Bayesian inference on biopolymer models

MOTIVATION

Most existing bioinformatics methods are limited to making point estimates of one variable, e.g. the optimal alignment, with fixed input values for all other variables, e.g. gap penalties and scoring matrices. While the requirement to specify parameters remains one of the more vexing issues in bioinformatics, it is a reflection of a larger issue: the need to broaden the view on statistical inference in bioinformatics.

RESULTS

The assignment of probabilities for all possible values of all unknown variables in a problem in the form of a posterior distribution is the goal of Bayesian inference. Here we show how this goal can be achieved for most bioinformatics methods that use dynamic programming. Specifically, a tutorial style description of a Bayesian inference procedure for segmentation of a sequence based on the heterogeneity in its composition is given. In addition, full Bayesian inference algorithms for sequence alignment are described.

AVAILABILITY

Software and a set of transparencies for a tutorial describing these ideas are available at http://www.wadsworth.org/res&res/bioinfo/

Inducible nitric oxide synthase expression is selectively induced in astrocytes isolated from adult human brain

Inducible nitric oxide synthase (iNOS) expression has been shown to be differentially regulated among different cell types and species. In cultures of primary human fetal glial cells, we have shown that astrocytes rather than microglia express iNOS. In the present study, we extended these findings to primary cultures of astrocytes and microglia derived from adult human brains. Mixed cultures of adult brain tissue were stimulated with IL-1beta and IFNgamma, a combination known to induce iNOS maximally in human fetal cells, and the expression of iNOS was determined by immunocytochemistry. Cell types were determined by morphology as well as immunocytochemistry for GFAP (astrocytes) and CD68 (microglia). The results showed that in cultures of adult human glia, iNOS was expressed following stimulation with cytokines, and the expression was restricted to astrocytes. Astrocyte iNOS immunoreactivity was detected both in the cytosol and in a discrete paranuclear region, a pattern noted in human fetal astrocytes. These results demonstrate that the ability to express iNOS is common to both fetal and adult human astrocytes.

Human Hsp70 and Hsp40 chaperone proteins facilitate human papillomavirus-11 E1 protein binding to the origin and stimulate cell-free DNA replication

Human papillomavirus replication initiator, the E1 helicase, binds weakly to the origin of DNA replication. Purified human chaperone proteins Hsp70 and Hsp40 (HDJ-1 and HDJ-2) independently and additively enhanced E1 binding to the origin. The interaction between E1 and Hsp70 was transient and required ATP hydrolysis, whereas Hsp40 bound to E1 directly and remained in the complex. A peptide of 20 residues spanning the HPD loop and helix II of the J domain of YDJ-1 also stimulated E1 binding to the origin, alone or in combination with Hsp70 or Hsp40. A mutated peptide (H34Q) had a reduced activity, while an adjacent or an overlapping peptide had no effect. Neither Hsp70 nor the J peptide altered the E1/DNA ratio in the complex. Electron microscopy showed that E1 mainly bound to DNA as a hexamer. In the presence of Hsp40, E1 primarily bound to DNA as a dihexamer. Preincubation of chaperones with viral E1 and template shortened the lag time and increased replication in a cell-free system. Since two helicases are essential for bidirectional replication of human papillomavirus DNA, these results demonstrate that, as in prokaryotes, chaperones play an important role in the assembly of preinitiation complexes on the origin.

IFNs are critical regulators of IL-1 receptor antagonist and IL-1 expression in human microglia

Because IL-1 is implicated in the pathogenesis of multiple sclerosis, and IFNs are known to alter disease course, we sought to determine whether IFNs can regulate the expression of IL-1 and IL-1R antagonist (IL-1Ra) in primary cultures of human microglia and astrocytes. We found that IL-1 and IL-1Ra are products of microglia but not astrocytes, and IFN-beta and IFN-gamma differentially modulate LPS- and cytokine-induced IL-1 and IL-1Ra. IFN-beta induces IL-1Ra and augments LPS- and IL-4-induced IL-1Ra, but suppresses LPS- and IL-1-induced IL-1, shifting the balance toward the expression of the IL-1Ra. Like IFN-beta, IFN-gamma suppresses the expression of both LPS and IL-1-induced IL-1beta. However, IFN-gamma also suppresses the expression of IFN-beta- and IL-4-induced IL-1Ra so that IFN-gamma may enhance or suppress IL-1 activity depending on the other cytokines present. IL-4 has similar effects to IFN-beta; however, other anti-inflammatory cytokines, did not regulate IL-1 or IL-1Ra in human microglia. Our data demonstrate a novel suppressive effect of IFN-beta and IL-4 on IL-1 activity in human microglia, suggesting that IFN-beta, a therapeutic agent used for multiple sclerosis, could have wider applications in the treatment of other central nervous system disorders in which IL-1 activity has been implicated in the pathogenesis.

Disassociation of sigma subunit from RNA polymerase of Xanthomonas oryzae pv. oryzae by phage Xp10 infection

The sigma subunit of Xanthomonas oryzae pv. oryzae is disassociated from host RNA polymerase after phage Xp10 infection. To clarify the possible mechanism for this observation, sigma subunit was purified and an antiserum against sigma subunit was prepared. Immunoprecipitation of RNA polymerase by the anti-core RNA polymerase antiserum, followed by immunoblotting with anti-sigma subunit antibody, revealed that sigma subunit was lost from RNA polymerase within 10 minutes after Xp10 infection. Loss of sigma subunit was not observed under other stress conditions including heat and cold stress, starvation and growth to stationary phase. Two-dimensional immunoblotting analysis did not reveal any covalent modification of either sigma subunit or RNA polymerase after Xp10 infection. These results suggest that separation of th subunit from RNA polymerase may be due to competition with other binding factors.

