Clinical value of amino acid imaging in paediatric brain tumours

Purpose: To evaluate single photon emission computed tomography (SPECT) using the amino acid l-3-[123I]-α-methyl tyrosine (IMT) and contrast enhanced magnetic resonance imaging (MRI) as diagnostic tools in primary paediatric brain tumours in respect of non-invasive tumour grading. Patients, materials, methods: 45 children with primary brain tumours were retrospectively evaluated. IMT uptake was quantified as tumour/nontumour- ratio, a 4-value-scale was used to measure gadolinium enhancement on contrast enhanced MRI. Statistical analyses were performed to evaluate IMT uptake and gadolinium enhancement in low (WHO I/II) and high (WHO III/ IV) grade tumours and to disclose a potential relationship of IMT uptake to disruption of blood brain barrier as measured in corresponding MRI scans. Results: IMT uptake above background level was observed in 35 of 45 patients. IMT uptake was slightly higher in high grade tumours but the difference failed to attain statistical significance. Grading of individual tumours was neither possible by IMT SPECT nor by gadolinium enhanced MRI. Conclusion: IMT is accumulated in most brain tumours in children. Tumour grading was not possible using IMT or contrast enhancement as determined by MRI. Neither morphological nor functional imaging can replace histology in paediatric brain tumours.

FRED Flow Diverter: A Study on Safety and Efficacy in a Consecutive Group of 50 Patients

BACKGROUND AND PURPOSE

Endovascular flow diverters are increasingly used for the treatment of cerebral aneurysms. We assessed the safety and efficacy of the Flow-Redirection Endoluminal Device (FRED) in a consecutive series of 50 patients.

MATERIALS AND METHODS

Inclusion criteria were wide-neck, blister-like, or fusiform/dissecting aneurysms independent of size, treated with the FRED between February 2014 and May 2015. Assessment criteria were aneurysm occlusion, manifest ischemic stroke, bleeding, or death. The occlusion rate was assessed at 3 months with flat panel CT and at 6 months with DSA by using the Raymond classification and the O'Kelly-Marotta grading scale.

RESULTS

Fifty patients with 52 aneurysms were treated with 54 FREDs; 20 patients were treated with the FRED and coils. Aneurysm size ranged from 2.0 to 18.5 mm. Deployment of the FRED was successful in all cases. There were no device-associated complications. One patient developed mild stroke symptoms that fully receded within days. There have been no late-term complications so far and no treatment-related mortality. Initial follow-up at 3 months showed complete occlusion in 72.3% of the overall study group, Six-month follow-up showed total and remnant-neck occlusion in 87.2% of patients, distributed over 81.5% of the FRED-only cases and 95.0% of the cases with combined treatment.

CONCLUSIONS

The FRED flow diverter is a safe device for the treatment of cerebral aneurysms of various types. Our data reveal high occlusion rates at 3 and 6 months, comparable with those in other flow diverters. Long-term occlusion rates are expected.

Comparison of Intracranial Aneurysms Treated by 2-D Versus 3-D Coils: A Matched-Pairs Analysis

OBJECTIVE

Knowledge on the influence of 2D and 3D coils to occlude intracranial aneurysms is poor. Therefore, aim of our analysis was to evaluate whether the use of 3-D versus 2-D coils alone may improve the efficacy of endovascular aneurysm treatment.

PATIENTS AND METHODS

We performed a matched pair analysis comparing aneurysms treated by 3-D coils as initial "framing" coils to aneurysms treated exclusively by 2-D coils. Number of coils, implanted coil length/volume, and associated packing density were calculated. Aneurysmal occlusion was assessed and monitored 6 months (DSA; magnetic resonance angiography (MRA)) and 18 months (MRA) after embolization. Periprocedural complications and retreatment rate of each group were analyzed.

RESULTS

Our retrospective analysis revealed 50 pairs. Concerning the 3-D group, number of coils (353 in total, median 7; p = 0.002), implanted coil length (55.69  ± 48.4 cm), implanted coil length per volume (5.92 mm/mm³), and packing density (30 %; p = 0.017) was higher than in the 2-D group (259 in total, median 5 coils; 38.52 ± 43.13 cm; 4.54 mm/mm³; 23 %). Occlusion was not significantly different immediately after treatment but at 6 and 18 months follow-up in favor of 3-D coils. Retreatment was performed in 2 cases of the 3-D group and in 3 cases of the 2-D group and therefore in a similar range (p = 0.564).

