Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs

We present a method for high-throughput alternative splicing detection in expressed sequence data. This method effectively copes with many of the problems inherent in making inferences about splicing and alternative splicing on the basis of EST sequences, which in addition to being fragmentary and full of sequencing errors, may also be chimeric, misoriented, or contaminated with genomic sequence. Our method, which relies both on the Partial Order Alignment (POA) program for constructing multiple sequence alignments, and its Heaviest Bundling function for generating consensus sequences, accounts for the real complexity of expressed sequence data by building and analyzing a single multiple sequence alignment containing all of the expressed sequences in a particular cluster aligned to genomic sequence. We illustrate application of this method to human UniGene Cluster Hs.1162, which contains expressed sequences from the human HLA-DMB gene. We have used this method to generate databases, published elsewhere, of splices and alternative splicing relationships for the human, mouse and rat genomes. We present statistics from these calculations, as well as the CPU time for running our method on expressed sequence clusters of varying size, to verify that it truly scales to complete genomes.

Development of studies of TPO gene and its application in nuclear medicine

Thyroperoxidase (TPO) is a glycosylated protein bound to the apical plasma membrane of thyrocytes. It is the key enzyme in the synthesis of thyroid hormones. Its gene structure and transcriptional regulation have been studied in detail. This article reviews the structure, function and transcriptional regulation of the TPO gene, and the relationship between TPO, thyroid diseases and radioactive iodide therapy.

5-Hydroxytryptamine-induced plasma extravasation in the rat knee joint is mediated by multiple prostaglandins

OBJECTIVE AND DESIGN

This study investigated whether prostaglandins (PGs) are involved in 5-hydroxytryptamine (5-HT)-induced synovial plasma extravasation.

MATERIALS AND METHODS

Male Sprague-Dawley rat knee joints were perfused with 5-HT and synovial capillary Evans Blue dye leakage was measured using spectrophotometry. Cyclooxygenase (COX) inhibitors and PG receptor subtype-selective antagonists were tested for the ability to reduce 5-HT-induced synovial plasma extravasation.

RESULTS

5-HT-induced plasma extravasation was inhibited by indomethacin. The COX-1 selective inhibitor SC-560 and the COX-2 selective inhibitor NS-398 were equally effective, indicating that both isoforms are involved. Antagonists selective for EP1, EP2 and DP receptor subtypes significantly attenuated the 5-HT-induced plasma extravasation. However, antagonists selective for FP, IP and TP subtypes failed to reduce 5-HT-induced plasma extravasation.

CONCLUSIONS

These results demonstrate that multiple, but selective, subtypes of PGs mediate synovial plasma extravasation produced by 5-HT, and suggest that PGs act downstream of 5-HT in the inflammatory cascade.

Alternatively folded choriogonadotropin analogs. Implications for hormone folding and biological activity

Most heterodimeric proteins are stabilized by intersubunit contacts or disulfide bonds. In contrast, human chorionic gonadotropin (hCG) and other glycoprotein hormones are secured by a strand of their beta-subunits that is wrapped around alpha-subunit loop 2 "like a seatbelt." During studies of hCG synthesis in COS-7 cells, we found that, when the seatbelt was prevented from forming the disulfide that normally "latches" it to the beta-subunit, its carboxyl-terminal end can "scan" the surface of the heterodimer and become latched by a disulfide to cysteines substituted for residues in the alpha-subunit. Analogs in which the seatbelt was latched to residues 35, 37, 41-43, and 56 of alpha-subunit loop 2 had similar lutropin activities to those of hCG; that in which it was latched to residue 92 at the carboxyl terminus had 10-20% the activity of hCG. Attachment of the seatbelt to alpha-subunit residues 45-51, 86, 88, 90, and 91 reduced lutropin activity substantially. These findings show that the heterodimer can form before the beta-subunit has folded completely and support the notions that the carboxyl-terminal end of the seatbelt, portions of alpha-subunit loop 2, and the end of the alpha-subunit carboxyl terminus do not participate in lutropin receptor interactions. They suggest also that several different architectures could have been sampled without disrupting hormone activity as the glycoprotein hormones diverged from other cysteine knot proteins.