The carboxyl-terminal region of the human papillomavirus type 16 E1 protein determines E2 protein specificity during DNA replication

The mechanism of DNA replication is conserved among papillomaviruses. The virus-encoded E1 and E2 proteins collaborate to target the origin and recruit host DNA replication proteins. Expression vectors of E1 and E2 proteins support homologous and heterologous papillomaviral origin replication in transiently transfected cells. Viral proteins from different genotypes can also collaborate, albeit with different efficiencies, indicating a certain degree of specificity in E1-E2 interactions. We report that, in the assays of our study, the human papillomavirus type 11 (HPV-11) E1 protein functioned with the HPV-16 E2 protein, whereas the HPV-16 E1 protein exhibited no detectable activity with the HPV-11 E2 protein. Taking advantage of this distinction, we used chimeric E1 proteins to delineate the E1 protein domains responsible for this specificity. Hybrids containing HPV-16 E1 amino-terminal residues up to residue 365 efficiently replicated either viral origin in the presence of either E2 protein. The reciprocal hybrids containing amino-terminal HPV-11 sequences exhibited a high activity with HPV-16 E2 but no activity with HPV-11 E2. Reciprocal hybrid proteins with the carboxyl-terminal 44 residues from either E1 had an intermediate property, but both collaborated more efficiently with HPV-16 E2 than with HPV-11 E2. In contrast, chimeras with a junction in the putative ATPase domain showed little or no activity with either E2 protein. We conclude that the E1 protein consists of distinct structural and functional domains, with the carboxyl-terminal 284 residues of the HPV-16 E1 protein being the primary determinant for E2 specificity during replication, and that chimeric exchanges in or bordering the ATPase domain inactivate the protein.

Bayesian adaptive sequence alignment algorithms

The selection of a scoring matrix and gap penalty parameters continues to be an important problem in sequence alignment. We describe here an algorithm, the 'Bayes block aligner, which bypasses this requirement. Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data. We compared the Bayes aligner with the popular Smith-Waterman algorithm with parameter settings from the literature which had been optimized for the identification of structural neighbors, and found that the Bayes aligner correctly identified more structural neighbors. In a detailed examination of the alignment of a pair of kinase and a pair of GTPase sequences, we illustrate the algorithm's potential to identify subsequences that are conserved to different degrees. In addition, this example shows that the Bayes aligner returns an alignment-free assessment of the distance between a pair of sequences.

Construction of an inducible nitric-oxide synthase gene transferring vector mediated by retrovirus

AIM

To construct an inducible nitric-oxide synthase (iNOS) gene transferring vector mediated by retrovirus.

METHODS

Recombinant DNA and polymerase chain reaction (PCR) amplification techniques were used.

RESULTS

With 2 steps of molecular cloning, the full-length cDNA encoding macrophage iNOS was isolated from plasmid pKSiNOS and subcloned into intermediate vector pSP72, adjusting the restriction enzyme sites in both 5'- and 3'-flanking ends of insert fragment. The retroviral vector pLNCXiNOS which contains iNOS coding region, cytomegalovirus promoter and neomycin resistance (neor) gene was further constructed. The authenticity of insertion size and orientation of iNOS sequence was verified by restriction mapping and PCR analysis with iNOS gene-specific primers.

CONCLUSION

Retroviral expression vector carrying iNOS fragment is obtained, which provides a material to establish a model of iNOS gene-modified neurons.

Selective inhibition of human glial inducible nitric oxide synthase by interferon-beta: implications for multiple sclerosis

Nitric oxide generated from the inducible nitric oxide synthase (iNOS) has been implicated in the pathogenesis of multiple sclerosis. Because significant species- and cell-specific differences exist in the expression of iNOS, we used primary human glial cell cultures to screen for an inhibitor of iNOS expression. Remarkably, among numerous soluble factors tested, interferon-beta (IFN-beta) alone showed a selective and potent inhibition of interleukin-1beta/interferon-gamma (IL-1beta/IFN-gamma)-induced iNOS expression in astrocytes. Inhibition of iNOS may provide a mechanism by which IFN-beta can ameliorate inflammation and cytotoxicity in the central nervous system of patients with multiple sclerosis.

Identification of neutral and acidic sphingomyelinases in Helicobacter pylori

We demonstrated for the first time the presence of sphingomyelinase (SMase) in Helicobacter pylori. Activation of SMase has been implicated as the cause of elevation of cellular ceramide levels and consequently of apoptosis. The data indicate that there are two classes of SMase, defined by their optimal pHs and cellular locations, existing in H. pylori. One is an Mg(2+)-dependent membrane-bound enzyme with an optimal activity at pH 7, and the other is an Mg(2+)-independent cytosolic enzyme with an optimal activity at pH 5. Bisalumin, a bismuth salt, was found to inhibit the activities of both forms of SMase regardless of the presence of Mg2+. By Western blot analysis, the membrane-bound SMases of H. pylori and Bacillus cereus were shown to be antigenically related and to have a similar denatured molecular mass of 28 kDa.

