Ensembl 2006

The Ensembl () project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.

Ensembl 2005

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

Assessment of a technique for 2D–3D registration of cerebral intra-arterial angiography

This study assesses the ability of a computer algorithm to perform automated 2D-3D registrations of digitally subtracted cerebral angiograms. The technique was tested on clinical studies of five patients with intracranial aneurysms. The automated procedure was compared against a gold standard manual registration, and achieved a mean registration accuracy of 1.3 mm (SD 0.6 mm). Two registration strategies were tested using coarse (128 x 128 pixel) or fine (256 x 256 pixel) images. The mean registration errors proved similar but registration of the lower resolution images was 3 times quicker (mean registration times 33 s, SD 13 s for low and 150 s SD 48 s for high resolution images). The automated techniques were considerably faster than manual registrations but achieved similar accuracy. The technique has several potential uses but is particularly applicable to endovascular treatment techniques.

Ensembl 2004

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

Epidemiology of hearing impairment at three Flemish Institutes for Deaf and Speech Defective Children

A retrospective analysis of 190 records of hearing impaired children up to the age of 14, all educated at one of three Flemish Institutes for Deaf and Speech Defective Children in Belgium, was performed. Until 1999, the well-known behavioral test (Ewing test) was used in the Flemish national screening program for hearing losses. Because it presented a lot of disadvantages, it has been replaced by Automated Auditory Brainstem Responses (AABR), enabling the Flemish national neonatal screening program to commence. This study is an extension of the preliminary results of a recently performed retrospective analysis in one Flemish institute of the hearing loss of patients that were diagnosed in the pre-AABR era. The authors analyzed the following data: etiology, risk factors of congenital hearing impairment, the patient's history from the moment of the first suspicion to diagnosis and treatment. The median age of the children was 8.5 years (2-14 year). In 66.5% the parents and/or grandparents were the first to raise suspicion, this was at a median age of approximately 9 months. The diagnosis was often made late, at a median age of 15 months (0-88 months). The etiology was unknown in 32.6% of the cases. The only cast-iron certain diagnoses were pre- and perinatal infections, syndromal and genetic hearing loss, and acquired infections (meningitis and measles). No risk factors of hearing loss, as they are stated by the Joint Committee on Infant Hearing, were found in more than 50% of the cases. Audiometry was performed in all cases, often supplemented with Auditory Brainstem Responses and/or click-evoked otoacoustic emissions, while other diagnostic investigations (imaging, genetics, etc.) were only variably performed. Finally, the authors confirm the need for universal neonatal screening, which only recently started in Belgium, and suggest that a detailed protocol should be established to pursue a coherent diagnostic policy.

Computerized analysis of resorbable polymer plates and screws for the rigid fixation of mandibular angle fractures

PURPOSE

This computer-based study used finite element analysis (FEA) to assess whether rigid fixation by resorbable polymer plates and screws can provide the required stiffness and strength for a typical mandibular angle fracture.

MATERIALS AND METHODS

Two separate 3-dimensional FEA models of the mandible were generated using 8-noded hexahedral elements. The jaw segments in 1 model were fixed with titanium plates and screws as those in common use today. The jaw segments in the other model were fixed with resorbable polymer plates and screws as used in a developmental product currently in trials. A commercial finite element solver was then applied to this mesh to compute stresses and bone interfragmentary displacements for both titanium fixation and resorbable fixation. Calculated displacements were compared with each other and to established norms for healthy bone regrowth. Calculated stresses were compared with the yield strength of each material. Finally, overall stress patterns in the fractured mandibles were compared with each other.

RESULTS

The study results indicate that titanium fixation more rigidly fixes the 2 bone segments in relative position. However, they also show that resorbable polymers provide sufficient stiffness to meet currently established norms for fracture immobility. Furthermore, the analyses show that resorbable polymers are capable of withstanding the stresses generated by the bite loads of postsurgical patients. The results indicate that mandibles, fixed with either titanium or resorbable materials, show nearly identical stress patterns.

CONCLUSIONS

The resorbable polymer-based plates and screws tested in this investigation are of adequate strength and stiffness for their successful application to the rigid fixation of mandibular angle fractures.

Ensembl 2002: accommodating comparative genomics

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

Cloned bullfrog skin sodium (fENaC) and xENaC subunits hybridize to form functional sodium channels

For many years the adult frog skin has been used as a model system to study transepithelial sodium transport. In other sodium transporting tissues the three homologous subunits of the sodium channel have been cloned. The aim of this study was to clone and characterize the amiloride inhibitable sodium channel (ENaC) in adult bullfrog (Rana catesbeiana) skin. Three transcripts corresponding to the alpha, beta, and gamma subunits of ENaC were cloned and sequenced. Co-expression of all three in Xenopus oocytes yielded a functional frog sodium channel (fENaC). Amiloride sensitivity and current voltage relationships suggested that its characteristics were similar to other ENaCs. Subunits from the Xenopus sodium channel (xENaC) and fENaC were combined in all possible triplets. Although functional amiloride inhibitable sodium channels were formed in every case, the amiloride sensitivities were not identical. Subunit combination studies suggested that the alpha subunit made a major contribution to amiloride sensitivity but interactions of beta and gamma were also seen. When the amiloride sensitivities of intact skin from adult R. catesbeiana and Xenopus laevis were compared, Rana also had a consistently higher affinity. Comparison of fENaC and xENaC sequences may provide insight into which amino acids beyond those already identified are critical for amiloride binding.

