

Endogenous pulmonary antibiotics.

The human lung produces a variety of peptides and proteins which have intrinsic antimicrobial activity. In general these molecules have broad spectra of antimicrobial activity, kill micro-organisms rapidly, and evade resistance generated by pathogens. In recent years it has become increasingly apparent that the antimicrobial peptides (AMPs) simultaneously possess immunomodulatory functions, suggesting complex roles for these molecules in regulating the clearance of, and immune response to, invading pathogens. These collective properties have stimulated considerable interest in the potential clinical application of endogenous AMPs. This article outlines the biology of AMPs, their pattern of expression in the lung, and their functions, with reference to both antimicrobial and immunomodulatory activity. We then consider the biological importance of AMPs, before concentrating on the potential to use AMPs to therapeutic effect. The principles discussed in the article apply to innate immune defence throughout the body, but particular emphasis is placed on AMPs in the lung and the potential application to pulmonary infection.

Anti-Bacterial Agents↗

Profile of adult rat sensory neuron loss, apoptosis and replacement after sciatic nerve crush.

Following permanent transection of the adult rat sciatic nerve, sensory neuron apoptosis in the contributing L4 and L5 dorsal root ganglia can be observed for at least 6 months afterwards. To establish the profile of any sensory neuron apoptosis and loss over time when axonal regeneration is allowed, serial sections of L4 and L5 ganglia were examined and the neurons counted using a stereological technique 1, 2 and 3 months after crushing the right sciatic nerve at mid-thigh level. Our results show that an identical degree of sensory neuron loss and apoptosis occurs 1 month after crush as at 1 month after permanent transection. However, at 3 months no neurons undergoing apoptosis could be observed and no significant loss could be detected in the ipsilateral ganglia when compared to unoperated controls. One explanation was a neuronal replacement mechanism, which was investigated by administering bromodeoxyuridine to rats for 1 month after sciatic nerve transection or crush, prior to detection using immunohistochemistry on sections of their ganglia after 2 months. The presence of bromodeoxyuridine in the nuclei of occasional cells that would be counted as neurons on the basis of size and morphology indicates that a process of apparent neurogenesis may underlie the profile of sensory neuron loss after axotomy.

Animals↗

Comparative genomic analysis of plant-associated bacteria.

This review deals with a comparative analysis of seven genome sequences from plant-associated bacteria. These are the genomes of Agrobacterium tumefaciens, Mesorhizobium loti, Sinorhizobium meliloti, Xanthomonas campestris pv campestris, Xanthomonas axonopodis pv citri, Xylella fastidiosa, and Ralstonia solanacearum. Genome structure and the metabolism pathways available highlight the compromise between the genome size and lifestyle. Despite the recognized importance of the type III secretion system in controlling host compatibility, its presence is not universal in all necrogenic pathogens. Hemolysins, hemagglutinins, and some adhesins, previously reported only for mammalian pathogens, are present in most organisms discussed. Different numbers and combinations of cell wall degrading enzymes and genes to overcome the oxidative burst generally induced by the plant host are characterized in these genomes. A total of 19 genes not involved in housekeeping functions were found common to all these bacteria.

Adaptation, Physiological↗

Separation of structural components in soil organic matter by diffusion ordered spectroscopy.

Diffusion ordered spectroscopy (DOSY) was applied to two extracts of organic matter from the surface horizon of an oak forest soil. It was possible to identify and confirm the presence of numerous aliphatic, aromatic, sugar, and amino acid components that could be separated on the basis of diffusion in DMSO-d6 and D2O. On average, sugar components were identified as the largest molecules in solution, with molecular masses up to approximately 1500 Da followed by the aliphatic and aromatic components. Amino acids with a range of molecular weights were also identified in the mixture. The summation of the individual slices from the DOSY experiment closely resembles the conventional 1H spectra of the material, indicating that the components identified with DOSY represent all the components present in the mixture. The separation of components in the mixture in organic solvent supports new findings that fulvic and humic acids are not cross-linked, high molecular weight macromolecules but are instead aggregates composed of relatively simple molecules that take on colloidal properties in the presence of metal ions in aqueous solution. Using the knowledge that these organic mixtures are combinations of relatively simple entities with well-documented reactivities and behavior will improve our ability to predict and model their interactions and fate under natural conditions.

Amino Acids↗

Significant overexpression of oligophrenin-1 in colorectal tumors detected by cDNA microarray analysis.

The human oligophrenin-1 gene is ubiquitously expressed at low levels and expressed at high levels in the developing neuroepithelium of the neural tube. Mutations in this gene have been related to the X-linked mental retardation. Using cDNA microarrays, we found evidence that oligophrenin-1 is strongly up-regulated in colorectal tumors. Semiquantitative reverse transcriptase polymerase chain reaction confirmed this finding. Thus, a well-known nervous system-associated human gene transcript may also be an important colorectal tumor marker and potential therapeutic target.