CONCLUSION

Initial use of 3-D coils revealed a higher packing density and a higher long-term occlusion. Therefore, we recommend initial use of 3-D coils.

Flat-Panel Computed Tomography (DYNA-CT) in Neuroradiology. From High-Resolution Imaging of Implants to One-Stop-Shopping for Acute Stroke

Originally aimed at improving standard radiography by providing higher absorption efficiency and a wider dynamic range, flat-panel detector technology has meanwhile got widely accepted in the neuroradiological community. Especially flat-panel detector computed tomography (FD-CT) using rotational C-arm mounted flat-panel detector technology is capable of volumetric imaging with a high spatial resolution. By providing CT-like images of the brain within the angio suite, FD-CT is able to rapidly visualize hemorrhage and may thus improve complication management without the need of patient transfer. As "Angiographic CT" FD-CT may be helpful during many diagnostic and neurointerventional procedures and for noninvasive monitoring and follow-up. In addition, spinal interventions and high-resolution imaging of the temporal bone might also benefit from FD-CT. Finally, using novel dynamic perfusion and angiographic protocols, FD-CT may provide functional information on brain perfusion and vasculature with the potential to replace standard imaging in selected acute stroke patients.

Dynamic Angiography and Perfusion Imaging Using Flat Detector CT in the Angiography Suite: A Pilot Study in Patients with Acute Middle Cerebral Artery Occlusions

BACKGROUND AND PURPOSE

Perfusion and angiographic imaging using intravenous contrast application to evaluate stroke patients is now technically feasible by flat detector CT performed by the angiographic system. The aim of this pilot study was to show the feasibility and qualitative comparability of a novel flat detector CT dynamic perfusion and angiographic imaging protocol in comparison with a multimodal stroke MR imaging protocol.

MATERIALS AND METHODS

In 12 patients with acute stroke, MR imaging and the novel flat detector CT protocol were performed before endovascular treatment. Perfusion parameter maps (MTT, TTP, CBV, CBF) and MIP/volume-rendering technique images obtained by using both modalities (MR imaging and flat detector CT) were compared.

RESULTS

Comparison of MIP/volume-rendering technique images demonstrated equivalent visibility of the occlusion site. Qualitative comparison of perfusion parameter maps by using ASPECTS revealed high Pearson correlation coefficients for parameters CBF, MTT, and TTP (0.95-0.98), while for CBV, the coefficient was lower (0.49).

CONCLUSIONS

We have shown the feasibility of a novel dynamic flat detector CT perfusion and angiographic protocol for the diagnosis and triage of patients with acute ischemic stroke. In a qualitative comparison, the parameter maps and MIP/volume-rendering technique images compared well with MR imaging. In our opinion, this flat detector CT application may substitute for multisection CT imaging in selected patients with acute stroke so that in the future, patients with acute stroke may be directly referred to the angiography suite, thereby avoiding transportation and saving time.

[Cerebrovascular complications of immunologically mediated heparin-induced thrombocytopenia]

Immunologically mediated heparin-induced thrombocytopenia (HIT) is a thrombotic disease caused by antibodies occurring after heparin exposure. Thrombocytopenia occurs within a few days after heparin exposure, about half of HIT-patients develop venous or arterial thrombotic complications. Neurological complications of HIT are mainly ischaemic stroke and sinus vein thrombosis. To ensure the primary clinical diagnosis functional and immunological assays for antibody detection are available. The probability for the occurrence of HIT depends on the nature of heparin employed (LMWH vs. UFH) and individual patient characteristics such as gender and primary disease (medical vs. surgical patients). In the case of suspected HIT heparin administration should be discontinued immediately and replaced by an alternative anticoagulation to prevent the expansion or development of further thrombotic complications. Herein we report a case of a patient suffering from HIT-associated embolic cerebral ischaemic stroke.

Monitoring of balloon test occlusion of the internal carotid artery by parametric color coding and perfusion imaging within the angio suite: first results

BACKGROUND

Temporary balloon test occlusion (BTO) might be performed prior to procedures in which occlusion of the internal carotid artery (ICA) might be necessary. We tested the hypothesis that parametric color coding (PCC) of angiographic series (digital subtraction angiography (DSA)) along with the assessment of cerebral blood volume (CBV) in the angiography suite would simplify and enhance the identification of candidates who are most likely to tolerate occlusion.

