Putting a human face on neurologic illness.
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Brain Diseases↗
Biomedical subjects
M O'Reilly
Publications and source records attributed to M O'Reilly.
Quantification of red blood cells using atomic force microscopy.
For humans the sizes and shapes of their red blood cells are important indicators of well being. In this study, the feasibility of using the atomic force microscope (AFM) to provide the sizes and shapes of red blood cells has been investigated. An immobilisation procedure has been developed that enabled red blood cells to be reliably imaged by contact AFM in air. The shapes of the red blood cells were readily apparent in the AFM images. Various cell quantification parameters were investigated, including thickness, width, surface area and volume. Excellent correlation was found between the AFM-derived immobilised mean cell volume (IMCV) parameter and the mean cell volume (MCV) parameter used in current haematological practice. The correlation between MCV and IMCV values has validated the immobilisation procedure by demonstrating that the significant cell shrinkage that occurs during immobilisation and drying does not introduce quantification artifacts. Reliable IMCV values were obtained by quantifying 100 red blood cells and this typically required 3-5 AFM images of 100 microm x 100 microm area. This work has demonstrated that the AFM can provide in a single test the red blood cell size and shape data needed in the assessment of human health.
Anemia, Macrocytic↗
New family of regulators in the environmental signaling pathway which activates the general stress transcription factor sigma(B) of Bacillus subtilis.
Expression of the general stress regulon of Bacillus subtilis is controlled by the alternative transcription factor sigma(B), which is activated when cells encounter growth-limiting energy or environmental stresses. The RsbT serine-threonine kinase is required to convey environmental stress signals to sigma(B), and this kinase activity is magnified in vitro by the RsbR protein, a positive regulator important for full in vivo response to salt or heat stress. Previous genetic analysis suggested that RsbR function is redundant with other unidentified regulators. A search of the translated B. subtilis genome found six paralogous proteins with significant similarity to RsbR: YetI, YezB, YkoB, YojH, YqhA, and YtvA. Their possible regulatory roles were investigated using three different approaches. First, genetic analysis found that null mutations in four of the six paralogous genes have marked effects on the sigma(B) environmental signaling pathway, either singly or in combination. The two exceptions were yetI and yezB, adjacent genes which appear to encode a split paralog. Second, biochemical analysis found that YkoB, YojH, and YqhA are specifically phosphorylated in vitro by the RsbT environmental signaling kinase, as had been previously shown for RsbR, which is phosphorylated on two threonine residues in its C-terminal region. Both residues are conserved in the three phosphorylated paralogs but are absent in the ones that were not substrates of RsbT: YetI and YezB, each of which bears only one of the conserved residues; and YtvA, which lacks both residues and instead possesses an N-terminal PAS domain. Third, analysis in the yeast two-hybrid system suggested that all six paralogs interact with each other and with the RsbR and RsbS environmental regulators. Our data indicate that (i) RsbR, YkoB, YojH, YqhA, and YtvA function in the environmental stress signaling pathway; (ii) YtvA acts as a positive regulator; and (iii) RsbR, YkoB, YojH, and YqhA collectively act as potent negative regulators whose loss increases sigma(B) activity more than 400-fold in unstressed cells.
Bacillus subtilis↗
How the multifunctional yeast Rap1p discriminates between DNA target sites: a crystallographic analysis.
Rap1p from Saccharomyces cerevisiae is a multifunctional, sequence-specific, DNA-binding protein involved in diverse cellular processes such as transcriptional activation and silencing, and is an essential factor for telomere length regulation and maintenance. In order to understand how Rap1p discriminates between its different DNA-binding sites, we have determined the crystal structure of the DNA-binding domain of the Rap1p (Rap1pDBD) in complex with two different DNA-binding sites. The first DNA sequence is the HMRE binding site found at silencers, which contains four base-pair substitutions in comparison to the telomeric binding site present in our earlier crystal structure of the Rap1pDBD-TeloA complex. The second complex contains an alternative telomeric binding site, TeloS, in which two half-sites are spaced closer together than in the TeloA complex. The determination of these structures was complicated by the presence of merohedral twinning in the crystals. Through identification of the twinning operator and determination of the twin fraction of the crystals, we were able to deconvolute the twinned intensities into their untwinned components, and to calculate electron density maps for both complexes. The structural information shows that the two domains present in the Rap1pDBD bind to these two biologically relevant binding sites through subtle side-chain movements at the protein-DNA interface, rather than through global domain rearrangements.
