Waved aCGH: to smooth or not to smooth

Array-based comparative genomic hybridization (aCGH) is a powerful tool to detect genomic imbalances in the human genome. The analysis of aCGH data sets has revealed the existence of a widespread technical artifact termed as ‘waves’, characterized by an undulating data profile along the chromosome. Here, we describe the development of a novel noise-reduction algorithm, waves aCGH correction algorithm (WACA), based on GC content and fragment size correction. WACA efficiently removes the wave artifact, thereby greatly improving the accuracy of aCGH data analysis. We describe the application of WACA to both real and simulated aCGH data sets, and demonstrate that our algorithm, by systematically correcting for all known sources of bias, is a significant improvement on existing aCGH noise reduction algorithms. WACA and associated files are freely available as Supplementary Data.

[Biological functions of cyclooxygenase 2: control of its expression and activity]

Cyclooxygenase (COX) plays a pivotal role in the biosynthesis of prostanoids. The identification of an inducible isoform, COX-2, besides the constitutive one, COX-1, suggested that the latter was dedicated to cytoprotection, whereas the former was responsible for inflammation and neoplasia. This oversimplification was amended due to the synthesis of new selective inhibitors of COX-2 and to the deletion of the COX-2 gene, which demonstrated the involvement of the inducible isoform in physiological as well as in pathological functions. Moreover, several reports describe effects of nonsteroidal anti-inflammatory drugs which do not result from the inhibition of COX activity.

Orbital color Doppler imaging of optic nerve tumors

OBJECTIVE

To report changes in retinal arterial and venous blood flow pattern in two patients with tumors involving the entire optic nerve.

METHODS

Retrospective review of one patient with clinical and neuroimaging characteristics typical of bilateral optic nerve gliomas and one patient with a probable meningioma of the left optic nerve sheath.

RESULTS

The optic nerve glioma patient had reduced peak systolic velocity of central retinal arteries bilaterally, while the patient with an optic nerve sheath meningioma had relatively low central retinal artery flow velocity and intermittent blood flow in the central retinal vein on the affected side.

CONCLUSIONS

Reduced retinal arterial flow velocities in the setting of optic nerve gliomas may correlate with the presence of optic nerve disease. Phasic blood flow in the central retinal vein with optic nerve sheath meningioma may be the reason that some patients with this tumor develop retinal choroidal venous anastomoses.

Abnormal development of the lesser wing of the sphenoid with microphthalmos and microcephaly

We report two patients with abnormal development of the lesser wing of the sphenoid bone, globe, optic nerve and cerebral hemisphere without stigmata of neurofibromatosis type 1. The lesser wing of the sphenoid bone was abnormally formed and was not ossified ipsilateral to the dysmorphic eye and underdeveloped cerebral hemisphere. Maldevelopment of the sphenoid wing may interfere with the normal closure of the optic vesicle and normal growth of encephalic structures, possibly by disturbing developmental tissue interactions. These patients may exhibit a type of restricted primary sphenoid dysplasia, while the sphenoid dysplasia of neurofibromatosis type 1 may be secondary to orbital or ocular neurofibromas and other factors associated with that disease.

The expression of thyrotropin receptor in the brain

The regulation of the thyroid gland by TSH is mediated by a heterotrimeric G protein-coupled receptor. Nonthyroid effects of TSH have been reported, and expression of its receptor has been described in adipocytes and lymphocytes. We have previously reported the existence of specific and saturable binding sites of TSH and specific TSH effects in primary cultured rat brain astroglial cells. We now report expression of the TSH receptor gene in these cells; the coding sequence of the corresponding complementary DNA is identical to that previously established in thyroid. Using specific antisense RNA probe, expression of this gene was detected in some isolated or clustered glial fibrillary acidic protein-positive primary cultured cells by in situ hybridization. With this technique, we further detected TSH receptor messenger RNA (mRNA) expression in rat brain cryoslices in both neuronal cells and astrocytes. Its presence predominated in neuron-rich areas (pyriform and postcingulate cortex, hippocampus, and hypothalamic nuclei) and was mostly colocalized with neuron-specific enolase. In astrocytes, this mRNA was detected in the ependymal cell layer and the subependymal zone, and several isolated cells were also found in the brain parenchyma. We also detected TSH receptor mRNA and protein in primary cultured human astrocytes. The protein was detected as well in both rat and human brain cryoslices. Together, these findings clearly demonstrate the expression of the TSH receptor gene in the brain in both neuronal cells and astrocytes.