MATERIALS AND METHODS

Fifteen patients underwent angiographic series (DSA) and perfusion imaging before and during BTO. Pre- and postocclusion DSA acquisitions were evaluated for venous delay by conventional methods ("eye balling") and by PCC measurements. Comparison of CBV values between the left and right hemisphere in 6 defined regions was performed.

RESULTS

Values of venous delay by eye balling and PCC showed a high correlation (r = 0.87, p < 0.01). Bland-Altman plot indicated slightly lower values (-0.05 s) by the PCC method. One of the 15 patients developed an asymmetrical CBV map with an increase in CBV of more than one standard deviation in 3 of the 6 regions of interest (ROIs). Acquisition of angiographic series and perfusion imaging did not prolong the test occlusion time.

CONCLUSION

PCC and CBV mapping are feasible during BTO. The use of PCC seems to simplify the ability to measure changes in venous filling delay. Perfusion imaging may show an increase in CBV in patients reaching the limits of cerebral autoregulation. These patients may be at risk for delayed infarction, even though they seem to tolerate temporary occlusion, and could be unsuitable candidates for permanent ICA occlusion.

Comparison of conventional CTA and volume perfusion CTA in evaluation of cerebral arterial vasculature in acute stroke

BACKGROUND AND PURPOSE

CTA-like datasets can be reconstructed from whole-brain VPCTA. The aim of our study was to compare VPCTA with CTA for detection of intracranial stenosis and occlusion in stroke patients. Omitting CTA from stroke CT could reduce radiation dose.

MATERIALS AND METHODS

One hundred sixty-three patients were included in this retrospective analysis. Inclusion criterion was suspected stroke within 4.5 hours after onset of symptoms. All examinations were performed on a 128-section multidetector CT scanner. Axial, coronal, and sagittal maximum intensity projections were reconstructed from CTA and from peak arterial phase of VPCTA. Images were scored for quality and presence of intracranial stenosis >50% or occlusion. For statistical analysis, the Wilcoxon signed-rank test and Fisher exact test were used, with a 2-tailed P value of .05 or less for statistical significance.

RESULTS

Average image quality was superior in CTA (P < .05). However, image quality dichotomized for diagnostic significance was without difference between CTA and VPCTA (P > .05). Comparative statistical analysis revealed no significant difference for detection of intracranial stenosis and occlusion between CTA and VPCTA (P > .05). Substitution of intracranial CTA by VPCTA would lower radiation dose by 0.5 mSv.

CONCLUSIONS

VPCTA is suited to assess the intracranial vasculature in patients with stroke and might have the potential to decrease radiation dose by substituting for intracranial CTA in stroke CT. Additional studies are necessary to further evaluate potential benefits of the dynamic nature of VPCTA.

Feasibility of cerebral blood volume mapping by flat panel detector CT in the angiography suite: first experience in patients with acute middle cerebral artery occlusions

BACKGROUND AND PURPOSE

A new FPCT application offers the possibility of perfusion (FPCT CBV) and parenchymal (FPCT) imaging within the angiography suite. We tested the hypothesis that findings in FPCT CBV and FPCT would correlate with those obtained using MSCT and PCT.

MATERIALS AND METHODS

In 16 patients with acute MCA occlusion, FPCT CBV was performed immediately posttreatment. The volume of tissue having abnormal CBV values was determined by FPCT CBV and PCT images. Stroke volume on follow-up MSCT was determined, CBV values in the effected parenchyma were measured, and FPCT images were reviewed.

RESULTS

In 6 cases, we found a FPCT CBV value identical or higher (hyperemia) in comparison with the contralateral side. In 10 cases, we found CBV lesions with values lower (oligemia) than the contralateral brain tissue. We found a high correlation of CBV lesion volume on FPCT CBV images to stroke volume on follow-up MSCT (r = 0.9, P < .05) in the oligemia group. Absolute FPCT CBV and PCT CBV values were comparable and showed good correlation (r = 0.9, P < .05). In 8 patients, contrast medium extravasation was visible.

CONCLUSIONS

The new FPCT application allows assessment of CBV in acute stroke patients. Our initial results indicate that these measurements may predict final infarct volume. The ability to assess this key parameter of cerebral perfusion within the angiographic suite may improve the management of these patients.

