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Biomedical subjects

J A Irving

Publications and source records attributed to J A Irving.

At least 19 recordsLinked to original sources
PubMed2004

Human clade B serpins (ov-serpins) belong to a cohort of evolutionarily dispersed intracellular proteinase inhibitor clades that protect cells from promiscuous proteolysis.

Serpins are unique among the various types of active site proteinase inhibitors because they covalently trap their targets by undergoing an irreversible conformational rearrangement. Members of the serpin superfamily are present in the three major domains of life (Bacteria, Archaea and Eukarya) as well as several eukaryotic viruses. The human genome encodes for at least 35 members that segregate evolutionarily into nine (A-I) distinct clades. Most of the human serpins are secreted and circulate in the bloodstream where they reside at critical checkpoints intersecting self-perpetuating proteolytic cascades such as those of the clotting, thrombolytic and complement systems. Unlike these circulating serpins, the clade B serpins (ov-serpins) lack signal peptides and reside primarily within cells. Most of the human clade B serpins inhibit serine and/or papain-like cysteine proteinases and protect cells from exogenous and endogenous proteinase-mediated injury. Moreover, as sequencing projects expand to the genomes of other species, it has become apparent that intracellular serpins belonging to distinct phylogenic clades are also present in the three major domains of life. As some of these serpins also guard cells against the deleterious effects of promiscuous proteolytic activity, we propose that this cytoprotective function, along with similarities in structure are common features of a cohort of intracellular serpin clades from a wide variety of species.

Amino Acid Sequence↗
PubMed2002

Florid infectious mononucleosis: clinicopathological correlation in acute tonsillectomy.

In patients with infectious mononucleosis (IM), acute tonsillectomy is advocated only in the minority who develop severe airway compromise. In such florid cases, the pathological diagnosis of IM, well known to morphologically simulate that of lymphoma, is particularly challenging. The present case describes a 15-year old male with a clinical course consistent with IM in whom acute tonsillectomy was performed due to progressive airway obstruction. The striking histological findings emphasize the need for close clinicopathological correlation. Recently available ancillary studies are described which both surgeon and pathologist should be familiar with in the differentiation of IM from other lymphoproliferative conditions.

Adolescent↗
PubMed2001

Protein structural alignments and functional genomics.

Structural genomics-the systematic solution of structures of the proteins of an organism-will increasingly often produce molecules of unknown function with no close relative of known function. Prediction of protein function from structure has thereby become a challenging problem of computational molecular biology. The strong conservation of active site conformations in homologous proteins suggests a method for identifying them. This depends on the relationship between size and goodness-of-fit of aligned substructures in homologous proteins. For all pairs of proteins studied, the root-mean-square deviation (RMSD) as a function of the number of residues aligned varies exponentially for large common substructures and linearly for small common substructures. The exponent of the dependence at large common substructures is well correlated with the RMSD of the core as originally calculated by Chothia and Lesk (EMBO J 1986;5:823-826), affording the possibility of reconciling different structural alignment procedures. In the region of small common substructures, reduced aligned subsets define active sites and can be used to suggest the locations of active sites in homologous proteins.

Bacillus subtilis↗
PubMed2001

Sequence, organization, chromosomal localization, and alternative splicing of the human serine protease inhibitor gene hurpin (PI13) which is upregulated in psoriasis.

Hurpin (protease inhibitor 13; PI13) is the most recently identified member of the ovalbumin family of serine protease inhibitors (serpins). It is expressed in human epidermal keratinocytes and is downregulated by exposure to ultraviolet irradiation. A role for hurpin in the proliferation or differentiation of keratinocytes has been proposed because of its strong expression in proliferating cells and its deregulated expression in the lesional epidermis of psoriatic patients. Here, we report the cloning, chromosomal localization, and complete sequence of the human hurpin gene. By PCR-based screening of the GeneBridge 4 radiation hybrid panel, we mapped the gene to chromosome 18q21.3, close to a known cluster of ov-serpin genes. Using the full-length cDNA for hurpin, we identified two clones from an arrayed genomic P1 placental library that contain the entire hurpin gene. Sequencing revealed that the gene covers 12.253 kb and is comprised of eight exons and seven introns. The exon--intron boundaries are identical in position and phasing to those in other members of the 18q serpin gene cluster, and analysis of hurpin variants indicated that modified functional inhibitors, differing only in the CD interhelical loop, can be generated by differential splicing of exon 3. These data show that hurpin is a typical member of the 18q ovalbumin-serpins most closely related to the serpins squamous-cell carcinoma antigens 1 and 2.

