Optical spectroscopic study of the effects of a single deoxyribose substitution in a ribose backbone: implications in RNA-RNA interaction

The 2'-OH group in the ribose sugars of an RNA molecule plays an important role in guiding tertiary interactions that stabilize different RNA structural motifs. Deoxyribose, or 2'-OH by 2'-H, substitution in both the single-stranded and the duplex part of an RNA backbone has been routinely used to evaluate what role the 2'-OH plays in different tertiary interactions that guide an RNA-RNA contact. A deoxyribose substitution not only has the effect of removing a hydrogen bond donating group, but also introduces a sugar moiety with a preference for C2'-endo pucker in a backbone of predominantly C3'-endo sugars. This study evaluates the effects of a single deoxyribose substitution in both single-stranded and double-helical forms of RNA oligomers. A single-stranded, nonrepetitive 7-mer oligoribonucleotide (7-mer RNA) and four different variants having the same base sequence but with a single deoxyribose sugar at different positions in the strands have been studied by ultraviolet (UV) absorption, circular dichroism (CD), and Fourier transform infrared (FTIR) spectroscopy. Duplexes were formed by association with the complementary strand of the 7-mer RNA. The results show that both RNA and DNA single strands have preorganized conformations with spectral properties resembling those of A- and B-form helices, respectively, with RNA being more heterogeneous than its DNA counterpart. A single deoxyribose substitution perturbs the structure of the RNA backbone, with the effect being more pronounced in the single-stranded than in the duplex structure. The perturbation depends on the position of the 2'-H substitution in the strand.

Influence of adrenal cortex on testicular activity in the toad during the breeding season

The aim of the present study was to determine the role of adrenals in gonadal activity in the male toad during the breeding season. Exogenous administration of corticosterone or metapyrone for 6 days inhibited adrenal delta5-3beta(delta 5-3 beta) hydroxysteroid (delta5-3beta-HSD) and testicular 17beta (17 beta) hydroxysteroid dehydrogenase (17beta-HSD) activities, decreased the serum levels of testosterone and inhibited spermatogenesis. When toads were treated with corticosterone a significant rise of serum corticosterone was noted while metapyrone treatment appeared to decrease serum corticosterone levels. It is concluded that adrenocortical hormone plays an indirect role in testicular activity in toads during the breeding season.

Viral IL-10 gene transfer decreases inflammation and cell adhesion molecule expression in a rat model of venous thrombosis

Post-thrombotic inflammation probably contributes to chronic venous insufficiency, and little effective treatment exists. IL-10 is an anti-inflammatory cytokine that previously has been shown to decrease perithrombotic inflammation and thrombosis. We investigated in a rat model whether local expression of viral IL-10 (vIL-10) in a segment of vein that undergoes thrombosis would confer an anti-inflammatory effect and how this effect might be mediated. Rats underwent inferior vena cava isolation, cannulation, and instillation of saline or adenovirus encoding either beta-galactosidase or vIL-10. Two days after transfection, thrombosis was induced, 2 days after this the rats underwent gadolinium (Gd)-enhanced magnetic resonance venography exam, and the vein segments were harvested. Tissue transfection was confirmed by either RT-PCR of vIL-10 or positive 5-bromo-4-chloro-3-indolyl beta-d-galactopyranoside (X-Gal) staining. vIL-10 significantly decreased both leukocyte vein wall extravasation and area of Gd enhancement compared with those in controls, suggesting decreased inflammation. Immunohistochemistry demonstrated decreased endothelial border staining of P- and E-selectin, while ELISA of vein tissue homogenates revealed significantly decreased P- and E-selectin and ICAM-1 levels in the vIL-10 group compared with those in controls. Importantly, native cellular IL-10 was not significantly different between the groups. However, neither clot weight nor coagulation indexes, including tissue factor activity, tissue factor Ag, or von Willebrand factor levels, were significantly affected by local vIL-10 expression. These data suggest that local transfection of vIL-10 decreases venous thrombosis-associated inflammation and cell adhesion molecule expression, but does not directly affect local procoagulant activity.