The use of 2 ipsilateral ureteral stents for relief of ureteral obstruction from extrinsic compression

PURPOSE

We present our early experience with the novel approach of placing 2 parallel stents simultaneously in extrinsically obstructed ureters in which single stents had failed. The increased stiffness of 2 stents reduces kinking and luminal compression, and the potential space between the stents likely preserves flow around as well as through them.

MATERIALS AND METHODS

Four patients recently presented with ureteral obstruction secondary to nonurinary tract malignancies. Previous stenting with a single 6F Double-J* stent had failed in all cases. Three patients experienced flank pain and 1 had persistent azotemia within 3 days of initial stent placement. All patients had significant residual sonographic hydronephrosis despite good stent position. In all cases cystoscopy/stent exchange was performed under local anesthesia with intravenous sedation. Parallel 4.7F Double-J stents were placed simultaneously over 2, 0.035 hydrophilic coated glide wires under fluoroscopic guidance after removal of the malfunctioning 6F stent.

RESULTS

Stent placement was uneventful in all 4 patients with prompt drainage of contrast material seen after parallel ipsilateral stent placement. Patients tolerated the double 4.7F parallel stents with no discernible difference in irritative symptoms compared to single 6F stents. Flank pain and azotemia resolved in 3 patients, and hydronephrosis improved in all 4 after placement of parallel Double-J stents. All patients remain alive with a mean followup of 5.8 months (range 4 to 8). Except for 1 patient who later underwent ureterolysis, each has subsequently had the stent changed every 3 months. No patient has required proximal urinary diversion (that is percutaneous nephrostomy tube).

CONCLUSIONS

Placement of 2 ipsilateral parallel ureteral stents simultaneously is an easy technique. It may obviate percutaneous nephrostomy tube placement in patients in whom drainage with a single stent failed, especially in cases of extrinsic ureteral compression.

Bilateral cheiro-oral syndrome

Eight cases of pure bilateral cheiro-oral syndrome (COS) are reported. The location and etiology of lesion were well defined in six cases, including pontine infarct in three, and brainstem hemorrhage, unilateral thalamic infarct and bilateral subdural hematoma in one patient each respectively. Neuroimaging and neurophysiological studies were normal in another two patients. Taken together with the previous five reported cases of bilateral COS, pons is the most frequent site for presentation even in the absence of associated brainstem signs.

Antiplatelet drugs induce apoptosis in cultured cancer cells

In order to understand if antiplatelet drugs possess direct antineoplastic property, we tested the apoptotic effect of 5 popularly marketed antiplatelet drugs in Taiwan in 6 cultured cancer cell lines (Hep 3B hepatocarcinoma, U87-MG malignant glioma, PC-3 prostate adenocarcinoma, HeLa cervical adenocarcinoma, HL-60 preleukemia and K-562 chronic myelogenous leukemia). While acetylsalicylate and flunarizine exerted no effect on these cancer cells, pentoxifyline (PTX), dipyridamole (DYA) and ticlopidine hydrochloride (T. HCl) displayed a time and dose-dependent apoptotic effect on them except for HL-60 and K-562 cells. PTX induced apoptosis in U87-MG, Hep 3B and HeLa cells, DYA in HeLa cells, while T. HCl in U87-MG, Hep 3B, PC-3 and HeLa cells. Adriamycin also provoked apoptotic effect in all 6 cell lines but neither PTX, DYA nor T. HCl acted synergy with adriamycin to HeLa cells, implicating that they may share a similar pathway for inducing apoptosis. Therefore, our results show that the antiplatelet drugs do possess antineoplastic property in vitro. A co-administration of antiplatelet drugs is noteworthy for an alternative adjunctive therapy in cancer patients.

Prediction of total cholesterol: high-density-lipoprotein-cholesterol ratio in young adults

Abnormal cholesterol fraction is an essential risk factor for atherosclerosis of large cerebral arteries in young Asians. In order to reduce the medical cost and social resource for cholesterol electrophoresis, especially in undeveloped and developing Asian countries, we evaluated the validity of Nanji's GUT score for predicting TC: HDLC ratio in this population. Results showed that GUT score only predicted 71% of them. We also tested the predictive power of CUT index, and predicting rate was 81%. Therefore, Nanji's GUT score is not an ideal surrogate for cholesterol electrophoresis. We recommend CUT index to screen for high-risk subjects till a new method can satisfy the economic pattern in Asian countries.

Extracting protein alignment models from the sequence database

Biologists often gain structural and functional insights into a protein sequence by constructing a multiple alignment model of the family. Here a program called Probe fully automates this process of model construction starting from a single sequence. Central to this program is a powerful new method to locate and align only those, often subtly, conserved patterns essential to the family as a whole. When applied to randomly chosen proteins, Probe found on average about four times as many relationships as a pairwise search and yielded many new discoveries. These include: an obscure subfamily of globins in the roundworm Caenorhabditis elegans ; two new superfamilies of metallohydrolases; a lipoyl/biotin swinging arm domain in bacterial membrane fusion proteins; and a DH domain in the yeast Bud3 and Fus2 proteins. By identifying distant relationships and merging families into superfamilies in this way, this analysis further confirms the notion that proteins evolved from relatively few ancient sequences. Moreover, this method automatically generates models of these ancient conserved regions for rapid and sensitive screening of sequences.