The Ensembl genome database project

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

The amount of scurfin protein determines peripheral T cell number and responsiveness

In the absence of the recently identified putative transcription factor scurfin, mice develop a lymphoproliferative disorder resulting in death by 3 wk of age from a pathology that resembles TGF-beta or CTLA-4 knockout mice. In this report, we characterize mice that overexpress the scurfin protein and demonstrate that these animals have a dramatically depressed immune system. Mice transgenic for the Foxp3 gene (which encodes the scurfin protein) have fewer T cells than their littermate controls, and those T cells that remain have poor proliferative and cytolytic responses and make little IL-2 after stimulation through the TCR. Although thymic development appears normal in these mice, peripheral lymphoid organs, particularly lymph nodes, are relatively acellular. In a separate transgenic line, forced expression of the gene specifically in the thymus can alter thymic development; however, this does not appear to affect peripheral T cells and is unable to prevent disease in mice lacking a functional Foxp3 gene, indicating that the scurfin protein acts on peripheral T cells. The data indicate a critical role for the Foxp3 gene product in the function of the immune system, with both the number and functionality of peripheral T cells under the aegis of the scurfin protein.

Aldosterone upregulates purinergic responses in larval amphibian skin epithelium

Bullfrog tadpoles respond to apical application of 100 microM amiloride, acetylcholine (ACh) or ATP with a sharp transient inward (apical to basolateral) cation current. In adult skin, amiloride blockable transepithelial Na+ transport is upregulated by the hormone aldosterone. Tadpoles were treated in vivo with aldosterone and changes in short circuit current (Isc) in response to apical application of ATP were determined. Bullfrog tadpoles were exposed to aldosterone (10(-6) M) for periods ranging from 3 h to 60 h. Skins from 60-h aldosterone-treated animals showed a two- to three-fold increase in apical ATP-activated short circuit current when compared to animals treated with vehicle alone. Sodium replacement with a large, nonpermeable cation resulted in no measurable increase in Isc after exposure to ligand, consistent with ATP activation of an inward cation current and not chloride efflux. Activation/desensitization time courses and treatment with blockers revealed no measurable differences between aldosterone-treated and non-treated skins. Activation by amiloride and ACh gave essentially identical results. Studies with RT/PCR showed significant increases over controls of levels of mRNA associated with P2X channels. Given these data, our working hypothesis is that all three ligands activate the same process that exhibits both purinergic and cholinergic characteristics. These data are consistent with aldosterone upregulation of ATP gated channels expressed in the apical membrane of larval frog skin.

Fluconazole for prophylaxis against candidal rectal colonization in the very low birth weight infant

BACKGROUND

Candidal infections are an important cause of morbidity and mortality in the very low birth weight (VLBW) infant. Current intervention focuses on treatment once candidal septicemia is either suspected or diagnosed. Studies have suggested that colonization with candidal species is an important risk factor for subsequent infection.

OBJECTIVE

To determine whether prophylactic fluconazole for the first 28 days of life results in a decreased incidence of candidal colonization in the VLBW infant.

RESEARCH DESIGN

Prospective, randomized, controlled, intention-to-treat design comparing prophylaxis with fluconazole versus placebo for the first 28 days of life.

SETTING

A tertiary level intensive care nursery in a major teaching hospital in Charleston, South Carolina.

PATIENTS

One hundred three infants with a birth weight of <1500 g, either inborn or outborn, who were admitted to the intensive care nursery between January 1998 and February 1999.

METHODS

Infants were enrolled within 72 hours of life with rectal cultures performed on the day of randomization (DOR), as well as day of life (DOL) 7, 14, and 28. Those infants with a birth weight of <1250 g had additional cultures on DOL 35, 49, and 56. Cultures were plated on selective media for isolation of candidal organisms. Infants were randomized to receive either fluconazole (6 mg/kg) or placebo on the DOR. Subsequent doses were given every 72 hours until DOL 7 and then every 24 hours until DOL 28. Medication was given either intravenously or by feeding tube once the infant had been gavage feeding for a 48-hour period without feeding intolerance. Aspartate aminotransferase and alanine aminotransferase levels were obtained on DOR and DOL 7, 14, and 28 to assess for fluconazole toxicity. The minimal inhibitory concentration to fluconazole was determined for all positive cultures to assess the development of resistance.

RESULTS

The infants who received fluconazole (n = 53) and placebo (n = 50) had no statistical difference in the major risk factors known to increase the chances of candidal septicemia in the VLBW infant. Rectal colonization by candidal species was detected in 8 of the 53 fluconazole-treated patients (15.1%) and in 23 of the 50 infants treated with placebo (46%). Fluconazole significantly reduced rectal colonization from DOL 14 through DOL 56 in all infants with a birth weight of <1250 g, and from DOL 14 through DOL 56 in all infants with a birth weight of 1250 to 1500 g. Alanine aminotransferase levels were higher in the fluconazole versus the placebo-treated group on DOL 14 (18.1 IU/L vs 15 IU/L), but no clinically significant abnormalities were observed. Candida albicans was the most common species isolated. There was no increase in species of Candida noted for their intrinsic resistance to fluconazole, and there was no statistically significant difference in the minimal inhibitory concentrations to fluconazole for all C albicans isolates in either group at any period.

CONCLUSION

Prophylactic administration of fluconazole to the VLBW infant for the first 28 days of life is safe and results in a decreased risk of rectal colonization by candidal species. Larger studies to determine the effect of prophylaxis on candidal septicemia and development of resistance in such a selective high-risk group are warranted before initiation of routine prophylaxis.fluconazole, very low birth weight infant, prophylaxis, candidal sepsis, sensitivities to fluconazole.

N-Acetylaspartate and creatine levels measured by (1)H MRS relate to recognition memory

OBJECTIVES

To investigate the relationship between recognition memory and metabolite levels in medial structures of the temporal lobes in the living human brain.

METHODS

Proton MRS ((1)H MRS) and the intracarotid amobarbital test were performed in 16 epileptic patients found suitable for temporal lobectomy. All patients had mesial temporal sclerosis. Metabolite ratios between N:-acetylaspartate (NAA), creatine and phosphocreatine (Cr + PCr), and choline-containing compounds (Cho) [NAA/(Cr + PCr), NAA/Cho, and NAA/(Cr + PCr + Cho)] were calculated for (1)H MRS voxels that included the amygdala, anterior half of the hippocampus, and underlying subiculum. Metabolite ratios were correlated with unilateral memory scores estimated by the intracarotid amobarbital test for words, objects, faces, and total score.