Lovastatin increases nitric oxide synthesis in IL-1 beta-stimulated smooth muscle cells

OBJECTIVE

Nitric oxide (NO) production by inducible NO synthase (iNOS) may play an important role in the pathogenesis of atherosclerosis. Although lovastatin has been shown to reduce the progression of atherosclerosis, it is not known whether it regulates NO production. We investigated the effects of lovastatin on NO synthesis and the mechanisms by which lovastatin exerts its effects in rat vascular smooth muscle cells.

METHODS

Primary cultures of the vascular smooth muscle cells were obtained from the media of the thoracic aorta of Sprague Dawley rats (200-250 g). Nitrite levels in the culture medium of rat vascular smooth muscle cells were determined colorimetrically.

RESULTS

Lovastatin (10(-5) mol/L) significantly increased interleukin-1 beta (IL-1 beta, 10 ng/mL)-induced nitrite accumulation in a time (0-24 hours)-dependent manner. Exogenous mevalonate and geranylgeranyl-pyrophosphate completely reversed the stimulatory effects of lovastatin on nitrite production. Furthermore, inhibition of Rho by C3 exoenzyme mimicked the increase in IL-1 beta-induced nitrite accumulation induced by lovastatin in the vascular smooth muscle cells.

CONCLUSION

These results demonstrate that lovastatin up-regulates NO formation in rat vascular smooth muscle cells stimulated by IL-1 beta, and the effect may be associated with the inhibition of Rho activity.

[Role of endogenous cholinergic nerve in esophageal dysmotility with reflux esophagitis]

OBJECTIVE

To study the role of endogenous cholinergic nerve in esophageal dysmotility with reflux esophagitis in a feline model.

METHODS

In 16 healthy cats under ketamine anesthesia (20 mg/kg), the abdominal parts of lower esophageal sphincter were cut open to establish the animal model for reflux esophagitis; esophageal motility was measured respectively preoperation and post-esophagitis. The activities of choline acetyltransferase (CHAT) and acetylcholinesterase(ACHE) in medial and distal esophageal body muscle was measured respectively with spectrophotometry, and compared to the normal cats(n = 8).

RESULTS

Reflux esophagitis can make distal esophageal peristaltic amplitude decrease, the distal esophageal peristaltic amplitude of cats with reflux esophagitis [above LES 1 cm: (22.65 +/- 16.53) mm Hg; above LES 3 cm:(39.94 +/- 14.78) mm Hg, P < 0.0001] was significantly lower than that of normal cats [above LES 1 cm: (63.71 +/- 21.34) mm Hg; above LES 3 cm: (73.65 +/- 23.42) mm Hg] and the conducting velocity of distal esophagus was slower than that of normal cats [(1.04 +/- 0.36) cm/s vs (1.39 +/- 0.46) cm/s, P < 0.05]. In the esophagus of reflux esophagitis group, CHAT activity was lower in the model, especially in the distal part [(81.01 +/- 22.03) U/g vs (230.13 +/- 30.10) U/g, P < 0.0001] and ACHE activity remains unchanged.

CONCLUSION

CHAT activity and pressure level were lower in the distal esophagus with reflux esophagitis compared to the normal cats. This study supported that reflux esophagitis can results in dysmotility of the distal esophagus and the abnormality of endogenous cholinergic innervation is one of the important mechanisms as far as the disorder of esophageal movement in reflux esophagitis.