3-Ketoglycoside-mediated metabolism of sucrose in E. coli as conferred by genes from Agrobacterium tumefaciens

Escherichia coli strains that did not have the ability to use sucrose as a sole carbon source gained this ability after receiving a cloned fragment of DNA from Agrobacterium tumefaciens. No invertase was detected in the sucrose-metabolizing E. coli, but evidence for the activity of certain enzymes, known to be produced by biotype 1 strains of Agrobacterium, were found. Evidence was found for the presence of D-glucoside 3-dehydrogenase (G3DH) and alpha-3-ketoglucosidase. The activity of enzyme extracts on 3-ketosucrose also indicated that 3-ketoglucose reductase, or some enzyme that acts on 3-ketoglucose, was present in the Suc+ E. coli as well. The fragment was found to complement a G3DH mutant of A. tumefaciens and was also found to confer chemotaxis towards sucrose in E. coli.

Molecular evolution and phylogeny of satellite RNA associated with bamboo mosaic potexvirus

Satellite RNA of bamboo mosaic potexvirus (satBaMV) is a linear RNA molecule which encodes a 20-kDa nonstructural protein. Sequences of seven different satBaMV isolates from bamboo hosts in three genera showed 0.7% to 7.5% base variation which spanned the whole RNA molecule. However, the putative 20-kDa open reading frame was all preserved in these isolates. The phylogenetic relationship based on the nucleotide sequence did not show particular grouping of satBaMV from the host in one genus; neither was the grouping of satBaMV evident by location of sampling. Putative secondary structures of the 3' untranslated regions showed a basic pattern with conserved hexanucleotides (ACCUAA) and polyadenylation signal (AAUAAA) located in the loop regions. Although the satBaMV-encoded 20-kDa protein is a nonstructural protein, its predicted secondary structure contains eight-stranded beta-sheets which may form "jelly-roll" structure similar to that found in capsid protein encoded by satellite virus of panicum mosaic virus.

Transient global amnesia and thalamic hemorrhage

A left rostral thalamic hematoma was found in a 52-year-old hypertensive man who suffered from a 10-h episode of transient global amnesia (TGA). A neuropsychological study revealed no cognitive impairment in a follow-up period for 5 years. The left rostral part of the thalamus appears to be responsible for his TGA, due probably to an interference of the mamillothalamic tract, ventroamygdalofugal pathway or dorsal noradrenergic bundle.

Acute diffuse phlegmonous esophagogastritis: report of a survived case

A 42-year-old man was admitted because of a persistent pain on swallowing together with epigastralgia, chest pain, fever, and shortness of breath for 5 days. An unbearable shortness of breath with a retrosternal pain was noted each time he tried to lie down. The patient also developed bilateral pleural effusion and pericardial effusion. Ten days after admission, he underwent an emergency laparotomy after an acute episode of severe epigastralgia with hematemesis and rebound tenderness limited to the epigastrium. Operative findings showed diffuse phlegmonous esophagogastritis. A near-total esophagectomy and a total gastrectomy were done. He lost 15 kilograms of body weight and was discharged 3 months later. The patient underwent reconstructive surgery 2 months after discharge, recovered well and regained his weight within one year.

Arthrographic evaluation of developmental dysplasia of the hip. Outcome prediction

Arthrograms of 35 hips in 33 children less than 2 years of age with typical development dysplasia of the hip were reviewed. After arthrograms were repeated for 11 hips 6 weeks following the initial test, results were classified into 6 types based on medial pooling ratio and morphology of the acetabular limbus. Using modified Severin's criteria for outcome evaluation, 7 of the 11 hips had been upgraded in type. All hips that were classified as Type I by arthrogram had Severin I results. The relation of arthrographic type and radiographic results was statistically significant. Immediate open reduction is recommended in hips classified as Type VI at first arthrogram or Type III and above at repeat arthrogram.

The lipoprotein profile of young adults with cerebral atherosclerosis

In order to elucidate the relationship between the lipoprotein profile and large cerebral artery atherosclerosis in the young adults living in developing Asian countries, the serum lipoprotein profile and the luminal diameter of large cerebral arteries (internal carotid, middle/anterior cerebral and vertebrobasilar arteries) were measured and correlated in 67 young Taiwanese with non-embolic cerebral infarct (CI). Totally 23 (21.9%) patients had atherosclerotic stenosis. A significant elevation of the serum total cholesterol (TC), triglyceride, total lipids, beta-lipoprotein (beta-LP) and pre-beta-LP level was found in atherosclerotic CI patients. But multiple regression analysis showed only the serum beta-LP (p = 0.0041) and TC (p = 0.0324) level to be the independent risk factors for atherosclerosis. Secondary dyslipoproteinemia is the main cause for hyperlipoproteinemia in our atherosclerotic patients. Therefore, an abnormal lipoprotein profile is linked to large cerebral artery atherosclerosis in young Asians regardless of ethnic group. A tailored program is recommended to modify the life style and dietary habit, as well as to gain access to secondary control for large cerebral atherosclerosis prevention in developing countries.