RESULTS

The total memory score, memory for objects and faces, and NAA/(Cr + PCr) were significantly lower for the hemisphere ipsilateral to the resection. The asymmetry indexes for NAA/(Cr + PCr) correlated with asymmetry indexes for words (rho = 0.82, p = 0.0001) and total memory (rho = 0. 72, p = 0.002). Analysis of memory scores and metabolite ratios from all 32 hemispheres revealed a correlation between NAA/(Cr + PCr) and memory for words (rho = 0.45, p = 0.009). A correlation between memory for words and NAA/(Cr + PCr) existed in the contralateral (rho = 0.58, p = 0.019) and in the right (rho = 0.51, p = 0.045) hemispheres, and a trend was found in the left hemispheres (rho = 0. 48, p = 0.06).

CONCLUSION

There is a correlation between memory for words and the NAA/(Cr + PCr) ratio from medial temporal structures in patients with mesial temporal sclerosis. The findings suggest that medial temporal structures and adjacent neocortex play a significant role in recognition memory in humans, particularly for words.

Cerebellar ataxia, anterior horn cell disease, learning difficulties, and dystonia: a new syndrome

The following case reports describe a new condition of cerebellar ataxia, anterior horn cell disease, dystonia, and learning difficulties. Four cases are described. The condition appears to be of autosomal recessive inheritance as the group is made up of two pairs of sisters. All cases were evident by 3 years of age. Anterior horn cell disease was of a type not previously described at this age in association with cerebellar ataxia. Further genetic studies suggest the condition is not allelic with spinal muscular atrophy having no evidence of deletion of the survival motor neurone gene.

Unilateral lesions of the globus pallidus: report of four patients presenting with focal or segmental dystonia

OBJECTIVES

To interpret clinical features after unilateral lesions of the globus pallidus on the basis of physiology of the basal ganglia.

METHODS

Four patients with unilateral lesions in the globus pallidus (GP) were clinically examined and the literature on patients with pallidal lesions was reviewed.

RESULTS

Three patients presented with contralateral dystonia largely confined to one arm in one case and one leg in two cases. One patient had predominant contralateral hemiparkinsonism manifested mainly as micrographia and mild dystonia in one arm. The cause of the lesions was unknown in two patients. In the other two symptoms had developed after head trauma and after anoxia. All lesions involved the internal segment of the GP. Two patients, including the patient with hemiparkinsonism, had additional involvement of the external segment of the GP. In the literature reports on 26 patients with bilateral lesions restricted to the GP only two with unilateral lesions were found. The patients with bilateral pallidal lesions manifested with dystonia, parkinsonism, or abulia. One of the patients with unilateral GP lesions had contralateral hemidystonia, the other contralateral arm tremor.

CONCLUSION

These cases emphasise the importance of the GP, particularly its internal segment, in the pathophysiology of dystonia.

Effects of three different doses of a bolus injection of gadodiamide: assessment of regional cerebral blood volume maps in a blinded reader study

BACKGROUND AND PURPOSE

Reconstruction of first-pass bolus information to derive regional cerebral blood volume (rCBV) maps is commonly performed in many centers; however, various protocols with different doses of paramagnetic contrast injections have been reported. We evaluated the dose dependency of rCBV maps in a brain tumor population by using three different doses of gadodiamide injection to evaluate their diagnostic accuracy in blinded reader sessions.

METHODS

Eighty-three patients with intraaxial brain tumors (72 gliomas) were studied at three centers and randomized to receive a bolus injection of 0.1, 0.2, or 0.3 mmol/kg per body weight of gadodiamide. rCBV maps were generated from T2*-weighted gradient-echo echoplanar sequences at 1.5 T. Data processing was performed according to the indicator dilution theory.

RESULTS

The mean contrast-to-noise ratio (CNR) was significantly different between gadodiamide doses of 0.1 and 0.2 mmol/kg (CNR = 8.7 and 15.7) and between 0.1 and 0.3 mmol/kg (CNR = 17.7). No significant difference was found between doses of 0.2 and 0.3 mmol/kg. Sensitivity for the differentiation of benign and malignant brain tumors was 80%, 95%, and 91%, and specificity was 45%, 54%, and 43% by blinded readings at 0.1, 0.2, and 0.3 mmol/ kg, respectively, as compared with histologic findings. Nonblinded readings had a sensitivity of 83%, 100%, and 90% and a specificity of 82%, 100%, and 73% at 0.1, 0.2, and 0.3 mmol/kg, respectively.

CONCLUSION

A dose of 0.2 mmol/kg of gadodiamide is recommended for reconstruction of rCBV maps if data are acquired with the T2*-weighted protocol described.

Haemochromatosis: novel gene discovery and the molecular pathophysiology of iron metabolism

The application of molecular genetics to haemochromatosis and experimental mutagenesis in animals has transformed our capacity to investigate the unique physiology of iron homeostasis-a key problem in biology and medicine. The identification of HFE, the principal determinant of adult haemochromatosis (HFE1; OMIM 235200) and TfR2, recently implicated in a rarer form of the inherited disorder (HFE3; OMIM 604250), and the promise of candidate genes for juvenile haemochromatosis (HFE2; OMIM 602390) and neonatal haemochromatosis (OMIM 231100) provide the foundation for important studies into the control mechanism of iron balance in humans. The rare conditions atransferrinaemia (OMIM 209300) and acaeruloplasminaemia (OMIM 604290), each associated with tissue iron overload, have already implicated the iron transport ligand transferrin and the copper transporter caeruloplasmin in the control of iron homeostasis. Gene mapping studies in animal mutants with anaemia due to defects in the uptake or tissue transfer of iron have yielded novel proteins involved in iron transport: DMT1 (brush border transporter of ferrous iron) in the mk/mk mouse, hephaestin (basolateral multi-copper ferroxidase) in the sex-linked anaemic mouse (sla) and ferroportin1 (basolateral iron exporter) in zebrafish weh mutants. The discovery of genes that determine heritable defects of iron absorption and regulation in animals and humans thus holds promise for a complete mechanistic understanding of the molecular pathophysiology of iron metabolism.