Germinal center-associated nuclear protein (GANP) has a phosphorylation-dependent DNA-primase activity that is up-regulated in germinal center regions

Antigen stimulation induces a rapid proliferation of B cells for expansion of specific B cell clones and their further differentiation into antibody-producing cells in germinal centers of T-dependent antigen-immunized mice. Previously, we identified a 210-kDa germinal center-associated nuclear protein (GANP) that is up-regulated selectively in germinal centers and carries an MCM-binding domain in the carboxyl-terminal side. In addition, here, we found a region (from 414 to 550 aa) in GANP molecule that is slightly similar to the known DNA-primase component p49. The recombinant GANP fragment covering this region synthesizes RNA primers for extension by DNA polymerase I with single-stranded DNA templates in vitro. GANP DNA-primase activity is controlled by phosphorylation at Ser(502) that is induced by CD40-mediated signaling in vitro and in the germinal center B cells stimulated with antigen in vivo. Overexpression of ganp cDNA in Daudi B cells caused the increased DNA synthesis more than the levels of the mock-transfectants. These evidences suggested that the novel DNA-primase GANP is involved in regulation of cell proliferation of antigen-driven B cells in germinal centers.

Early treatment of wounds polluted by sea water

During construction or training at sea, wounds are commonly seen and irresistibly polluted by sea water. An early and proper treatment of wounds polluted by sea water is very important for wound healing and function recovery of extremities. Some wounds even result in vegetation. In this study, we have reported the treatment results of 132 cases of wounds polluted by sea water admitted from 1985 to 1999.

Transmission of mouse senile amyloidosis

SUMMARY

In mouse senile amyloidosis, apolipoprotein A-II polymerizes into amyloid fibrils (AApoAII) and deposits systemically. Peripheral injection of AApoAII fibrils into young mice induces systemic amyloidosis (Higuchi et al, 1998). We isolated AApoAII amyloid fibrils from the livers of old R1.P1-Apoa2(c) mice and injected them with feeding needles into the stomachs of young R1.P1-Apoa2(c) mice for 5 consecutive days. After 2 months, all mice had AApoAII deposits in the lamina propria of the small intestine. Amyloid deposition extended to the tongue, stomach, heart, and liver at 3 and 4 months after feeding. AApoAII suspended in drinking water also induced amyloidosis. Amyloid deposition was induced in young mice reared in the same cage for 3 months with old mice who had severe amyloidosis. Detection of AApoAII in feces of old mice and induction of amyloidosis by the injection of an amyloid fraction of feces suggested the propagation of amyloidosis by eating feces. Here, we substantiate the transmissibility of AApoAII amyloidosis and present a possible pathogenesis of amyloidosis, ie, oral transmission of amyloid fibril conformation, where we assert that exogenous amyloid fibrils act as templates and change the conformation of endogenous amyloid protein to polymerize into amyloid fibrils.

[Geostrophic deviation analysis of regional effects of protective forest system in reducing windspeed in north Liaoning plain]

East Asian synoptic charts and ground wind data in April and May of four counties of north Liaoning plain were selected to calculate the regional effects of protective forest system in reducing windspeed by geostrophic deviation method. The results show that the protection effects increased with increasing forestration area. Different protection effects of protective forest appeared at different daytime, with the greatest at 14:00 and smallest at 2:00, and the average windspeed reduced 13.3%. The characteristics of the geostrophic deviation method was also discussed.

Threading of a glycosylated protein loop through a protein hole: implications for combination of human chorionic gonadotropin subunits

Chorionic gonadotropin (hCG) is a heterodimeric placental glycoprotein hormone essential for human reproduction. Twenty hCG beta-subunit residues, termed the seatbelt, are wrapped around alpha-subunit loop 2 (alpha 2) and their positions "latched" by a disulfide formed by cysteines at the end of the seatbelt (Cys 110) and in the beta-subunit core (Cys 26). This unique arrangement explains the stability of the heterodimer but raises questions as to how the two subunits combine. The seatbelt is latched in the free beta-subunit. If the seatbelt remained latched during the process of subunit combination, formation of the heterodimer would require alpha 2 and its attached oligosaccharide to be threaded through a small beta-subunit hole. The subunits are known to combine during oxidizing conditions in vitro, and studies described here tested the idea that this requires transient disruption of the latch disulfide, possibly as a consequence of the thioredoxin activity reported in hCG. We observed that alkylating agents did not modify either cysteine in the latch disulfide (Cys 26 or Cys 110) during heterodimer formation in several oxidizing conditions and had minimal influence on these cysteines during combination in the presence of mild reductants (1--3 mM beta-mercaptoethanol). Reducing agents appeared to accelerate subunit combination by disrupting a disulfide (Cys 93--Cys 100) that forms a loop within the seatbelt, thereby increasing the size of the beta-subunit hole. We propose a mechanism for hCG assembly in vitro that depends on movements of alpha 2 and the seatbelt and suggest that the process of glycoprotein hormone subunit combination may be useful for studying the movements of loops during protein folding.

