Complete DNA sequence of yeast chromosome XI

The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.

Genome fingerprinting of Pseudomonas aeruginosa indicates colonization of cystic fibrosis siblings with closely related strains

The epidemiology of Pseudomonas aeruginosa infection at a cystic fibrosis (CF) center was monitored over a 3-year period. A total of 835 isolates from 72 unrelated patients and 22 siblings with CF were analyzed by genome fingerprinting and serotyping, bacteriophage typing, and pyocin typing. For genome fingerprinting, bacterial chromosomes were digested with one of the restriction endonucleases SpeI, DraI, XbaI, SspI, and NheI, which cut only rarely, and subsequently separated by field inversion gel electrophoresis. The physical genome analysis allowed us to classify P. aeruginosa strains in terms of DNA relatedness. Related strains differed by fewer than six DraI bands in the fingerprint, whereas unrelated strains differed by more than 20 DraI bands. All unrelated CF patients were colonized with different strains. The absence of a nosocomial spread of organisms at the CF center was attributed to the strict hygiene measures observed at the hospital. CF siblings were harboring either identical or closely related strains; transmission within the family is thought to be the most likely cause.

Epidemiology of chronic Pseudomonas aeruginosa infections in cystic fibrosis

The epidemiology of chronic colonization of airways with Pseudomonas aeruginosa was monitored in 44 patients with cystic fibrosis (CF) by DraI/SpeI macrorestriction analyses of 489 isolates. Sequential P. aeruginosa isolates (144) that had been collected from 32 CF patients over < or = 2.5 years were investigated, and 12 patients were followed for 8 years after onset of colonization. Forty-eight different genotypes were uncovered from 481 typeable isolates. Ten genotypes were found in > 1 unrelated CF patient. The 6 most frequent clones were identified in 58% of isolates. Ten of the 12 patients monitored for 8 years were harboring their initially acquired P. aeruginosa clone at all times, with subtle shifts of fragment patterns indicating subclonal variation. During colonization, the bacteria gradually lost pyocin and phage typing responses, supporting the view that genotypically discordant P. aeruginosa strains develop a common phenotype.

Nosocomial acquisition of Pseudomonas aeruginosa by cystic fibrosis patients

During a 4-year period, at least 12 of 40 patients with cystic fibrosis (CF) who were newly colonized with Pseudomonas aeruginosa had acquired it at CF recreation camps, clinics, or rehabilitation centers. After introduction of hygienic precautions at the CF clinic, only a single episode of nosocomial transmission of P. aeruginosa was detected at the CF ward during the subsequent 2 years.

New approaches in genome analysis by pulsed-field gel electrophoresis: application to the analysis of Pseudomonas species

A general method for the evaluation of macrorestriction fragment patterns is presented and its applicability to the taxonomy of bacteria is demonstrated for 32 Pseudomonas species. Strains were differentiated at the species and subspecies level by genome size and macrorestriction fragment fingerprints of the chromosome that had been separated on pulsed-field gels. The relatedness of bacteria was ascertained from the similarity of AsnI, DraI, SpeI, SspI or XbaI fragment patterns. In general, the dendrograms calculated from the genome fingerprints corresponded with the phylogenetic classification obtained from phenotypic marker or nucleic acid hybridization analysis, but several exceptions were noted. The techniques and algorithms presented herein are generally applicable to the genome analysis of bacteria, lower eukaryotes, and DNA fragments cloned in yeast artificial chromosomes.

A physical genome map of Pseudomonas aeruginosa PAO

A complete macrorestriction map of the 5.9 Mb genome of Pseudomonas aeruginosa PAO (DSM 1707) was constructed by the combination of various one- and two-dimensional pulsed field gel electrophoresis techniques. A total of 51 restriction sites (36 SpeI sites, 15 DpnI sites) were placed on the physical map yielding an average resolution of 110 kb. Several genes encoding virulence factors and enzymes of metabolic pathways were located on the anonymous map by Southern hybridization. Distances between the gene loci were similar on the genetic and physical maps, suggesting an even distribution of genome mobility throughout the bacterial chromosome. The four rRNA operons were organized in pairs of inverted repeats. The two-dimensional macro-restriction techniques described herein are generally applicable for the genome mapping of any prokaryote and lower eukaryote which yields resolvable fragment patterns on two-dimensional pulsed field gels.

