cisRED: a database system for genome-scale computational discovery of regulatory elements

We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (www.cisred.org). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally.

[Cytokine expression in effusions of secretory otitis media]

OBJECTIVE

To assess the cytokine level in effusions of secretary otitis media and it's relationship with clinical index. To further study the inflammatory mechanism of otitis media with effusion.

METHOD

The concentration of TNF-alpha and TNFsolR II was quantitatively determined using enzyme-linked immunosorbent assay and it was correlated with clinical index in otitis media with effusion using stepwise regression analysis.

RESULT

TNF-alpha and TNFsolR II was found in 100% effusions. Mean values of TNF-alpha were (3.42 +/- 2.25) ng/g total protein. Mean values of TNFsolR II were (405.80 +/- 216.53) ng/g total protein. Mean values of TNFsolR II index was (154.18 +/- 90.45) U. There was a significant decrease of TNFsolR II and TNFsolR II index in patients who recurred (P < 0.05).

CONCLUSION

Cytokine TNF-alpha and TNFsolR II are important inflammatory medium which exist in all otitis media effusions. The decrease of the level of TNFsolR II and TNFsolR II index present significantly in middle ear effusions with recurrence, but there is no any relation of TNF-alpha in middle ear effusions with recurrence.

Specific sequences outside the E-box are required for proper per expression and behavioral rescue

A 69 bp circadian regulatory sequence (CRS) upstream of the per gene is sufficient to drive circadian transcription, mediate proper spatial expression, and rescue behavioral rhythmicity in per01 flies. Within the CRS, an E-box is required for transcriptional activation by two basic-helix-loop-helix (bHLH) PERARNT-SIM (PAS) transcription factors, dCLOCK (dCLK) and CYCLE (CYC). To define sequences within the CRS that are required for spatial expression, circadian expression, and behavioral rhythmicity, a series of mutants that alter blocks of 3 to 12 nucleotides across the entire CRS were used to drive lacZ or per expression in vivo. As expected, the E-box within the CRS is necessary for high-level expression and behavioral rhythmicity, but sequences outside the E-box are also required for transcriptional activation, proper spatial expression, and behavioral rhythmicity. These results indicate that the dCLK-CYC target site extends beyond the E-box and that factors other than dCLK and CYC modulate per transcription.

Bleomycin-induced pulmonary fibrosis is independent of eosinophils

Eosinophils have been shown to increase in tissues during many fibrotic conditions and consequently have been suggested to contribute to the development of fibrosis. This study tested the hypothesis that eosinophils are essential in the development of lung fibrosis in mice in response to bleomycin (BLM). Anti-IL-5 antibody was administered intraperitoneally into mice 2 h prior to endotracheal BLM inoculation and thereafter, every other day. Lung eosinophilia was evaluated by measurement of eosinophil peroxidase activity and confirmed by eosinophil counts in histologic sections. Lung fibrosis was evaluated by hydroxyproline content and confirmed by collagen staining in histological sections. Results demonstrated that BLM induced pronounced lung eosinophilia, which was maximal 7 days after BLM treatment and remained elevated through day 14, in C57B1/6 SCID mice and CBA/J mice. In contrast, eosinophilia was a minor component in the lungs of wildtype C57B1/6 mice after BLM treatment, although lung fibrosis developed similarly in all three strains of mice. Treatment with anti-IL-5 completely abrogated eosinophilia but failed to block pulmonary fibrosis induced by BLM in all mouse strains, including C57B1/6 SCID, wildtype C57B1/6 mice, and CBA/J mice. Analysis of cytokine mRNA by RNase-protection assay in C57B1/6 SCID mice indicated that BLM treatment caused enhanced expression of the cytokines, TNF-alpha, and IL-6 at days 3, 7, and 14 post-BLM inoculation, regardless of whether eosinophils were depleted by anti-IL-5. Finally, the importance of eosinophils in lung fibrosis was examined in IL-5 gene knockout mice (IL-5tm1Kopf). BLM treatment induced significant lung fibrosis in IL-5 knockout mice in the absence of eosinophilia. These findings indicate that eosinophils are not an absolute requirement for BLM-induced pulmonary fibrosis in the mouse.

Melatonin does not shift circadian phase in baboons

It has been suggested that the pineal hormone melatonin can modulate circadian rhythmicity and may have clinical utility in treating biological clock disorders. Thus, there is considerable clinical interest in using melatonin to treat disorders, such as jet-lag. Yet, despite growing enthusiasm for the use of melatonin, it is not clear whether melatonin indeed shifts the circadian phase in humans and other primate species. Thus, to assess whether melatonin can influence circadian phase, we studied the phase-shifting effects of melatonin on baboons to provide insights into the role of melatonin. Mel- atonin was administered orally to baboons (0.5, 3, 5, or 10 mg) either in the early morning hours from circadian time (CT) 0 to CT3 or late in the afternoon from CT9 to CT12, and changes in circadian phase were assessed. Surprisingly, at all doses and times tested, melatonin did not shift circadian phase. Physical activity was reduced after 5- and 10-mg doses given late in the afternoon, but not after doses given early in the morning. These observations suggest that melatonin does not shift circadian phase in baboons using doses similar to those prescribed for treating human circadian system disorders.