The functions of human papillomavirus type 11 E1, E2, and E2C proteins in cell-free DNA replication

We examined the functions of human papillomavirus type 11 (HPV-11) E1 and E2 proteins purified from Sf9 cells infected with recombinant baculoviruses in cell-free HPV-11 origin (ori) replication. The E1 protein binds specifically to a wild type but not to a mutated sequence in the ori spanning nucleotide position 1. It also has a relatively strong affinity for nonspecific DNA. A neutralizing antiserum directed against the amino-terminal one-third of the E1 protein totally abolishes initiation and elongation, suggesting that it functions as an initiator and a helicase at the replication fork. An antiserum against the carboxyl-terminal portion of E1 protein abolished replication only when added prior to initiation. Thus this portion of E1 is hidden in the replication complexes. The HPV-11 E2 protein appears not to be essential for elongation, but it must be present in the preinitiation complex for the E1 protein to recruit host DNA replication machinery to the ori. E2 antiserum added after preincubation in the absence of the cell extracts totally abolished replication. An identical conclusion is also reached for the bovine papillomavirus type 1 E2 protein. Finally, the HPV-11 E2C protein lacking the transacting domain of the full-length E2 protein partially inhibits E2-dependent ori replication.

Delayed transhemispheric c-fos gene expression after focal cerebral ischemia-reperfusion in rats

Using a unilateral, focal, cortical, ischemia-reperfusion rat model, c-fos mRNA and Fos immunoreactivity in the brain were investigated. The study was divided into a series of reperfusion intervals which were carried out for a period of up to 7 days. The c-fos mRNA peaked in the ischemic cortex (about 15-fold) after 30 minutes of ischemia followed by 1 hour of reperfusion and dropped to baseline level after 1 day of reperfusion. Increased expression switched to the bilateral retrosplenial and frontal cortex, as well as the left (nonischemic) parietal cortex, at 3- or 5-days of reperfusion (about three- to fourfold). Fos immunohistochemical staining correlated positively with the surge of c-fos mRNA. Nuclear run-off transcription assays further indicated that the increase in c-fos mRNA was regulated at the transcriptional level not only in the ischemic cortex (30 min of ischemia, followed by 1 h of reperfusion) but also in the contralateral counterpart (30 min of ischemia, followed by 3 d of reperfusion). A link between altered gene expression and diaschisis is suggested. The distant/delayed c-fos expression is probably caused by loss of inhibition from the ischemic cortex through a polysynaptic transneural pathway.

Fibromuscular dysplasia associated with intracranial giant aneurysm: report of a case

Although the correlation between fibromuscular dysplasia (FMD) and intracranial aneurysm is well established, the combination of FMD with a giant aneurysm is rare. This paper reports a patient with extracranial FMD associated with a giant intracavernous aneurysm compromising the trigeminal and abducens nerve. A review of the literature uncovered only four documented cases of FMD with concurrent giant intracranial aneurysms. The present case adds further weight to the argument for including FMD in the differential diagnosis list when confronted with a patient with a giant intracranial aneurysm. Absence of adequate collaterals in this patient eliminated ligation as a treatment strategy for the aneurysm.

Satellite RNA associated with bamboo mosaic potexvirus shares similarity with satellites associated with sobemoviruses

A putative nonstructural protein encoded by a satellite RNA associated with bamboo mosaic potexvirus shares 46% identity with the capsid protein of satellite virus of panicum mosaic sobemovirus. The sequence similarity among satellite plant viruses which have no apparent relationship implies a common origin.

Gibbs motif sampling: detection of bacterial outer membrane protein repeats

The detection and alignment of locally conserved regions (motifs) in multiple sequences can provide insight into protein structure, function, and evolution. A new Gibbs sampling algorithm is described that detects motif-encoding regions in sequences and optimally partitions them into distinct motif models; this is illustrated using a set of immunoglobulin fold proteins. When applied to sequences sharing a single motif, the sampler can be used to classify motif regions into related submodels, as is illustrated using helix-turn-helix DNA-binding proteins. Other statistically based procedures are described for searching a database for sequences matching motifs found by the sampler. When applied to a set of 32 very distantly related bacterial integral outer membrane proteins, the sampler revealed that they share a subtle, repetitive motif. Although BLAST (Altschul SF et al., 1990, J Mol Biol 215:403-410) fails to detect significant pairwise similarity between any of the sequences, the repeats present in these outer membrane proteins, taken as a whole, are highly significant (based on a generally applicable statistical test for motifs described here). Analysis of bacterial porins with known trimeric beta-barrel structure and related proteins reveals a similar repetitive motif corresponding to alternating membrane-spanning beta-strands. These beta-strands occur on the membrane interface (as opposed to the trimeric interface) of the beta-barrel. The broad conservation and structural location of these repeats suggests that they play important functional roles.

Amphotericin B-induced leukoencephalopathy in a patient with cryptococcal meningitis

A 43-year-old male was diagnosed as having cryptococcal meningitis based on his clinical condition, cerebrospinal fluid (CSF) profile and high titer CSF cryptococcal antigen. The patient received intravenous amphotericin B at a total dose of 91 mg over 5 days. The therapy was then abandoned due to acute hepatorenal failure. The patient's neurologic status remained stable for 2 months, after which he began experiencing somnolence, confusion and a personality change. Cranial computed tomography revealed multifocal white matter lesions, and a brain biopsy showed a demyelination change with concurrent IgM and C1q deposition. A clinical diagnosis of amphotericin B-induced leukoencephalopathy was made. The patient's clinical condition was partially reversed after low-dose steroid therapy.