Studies on the Interaction of Surfactants with Cationic Dye by Absorption Spectroscopy

The interaction of methyl violet, a cationic dye, with various surfactants, viz. anionic (SDS), nonionic (Triton X-100), and cationic (CTAB), has been investigated spectrophotometrically in submicellar and micellar concentration range. While in the submicellar concentration region of SDS the higher aggregates of the dye are found, in the micellar concentration region the monomer of the dye predominates. With nonionic surfactant the dye is solubilized primarily as the monomer. CTAB produces no perturbation to the visible spectra of the dye. In the presence of strong electrolytes such as NaNO(3) and NaCl the dye aggregates are formed at a much lower SDS concentrations. Copyright 2000 Academic Press.

Application of K-nearest neighbors algorithm on breast cancer diagnosis problem

This paper addresses the Breast Cancer diagnosis problem as a pattern classification problem. Specifically, this problem is studied using the Wisconsin-Madison Breast Cancer data set. The K-nearest neighbors algorithm is employed as the classifier. Conceptually and implementation-wise, the K-nearest neighbors algorithm is simpler than the other techniques that have been applied to this problem. In addition, the Knearest neighbors algorithm produces the overall classification result 1.17% better than the best result known for this problem.

Comparison of tRNA activity under homologous and heterologous conditions during the reproductive cycle of Heteropneustes fossilis

Rate of protein synthesis in ovary is analyzed throughout the annual reproductive cycle of H. fossilis. It is highest during previtellogenic phase and lowest during post spawning phase. The variation pattern matches with aminoacylation capacity of tRNA. The aminoacylation capacity of tRNA is compared in the two phases under homologous and heterologous conditions. Both tRNA and aRS are obtained from the same phase under homologous conditions and from different phases under heterologous conditions. Aminoacylation capacity is also compared in ovary and liver under homologous and heterologous conditions. Both tRNA and aRS show higher activity in previtellogenic phase. However, tRNA contributes more for higher aminoacylation activity. Transfer RNA fractionates into similar isoacceptors during the two phases. This indicates that the primary structure of tRNA may not change during the reproductive cycle. Therefore, it is suggested that the difference in aminoacylation activity may be due to post-transcriptional modifications of tRNA leading to conformational changes. Gm modification and 2-O' methylation of tRNA are reported earlier to vary during the reproductive cycle [2]. The results support the earlier suggestion of conformational changes in tRNA in 'active' and 'inactive' forms in previtellogenic and post spawning phases respectively. Aminoacylation capacity of tRNA shows organ specificity. It is high in ovary than in liver. Poor aminoacylation capacity is shown under heterologous conditions. This may be due to incompatible aRS related to specific amino acid pool in the tissue, or post transcriptional changes in tRNA, which may not allow cross acylation with full efficiency.

Antitesticular effect of copper chloride in albino rats

Copper chloride treatment adversely affects testicular activity in albino rats. To investigate its antitesticular effects mature (120 days) Wistar strain albino rats were treated intraperitoneally (i.p.) with copper chloride at doses of 1000, 2000 and 3000 micrograms/kg body weight/day for 26 days. Significant reduction of testicular and accessory sex organs (seminal vesicle, ventral prostate) weight, along with inhibition of testicular delta 5-3 beta-hydroxysteroid dehydrogenase (delta 5-3 beta-HSD) and 17 beta-hydroxysteroid dehydrogenase (17 beta-HSD) activity and reduction in plasma testosterone level, were observed at the doses of 2000 and 3000 micrograms/kg body weight/day. The degree of inhibition in all the parameters were increased with the increase of dosage. But no significant change was observed in the above parameters when the animals were treated with 1000 micrograms/kg body weight/day dose. This suggests that copper produces a suppressive influence on male reproductive activity, mainly on testicular weight and steroidogenesis and accessory sex organ weight in a dose-dependent manner.