Alternative Splicing↗
PubMed2001

The nursing shortage--it's back!

Nursing shortages have been cyclic events during the 1970s, 1980s, and early 1990s. Recent downsizings and reengineerings have witnessed professional nurses in reduction of workforce actions. Acute-care settings, with goals of increased productivity and cost reduction, have decreased ratios of professional to nonlicensed staff frequently forcing nurses to practice with fewer resources and in diverse healthcare settings. As inpatient settings find a higher acuity level of patients receiving care from a "leaner" high-percentage agency workforce, many experts believe we are beginning to experience a new wave of shortages that will be more critical than those of the past. Hospitals and other healthcare practice sites will experience a shortage of professionals necessary to provide care to patients and will be competing for those scarce resources. This article presents a discussion of the important factors of supply and demand related to the shortage and possible strategies for hospitals to use when approaching the large and complex challenge.

Delivery of Health Care↗
PubMed2001

Validation of the Hasford score in a demographic study in chronic granulocytic leukaemia.

Chronic granulocytic leukaemia (CGL) is a rare disease. For most patients the only curative treatment (an allogeneic stem cell transplant) is not available. Survival varies between a few months to many years from diagnosis, and an accurate prediction of the duration of survival could help patients and clinicians make informed decisions about the many treatment options. In 1984, the Sokal score was introduced to stratify patients into risk groups. Recently, a new prognostic scoring system was proposed by Hasford and co-workers for interferon treated patients. We have analysed survival on an unselected population based cohort of patients using both the Hasford and the Sokal scores. In the group overall, neither score was predictive of survival, but in younger patients (< 60 years) treated with interferon, the Hasford score was highly predictive of survival, dividing patients into groups with a five year survival of 77% (45 patients) v 33% (six patients) v 14% (31 patients) (p = 0.01).

Adolescent↗
PubMed2001

Mismatch repair defects as a cause of resistance to cytotoxic drugs.

In this short review, we aim to bring together the most recent evidence implicating mismatch repair pathway defects as a cause of drug resistance to a spectrum of chemotherapeutic agents in a variety of cancers. Experimental and clinical studies are discussed and possible strategies that may be employed to overcome the multidrug resistant phenotype afforded by such defects.

Base Pair Mismatch↗
PubMed2000

Simple modifications of the serpin reactive site loop convert SCCA2 into a cysteine proteinase inhibitor: a critical role for the P3' proline in facilitating RSL cleavage.

The human squamous cell carcinoma antigens (SCCA) 1 and 2 are members of the serpin family that are 92% identical in their amino acid sequence. Despite this similarity, they inhibit distinct classes of proteinases. SCCA1 neutralizes the papain-like cysteine proteinases, cathepsins (cat) S, L, and K; and SCCA2 inhibits the chymotrypsin-like serine proteinases, catG and human mast cell chymase. SCCA2 also can inhibit catS, as well as other papain-like cysteine proteinases, albeit at a rate 50-fold less than that of SCCA1. Analysis of the mechanism of inhibition by SCCA1 revealed that the reactive site loop (RSL) is important for cysteine proteinase inhibition. The inhibition of catS by a mutant SCCA2 containing the RSL of SCCA1 is comparable to that of wild-type SCCA1. This finding suggested that there were no motifs outside and only eight residues within the RSL that were directing catS-specific inhibition. The purpose of this study was to determine which of these residues might account for the marked difference in the ability of SCCA1 and SCCA2 to inhibit papain-like cysteine proteinases. SCCA2 molecules containing different RSL mutations showed that no single amino acid substitution could convert SCCA2 into a more potent cysteine proteinase inhibitor. Rather, different combinations of mutations led to incremental increases in catS inhibitory activity with residues in four positions (P1, P3', P4', and P11') accounting for 80% of the difference in activity between SCCA1 and SCCA2. Interestingly, the RSL cleavage site differed between wild-type SCCA2 and this mutant. Moreover, these data established the importance of a Pro residue in the P3' position for efficient inhibition of catS by both wild-type SCCA1 and mutated SCCA2. Molecular modeling studies suggested that this residue might facilitate positioning of the RSL within the active site of the cysteine proteinase.