Bilateral cheiro-oral syndrome and traumatic subdural hematoma

Typical bilateral cheiro-oral syndrome was encountered in a 74-year-old man who had bilateral subdural hematoma after a minor head injury. The delayed grave neurologic deficits occurred 1 month later without expansion of the hematoma. Removal of the lesions reversed both cheiro-oral syndrome and his late-onset neurological disabilities.

Isolated vertiginous dysequilibrium due to bilateral caudal cerebellar infarction

We present a 74-year-old woman who developed a sudden onset of vertigo, vomiting, and axial retropulsion without limb ataxia. A clinical diagnosis of acute peripheral labyrinthine lesion was made initially. However, magnetic resonance imaging demonstrated a small infarct area involving the caudal part of the cerebellar vermis and medial cerebellar hemispheres on both sides. We emphasize that a cautious attitude should be taken in managing patients with isolated vestibular dysfunction, especially in aged person or those associated with stroke risk factor.

Asymptomatic sacral arachnoid cyst in a patient with ankylosing spondylitis

A sacral arachnoid cyst was found incidentally in a patient with ankylosing spondylitis. The clinical manifestations were perithecal bony erosions and thecal sac displacement while no associated neurological deficit was detected. This peculiar situation is of special interest as cauda equina syndrome invariably presented in such clinical complex. The pathogenesis of the arachnoid cyst remains unclear. And surgical intervention is only indicated in patients with evidence of nerve root compression.

A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes

A highly conserved sequence was found in rRNA gene internal transcribed spacer 1 (ITS1) among flowering plant species. The sequence, GGCRY-(4 to 7 n)-GYGYCAAGGAA (where Y = C or T; R = G or A) is located in the central region of ITS1, and is present in published sequences from a wide range of flowering plants. The rest of ITS1 is highly variable in sequence. Therefore, the conserved motif within ITS1 may have a key function in the processing of rRNA gene transcripts. Furthermore, identification of such a conserved motif will help facilitate alignment of sequences for phylogenetic analysis.

Suppression of ischemia-induced fos expression and AP-1 activity by an antisense oligodeoxynucleotide to c-fos mRNA

Activation of c-fos, an immediate early gene, and the subsequent expression of the Fos protein have been noted following focal cerebral ischemia. Fos and Jun form a heterodimer as activator protein 1 (AP-1), which transregulates the expression of several genes. To study the postischemic events related to c-fos expression, we suppressed the expression of c-fos by intraventricular infusion of an antisense oligodeoxynucleotide (anti-rncfosr115) of c-fos mRNA. The effectiveness of anti-rncfosr115 was confirmed first by its capability to block in vitro c-fos mRNA translation. In vivo, after intraventricular infusion of 32P-labeled anti-rncfosr115, the oligodeoxynucleotide was internalized within 6 hours and detectable also in the nucleic acids fraction up to 41 hours. Treatment of the recovered nucleic acids with RNase H separated the labeled oligodeoxynucleotide from the nucleic acid fraction, indicating an association of the antisense oligodeoxynucleotide and cellular RNA after uptake. When focal cerebral ischemia was induced 16 hours after the infusion of anti-rncfosr115, the postischemic increase in Fos expression and AP-1 binding activity were suppressed. Specificity of the effect of anti-rncfosr115 was suggested by its failure to suppress the DNA binding activity of nuclear cyclic AMP response elements. These results support the hypothesis that increased AP-1 binding activity following focal cerebral ischemia is dependent on Fos expression and can be inhibited in vivo by antisense c-fos oligodeoxynucleotides.

Cell-free replication of the human papillomavirus DNA with homologous viral E1 and E2 proteins and human cell extracts

We have established the first homologous cell-free DNA replication system for a papillomavirus. The replication of the human papillomavirus type 11 (HPV-11) origin was achieved by using human 293 cell extracts supplemented with the HPV-11 E1 and E2 proteins purified from insect cells infected with recombinant baculoviruses. Efficient replication depends on the HPV-11 origin, the HPV-11 E1 and E2 proteins, as well as human DNA polymerase alpha, delta, replication protein A, topoisomerase I, and topoisomerase II. High concentrations of E1 protein also promoted a low level of origin-independent replication which was suppressed by the addition of the E2 protein, whereas E2 protein stimulated origin-dependent replication. We also show that an intact E2 protein binding site was absolutely necessary for origin activity, as a strong HPV-11 origin was rendered inactive when one half-site of each of the three E2 binding sites was mutated. In contrast, there was only a relatively small reduction in this mutant origin activity when the cell extracts were supplemented with the bovine papillomavirus type 1 (BPV-1) proteins. These results suggest that the HPV-11 E2 protein plays a primary role in HPV origin recognition. Furthermore, unlike transient replication in which HPV-11 and BPV-1 viral proteins promote efficient replication of homologous and heterologous origins, efficient cell-free replication took place only with the homologous combinations.

A case of Graves' diseases associated with intracranial moyamoya vessels and tubular stenosis of extracranial internal carotid arteries

A 28-year-old woman presented with a clinical picture of hyperthyroidism, goiter, ophthalmopathy, and an ensuing ischemic stroke. Cerebral angiography demonstrated moyamoya vessels around the Willis's circle and tubular stenosis of the bilateral extracranial internal carotid arteries. The combination of the above angiographic abnormalities occurring in a patient with Graves' disease is extremely rare. A pathogenic link between Graves' disease and certain specific vascular disorders is suspected.

