John Murphy - Academia.edu (original) (raw)

Papers by John Murphy

A hybrid toxin targeted to melanotropin receptors and selectively cytotoxic to melanoma cell line... more A hybrid toxin targeted to melanotropin receptors and selectively cytotoxic to melanoma cell lines in vitro has recently been developed. The toxin, a recombinant fusion protein (designated l)ABlm-MSII), contains the peptide sequences of a-melanocyte-stimulating hormone (Â«- MSI I) and the catalytic (cytotoxic; Fragment A) and lipophilic (part of Fragment B) domains of diphtheria toxin. In the present study, binding of

This paper summarizes preliminary efforts at the Idaho National Engineering and Environmental Lab... more This paper summarizes preliminary efforts at the Idaho National Engineering and Environmental Laboratory (INEEL) to develop a simplified methodology for estimating risk reduction resulting from waste management operations. The method involves constructing human safety and health site risk curves resulting from waste and materials stored at the INEEL. Risk from waste management activities at the site is also analyzed. Finally,

Kernan/Climate Change Impacts on Freshwater Ecosystems, 2010

... Piet FM Verdonschot, Daniel Hering, John Murphy, Sonja C. Jähnig, Neil L. Rose, Wolfram Graf,... more ... Piet FM Verdonschot, Daniel Hering, John Murphy, Sonja C. Jähnig, Neil L. Rose, Wolfram Graf, Karel ... The effects of climate change on hydraulics and morphology at the reach scale ... which are often readily available, are sufficient to characterize flow regime (eg Clausen & Biggs ...

Converged Networking, 2003

Methods in enzymology, 2000

... Sci. USA 91, 3127 (1994). 6 M. Yamizumi, E. Mekada, T. Uchida, and Y. Okada, Cell 15, 245 (19... more ... Sci. USA 91, 3127 (1994). 6 M. Yamizumi, E. Mekada, T. Uchida, and Y. Okada, Cell 15, 245 (1978). DB Cawley, HR Herschman, DG Gilliland, and RJ Collier, Cell 22, 563 (1980). 8 JR Murphy, W. Bishai, M. Borowski, A. Miyanohara, J. Boyd, and S. Nagle, Proc. Nad. Acad. Sci. ...

Nature, Jan 30, 1998

The virulent phenotype of the pathogenic bacterium Corynebacterium diphtheriae is conferred by di... more The virulent phenotype of the pathogenic bacterium Corynebacterium diphtheriae is conferred by diphtheria toxin, whose expression is an adaptive response to low concentrations of iron. The expression of the toxin gene (tox) is regulated by the repressor DtxR, which is activated by transition metal ions. X-ray crystal structures of DtxR with and without (apo-form) its coordinated transition metal ion have established the general architecture of the repressor, identified the location of the metal-binding sites, and revealed a metal-ion-triggered subunit-subunit 'caliper-like' conformational change. Here we report the three-dimensional crystal structure of the complex between a biologically active Ni(II)-bound DtxR(C102D) mutant, in which a cysteine is replaced by an aspartate at residue 102, and a 33-base-pair DNA segment containing the toxin operator toxO. This structure shows that DNA interacts with two dimeric repressor proteins bound to opposite sides of the tox operator. ...

Digestive diseases and sciences, 1997

Activated mucosal T lymphocytes correlate with the intestinal inflammation of inflammatory bowel ... more Activated mucosal T lymphocytes correlate with the intestinal inflammation of inflammatory bowel disease. Activated T cells elaborate interferon-gamma (IFN-gamma) and express high-affinity interleukin-2 (IL-2) receptors. The IL-2/diphtheria toxin fusion protein (DAB389IL-2) has been shown to specifically kill high affinity IL-2 receptor-bearing cells. We tested whether DAB389IL-2 could specifically target activated lamina propria lymphocytes. Lymphocytes were activated in vitro with phytohemagglutinin and IL-2 for 24-48 hr. Toxin efficacy was determined by the [14C]leucine incorporation, IFN-gamma ELISA, and flow cytometry. DAB389IL-2 (10(-11) M) inhibited protein synthesis by 80% in activated lamina propria lymphocytes. This inhibition was blocked by coculture of either excess IL-2 or a nonfunctional IL-2 diphtheria toxin mutant protein. DAB389IL-2 (10(-12) M) also significantly reduced the numbers of activated helper T cells and IFN-gamma levels in 24-hr cultures. DAB389IL-2 speci...