Amino Acid Sequence↗
PubMed2000

Population-based study of the pattern of molecular markers of minimal residual disease in childhood and adult acute lymphoblastic leukemia: an assessment of the practical difficulty of representative sampling for trial purposes. Northern Region Haematology Group.

BACKGROUND: The prevalence, in unselected patients with acute lymphoblastic leukaemia (ALL), of clonal rearrangements suitable for minimal residual disease (MRD) studies has not been formally investigated. PROCEDURE: This was a prospective, demographic study of the frequency of molecular markers of MRD in all patients with ALL presenting over 5 years within the Northern Health Region of England (population 3.1 million). Presentation marrow samples were examined to detect informative markers. RESULTS: One hundred twenty-four children (age <15 years) developed non-Burkitt ALL. No material was available for study in 21. Eighty-six had clonal gene rearrangements (BCR/ABL, immunoglobulin heavy chain (IGH) and/or T cell receptor (TCR) gene rearrangements). All entered remission; 84 (68% of the original cohort) survived to become eligible for MRD studies. One hundred sixteen adults developed ALL, of whom 48 were not studied due to insufficient cellular material in the bone marrow aspirate or to logistical problems in central referral of samples from other hospitals. Material from elderly adults (age >55 years) was less likely to be sent for analysis, 36% vs. 59% (P = 0.024). Thirty-eight had BCR/ABL and/or IGH/TCR gene rearrangements. Thirty-one (27% of the original cohort) entered remission and became eligible for MRD studies. Informative gene rearrangements were more common in children than adults (83% vs. 63%, P < 0.003). CONCLUSIONS: The results reveal substantial potential, unintentional, selection bias. Large-scale multicentre studies of MRD in children may well produce clinically relevant and representative data. Those who mount similar studies in adults should not assume they will be similarly representative or as successful in accrual of material.

Adolescent↗
PubMed2000

Mitotic arrest of endometrial epithelium after paclitaxel therapy for breast cancer.

We report the histopathologic findings in endometrial curettings from a 31-year-old woman with dysfunctional uterine bleeding who had received paclitaxel therapy for breast carcinoma. Paclitaxel, a member of the taxane family of antineoplastic agents that is used in the treatment of breast carcinoma, ovarian carcinoma, and non-small cell lung carcinoma, acts by the simultaneous promotion of tubulin assembly into microtubules and inhibition of microtubule disassembly. The curettings in this case showed fragmented menstrual phase endometrium with striking numbers of mitotic figures. Cell divisions were arrested in metaphase. Glandular epithelial cells showed strong immunoreactivity for bcl-2 and MIB-1. We attribute this marked morphologic effect to paclitaxel-induced mitotic arrest of the endometrium.

Adenocarcinoma↗
PubMed2000

Phylogeny of the serpin superfamily: implications of patterns of amino acid conservation for structure and function.

We present a comprehensive alignment and phylogenetic analysis of the serpins, a superfamily of proteins with known members in higher animals, nematodes, insects, plants, and viruses. We analyze, compare, and classify 219 proteins representative of eight major and eight minor subfamilies, using a novel technique of consensus analysis. Patterns of sequence conservation characterize the family as a whole, with a clear relationship to the mechanism of function. Variations of these patterns within phylogenetically distinct groups can be correlated with the divergence of structure and function. The goals of this work are to provide a carefully curated alignment of serpin sequences, to describe patterns of conservation and divergence, and to derive a phylogenetic tree expressing the relationships among the members of this family. We extend earlier studies by Huber and Carrell as well as by Marshall, after whose publication the serpin family has grown functionally, taxonomically, and structurally. We used gene and protein sequence data, crystal structures, and chromosomal location where available. The results illuminate structure-function relationships in serpins, suggesting roles for conserved residues in the mechanism of conformational change. The phylogeny provides a rational evolutionary framework to classify serpins and enables identification of conserved amino acids. Patterns of conservation also provide an initial point of comparison for genes identified by the various genome projects. New homologs emerging from sequencing projects can either take their place within the current classification or, if necessary, extend it.