Amino Acid Sequence↗
An interactive approach to treating prostate cancer.
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Humans↗
An assessment of the aggressive potential of radiolucencies related to the mandibular molar teeth.
AIM: The purpose of this study was to outline the radiographic appearance of radiolucent lesions related to the molar teeth and to determine which features indicate aggressive lesions. PATIENTS AND METHODS: Panoramic radiographs were reviewed in 66 patients with radiolucencies related to the molar teeth. The radiographic appearances of the lesions were assessed with regard to location and size, and the relationship to the molar teeth. Radiographic evidence of aggression was assessed and pathology reviewed. RESULTS: Nineteen patients had aggressive and 47 had non-aggressive radiolucent lesions. The aggressive lesions included keratocysts, unicystic ameloblastoma, adenoid cystic carcinoma, giant cell granuloma, myxofibroma, chondroblastic osteosarcoma, mestastases and squamous cell carcinoma of the tongue invading the mandible. CONCLUSION: The differential diagnosis of radiolucent lesions in the mandible can be difficult using panoramic radiographs alone. Helpful features in determining aggression were older patients, larger lesions, Lodwick type IC tumour border, condition of the mandibular cortex, movement of adjacent teeth and the relationship of the inferior alveolar canal.
Adult↗
Expression of a new operon from Bacillus subtilis, ykzB-ykoL, under the control of the TnrA and PhoP-phoR global regulators.
The ykzB and ykoL genes encode two peptides, of 51 and 60 amino acids, the functions of which are unknown. The ykzB and tnrA genes are contiguous and transcribed divergently. Expression of ykzB and ykoL is induced by glutamate and is under the control of the TnrA global regulator of nitrogen utilization. TnrA regulated its own synthesis in glutamate minimal medium. Two DNA sequences (TnrAB1 and TnrAB2) homologous to the TnrA binding site are present in the region between tnrA and ykzB. Deletion mapping indicated that the TnrAB2 binding site was involved in activation of the ykzB promoter. In addition, transcription of tnrA depends on the presence of the TnrAB1 binding site. The ykzB and ykoL genes are probably in the same transcriptional unit. A single promoter involved in transcription in the presence of glutamate was mapped by primer extension. ykoL expression was induced by phosphate limitation and depended on the PhoP-PhoR two-component regulatory system. Its promoter was mapped to the region between ykoL and ykzB. Four boxes similar to the PhoP binding site are present upstream from the ykoL promoter. These boxes are probably recognized by PhoP approximately P during the activation of transcription in phosphate limitation conditions.
Bacillus subtilis↗
Ribozyme-based therapeutic approaches for autosomal dominant retinitis pigmentosa.
PURPOSE: To design, generate, and compare in vitro a range of hammerhead ribozymes targeting retinal transcripts implicated in autosomal dominant retinitis pigmentosa (adRP) and thereby identify ribozymes that may be valuable as therapeutic agents for adRP. To address mutational heterogeneity in rhodopsin and peripherin-linked adRP using mutation-independent ribozyme-based therapeutic approaches. METHODS: Ribozyme and cDNAs constructs were cloned into pcDNA3 and expressed in vitro from the T7 promoter. Cleavage reactions were separated on polyacrylamide gels, visualized by autoradiography, and quantified using an instant imager. Ribozymes targeting rhodopsin and peripherin transcripts in a mutation-independent manner (Rz9, Rz10, and Rz40) and a multimeric ribozyme (RzMM) targeting rhodopsin transcripts were evaluated for in vitro activity. Parameters such as V:(max), K:(m), k(2) and k(-1) were established for each ribozyme. RESULTS: Four ribozymes targeting retinal transcripts were evaluated. Mutation-independent ribozymes targeting degenerate sites or untranslated regions in retinal transcripts resulted in cleavage products of predicted size, whereas transcripts from modified replacement genes remained intact. Detailed kinetic evaluation of ribozymes revealed substantial differences in cleavage rates between ribozymes. CONCLUSIONS: Mutation-independent hammerhead ribozymes targeting rhodopsin and peripherin have been screened in vitro, and a number of extremely efficient ribozymes identified subsequent to detailed kinetic analyses, suggesting that these ribozymes may provide mutation-independent methods of treating adRP. These are the first ribozymes reported that potentially will provide benefit for inherited retinopathies.
