Biomedical subjects

John Parkinson

Publications and source records attributed to John Parkinson.

At least 19 recordsLinked to original sources

PubMed2024

Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens.

The present study was undertaken to profile and compare the cecal microbial communities in conventionally (CONV) grown and raised without antibiotics (RWA) broiler chickens. Three hundred chickens were collected from five CONV and five RWA chicken farms on days 10, 24, and 35 of age. Microbial genomic DNA was extracted from cecal contents, and the V4-V5 hypervariable regions of the 16S rRNA gene were amplified and sequenced. Analysis of 16S rRNA sequence data indicated significant differences in the cecal microbial diversity and composition between CONV and RWA chickens on days 10, 24, and 35 days of age. On days 10 and 24, CONV chickens had higher richness and diversity of the cecal microbiome relative to RWA chickens. However, on day 35, this pattern reversed such that RWA chickens had higher richness and diversity of the cecal microbiome than the CONV groups. On days 10 and 24, the microbiomes of both CONV and RWA chickens were dominated by members of the phylum Firmicutes. On day 35, while Firmicutes remained dominant in the RWA chickens, the microbiome of CONV chickens exhibited am abundance of Bacteroidetes. The cecal microbiome of CONV chickens was enriched with the genus Faecalibacterium, Pseudoflavonifractor, unclassified Clostridium_IV, Bacteroides, Alistipes, and Butyricimonas, whereas the cecal microbiome of RWA chickens was enriched with genus Anaerofilum, Butyricicoccu, Clostridium_XlVb and unclassified Lachnospiraceae. Overall, the cecal microbiome richness, diversity, and composition were greatly influenced by the management program applied in these farms. These findings provide a foundation for further research on tailoring feed formulation or developing a consortium to modify the gut microbiome composition of RWA chickens.

Animals↗

PubMed2006

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

Biological Evolution↗

PubMed2005

Large-scale modelling as a route to multiple surface comparisons of the CCP module family.

Numerous mammalian proteins are constructed from a limited repertoire of module-types. Proteins belonging to the regulators of complement activation family--crucial for ensuring a complement-mediated immune response is targeted against infectious agents--are composed solely of complement control protein (CCP) modules. In the current study, CCP module sequences were grouped to allow selection of the most appropriate experimentally determined structures to serve as templates in an automated large-scale structure modelling procedure. The resulting 135 individual CCP module models, valuable in their own right, are available at the online database http://www.bru.ed.ac.uk/~dinesh/ccp-db.html. Comparisons of surface properties within a particular family of modules should be more informative than sequence alignments alone. A comparison of surface electrostatic features was undertaken for the first 28 CCP modules of complement receptor type 1 (CR1). Assignments to clusters based on surface properties differ from assignments to clusters based on sequences. This observation might reflect adaptive evolution of surface-exposed residues involved in protein-protein interactions. This illustrative example of a multiple surface-comparison was indeed able to pinpoint functional sites in CR1.

Amino Acid Sequence↗

PubMed2005

Interaction network containing conserved and essential protein complexes in Escherichia coli.

Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (approximately 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data. This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.

Alleles↗

PubMed2005

PartiGeneDB--collating partial genomes.

Owing to the high costs involved, only 28 eukaryotic genomes have been fully sequenced to date. On the other hand, an increasing number of projects have been initiated to generate survey sequence data for a large number of other eukaryotic organisms. For the most part, these data are poorly organized and difficult to analyse. Here, we present PartiGeneDB (http://www.partigenedb.org), a publicly available database resource, which collates and processes these sequence datasets on a species-specific basis to form non-redundant sets of gene objects-which we term partial genomes. Users may query the database to identify particular genes of interest either on the basis of sequence similarity or via the use of simple text searches for specific patterns of BLAST annotation. Alternatively, users can examine entire partial genome datasets on the basis of relative expression of gene objects or by the use of an interactive Java-based tool (SimiTri), which displays sequence similarity relationships for a large number of sequence objects in a single graphic. PartiGeneDB facilitates regular incremental updates of new sequence datasets associated with both new and exisitng species. PartiGeneDB currently contains the assembled partial genomes derived from 1.83 million sequences associated with 247 different eukaryotes.

Databases, Nucleic Acid↗

PubMed2005

Potential roles for diatomists in nanotechnology.

Diatoms produce diverse three-dimensional structures that, due to their exponential rate of growth, may be of use in the manufacture of components for nanotechnology as an alternative to present linear lithographic techniques. Vapor replacement of the silicon permits the conversion of diatom silica valves and other structures to metal/ceramics, with no loss of structure. The literature on diatom nanotechnology is reviewed, along with suggestions on how diatomists might enhance this emerging technology. There is a need for a systematics based catalog of parts (via genomics technologies), improved diatom culture techniques, better understanding of the mechanisms of diatom morphogenesis and motility, and genetic manipulation, mutagenesis, and selection, as via the chemostat-like compustat. Given the self-motility of raphid diatoms, they could form the basis for industrially useful nanobots.