Therapeutic hypothermia for space-occupying Herpes simplex virus encephalitis

Development of space-occupying edema in patients with severe Herpes simplex virus encephalitis is a major factor for high morbidity and mortality. Conventional intracranial pressure-lowering modalities are limited and more aggressive treatment options for such patients have rarely been described. This article reports on a HIV-positive patient with Herpes simplex type 2 encephalitis and elevated intracranial pressure refractory to medical therapy. Induced moderate hypothermia of 33 °C resulted in fast and sustained control of intracranial pressure. After three months, the patient had a fairly good functional outcome with a Glasgow Outcome Scale score of 4.

Flat detector CT in the evaluation of brain parenchyma, intracranial vasculature, and cerebral blood volume: a pilot study in patients with acute symptoms of cerebral ischemia

BACKGROUND AND PURPOSE

The viability of both brain parenchyma and vascular anatomy is important in estimating the risk and potential benefit of revascularization in patients with acute cerebral ischemia. We tested the hypothesis that when used in conjunction with IV contrast, FD-CT imaging would provide both anatomic and physiologic information that would correlate well with that obtained by using standard multisection CT techniques.

MATERIALS AND METHODS

Imaging of brain parenchyma (FD-CT), cerebral vasculature (FD-CTA), and cerebral blood volume (FD-CBV) was performed in 10 patients. All patients also underwent conventional multisection CT, CTA, CTP (including CBV, CTP-CBV), and conventional catheter angiography. Correlation of the corresponding images was performed by 2 experienced neuroradiologists.

RESULTS

There was good correlation of the CBV color maps and absolute values between FD-CBV and CTP-CBV (correlation coefficient, 0.72; P < .001). The Bland-Altman test showed a mean difference of CBV values between FD-CT and CTP-CBV of 0.04 ± 0.55 mL/100 mL. All vascular lesions identified with standard CTA were also visualized with FD-CTA. Visualization of brain parenchyma by using FD-CT was poor compared with that obtained by using standard CT.

CONCLUSIONS

Both imaging of the cerebral vasculature and measurements of CBV by using FD-CT are feasible. The resulting vascular images and CBV measurements compared well with ones made by using standard CT techniques. The ability to measure CBV and also visualize cerebral vasculature in the angiography suite may offer significant advantages in the management of patients. FD-CT is not yet equivalent to CT for imaging of brain parenchyma.

Obliterating intracranial vasculopathy mimicking multiple sclerosis

BACKGROUND

The first ever diagnosis of multiple sclerosis (MS) requires consideration of both diagnostic criteria and differential diagnosis. Clinicians are particularly challenged by rare conditions which may mimic MS symptoms and relapses.

CASE REPORT

We report the case of a young female patient who presented with relapsing left hemispheric symptoms that were highly suspicious of MS but were caused by an idiopathic occlusive angiopathy of the circle of Willis.

CONCLUSION

Occlusive disease of the great cerebral arteries in young patients is a rare but important differential diagnosis of MS. It has to be considered in patients presenting with the first symptoms suspicious of MS as substantial treatment consequences will arise.

[Clinical value of amino acid imaging in paediatric brain tumours. Comparison with MRI]

PURPOSE

To evaluate single photon emission computed tomography (SPECT) using the amino acid l-3-[123I]-alpha-methyl tyrosine (IMT) and contrast enhanced magnetic resonance imaging (MRI) as diagnostic tools in primary paediatric brain tumours in respect of non-invasive tumour grading. Patients, materials, methods: 45 children with primary brain tumours were retrospectively evaluated. IMT uptake was quantified as tumour/nontumour-ratio, a 4-value-scale was used to measure gadolinium enhancement on contrast enhanced MRI. Statistical analyses were performed to evaluate IMT uptake and gadolinium enhancement in low (WHO I/II) and high (WHO III/IV) grade tumours and to disclose a potential relationship of IMT uptake to disruption of blood brain barrier as measured in corresponding MRI scans.

RESULTS

IMT uptake above background level was observed in 35 of 45 patients. IMT uptake was slightly higher in high grade tumours but the difference failed to attain statistical significance. Grading of individual tumours was neither possible by IMT SPECT nor by gadolinium enhanced MRI.

CONCLUSION

IMT is accumulated in most brain tumours in children. Tumour grading was not possible using IMT or contrast enhancement as determined by MRI. Neither morphological nor functional imaging can replace histology in paediatric brain tumours.