Autoradiography↗
Tuberculosis of the breast presenting as carcinoma.
Breast infections caused by Mycobacterium tuberculosis, although rare in western countries, should not be forgotten as a cause of a breast lump presenting clinically and radiologically as a carcinoma in the older patient who gives a history of previous tuberculosis. We report the case of an 84-year-old woman with a breast lump showing noncaseating granulomas on histology who developed a sinus track after excision biopsy of the lump. The patient responded to empiric treatment with anti-tuberculosis drugs and remains well 2 years after presentation.
Aged↗
A sandwich enzyme-linked immunoabsorbent assay for measurement of picogram quantities of murine granulocyte colony-stimulating factor.
Granulocyte colony-stimulating factor (G-CSF) stimulates the proliferation and differentiation of hematopoietic progenitor cells of the neutrophil lineage. Measurement of murine G-CSF levels will allow examination of its role in host defense using murine models. Therefore, we developed a sensitive sandwich enzyme-linked immunoabsorbent assay (ELISA) for murine G-CSF. A polyclonal antibody to recombinant murine G-CSF was produced in rabbits and isolated using a protein A column. This purified native IgG served as the capture antibody and a portion of the IgG was biotinylated to serve as the developing antibody. Specificity was verified by lack of reactivity to GM-CSF, IL-6, IL-3, prolactin, and growth hormone. The lower limit of sensitivity routinely extended to 16 pg/ml in multiple ELISAs. Intra-assay coefficient of variation (CV) ranged from 3.4 to 21.5% across the detection limits of the assay, with the greatest variance occurring near the standard curve maximum. Interassay CV ranged from 11.5 to 23.3%. The ability of the ELISA to detect G-CSF in different sample preparations was examined in RPMI 1640 with 10% FCS, Hanks balanced salt solution, PBS/Tween-20/2% FCS, and the dilution media for ELISA (10% BLOTTO/PBS/0.05% Tween-20). Average recovery in these media ranged from 98 to 107%. Heparin anti-coagulated normal mouse plasma had a suppressive effect on the ELISA that varied between individual mice. Recovery was also determined from liver, spleen, and lung homogenate suspensions at dilutions of 1:5, 1:10, and 1:20 in dilution buffer. Recovery from liver was optimal at the 1:10 and 1:20 dilutions at 105%, with that of the 1:5 dilution at 135%. Recovery from spleen ranged from 94 to 96%. Lung homogenate displayed enhanced recovery (139% or greater) across all dilutions. The ability of the assay to detect G-CSF was explored by measurement of G-CSF levels in peritoneal lavage following polymicrobial intra-abdominal infection. Peak levels of G-CSF production occurred at 16 h after cecal ligation and puncture surgery with 18- and 21-guage needles (75.7 ng/ml and 111.4 ng/ml, respectively) as compared to the sham animals (0.61 ng/ml). The assay was found to be specific, sensitive, and accurate for measurement of murine G-CSF in a variety of sample types.
Animals↗
The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex.