Journal of bacteriology, 1995

A plasmid of 45 kb, designated pNOB8, was found in high copy number in a new heterotrophic Sulfol... more A plasmid of 45 kb, designated pNOB8, was found in high copy number in a new heterotrophic Sulfolobus isolate, NOB8H2, from Japan. Dissemination of the plasmid occurred in six cultures of nine different Sulfolobus strains when small amounts of the donor were added. These mixed cultures exhibited a high average copy number of the plasmid, between 20 and 40 per chromosome, and showed a marked growth retardation. Horizontal transfer of pNOB8 was proved by isolating transcipients from mating mixtures via single colonies. In these isolates, the copy number of the plasmid appeared to be subject to a control mechanism. Cell-free filtrates of donor cultures did not transmit the plasmid, and plating of the donor on lawns of recipients did not result in plaque formation, suggesting that the transfer was not mediated by a virus. Rapid formation of cell-to-cell contacts between differently stained donor and recipient partners was demonstrated after the two strains were mixed. Electron microscop...

Journal of dairy science, 1987

The objective was to develop a method for estimating intestinal availability of rumen undegradabl... more The objective was to develop a method for estimating intestinal availability of rumen undegradable protein. One-gram samples of six feedstuffs were placed into small (3.5 X 5.5 cm) nylon bags (pore size 48 micron). Bags were heat sealed and ruminally incubated in a polyester mesh (lingerie) bag in quadruplicate for each of six time periods (0, 2, 4, 8, 12, 24 h). Two bags from each rumen incubation time were inserted into the small intestine via a duodenal cannula at the rate of one bag per 45 min. Bags were mechanically washed either upon removal from the rumen--for determination of rumen degradability, or when recovered from the feces--for estimation of intestinal availability. Dried bags plus contents were digested intact for nitrogen analysis. Rumen degradable protein and apparent intestinal availability of undegradable protein (based on 8 h of rumen incubation) for corn gluten meal, fish meal, meat and bone meal, soybean meal, canola meal, and alfalfa hay, respectively, were 11...

We show that dramatic reductions in the maximum utilization of congested links in a network ("hot... more We show that dramatic reductions in the maximum utilization of congested links in a network ("hot spots") can be achieved using the dual solution of the multi-commodity flow problem to set the link weights. Using a modern Linear Programming (LP) software package the time required to compute solutions is up to two orders of magnitude faster than schemes reliant on search techniques. Approximate solutions using split routing and single path routing are shown to produce near-optimal results. Single path solutions allow the use of MPLS over OSPF with a vastly reduced administrative overhead. We also show that sub-optimal (but vastly improved) solutions can be found so that MPLS need not be deployed at all.

A central feature of arid soils is their spatial variability. In particular, the Aislands of fert... more A central feature of arid soils is their spatial variability. In particular, the Aislands of fertility@ phenomenon characterizes these systems, causing regular patterns in carbon and nutrient concentrations in soils on both a horizontal and vertical scale. This paper reviews sampling techniques and associated problems associated with characterizing soils in general and addresses some issues that are particularly important to

The climateprediction.com project aims to make use of the idle time on home, office and school PC... more The climateprediction.com project aims to make use of the idle time on home, office and school PCs to make a many thousand member ensemble of climate model runs from 1950 to 2050. These runs will be used to assess the uncertainty in projections of climate change out to 2050. Ensemble members will have different representations of the physics of the

PloS one, 2014

The human ZFP36 zinc finger protein family consists of ZFP36, ZFP36L1, and ZFP36L2. These protein... more The human ZFP36 zinc finger protein family consists of ZFP36, ZFP36L1, and ZFP36L2. These proteins regulate various cellular processes, including cell apoptosis, by binding to adenine uridine rich elements in the 3' untranslated regions of sets of target mRNAs to promote their degradation. The pro-apoptotic and other functions of ZFP36 family members have been implicated in the pathogenesis of lymphoid malignancies. To identify candidate mRNAs that are targeted in the pro-apoptotic response by ZFP36L1, we reverse-engineered a gene regulatory network for all three ZFP36 family members using the 'maximum information coefficient' (MIC) for target gene inference on a large microarray gene expression dataset representing cells of diverse histological origin. Of the three inferred ZFP36L1 mRNA targets that were identified, we focussed on experimental validation of mRNA for the pro-survival protein, BCL2, as a target for ZFP36L1. RNA electrophoretic mobility shift assay experim...

Blood, Jan 8, 2015

An important negative regulator of factor VIIIa (FVIIIa) cofactor activity is A2 subunit dissocia... more An important negative regulator of factor VIIIa (FVIIIa) cofactor activity is A2 subunit dissociation. FVIII molecules with stabilized activity have been generated by elimination of charged residues at the A1-A2 and A2-A3 interfaces. These molecules exhibited reduced decay rates as part of the enzymatic factor Xa generation complex and retained their activities under thermal and chemical denaturing conditions. We describe here the potency and efficacy of 1 such stability variant, D519V/E665V, derived from B domain-deleted FVIII (BDD-FVIII). The major effect of A2 stabilization was on cofactor activity. D519V/E665V potency was increased twofold by the 2-stage chromogenic assay relative to BDD-FVIII. D519V/E665V demonstrated enhanced thrombin generation responses (fivefold by peak thrombin) relative to BDD-FVIII. In vivo consequences of enhanced cofactor activity of D519V/E665V included >fourfold increased maximal platelet-fibrin deposition after laser injury and twofold increased ...