Multiple levels of regulation of selenoprotein biosynthesis revealed from the analysis of human glioma cell lines

To gain a better understanding of the biological consequences of the exposure of tumor cells to selenium, we evaluated the selenium-dependent responses of two selenoproteins (glutathione peroxidase and the recently characterized 15-kDa selenoprotein) in three human glioma cell lines. Protein levels, mRNA levels, and the relative distribution of the two selenocysteine tRNA isoacceptors (designated mcm(5)U and mcm(5)Um) were determined for standard as well as selenium-supplemented conditions. The human malignant glioma cell lines D54, U251, and U87 were maintained in normal or selenium-supplemented (30 nM sodium selenite) conditions. Northern blot analysis demonstrated only minor increases in steady-state GSHPx-1 mRNA in response to selenium addition. Baseline glutathione peroxidase activity was 10.7 +/- 0.7, 7.6 +/- 0.7, and 4.3 +/- 0.7 nmol NADPH oxidized/min/mg protein for D54, U251, and U87, respectively, as determined by the standard coupled spectrophotometric assay. Glutathione peroxidase activity increased in a cell line-specific manner to 19.7 +/- 1.4, 15.6 +/- 2.1, and 6. 7 +/- 0.5 nmol NADPH oxidized/min/mg protein, respectively, as did a proportional increase in cellular resistance to H(2)O(2), in response to added selenium. The 15-kDa selenoprotein mRNA levels likewise remained constant despite selenium supplementation. The selenium-dependent change in distribution between the two selenocysteine tRNA isoacceptors also occurred in a cell line-specific manner. The percentage of the methylated isoacceptor, mcm(5)Um, changed from 35.5 to 47.2 for D54, from 38.1 to 47.3 for U251, and from 49.0 to 47.6 for U87. These data represent the first time that selenium-dependent changes in selenoprotein mRNA and protein levels, as well as selenocysteine tRNA distribution, were examined in human glioma cell lines.

Developing circadian rhythmicity

Circadian rhythms are endogenously generated rhythms with a period length of about 24-hours. Evidence gathered over the past decade indicates that the circadian timing system develops prenatally, and the suprachiasmatic nuclei, the site of a circadian clock, is present by midgestation in human and nonhuman primates. Recent evidence also shows that the circadian system of primate infants is responsive to light at very premature stages and that low intensity lighting can regulate the developing clock. After birth, there is progressive maturation of the circadian system outputs, with pronounced rhythms in sleep-wake and hormone secretion generally developing after 2 months of age. With the continued elucidation of circadian system development and influences on human physiology and illness, it is anticipated that consideration of circadian biology will become an increasingly important component of neonatal care.

Study of phonon dispersion in silicon and germanium at long wavelengths using picosecond ultrasonics

We have studied the dispersion of long wavelength longitudinal phonons in silicon and germanium using ultrasonic techniques. For long wavelengths, the acoustic phonon dispersion relation is of the form omega(k) approximately ck-gammak(3), where c is the speed of sound and gamma measures the lowest-order phonon dispersion. By sending an ultrasonic pulse of length a few hundred angstroms into a crystal and measuring the change of the pulse shape with propagation distance, we are able to determine the parameter gamma. The results are compared with lattice dynamics models.

Knowledge-based grouping of modeled HLA peptide complexes

Human leukocyte antigens are the most polymorphic of human genes and multiple sequence alignment shows that such polymorphisms are clustered in the functional peptide binding domains. Because of such polymorphism among the peptide binding residues, the prediction of peptides that bind to specific HLA molecules is very difficult. In recent years two different types of computer based prediction methods have been developed and both the methods have their own advantages and disadvantages. The nonavailability of allele specific binding data restricts the use of knowledge-based prediction methods for a wide range of HLA alleles. Alternatively, the modeling scheme appears to be a promising predictive tool for the selection of peptides that bind to specific HLA molecules. The scoring of the modeled HLA-peptide complexes is a major concern. The use of knowledge based rules (van der Waals clashes and solvent exposed hydrophobic residues) to distinguish binders from nonbinders is applied in the present study. The rules based on (1) number of observed atomic clashes between the modeled peptide and the HLA structure, and (2) number of solvent exposed hydrophobic residues on the modeled peptide effectively discriminate experimentally known binders from poor/nonbinders. Solved crystal complexes show no vdW Clash (vdWC) in 95% cases and no solvent exposed hydrophobic peptide residues (SEHPR) were seen in 86% cases. In our attempt to compare experimental binding data with the predicted scores by this scoring scheme, 77% of the peptides are correctly grouped as good binders with a sensitivity of 71%.

HLA alleles in patients with Guillain-Barre syndrome

OBJECTIVE

To determine whether genetic factors may work in concert with autoimmune factors in the pathogenesis of Guillain-Barre syndrome (GBS).

METHODS

We determined the differences in the distribution of HLA alleles between GBS patients and normal controls. HLA-DQA, -DQB and -DRB alleles were typed by the sequence specific primer polymerase chain reaction (PCR-SSP) methods in 47 GBS, 7 patients with Campylobacter jejuni (CJ) enteritis and 50 normal controls.

RESULTS

There were no differences in the frequency of HLA-DQA, -DQB and -DRB among GBS group, CJ group, normal controls and GBS subgroups with respect to recent CJ infection, GM1 IgG and GM1 IgM antibodies (P > 0.05). There was an increasing tendency of DQA1 * 0301 (P = 0.056, RR = 2.991) in the subgroup with GM1 IgG antibodies and DQA1 * 0302 (P = 0.087, RR = 3.587) in the subgroup with recent CJ infection. No difference was found among GBS, CJ enteritis patients and normal controls.

CONCLUSIONS

The increasing tendency of the two alleles suggests that there may be some relation between genetic factors and immunological factors, but a definite conclusion waits for more cases.

Are A3 adenosine receptors expressed in the brain?

