Contact-site cross-linking agents

Summary Contact-site cross-linking agents comprise a heterogeneous grouping of cross-linkers which share the common property of being able to cross-link only very closely juxtaposed residues in macromolecular complexes. We have defined contact-site cross-linking arbitrarily as the covalent joining of residues such that they are constrained to a distance which is equivalent to or less than their closest possible steric approach prior to becoming linked (1). We recognize two classes of contact-site cross-linkers, bridge type and zero-length type. The former, such as formaldehyde, become incorporated during cross-linking as one-atom bridges. The latter, such as the carbodiimides, operate as condensing agents with the result that the cross-linked residues become interjoined directly. Contact-site cross-linkers have been used in several ways as specific probes of both the static and dynamic aspects of macromolecular structure. They can yield precise structural information about macromolecular contacts when actual sites of cross-linking are determined by peptide or nucleotide mapping techniques. In this way exact contacs between histones in the nucleosome, between protein and RNA in the ribosome, and between RNA polymerase and DNA have been determined. Contact-site cross-linkers have also been used to probe the perturbation of contacts following macromolecular conformational changes. Certain histonehistone ‘cross-linkable’ sites are rendered unreactive after induction of chromatin conformational changes thus serving to localize sites of perturbation.     

Heterogeneity of Intermediate Filament Expression in Vascular Smooth Muscle: A Gradient in Desmin Positive Cells from the Rat Aortic Arch to the Level of the Arteria Iliaca Communis

The display of the two distinct intermediate filament proteins, desmin and vimentin, in rat vascular smooth muscle tissue was studied by immunofluorescence microscopy on frozen sections of aorta and other blood vessels. Vascular smooth muscle cells present in these vessels always appeared rich in vimentin. However, staining of sections covering six distinct but contiguous parts of the aorta showed that the number of desmin containing cells was low distal to the truncus brachiocephalicus, but increases until in distal parts of the aorta and in the arteria iliaca communis almost all cells appear positive for desmin. Thus blood vessels show heterogeneity of intermediate filament expression not only in cross-section but can also display heterogeneity along their length. Muscular arteries such as the renal artery and the arteria femoralis, as well as arterioles and veins including the vena jugularis and the vena cava also contain desmin. Thus it may be that low numbers of desmin-positive cells are typical of elastic arteries, while muscular arteries and other blood vessels are characterized by large numbers of desmin-positive cells. We discuss whether desmin-positive and desmin-negative vascular smooth muscle cells may perform different functions and raise the possibility that desmin expression may coincide with the turn on of a specially regulated contractility program.     

The subcellular distribution of dystrophin in mouse skeletal, cardiac, and smooth muscle

We use a highly specific and sensitive antibody to further characterize the distribution of dystrophin in skeletal, cardiac, and smooth muscle. No evidence for localization other than at the cell surface is apparent in skeletal muscle and no 427-kD dystrophin labeling was detected in sciatic nerve. An elevated concentration of dystrophin appears at the myotendinous junction and the neuromuscular junction, labeling in the latter being more intense specifically in the troughs of the synaptic folds. In cardiac muscle the distribution of dystrophin is limited to the surface plasma membrane but is notably absent from the membrane that overlays adherens junctions of the intercalated disks. In smooth muscle, the plasma membrane labeling is considerably less abundant than in cardiac or skeletal muscle and is found in areas of membrane underlain by membranous vesicles. As in cardiac muscle, smooth muscle dystrophin seems to be excluded from membrane above densities that mark adherens junctions. Dystrophin appears as a doublet on Western blots of skeletal and cardiac muscle, and as a single band of lower abundance in smooth muscle that corresponds most closely in molecular weight to the upper band of the striated muscle doublet. The lower band of the doublet in striated muscle appears to lack a portion of the carboxyl terminus and may represent a dystrophin isoform. Isoform differences and the presence of dystrophin on different specialized membrane surfaces imply multiple functional roles for the dystrophin protein.     

Mechanisms of food selection in Daphnia

A conceptual behavioural and mechanistic Holling-type model of food selection in Daphnia pulicaria is derived from SEM observations with animals feeding on mixtures of spherical-cylindrical diatoms, oblongate green algae, and filamentous cyanobacteria, as well as ultrafine particles. The algae used were Stephanodiscus hantzschii (<- 6 µm length), Monoraphidium setiforme ( 20 µm), and Oscillatoria aghardii (strands, >- 80 µm). Cell (strand) selection can occur at any or all of three stages: (i) interception from the feeding currents, (ii) collection and channeling to the food groove, and (iii) compaction and transport to the mouth. During each stage, given equal initial cell densities, elongate cells are more likely to escape collection than spherical cells and are more likely to be rejected. In addition, filaments require increased handling time at stages (ii) and (iii) and promote entanglement with limb 5 and the postabdominal claw. Food is collected primarily with the aid of limbs 3 (and 4), but limbs 1 and 2 also intervene. Neither the leaky sieve hypothesis alone nor any other single-process hypothesis explains the observations on examined in corpore positions, morphology, and derived movements of the feeding limbs. Attachment and mucus appear to be important for the ingestion of bacteria and ultrafine particles.The model is consistent with many experimental results of differential feeding by Daphnia pulicaria on mixtures of variously shaped algae and other observations on Daphnia feeding behaviour. The paradigm of invariate, nonselective feeding by Daphnia is rejected.     

IL-7 up-regulates the expression of IL-8 from resting and stimulated human blood monocytes.