Dehydration confounds the assessment of brain atrophy

Computerized brain volumetry has potential value for diagnosis and the follow-up evaluation of degenerative disorders. A potential pitfall of this method is the extent of physiologic variations in brain volume. The authors show that dehydration and rehydration can significantly change brain volume: lack of fluid intake for 16 hours decreased brain volume by 0.55% (SD, +/-0.69), and after rehydration total cerebral volume increased by 0.72% (SD, +/-0.21).

O-(2-[18F]fluorethyl)-L-tyrosine PET in the clinical evaluation of primary brain tumours

PURPOSE

The aim of this study was to evaluate the differential uptake of O-(2-[18F]fluorethyl)-L-tyrosine (FET) in suspected primary brain tumours.

METHODS

Positron emission tomography (PET) was performed in 44 patients referred for the evaluation of a suspected brain tumour. Acquisition consisted of four 10-min frames starting upon i.v. injection of FET. Tumour uptake was calculated as the ratio of maximal tumour intensity to mean activity within a reference region (FETmax).

RESULTS

FET uptake above the cortical level was observed in 35/44 lesions. All histologically confirmed gliomas and many other lesions showed FET uptake to a variable extent. No uptake was observed in nine lesions (one inflammatory lesion, one dysembryoplastic neuroepithelial tumour, one mature teratoma, six lesions without histological confirmation). An analysis of uptake dynamics was done in the patients with increased FET uptake (22 gliomas, three lymphomas, three non-neoplastic lesions, three lesions with unknown histology and four other primaries). Upon classification of tumours into low (i.e. WHO I and II) and high grade (i.e. WHO III and IV), a significant difference in FETmax between the two categories was observed only in the first image frame (0-10 min p.i.), with FETmax=2.0 in low-grade and 3.2 in high-grade tumours (p<0.05); no significant differences were found in frame 4 (30-40 min p.i.), with FETmax=2.4 vs 2.7. Similar results were obtained when the analysis was applied only to astrocytic tumours (2.0 vs 3.1 in the first frame; 2.4 vs 2.6 in the fourth frame).

CONCLUSION

These initial results indicate that FET PET is a useful method to identify malignant brain lesions. It appears that high- and low-grade brain tumours exhibit a different uptake kinetics of FET. A kinetic analysis of FET PET may provide additional information in the differentiation of suspected brain lesions.

Vascular Anastomosing by Gluing - an Experimental Study

BACKGROUND

Performing anastomoses by stitching is very time-consuming. We therefore looked for an alternative technique and used a relatively new surgical adhesive.

METHODS

Ten anastomoses between the aorta and a prosthesis were performed on five pigs (Deutsche Landrasse) using surgical glue (BioGlue). The proximal anastomoses between the abdominal aorta and the prostheses were performed end-to-side just below the renal arteries, the distal anastomoses in an end-to-end fashion just above the iliac bifurcation. The aorta between the anastomoses was ligated and resected. The animals were sacrificed between one week and up to four months after operation and anastomoses were analysed by angiography, CT angiography, angioscopy, and histology.

RESULTS

Angiography and CT angiography revealed that all anastomoses were patent. No aneurysms were found at the site of anastomoses. No haematomas were detected. Angioscopy revealed well-healed connections between the original aorta and the prosthesis.

CONCLUSIONS

We could demonstrate that anastomoses between the aorta and a prosthesis can be performed safely using a surgical adhesive. Further investigations of these anastomoses, especially over the long term, using calcified aortas, are necessary.

Magnetic resonance imaging protocols for examination of the neurocranium at 3 T

The increasing availability of high-field (3 T) MR scanners requires adapting and optimizing clinical imaging protocols to exploit the theoretically higher signal-to-noise ratio (SNR) of the higher field strength. Our aim was to establish reliable and stable protocols meeting the clinical demands for imaging the neurocranium at 3 T. Two hundred patients with a broad range of indications received an examination of the neurocranium with an appropriate assortment of imaging techniques at 3 T. Several imaging parameters were optimized. Keeping scan times comparable to those at 1.5 T we increased spatial resolution. Contrast-enhanced and non-enhanced T1-weighted imaging was best applying gradient-echo and inversion recovery (rather than spin-echo) techniques, respectively. For fluid-attenuated inversion recovery (FLAIR) imaging a TE of 120 ms yielded optimum contrast-to-noise ratio (CNR). High-resolution isotropic 3D data sets were acquired within reasonable scan times. Some artifacts were pronounced, but generally imaging profited from the higher SNR. We present a set of optimized examination protocols for neuroimaging at 3 T, which proved to be reliable in a clinical routine setting.