Neovascularization during venous thrombosis organization: a preliminary study

PURPOSE

Thrombus organization after venous thromboembolism leading to recanalization occurs at a variable rate. The angiogenic chemokine interleukin-8 (IL-8) has been found in thrombus months after thrombus initiation. We hypothesize that thrombus organization involves neovascularization and leukocyte influx and that IL-8 administered at thrombus induction will promote thrombus organization.

METHODS

A group of rats underwent inferior vena caval occlusive thrombosis. At thrombus induction and every 24 hours, the rats were administered IL-8 (1 microgram) or serum albumin. The rats were killed at either day 4, day 8, or day 12, and, at death, colloidal carbon was perfused via the heart. The inferior vena cava was isolated, measured, weighed, and formalin fixed. The sections were stained with anti-polymorphonuclear leukocyte antibody, the endothelial marker factor VIII-related antigen, and with hematoxylin and eosin. Thrombus neovascularization (colloidal carbon) with morphometric analysis was normalized to the total thrombus area. In addition, the rats underwent perfusion with fluorescein isothiocyanate dextran (molecular weight, 150,000) at death to correlate with colloidal carbon perfusion, and thrombus fluorescence was determined.

RESULTS

Thrombus cellularity initially involved neutrophils, followed by monocytes. Significantly more neutrophils, monocytes, and cells that were defined as spindle shaped (fibroblasts and endothelial cells) were noted in the animals treated with IL-8. Neovascularization was significantly increased at day 4 in the animals treated with IL-8 versus the animals treated with serum albumin and was corroborated with a significant increase in thrombus fluorescein isothiocyanate dextran fluorescence at day 4 in the rats treated with IL-8. Colloidal carbon perfusion was noted within vascular channels without extravasation and colocalized with factor VIII-related antigen.

CONCLUSION

This study shows that thrombus organization involves neovascularization and that IL-8 augments thrombus organization.

Dexamethasone suppresses vascular smooth muscle cell proliferation

BACKGROUND

Experimental studies in vivo have demonstrated that dexamethasone inhibits neointimal hyperplasia following arterial injury. The mechanisms of this inhibition have not been clearly defined. Our objective was to test the hypothesis that dexamethasone directly suppresses smooth muscle cell (SMC) proliferation by inhibiting cell cycle progression and the expression of key cell cycle-dependent genes.

METHODS

Cultured rat aortic SMC were treated with incremental concentrations of dexamethasone and cell number was determined after 72 h. To determine if dexamethasone inhibited cell cycle progression, cells were synchronized, then restimulated to enter the cell cycle, and treated with or without dexamethasone. DNA synthesis was determined 24 h after restimulation by measuring [3H]thymidine incorporation. To define the point of action of dexamethasone in the cell cycle, synchronized SMC were treated with dexamethasone (10(-7) M) at various time points after entry into the cell cycle. Flow cytometry and Northern blots were performed to examine cell cycle progression and the expression of smooth muscle cell cycle-dependent genes c-fos, c-myc, and thymidine kinase (TK).

RESULTS

Dexamethasone treatment induced a concentration-dependent inhibition of SMC proliferation and DNA synthesis. The cell cycle progression of synchronized SMC from G1 into S phase was inhibited by dexamethasone, even when added as late as 16 h after restimulation. The expression of TK was suppressed by dexamethasone, while c-fos and c-myc were not affected.

CONCLUSIONS

Dexamethasone inhibits the proliferation of SMC in a concentration-dependent fashion. This inhibition is associated with a block in cell cycle progression late in G1 phase of the cell cycle. Consistent with this finding, dexamethasone does not alter the expression of the early cell cycle-dependent genes c-fos and c-myc, but significantly inhibits the expression of TK, a marker of late G1 phase.