Positron emission tomography in imaging spinal cord tumors

The ability of positron emission tomography (PET) to detect spinal cord tumors was studied prospectively in 14 patients presenting over a 5-year period. Abnormal uptake by [18F]-fluorodeoxyglucose (FDG) or 11C-methionine was detected in all except one. These data were assessed in relation to magnetic resonance imaging (MRI) findings with regard to tumor type and extent preoperatively, findings at operation, and subsequent clinical course. The group consisted of six astrocytomas, five ependymomas, one mixed ependymoma and astrocytoma, one schwannoma, and one ganglioglioma, all confirmed histologically. This is the largest study comparing spinal PET to MRI. Accurate preoperative correlation between PET and MRI was found in all eight patients scanned at first presentation. The PET uptake was in keeping with the low-grade histology of the tumors. Postoperatively, PET and MRI findings were in agreement in nine patients. In eight of these the findings were in keeping with the subsequent clinical course. In three patients, however, the PET findings were at variance with the clinical course and MRI findings. In one, persistent FDG uptake after radiotherapy was seen where there was subsequent tumor resolution. In two patients with low-grade astrocytomas, scanned with FDG and 11C-methionine, respectively, tracer was not taken up by residual tumor. In this small group of patients, PET did not provide additional useful information. This could be because all tumors studied were low grade and the limited spatial resolution of PET does not lend itself to imaging small spinal cord tumors. The prospective study of larger numbers of patients with a wider range of tumor types is required, but this might be difficult to achieve given the rarity of spinal cord tumors.

Sequence analysis of bacterial DNA in the colon and stomach of the Tyrolean Iceman

The male human body found in an Alpine glacier on September 19, 1991 ("Tyrolean Iceman") has, for the first time in history, given scientists a chance to perform detailed anatomical, histological, and molecular investigations on the organs of a person from the Neolithic Age (5350-5100 B.P.). In the present study, tissue samples aseptically taken from the stomach and the colon of the mummy were utilized for DNA extraction, and the DNA was PCR-amplified, using primer pairs designed to bind to fragments of the 16s ribosomal RNA gene (16s rDNA) of a broad range of bacteria. The PCR products were cloned in plasmid vectors, and the recombinant clones (amplicons) were sequenced. The sequence data were finally used for scanning data libraries containing the corresponding sequences of present-day bacteria, to infer the putative ecophysiology of the ancient ones. The same procedure was repeated on some fragments of grass from the clothing found near the corpse. These fragments were taken as a control of the microbiological situation of the glacier. The results show that the flora of the Iceman's stomach is entirely composed of Burkholderia pickettii, an organism commonly found in aquatic habitats. The colon, on the other hand, contains several members of the fecal flora of humans, such as Clostridium perfringens, C. ghonii, C. sordellii, Eubacterium tenue, and Bacteroides sp. The Iceman's colon, however, was found to contain, rather unexpectedly, also some members of the genus Vibrio. The results are discussed in light of what is known about the preservation of microbial DNA at the Iceman's site and of previous parasitological studies performed on the Iceman himself and on human coprolites.

Novel oral treatment of Gaucher's disease with N-butyldeoxynojirimycin (OGT 918) to decrease substrate biosynthesis

BACKGROUND

Current treatment for Gaucher's disease involves administration of intravenous glucocerebrosidase to degrade glucocerebroside stored in lysosomes. Lowering the rate of biosynthesis of glucocerebroside should decrease accumulation of this substrate. We investigated the safety and efficacy of OGT 918 (N-butyldeoxynojirimycin), an inhibitor of glucosyltransferase, as a novel oral treatment for non-neuronopathic Gaucher's disease.

METHODS

We recruited, into a 1-year open-label study, 28 adults (seven with previous splenectomies) from four national Gaucher's referral clinics, who were unable or unwilling to receive enzyme treatment. We measured liver and spleen volume by computed tomography or magnetic resonance imaging at baseline and at months 6 and 12, and biochemical and haematological variables monthly, including chitotriosidase activity (a sensitive marker of Gaucher's disease activity). Patients were started on 100 mg oral OGT 918 three times daily.

FINDINGS

Baseline liver volumes were 1.1-2.7 times normal and spleen volumes 5.1-24.8 times normal. At 12 months, mean liver and spleen volumes were significantly lowered by 12% (95% CI 7.8-16.4) and 19% (14.3-23.7), respectively (each p<0.001). Haematological variables improved slightly. Mean organ volume and blood counts improved continually between 6 months and 12 months of treatment. Mean chitotriosidase concentrations fell by 16.4% over 12 months (p<.0001). Six patients withdrew because of gastrointestinal complaints (two), personal reasons (two), or severe pre-existing disease (two). The most frequent adverse effect was diarrhoea, which occurred in 79% of patients shortly after the start of treatment.

INTERPRETATION

Decrease of substrate formation by OGT 918 improves key clinical features of non-neuronopathic Gaucher's disease. The strategy justifies further trials in this and other glycosphingolipid storage disorders.