An increasing number of reports suggest a role for A3 adenosine receptors (A3ARs) in mediating adenosine action in the central nervous system. However, studies of A3AR localization in the brain have yet to be performed. To provide insights into the central sites of A3AR action, we compared patterns of A1 and A3AR mRNA and binding site expression in the brains of rats, mice and humans. We also assessed whether A3 agonists are selective for A3ARs. Whereas it was possible to detect high-level A1AR expression in many brain regions, it was not possible to detect either A3AR gene or binding site expression in the central nervous system. When we examined the affinities of the A3AR agonists CI-IAB-MECA and IAB-MECA for A1ARs, we found that these compounds bound to A1ARs with high affinity. These observations suggest that studies using A3-agonists need to consider potential effects of A1ARs activation, as A1ARs are abundantly expressed in the nervous system whereas A3AR expression in the brain cannot be directly demonstrated.

Mechanisms of human mitochondrial DNA maintenance: the determining role of primary sequence and length over function

Although the regulation of mitochondrial DNA (mtDNA) copy number is performed by nuclear-coded factors, very little is known about the mechanisms controlling this process. We attempted to introduce nonhuman ape mtDNA into human cells harboring either no mtDNA or mutated mtDNAs (partial deletion and tRNA gene point mutation). Unexpectedly, only cells containing no mtDNA could be repopulated with nonhuman ape mtDNA. Cells containing a defective human mtDNA did not incorporate or maintain ape mtDNA and therefore died under selection for oxidative phosphorylation function. On the other hand, foreign human mtDNA was readily incorporated and maintained in these cells. The suicidal preference for self-mtDNA showed that functional parameters associated with oxidative phosphorylation are less relevant to mtDNA maintenance and copy number control than recognition of mtDNA self-determinants. Non-self-mtDNA could not be maintained into cells with mtDNA even if no selection for oxidative phosphorylation was applied. The repopulation kinetics of several mtDNA forms after severe depletion by ethidium bromide treatment showed that replication and maintenance of mtDNA in human cells are highly dependent on molecular features, because partially deleted mtDNA molecules repopulated cells significantly faster than full-length mtDNA. Taken together, our results suggest that mtDNA copy number may be controlled by competition for limiting levels of trans-acting factors that recognize primarily mtDNA molecular features. In agreement with this hypothesis, marked variations in mtDNA levels did not affect the transcription of nuclear-coded factors involved in mtDNA replication.

Relationship between pathogenesis of Guillain-Barre syndrome and Penner's serotypes of Campylobacter jejuni

OBJECTIVE

To investigate the relationship between the pathogenesis of Guillain-Barre syndrome (GBS) and Campylobacter jejuni (C. jejuni) in China.

METHODS

C. jejuni strains were isolated from fresh stools of 47 GBS patients in Beijing area from 1995 to 1997 by modified Skirrow's method. Serotyping of C. jejuni was performed with Penner's method in 47 GBS patients and 171 patients with C. jejuni enteritis in our hospital during the same period. The stools from which no C. jejuni strains could be isolated were typed by PCR-RFLP (restriction fragment length polymorphism) method.

RESULTS

Six C. jejuni strains were isolated by Skirrow's method, including 3 strains of Penner serotype 2, 1 Penner serotype 4, 1 Penner serotype 19 and 1 Penner serotype 26. Three strains of DNA-I, which was equal to the same type of Penner serotype 19, were found by PCR-RFLP method.

CONCLUSION

C. jejuni isolated from Beijing area are similar to those reported in literature, which once more confirms the molecular mimicry pathogenetic theory of GBS caused by C. jejuni infection in China. The similarities of serotypes between C. jejuni strains from GBS patients and those from C. jejuni enteritis patients may explain the high incidence of GBS following C. jejuni infection in China.

[The relationship between Guillain-Barre syndrome and serotypes of Campylobacter jejuni isolated from the patients]

OBJECTIVE

To investigate the relationship between Campylobacter jejuni (CJ) serotype and the high incidence of Guillain-Barre syndrome (GBS) following CJ enteritis in China.

METHODS

CJ was isolated from fresh stool of 47 GBS patients in Beijing area from 1995-1997 with a combination of Skirrow method and micro-filtration method. Serotyping of the CJ strains was performed with passive hemagglutination method with standard serum from CDC. 171 CJ strains from CJ enteritis in our hospital in the same period were serotyped with the same method. The stool from which no CJ could be isolated was typed with PCR-RFLP method.

RESULTS

3 Penner 2, 1 Penner 4, 1 Penner 19 and 1 Penner 26 strains were isolated and serotyped. Three strains which could not be isolated were found by PCR-RFLP method to be DNA-I, which is equivalent to the type of Penner 19. There were some CJ strains which could be typed with serum from CDC.

CONCLUSION

CJ from GBS patients in Beijing area are similar to those reported in the world; it is suggested that CJ may cause GBS by molecular mimicry mechanism in China. The most common serotype of CJ from GBS was reported to be Penner 19 in Japan, while it was rare in CJ enteritis. However, the similarity of the serotypes between CJ from GBS patients and CJ from enteritis patients may explain the high incidence of GBS following CJ infection in China. Penner 26 is reported to be isolated from GBS patients for the first time.