Expression of three Caenorhabditis elegans N-acetylglucosaminyltransferase I genes during development

UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1, 2-N-acetylglucosaminyltransferase I (GnT I) is a key enzyme in the synthesis of Asn-linked complex and hybrid glycans. Studies on mice with a null mutation in the GnT I gene have indicated that N-glycans play critical roles in mammalian morphogenesis. This paper presents studies on N-glycans during the development of the nematode Caenorhabditis elegans. We have cloned cDNAs for three predicted C. elegans genes homologous to mammalian GnT I (designated gly-12, gly-13, and gly-14). All three cDNAs encode proteins (467, 449, and 437 amino acids, respectively) with the domain structure typical of previously cloned Golgi-type glycosyltransferases. Expression in both insect cells and transgenic worms showed that gly-12 and gly-14, but not gly-13, encode active GnT I. All three genes were expressed throughout worm development (embryo, larval stages L1-L4, and adult worms). The gly-12 and gly-13 promoters were expressed from embryogenesis to adulthood in many tissues. The gly-14 promoter was expressed only in gut cells from L1 to adult developmental stages. Transgenic worms that overexpress any one of the three genes show no obvious phenotypic defects. The data indicate that C. elegans is a suitable model for further study of the role of complex N-glycans in development.

Endoprosthetic treatment of metastatic pathological fractures

Due to a prolonged time of survival patients with lowrisk skeletal dissemination may develop a local relapse after surgical treatment of a pathological fracture. In a series of 180 patients with bone metastases of breast cancer, a local metastatic recurrency was observed 8-36 months after operative treatment in 12 patients. All of them had a receptor-positive primary and were free from visceral metastases; only one had received radiotherapy postoperatively. Patients with low-risk disease therefore should undergo more radial surgical procedures than patients with poor prognosis, in whom reconstitution of stability represents the most important therapeutic goal. In cases with low-risk disease and histologically proven residual tumour a postoperative irradiation should be administered as a rule.

Comparison of tRNA conformation during different phases of reproduction

The present study is a comparison of tRNA conformation from ovary of Heteropneustes fossilis in its active phase of reproduction (when it is highly engaged in protein synthesis i.e. previtellogenic phase) with inactive phase (when tRNA is mainly stored in mature ovary i.e. spawning phase). Transfer RNA of active phase is shown to be compact, flexible and susceptible towards nuclease. Compact tRNA structure is evidenced by higher hyperchromicity and presence of relatively less Gm modifications thereby allowing adequate hydrogen bonding between D loop and T loop. Higher sensitivity of tRNA towards Mg++ reflects its higher flexibility towards internal environment. This structure of tRNA may be required for active protein synthesis. On the other hand tRNA of inactive phase is shown to be relaxed but resistant towards nuclease which may be favoured for storage in mature ova of a teleost as maternal carry over.

Removal of 106 amino acids from the N-terminus of UDP-GlcNAc: alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I does not inactivate the enzyme

UDP-GlcNAc: alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnTI, EC 2.4.1.101) plays an essential role in the conversion of oligomannose to complex and hybrid N-glycans. Rabbit GnTI is 447 residues long and has a short four-residue N-terminal cytoplasmic tail, a 25-residue putative signal-anchor hydrophobic domain, a stem region of undetermined length and a large C-terminal catalytic domain, a structure typical of all glycosyltransferases cloned to date. Comparison of the amino acid sequences for human, rabbit, mouse, rat, chicken, frog and Caenorhabditis elegans GnTI was used to obtain a secondary structure prediction for the enzyme which suggested that the location of the junction between the stem and the catalytic domain was at about residue 106. To test this hypothesis, several hybrid constructs containing GnT I with N- and C-terminal truncations fused to a mellitin signal sequence were inserted into the genome of Autographa californica nuclear polyhedrosis virus (AcMNPV), Sf9 insect cells were infected with the recombinant baculovirus and supernatants were assayed for GnTI activity. Removal of 29, 84 and 106 N-terminal amino acids had no effect on GnTI activity; however, removal of a further 14 amino acids resulted in complete loss of activity. Western blot analysis showed strong protein bands for all truncated enzymes except for the construct lacking 120 N-terminal residues indicating proteolysis or defective expression or secretion of this protein. The data indicate that the stem is at least 77 residues long.

