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Biomedical subjects

H R Clarke

Publications and source records attributed to H R Clarke.

15 recordsLinked to original sources
PubMed1998

Crystal structure of the catalytic domain of human tumor necrosis factor-alpha-converting enzyme.

Tumor necrosis factor-alpha (TNFalpha) is a cytokine that induces protective inflammatory reactions and kills tumor cells but also causes severe damage when produced in excess, as in rheumatoid arthritis and septic shock. Soluble TNFalpha is released from its membrane-bound precursor by a membrane-anchored proteinase, recently identified as a multidomain metalloproteinase called TNFalpha-converting enzyme or TACE. We have cocrystallized the catalytic domain of TACE with a hydroxamic acid inhibitor and have solved its 2.0 A crystal structure. This structure reveals a polypeptide fold and a catalytic zinc environment resembling that of the snake venom metalloproteinases, identifying TACE as a member of the adamalysin/ADAM family. However, a number of large insertion loops generate unique surface features. The pro-TNFalpha cleavage site fits to the active site of TACE but seems also to be determined by its position relative to the base of the compact trimeric TNFalpha cone. The active-site cleft of TACE shares properties with the matrix metalloproteinases but exhibits unique features such as a deep S3' pocket merging with the S1' specificity pocket below the surface. The structure thus opens a different approach toward the design of specific synthetic TACE inhibitors, which could act as effective therapeutic agents in vivo to modulate TNFalpha-induced pathophysiological effects, and might also help to control related shedding processes.

ADAM Proteins↗
PubMed1998

Expression and purification of correctly processed, active human TACE catalytic domain in Saccharomyces cerevisiae.

Human tumor necrosis factor-alpha (TNF alpha) converting enzyme (TACE) releases soluble TNF alpha from cells. It is a member of the adamalysin family of metalloproteases. A truncated form of TACE cDNA was expressed in Saccharomyces cerevisiae and purified to homogeneity in order to study TACE structure and function. Recombinant TACE was expressed as a preproprotein including the pro- and catalytic (PROCAT) domains fused to the yeast alpha-factor leader. A C-terminal immunoreactive FLAG peptide was added for Western blot detection and anti-FLAG antibody column purification. We constructed two glycosylation mutant PROCAT TACE isoforms to facilitate purification. A PROCAT isoform, mutated to eliminate two N-linked glycosylation sites, was buffer exchanged and purified to homogeneity by ion exchange chromatography and an anti-FLAG antibody affinity step. N-terminal sequence analysis showed that the mutant preproprotein was processed in yeast at the furin protease cleavage site and yielded an active catalytic domain which has TNF alpha peptide-specific protease activity. Mass spectrometry of the purified catalytic domain showed that removal of both N-linked sites results in a homogeneous sized polypeptide lacking further posttranslational modifications.

ADAM Proteins↗
PubMed1996

Labor immigration and capital flows: long-term Australian, Canadian and United States experience.

"Evidence on labor immigration and capital inflows to three high labor-immigration economies (Australia, Canada, the United States) is examined over periods ranging from 1820-1870 through to 1991. Data show a close association between capital flows and immigration, although causality implications are ambiguous. For the United States, the relation between factor flows is more complex than for the other countries, but flows to the United States have influenced those to smaller economies. All three nations have been subjected to common immigrant push factors through to 1930-1950 but, since World War II, linkages between factor flows have altered. Post-World War II U.S. immigration restrictions have become more important as a global determinant of labor flows, with factor flow policymaking becoming increasingly internationally interdependent."

Americas↗
PubMed1995

Population growth and the benefits from optimally priced externalities.

"In this article we show that, considering only economic effects, even if population growth, by natural increase or immigration, increases congestion, pollution, and other forms of external costs, that provided pre-existing citizens own the resources giving rise to the externalities, and provided they efficiently price usage of such, that existing citizens must, in net average terms, be better off with population growth than without it. In simple terms the increased revenues they gain from efficient pricing at increased demand levels will be strictly greater than the monetary value of the increased external costs together with the higher tax costs they incur as consumers of the resources."

Cost-Benefit Analysis↗
PubMed1994

Wound-induced and developmental activation of a poplar tree chitinase gene promoter in transgenic tobacco.