Bilateral orbital hemorrhage in a newborn

PURPOSE

To report a case of severe bilateral proptosis resulting from orbital hemorrhage in a newborn and to discuss the differential diagnoses and management.

METHOD

Case report of a 13-day-old male infant with bilateral proptosis since birth. The proptosis was monitored with clinical examinations and computed tomography as well as magnetic resonance imaging (MRI) scans, and it was managed with antibiotic ointment and patching. The MRI scans demonstrated bilateral subperiosteal orbital hemorrhage.

RESULTS

Proptosis decreased, and there was successful, complete recovery without untoward sequelae in 14 days; follow-up indicated no late complications at age 1 year.

CONCLUSION

Spontaneous orbital hemorrhage, unilateral or bilateral, is uncommon in an otherwise healthy newborn without apparent history of birth trauma. Magnetic resonance imaging scans are helpful in making the diagnosis of subperiosteal hemorrhage, and conservative management is advised.

Canalis basilaris medianus: MRI

We report the MRI appearances of an developmental anatomical variant of the basiocciput, with neuroimaging findings (CT and MRI). Such variants are commonly asymptomatic, but may be associated with episodes of meningitis.

Ophthalmological and intracranial anomalies in patients with clinical anophthalmos

PURPOSE

To better describe the clinical and neuroimaging spectrum of abnormalities in clinical anophthalmos.

METHODS

We performed a retrospective review of all 17 patients admitted to the King Khaled Eye Specialist Hospital with clinical anophthalmos over a 15 year period who had a complete ophthalmological examination documented and received computed tomographic (CT) imaging of the orbits and brain.

RESULTS

Patients with clinical anophthalmos had a high incidence of developmental abnormalities involving both eyes (15/17 patients, 88%), the brain (12/17 patients, 71%) and the body (7/12, 58%). The incidence of central nervous system anomalies reached 100% in patients with bilateral small optic nerves on CT scan.

CONCLUSIONS

Patients with clinical anophthalmos share a similar constellation of neurological, somatic and neuroradiological abnormalities as patients with microphthalmos, septo-optic dysplasia and clinical optic nerve hypoplasia. This fact may provide insight into developmental abnormalities of the afferent visual system and brain.

Marble brain syndrome: osteopetrosis, renal acidosis and calcification of the brain

Cerebral calcification in children is frequently associated with systemic metabolic disease. We present a case of "marble brain syndrome", which showed this abnormality.

Detection of optic nerve involvement in retinoblastoma with enhanced computed tomography

PURPOSE

The study was designed to evaluate the value of enhanced computed tomography (CT) as a non-invasive test in the detection of optic nerve invasion in retinoblastoma.

METHODS

Nineteen eyes in 17 consecutive retinoblastoma patients underwent CT studies performed with high spatial resolution (512 x 512) and 1.5 mm sections, both with enhancement and without enhancement. If the central retinal vessels (CRV) were subjectively visualised with intravenous enhancement, the optic nerve was considered to be free of retinoblastoma. Nineteen enucleated globes were processed for histopathology, and the optic disc and nerve examined with light microscopy for the presence or absence of tumour and the level of involvement.

RESULTS

The correlation between the visualisation of CRV and the presence or absence of optic nerve involvement histopathologically was found to be highly significant (p = 0.0006, Fisher exact test).

CONCLUSION

In high spatial resolution CT with enhancement and 1.5 mm or thinner sections, non-visualisation of the CRV appears to be a reliable indicator of optic nerve invasion with retinoblastoma.