Intractable hiccup due to multiple sclerosis: MR imaging of medullary plaque

We describe a 31-year-old man with clinically definite multiple sclerosis who presented with intractable hiccup for one month prior to admission. The responsible lesion was confirmed by magnetic resonance imaging to be a plaque in the ventral paramedian portion of the medulla oblongata.

Unilateral cheiro-oral syndrome in a patient with bilateral subdural hematomas

We report a 49-year-old man with acute intermittent perioral and distal hand sensory dysfunction on the left side (cheiro-oral syndrome). The responsible lesion was confirmed by magnetic resonance imaging to be bilateral subdural hematomas with the larger side compressing the middle and lower thirds of the right postcentral gyrus. We emphasize that subdural hematoma should be considered in the differential diagnosis of cheiro-oral syndrome.

Evolutionary diversification of fungal endophytes of tall fescue grass by hybridization with Epichloë species

The mutualistic associations of tall fescue (Festuca arundinacea) with seed-borne fungal symbionts (endophytes) are important for fitness of the grass host and its survival under biotic and abiotic stress. The tall fescue endophytes are asexual relatives of biological species (mating populations) of genus Epichloë (Clavicipitaceae), sexual fungi that cause grass choke disease. Isozyme studies have suggested considerable genetic diversity among endophytes of tall fescue. Phylogenetic relationships among seven isolates from tall fescue, three from meadow fescue (a probable ancestor of tall fescue), and nine Epichloë isolates from other host species were investigated by comparing sequences of noncoding segments of the beta-tubulin (tub2) and rRNA (rrn) genes. Whereas each Epichloë isolate and meadow fescue endophyte had only a single tub2 gene, most tall fescue endophytes had two or three distinct tub2 copies. Phylogenetic analysis of tub2 sequences indicated that the presence of multiple copies in the tall fescue endophytes was a consequence of hybridization with Epichloë species. At least three hybridization events account for the distribution and relationships of tub2 genes. These results suggest that interspecific hybridization is the major cause of genetic diversification of the tall fescue endophytes.

Effect of cholinesterase inhibition in vitro by huperzine analogs

Huperzine (Hup) A and B were first discovered and studied by Chinese. Fourteen analogs of Hup were tested for their anticholinesterase (anti-ChE) activity by colorimetric method using rat erythrocyte membrane and serum as enzyme sources. Hup-A showed the highest anti-AChE potency. The anti-BuChE activity of (-)dihydro and (-)tetrahydro analogs were potent than those of Hup-A. Their anti-AChE activities were comparable to those of physostigmine and galanthamine. Dihydro analog inhibition was of the mixed competitive type with a Ki value of 0.12 mumol.L-1. Tetrahydro analog inhibition was of the competitive type with a Ki value of 0.56 mumol.L-1. They were different from isoflurophate to bond to AChE in a reversible manner.

[Correction of tetralogy of Fallot in patients with a single pulmonary artery]

2249 patients underwent correction of tetralogy of fallot in our department. 23 of them were with unilateral absence of pulmonary artery, 19 absence of the left pulmonary artery, 4 absence of the right pulmonary artery. The age at operation ranged from 4 to 21 years. Valve-containing conduits were used in 9 patients and right ventricular outflow patch in 14 patients. There were two operative death who both had hypoplasia of the left ventricle. All survivors had good early and late results. Outflow patch with a single valve should be used in tetralogy of fallot with a single pulmonary artery and pulmonary valve ring stenosis. Aorticvalved homograft conduit is suit for the patient with anomalous coronary or pulmonary atresia.

Quantifying the vitamin K requirement of juvenile marine shrimp (Penaeus monodon) with menadione

A feeding trial was conducted to estimate the optimum dietary vitamin K requirement for juvenile marine shrimp, Penaeus monodon. Purified diets with eight levels (0, 5, 10, 20, 50, 80, 160 and 320 mg/kg) of supplemental menadione were fed to P. monodon (mean weight 1.33 +/- 0.05 g) for 12 wk. Each diet was fed to three replicate groups of shrimp. Shrimp fed diets supplemented with vitamin K (5-320 mg/kg) had significantly (P < 0.05) higher weight gain and feed efficiency than those fed the unsupplemented control diet. Shrimp fed diets supplemented with > or = 50 mg/kg vitamin K had higher protein efficiency ratios than shrimp fed the control diet. Calcium deposition in shrimp generally increased as dietary vitamin K supplementation increased. Vitamin K-dependent carboxylase activity was highest in shrimp fed the control diet, followed by shrimp fed 5-160 mg menadione/kg diet, and lowest in those fed 320 mg menadione/kg diet. Vitamin K-dependent protein precursor concentrations were high in shrimp fed 0-10 mg menadione/kg diet, lower in those fed 20 mg/kg, and lowest in shrimp fed > or = 50 mg/kg diet. Protein efficiency ratio and vitamin K-dependent protein precursor concentration analyzed by broken-line regression indicated that the adequate dietary vitamin K concentration in growing P. monodon is 30-40 mg/kg diet.

Low dose propranolol-induced delirium: 3 cases report and a review of literature

Delirium in 3 elderly patients with recent cerebral infarction and pre-existing brain dysfunction receiving low dose propranolol is described. The dose ranged from 30 to 60 mg/day and the interval between delirium onset and drug initiation was 3-7 days. One patient exhibited ictal mydriasis and sinus tachycardia. Hypoalbuminemia was found in 1 patient. Discontinuation of propranolol abolished their delirious pictures 2-5 days later. Their delirium may be attributed to central beta blockade or anticholinergic effect. Preexisting brain damage, old age and hypoalbuminemia may predispose such patients to neuropharmacotoxicity of low dose propranolol.