The effect of interleukin-6 on the proliferation of prostate cancer cells in vitro and the modulation of this procedure

The role of interleukin-6 (IL-6) in the growth of an androgen-independent prostate cancer cell line (PC-3 m) was defined and the effect of dexamethasone, which was previously shown to modulate IL-6/IL-6 receptor (IL-6R) on this procedure was investigated. By using a pretty sensitive and specific enzyme immunoassay (ELISA), it was found that PC-3 m produced certain IL-6, but there was no difference in IL-6 secretion between the group with or without dexamethasone treatment. It was also found that PC-3 m cells could not be stimulated to grow by exogenous IL-6 (P > 0.05), while it could be inhibited to grow by anti-IL-6 monoclonal antibody and dexamethasone with a dose-dependent fashion. Our observation indicated that IL-6 acted as an autocrine growth factor for PC-3 m, and dexamethasone could inhibit cell proliferation by a mechanism independent of its effect on IL-6 mRNA expression.

Efficient pyridinylmethyl functionalization: synthesis of 10, 10-Bis[(2-fluoro-4-pyridinyl)methyl]-9(10H)-anthracenone (DMP 543), an acetylcholine release enhancing agent

2-Fluoro-4-methylpyridine (3) is efficiently functionalized by chlorination, hydrolysis and methanesulfonylation into the novel alkylating agent 7. This mesylate is used for the bisalkylation of anthrone under carefully defined conditions to prepare the cognition enhancer drug candidate 1. This process proceeds in up to 37% overall yield and is adaptable for large scale synthesis.

A commercial preparation of catalase inhibits nitric oxide production by activated murine macrophages: role of arginase

Catalase is widely used as a pharmacological probe to evaluate the role of hydrogen peroxide in antimicrobial activities of phagocytic cells. This report demonstrates that the ability of a commercial preparation of catalase to inhibit concomitantly macrophage antimycobacterial activity and production of reactive nitrogen intermediates can be attributed, at least in part, to the depletion of L-arginine by contaminating arginase. In experimental systems that employ pharmacological probes, the existence of nonspecific effects should be considered in data interpretation.

Toxicity of nitrogen oxides and related oxidants on mycobacteria: M. tuberculosis is resistant to peroxynitrite anion

OBJECTIVE

To test the toxicity of reactive nitrogen intermediates (RNI), including authentic nitric oxide (NO), nitrogen dioxide (NO2), and peroxynitrite anion (ONOO-), a potent oxidant derived from NO and superoxide anion, on various mycobacterial strains including M. tuberculosis.

DESIGN

Relatively avirulent mycobacteria including M. smegmatis and BCG, as well as the pathogenic M. Bovis Ravenel and M. tuberculosis Erdman and the clinical isolate M160 (also known as the C strain) were tested for their susceptibility to the toxic effects of NO, NO2, and ONOO-, Deaerated, NO-saturated solutions as well as an anaerobic in vitro system in which mycobacteria can be exposed to desired concentrations of authentic NO or NO2, were employed in these studies. An in vitro ONOO- killing assay was used to examine the adverse effects of this NO-derived oxidant on the various strains of mycobacteria.