Tuberous sclerosis in infancy

PURPOSE

To report two infants with tuberous sclerosis who initially were considered to have retinoblastoma.

PATIENTS AND METHODS

An 8-day-old infant was referred with small tumors in the posterior poles of both eyes. A left microphthalmos with ciliochoroidal coloboma was present. Computed tomographic (CT) scanning of the brain showed scattered high-density subependymal foci in the lateral ventricle thought to be consistent with calcification resulting from intrauterine viral infection. Argon laser photocoagulation was applied to lesions in the right eye. Because one tumor was situated on the retina straddling the coloboma in the left eye, external beam radiotherapy was administered. A 5-month-old girl presented with a large mass in a left microphthalmic eye. Calcification was present on B-scan ultrasonography and CT scanning. Vitreous seeding was noted to originate from the tumor. The contralateral eye manifested four small gray translucent retinal tumors in the posterior pole. CT scan and magnetic resonance imaging (MRI) revealed multiple periventricular subependymal lesions, including one at the foramen of Monro.

RESULTS

Repeated examinations in the younger child under anesthesia revealed small new retinal lesions that appeared to enlarge gradually. She developed intractable seizures and her electroencephalogram revealed a modified hypsarrhythmia recording. A careful review of available CT scans and MRI displays suggested the diagnosis of tuberous sclerosis. The child's most recent examination under anesthesia revealed multiple newly developed hamartomas. In the older child, prompt diagnosis was made on the basis of the intracranial radiologic findings.

CONCLUSION

Retinal hamartoma presentation may vary in infancy. Small, initially fleck-like gliotic lesions appear to enlarge gradually and eventually may form gray, translucent tumors. Large astrocytic hamartomas of the retina associated with tuberous sclerosis may resemble retinoblastoma, particularly if the mass is large, calcified, and associated with vitreous seeding. Although ophthalmic presentation was reminiscent of retinoblastoma in both patients, radiologic evidence of subependymal hamartomas pathognomic for tuberous sclerosis helped establish the correct diagnosis. We stress the importance of intracranial radiologic findings in this regard.

A gas chromatographic separation for the h and C stable isotope ratio determination of coal compounds

A new, completely automated gas chromatography technique has been developed to separate the different gaseous compounds produced during underground coal gasification for their (13)C/(12)C and D/H isotope ratio measurements. The technique was designed for separation and collection of H(2), CO, CO(2), H(2)O, H(2)S, CH(4), and heavier hydrocarbons. These gaseous compounds are perfectly separated by the gas-phase chromatograph and quantitatively sent to seven combustion and collection lines. H(2), CO, CH(4), and heavier hydrocarbons are quantitatively oxidized to CO(2) and/or H(2)O. The isotopic analyses are performed by the sealed-tube method. The zinc method is used for reduction of both water and H(2)S to hydrogen for D/H analysis. Including all preparation steps, the reproducibility of isotope abundance values, for a quantity higher than or equal to 0.1 mL of individual components in a mixture (5 mL of gases being initially injected in the gas chromatograph), is ±0.1‰ for δ(13)C(PDB) and ±6‰ for δD(SMOW).

Snaring of the target vessel in less invasive bypass operations does not cause endothelial dysfunction

BACKGROUND

Minimally invasive coronary artery bypass grafting aims to achieve less patient discomfort and a more rapid return to active life. Most approaches have used maintenance of the beating heart and control of the target coronary vessel by different hemostatic devices. The purpose of this study was to assess the effects of commonly used coronary artery snares and of the occlusion of the coronary vessel necessary for minimally invasive coronary artery operations on coronary endothelial function.

METHODS

Coronary artery bypass grafting with an internal mammary artery to left anterior descending artery anastomosis was performed in a porcine model with a 30-minute period of ischemia and a subsequent 30-minute period of reperfusion, using snares on either side of the anastomotic site to achieve hemostasis of the operative field. Endothelium-dependent relaxation to serotonin was studied in conventional organ chamber experiments with rings taken from the left anterior descending artery at the proximal snare site, the anastomotic site in the segment that underwent the ischemia-reperfusion cycle, the distal snare site, and at a control segment. Responses to potassium chloride and bradykinin were also compared.

