The Escherichia coli dam DNA methyltransferase modifies DNA in a highly processive reaction

The Escherichia coli dam adenine-N6 methyltransferase modifies DNA at GATC sequences. It is involved in post-replicative mismatch repair, control of DNA replication and gene regulation. We show that E. coli dam acts as a functional monomer and methylates only one strand of the DNA in each binding event. The preferred way of ternary complex assembly is that the enzyme first binds to DNA and then to S-adenosylmethionine. The enzyme methylates an oligonucleotide containing two dam sites and a 879 bp PCR product with four sites in a fully processive reaction. On lambda-DNA comprising 48,502 bp and 116 dam sites, E. coli dam scans 3000 dam sites per binding event in a random walk, that on average leads to a processive methylation of 55 sites. Processive methylation of DNA considerably accelerates DNA methylation. The highly processive mechanism of E. coli dam could explain why small amounts of E. coli dam are able to maintain the methylation state of dam sites during DNA replication. Furthermore, our data support the general rule that solitary DNA methyltransferase modify DNA processively whereas methyltransferases belonging to a restriction-modification system show a distributive mechanism, because processive methylation of DNA would interfere with the biological function of restriction-modification systems.     

Purkinje cell size is reduced in cerebellum of patients with autism

1. The authors' goal was to compare the size and density of Purkinje cells in the cerebellum of subjects with and without autism. Blocks of cerebellum were dissected at autopsy from the brains of age, sex- and postmortem-intervaled (PMI) groups of autistic and normal control individuals (N = 5 per group). Frozen, unfixed blocks were sectioned and stained with 1% cresyl violet.2. The linear, molecular, granular densities and cross-sectional area of Purkinje cells were measured using computer-assisted image analysis. The average cross-sectional areas of Purkinje cells of the patients with autism were smaller by 24% when compared to the normal subjects. Two of the five autistic subjects had mean Purkinje cell sizes that corresponded to greater than 50% reduction in size. There was a substantial effect size difference in Purkinje cell size (² = 0.29) between control and autistic brains (F(1, 8) = 3.32, P = 0.106). No differences in Purkinje cell densities were observed between the two groups.3. These data indicate the possibility of Purkinje cell atrophy in autism with significant neurohistological heterogeneity among individuals diagnosed with this disorder.     

Optimizing MRI sequences and images for MRI-based stereotactic radiosurgery treatment planning

AimDevelopment of MRI sequences and processing methods for the production of images appropriate for direct use in stereotactic radiosurgery (SRS) treatment planning.BackgroundMRI is useful in SRS treatment planning, especially for patients with brain lesions or anatomical targets that are poorly distinguished by CT, but its use requires further refinement. This methodology seeks to optimize MRI sequences to generate distortion-free and clinically relevant MR images for MRI-only SRS treatment planning.Materials and methodsWe used commercially available SRS MRI-guided radiotherapy phantoms and eight patients to optimize sequences for patient imaging. Workflow involved the choice of correct MRI sequence(s), optimization of the sequence parameters, evaluation of image quality (artifact free and clinically relevant), measurement of geometrical distortion, and evaluation of the accuracy of our offline correction algorithm.ResultsCT images showed a maximum deviation of 1.3 mm and minimum deviation of 0.4 mm from true fiducial position for SRS coordinate definition. Interestingly, uncorrected MR images showed maximum deviation of 1.2 mm and minimum of 0.4 mm, comparable to CT images used for SRS coordinate definition. After geometrical correction, we observed a maximum deviation of 1.1 mm and minimum deviation of only 0.3 mm.ConclusionOur optimized MRI pulse sequences and image correction technique show promising results; MR images produced under these conditions are appropriate for direct use in SRS treatment planning.     

Identification of the "missing domain" of the rat copper-transporting ATPase, atp7b: insight into the structural and metal binding characteristics of its N-terminal copper-binding domain

Wilson disease is an autosomal disorder of copper transport caused by mutations in the ATP7B gene encoding a copper-transporting P-type ATPase. The Long Evans Cinnamon (LEC) rat is an established animal model for Wilson disease. We have used structural homology modelling of the N-terminal copper-binding region of the rat atp7b protein (rCBD) to reveal the presence of a domain, the fourth domain (rD4), which was previously thought to be missing from rCBD. Although the CXXC motif is absent from rD4, the overall fold is preserved. Using a wide range of techniques, rCBD is shown to undergo metal-induced secondary and tertiary structural changes similar to WCBD. Competition 65Zn(II)-blot experiments with rCBD demonstrate a binding cooperativity unique to Cu(I). Far-UV circular dichroism (CD) spectra suggest significant secondary structural transformation occurring when 2-3 molar equivalents of Cu(I) is added. Near-UV CD spectra, which indicate tertiary structural transformations, show a proportional decrease in rCBD disulfide bonds upon the incremental addition of Cu(I), and a maximum 5:1 Cu(I) to protein ratio. The similarity of these results to those obtained for the Wilson disease N-terminal copper-binding region (WCBD), which has six copper-binding domains, suggests that the metal-dependent conformational changes observed in both proteins may be largely determined by the protein-protein interactions taking place between the heavy metal-associated (HMA) domains, and remain largely unaffected by the absence of one of the six CXXC copper-binding sites.     

Sclerosing angiomatoid nodular transformation of the spleen (SANT) in a patient with clear cell carcinoma of the uterus: a case report

Background

Sclerosing angiomatoid nodular transformation of the spleen is a very rare benign vascular lesion recently described. Usually, sclerosing angiomatoid nodular transformation of the spleen is an incidental finding; the association with malignant tumors is extremely rare. To the best of our knowledge, we report the first case of sclerosing angiomatoid nodular transformation of the spleen associated with uterine clear cell carcinoma.