RESULTS

Both NO and NO2 exhibit antimycobacterial activity, with the former being more potent. Results obtained using ONOO- killing assay revealed that while avirulent mycobacteria including BCG and M. smegmatis are susceptible to this NO-derived oxidant, the virulent Erdman strain of M. tuberculosis and M. bovis, as well as the clinical tuberculous isolate M160, are remarkably resistant.

CONCLUSION

These results suggest that the interactions between RNI and various species of mycobacteria could be highly specific. And since activated macrophages produce peroxynitrite, the significance of the ONOO- resistance of M. tuberculosis strains in relation to intracellular survival deserves further investigation.

Newcastle disease virus activates macrophages for anti-tumor activity

Newcastle Disease Virus (NDV), an agent with interesting immune stimulatory and anti-tumor activity, was investigated for its capacity to activate anti-tumor activity in murine macrophages in vitro and in vivo. Direct macrophage activation was seen under a variety of experimental conditions using two different strains of NDV, different sources of macrophages (spleen and peritoneum) and different strains of mice (DBA/2, C57BL/6, 615). Various macrophage enzymes (ADA, iNOS, lysozyme, acid phosphatase) became upregulated and anti-tumor effector molecules such as nitric oxide (NO) and TNF-alpha were found in the supernatant. NDV activated macrophages performed anti-tumor activity in vitro such as anti-tumor cytostasis and anti-tumor cytotoxicity. The cytotoxic anti-tumor activity was broad and active against all tumor lines tested including mammary carcinoma, lung carcinoma, mastocytoma and immune escape variants (lymphoma). Macrophage activation via BCG/LPS also caused a broad range anti-tumor cytotoxic activity while activation via mixed lymphocyte culture conditioned medium had restricted anti-tumor activity. Anti-tumor activity of NDV activated macrophages could be transfered in vivo. Transfer of macrophages which had not been appropriately activated exerted either no effect or a tumor growth augmenting effect. Repeated intravenous transfer of NDV activated macrophages exerted a significant suppressive effect on pulmonary metastases in a mammary carcinoma tumor model as well as in a lung carcinoma model. Taken together these results demonstrate that NDV can strongly activate macrophages to perform anti-tumor activities in vitro and in vivo.

Newcastle disease virus activates macrophages for anti-tumor activity

Newcastle Disease Virus (NDV), an agent with interesting immune stimulatory and anti-tumor activity, was investigated for its capacity to activate anti-tumor activity in murine macrophages in vitro and in vivo. Direct macrophage activation was seen under a variety of experimental conditions using two different strains of NDV, different sources of macrophages (spleen and peritoneum) and different strains of mice (DBA/2, C57BL/6, 615). Various macrophage enzymes (ADA, iNOS, lysozyme, acid phosphatase) became upregulated and anti-tumor effector molecules such as nitric oxide (NO) and TNF-alpha were found in the supernatant. NDV activated macrophages performed anti-tumor activity in vitro such as anti-tumor cytostasis and anti-tumor cytotoxicity. The cytotoxic anti-tumor activity was broad and active against all tumor lines tested including mammary carcinoma, lung carcinoma, mastocytoma and immune escape variants (lymphoma). Macrophage activation via BCG/LPS also caused a broad range anti-tumor cytotoxic activity while activation via mixed lymphocyte culture conditioned medium had restricted anti-tumor activity. Anti-tumor activity of NDV activated macrophages could be transfered in vivo. Transfer of macrophages which had not been appropriately activated exerted either no effect or a tumor growth augmenting effect. Repeated intravenous transfer of NDV activated macrophages exerted a significant suppressive effect on pulmonary metastases in a mammary carcinoma tumor model as well as in a lung carcinoma model. Taken together these results demonstrate that NDV can strongly activate macrophages to perform anti-tumor activities in vitro and in vivo.

[DNase I sensitivity of nucleus and chromatin in six different tissues of old rates]

In order to investigate the mechanism of aging, we studied the DNase I sensitivity of nucleus and chromatin in six different tissue (heart, liver, spleen, lung, kidney and brain of old and weanling wistar rats. The results showed that the DNase I digestive sensitivity levels of nucleus and chromatin in the tissue of the old rats were lower than those of the weanling rats respectively that in the old rats, the DNase I digestive sensitively in the tissue varied, the lowest sensitivity was in brain (P < 0.01); and that in the weanling rats, lowest DNase I digestive sensitivity of nucleus and chromatin was also in the brain, but the difference was not significant.