Biomimetics↗

PubMed2005

Differential inhibition of inducible T cell cytokine secretion by potent iron chelators.

Effector functions and proliferation of T helper (Th) cells are influenced by cytokines in the environment. Th1 cells respond to a synergistic effect of interleukin-12 (IL-12) and interleukin-18 (IL-18) to secrete interferon-gamma (IFN-gamma). In contrast, Th2 cells respond to interleukin-4 (IL-4) to secrete IL-4, interleukin-13 (IL-13), interleukin-5 (IL-5), and interleukin-10 (IL-10). The authors were interested in identifying nonpeptide inhibitors of the Th1 response selective for the IL-12/IL-18-mediated secretion of IFN-gamma while leaving the IL-4-mediated Th2 cytokine secretion relatively intact. The authors established a screening protocol using human peripheral blood mononuclear cells (PBMCs) and identified the hydrazino anthranilate compound 1 as a potent inhibitor of IL-12/IL-18-mediated IFN-gamma secretion from CD3(+) cells with an IC(50) around 200 nM. The inhibitor was specific because it had virtually no effect on IL-4-mediated IL-13 release from the same population of cells. Further work established that compound 1 was a potent intracellular iron chelator that inhibited both IL-12/IL-18- and IL-4-mediated T cell proliferation. Iron chelation affects multiple cellular pathways in T cells. Thus, the IL-12/IL-18-mediated proliferation and IFN-gamma secretion are very sensitive to intracellular iron concentration. However, the IL-4-mediated IL-13 secretion does not correlate with proliferation and is partially resistant to potent iron chelation.

Cell Differentiation↗

PubMed2004

A transcriptomic analysis of the phylum Nematoda.

The phylum Nematoda occupies a huge range of ecological niches, from free-living microbivores to human parasites. We analyzed the genomic biology of the phylum using 265,494 expressed-sequence tag sequences, corresponding to 93,645 putative genes, from 30 species, including 28 parasites. From 35% to 70% of each species' genes had significant similarity to proteins from the model nematode Caenorhabditis elegans. More than half of the putative genes were unique to the phylum, and 23% were unique to the species from which they were derived. We have not yet come close to exhausting the genomic diversity of the phylum. We identified more than 2,600 different known protein domains, some of which had differential abundances between major taxonomic groups of nematodes. We also defined 4,228 nematode-specific protein families from nematode-restricted genes: this class of genes probably underpins species- and higher-level taxonomic disparity. Nematode-specific families are particularly interesting as drug and vaccine targets.

Animals↗

PubMed2004

Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites.

BACKGROUND: Parasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied model nematode parasite of rodents, which secretes products known to modulate host immunity. RESULTS: Taking a genomic approach to characterize potential secreted products, we analyzed expressed sequence tag (EST) sequences for putative amino-terminal secretory signals. We sequenced ESTs from a cDNA library constructed by oligo-capping to select full-length cDNAs, as well as from conventional cDNA libraries. SignalP analysis was applied to predicted open reading frames, to identify potential signal peptides and anchors. Among 1,234 ESTs, 197 (~16%) contain predicted 5' signal sequences, with 176 classified as conventional signal peptides and 21 as signal anchors. ESTs cluster into 742 distinct genes, of which 135 (18%) bear predicted signal-sequence coding regions. Comparisons of clusters with homologs from Caenorhabditis elegans and more distantly related organisms reveal that the majority (65% at P < e-10) of signal peptide-bearing sequences from N. brasiliensis show no similarity to previously reported genes, and less than 10% align to conserved genes recorded outside the phylum Nematoda. Of all novel sequences identified, 32% contained predicted signal peptides, whereas this was the case for only 3.4% of conserved genes with sequence homologies beyond the Nematoda. CONCLUSIONS: These results indicate that secreted proteins may be undergoing accelerated evolution, either because of relaxed functional constraints, or in response to stronger selective pressure from host immunity.

Animals↗

PubMed2004

Metabolic and functional protection by selective inhibition of nitric oxide synthase 2 during ischemia-reperfusion in isolated perfused hearts.