Case presentation

A 49-year-old Arabic woman presented to our institute with abdominal pain and distention. An abdominal computed tomographic scan was obtained, which showed a 14-cm uterine malignant tumor and a 4-cm isolated splenic nodule suggesting a metastatic lesion. The tumor was limited to the uterus but did not extend beyond. The patient underwent surgical treatment, and the histopathological examination of the resected uterine and splenic specimens disclosed invasive uterine clear cell carcinoma and sclerosing angiomatoid nodular transformation of the spleen, respectively. The patient had no signs of the disease 17 months after surgical treatment.

Conclusions

Sclerosing angiomatoid nodular transformation of the spleen is a very rare benign disease with a misleading presentation when associated with a malignant tumor. Pathological assessment of the resected spleen is the only way to achieve the correct diagnosis.

     

The glycophospholipid anchor of Thy-1. Biosynthetic labeling experiments with wild-type and class E Thy-1 negative lymphomas

The Thy-1 antigen of the surface of lymphocytes and neurons is anchored to the plasma membrane via a glycophospholipid moiety. In contrast, the Thy-1 synthesized by the class E Thy-1 negative mutant lymphoma is secreted as a hydrophilic species. The present investigation uses the approach of biosynthetic labeling to investigate further the structure of the intracellular Thy-1 of wild-type cells and the secreted Thy-1 of these mutant cells. In the wild-type cells, Thy-1 can be labeled with [3H] mannose, [3H]galactose, [3H]fucose, [3H]ethanolamine, and [3H]palmitic acid. In the latter two cases the label is recovered almost exclusively in a detergent-binding Pronase fragment of the protein. The incorporated label is in the form of [3H]ethanolamine, or [3H]palmitate and stearate, respectively. Reductive methylation of biosynthetically labeled Thy-1 and a nonradioactive sample of Thy-1 shows that [3H]ethanolamine is incorporated equally into two residues of ethanolamine, only one of which has a free amino group. A single residue of glucosamine with a free amino group is also detected. Each of the sugar precursors is incorporated with extensive conservation of chemical identity. In the class E cells, each of the labeled sugars but neither [3H]ethanolamine nor [3H]palmitate is incorporated into Thy-1. The anchor moiety therefore appears to be entirely missing, although N-linked oligosaccharide processing is essentially normal. We postulate that the anchor deficiency in the mutant cells results from a biosynthetic lesion.     

Dynamics and longevity of the glycolipid-anchored membrane protein, Thy- 1

Thy-1 and a number of other proteins are anchored to the outer hemi-leaflet of membranes by a glycolipid moiety containing ethanolamine phosphate, mannose, glucosamine, and phosphatidylinositol. They nevertheless have the striking property of being able to transduce signals across the plasma membrane. We here demonstrate, for the BW5147 murine T lymphoma, that (a) greater than 90% of Thy-1 is at the cell surface, (b) Thy-1 is about one order of magnitude less concentrated in coated pits than the transferrin receptor or H-2 antigens, (c) Thy-1 undergoes at most very limited endocytosis or diacytosis, and (d) Thy-1 has an unusually slow turnover rate. Several similar observations have also been made for a second glycolipid-anchored protein, the T cell activating protein. Thus, the absence of cytoplasmic and trans-membrane domains may result in lipid-anchored proteins being confined to the cell surface and being free from constraints which affect the turnover of transmembrane proteins.     

The phenotype of five classes of T lymphoma mutants. Defective glycophospholipid anchoring, rapid degradation, and secretion of Thy-1 glycoprotein

Thy-1 glycoprotein is a member of a class of proteins which are anchored to the plasma membrane via a covalently bound glycophospholipid. The biosynthesis and anchoring of Thy-1 were investigated in a family of wild-type and mutant (complementation groups A, B, C, E, and F) T lymphomas. The mutants all synthesize Thy-1 but fail to express it on the cell surface. Analysis of the size of D-[2-3H]mannose-labeled dolichol-linked oligosaccharides showed that the class E mutant is the only cell line which does not synthesize dolichol-P-P-Glc3Man9GlcNAc2. Turnover and possible secretion of Thy-1 by mutant T lymphoma cells were documented in D-[2-3H]mannose pulse-chase experiments. The turnover of [3H]Thy-1 for all wild-type cells is considerably slower than for the mutant cells. Class B and E cells release appreciably more [3H]Thy-1 than wild-type cells. Additional experiments were performed to determine the electrophoretic mobility and hydrophobicity of cell-associated and released forms of Thy-1 labeled overnight with [3H]mannose. All wild-type and class A, C, E, and F mutant cells contain a major Triton X-114 binding species of cell-associated [3H]Thy-1. All extracellular [3H]Thy-1 was almost exclusively hydrophilic. The presence of two Thy-1 anchor components, ethanolamine and palmitate, was investigated. Biosynthetic labeling with [3H]palmitic acid showed that all of the wild-type cells but none of the mutants incorporated this anchor precursor into Thy-1. In [3H]ethanolamine-labeling experiments, incorporation was detected in the Thy-1 of all wild-type cells and in two mutants, S1A-b and T1M1-c. Based on the above studies, the phenotype of Thy-1 negative T lymphoma mutants can be re-evaluated. In classes A and F, dolichol-linked oligosaccharides appear normal and no anchor is detected. In class B, dolichol-linked oligosaccharides appear normal, a partial anchor may be present, and a substantial amount of Thy-1 is released. In class C, dolichol-linked oligosaccharides appear normal and a partial anchor may be present. In class E, truncated dolichol-linked oligosaccharides are formed, no anchor is detected, but a substantial amount of newly synthesized Thy-1 is released. These observations are discussed with reference to the possibility that the lesions which characterize the mutants pertain to the biosynthesis of the glycophospholipid moiety of Thy-1.