Wounding hybrid poplar (Populus trichocarpa x P. deltoides) trees results in the expression of novel wound-inducible (win) mRNAs thought to encode proteins involved in defense against pests and pathogens. Members of the win6 gene family encode acidic multi-domain chitinases, with combined structure and charge characteristics that differ from previously described chitinases. Win6 expression has been shown to occur in pooled unwounded leaves of a wounded (on multiple leaves) poplar plant. Here we demonstrate that wounding a single leaf induces win6 expression locally, in the wounded leaf, and remotely, in specific unwounded leaves with strong vascular connections to the wounded leaf. We also demonstrate that a win6 promoter-beta-glucuronidase (GUS) gene fusion (win6-GUS) responds to wounding locally and remotely in transgenic tobacco. These data indicate that the poplar win6 promoter has regulatory elements that are responsive to 'wound signals' in the heterologous host. In addition, win6-GUS is developmentally activated in unwounded young leaves and floral tissues of transgenic tobacco. Similar developmental expression patterns are found to occur for win6 in poplar trees, demonstrating that a herbaceous plant can serve as a host for woody tree transgene analysis and can accurately predict expression patterns in tree tissues (e.g. flowers) that would be difficult to study in free-living trees.

Adaptation, Biological↗
PubMed1994

The welfare effects of labour force growth with internationally mobile capital.

"This paper examines some economic effects of population growth, due to natural increase and immigration.... An objective is to assess how immigration and natural labour supply growth impact on international equilibrium when trade in produced inputs is induced by population changes. For the most part our analysis is based on theories on international factor mobility.... Natural population growth will be analysed as a byproduct of the factor mobility studies."

Commerce↗
PubMed1994

Entry charges on immigrants.

The author analyzes "the various arguments that can be advanced for imposing fees on immigrants to optimize...resident gains.... This article discusses cost recovery and emphasizes the costs of multiculturalism as a possible basis for fees. It then analyzes the effects of inelastic immigrant supplies in providing an optimal tariff motivation for monopsonistically restricting labor flows and deals with the second-best problem of devising an optimal fee policy to accompany a possibly suboptimal immigration quota. Next, attention turns to the role of priceable externalities. Externalities which are expensive to price because of transactions costs are analyzed. Finally, along with summarization of major conclusions, the author considers if, even in the economic interests of existing residents, entry rights should be sold."

Demography↗
PubMed1993

Immigration and economic welfare: resource and environmental aspects.

"The relation between immigration and the economic welfare of residents is analyzed for resource-rich economies (such as Australia) both under competitive conditions and when various distortions are present. Immigration provides efficiency gains for residents under distortion-free competition for standard 'gains from trade' reasons. Such reasons, however, tend to be ignored by immigration and 'optimal population' theorists who raise the issue of restricting immigration without explicitly referring to the distortions. In situations where distortions and externalities are present, we argue that it is generally preferable to devise policies which specifically target the distortions than to restrict immigration."

Australia↗
PubMed1992

Molecular signals in the interactions between plants and microbes.

The field of plant-microbe interactions has witnessed several recent breakthroughs, such as the molecular details of vir gene induction, identification of Nod factors, and the cloning and characterization of avr genes. Other breakthroughs, such as the cloning and characterization of R genes, appear imminent. Parallels to mammalian systems are emerging in the world of plant-microbe interactions, for example, ion channels formed by Rhizobium proteins, similarities of hrp genes to pathogenicity genes of mammalian pathogens, and plant signal transduction via calcium and protein phosphorylation. We remain, however, largely ignorant of many facets of signaling in plant-microbe interactions. We know little about how microbial signals are perceived by plants or how subsequent signal transduction occurs within plant cells and are probably unaware of many of the microbe-generated signals to which plants respond or of plant-generated signals to which bacteria and fungi respond. Contributions from those working on the genetics, molecular biology, and physiology of bacteria, fungi, and plants will be required to address these questions. The many nonpathogenic plant-microbe interactions in addition to the Rhizobium-plant interaction remain relatively unexplored. Genetic and molecular approaches are being initiated to investigate the signaling that is likely to underlie interactions such as those between mycorrhizal fungi and plant roots and between epiphytic bacteria and plant leaf surfaces. The importance of these interactions to plant growth and development makes it likely that they will figure more prominently at future symposia.(ABSTRACT TRUNCATED AT 250 WORDS)

Plant Physiological Phenomena↗
PubMed1991

Populus chitinase genes: structure, organization, and similarity of translated sequences to herbaceous plant chitinases.