PCR amplification of megabase DNA with tagged random primers (T-PCR)

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Physical genome analysis of bacteria

Pulsed-field gel electrophoresis (PFGE) is a general analytical tool to separate large DNA molecules and may therefore be applied to problems from all areas of bacteriology. The genome size of bacteria covers the range of 0.6 to 10 megabase pairs. For genome fingerprinting, the bacterial chromosome is cleaved with a restriction endonuclease that gives a resolvable and informative number of five to one hundred fragments on the PFGE gel. Restriction enzymes are chosen according to GC content, degree of methylation, and codon usage of the respective bacterial genus. Macrorestriction fingerprinting allows the identification of bacterial strains and the distinction between related and unrelated strains. If fragment patterns of several restriction digestions are quantitatively evaluated, strains can be classified according to genetic relatedness at the level of genus, species, and biovar. In particular, members of a clonal lineage can be uncovered. Hence, any problem from applied, environmental, and clinical microbiology may be addressed by PFGE restriction analysis where the spatiotemporal spread of a bacterial clone is of interest. In bacterial genomics, PFGE is employed for the top-down construction of macrorestriction maps of the chromosome which yields data about genome organization, mobile genetic elements, and the arrangement of gene loci and gene families. The genomic diversity of a bacterial species is elucidated by comparative chromosome mapping. Map positions of restriction sites and gene loci of interest serve as landmarks to assess the extent of gross chromosomal modification, namely insertions, deletions and inversions. Intra- and interspecies comparisons of genome organization provide insights into the structure and diversity of bacterial populations and the phylogeny of bacterial taxa.

Simultaneous on-line DNA sequencing on both strands with two fluorescent dyes

We describe an automated DNA-sequencing technique which allows both the simultaneous sequencing from the two strands of double-stranded templates and the subsequent detection of the sequencing products online and in parallel. The technique is based on hardware technology also used in the ALF DNA sequencer (Pharmacia, Uppsala). A helium-neon laser was mounted into the sequencing device additionally to the standard argon laser. Two different primers, labeled with either fluorescein or Texas red, are used in a single sequencing reaction resulting in an output of two sequences. Both sequencing products are then analyzed on-line in the same lanes of a gel. This technique is especially useful for the complete sequencing of DNA fragments up to 1 kb. High accuracy sequencing of PCR products in double-stranded form can now be accomplished in only one sequencing reaction.

Gelfoam for closure of large percutaneous transhepatic and transsplenic puncture tracts in pediatric patients

PURPOSE

Evaluation of the efficacy and safety of Gelfoam for the closure of transhepatic or transsplenic parenchymal puncture tracts with large-bore sheaths in pediatric patients.

MATERIALS AND METHODS

Between January 2012 and May 2013, 8 percutaneous transhepatic accesses and 3 percutaneous transsplenic accesses were closed using percutaneous Gelfoam in pediatric patients. The primary study endpoints to determine treatment efficacy and safety were patient survival, technical success defined as successful closure of the puncture tract without signs of bleeding, and complication rates. The secondary study endpoints were the occurrence of local and systemic inflammation.

RESULTS

Overall survival was 100 % with a median follow-up of 256 days. The procedure was technically successful in 10 of 11 procedures. One patient suffered from bleeding, which was successfully managed by a single blood transfusion. No re-bleeding was detected during follow-up and no surgical interventions were necessary. No signs of local or systemic infections related to the Gelfoam application occurred.

CONCLUSION

Percutaneous Gelfoam application is an effective and safe technique for the closure of transhepatic or transsplenic accesses in pediatric patients.

KEY POINTS

Interventional closure of large transhepatic and transsplenic parenchymal accesses in children after interventional treatment is recommended to avoid bleeding. Gelfoam application does not cause artifacts in magnetic resonance imaging and does not increase the risk of local or systemic inflammation in comparison to permanent embolic agents. Thus, especially children under immunosuppressive therapy can benefit from the application of Gelfoam.

Characterization of HIV type 1 from Romanian children: lack of correlation between V3 loop amino acid sequence and syncytium formation in MT-2 cells

The biological properties and amino acid sequences of the third variable domain (V3 loop and flanking regions) of the env region of 34 HIV-1 isolates obtained from Romanian children were analyzed. Unambiguous nucleic acid sequences were obtained from 31 isolates. The derived V3 amino acid sequences were highly homologous (93-100%) and clustered with the HIV-1 subtype F Romanian consensus. Five of the 31 isolates presented a syncytium-inducing phenotype in MT-2 cells and established continuous viral replication in various CD4+ cell lines (rapid/high phenotype). The V3 sequence from one of these isolates showed a slightly lesser degree of homology with the consensus sequence. The presence of positively charged amino acids at positions 306 and 320 has been strongly associated with the ability to induce syncytia in MT-2 cells, whereas negatively or uncharged amino acids at these positions are present in non-syncytium-inducing isolates (slow/low phenotype). There was, however, no correlation between phenotype and amino acid sequence in the five syncytium-inducing isolates; negatively or uncharged amino acids were conserved at positions 306 and 320 for all 31 isolates in sequences obtained from PBMCs. A tendency toward a more positive net charge in the V3 loop of syncytium-inducing isolates was noted. These data confirm the recent observations that HIV-1 isolates from Romania not only cluster in subtype F, but also show a high degree of interpatient homogeneity in the V3 region.(ABSTRACT TRUNCATED AT 250 WORDS)