Diversity of Microorganisms Isolated from Amber

> Abstract Claims that organisms can be cultured from amber, if substantiated, would be significant contributions to our understanding of the evolution, tenacity, and potential spread of life. Three reports on the isolation of organisms from amber have been published. Cano and Borucki recently reported the isolation of Bacillus sphaericus and Lambert et al. have described a new species designated Staphylococcus succinus from 25-40 million year old Dominican amber. These characterized organisms were phylogenetically distant from extant relatives and the Staphylococcus sp. sufficiently far removed from other extant staphylococci to be considered a new species. Here we report the culture of bacteria from Dominican and previously untested 120 million year old Israeli (Lebanese lode) amber. Twenty-seven isolates from the amber matrix have been characterized by fatty-acid profiles (FAME) and/or 16S rRNA sequencing. We also performed a terminal restriction fragment pattern (TRF) analysis of the original amber before prolonged culture by consensus primer amplification of the 16S rRNA followed by restriction enzyme digestion of the amplicons. Sample TRFs were consistent with a sparse bacterial assemblage and included at least five of the isolated organisms. Finally, we microscopically mapped the internal topography of an amber slice.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p58.html

System memory in violent incidents: evidence from patterns of reoccurrence

For 20% of a sample of 1,078 violent incidents reported in British bars and pubs, another incident was reported at the same premises within 6 months. Log-survival analysis revealed nonrandom sequences that demonstrate a system memory effect separate from any biases involving particular venues. The rate of reoccurrence was not constant during the 6 months following incidents but was significantly higher for Weeks 1-4, approximated to the mean value for Weeks 5-12, and declined for Weeks 13-26. Reoccurrence was particularly likely in the first 3-4 days after an incident. Risk of reoccurrence was further increased for incidents that involved either threats or the exit and return of the assailants within that original incident. Results support the view that "violence breeds violence" and demonstrate the need for increased staff vigilance for up to 12 weeks following a violent incident, and particularly during the first few days and weeks.

Interictal regional slow activity in temporal lobe epilepsy correlates with lateral temporal hypometabolism as imaged with 18FDG PET: neurophysiological and metabolic implications

OBJECTIVES

The phenomenon of interictal regional slow activity (IRSA) in temporal lobe epilepsy and its relation with cerebral glucose metabolism, clinical data, MRI, and histopathological findings was studied.

METHODS

Interictal 18F-fluorodeoxyglucose positron emission tomography (FDG PET) was performed under continuous scalp EEG monitoring in 28 patients with temporal lobe epilepsy not associated with intracranial foreign tissue lesions, all of whom subsequently underwent resective surgery. Regions of interest (ROIs) were drawn according to a standard template. IRSA was considered lateralised when showing a 4:1 or greater ratio of predominance on one side.

RESULTS

Sixteen patients (57%) had lateralised IRSA which was always ipsilateral to the resection and of maximal amplitude over the temporal areas. Its presence was significantly related to the presence of hypometabolism in the lateral temporal neocortex (p=0.0009). Logistic regression of the asymmetry indices for all measured cerebral regions confirmed a strong association between IRSA and decreased metabolism of the posterior lateral temporal neocortex only (p=0.009). No significant relation could be shown between slow activity and age at onset, duration of the epilepsy, seizure frequency, and MRI evidence for hippocampal atrophy. Furthermore, IRSA was not specifically related to mesial temporal sclerosis or any other pathology.

CONCLUSIONS

Interictal regional slowing in patients with temporal lobe epilepsy not associated with a mass lesion is topographically related to the epileptogenic area and therefore has a reliable lateralising, and possibly localising, value. Its presence is irrelevant to the severity or chronicity of the epilepsy as well as to lateral deactivation secondary to neuronal loss in the mesial temporal structures. Although slow EEG activity is generally considered as a non-specific sign of functional disturbance, interictal regional slowing in temporal lobe epilepsy should be conceptualised as a distinct electrographic phenomenon which is directly related to the epileptogenic abnormality. The strong correlation between interictal regional slowing and lateral temporal hypometabolism suggests in turn that the second may delineate a field of reduced neuronal inhibition which can receive interictal and ictal propagation.

Independent recovery of memory and language functioning during the Intracarotid Sodium Amytal Test

Memory and language recovery during the Intracarotid Sodium Amytal Test (IAP) was investigated in 49 left-hemisphere-dominant patients with unilateral temporal epileptic seizure foci. Memory was assessed by presenting items (words, objects, and faces) immediately after injection, and testing for recognition memory 10 min after motoric recovery. To assess language the patients responded verbally to the same items during memory presentation. Memory for the individual items was found to be independent of their presentation order and language functioning was impaired only with the dominant-hemisphere injection, recovering during the presentation of the memory items. These results suggest that the encoding of material remains at a constant level throughout the initial active phase of the IAP, whereas language functioning recovers independently.

Neuroimaging and spectroscopy in children with epileptic encephalopathies

AIMS

To investigate the nature of the unifocal cortical abnormalities on FDG positron emission tomography (PET) in children with an epileptic encephalopathy but no focal abnormality on electroencephalogram or standard magnetic resonance imaging (MRI).

METHODS

Repeat FDG PET, surface rendered high resolution MRI, and single voxel magnetic resonance proton spectroscopy of the areas of abnormal metabolism compared to the contralateral side in 11 children aged 2 to 12 years. Imaging was repeated after a median of 13 months.

RESULTS

Visual analysis of repeat FDG PET revealed similar abnormalities in 10 of 11 children. Semiquantitative analysis revealed similar sited abnormalities in eight children. One child with ictal hypermetabolism initially had an inconsistent second scan. Magnetic resonance spectra in three children showed the N-acetyl-aspartate/choline ratio was lower in the hypometabolic focus than in the reciprocal area on the opposite side, in two children it was higher, and in one child it was equal. Surface rendered MRI was normal in seven of eight children, and showed temporal lobe asymmetry in one.

CONCLUSION

In children with established epileptic encephalopathies most hypometabolic areas on FDG PET are stable over time. While focal neuronal loss is likely in these areas in some children, microdysplasias or other focal cortical dysplasias are probable in others.

Staphylococcus succinus sp. nov., isolated from Dominican amber

Two bacterial isolates, designated AMG-D1T and AMG-D2, were recovered from 25-35-million-year-old Dominican amber. AMG-D1T and AMG-D2 biochemically most closely resemble Staphylococcus xylosus; they differ physiologically from other staphylococci. Fatty acid analysis and comparisons with extensive databases were unable to show relatedness to any specific taxon. Moreover, AMG-D1T and AMG-D2 contain tuberculostearic acid and meso-diaminopimelic acid, characteristic of the G + C-rich coryneform bacteria, as opposed to L-lysine characteristic of staphylococci. AMG-D1T and AMG-D2 have a G + C ratio of 35 mol%. Phylogenetic analysis with the 16S rRNA gene indicated that AMG-D1T and AMG-D2 were most closely related to Staphylococcus equorum, S. xylosus, Staphylococcus saprophyticus and other novobiocin-resistant staphylococci. Stringent DNA-DNA hybridization studies with AMG-D1T revealed similarities of 38% with S. equorum, 23% with S. xylosus and 6% with S. saprophyticus. The results indicate that AMG-D1T and AMG-D2 represent a novel species, which was named Staphylococcus succinus sp. nov. The type strain of the new species is AMG-D1 (ATCC 700337).