Amino Acid Sequence↗
PubMed2000

A single amino acid substitution affects substrate specificity in cysteine proteinases from Fasciola hepatica.

The trematode Fasciola hepatica secretes a number of cathepsin L-like proteases that are proposed to be involved in feeding, migration, and immune evasion by the parasite. To date, six full cDNA sequences encoding cathepsin L preproproteins have been identified. Previous studies have demonstrated that one of these cathepsins (L2) is unusual in that it is able to cleave substrates with a proline in the P2 position, translating into an unusual ability (for a cysteine proteinase) to clot fibrinogen. In this study, we report the sequence of a novel cathepsin (L5) and compare the substrate specificity of a recombinant enzyme with that of recombinant cathepsin L2. Despite sharing 80% sequence identity with cathepsin L2, cathepsin L5 does not exhibit substantial catalytic activity against substrates containing proline in the P2 position. Molecular modeling studies suggested that a single amino acid change (L69Y) in the mature proteinases may account for the difference in specificity at the S2 subsite. Recombinant cathepsin L5/L69Y was expressed in yeast and a substantial increase in the ability of this variant to accommodate substrates with a proline residue in the P2 position was observed. Thus, we have identified a single amino acid substitution that can substantially influence the architecture of the S2 subsite of F. hepatica cathepsin L proteases.

Amino Acid Sequence↗
PubMed1999

Human ovalbumin serpin evolution: phylogenic analysis, gene organization, and identification of new PI8-related genes suggest that two interchromosomal and several intrachromosomal duplications generated the gene clusters at 18q21-q23 and 6p25.

The human ovalbumin (ov) serpins are associated with tumorigenesis, inflammation, and protection from autolysis by granule proteinases. Their genes are located at 18q21 or 6p25, falling into two structurally very similar but distinct categories depending on the presence or absence of a particular exon. Analysis of ov-serpin gene structure provides an opportunity to elucidate the mechanisms contributing to the formation of the larger serpin gene superfamily. Here we have identified a new gene (PI8L1) at 6p25 that is 72% identical to the 18q21 gene PI8. FISH analysis using the 3' untranslated region of PI8 yielded an additional signal at 18q23, separable from the known 18q21.3 signal by the t(1;18)(p32;q23) chromosomal translocation. The presence of more than one PI8-related gene was confirmed by analysis of human genomic DNA using the same probe. Cloning and analysis of PI8 showed that its intron number and phasing are identical to those of the 6p25 genes PI6, PI9, and ELANH2, and it lacks the interhelical variable loop exon found in other 18q21 genes. PCR analysis demonstrated that PI5 at 18q21 also lacks this exon, indicating that it is organized identically to the 6p25 genes. By contrast, PI10 and megsin have this exon and resemble the other 18q21 genes, PLANH2, SCCA-1, and SCCA-2, in structure. Using these data with an ov-serpin phylogenic tree we have constructed, we propose that the ov-serpin gene clusters arose via interchromosomal duplication of PI5 (or a precursor) to 6p25, followed by duplication at 6p25, and a more recent interchromosomal duplication from 6p25 to 18q to yield PI8.

3' Untranslated Regions↗
PubMed1999

Serpins in the Caenorhabditis elegans genome.

Data mining in genome sequences can identify distant homologues of known protein families, and is most powerful if solved structures are available to reveal the three-dimensional implications of very dissimilar sequences. Here we describe putative serpin sequences identified with very high statistical significance in the Caenorhabditis elegans genome. When mapped onto vertebrate serpins such as alpha1-antitrypsin, they suggest novel structural features. Some appear complete, some show extensive deletions, and others appear to contain only the C-terminal part of the known serpin fold, probably in partnership with N-terminal regions that have conformations unlike those of known serpins. The observation of such striking sequence similarity, in proteins that must have significantly different overall structures, substantially extends the structural characteristics of the serpin family of proteins.