Suppression of a mitochondrial tRNA gene mutation phenotype associated with changes in the nuclear background

We previously have characterized a pathogenic mtDNA mutation in the tRNAAsn gene. This mutation (G5703A) was associated with a severe mitochondrial protein synthesis defect and a reduction in steady-state levels of tRNAAsn. We now show that, although transmitochondrial cybrids harboring homoplasmic levels of the mutation do not survive in galactose medium, several galactose-resistant clones could be obtained. These cell lines had restored oxidative phosphorylation function and 2-fold higher steady-state levels of tRNAAsn when compared with the parental mutant cell line. The revertant lines contained apparently homoplasmic levels of the mutation and no other detectable alteration in the tRNAAsn gene. To investigate the origin of the suppression, we transferred mtDNA from the revertants (143B/206 TK-) to a different nuclear background (143B/207 TK-, 8AGr). These new transmitochondrial cybrids became defective once again in oxidative phosphorylation and regained galactose sensitivity. However, galactose-resistant clones could also be obtained by growing the 8AGr transmitochondrial cybrids under selection. Because the original rate of reversion was higher than that expected by a classic second site nuclear mutation, and because of the aneuploid features of these cell lines, we searched for the presence of chromosomal alterations that could be associated with the revertant phenotype. These studies, however, did not reveal any gross changes. Our results suggest that modulation of the dosage or expression of unknown nuclear-coded factor(s) can compensate for a pathogenic mitochondrial tRNA gene mutation, suggesting new strategies for therapeutic intervention.

The biological clock of very premature primate infants is responsive to light

Each year more than 250,000 infants in the United States are exposed to artificial lighting in hospital nurseries with little consideration given to environmental lighting cycles. Essential in determining whether environmental lighting cycles need to be considered in hospital nurseries is identifying when the infant's endogenous circadian clock becomes responsive to light. Using a non-human primate model of the developing human, we examined when the circadian clock, located in the hypothalamic suprachiasmatic nuclei (SCN), becomes responsive to light. Preterm infant baboons of different ages were exposed to light (5,000 lux) at night, and then changes in SCN metabolic activity and gene expression were assessed. After exposure to bright light at night, robust increases in SCN metabolic activity and gene expression were seen at ages that were equivalent to human infants at 24 weeks after conception. These data provide direct evidence that the biological clock of very premature primate infants is responsive to light.

The 69 bp circadian regulatory sequence (CRS) mediates per-like developmental, spatial, and circadian expression and behavioral rescue in Drosophila

The period (per) gene is an essential component of the circadian timekeeping mechanism in Drosophila. This gene is expressed in a circadian manner, giving rise to a protein that feeds-back to regulate its own transcription. A 69 bp clock regulatory sequence (CRS) has been identified previously upstream of the period gene. The CRS confers wild-type mRNA cycling when used to drive a lacZ reporter gene in transgenic flies. To determine whether the CRS also mediates proper developmental and spatial expression and behavioral rescue, we used the CRS to drive either lacZ or per in transgenic flies. The results show that the CRS is able to activate expression in pacemaker neuron precursors in larvae and essentially all tissues that normally express per in pupae and adults. The CRS is sufficient to rescue circadian feedback loop function and behavioral rhythms in per01 flies. However, the period of locomotor activity rhythms shortens if a stronger basal promoter is used. This study shows that regulatory elements sufficient for clock-dependent and tissue-specific per expression in larvae, pupae, and adults are present in the CRS and that the period of adult locomotor activity rhythms is dependent, in part, on the overall level of per transcripts.

T cell independence of bleomycin-induced pulmonary fibrosis

The role of T cells and cytokines in bleomycin (BLM)-induced fibrosis was evaluated in susceptible and resistant strains of normal and SCID mice. Histology and hydroxyproline analysis showed that BLM induced pulmonary fibrosis in C57BL/6 and (C57BL/6 x BALB/c)F1 mice, whereas BALB/c mice were resistant to the disease. To test whether lymphocytes were required for the induction of BLM-induced pulmonary fibrosis, SCID mice were injected intratracheally with BLM and evaluated for the development of pulmonary inflammation and fibrosis. Similar morphological changes and increases in hydroxyproline were observed in both C57BL/6 SCID and (C57BL/6 x CB.17)F1 SCID animals compared to those seen in wild-type C57BL/6 and (C57BL/6 x BALB/c)F1 mice. In contrast, CB.17 SCID mice, which are genetically similar to BALB/c mice, were resistant to disease induction. Analysis of the cellular infiltrate in BLM-treated C57Bl/6 SCID mice confirmed a lack of T cells in the lungs of SCID mice and demonstrated a pronounced accumulation of eosinophils in areas of developing pulmonary fibrosis. NK cells were significantly elevated in untreated SCID mice and did not increase further after BLM treatment. Analysis of selected cytokines 1 day after initiation of BLM-induced pulmonary fibrosis indicated that the levels of TNF-alpha and IFN-gamma appeared to segregate with fibrosis in both the SCID and wild-type mice. The data demonstrate that T cells are not required for the induction of fibrosis by BLM and suggest that responses by non-lymphoid cells may be sufficient for the induction of fibrosis.

Brain natriuretic peptide enhances the endothelium-independent cAMP and vasorelaxant responses of calcitonin gene-related peptide in rat aorta