Temporal architecture of violent incidents

Five hundred five reports of violent incidents in British pubs and bars were studied by using logical pathway modeling to provide information on the processes underlying work-related violence. Logical pathway modeling is innovative in examining and mapping sequences in real incidents at a population level. The data reveal the most common pathway to be misbehavior by customers, intervention by staff (before any physically violent act), physical attack on staff, and injury to staff. The data also highlight the likelihood of further action after assailants have exited and identify stages in incidents at which most staff and customer injuries and damage to property occur. Results assist in the design of strategies to reduce the risk from future violence, particularly by training staff to recognize and to handle potentially violent situations and to maintain vigilance and security following problem incidents.

Amiloride analog stimulation of short-circuit current in larval frog skin epithelium

The skin of the bullfrog Rana catesbeiana tadpole contains an apical non-selective cation channel that is activated by amiloride. This is in contrast to the adult skin, which has a highly Na+-selective channel that is blocked by amiloride. The purpose of the present study was to characterize further the nature of the tadpole channel using amiloride and its analogs benzamil, dimethyl amiloride (DMA), 5-(N-ethyl-N-isopropyl)-amiloride (EIPA) and methyl isobutyl amiloride (MIBA). Tadpole skins were mounted in modified Ussing chambers with Ca2+-free KCl or NaCl Ringer on the apical side and standard NaCl Ringer (containing 2 mmol l-1 Ca2+) on the basolateral side. Drugs were added to the apical solution at concentrations between 0.1 and 1000 micromol l-1. Amiloride caused the short-circuit current (Isc) to increase rapidly from near zero to a peak of approximately 30-50 microA and then to decline back towards zero over several seconds. The peak response was largest at 100 micromol l-1. The rate of decline was noticeably faster at the higher concentrations. Benzamil and DMA had similar time courses to amiloride, but with smaller effects on Isc. The largest peak responses occurred at 5-50 micromol l-1. EIPA and MIBA gave small responses at 1-10 micromol l-1 and, at higher concentrations (50-500 micromol l-1), the responses consisted of rapid, small increases in Isc followed by rapid decreases. The largest peak response occurred at 10 micromol l-1 for both drugs. After apical membrane resistance had been reduced by nystatin, addition of analogs to the apical solution caused no change in Isc or transepithelial resistance. This suggests that the decline in Isc after amiloride analog treatment was not due to increases in the resistance of the basolateral membrane. N-(6-Aminohexyl)-5-chloro-1-naphthalenesulfonamide hydrochloride (W-7) blocked stimulation by all of the analogs. These data are consistent with amiloride analogs acting as both activators and inhibitors of short-circuit current in tadpole skin and extend the list of ligands that activate these channels.

Psychosocial factors predicting employee sickness absence during economic decline

Psychosocial factors such as work characteristics, life events, social support, and personality were examined as predictors of the change in medically certified sickness absence observed during a period of severe economic decline. Longitudinal data, derived from self-reports and register-based information relating to 763 local government employees, were collected at 3 points during a 5-year period: before the economic decline, during the nadir of that decline, and immediately after the nadir. After the effects of prior absence and demographic and lifestyle variables had been partialed out, the results of multiple Poisson regression analyses showed that work characteristics play a major role in forthcoming sickness absences. Negative life events and the personality trait sense of coherence (in women) also predicted forthcoming absence rate. Social support did not relate to absences either in men or in women.

Nurses' evaluations of sources of information about HIV and AIDS

Reviews of the literature indicate that nurses feel ill-informed about HIV/AIDS and that poor knowledge is associated with anxiety and negative attitudes towards infected patients and their care. Although some studies have sought to identify the sources of HIV/AIDS information available to nurses, few have attempted to understand how nurses evaluate such sources. In this study in 1992, 15 sources of HIV/AIDS information were identified during group discussions with nursing staff and nurse tutors. 277 nursing staff evaluated each of the sources in terms of perceived frequency (how often the source is used) and six items chosen to assess the usability and usefulness of each source (e.g. how informative the source is, how easy it is to understand). The results indicate that in-service training, basic training and professional colleagues are the sources evaluated most highly while posters and advertisements, television and radio and popular newspapers are the most frequently used sources of information. Trades unions' journals and pamphlets are the least frequently used sources of information and receive only modest evaluations. 20% of respondents report never having received any training regarding HIV and AIDS. Implications for the future provision of HIV/AIDS information and directions for further research are discussed.

The effectiveness of psychiatric treatment for HIV-infected patients

The study sought to determine the effectiveness of a model program of psychiatric care for human immunodeficiency virus (HIV)-infected patients. This was a cohort study of 126 HIV-positive outpatients referred for psychiatric evaluation and treatment (average follow up of 14 months) in a HIV-dedicated primary-care outpatient clinic in the inner city. A global outcome measure (encompassing symptom relief, functioning, and HIV-risk behaviors), and a measure of abstinence from alcohol and illicit substances were used. Fifty percent of patients improved, with 19% "nearly well" at follow-up. Abstinence was achieved 48% of the time. Good compliance with treatment and the absence of injection drug use were the primary predictors of good outcomes. Of the compliant patients, 94% improved, with 45.7% being nearly well. Psychiatric treatment of HIV-infected patients is effective when located in the HIV primary-care setting and administered by a multidisciplinary team under the direction of a psychiatrist, using evidence-based interventions.