[Dose reduction of radiographs of the pediatric pelvis for diagnosing hip dysplasia using a digital flat-panel detector system]

PURPOSE

To evaluate a possible dose reduction in pediatric pelvic radiographs in congenital hip dysplasia using a digital flat-panel system instead of a phosphor-storage system.

MATERIALS AND METHODS

During a six-month period, all pediatric patients referred for pelvic radiography for the evaluation of congenital hip dysplasia were randomly assigned to be examined by either a phosphor-storage system or a digital flat-panel system, whereby the latter system was operated with half the radiation dose. Thirty pairs of radiographs were assessed for the visibility of 16 anatomic details and for 5 orthopedic-radiographic measurements (5-point scale with 1 = excellent; three independent observers). The projection indices of Ball and Kommenda and of Tönnis and Brunken were calculated for all radiographs. The Student's t-test was used to compare the flat-panel and the phosphor-storage radiographs for observers' assessments, patients' age and projection indices.

RESULTS

In a total of 7560 observations, the scores for the visibility of anatomic details and orthopedic-radiographic measurements were respectively 2.72 and 2.64 for the flat-panel system and 2.93 and 2.79 for the phosphor-storage system. No significant differences were found between both systems (p > 0.05) and between patient age and projection indices (p > 0.05).

CONCLUSION

Pediatric pelvic radiographs can be obtained with a digital flat-panel system using half the radiation dose instead of a phosphor-storage system without sacrificing relevant information in the diagnosis of congenital hip dysplasia.

[HIV-associated cerebral toxoplasmosis -- review and retrospective analysis of 36 patients]

Highly active antiretroviral therapy (HAART) has resulted in a reduction of morbidity and mortality in HIV-associated cerebral opportunistic infection. Before HAART, up to 50% of all HIV-infected patients in Europe developed cerebral toxoplasmosis, an encephalitis caused by reactivation of Toxoplasma gondii infection. Although potent therapeutical options exist, the prognosis is still poor. We describe the course of 36 AIDS patients with cerebral toxoplasmosis and present a review of clinical signs, diagnosis, therapy, and survival times. The main criteria for differential diagnosis from other secondary neuromanifestations such as primary CNS lymphoma, progressive multifocal leukencephalopathy, abscesses, and ischemic infarctions are described. Indications and problems of stereotactic biopsy are discussed.

Response of Arabidopsis to iron deficiency stress as revealed by microarray analysis

Gene expression in response to Fe deficiency was analyzed in Arabidopsis roots and shoots through the use of a cDNA collection representing at least 6,000 individual gene sequences. Arabidopsis seedlings were grown 1, 3, and 7 d in the absence of Fe, and gene expression in roots and shoots was investigated. Following confirmation of data and normalization methods, expression of several sequences encoding enzymes known to be affected by Fe deficiency was investigated by microarray analysis. Confirmation of literature reports, particularly for changes in enzyme activity, was not always possible, but changes in gene expression could be confirmed. An expression analysis of genes in glycolysis, the tricarboxylic acid cycle, and oxidative pentose phosphate pathway revealed an induction of several enzymes within 3 d of Fe-deficient growth, indicating an increase in respiration in response to Fe deficiency. In roots, transcription of sequences corresponding to enzymes of anaerobic respiration was also induced, whereas in shoots, the induction of several genes in gluconeogenesis, starch degradation, and phloem loading was observed. Thus, it seemed likely that the energy demand in roots required for the Fe deficiency response exceeded the capacity of oxidative phosphorylation, and an increase in carbon import and anaerobic respiration were required to maintain metabolism.

Integrated studies on plant biology using multiparallel techniques

Plant biology, especially the fields of molecular genetics and molecular physiology, is currently undergoing a change in paradigm from 'vertical' analysis of the role(s) of one or a few genes to 'horizontal' holistic approaches, studying the function of many or even all of the genes of an organism simultaneously. This change is leading us beyond genomes to transcriptomes, proteomes and metabalomes, and to an understanding of life at an entirely new level. Profiling strategies are putting this change into effect through the generation of large amounts of data, requiring that current bioinformatic approaches adapt and grow in order to make the most of these data.