Biomarkers, Tumor↗

The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome.

Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.

Expressed Sequence Tags↗

The application of 1H HR-MAS NMR spectroscopy for the study of structures and associations of organic components at the solid-aqueous interface of a whole soil.

High resolution-magic angle spinning nuclear magnetic resonance (HR-MAS NMR) allows the application of solution-state NMR experiments to samples that are not fully soluble and contain solids. Only the species in contact with the solvent system employed become NMR observable. In this study utilizing D2O as the solvent system we show it is possible to examine the structures at the solid-aqueous interface of a whole soil. Combining one- and two-dimensional HR-MAS NMR allowed, for the first time, the identification of fatty acids, aliphatic esters, and ethers/ alcohols as prominent species at the solid-aqueous interface of the soil with signals from sugars and amino acids also apparent. Few, if any signals from aromatic protons were observed when the soil was swollen in aqueous media, although these signals are observed in extracts from the same soil and when the soil is swollen with a more penetrating solvent(DMSO-d6)which is known to disassociate hydrogen bonds. These findings indicate that the soil aromatic moieties are protected in hydrophobic regions which are not water accessible. Furthermore, when the soil was amended with a herbicide (trifluralin), direct observations of interactions between the protons on a xenobiotic and the surrounding soil matrix were possible for the first time. HR-MAS promises to be a method that can be widely applicable to a range of complex environmental samples without the need for extraction, pretreatment, or purification.

Environmental Monitoring↗

Adenoviral augmentation of elafin protects the lung against acute injury mediated by activated neutrophils and bacterial infection.

During acute pulmonary infection, tissue injury may be secondary to the effects of bacterial products or to the effects of the host inflammatory response. An attractive strategy for tissue protection in this setting would combine antimicrobial activity with inhibition of human neutrophil elastase (HNE), a key effector of neutrophil-mediated tissue injury. We postulated that genetic augmentation of elafin (an endogenous inhibitor of HNE with intrinsic antimicrobial activity) could protect the lung against acute inflammatory injury without detriment to host defense. A replication-deficient adenovirus encoding elafin cDNA significantly protected A549 cells against the injurious effects of both HNE and whole activated human neutrophils in vitro. Intratracheal replication-deficient adenovirus encoding elafin cDNA significantly protected murine lungs against injury mediated by Pseudomonas aeruginosa in vivo. Genetic augmentation of elafin therefore has the capacity to protect the lung against the injurious effects of both bacterial pathogens resistant to conventional antibiotics and activated neutrophils.

Acute Disease↗

Regulation of adenovirus-mediated elafin transgene expression by bacterial lipopolysaccharide.

Lipopolysaccharide (LPS) is a mediator of inflammatory lung injury. Selective augmentation of host defense molecules such as elafin (an elastase inhibitor with antimicrobial activity) at the onset of pulmonary inflammation is an attractive potential therapeutic strategy. The aim of this study was to determine whether elafin expression could be induced by LPS administered after transfection with adenovirus (Ad) encoding human elafin downstream of the murine cytomegalovirus (CMV) promoter (known to be potentially responsive to LPS). In addition, we aimed to determine the effect of local elafin augmentation on neutrophil migration to the lung. LPS significantly up-regulated elafin expression from pulmonary epithelial cells transfected with Ad-elafin in vitro. In murine airways expression of human elafin was achieved using doses low enough (3 x 10(7) plaque forming units) to circumvent overt vector-induced inflammation. LPS significantly up-regulated human elafin secretion in murine airways treated with Ad-elafin [117 ng/ml in bronchoalveolar lavage fluid (BALF) after LPS administration, 5.9 ng/ml after PBS, p < 0.01)]. Over-expression of elafin significantly augmented LPS-mediated neutrophil migration into the airways in vivo (1.30 x 10(6) neutrophils in BALF after Ad-elafin/LPS treatment, 0.54 x 10(6) after Ad-lacZ/LPS (p < 0.05), 0.63 x 10(6) after PBS/LPS (p < 0.05)) and significantly enhanced human neutrophil migration in vitro. These data suggest novel functions for elafin in neutrophil migration, and that judicious selection of promoters may allow single, low-dose adenoviral administration to effect inflammation-specific expression of potentially therapeutic transgenes.

Adenoviridae↗

Human semaphorin 6B [(HSA)SEMA6B], a novel human class 6 semaphorin gene: alternative splicing and all-trans-retinoic acid-dependent downregulation in glioblastoma cell lines.