Central corneal thickness in normal, glaucomatous, and ocular hypertensive eyes

OBJECTIVE

To determine the relationship between central corneal thickness (CCT) and applanation intraocular pressure (IOP) in normal, glaucomatous, and ocular hypertensive eyes.

METHODS

One hundred nine subjects (184 eyes) were studied. Forty-eight patients (74 eyes) had glaucoma, 28 patients (51 eyes) had ocular hypertension, and 33 patients (59 eyes) were normal. Intraocular pressure as measured by applanation tonometry, refractive status, CCT, and axial length were measured for all subjects.

RESULTS

The CCT (mean +/- SD) of eyes with ocular hypertension was significantly greater (0.606 +/- 0.041 mm) than that of glaucomatous eyes (0.554 +/- 0.022 mm) (P < .001) or of normal controls (0.561 +/- 0.026 mm) (P < .001). There was no significant difference in CCT between normal and glaucomatous eyes (P = .40). The axial length (mean +/- SD) of eyes with ocular hypertension (23.54 +/- 1.34 mm) was not different compared with glaucomatous eyes (23.93 +/- 0.96 mm) (P = .13) or normal eyes (23.62 +/- 1.21 mm) (P = .83). There was no significant difference between the axial length for glaucomatous eyes compared with normal eyes (P = .18). Those eyes with glaucoma being treated with topical dorzolamide hydrochloride had a significantly increased CCT (0.560 +/- 0.025 mm) compared with those eyes with glaucoma not being treated with dorzolamide (0.551 +/- 0.20 mm) (P = .02).

CONCLUSIONS

The mean CCT is increased in eyes with ocular hypertension when compared with normal or glaucomatous eyes, which confirms the findings of other investigators. Increased CCT may give an artificially high IOP measurement by applanation tonometry. The CCT must be considered when developing a treatment approach for patients with ocular hypertension.

Progressive facial hemiatrophy: MRI appearances

The cranial CT and MRI appearances of a 14-year-old girl with Parry-Romberg syndrome and epilepsy are described. The findings are compared with the two published descriptions of MRI and CT in such patients. MRI appearances in our patient differ from those published and may be consistent with a vascular malformation. The one published report on the intracranial histopathology of a patient with Parry-Romberg syndrome and epilepsy states that a microscopic vascular malformation was found. We discuss the relationship between radiological and pathological findings. The possible aetiologies of Parry-Romberg syndrome (vascular malformation, immunological, trauma, sympathetic innervation, hereditary, slow virus) are discussed. We suggest that Parry-Romberg syndrome could be regarded as a neurocutaneous syndrome, a component of which includes intracerebral vascular dysplasia. In this and the other three cases of Parry-Romberg syndrome with epilepsy, the sensitivity of MRI in detecting intracranial lesions is demonstrated. Recommendations for imaging these patients are proposed.

Histologic, molecular, and radiologic characterization of resolving cerebral posttransplant lymphoproliferative disorder

Lymphoproliferative disorders (LPDs) are commoner in pediatric versus adult immunosuppressed transplant recipients, and frequently involve the central nervous system. In these circumstances, the justification for biopsy is heavily influenced by the likely diagnostic yield. The present study centers on a 12-y-old renal transplant patient who developed multifocal cerebral LPD and had serial magnetic resonance (MR) examinations during the course of her illness from which she has completely recovered upon reduction of immunosuppression. She underwent stereotaxic biopsy, which was analyzed by both immunocytochemistry and polymerase chain reaction to examine the general question of how to release the maximum amount of information contained within, as well as to obtain a tissue diagnosis in this particular case. We show that a combination of these methods permits identification of the immunophenotype, lineage, clonality, viral involvement, and origin of abnormal cellular infiltrates. The biopsy also showed a novel histologic pattern of LPD, comprising numerous benign T cells obscuring a tiny clone of B cells. The MR examinations documented, for the first time, the differences in signal that accompany clinical resolution at both biopsied and nonbiopsied sites, showing that the latter may be associated with reduction, but not elimination, of MR signal abnormality. We conclude: 1) a combination of conventional and polymerase chain reaction analysis offers the greatest diagnostic yield from stereotaxic biopsies, even when the available tissue is minimal; 2) a focal polyclonal T cell infiltrate should prompt further investigation to exclude an underlying B cell lesion.

Focal abnormalities detected by 18FDG PET in epileptic encephalopathies

A prospective study of 32 children with epileptic encephalopathies 12 years or younger revealed a high incidence of focal cortical metabolic defects on 18-fluorodeoxyglucose positron emission tomography (PET) not suspected from clinical, EEG, or magnetic resonance imaging findings. PET scans were normal in all five children with typical de novo Lennox-Gastaut syndrome but showed cortical metabolic abnormalities in three out of four with atypical de novo Lennox-Gastaut syndrome, five out of six with Lennox-Gastaut syndrome following infantile spasms, six out of eight with severe myoclonic epilepsy in infancy, one out of two with epilepsy with myoclonic-astatic seizures, and four out of six with an unclassified epileptic encephalopathy. This suggests that some children with epileptic encephalopathies previously thought to have primary generalised seizures or seizures due to multifocal pathology may have unifocal cortical origin for their seizures. Such an origin may be amenable to surgery.

Episodic memory dysfunction during sodium amytal testing of epileptic patients in relation to posterior cerebral artery perfusion

The effect of filling of the posterior cerebral artery (PCA) on memory performance during the intracarotid sodium amytal test (IAP) was investigated in 57 patients with unilateral temporal epileptic seizure foci under consideration for surgical therapy. Memory functioning was tested following injection of the internal carotid artery contralateral and ipsilateral to the side of seizure focus. In both cases, patients with PCA filling observed using conventional angiography showed a greater memory deficit, although this effect was more robust with contralateral injections. In a subsample of patients with left hemisphere dominance for language, the effect of PCA filling on memory performance was only significant when the right hemisphere was injected. The implications of these findings are discussed in terms of the validity of the IAP test and the different factors that need to be taken into account when interpreting IAP memory performance.