Poplar trees have at least two different chitinase genes, win6 and win8, which are systemically wound-inducible and belong to multigene families [Proc Natl Acad Sci USA 86: 7895-7899]. On one genomic clone that we have partially sequenced, there are three win6 genes which are transcriptionally oriented in the same direction. Between two of the win6 genes is a gene that we have designated chitinase X (chiX), which appears to be a pseudogene belonging to a multigene family distinct from win6 and win8. The win6 and chiX genes we have sequenced contain two AT-rich introns that correspond in location to those in a basic chitinase gene from tobacco. The predicted Win6 proteins have a putative signal peptide, a cysteine-rich 'hevein' domain, a hinge region, and a catalytic domain as described in Shinshi et al. [Plant Mol Biol 14: 357-368]. The predicted Win8 protein, by contrast, completely lacks a hinge region. Both Win6 and Win8 are expected to be highly acidic (with a calculated net charge of -15 to -17), whereas ChiX proteins are likely to be basic. Based on an inferred phylogeny, the catalytic domain of ChiX is more closely related to the basic chitinases of herbaceous plants than are either Win6 or Win8.

Amino Acid Sequence↗
PubMed1990

Systemically wound-responsive genes in poplar trees encode proteins similar to sweet potato sporamins and legume Kunitz trypsin inhibitors.

When the lower leaves of hybrid poplar trees are mechanically wounded, several novel mRNAs accumulate in the unwounded upper leaves (Parsons TJ, Bradshaw HD, Gordon MP: Systemic accumulation of specific mRNAs in response to wounding in poplar trees, Proc Natl Acad Sci USA, in press). A partial cDNA clone corresponding to a transcript from the wound-responsive gene designated win 3 (wound-inducible) has been cloned by differential hybridization to 32P-labelled cDNA from the leaves of wounded trees. Northern blots show a large accumulation of win 3 transcripts in the unwounded leaves of wounded trees. Southern blot analysis of poplar DNA suggests that win 3 is a member of a multigene family. The nucleotide sequences of several win 3 cDNA clones have been determined, indicating that at least three win 3 gene family members are transcribed. A genomic clone of a win 3 gene family member has been isolated and a 1.5 kb Hind III fragment containing the predicted protein-coding and 5' upstream regions has been sequenced. The putative win 3 gene product is similar to the major soluble proteins of sweet potato tubers, sporamin A and sporamin B. Both Win3 and the sporamins share significant amino acid sequence identity with Kunitz-type trypsin inhibitors from legume seeds. The Kunitz family of proteinase inhibitors thus joints three other proteinase inhibitor families which are systemically responsive to wounding.

Amino Acid Sequence↗
PubMed1989

Association between a specific apolipoprotein B mutation and familial defective apolipoprotein B-100.

Familial defective apolipoprotein (apo) B-100 is a genetic disease that leads to hypercholesterolemia and to an increased serum concentration of low density lipoproteins that bind defectively to the apoB,E(LDL) receptor. The disorder appears to result from a mutation in the gene for apoB-100. Extensive sequence analysis of the two alleles of one subject heterozygous for the disorder has revealed a previously unreported mutation in the codon for amino acid 3500 that results in the substitution of glutamine for arginine. This same mutant allele occurs in six other, unrelated subjects and in eight affected relatives in two of these families. A partial haplotype of this mutant apoB-100 allele was constructed by sequence analysis and restriction enzyme digestion at positions where variations in the apoB-100 are known to occur. This haplotype is the same in three probands and four affected members of one family and lacks a polymorphic Xba I site whose presence has been correlated with high cholesterol levels. Thus, it appears that the mutation in the codon for amino acid 3500 (CGG----CAG), a CG mutational "hot spot," defines a minor apoB-100 allele associated with defective low density lipoproteins and hypercholesterolemia.

Alleles↗
PubMed1989

Type III hyperlipoproteinemia associated with apolipoprotein E phenotype E3/3. Structure and genetics of an apolipoprotein E3 variant.

A family has been described in which type III hyperlipoproteinemia is associated with apo E phenotype E3/3 (Havel, R. J., L. Kotite, J. P. Kane, P. Tun, and T. Bersot. 1983. J. Clin. Invest. 72:379-387). In the current study, the structure of apo E from the propositus of this family was determined using both protein and DNA analyses. The propositus is heterozygous for two different apo E alleles, one coding for normal apo E3 and one for a previously undescribed variant apo E3 in which arginine replaces cysteine at residue 112 and cysteine replaces arginine at residue 142. Apo E gene analysis of nine other family members spanning four generations indicated that only those five members having type III hyperlipoproteinemia possess the variant apo E3. Like the propositus, all five are heterozygous for this variant, suggesting that the disorder in this family is transmitted in a dominant fashion. The variant apo E3 was defective in its ability to bind to lipoprotein receptors, and this functional defect probably contributes to the expression of type III hyperlipoproteinemia in this family.

Adult↗