Putrescine activates oxidative stress dependent apoptotic death in ornithine decarboxylase overproducing mouse myeloma cells

Accumulation of putrescine in ornithine decarboxylase overproducing cells provokes apoptotic death that is inhibited by 2-difluoromethylornithine, a specific inhibitor of ODC. The apoptotic process provoked by putrescine involves the release of cytochrome c from the mitochondria and activation of caspases cascades demonstrated by the cleavage of caspase-2, polyA-ribose polymerase (PARP), and proteolytic cleavage of the translation initiation factor 4G (eIF4G). The general caspases inhibitor BD-fmk inhibits PARP cleavage but not cell death. Aminoguanidine, an inhibitor of amine oxidases, inhibits the cleavage of PARP and cell death, whereas the antioxidant BHA inhibits PARP cleavage but not cell death. The intracellular Ca2+ chelator 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid tetra(acetoxymethyl) ester (BAPTA/AM) inhibits both PARP cleavage and cell death. Although the ability of BAPTA/AM to inhibit the induction of apoptosis may suggest that the accumulating putrescine stimulates the release of Ca2+, such a Ca2+ elevation was not observed. We suggest that the accumulation of putrescine leads to oxidative stress that causes cell death.     

DNA polymorphism in cytokine genes based on length variation in simple-sequence tandem repeats

The possibility of the involvement of cytokines in the genetic predisposition to various diseases has been suggested by a large variety of studies. However, the study of potential disease linkage of cytokine genes has been hampered by a lack of sufficiently polymorphic markers at the restriction fragment length polymorphism (RFLP) level. We have investigated the distribution, the length polymorphism, the informativeness, and the efficiency of analysis, of simple-sequence tandem repeats in the mouse cytokine genes. Highly polymorphic sequences have been identified in the IL-1, IL-1ra, IL-2, IL-4, IL-6, IL-7, and IFN- genes. The utility and the value of these sequences as gene markers is exemplified by mapping the IL-7 gene to mouse chromosome 3 close to pgk-1ps3 and Car-2 loci and the IFN- gene to chrrmosome 10 near the pg locus. Advantages of short tandemly repeated sequences as genetic markers are discussed in comparison with RFLPs.     

Problems and approaches in covalent attachment of peptides and proteins to inorganic surfaces for biosensor applications

Summary Some of the fundamental problems in covalent attachment of peptides and proteins to putative biosensor surfaces are reviewed and specific approaches to these problems discussed. In addition, selected aspects of our recent work utilizing self-assembled monolayer (SAM) systems designed to react selectively with the thiol side chain of Cys in proteins are presented. Uniform attachment of a 21-amino acid peptide antigen through a single Cys residue with retention of biological function (antibody binding) has been attained. Further work with this system may lead to solutions for some of the problems which currently prevent the development of reliable biosensors for industrial and medical use.This paper was presented at a Symposium on Enzyme Electrodes held at the Annual Meeting of the Society of Industrial Microbiology, and the Canadian Society of Microbiologists, in Toronto, Canada (August 3, 1993).     

The degenerate primer design problem: theory and applications.

A PCR primer sequence is called degenerate if some of its positions have several possible bases. The degeneracy of the primer is the number of unique sequence combinations it contains. We study the problem of designing a pair of primers with prescribed degeneracy that match a maximum number of given input sequences. Such problems occur when studying a family of genes that is known only in part, or is known in a related species. We prove that various simplified versions of the problem are hard, show the polynomiality of some restricted cases, and develop approximation algorithms for one variant. Based on these algorithms, we implemented a program called HYDEN for designing highly degenerate primers for a set of genomic sequences. We report on the success of the program in several applications, one of which is an experimental scheme for identifying all human olfactory receptor (OR) genes. In that project, HYDEN was used to design primers with degeneracies up to 10(10) that amplified with high specificity many novel genes of that family, tripling the number of OR genes known at the time.     

Novel mutations and hot-spots in patients with purine nucleoside phosphorylase deficiency

Purine nucleoside phosphorylase (PNP) deficiency results in severe immune dysfunction and early death from infections. Lymphopenia, reduced serum uric acid, and abnormal PNP enzymatic activity assist in the diagnosis of PNP-deficient patients. Analysis of the gene encoding PNP in these patients reveals several recurring mutations. Identification of these hot-spots for mutation may allow faster confirmation of the diagnosis in suspected cases.     