Alignment of Sfi I sites with the Not I restriction map of Schizosaccharomyces pombe genome

A Sfi I restriction map of the fission yeast Schizosaccharomyces pombe genome was aligned with the Not I restriction map. There are 16 Sfi I sites in the S. pombe genome. Three Sfi I sites are on chromosome III which is devoid of Not I sites. The sizes of the entire genome and individual chromosomes, calculated from the Sfi I fragment sizes, are consistent with that calculated from the Not I fragment sizes. The Sfi I map provides greater physical characterization of the S. pombe genome and further validates the use of S. pombe chromosomal DNA as size standard. These maps have allowed detection of polymorphism on all three chromosomes.

Pulsed-field gel electrophoresis analysis of a Pseudomonas aeruginosa pathovar

This paper presents the genome organization and mobility of Pseudomonas aeruginosa strains that had been isolated in half-year intervals from 30 patients with cystic fibrosis since the onset of colonization over a 2- to 8-year period. The chromosomes were digested with DraI or SpeI, separated by pulsed-field gel electrophoresis, blotted and hybridized with probes encoding housekeeping or virulence genes. Strains were differentiated by relatedness of macrorestriction fingerprints. After some turnover of strains during the first two years of colonization, each patient had acquired a set of strains that diversified during the course of the disease. In the majority of patients, two clonal lineages were found to account for colonization in the air passages but each lung habitat was characterized by some specific signature of bands in the macrorestriction fragment pattern.

Evaluation of the diagnostic accuracy of CEUS in children with benign and malignant liver lesions and portal vein anomalies

OBJECTIVE

Comparison of the diagnostic findings of MRI, CT and CEUS in children with benign and malignant and portal venous anomalies of the liver.

MATERIALS/METHODS

Retrospective analysis of the diagnostic findings of CEUS, MRI and CT scans in 56 children (age 0-17 years) with a total of 60 benign and malignant liver lesions and anomalies of the portal vein/perfusion. All patients underwent CEUS using sulphur hexafluoride microbubbles and a multi-frequency probe (1-5 MHz, 6-9 MHz). Cine-loops were stored up to 3 minutes. MRI was performed in 38 lesions. CT was performed in 8 lesions.

RESULTS

Out of the 56 patients 49 liver lesions (48 benign, 1 malignant), 9 anomalies of the portal vein/perfusion and 2 of the biliary system were detected. 16/49 lesions were analyzed histopathologically. Using CEUS, the characterization of the lesions was possible in 45 out of 49 cases. In 32 cases, CEUS provided the exact diagnosis. Only two benign lesions were falsely categorized as malignant.Findings of MRI and CEUS were concordant in 84% of cases (n = 32/38). CEUS considered 1 benign lesion to be malignant. 2 lesions were not detectable and in 3 lesions no definite diagnosis was established using MRI.Findings of CT and CEUS were concordant in 5 of 8 cases. In 21 lesions CEUS as the only imaging modality was found to be sufficient for diagnostics.

CONCLUSION

Despite the restricted indications for using CEUS in children, it offers a high diagnostic detection rate (93%) for characterization of liver lesions and portal vein anomalies.

Separation of up to 1000 bases on a modified A.L.F. DNA sequencer

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Top-down construction of an ordered Schizosaccharomyces pombe cosmid library

A very rapid and efficient method for sorting and ordering large numbers of clones is presented. This top-down mapping approach divides the entire ordering problem into many smaller tasks and analyzes in parallel a gridded membrane array of clones by hybridization with probe pools. The strategy was tested on a 15-fold-coverage Schizosaccharomyces pombe cosmid library. About 1600 clones were assigned to chromosomes and to regions defined by the Not I and Sfi I restriction maps. Then, the clones were ordered into 20 contigs, which is consistent with statistical expectations for the degree of genome coverage used. The parallel ordering of clones and the computer-based analysis of digitized images make this approach very efficient; it is about 8-fold faster than existing methods. Only 61 hybridizations were needed to order 1600 clones.

Sequencing and analysis of 51.6 kilobases on the left arm of chromosome XI from Saccharomyces cerevisiae reveals 23 open reading frames including the FAS1 gene

We have sequenced two segments containing a total of 51.6 kb of the left arm from chromosome XI of Saccharomyces cerevisiae. The first segment of 38.5 kb contains 18 open reading frames (ORFs) of more than 100 amino acid residues. Five ORFs encode known yeast genes, including the fatty acid synthase gene (FAS1). Three new yeast genes were discovered with homologies to non-yeast genes and ten new genes without homologies to any known sequences. The second segment of 13 kb contains five ORFs with two known yeast genes and three unknown genes. The sequences from cosmid pUKG041 were obtained entirely with the walking primer strategy resulting in a very low overall sequence redundancy of 2.8 and an average reading length of 443 bases.