Acarbose is a naturally occurring pseudo-tetrasaccharide. It has been used in conjunction with other drugs in the treatment of diabetes where it acts as an inhibitor of intestinal glucosidases. To probe the interactions of acarbose with other carbohydrate recognition enzymes, the crystal structure of E. coli maltodextrin phosphorylase (MalP) complexed with acarbose has been determined at 2.95 A resolution and refined to crystallographic R-values of R (Rfree) = 0.241 (0.293), respectively. Acarbose adopts a conformation that is close to its major minimum free energy conformation in the MalP-acarbose structure. The acarviosine moiety of acarbose occupies sub-sites +1 and +2 and the disaccharide sub-sites +3 and +4. (The site of phosphorolysis is between sub-sites -1 and +1.) This is the first identification of sub-sites +3 and +4 of MalP. Interactions of the glucosyl residues in sub-sites +2 and +4 are dominated by carbohydrate stacking interactions with tyrosine residues. These tyrosines (Tyr280 and Tyr613, respectively, in the rabbit muscle phosphorylase numbering scheme) are conserved in all species of phosphorylase. A glycerol molecule from the cryoprotectant occupies sub-site -1. The identification of four oligosaccharide sub-sites, that extend from the interior of the phosphorylase close to the catalytic site to the exterior surface of MalP, provides a structural rationalization of the substrate selectivity of MalP for a pentasaccharide substrate. Crystallographic binding studies of acarbose with amylases, glucoamylases, and glycosyltranferases and NMR studies of acarbose in solution have shown that acarbose can adopt two different conformations. This flexibility allows acarbose to target a number of different enzymes. The two alternative conformations of acarbose when bound to different carbohydrate enzymes are discussed.
Acarbose↗
Telomerases.
Telomerases are RNA-dependent polymerases that catalyse the synthesis of the telomeric DNA at the tips of eukaryotic chromosomes. The recent identification of the catalytic subunit of telomerases from several different species suggests that the core of the telomerase is conserved. The proposed sequence and structural homology between the telomerase catalytic subunit and reverse transcriptases, together with a wealth of genetic and biochemical information, has led to significant advances in our understanding of the mechanism by which telomerases synthesise telomeric DNA.
Amino Acid Sequence↗
Indirect versus direct measurement of brachial plexus depth.
UNLABELLED: Supraclavicular nerve blocks are effective but may be complicated by pneumothorax. We hypothesized that, to avoid this complication, the depths of the brachial plexus and the lung could be estimated to guide needle placement. In 17 patients undergoing surgical relief of thoracic outlet syndrome, we designated a point on the skin midway between the clavicle and the trapezius muscle, in line with the most lateral point of the arterial pulsation in the supraclavicular fossa, to make preoperative height measurements relative to the clavicle and then intraoperative depth measurements of the plexus, artery, and pleura. The height of the reference point above the top of clavicle did not differ significantly from the depth of the plexus. The height of the reference point above the top, middle, and bottom of the clavicle differed significantly from the pleural depth (P = 0.0001, P = 0.0001, P = 0.0005, respectively). Patient weight correlated significantly with the depth of the plexus (P = 0.004, r2 = 0.45), artery (P = 0.0003, r2 = 0.42), and pleura (P = 0.0003, r2 = 0.58). We conclude that it is possible to accurately estimate the depth of the brachial plexus in the supraclavicular fossa. IMPLICATIONS: In this study, we sought to minimize the risk of pneumothorax when approaching the brachial plexus through the supraclavicular fossa by developing a technique that could accurately estimate the depth of the nerves, within a range that is well clear of the lung.
Adult↗
Immunopathologic responses to non-lethal sepsis.
Although sepsis causes significant morbidity and mortality, its basic pathology is still not well understood. We investigated the inflammatory and physiologic alterations of non-lethal sepsis using cecal ligation and puncture (CLP), a model that induces peritonitis due to mixed intestinal flora, reproducing the complex immunology of sepsis. Groups of mice were subjected to CLP (25G needle) or sham surgery, had minimitters implanted to continuously monitor temperature and activity, and were sacrificed daily for 6 days. There was significant hypothermia (6-13 hrs post-surgery), and decreases in activity (to day 4) and weight (to day 3) but no mortality in the CLP group. Blood analyses of the CLP-treated mice showed reduced hemoglobin, platelets, lymphocytes, monocytes, and neutrophils, compared to sham animals. Both groups had nearly equivalent neutrophil influx into the peritoneum. Plasma and peritoneal G-CSF, IL-6, as well as the murine chemokines KC and MIP2-alpha were significantly higher in the CLP-treated mice at day 1. Plasma and peritoneal TNF were low (<70 pg/mL). While there was elevated IL-1beta in the peritoneum of the CLP-treated mice, this cytokine was not detected in the plasma in either treatment group. Cytokines were not detected in the pulmonary airspace of the CLP-treated mice and PMNs were not recruited to this site. Our data shows altered immunopathology in non-lethal sepsis with significant blood and cytokine alterations. Since there was 100% survival, the inflammatory response was appropriate and probably even protective.