Small scale membrane mechanics

Large scale changes to lipid bilayer shapes are well represented by the Helfrich model. However, there are membrane processes that take place at smaller length scales that this model cannot address. In this work, we present a one-dimensional continuum model that captures the mechanics of the lipid bilayer membrane at the length scale of the lipids themselves. The model is developed using the Cosserat theory of surfaces with lipid orientation, or ‘tilt’, as the fundamental degree of freedom. The Helfrich model can be recovered as a special case when the curvatures are small and the lipid tilt is everywhere zero. We use the tilt model to study local membrane deformations in response to a protein inclusion. Parameter estimates and boundary conditions are obtained from a coarse-grained molecular model using dissipative particle dynamics (DPD) to capture the same phenomenon. The continuum model is able to reproduce the membrane bending, stretch and lipid tilt as seen in the DPD model. The lipid tilt angle relaxes to the bulk tilt angle within 5–6 nm from the protein inclusion. Importantly, for large tilt gradients induced by the proteins, the tilt energy contribution is larger than the bending energy contribution. Thus, the continuum model of tilt accurately captures behaviors at length scales shorter than the membrane thickness.     

Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production

Systemic lupus erythematosus (SLE) is a clinically heterogeneous, systemic autoimmune disease characterized by autoantibody formation. Previously published genome-wide association studies (GWAS) have investigated SLE as a single phenotype. Therefore, we conducted a GWAS to identify genetic factors associated with anti–dsDNA autoantibody production, a SLE–related autoantibody with diagnostic and clinical importance. Using two independent datasets, over 400,000 single nucleotide polymorphisms (SNPs) were studied in a total of 1,717 SLE cases and 4,813 healthy controls. Anti–dsDNA autoantibody positive (anti–dsDNA +, n = 811) and anti–dsDNA autoantibody negative (anti–dsDNA –, n = 906) SLE cases were compared to healthy controls and to each other to identify SNPs associated specifically with these SLE subtypes. SNPs in the previously identified SLE susceptibility loci STAT4, IRF5, ITGAM, and the major histocompatibility complex were strongly associated with anti–dsDNA + SLE. Far fewer and weaker associations were observed for anti–dsDNA – SLE. For example, rs7574865 in STAT4 had an OR for anti–dsDNA + SLE of 1.77 (95% CI 1.57–1.99, p = 2.0E-20) compared to an OR for anti–dsDNA – SLE of 1.26 (95% CI 1.12–1.41, p = 2.4E-04), with p_{heterogeneity}<0.0005. SNPs in the SLE susceptibility loci BANK1, KIAA1542, and UBE2L3 showed evidence of association with anti–dsDNA + SLE and were not associated with anti–dsDNA – SLE. In conclusion, we identified differential genetic associations with SLE based on anti–dsDNA autoantibody production. Many previously identified SLE susceptibility loci may confer disease risk through their role in autoantibody production and be more accurately described as autoantibody propensity loci. Lack of strong SNP associations may suggest that other types of genetic variation or non-genetic factors such as environmental exposures have a greater impact on susceptibility to anti–dsDNA – SLE.     

A comprehensive analysis of shared loci between systemic lupus erythematosus (SLE) and sixteen autoimmune diseases reveals limited genetic overlap

In spite of the well-known clustering of multiple autoimmune disorders in families, analyses of specific shared genes and polymorphisms between systemic lupus erythematosus (SLE) and other autoimmune diseases (ADs) have been limited. Therefore, we comprehensively tested autoimmune variants for association with SLE, aiming to identify pleiotropic genetic associations between these diseases. We compiled a list of 446 non–Major Histocompatibility Complex (MHC) variants identified in genome-wide association studies (GWAS) of populations of European ancestry across 17 ADs. We then tested these variants in our combined Caucasian SLE cohorts of 1,500 cases and 5,706 controls. We tested a subset of these polymorphisms in an independent Caucasian replication cohort of 2,085 SLE cases and 2,854 controls, allowing the computation of a meta-analysis between all cohorts. We have uncovered novel shared SLE loci that passed multiple comparisons adjustment, including the VTCN1 (rs12046117, P = 2.02×10⁻⁰⁶) region. We observed that the loci shared among the most ADs include IL23R, OLIG3/TNFAIP3, and IL2RA. Given the lack of a universal autoimmune risk locus outside of the MHC and variable specificities for different diseases, our data suggests partial pleiotropy among ADs. Hierarchical clustering of ADs suggested that the most genetically related ADs appear to be type 1 diabetes with rheumatoid arthritis and Crohn''s disease with ulcerative colitis. These findings support a relatively distinct genetic susceptibility for SLE. For many of the shared GWAS autoimmune loci, we found no evidence for association with SLE, including IL23R. Also, several established SLE loci are apparently not associated with other ADs, including the ITGAM-ITGAX and TNFSF4 regions. This study represents the most comprehensive evaluation of shared autoimmune loci to date, supports a relatively distinct non–MHC genetic susceptibility for SLE, provides further evidence for previously and newly identified shared genes in SLE, and highlights the value of studies of potentially pleiotropic genes in autoimmune diseases.