Calcitonin gene-related peptide (CGRP) causes vasorelaxation in rat aorta involving endothelium/nitric oxide (NO)-dependent elevations of both cAMP and cGMP levels. When endothelium is removed, preincubation with exogenous NO uncovers and potentiates direct (endothelium-independent) cAMP elevations and vasorelaxations caused by CGRP. This enhancing effect of NO potentially involves elevation of cGMP and inhibition of Type III (cGMP-inhibitable) phosphodiesterase, causing accumulation of cAMP. However, NO may have other actions. The aim of the present study was to determine if brain natriuretic peptide (BNP), which elevates cGMP levels independent of NO, could enhance cAMP accumulations and vasorelaxations induced by CGRP in rat aortic rings denuded of endothelium. When added separately, neither CGRP (100 nM) nor BNP (10 nM) altered cAMP levels. When added in combination, CGRP (100 nM) and BNP (10 nM) significantly elevated cAMP levels (from control of 0.95+/-0.08 to 1.53+/-0.09 pmol/mg protein) at 2 min. BNP (10 nM) elevated cGMP levels 10-fold at 2 min and this response was not altered by co-administration of CGRP (100 nM). Pretreatment with BNP at concentrations as low as 1 nM in endothelium-denuded aortic rings greatly enhanced the direct vasorelaxant effects of CGRP (100 nM) (from control of 0% to 57.6+/-6.8% relaxation of phenylephrine-precontractions). Our findings indicate that BNP enhances direct (endothelium-independent) cAMP elevations and vasorelaxations caused by CGRP in rat aorta, thus supporting the concept that cGMP inhibits cAMP metabolism and enhances CGRP-induced responses in aortic smooth muscle cells.

[Pathogenesis of acute coronary syndromes]

Coronary artery diseases may categorized into asymptomatic disease, angina pectoris, myocardial infarction, chronic heart failure, and sudden coronary death. Unstable angina, acute myocardial infarction, and sudden cardiac death are known as the acute coronary syndromes. Coronary atheroma is unstable in the patients with acute coronary syndromes. Stable plaques will be unstable when dynamic alterations occur. The alterations are plaque rupture, plaque hemorrhage, coronary thrombosis and vasospasm. They act each other. We analysed the histopathology of coronary arteries who died of acute myocardial infarction in 85 cases. It showed that the risk factors of plaque rupture are clusters of form cells, eccentric plaque with soft lipid rich core, and thinning of fibrous cap in atheroma. Most of these cases ruptured at edge of the atheroma.

A disease-associated G5703A mutation in human mitochondrial DNA causes a conformational change and a marked decrease in steady-state levels of mitochondrial tRNA(Asn)

We introduced mitochondrial DNA (mtDNA) from a patient with a mitochondrial myopathy into established mtDNA-less human osteosarcoma cells. The resulting transmitochondrial cybrid lines, containing either exclusively wild-type or mutated (G5703A transition in the tRNA[Asn] gene) mtDNA, were characterized and analyzed for oxidative phosphorylation function and steady-state levels of different RNA species. Functional studies showed that the G5703A mutation severely impairs oxidative phosphorylation function and mitochondrial protein synthesis. We detected a marked reduction in tRNA(Asn) steady-state levels which was not associated with an accumulation of intermediate transcripts containing tRNA(Asn) sequences or decreased transcription. Native polyacrylamide gel electrophoresis showed that the residual tRNA(Asn) fraction in mutant cybrids had an altered conformation, suggesting that the mutation destabilized the tRNA(Asn) secondary or tertiary structure. Our results suggest that the G5703 mutation causes a conformational change in the tRNA(Asn) which may impair aminoacylation. This alteration leads to a severe reduction in the functional tRNA(Asn) pool by increasing its in vivo degradation by mitochondrial RNases.

Anti-acetylcholinesterase antibody in myasthenic syndrome

OBJECTIVE

To examine the relationship between antibodies to acetylcholinesterase and myasthenic syndrome.

METHODS

Serum class specific antibodies to acetylcholinesterase and acetylcholine receptor were prepared with solid phase enzyme-linked immunosorbent assay in 51 patients with myasthenic syndrome, 31 controls with other neurological diseases (diseased controls) and 44 normal controls.

RESULTS

The positive rate of anti-acetylcholinesterase antibody in patients with myasthenic syndrome was 25%, while the results of the other two control groups were negative. Furthermore, the positive rate in patients without myasthenia gravis was 45%, which was much higher than that (13%) in those with myasthenic gravis.

CONCLUSION

Anti-acetylcholinesterase antibody may play a role in the pathogenesis of myasthenic syndrome.

A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster

Genes expressed under circadian-clock control are found in organisms ranging from prokaryotes to humans. In Drosophila melanogaster, the period (per) gene, which is required for clock function, is transcribed in a circadian manner. We have identified a circadian transcriptional enhancer within a 69-bp DNA fragment upstream of the per gene. This enhancer drives high-amplitude mRNA cycling under light-dark-cycling or constant-dark conditions, and this activity is per protein (PER) dependent. An E-box sequence within this 69-bp fragment is necessary for high-level expression, but not for rhythmic expression, indicating that PER mediates circadian transcription through other sequences in this fragment.

Functional and structural features of a tandem duplication of the human mtDNA promoter region

An approximately 260-bp tandem duplication of the human mtDNA regulatory region has been identified in patients with mitochondrial disorders and in a specific Caucasian haplogroup. The functional significance of this mtDNA duplication was difficult to assess, because it was present at very low levels in human tissues. We have isolated several transmitochondrial cybrid lines harboring this mutation, one of which (clone CA17.1) was essentially homoplasmic for the duplication. Oxidative-phosphorylation function was not impaired in clone CA17.1, suggesting that this mtDNA alteration is not pathogenic. mtDNA copy number and steady-state levels of heavy- and light-strand transcripts were unaltered in clone CA 17.1. The steady-state levels of RNAs made from the two promoters (either from the heavy-strand or from the light-strand) were also similar, indicating that oppositely oriented promoters did not interfere with each other.