We have identified a novel human gene related to the class 6 semaphorin family of axon guidance molecules, termed human semaphorin 6B or (HSA)SEMA6B. Two splicing variants of this gene were identified by RT-PCR: (HSA)SEMA6B.1 (short isoform) and (HSA)SEMA6B.2 (longer isoform). Computational analysis suggests that these isoforms correspond to putative secreted and transmembranous semaphorins, respectively. The levels of (HSA)SEMA6B expression were evaluated by Northern blot analysis in different tissues and in some pathological and pharmacological conditions. We observed that (HSA)SEMA6B is highly expressed in human brain and at lower levels in a variety of other tissues. Interestingly, the (HSA)SEMA6B transcript was downregulated in two different human glioblastoma cell lines (T98G and A172) upon prolonged treatment with all-trans-retinoic acid, an anti-tumor and differentiation-inducing agent.

Alternative Splicing↗

Circulating tumor-derived DNA may permit the early diagnosis of head and neck squamous cell carcinomas.

A series of eight microsatellite loci were assayed for both loss of heterozygosity and new mutated alleles in 91 head and neck squamous cell carcinomas. In 58 cases, alterations were detected and used as markers for assaying the presence of circulating tumor-derived DNA in the patients' plasma. This was unambiguously detected in 17 cases. The probability of detecting circulating DNA was independent of tumor stage and was found to be present even in some individuals with stage I tumors. The presence of such DNA, however, could not be correlated with disease outcome or other significant clinical parameters, suggesting that it has no prognostic significance. The results indicate that circulating tumor-derived DNA could be used as a means of early diagnosis of head and neck tumors.

Alleles↗

Effects of hydrostatic pressure on the Leptospira interrogans: high immunogenicity of the pressure-inactivated serovar hardjo.

The Hardjoprajitno strain of Leptospira interrogans serovar hardjo was subjected to different hydrostatic pressures. Complete inactivation occurred when the leptospires were treated with 2 kbar for 60 min. Electron microscopy showed dislocation of the outer membrane, partial loss of the helical shape and extrusion of the axial filament from the cytoplasmic cylinder of the pressurized leptospires. When the pressure-treated leptospires were inoculated into rabbits they were highly immunogenic. The sera of these animals presented a titer of 2048 in the microscopic serum agglutination reaction. Fluorescence measurements indicated that the action of pressure on the leptospires might have resulted from perturbation on membrane protein components, permitting the binding of the fluorescent probe bis (8-anilinonaphthalene-1-sulfonate) (Bis-ANS). This is the first report of the use of hydrostatic pressure to inactivate pathogenic bacteria with the potential to lead to a vaccine.

Anilino Naphthalenesulfonates↗

Microsatellite instability as a tool for the classification of gastric cancer.

Microsatellite instability (MSI) is a common feature of gastric cancers that reflects underlying mismatch-repair deficiency in the tumor, caused most frequently by methylation of the hMLH1 promoter. Tumors with MSI have been found to inactivate certain target genes by permitting an increased frequency of mutations in mononucleotide runs in their coding regions. Gastric tumors with MSI have a distinct clinicopathological profile with a relatively good prognosis. Using the simple and robust methodologies available, MSI detection in gastrointestinal tumors promises to be one of the first widely used molecular prognostic tests for human cancer. Here, we review the molecular context of this exciting prospect with respect to one of the world's most prevalent cancers, that of the stomach.

Adaptor Proteins, Signal Transducing↗

Genetic variability and molecular identification of Brazilian Biomphalaria species (Mollusca: Planorbidae).

Freshwater snails belonging to the genus Biomphalaria are intermediate hosts of the trematode Schistosoma mansoni in the Neotropical region and Africa. In Brazil, one subspecies and ten species of Biomphalaria have been identified: B. glabrata, B. tenagophila, B. straminea, B. occidentalis, B. peregrina, B. kuhniana, B. schrammi, B. amazonica, B. oligoza, B. intermedia and B.t. guaibensis. However, only the first three species are found naturally infected with S. mansoni. The classical identification of these planorbids is based on comparison of morphological characteristics of the shell and male and female reproductive organs, which is greatly complicated by the extensive intra-specific variation. Several molecular techniques have been used in studies on the identification, genetic structure as well as phylogenetic relationships between these groups of organisms. Using the randomly amplified polymorphic DNAs (RAPD) analysis we demonstrated that B. glabrata exhibits a remarkable degree of intra-specific polymorphism. Thus, the genetics of the snail host may be more important to the epidemiology of schistosomiasis than those of the parasite itself. Using the simple sequence repeat anchored polymerase chain reaction (SSR-PCR) in intra-populational and intra-specific studies we have demonstrated that snails belonging to the B. straminea complex (B. straminea, B. kuhniana and B. intermedia) clearly presented higher heterogeneity. Using the low stringency polymerase chain reaction (LS-PCR) technique we were able to separate B. glabrata from B. tenagophila and B. tenagophila from B. occidentalis. To separate all Brazilian Biomphalaria species we used the restriction fragment length polymorphism (PCR-RFLP) of the internal transcribed spacer region (ITS) of the DNA gene. The method also proved to be efficient for the specific identification of DNA extracted from snail eggs. Recently we have sequenced the ITS2 region for phylogenetic studies of all Biomphalaria snails from Brazil.