RESULTS

There were no significant differences in endothelium-dependent relaxation values among the four sites studied.

CONCLUSIONS

These results confirm that snaring of the coronary artery for achieving hemostasis at the anastomotic site when performing coronary artery bypass grafting on the beating heart does not cause endothelial dysfunction.

Mediation by arachidonic acid metabolites of the H2O2-induced stimulation of mitogen-activated protein kinases (extracellular-signal-regulated kinase and c-Jun NH2-terminal kinase)

Reactive oxygen species modulate major cellular functions by mechanisms which are still poorly understood. Recently, H2O2 has been reported to stimulate the activity of the mitogen-activated protein kinases (MAPKs) ERK and JNK, and the expression of the proto-oncogenes c-fos and c-jun. As their expression is enhanced by H2O2 in astrocytes, we studied whether these MAPKs were stimulated by H2O2 in primary cultured astrocytes. The result was positive, a maximum of stimulation being reached with 200 microM H2O2 (0.3 pmol H2O2/cell) for both ERK and JNK. ERK was previously reported to stimulate cytosolic phospholipase A2 phosphorylation and activity. H2O2 stimulated the release of arachidonic acid in astrocytes, as already reported in other cell types. We found also that cPLA2 phosphorylation was increased by H2O2. Moreover, the stimulation by H2O2 of ERK and JNK was decreased by phospholipase A2 activity inhibitors. When astrocytes were incubated first with eicosatetraynoic acid, a structural analogue competing in arachidonic acid metabolism, the stimulation of JNK by H2O was also inhibited, suggesting the involvement of arachidonic acid metabolites. Cyclooxygenase or cytochrome P450 monooxygenase inhibitors failed in decreasing the MAPK stimulation by H2O2, whereas lipoxygenase inhibitors completely abolished that of JNK. Mitogenicity has been reported to be stimulated by H2O2 in other cell types. Although ERK was strongly and durably stimulated by 200 microM H2O2 in astrocytes, at the same extent as by mitogenic growth factors, basal thymidine incorporation rate was decreased by more than 80% after 12-15 h. Moreover, the stimulation of thymidine incorporation induced by basic fibroblast growth factor was transiently abolished by H2O2. Furthermore, H2O2 likely induced the expression of CL100/PAC1/MKP-1, a dual specificity phosphatase which has been implicated in ERK and JNK inactivation in the nucleus. Finally, the prior treatment of astrocytes with MK886, a 5-lipoxygenase-activating protein inhibitor, prevented JNK from stimulation, but did not prevent thymidine incorporation from inhibition, both induced by H2O2. These results strongly suggest an involvement of arachidonic acid and/or its metabolites in the stimulation of both ERK and JNK following the oxidative stress evoked by H2O2, which induced a cell cycle arrest probably independent of the stimulation of JNK.

Long-term effect of forskolin on the activation of adenylyl cyclase in astrocytes

Long-term (48-h) forskolin treatment of rat astroglial cells led to a slight decrease (30-40%) in the response to isoproterenol, vasoactive-intestinal peptide, guanyl 5'-(beta gamma-imido)diphosphate, guanosine 5'-O-(3-thiotriphosphate) [GTP(S)], and AIF4- in crude membrane fractions. In contrast, the acute stimulatory effect of forskolin was increased by 1.25-1.5-fold. These two opposite effects of forskolin were mediated by a cyclic AMP-dependent mechanism. No changes in Gs alpha, Gi alpha, or G beta protein levels could be determined by immunoblotting using specific antisera. No significant differences were observed in the ability of G proteins extracted from control and forskolin-treated cells to reconstitute a full adenylyl cyclase activity in membranes from S49 cyc- cells, lacking Gs alpha protein. Gs alpha proteins were detected in two pools of membranes, one in the heavy sucrose fractions and the other in light sucrose fractions. Forskolin treatment of the cells shifted Gs alpha protein toward the light-density membranes. We did not find any significant change in the distribution of adenylyl cyclase. In contrast to the decreased stimulation of adenylyl cyclase activity by agonists acting via Gs alpha, observed in the crude membrane fraction, the responses of adenylyl cyclase to forskolin as well as to GTP(S) were increased in the purified plasma membrane fractions. These results may indicate that sensitization of the catalyst appears to be the dominant component in the astroglial cell response to long-term treatment by forskolin.