BACKGROUND: Drugs that selectively block nitric oxide synthase (NOS) 2 enzyme activity by inhibiting dimerization of NOS2 monomers have recently been developed. METHODS AND RESULTS: To investigate whether selective inhibition of NOS2 is cardioprotective, rats were pretreated for 2 days with BBS2, an inhibitor of NOS2 dimerization, at 15 mg/kg SC. Isolated buffer-perfused hearts from treated (n=9) and control (n=7) hearts were subjected to 20 minutes of ischemia followed by 60 minutes of reperfusion. NOS2 protein was upregulated in all hearts at the end of ischemia and of reperfusion; NOS2 enzyme activity was 60% lower in hearts from the treated animals. In the treated hearts, the increase in end-diastolic pressure was significantly attenuated at the end of ischemia, and the return of developed pressure at reperfusion was greater (P<0.05). Creatine kinase release at reperfusion was lower in treated hearts than in controls (P=0.02). At the end of ischemia and of reperfusion, myocardial ATP levels were significantly higher in the treated hearts than in controls (P<0.05). In the treated hearts under ischemic conditions, lactate content was higher and the lactate/pyruvate ratio was lower than in controls (P<0.05); GAPDH activity was higher; and G-3-P and aldose reductase activity were lower. At reperfusion, in the treated hearts, there was less histological damage and less apoptosis of cardiac muscle cells. CONCLUSIONS: Pretreatment with BBS2, a selective inhibitor of NOS2, improves contractile performance, preserves myocardial ATP, and reduces damage and death of cardiac myocytes during ischemia and reperfusion of isolated buffer-perfused rat hearts.

Adenosine Triphosphate↗

PubMed2004

PartiGene--constructing partial genomes.

UNLABELLED: Expressed sequence tags (ESTs) offer a low-cost approach to gene discovery and are being used by an increasing number of laboratories to obtain sequence information for a wide variety of organisms. The challenge lies in processing and organizing this data within a genomic context to facilitate large scale analyses. Here we present PartiGene, an integrated sequence analysis suite that uses freely available public domain software to (1) process raw trace chromatograms into sequence objects suitable for submission to dbEST; (2) place these sequences within a genomic context; (3) perform customizable first-pass annotation of the data; and (4) present the data as HTML tables and an SQL database resource. PartiGene has been used to create a number of non-model organism database resources including NEMBASE (http://www.nematodes.org) and LumbriBase (http://www.earthworms.org/). The packages are readily portable, freely available and can be run on simple Linux-based workstations. AVAILABILITY: PartiGene is available from http://www.nematodes.org/PartiGene and also forms part of the EST analysis software, associated with the Natural Environmental Research Council (UK) Bio-Linux project (http://envgen.nox.ac.uk/biolinux.html).

Chromatography↗

PubMed2004

NEMBASE: a resource for parasitic nematode ESTs.

NEMBASE (available at http://www.nematodes.org) is a publicly available online database providing access to the sequence and associated meta-data currently being generated as part of the Edinburgh-Wellcome Trust Sanger Institute parasitic nematode EST project. NEMBASE currently holds approximately 100 000 sequences from 10 different species of nematode. To facilitate ease of use, sequences have been processed to generate a non-redundant set of gene objects ('partial genome') for each species. Users may query the database on the basis of BLAST annotation, sequence similarity or expression profiles. NEMBASE also features an interactive Java-based tool (SimiTri) which allows the simultaneous display and analysis of the relative similarity relationships of groups of sequences to three different databases. NEMBASE is currently being expanded to include sequence data from other nematode species. Other developments include access to accurate peptide predictions, improved functional annotation and incorporation of automated processes allowing rapid analysis of nematode-specific gene families.

Animals↗

PubMed2004

Expressed sequence tags: analysis and annotation.

Expressed sequence tags (ESTs) present a special set of problems for bioinformatic analysis. They are partial and error-prone, and large datasets can have significant internal redundancy. To facilitate analysis of small EST datasets from in-house projects, we present an integrated "pipeline" of tools that take EST data from sequence trace to database submission. These tools also can be used to provide clustering of ESTs into putative genes and to annotate these genes with preliminary sequence similarity searches. The systems are written to use the public-domain LINUX environment and other openly available analytical tools.

Computational Biology↗

PubMed2003

Inducible nitric oxide synthase dimerization inhibitor prevents cardiovascular and renal morbidity in sheep with combined burn and smoke inhalation injury.