Amino Acid Sequence↗
PubMed1999

Analysis of CD34 populations in mobilised peripheral blood stem cell harvests and in bone marrow by fluorescent in situ hybridisation for the bcr/abl gene fusion in patients with chronic granulocytic leukaemia.

For those patients ineligible for allogeneic bone marrow transplant and who are non-responsive to interferon, autotransplant with peripheral blood stem cells (PBSC) mobilised after intensive chemotherapy, may provide a novel approach to improve prognosis in patients with chronic granulocytic leukaemia. PBSC harvests are assessed for CD34-positive cell numbers, which serve as an indicator of engraftment potential, and are also analysed cytogenetically to ascertain tumour cell contamination. However, a more accurate assessment of PBSC harvest contamination requires investigation of the Philadelphia (Ph) status of the CD34pos population, in which the cells that provide long-term engraftment are contained. In this study, we have analysed these levels in mobilised PBSC and also in bone marrow (BM) harvests, taken several weeks prior to mobilising chemotherapy. Using fluorescent in situ hybridisation for the bcr/abl gene fusion, we have shown that the median number of Ph negative cells in CD34pos isolated populations was 14.95% in BM compared to 79.05% in PBSC harvests and that in all PBSC samples tested, Ph positivity in CD34pos populations was always detectable either by FISH or one round PCR methods. In paired assessments of both PBSC and BM harvests, higher levels of Ph negative CD34pos cells (> or = 14%) isolated from BM harvests, taken prior to intensive chemotherapy, correlated with higher levels of Ph negative CD34pos cells (> or = 78.5%) in PBSC harvests. These data may aid in the selection of patients for whom PBSC harvesting, after mobilisation, is more likely to achieve an autograft product containing predominantly Ph negative CD34pos cells and may exclude those patients for whom the risk, morbidity and expense of stem cell harvesting may have no apparent benefit over a chronic phase BM harvest.

Adult↗
PubMed1998

Molecular remission in Philadelphia-positive adult acute lymphoblastic leukaemia rapidly induced by conventional-dose chemotherapy.

This report describes a patient presenting with Ph-positive ALL. RT-PCR analysis of diagnostic marrow revealed the presence of three bcr/abl transcripts; the ALL type ela2 along with the CML types, b2a2 and b3a2. After initial induction therapy, bcr/abl transcripts were only detectable after two rounds of PCR but after MIDAC consolidation, remission samples were two-round negative. The relationship between the unusual molecular biological profile of this leukaemia and the rapid attainment of molecular remission is discussed.

Adult↗
PubMed1998

Collection of Philadelphia-negative peripheral blood progenitor cells in unselected patients with chronic granulocytic leukaemia. Northern Regional Haematology Group.

Thirty unselected patients with chronic granulocytic leukaemia (CGL), age range 22-59 years, were treated with intensive chemotherapy and G-CSF to mobilize peripheral blood progenitor cells (PBPC). Chemotherapy was well tolerated and PBPC were collected by leukapheresis early during white cell recovery. PBPC collections considered adequate for engraftment were collected in 21 patients. Cytogenetic analysis of all collections in these patients showed >75% Ph negativity (range 79-100%) in 10. Successful collections, ie those >75% Ph negative and with total cell count of >1 x 10(6) CD34+ve cells/kg or >20 x 10(4) CFU-GM/kg were further analysed by Southern blot or RT-PCR. All samples were positive for the bcr/abl transcript. Patients with a low Sokal score (<0.8) were more likely to achieve a successful collection. In contrast, there was no association between transcript expression and likelihood of successful collection. We have confirmed that it is possible to mobilize and collect Ph-negative enriched PBPC in unselected patients with CGL. This procedure is more likely to be successful earlier rather than later in the course of the disease. Whether such collections will give an advantage over unmanipulated autologous bone marrow transplantation in CGL requires further study, but our experience suggests that suitable material for autologous rescue can be obtained from approximately one third of eligible, unselected young patients.

Adult↗