Evidence for cAMP-dependent platelet ectoprotein kinase activity that phosphorylates platelet glycoprotein IV (CD36)

The dephosphorylating enzyme alkaline phosphatase, by removing phosphate groups from the external platelet membrane proteins, modulates platelet activation (Hatmi, M., Haye, B., Gavaret, J. M., Vargaftig, B. B., and Jacquemin, C. (1991) Br. J. Pharmacol. 104, 554-558). This observation, together with findings reported by others (Ehrlich, Y. H., Davis, T. B., Bock, E., Kornecki, E., and Lenox, R. H. (1986) Nature 320, 67-70; Dusenbery, K. E., Mendiola, J. R., and Skubitz, K. M. (1988) Biochem. Biophys. Res. Commun. 153, 7-13), indicate the existence of ectoprotein kinase activity on the blood platelet surface. In this study, we demonstrate that washed human platelets phosphorylate the synthetic heptapeptide kemptide in a cAMP-dependent mode. The intensity of the phosphorylation was concentration-dependent for kemptide. In addition, incubation of platelets with [gamma-32P]ATP resulted in a rapid incorporation of [32P] phosphate into proteins at the outer membrane surface that was sensitive to alkaline phosphatase treatment. When cAMP was added to the medium, major phosphorylation of an 88-kDa ectoprotein occurred. Its isoelectric point determined by isoelectric focusing SDS-polyacrylamide gel electrophoresis was around pH 6.2. Phosphorylations of this 88-kDa polypeptide and of the exogenous kemptide substrate were both prevented by the specific protein kinase A inhibitor peptide. When platelets were preincubated with [32P]inorganic phosphate to label intracellular proteins, the protein phosphorylation pattern was different from that obtained with [gamma-32P]ATP, indicating that the latter occurred at the outer surface of the cells. Prostacyclin, which induces the increase of intracellular cAMP levels and, consequently, its liberation into the extracellular medium, increased phosphorylation of both kemptide and platelet 88-kDa polypeptide. The major protein of 88-kDa, which was phosphorylated in the presence of cAMP and external [gamma-32P]ATP, was identified by immunoprecipitation to GPIV (CD36), one of thrombospondin and collagen binding sites on platelets. The phosphorylation of CD36 also occurred in platelet-rich plasma, suggesting a physiological role for this ectoenzyme. In the present study, we clearly demonstrate the presence of an ectoprotein kinase A activity at the surface of intact human platelets, and we revealed its principal endogenous substrate as being CD36.

Endothelial effects of hemostatic devices for continuous cardioplegia or minimally invasive operations

BACKGROUND

Improvements in myocardial protection may include the continuous delivery of normothermic blood cardioplegia. Technical aids are required for optimal visualization of the operative field during the performance of coronary anastomoses if cardioplegia is to be given continuously or during minimally invasive operations. However, the effects of the different hemostatic devices on coronary endothelial function are unknown.

METHODS

We compared the effects on endothelial function of two commonly used hemostatic techniques, coronary clamping and gas jet insufflation, with those of a technique using extravascular balloon occlusion to mimic systolic luminal closure by the surrounding myocardium. The three techniques were applied for 15 minutes on porcine epicardial coronary arteries from explanted hearts. For coronary clamping, standard bulldog clamps were used. Gas jet insufflation was applied by blowing oxygen (12 L/min) tangentially at a 45-degree angle 1 cm away from a 3-mm arteriotomy. Extravascular balloon occlusion was achieved with a needle-tipped silicone loop, the midportion of which, once positioned beneath the coronary artery, was inflated to push a myocardial "cushion" against the back of the vessel until its occlusion. Control rings were taken from the same coronary artery. The endothelial function of control and instrumented arterial rings was then studied in organ chambers filled with modified Krebs-Ringer bicarbonate solution.