A complete BAC-based physical map of the Arabidopsis thaliana genome

Arabidopsis thaliana is a small flowering plant that serves as the major model system in plant molecular genetics. The efforts of many scientists have produced genetic maps that provide extensive coverage of the genome (http://genome-www. stanford.edu/Arabidopsis/maps.html). Recently, detailed YAC, BAC, P1 and cosmid-based physical maps (that is, representations of genomic regions as sets of overlapping clones of corresponding libraries) have been established that extend over wide genomic areas ranging from several hundreds of kilobases to entire chromosomes. These maps provide an entry to gain deeper insight into the A. thaliana genome structure. A. thaliana has been chosen as the subject of the first large-scale project intended to determine the full genome sequence of a plant. This sequencing project, together with the increasing interest in map-based gene cloning, has highlighted the requirement for a complete and accurate physical map of this plant species. To supply the scientific community with a high-quality resource, we present here a complete physical map of A. thaliana using essentially the IGF BAC library. The map consists of 27 contigs that cover the entire genome, except for the presumptive centromeric regions, nucleolar organization regions (NOR) and telomeric areas. This is the first reported map of a complex organism based entirely on BAC clones and it represents the most homogeneous and complete physical map established to date for any plant genome. Furthermore, the analysis performed here serves as a model for an efficient physical mapping procedure using BAC clones that can be applied to other complex genomes.

Transfer of rps19 to the nucleus involves the gain of an RNP-binding motif which may functionally replace RPS13 in Arabidopsis mitochondria

The discovery of disrupted rps19 genes in Arabidopsis mitochondria prompted speculation about the transfer to the nuclear compartment. We here describe the functional gene transfer of rps19 into the nucleus of Arabidopsis. Molecular cloning and sequence analysis of rps19 show that the nuclear gene encodes a long N-terminal extension. Import studies of the precursor protein indicate that only a small part of this extension is cleaved off during import. The larger part of the extension, which shows high similarity to conserved RNA-binding domains of the RNP-CS type, became part of the S19 protein. In the Escherichia coli ribosome S19 forms an RNA-binding complex as heterodimer with S13. By using immuno-analysis and import studies we show that a eubacterial-like S13 protein is absent from Arabidopsis mitochondria, and is not substituted by either a chloroplastic or a cytosolic homologue of this ribosomal protein. We therefore propose that either a highly diverged or missing RPS13 has been functionally replaced by an RNP domain that most likely derived from a glycine-rich RNA-binding protein. These results represent the first case of a functional replacement of a ribosomal protein by a common RNA-binding domain and offer a new view on the flexibility of biological systems in using well-adapted functional domains for different jobs.

On the identification of group II introns in nucleotide sequence data

Four different consensus sequences (GTI, group II identifiers) have been derived from domains V of known group II introns and are used as query input sequences for sensitive database screenings with the FASTA and LFASTA programs. The set of four GTI sequences can identify all domains V of the 96 known group II introns in the completely sequenced chloroplast genomes of Marchantia polymorpha, Epifagus virginiana, Oryza sativa, Nicotiana tabacum and the completely sequenced mitochondrial genomes of Saccharomyces cerevisiae, Podospora anserina, Schizosaccharomyces pombe and Marchantia polymorpha. Seven moderately high-scoring hits can easily be rejected as false-positives since they do not fulfil secondary structure requirements. Large FASTA outputs obtained after screening the entire nucleotide sequence database are evaluated in a second step by a program (D5SCAN) that allows the assignment of variable selection criteria for potential domain V secondary structures. Database searches with these routines yield evidence for several group II intron sequences previously unrecognized. These include novel intron structures in the cyanobacterium Synechocystis and in the mitochondrial genomes of Marchantia, soybean, pea, broad bean, sugar beet and a heterobasidiomycete. Potential intron remnants are found contributing to the secondary structure of rRNAs in several trypanosome species. At a given sensitivity of 95% positively identified true domains V, the search routine produces one false positive hit per 10,000 kb.

An adenine nucleotide translocator gene from Arabidopsis thaliana

The sequence of an adenine nucleotide translocator (ANT) gene of Arabidopsis contains three introns, the first of which is located upstream of the assumed initiation codon. The presequence characteristic for plant ANTs is processed also in Arabidopsis as suggested by Western blot analysis, most likely at the conserved cleavage site.