Animals↗

Genome sequencing networks.

Genome sequencing projects have been undertaken in one of three ways: in a purpose-built and professionally staffed genome centre, by a small number of traditional research laboratories or by an extensive network of traditional research laboratories that are linked by the Internet. Sequencing networks are an attractive option in many circumstances as they are easy to create, bring together diverse types of expertise, integrate the eventual users of a genome sequence with its determination and generally foster a collaborative spirit.

Genome↗

Analysis of Vgamma/Jbeta trans-rearrangements in paediatric patients undergoing chemotherapy.

The frequency of the hybrid Vgamma/Jbeta trans-rearrangement in peripheral blood lymphocytes (PBLs) was analysed in a transversal study of paediatric patients (n = 210) with acute lymphoblastic leukaemia (ALL) and solid tumours (ST). Different amounts of DNA were used as the template for a nested polymerase chain reaction to evaluate the frequency of hybrid Vgamma/Jbeta genes, using silver-stained gels. The frequency of the rearrangement was evaluated in groups before, during and after therapy. A greatly increased frequency of Vgamma/Jbeta trans-rearrangement was found in PBLs of both groups of patients during exposure to chemotherapeutic agents compared with patients before chemotherapy. In patients who had finished treatment, the frequency of the rearrangement fell promptly to the baseline levels in ST but showed a slow decrease in ALL in those in whom increased levels could be found until 4 years after the end of treatment. We hypothesize that the chemotherapeutic agents are able to induce the Vgamma/Jbeta trans-rearrangement, but this is transient in most cases. The exact relationship between the persistence of the rearrangement and the occurrence of secondary leukaemia remains to be determined.

Anthracyclines↗

X-ray turns a blind eye to ferrous metal.

The case is reported of a 31-year-old man with a retained metallic intraocular foreign body (IOFB) in the left eye who underwent magnetic resonance imaging (MRI) for investigation of a subsequent unrelated brachial plexus injury Despite the patient providing good history of IOFB, the decision to proceed with MRI was based on screening orbit X-ray which was reported as normal. A review of published reports regarding screening recommendations for MRI for patients with IOFB is provided. A minimum recommendation is for prescreening questionnaire; belief of the patient history is critical. If there is any doubt after history and examination by an ophthalmologist, then computed tomography imaging of the orbits is recommended. Whether screening by plain X-ray imaging is worthwhile is debatable as the sensitivity and specificity of this modality is poor.

Adult↗

A prospective study of AIDS-associated cryptococcal meningitis in Thailand treated with high-dose amphotericin B.

OBJECTIVE: To assess kinetic of cryptococci in the cerebrospinal fluid (CSF) and outcome of AIDS-associated cyptococcal meningitis after high-dose amphotericin B. PATIENTS AND METHODS: A prospective study involving Thai adults (n=106) with cryptococcal meningitis associated with AIDS was conducted to determine the kinetic of cryptococci in CSF and prognostic factors affecting survival after high-dose amphotericin B (0.7 mg/kg/day) followed by oral azole treatment. Cerebrospinal fluids were collected for cryptococcal count and culture at weekly intervals for at least 2 weeks or until CSF cultures were negative for cryptococci. All patients were followed monthly for 1 year or until death in order to detect relapse or occurrence of any other opportunistic infection. RESULTS: A total of 106 AIDS patients with cryptococcal meningitis were enrolled. The geometric mean (range) total and viable cryptococcal counts in CSF on admission were 430,000 (1000 to 3.4 x 10(7)) and 31,000 (10 to 1.4 x 10(7)) per ml, respectively. Both total and viable cryptococcal counts declined monoexponentially with an elimination half life of 4 days. The cumulative CSF yeast clearance rates were 38% and 56% at 2 and 4 weeks, respectively. Early death was associated significantly with previous history of weight loss [relative risk (RR)=2.2; 95% CI, 1.2-3.9], Glasgow Coma Score <13 (RR=2.33; 95% CI, 1.55-3.50), and hypoalbuminaemia (P<0.001). Later mortality was associated delayed CSF yeast clearance (RR=3.6; 95% CI, 1.9--6.4) and relapse (RR=3.9; 95% CI, 1.4-10.8). CONCLUSION: High-dose amphotericin B was not as effective as previously thought. Cumulative mortality at 2 weeks, 4 weeks and 1 year were 16%, 24% and 76%, respectively.

AIDS-Related Opportunistic Infections↗