Wall composition in intravascular ultrasound layered appearance of human coronary artery

To evaluate the impact of histological factors on the appearance of the wall of the coronary artery by intravascular ultrasound (IVUS), we performed an in vitro study of 34 coronary artery segments from eight autopsied patients. We assumed the coronary cross section to be divided into four equal parts, and assessed the quadrants with maximal and minimal wall thickness by IVUS (30 MHz; 4.3 Fr; 1800 rpm) and by a histological study. The histological layer thickness and composition were also evaluated in terms of their contribution to the appearance of the ultrasound layer. Fifty-eight quadrants were clearly visible on ultrasound. A three-layered appearance, with inner echogenic, subjacent sonolucent, and outer echogenic layers, was observed in 32 quadrants, while 26 quadrants showed a two-layered appearance with inner and outer echogenic layers. The thickness of the inner echogenic layer (0.77 +/- 0.38 mm) was moderately correlated with the intimal thickness (0.51 +/- 0.45 mm; r = 0.85, standard error of estimate [SEE] = 0.24 mm); however, the correlation was significantly improved when the thickness of the inner echogenic plus sonolucent layers (0.89 +/- 0.47 mm) was compared with that of the intima plus media (0.69 +/- 0.47 mm; r = 0.94, SEE = 0.15 mm; P = 0.012 between the coefficients). Discriminant analysis showed that intimal hyalinization, associated with intimal thickening, was strongly related to the presence of the three-layered appearance on IVUS (F to enter 40.0, P < 0.0001). These results indicate that the ultrasound layered appearance of human coronary arteries varies with histological alterations. We suggest that the thickness of the inner echogenic plus sonolucent layers on IVUS represents the intimal plus medial thickness observed by histology, and that the use of this value may be appropriate in the assessment of coronary wall thickening associated with atherosclerosis.

Functional and molecular mitochondrial abnormalities associated with a C --> T transition at position 3256 of the human mitochondrial genome. The effects of a pathogenic mitochondrial tRNA point mutation in organelle translation and RNA processing

We have previously identified a mitochondrial DNA polymorphism (a C --> T transition at position 3256, within the mitochondrial tRNALeu(UUR) gene in a patient with a multisystem disorder. Although there were several indicators suggesting a pathogenetic role for this mtDNA polymorphism, its heteroplasmic nature made functional and molecular studies difficult to interpret. We have now fused enucleated fibroblasts from the patient with a mtDNA-less cell line to generate transmitochondrial cybrids harboring different proportions of mutated and wild-type mtDNA. Individual clones harboring essentially 100% wild-type or > 99% mutated mtDNAs were characterized and studied for respiratory capacity, respiratory chain enzymes activity, mitochondrial protein synthesis, and RNA steady-state levels and processing. Our results showed that cell lines containing exclusively mutated mtDNAs respire poorly, overproduce lactic acid, and have significantly impaired activity of respiratory complexes I and IV. Molecular studies showed that mutant clones have a decrease in steady-state levels of mitochondrial tRNALeu(UUR), and a partial impairment of mitochondrial protein synthesis and steady-state levels, suggesting that these molecular abnormalities are involved in the pathogenetic mechanism of the mtDNA 3256 mutation.

Alterations of bone matrix protein mRNA expression in rat aorta in vitro

We examined the expression of matrix Gla protein (MGP), osteopontin (OPN), and osteonectin (ON) mRNAs in aortic rings excised from 3-month-, 10-month-, and 2-week-old rats during 72-hour incubations in serum-free media. In the aortic rings from 3-month-old rats, the expression of MGP mRNA was strong before incubation and increased during the 72-hour incubation. The expression of OPN mRNA was first detected after a 5-hour incubation and increased thereafter, and that of ON mRNA was strong before the incubation and decreased during the incubation. The expression of MGP and OPN mRNAs in 10-month- and 2-week-old rats was similar to that in 3-month-old rats. In contrast, expression of ON mRNA in 10-month-old rats and the expression of ON mRNA in 2-week-old rats was stronger than that in 3-month-old rats at every incubation period. In situ hybridization and immunohistochemistry identified the MGP, OPN, and ON mRNA-expressing cells as vascular smooth muscle cells. These results suggest that the expression of these mRNAs was regulated in incubation time-dependent and age-specific ways. We believe that this organ culture model is useful for further studies of the function of these bone matrix proteins and regulation of their expression in the vessel wall.

A comprehensive characterization of lymphoepithelial cyst associated with the pancreas

BACKGROUND

Lymphoepithelial cyst of the pancreas is a rare but distinctive cystic lesion lined by a mature, keratinizing squamous epithelium and surrounded by lymphoid tissue.

METHODS

To gain more insights into this entity, we describe 5 examples of lymphoepithelial cyst of the pancreas (2 of which were briefly described before) and compare them with similar cases in the literature for a total of 19 cases.

RESULTS

The male:female ratio was 16:3; patients' ages ranged from 32 to 73 years (mean and median 51). The lymphoepithelial cyst was incidentally found at autopsy in 4 patients (21%) or during evaluation for unrelated diseases in another 4 patients (21%). In the remaining 11 patients, the cyst was associated with abdominal pain in 9 (47% of all patients), nausea/vomiting in 3 (16%), diarrhea in 1 (5%), and nonspecific systemic symptoms in 6 (32%) (some patients had more than 1 associated symptom). Computed axial tomography scan, with or without ultrasonographic study, was done in 16 cases and uniformly displayed a single, well-circumscribed, cystic mass protruding beyond the surface of the pancreas; the rest of the pancreas was normal. Intraoperatively, the cyst was readily apparent once the lesser sac was entered and the surface of the pancreas exposed; the cyst was located at the head (3 cases), neck (1 case), body (6 cases), and tail (9 cases). Surgery was done for all 15 clinical cases and included local excision of the cyst with a thin rim of attached, underlying pancreas (6 cases), or distal pancreatectomy with (4 cases) or without (3 cases) splenectomy. Follow-up information, available in 7 cases, showed that all symptoms disappeared and the patients were alive and well up to 6 years after surgery.