Expression of immediate early gene and growth factor mRNAs in a focal cerebral ischemia model in the rat

BACKGROUND AND PURPOSE

Increased release of excitatory neurotransmitters leading to activation of signal transduction has been noted after cerebral ischemia. One of the biochemical events in the signaling processes is an alteration of gene expression. A focal cerebral ischemia-reperfusion model in the rat was used to study the postischemic alteration of selected proto-oncogene and neurotrophin gene expression.

METHODS

Focal ischemia in the cerebral cortex irrigated by the right middle cerebral artery was induced by temporary occlusion of the right middle cerebral artery and both common carotid arteries for 30 or 90 minutes. Expression of selected proto-oncogenes and neurotrophin genes was studied with Northern blot analysis and in situ hybridization.

RESULTS

Northern blot analysis showed that an increase in the expression of selected proto-oncogenes including c-fos, c-jun, jun B, zif/268, and nur 77 were noted 30 to 90 minutes into postischemic reperfusion. In situ hybridization revealed different regional distribution of c-fos mRNA signal under different experimental conditions. Nuclear run-on experiments showed that the increase in c-fos and jun B mRNA signals was due to an increase in the transcription rate. An increase in AP-1 binding activity in the ischemic cortex was also noted. Increased expression of brain-derived neurotrophic factor and nerve growth factor mRNAs were noted subsequent to the expression of immediate early genes in the ischemic cortex and adjacent areas in a biphasic pattern.

CONCLUSIONS

Results are in agreement with the contention that increased c-fos and jun B expression leads to increased AP-1 binding activity, which in turn has been linked to the enhanced expression of neurotrophin genes.

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

A wealth of protein and DNA sequence data is being generated by genome projects and other sequencing efforts. A crucial barrier to deciphering these sequences and understanding the relations among them is the difficulty of detecting subtle local residue patterns common to multiple sequences. Such patterns frequently reflect similar molecular structures and biological properties. A mathematical definition of this "local multiple alignment" problem suitable for full computer automation has been used to develop a new and sensitive algorithm, based on the statistical method of iterative sampling. This algorithm finds an optimized local alignment model for N sequences in N-linear time, requiring only seconds on current workstations, and allows the simultaneous detection and optimization of multiple patterns and pattern repeats. The method is illustrated as applied to helix-turn-helix proteins, lipocalins, and prenyltransferases.

Babinski-Nageotte syndrome: a case report

A 68-year-old man developed a sudden onset of the left Wallenberg's syndrome with additional left hypoglossal nerve palsy and contralateral hemiparesis sparing the face. The clinical constellation, known as Babinski-Nageotte syndrome, is regarded as a combination of the medial and lateral medullary syndrome. Magnetic resonance imaging showed potential of in vivo confirmation of the underlying vascular insult, which clearly demonstrated an infarct area in the left half of the medulla oblongata.

Intractable hiccup caused by medulla oblongata lesions

Intractable hiccup is a rare manifestation of a brainstem lesion. We present five cases of intractable hiccups associated with medulla oblongata lesions: three of these had brainstem infarction compatible with Wallenberg's lateral medullary syndrome; one, clinically probable multiple sclerosis with a medullary lesion; and one, choroid plexus papilloma of the fourth ventricle with medullary compression. Using magnetic resonance imaging, it was demonstrated that the lesions affecting the dorsal and/or lateral medulla oblongata were responsible for the intractable hiccups.

Two independent intracranial arteriovenous malformations: a case report

Two independent intracranial arteriovenous malformations occurring to a single patient is rarely seen. A 23-year-old female suffered from a sudden onset weakness of the left side extremities and a generalized tonic-clonic seizure. A cranial CT revealed an intracranial hemorrhage in the right posterior temporal region and a highly enhanced mass in the left frontal lobe. On MR images, combination of subacute hematoma and serpentine vascular shadows in the right temporal area as well as clusters of vessels in the left frontal lobe were seen. Cerebral angiography confirmed one AVM in the right posterior temporal and the other the left frontal cortex.

Unilateral symptomatic palatal myoclonus: MRI evidence of contralateral inferior olivary lesion

Symptomatic palatal myoclonus is a rare syndrome of segmental myoclonus which is thought to occur after damage to certain brainstem or cerebellar structures. We report two patients with unilateral PM, who showed hypertrophy of the inferior olivary nucleus on magnetic resonance imaging. In the first patient this was due to a left pontine tegmental hemorrhage, and a right-sided oculo-palato-facial myoclonus developed one month after the episode. The second one had a basilar artery occlusion with ischemic infarcts at the basis pontis, dorso-lateral aspects of the left pons, and left cerebellar dentate nucleus, as well as the occipital lobe. A delayed left oculopalatal myoclonus was recognized 3 months later. Interruption of the "dentato-rubro-olivary pathway" by the lesion with ensuing neuronal loss, cytoplasmic vacuolation, and astrocytic proliferation in the inferior olive, together with an increase of water content as mobile proton may cause the MR signal abnormalities in patients with unilateral symptomatic palatal myoclonus.