Animals↗
Endotoxin, sepsis, and the primrose path.
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Animals↗
Angiostatin induces endothelial cell apoptosis and activation of focal adhesion kinase independently of the integrin-binding motif RGD.
Angiostatin, a fragment of plasminogen, has been identified and characterized as an endogenous inhibitor of neovascularization. We show that angiostatin treatment of endothelial cells in the absence of growth factors results in an increased apoptotic index whereas the proliferation index is unchanged. Angiostatin also inhibits migration and tube formation of endothelial cells. Angiostatin treatment has no effect on growth factor-induced signal transduction but leads to an RGD-independent induction of the kinase activity of focal adhesion kinase, suggesting that the biological effects of angiostatin relate to subversion of adhesion plaque formation in endothelial cells.
Angiostatins↗
Liver biopsy pathology in human immunodeficiency virus infection.
OBJECTIVES: To determine the hepatic changes in patients with human immunodeficiency virus (HIV) infection in Dublin and to assess the usefulness of liver biopsy in this condition. DESIGN: A consecutive series of liver biopsies was examined retrospectively and correlated with clinical findings. METHODS: A histological review was conducted of specimens from all patients who had undergone liver biopsy in a tertiary referral centre for HIV-infected patients in Dublin. RESULTS: Thirty-nine liver biopsies were studied from 36 patients. Thirty-one (86%) showed pathological changes. Non-specific changes were most frequent, followed by viral-induced chronic hepatitis (15 cases). Acute hepatitis was documented in five and cirrhosis in four cases. Five biopsies performed for pyrexia of unknown origin (PUO) or suspected tuberculosis showed granulomas. Organisms were rarely identified (2) and bile duct changes were uncommon. CONCLUSIONS: Liver biopsy was useful in detecting primary hepatic pathology and, in some cases, the cause of PUO, but not useful in detecting opportunistic infections despite their known presence in other organs.
Acute Disease↗
TGF-beta1 up-regulates the mRNA for the Na+/Ca2+ exchanger in neonatal rat cardiac myocytes.
Northern analyses of neonatal cardiac myocytes demonstrated that TGF-beta1 (5 ng/ml) stimulates and IL-1beta (5 ng/ml) decreases the steady-state levels of the mRNA coding for the Na+/Ca2+ exchanger. This is in agreement with the effects of TGF-beta1 and IL-1beta on beating rate and calcium uptake, suggesting that such effects might be mediated, at least partially, through up-regulation of the Na+/Ca2+ exchanger. Basal and TGF-beta1 stimulated mRNA levels were inhibited by the PKC inhibitors H7 (10 microM) and GF109203X (250 nM). In addition, apigenin (12.5 microM), a MAP kinase inhibitor, was able to inhibit basal mRNA levels for the exchanger. Cycloheximide (35.5 microM) had no effect on basal mRNA levels for the exchanger but steady-state levels were diminished in cells treated with TGF-beta1. Finally, actinomycin D (10 microM) inhibited both basal and TGF-beta1 stimulated mRNA levels, though with a more pronounced effect in the presence of TGF-beta1. These results suggest that a complex mechanism of regulation exists for the exchanger and that PKC and possibly MAP kinases might be involved. The up-regulation of this important protein for calcium extrusion, induced by TGF-beta1, might prepare cells to better overcome the calcium overload which occurs under cellular stress and might explain some of the cytoprotective effects of TGF-beta1.
Animals↗