CONCLUSIONS

This rare cyst of the pancreas has a uniform and characteristic clinicopathologic profile, enabling easy and accurate diagnosis. Although the histogenesis of lymphoepithelial cysts is not known, they are benign and can be cured by local excision.

Segregation patterns of a novel mutation in the mitochondrial tRNA glutamic acid gene associated with myopathy and diabetes mellitus

We have identified a novel mtDNA mutation in a 29-year-old man with myopathy and diabetes mellitus. This T-->C transition at mtDNA position 14709 alters an evolutionarily conserved nucleotide in the region specifying for the anticodon loop of the mitochondrial tRNA(Glu). The nt-14709 mutation was heteroplasmic but present at very high levels in the patient's muscle, white blood cells (WBCs), and hair follicles; lower proportions of mutated mtDNA were observed in WBCs and hair follicles of all examined maternal relatives. In the patient's muscle, abnormal fibers showed mitochondrial proliferation, severe focal defects in cytochrome c oxidase activity, and absence of cross-reacting material for mitochondrially synthesized polypeptides. These fibers had higher levels of mutated mtDNA than did surrounding "normal" fibers. Although the percentage of mutated mtDNA in WBCs from family members were distributed around the percentage observed in the mothers, the pattern was different in hair follicles, where the mutated population tended to increase in subsequent generations. PCR/RFLP analysis of single hairs showed that the intercellular variations in the percentage of mutated mtDNA differed among family members, with younger generations having a more homogeneous distribution of mutated mtDNA in different hair follicles. These results suggest that the intercellular distribution of the mutated and wild-type mtDNA populations may drift toward homogeneity in subsequent generations.

GM1 antibody in Guillain-Barre syndrome after Campylobacter jejuni infection

Fecal culture of Campylobacter jejuni was prepared by the method of Skirrow, and serum class specific antibodies (IgG, IgM and IgA) to Campylobacter jejuni and serum class specific antibodies (IgG IgM) to GM1 were prepared with solid phase enzyme linked immunasorbent assay in 16 cases of Guillain-Barre syndrome (GBS), 32 controls with other neurological diseases (disease controls) and 90 normal controls. The results showed that the incidence of Campylobacter jejuni infection, especially recent infections, in the group with Guillain-Barre syndrome was much higher than that in the two control groups, and that the positive rate of GM1 antibody was also much higher in the GBS group than in the two control groups. The results suggest that Campylobacter jejuni infection may be one of the important precipitating factors of Guillain-Barre syndrome and play an important role in the epidemiological pattern of Guillain-Barre syndrome in China. It damages the myelin of peripheral nerves through induction of GM1 antibody production.

Phenotype-genotype correlations in skeletal muscle of patients with mtDNA deletions

Large-scale deletions of mitochondrial DNA (mtDNA) have been associated with a subgroup of mitochondrial encephalomyopathies, usually characterized by progressive external ophthalmoplegia (PEO) and mitochondrial proliferation in muscle fibers. We and others have shown that muscle from patients with mtDNA deletions have variable cytochrome c oxidase (COX) deficiency and reduction of mitochondrially-synthesized polypeptides in affected muscle fibers. The present work summarizes the phenotype-genotype correlations observed in patients' muscle. In situ hybridization revealed that, while most COX-deficient fibers had increased levels of mutant mtDNA, they almost invariably had reduced levels of normal mtDNA. PCR quantitation of both deleted and wild-type mtDNAs in normal and respiration-deficient muscle fibers from patients with the "common deletion" showed that deleted mtDNAs were present in normal fibers (31 +/- 26%), but their percentages were much higher in affected fibers (95% +/- 2%). Absolute levels of deleted mtDNA were also increased in affected fibers, whereas absolute levels of wild-type mtDNA were significantly reduced. Taken together, our results suggest that although a specific ratio between mutant and wild-type mitochondrial genomes is probably the major determinant of the respiratory chain deficiency associated with mtDNA deletions, the reduction in the absolute amounts of wild-type mtDNA may also play a significant pathogenetic role.

Effects of gender, birth order, and other correlates on childhood mortality in China

Using data from the 1988 Two-Per-Thousand Survey of Fertility and Birth Control, this paper examines the effects of gender, birth order, and other correlates of childhood mortality in China. Controlling for family-level factors, childhood mortality is found to be associated with the child's gender and birth order. Among firstborn children the difference between male and female childhood mortality is not statistically significant, but among others, female children between ages 1 and 5 experience higher mortality than male children. Childhood mortality is slightly higher for children who have older brothers only than for those who have older sisters only, and it is highest for those who have both older brothers and sisters. Other factors affecting childhood mortality in China include mortality of older siblings, birth interval, urban/rural residence, mother's level of education, and mother's occupation. All interactive effects between gender and family-level characteristics are found to be statistically insignificant.

Regulation of human DNA polymerase delta during the cell cycle

The expression of polymerase delta (pol delta) during the cell cycle was studied in Molt 4 cells separated by counter-flow centrifugal elutriation. Northern blotting showed that pol delta mRNA levels increased by 3-fold at the G1/S border. Levels of pol delta protein determined by Western blotting also peaked at the G1/S border with qualitatively similar changes as the mRNA levels. Thus, pol delta gene expression appears to be regulated during the cell cycle at the transcriptional level. The mRNA half-life for pol delta was determined to be about 8 h and the protein half-life about 10 h. Parallel examination of the expression of proliferating cell nuclear antigen showed that the mRNA levels also increased about 2-fold at the G1/S border, while the protein levels of proliferating cell nuclear antigen increased steadily through the whole cell cycle period, and remained high at G2/M. Analysis of pol alpha expression showed qualitatively similar behavior as pol delta, but the magnitude of the changes were higher. Pulse labeling of cells metabolically arrested in G1,S, or G2/M with 32Pi showed that pol delta is a phosphoprotein and that it is most actively phosphorylated during the S phase.