Cytotoxic Anticancer Drugs: Models and Concepts for Drug Discovery and Development, 1992

The genetic replacement of either the native diphtheria toxin or Pseudomonas exotoxin A receptor ... more The genetic replacement of either the native diphtheria toxin or Pseudomonas exotoxin A receptor binding domain with eukaryotic cell receptor-specific polypeptide hormones or growth factor sequences has resulted in the development of a new class of biological response modifier — the fusion toxin (1–6). The first of these fusion toxins, DAB486-IL-2, is currently in human Phase I clinical trials and

This paper gives the reasons for the effectiveness of the hot spot remover proposed by Murphy et ... more This paper gives the reasons for the effectiveness of the hot spot remover proposed by Murphy et al (5). The dual solution of a linear programming problem is used to calculate a new set of OSPF weights. We explain why it is often possible to greatly reduce maximum link utilization with only a very few weight changes. Some numerical examples

Transplantation, 2003

Background. Antibodies to endothelial derived nonhuman leukocyte antigens (HLA) have been associa... more Background. Antibodies to endothelial derived nonhuman leukocyte antigens (HLA) have been associated with transplant (Tx)-associated coronary artery disease (CAD) after cardiac transplantation; however, few have been identified. The aim of this study was to screen a human coronary artery endothelial cell cDNA library with patient sera to establish the diversity and nature of the target antigens. Methods. A human coronary artery endothelial cell cDNA library was screened with sera from seven longterm cardiac transplant patients with angiographically diagnosed TxCAD and sera from five healthy volunteers. Results. Of the seven patients' sera, five showed reactivity, as did sera from two of the five normal subjects. Eighteen positive cDNA clones were isolated by TxCAD sera; DNA sequence analysis and DNA database searching identified all but one clone; 16 were nuclear or cytoplasmic proteins and 1 of them was the cell surface protein neuropilin 2. Five clones were targeted by normal sera. A different spectrum of reactive clones was identified by the sera of each patient where reactive clones were evident. Conclusions. A high diversity of non-HLA antigens, probably autoantigens, are involved in the pathogenesis of TxCAD.

The Journal of cell biology, 1993

Coronin is an actin-binding protein in Dictyostelium discoideum that is enriched at the leading e... more Coronin is an actin-binding protein in Dictyostelium discoideum that is enriched at the leading edge of the cells and in projections of the cell surface called crowns. The polypeptide sequence of coronin is distinguished by its similarities to the beta-subunits of trimeric G proteins (E. L. de Hostos, B. Bradtke, F. Lottspeich, R. Guggenheim, and G. Gerisch, 1991. EMBO (Eur. Mol. Biol. Organ.) J. 10:4097-4104). To elucidate the in vivo function of coronin, null mutants have been generated by gene replacement. The mutant cells lacking coronin grow and migrate more slowly than wild-type cells. When these cor- cells grow in liquid medium they become multinucleate, indicating a role of coronin in cytokinesis. To explore this role, coronin has been localized in mitotic wild-type cells by immunofluorescence labeling. During separation of the daughter cells, coronin is strongly accumulated at their distal portions including the leading edges. This contrasts with the localization of myosin ...

The Journal of cell biology, 1995

A gene trap-type targeting vector was designed to inactivate the beta 1 integrin gene in embryoni... more A gene trap-type targeting vector was designed to inactivate the beta 1 integrin gene in embryonic stem (ES) cells. Using this vector more than 50% of the ES cell clones acquired a disruption in the beta 1 integrin gene and a single clone was mutated in both alleles. The homozygous mutant did not produce beta 1 integrin mRNA or protein, while alpha 3, alpha 5, and alpha 6 integrin subunits were transcribed but not detectable on the cell surface. Heterozygous mutants showed reduced beta 1 expression and surface localization of alpha/beta 1 heterodimers. The alpha V subunit expression was not impaired on any of the mutants. Homozygous ES cell mutants lacked adhesiveness for laminin and fibronectin but not for vitronectin and showed a reduced association with a fibroblast feeder layer. Furthermore, they did not migrate towards chemoattractants in fibroblast medium. None of these functions were impaired in heterozygous mutants. Scanning electron microscopy revealed that homozygous cells...