FTIR spectroscopic studies of oligonucleotides that model a triple-helical domain in self-splicing group I introns

Fourier Transform infrared (FTIR) spectroscopy was used to characterize the Mg2+ dependent association of a 23-mer mixed ribo-deoxyribonucleotide (23-mer RNA) and a 7-mer oligoribonucleotide (7-mer RNA) that models the triple-helical domain of a self-splicing group I intron [Sarkar et al. (1996) Biochemistry 35, 4678-4688]. To elucidate the effect of deoxyribose substitution in the entire backbone, as well as at specific positions, in the assembly of the triple-helical domain, parallel studies were carried out on the association of pure deoxyribonucleotides having base sequences corresponding to the oligoribonucleotides and also between 23-mer RNA and two 7-mer RNA variants. In the variants, either the ribose attached to G451 or the ribose attached to U453 was changed to deoxyribose. FTIR-monitored thermal denaturation of the two 23-mer hairpins shows two distinct melting regions in 1 M NaCl, in case of the RNA hairpin but not for the 23-mer DNA. Triple-helix association between the two strands (7-mer and 23-mer) studied by FTIR show that only when both strands are RNA, association takes place with the formation of the P6 helix. Our results also show that the interactions between the two RNA strands involve some participation of the riboses, which could also involve the 2'-OH groups of the RNA backbone. The assembly of the triple-helical domain is not possible with a deoxyribose backbone and is completely perturbed even when only one ribose at either G451 or U453 position is substituted by deoxyribose.

Thrombocytopenic coagulopathy (Kasabach-Merritt phenomenon) is associated with Kaposiform hemangioendothelioma and not with common infantile hemangioma

Children with a large vascular tumor and associated Kasabach-Merritt coagulopathy respond inconsistently to therapy and have a high mortality rate. For this reason, we undertook a retrospective study of 21 such patients, and focused on clinical, radiographic, and histopathologic features. The male to female ratio was 1:1.6. Tumor was noted at birth in 50 percent of patients; the remainder appeared throughout infancy. The location was cervicofacial (n = 2), shoulder/upper limb (n = 4), trunk including retroperitoneum (n = 11), and lower limb (n = 4). These tumors grew rapidly to large size and were characterized by cutaneous purpura, edema, and an advancing ecchymotic margin. In contrast to common hemangioma, magnetic resonance imaging showed diffuse enhancement with ill-defined margins, cutaneous thickening, stranding of subcutaneous fat, hemosiderin deposits, and small feeding and draining vessels. All tumors were Kaposiform hemangioendothelioma (KHE); none were infantile hemangioma. Light microscopy showed irregular lobules or sheets of poorly formed, small vascular channels infiltrating and entrapping normal tissues. Characteristic features included spindle-shaped endothelial cells, diminished pericytes and mast cells, microthrombi, and hemosiderin deposits. Wide endothelial intercellular gaps and incomplete basement membranes were seen by electron microscopy. Dilated, hyperplastic, lymphaticoid channels were prominent in one tumor. KHE in 14 infants was treated with interferon alpha-2a: 6 had accelerated regression; 2 had stabilization of growth; and 6 evidenced no response. The mortality rate was 24 percent (5 of 21); this included three infants with retroperitoneal KHE. Kasabach-Merritt phenomenon does not occur with common hemangioma. Rather it is associated with the more aggressive KHE and rarely with other vascular neoplasms. Variable response to current pharmacologic therapy underscores our inadequate knowledge of the pathogenesis of thrombocytopenia in KHE.