The alpha-1,3-galactosyltransferase knockout mouse. Implications for xenotransplantation

Organ xenografts in discordant combinations such as pig-to-man undergo hyperacute rejection due to the presence of naturally occurring human anti-pig xenoantibodies. The galactose alpha(1,3)-galactose epitope on glycolipids and glycoproteins is the major porcine xenoantigen recognized by these xenoantibodies. This epitope is formed by alpha(1,3)-galactosyltransferase, which is present in all mammals except man, apes, and Old World monkeys. We have generated mice lacking this major xenoantigen by inactivating the alpha(1,3)-galactosyltransferase gene. These mice are viable and have normal organs but develop cataracts. Substantially less xenoantibody from human serum binds to cells and tissues of these mice compared with normal mice. Similarly, there is less activation of human complement on cells from mice lacking the galactose alpha(1,3)-galactose epitope. These mice confirm the importance of the galactose alpha(1,3)-galactose epitope in human xenoreactivity and the logic of continuing efforts to generate pigs that lack this epitope as a source of donor organs.

Mammalian AMP-activated protein kinase subfamily

The mammalian 5'-AMP-activated protein kinase (AMPK) is related to a growing family of protein kinases in yeast and plants that are regulated by nutritional stress. We find the most prominent expressed form of the hepatic AMPK catalytic subunit (alpha 1) is distinct from the previously cloned kinase subunit (alpha 2). The alpha 1 (548 residues) and alpha 2 (552 residues) isoforms have 90% amino acid sequence identity within the catalytic core but only 61% identity elsewhere. The tissue distribution of the AMPK activity most closely parallels the low abundance 6-kilobase alpha 1 mRNA distribution and the alpha 1 immunoreactivity rather than alpha 2, with substantial amounts in kidney, liver, lung, heart, and brain. Both alpha 1 and alpha 2 isoforms are stimulated by AMP and contain noncatalytic beta and gamma subunits. The liver alpha 1 isoform accounts for approximately 94% of the enzyme activity measured using the SAMS peptide substrate. The tissue distribution of the alpha 2 immunoreactivity parallels the alpha 2 8.5-kilobase mRNA and is most prominent in skeletal muscle, heart, and liver. Isoforms of the beta and gamma subunits present in the human genome sequence reveal that the AMPK consists of a family of isoenzymes.

Studies evaluating the antitumor activity and toxicity of interleukin-15, a new T cell growth factor: comparison with interleukin-2

Interleukin-15 is a new cytokine that stimulates the proliferation of T cells and other cells of the immune system. Some of the biological properties of interleukin-15 overlap that of interleukin-2. Using murine models, the present studies have shown that interleukin-15, in vivo, is three to four times more potent than interleukin-2 in generating cytolytic effector splenocytes that lyse YAC target cells. It is approximately one-third as potent as interleukin-2 in inducing specific cytolytic cells that lyse allogeneic target cells. Interleukin-15 is approximately half as potent as interleukin-2 in suppressing pulmonary metastasis induced by MCA-205 tumor cells. The dose of interleukin-15 required to induce pulmonary vascular leak in mice is six times higher than that required for interleukin-2. These results support the view that interleukin-15 exhibits a therapeutic index that is superior to interleukin-2.

White matter signal hyperintensities in the brains of patients with late paraphrenia and the normal, community-living elderly

We determined the prevalence and anatomical location of areas of white matter hyperintensity visualized by magnetic resonance imaging in the brains of 38 late paraphrenic patients with an onset of psychotic illness after the age of 60 and 31 healthy aged community volunteers. All degrees of white matter signal hyperintensity were very common in both groups, and there was no excess of such changes in the brain of patients. Periventricular white matter and subcortical grey matter hyperintensities were significantly associated with both measured diastolic and systolic blood pressure in patients and control subjects. Periventricular and deep white matter, together with subcortical grey matter hyperintensities, were significantly associated with increased age. The excess of such presumed brain-imaging abnormalities previously reported in patients with an onset of psychosis late in life may be a consequence of earlier authors' failure to include examination of appropriate community control populations and to carefully exclude patients with evidence of stroke.

Catalytic subunits of the porcine and rat 5'-AMP-activated protein kinase are members of the SNF1 protein kinase family

The 5'-AMP-activated protein kinase (AMPK) regulates the fatty acid and sterol synthesizing pathways via phosphorylation of acetyl-CoA carboxylase and HMG-CoA reductase, respectively. Highly purified kinase from porcine liver contains three apparent subunits of molecular mass 63 kDa, 40 kDa and 38 kDa. Peptide sequencing of the 63 kDa protein (AMPK63cat) revealed that this polypeptide is the catalytic subunit of the kinase. Porcine peptide sequences were used to clone by RT-PCR partial length cDNAs for the catalytic domains of the porcine AMPK63cat, and its rat homolog, which were virtually identical in deduced amino acid sequence. Screening of a rat liver cDNA library with these partial length cDNAs and with degenerate oligonucleotides yielded several unique clones, some of which had a 142 bp deletion in the catalytic domain of the kinase. A consensus full-length sequence with a 1.7 kb open reading frame has been constructed from overlapping library and PCR-derived clones. A large mRNA for rat AMPK63cat (8.5 kb) is expressed in nearly all rat tissues, with highest levels detectable in heart and skeletal muscle. Using PCR, the presence of two mRNA species with or without the 142 bp deletion in the catalytic domain was noted in all rat tissues examined. Comparison of the deduced protein sequence of AMPK63cat reveals highly conserved homologies in both the catalytic and non-catalytic domains to several members of the SNF1 kinase family, including kinases from Arabidopsis, barley, rye, and S. cerevesiae, as well as to other mammalian kinases and to a C. elegans kinase. The high evolutionary conservation of both kinase structure and function (metabolite sensing) coupled with their pattern of tissue/organism expression suggest that the mammalian members of this kinase family likely play wider roles than the regulation of cellular lipid metabolism.