Dihydrofolate reductase of Drosophila. Cloning and expression of a gene with a rare transcript

Traditionally, dihydrofolate reductase (DHFR) has been isolated and the corresponding gene cloned from drug-resistant cell lines which have amplified DHFR genes after selection. A Dhfr sequence has now been obtained by nested polymerase chain reaction (PCR) from Drosophila bearing a single gene copy. Using the PCR-amplified partial cDNA as a probe, Dhfr was cloned by screening a Drosophila genomic library. It consists of regulatory regions as well as a 599-nucleotide coding region with a single 50-base pair (bp) intron and encodes a protein of 182 amino acids. Previously we have shown that the enzyme has kinetic properties characteristic of both "prokaryotic" and "eukaryotic" DHFRs. Here we show that the organization of Drosophila Dhfr is strikingly different from its mammalian counterparts and most similar to that of mosquito. A 790-bp transcript was detected by Northern blot analysis, with a single transcription start site located 27 bp upstream of ATG codon. The Drosophila genome contains a single Dhfr copy at 89E and a selected cell line has not amplified the gene. Confirmation of the identity of this gene has been obtained by kinetic studies of recombinant DHFR over-expressed in Escherichia coli cells.

DNA polymerase delta is involved in the cellular response to UV damage in human cells

We have used antibodies specific for either polymerase delta (pol delta) or its accessory protein, proliferating cell nuclear antigen (PCNA), to demonstrate that they can markedly inhibit the capacity of HeLa nuclear extracts to effect repair of UV-damaged plasmid DNA. This provides the first unambiguous evidence for the involvement of pol delta in DNA repair synthesis. The mRNA levels of both pol delta and PCNA were significantly stimulated subsequent to UV irradiation of cultured cells, providing the first evidence that the cellular response to UV damage may involve regulation of pol delta and PCNA at the gene level. Thus, DNA polymerase delta and its accessory proteins, in addition to their function in replicative DNA synthesis, also function in DNA repair synthesis.

N omega-nitro-L-arginine inhibits vasodilations and elevations of both cyclic AMP and cyclic GMP levels in rat aorta induced by calcitonin gene-related peptide (CGRP)

Our previous studies showed that vasodilations and elevations of both cyclic AMP and cyclic GMP levels in rat aorta induced by rat calcitonin gene-related peptide (rCGRP) are inhibited by hemoglobin and methylene blue, blockers of the endothelium-derived relaxant factor (EDRF, now recognized as nitric oxide [NO]). In the present study, we used N omega-nitro-L-arginine (L-NNA), a selective inhibitor of nitric oxide synthase, to test whether rCGRP-induced relaxations and cyclic AMP and cyclic GMP responses in rat aorta require de novo synthesis of NO. L-NNA (30 microM, 15 min) inhibited by 84, 76 and 73% the relaxations induced by rCGRP at 1, 10 and 100 nM, respectively. D-NNA (30 microM), which does not inhibit nitric oxide synthase, did not block rCGRP-induced vasorelaxations. Addition of L-arginine (3 mM) 5 min before L-NNA completely prevented the L-NNA-inhibition of CGRP-induced relaxations. L-NNA (30 microM, 15 min) also inhibited the elevations of both cyclic AMP and cyclic GMP levels caused by CGRP (100 nM). The data suggest that de novo synthesis of nitric oxide from its precursor L-arginine is required for rCGRP to induce vasodilations and elevations of both cyclic AMP and cyclic GMP levels in rat aorta.

Nitroglycerin (exogenous nitric oxide) substitutes for endothelium-derived nitric oxide in potentiating vasorelaxations and cyclic AMP elevations induced by calcitonin gene-related peptide (CGRP) in rat aorta

Rat calcitonin gene-related peptide (rCGRP) causes endothelium-dependent vasorelaxations via a dual signal transduction mechanism involving elevations of both cyclic AMP and cyclic GMP levels in rat aorta. These responses are all dependent on de novo synthesis of nitric oxide (NO) in endothelial cells and appear to involve a mechanistic link between cyclic GMP and cyclic AMP responses in smooth muscle cells. The present study determined whether NO from an exogenous source (i.e. added nitroglycerin) could substitute for endogenous NO in rCGRP-induced responses in endothelium-denuded aorta. Nitroglycerin (1 microM) significantly elevated cyclic GMP levels by 20-fold and 3.3-fold and cyclic AMP levels by 26% and 22% at 1 and 2 min, respectively. By itself, rCGRP (100 nM) did not significantly elevate cyclic AMP levels. In combination, however, nitroglycerin and rCGRP caused more-than-additive cyclic AMP elevations (41% above basal at 1 and 2 min). Nitroglycerin also potentiated rCGRP-induced vasorelaxations in endothelium-denuded rings, thus uncovering a direct (endothelium-independent) relaxant effect of rCGRP in rat aorta. The data indicate that exogenous NO can substitute for endogenous NO in rCGRP-induced relaxant and cyclic AMP responses in aorta. This nitroglycerin-induced potentiation of CGRP effects likely involves inhibition of cyclic-GMP-inhibited-phosphodiesterase in smooth muscle cells, thus allowing cyclic AMP to accumulate and mediate the direct vasodilator effects of rCGRP.