RESULTS

Contractions to potassium chloride and prostaglandin F2 alpha and endothelium-independent relaxation to sin-1, a nitric oxide donor, were unaffected in all groups. Endothelium-dependent relaxation to serotonin was impaired after clamping and preserved after gas jet insufflation and extravascular balloon occlusion. Maximal endothelium-dependent relaxation to serotonin was as follows: for coronary clamping, 63% +/- 6% versus 87% +/- 3% in controls; for gas jet insufflation, 67% +/- 12% versus 88% +/- 7%; and for extraluminal balloon occlusion, 79% +/- 6% versus 85% +/- 5%.

CONCLUSIONS

Whereas commonly used hemostatic devices may impair endothelial function, extravascular balloon occlusion appears to achieve effective hemostasis while preserving endothelial integrity.

Monohydroperoxidized fatty acids but not 4-hydroxynonenal induced acute cardiac cell damage

Unsaturated fatty acids constitutive of cardiac membranal lipid matrix are one of the primary targets for reactive oxygen species generated during ischemia-reperfusion cycle. Lipid peroxidation is a cascade of intricate reactions involving the successive formations of fatty acids hydroperoxides and aldehydic compounds such as alkenals derived from the oxidative fragmentation of these hydroperoxides. The potential deleterious effects of different classes of lipid peroxidation products on cardiac cells were compared using three in vitro approaches: (i) cardiomyocyte integrity, (ii) electromechanical activity of papillary muscle, and (iii) atrial contractility. The following products of lipid peroxidation were tested: (i) photoperoxidized arachidonic acid pooling hydroperoxidized derivatives and aldehydic compounds, (ii) fatty acids hydroperoxides, and (iii) 4-hydroxynonenal, a characteristic alkenal derived from the oxidative fragmentation of hydroperoxidized n-6 fatty acids. Only fatty acids hydroperoxides induced drastic loss of cellular integrity and severe disturbances in electromechanical activity of cardiomyocytes. 4-hydroxynonenal induced only a slight leak of lactate dehydrogenase at high concentrations and did not modify the electromechanical behavior of cardiac preparations. Under our conditions, monohydroperoxidized fatty acids but not 4-hydroxynonenal induced acute cardiac cell damages. In conclusion, lipid hydroperoxides can be considered both as markers of oxidative injury and relay sources of oxidative stress.

Stimulation of mitogen-activated protein kinase by thyrotropin in primary cultured human thyroid follicles

In the thyroid, thyrotropin (TSH) stimulates both growth and function, and stimulates the production of cAMP which reproduces most of the effects of TSH. Here, we report evidence that TSH stimulates the mitogen-activated protein (MAP) kinase cascade through a cAMP-independent pathway, in human thyroid. TSH stimulated MAP kinase activity (4-9-fold the basal level) measured in the cytosolic fractions of primary cultured thyroid follicles. Maximal activity was reached after 20 min and remained sustained for 1-3 h, TSH being as potent as EGF; EC50 was 1.5 nM TSH. Only a single isoform of MAP kinase (p42) was detected in the follicles. p42 was phosphorylated on tyrosine residues and showed a reduced electrophoretic mobility in follicles stimulated by TSH. All these effects on MAP kinase were decreased by preincubation of the follicles with human anti-TSH receptor antibodies. The stimulation of MAP kinase by TSH was neither blocked by pertussis toxin nor reproduced by forskolin, cholera toxin, or 8-bromo-cAMP. In conclusion, in human thyroid cells, in contrast with previous observations on dog thyroid cells, TSH stimulates strongly MAP kinase through a pertussis toxin-insensitive and cAMP-independent pathway.