Blood monocytes are important cellular sources of a vast array of bioactive substances, including regulatory and chemotactic cytokines. The regulation of these cytokines is of critical importance to the expression of acute and chronic inflammatory responses. IL-7, a T and B cell-activating cytokine, has recently been shown to have stimulatory effects on the expression of several monocyte-derived proinflammatory cytokines. We now describe the induction of IL-8 mRNA and extracellular protein from human blood monocytes by IL-7. The up-regulation of IL-8 mRNA by IL-7 was not altered by concomitant treatment with cycloheximide, suggesting that the direct stimulatory effects of IL-7 were not dependent upon de novo protein synthesis. In addition, IL-7 significantly potentiated the production of IL-8 from LPS-, TNF-, and IL-1-treated peripheral blood monocytes. Our findings suggest that IL-7 may play a critical role in the modulation of macrophage-derived cytokine expression and may function in vivo as an important proinflammatory cytokine.     

Fidelity of mammalian DNA replication and replicative DNA polymerases.

Current models suggest that two or more DNA polymerases may be required for high-fidelity semiconservative DNA replication in eukaryotic cells. In the present study, we directly compare the fidelity of SV40 origin-dependent DNA replication in human cell extracts to the fidelity of mammalian DNA polymerases alpha, delta, and epsilon using lacZ alpha of M13mp2 as a reporter gene. Their fidelity, in decreasing order, is replication greater than or equal to pol epsilon greater than pol delta greater than pol alpha. DNA sequence analysis of mutants derived from extract reactions suggests that replication is accurate when considering single-base substitutions, single-base frameshifts, and larger deletions. The exonuclease-containing calf thymus DNA polymerase epsilon is also highly accurate. When high concentrations of deoxynucleoside triphosphates and deoxyguanosine monophosphate are included in the pol epsilon reaction, both base substitution and frameshift error rates increase. This response suggests that exonucleolytic proofreading contributes to the high base substitution and frameshift fidelity. Exonuclease-containing calf thymus DNA polymerase delta, which requires proliferating cell nuclear antigen for efficient synthesis, is significantly less accurate than pol epsilon. In contrast to pol epsilon, pol delta generates errors during synthesis at a relatively modest concentration of deoxynucleoside triphosphates (100 microM), and the error rate did not increase upon addition of adenosine monophosphate. Thus, we are as yet unable to demonstrate that exonucleolytic proofreading contributes to accuracy during synthesis by DNA polymerase delta. The four-subunit DNA polymerase alpha-primase complex from both HeLa cells and calf thymus is the least accurate replicative polymerase. Fidelity is similar whether the enzyme is assayed immediately after purification or after being stored frozen.(ABSTRACT TRUNCATED AT 250 WORDS)     

Purification and characterization of DNA polymerase II from the yeast Saccharomyces cerevisiae. Identification of the catalytic core and a possible holoenzyme form of the enzyme

We have purified yeast DNA polymerase II to near homogeneity as a 145-kDa polypeptide. During the course of this purification we have detected and purified a novel form of DNA polymerase II that we designate as DNA polymerase II. The most highly purified preparations of DNA polymerase II are composed of polypeptides with molecular masses of 200, 80, 34, 30, and 29 kDa. Immunological analysis and peptide mapping of DNA polymerase II and the 200-kDa subunit of DNA polymerase II indicate that the 145-kDa DNA polymerase II polypeptide is derived from the 200-kDa polypeptide of DNA polymerase II. Activity gel analysis shows that the 145- and the 200-kDa polypeptides have catalytic function. The polypeptides present in the DNA polymerase II preparation copurify with the polymerase activity with a constant relative stoichiometry during chromatography over five columns and co-sediment with the activity during glycerol gradient centrifugation, suggesting that this complex may be a holoenzyme form of DNA polymerase II. Both forms of DNA polymerase II possess a 3'-5' exonuclease activity that remains tightly associated with the polymerase activity during purification. DNA polymerase II is similar to the proliferating cell nuclear antigen (PCNA)-independent form of mammalian DNA polymerase delta in its resistance to butylpheny-dGTP, template specificity, stimulation of polymerase and exonuclease activity by KCl, and high processivity. Although calf thymus PCNA does not stimulate the activity of DNA polymerase II on poly(dA):oligo(dT), possibly due to the limited length of the template, the high processivity of yeast DNA polymerase II on this template can be further increased by the addition of PCNA, suggesting that conditions may exist for interactions between PCNA and yeast DNA polymerase II.     

Skewed X inactivation in a female MZ twin results in Duchenne muscular dystrophy.

One of female MZ twins presented with muscular dystrophy. Physical examination, creatine phosphokinase levels, and muscle biopsy were consistent with Duchenne muscular dystrophy (DMD). However, because of her sex she was diagnosed as having limb-girdle muscular dystrophy. With cDNA probes to the DMD gene, a gene deletion was detected in the twins and their mother. The de novo mutation which arose in the mother was shown by novel junction fragments generated by HindIII, PstI, or TaqI when probed with cDNA8. Additional evidence of a large gene deletion was given by novel SfiI junction fragments detected by probes p20, J-Bir, and J-66 on pulsed-field gel electrophoresis (PFGE). Immunoblot analysis of muscle from the affected twin showed dystrophin of normal size but of reduced amount. Immunofluorescent visualization of dystrophin revealed foci of dystrophin-positive fibers adjacent to foci of dystrophin-negative fibers. These data indicate that the affected twin is a manifesting carrier of an abnormal DMD gene, her myopathy being a direct result of underexpression of dystrophin. Cytogenetic analysis revealed normal karyotypes, eliminating the possibility of a translocation affecting DMD gene function. Both linkage analysis and DNA fingerprint analysis revealed that each twin has two different X chromosomes, eliminating the possibility of uniparental disomy as a mechanism for DMD expression. On the basis of methylation differences of the paternal and maternal X chromosomes in these MZ twins, we propose uneven lyonization (X chromosome inactivation) as the underlying mechanism for disease expression in the affected female.