Inducible nitric oxide synthase (iNOS) is implicated in the pathogenesis of acute respiratory distress syndrome (ARDS). ARDS treatment is frequently complicated by significant extrapulmonary comorbidity. This study was designed to clarify the role of iNOS in mediating extrapulmonary comorbidity in sheep after combined burn and smoke inhalation injuries using a potent and highly selective iNOS dimerization inhibitor, BBS-2. Twenty-two female sheep were operatively prepared. After 5 days of recovery, tracheostomy was performed under ketamine-halothane anesthesia. Sheep were given a 40% total body surface third-degree burns and insufflated with cotton smoke (48 breaths, <40 degrees C). Sheep were divided into four groups: noninjured and nontreated (sham group; n = 6), noninjured but treated with BBS-2 (sham/BBS-2 group; n = 4), injured but nontreated (control group, n = 6), and injured but treated with 100 microg.kg-1.h-1 BBS-2 (BBS-2 group; n = 6). Evaluation was in a laboratory intensive care unit setting for 48 h. The sham group had stable cardiopulmonary and systemic hemodynamics. Control animals showed multiple signs of morbidity. Decreased left ventricular stroke work index and stroke volume index with elevated left atrial pressure indicated myocardial depression. Systemic vascular leak was evidenced by robust hemoconcentration, decreased plasma oncotic pressure, and increased transvascular fluid flux into the lymphatic system. Finally, severely impaired renal function (urinary output) was associated with adverse net fluid balance. Treatment with BBS-2 prevented all these morbidities without adversely effecting cardiovascular hemodynamics such as cardiac index and mean arterial pressure. The results identify a major role for iNOS in mediating extrapulmonary comorbidity in a clinically relevant and severe trauma model and support the use of highly selective iNOS inhibitors as novel treatments in critical care medicine.

Animals↗

PubMed2003

SimiTri--visualizing similarity relationships for groups of sequences.

Global sequence comparisons between large datasets, such as those arising from genome projects, can be problematic to display and analyze. We have developed SimiTri, a Java/Perl-based application, which allows simultaneous display and analysis of relative similarity relationships of the dataset of interest to three different databases. We illustrate its utility in identifying Caenorhabditis elegans genes that have distinct patterns of phylogenetic affinity suggestive of horizontal gene transfer. SimiTri is freely downloadable from http://www.nematodes.org/SimiTri/ and the source code is freely available from the authors.

Animals↗

PubMed2003

400000 nematode ESTs on the Net.

The parasitic nematode expressed sequence tag (EST) project, a collaboration between University of Edinburgh and the Wellcome Trust Sanger Institute in the UK and the Genome Sequencing Center, St Louis, MO, USA, is currently generating sequence information from >30 different species of nematode. Over 400000 nematode ESTs are now available and at least another 130000 are planned. Here, an update is provided on the status of the project and describes the database tools being developed to disseminate these data.

Animals↗

PubMed2002

Effects of selective inhibitors of nitric oxide synthase-2 dimerization on acute cardiac allograft rejection.

BACKGROUND: Nitric oxide synthase-2 (NOS2) is expressed during acute cardiac allograft rejection in association with myocardial inflammation, contractile dysfunction, and death of cardiomyocytes by necrosis and apoptosis. Recently, allosteric inhibitors of NOS2 monomer dimerization that block NOS2 activity have been developed. METHODS AND RESULTS: To investigate effects of selective NOS2 blockade, 15 mg/kg of BBS-1 or BBS-2 was administered twice daily subcutaneously to rats starting the day of heterotopic heart transplantation. Cardiac allograft survival was increased significantly, from 6.8 days in controls to 13.3 and to 14.2 days in NOS2-inhibited allografts. At day 5 after heart transplantation, synthesis of NOx was reduced by 53%. There were significantly fewer T lymphocytes and macrophages in the inflammatory infiltrate, as well as less edema and cardiomyocyte damage, and the International Society of Heart and Lung Transplantation score fell from 5 to 4 and 3.5. NOS2 and nitrotyrosine immunostaining and the mean numbers of apoptotic cells and of apoptotic cardiomyocytes were significantly diminished in the treated allografts. CONCLUSIONS: The data indicate that selective inhibition of NOS2 dimerization prolongs survival and reduces myocardial inflammation and cardiomyocyte damage in acute cardiac allograft rejection.

Acute Disease↗

PubMed2002

Making sense of EST sequences by CLOBBing them.

BACKGROUND: Expressed sequence tags (ESTs) are single pass reads from randomly selected cDNA clones. They provide a highly cost-effective method to access and identify expressed genes. However, they are often prone to sequencing errors and typically define incomplete transcripts. To increase the amount of information obtainable from ESTs and reduce sequencing errors, it is necessary to cluster ESTs into groups sharing significant sequence similarity. RESULTS: As part of our ongoing EST programs investigating 'orphan' genomes, we have developed a clustering algorithm, CLOBB (Cluster on the basis of BLAST similarity) to identify and cluster ESTs. CLOBB may be used incrementally, preserving original cluster designations. It tracks cluster-specific events such as merging, identifies 'superclusters' of related clusters and avoids the expansion of chimeric clusters. Based on the Perl scripting language, CLOBB is highly portable relying only on a local installation of NCBI's freely available BLAST executable and can be usefully applied to > 95 % of the current EST datasets. Analysis of the Danio rerio EST dataset demonstrates that CLOBB compares favourably with two less portable systems, UniGene and TIGR Gene Indices. CONCLUSIONS: CLOBB provides a highly portable EST clustering solution and is freely downloaded from: http://www.nematodes.org/CLOBB

Algorithms↗