[Determination of nifedipine content and its uniformity in tablets by high performance liquid chromatography]

An HPLC method with diazepam as internal standard was developed to determine nifedipine content and its uniformity in tablets. The analytical column was a C18 column, the mobile phase consisted of V (methanol):V(triethylamine, pH 5.20) = 68:32. The detection was carried out with UV detector (lambda = 237 nm). Under this condition, the linear range was wide(8-80 mg/L) and the recovery was high (99.86%). The proposed method is simple and accurate and the decomposed product can be separated as well. Therefore, the quality of nifedipine tablets can be effectively controlled.

In situ light-scattering measurements of morphologically evolving flame-synthesized oxide nanoaggregates

Nonspherical Al2O3 aggregates produced in a laminar counterflow nonpremixed methane flame were investigated with an in situ laser light-scattering (LLS) technique in combination with a thermophoretic sampling-transmission electron microscope (TS-TEM) method. These flame-synthesized nanoparticles clearly underwent morphological changes following their formation (from precursor trimethylaluminum hydrolysis), mainly as a result of aggregation and sintering processes in the approximately 3.3 x 10(4) K/s heating environment. To characterize this particulate morphological evolution conveniently we made multiangular absolute LLS measurements and interpreted them based on the Rayleigh-Debye-Gans scattering theory for fractal aggregates. Optically determined fractal dimension D(f), mean radius of gyration, aggregate size distribution, and local particle volume fraction phi(p) were found to be consistent with our independent ex situ TS-TEM experiments. D(f) (optically inferred) increased from 1.60 to 1.84 with axial position, confirming the morphological evolution of alumina aggregates owing to finite-rate, spatially resolved high-temperature sintering. An extension of our TS-TEM method was successfully applied, for the first time to our knowledge, to inorganic particles. Phi(p) inferred by means of this ex situ technique generally agreed with that from the in situ LLS technique, supporting our interpretation of both measurements. Moreover, an optically inferred net sintering rate of alumina aggregates approaching the flame was estimated to be consistent with the available TEM data. The LLS methods and results presented here are expected to permit more comprehensive mechanistic analyses of nanoaggregate sintering and coagulation kinetics in such flame environments, ultimately improving the modeling of more-complex (e.g., turbulent, high-pressure) combustion systems involving nanoparticle formation and evolution.

Identification and characterization of immunoreactive calcitonin gene-related peptide from lymphocytes of the rat

There is accumulating evidence that the immune system can produce neuropeptides. In the light of these facts, we obtained direct evidences to prove that T lymphocytes also synthesize and secrete calcitonin gene-related peptide (CGRP), a neuropeptide localized within primary sensory nerves. By using CGRP specific RIA, CGRP-like immunoreactivity (LI) was found in the extracts of rat lymphocytes from thymus and mesenteric lymph node. The intracellular concentration of lymphocyte-derived CGRP-LI of rat thymus and mesenteric lymph node was 745+/-39 and 447+/-33 fg/10(6) cells, respectively. CGRP-LI in lymphocytes was shown to co-elute with synthetic rat CGRP and sensory neuron-derived CGRP by reverse-phase HPLC. In addition, the CGRP-LI located in the T lymphocytes was also shown by immunocytochemical method examined by electron microscopy. The CGRP mRNA detected by RT-PCR was also present in these lymphocytes and was also identified to be the same one in sensory neurons. These data suggest that CGRP is synthesized and secreted in T lymphocytes of both thymus and lymph node in the rat, and this is identified to be the same one in neuronal tissue. Lymphocyte-derived CGRP may act in an autocrine/paracrine mode and play an important role in certain physiological and pathophysiological conditions.