Super selective percutaneous transhepatic coil embolization of intrahepatic pseudoaneurysm after pediatric liver transplantation: a case report

Background

Intrahepatic arterial pseudoaneurysms are a rare, life-threatening complication after pediatric liver transplantation. Treatment of choice represents interventional radiological management with endovascular embolization of the segmental artery proximal and distal to the aneurysm. However, this technique results in loss of arterial perfusion distal to the aneurysm with subsegment arterial ischemia.

Case presentation

We report a case of a 1-year-old girl with a pseudoaneurysm in the split-liver graft. Direct percutaneous, transhepatic access to the pseudoaneurysm was performed followed by super selective coil application into the aneurysm.

Conclusion

Super selective percutaneous, transhepatic coil application is feasible even in pediatric patients after liver transplantation and results in preservation of the entire course of the liver artery.

The nasal polyps as a tool for basic research in cystic fibrosis

Total RNA and mRNA were prepared from cystic fibrosis (CF) and control nasal polyps and nasal epithelial cells. Genomic clones from the chromosomal region of the CF locus were screened by northern blots. A representative cDNA library from nasal polyps was cloned in the vector lambda gt10. For the construction of a physical genomic map around the CF locus single gene markers were isolated from metaphase 1:7q2qter chromosomes by laser micro-dissection and subsequent microcloning. A linkage study with the polymorphic markers met-H, met-D, and pJ3.11 was performed in 53 German CF families with at least 2 children. No significant correlation of any haplotype on the CF chromosomes with the clinical severity of the course of the disease could be observed, which provides evidence that cystic fibrosis is genetically homogeneous.

Differential expression and regulation of GTPases (RhoA and Rac2) and GDIs (LyGDI and RhoGDI) in neutrophils from patients with severe congenital neutropenia

Severe congenital neutropenia (SCN) or Kostmann syndrome is a disorder of myelopoiesis characterized by a maturation arrest at the stage of promyelocytes or myelocytes in bone marrow and absolute neutrophil counts less than 200/microL in peripheral blood. Treatment of these patients with granulocyte colony-stimulating factor (G-CSF) leads to a significant increase in circulating neutrophils and a reduction in infection-related events in more than 95% of the patients. To date, little is known regarding the underlying pathomechanism of SCN. G-CSF-induced neutrophils of patients with SCN are functionally defective (eg, chemotaxis, superoxide anion generation, Ca(++ )mobilization). Two guanosine triphosphatases (GTPases), Rac2 and RhoA, were described to be involved in many neutrophil functions. The expression of these GTPases and their regulation in patients' neutrophils were of interest. This study determined that the guanosine diphosphate (GDP)-dissociation inhibitor RhoGDI is overexpressed at the protein level in patients' neutrophils and that overexpression is a result of G-CSF treatment. RhoA and LyGDI are expressed at similar levels, whereas Rac2 shows a decreased expression. In addition, association of Rac2 and RhoGDI or LyGDI is abrogated or not detectable based on the low Rac2 expression in patients' neutrophils. (Blood. 2000;95:2947-2953)

Automated low-redundancy large-scale DNA sequencing by primer walking

Low-redundancy automated DNA sequencing by primer walking is described. T7 DNA polymerase is used together with computer-selected walking primers and fluorescein-dATP as internal label to sequence large plasmids or cosmids directly on a standard DNA sequencer with an error rate below 1% up to 500 bases (in the unedited raw data). The low error rate allows efficient sequencing with low (2-3 times) redundancy. Plasmid subclones covering 20 kb of a cosmid insert were sequenced with an overall redundancy of 2.7 in the course of the European community Saccharomyces cerevisiae genome sequencing project. Neighboring plasmid subclones were linked by direct cosmid sequencing. Sets of ten walking primers are synthesized on the EMBL multiple segmental DNA synthesizer at low costs and used for sequencing with greater than 95% efficiency. The accuracy of the directed approach is improved by simultaneous walking on both strands by designing two primers in opposite directions in the same starting region. One primer is used to confirm sequence data on the opposite strand, and the other primer to obtain new sequence data.

[Percutaneous thrombus aspiration and thrombolysis for the treatment of acute portal vein thrombosis in a 5-year-old child]

Early portal vein thrombosis is a frequent and severe complication following pediatric liver transplantation. The clinical presentation is characterized by signs and symptoms of portal hypertension such as ascites and digestive hemorrhage. Primary treatment consists of heparin therapy. In the case of persistent or progressive thrombosis or symptoms, surgical thrombectomy or retransplantation should be considered. However, surgical intervention is associated with significant morbidity and mortality. We report on successful minimally invasive percutaneous thrombus aspiration and thrombolysis for the treatment of acute portal vein thrombosis in a 5-year-old child post liver transplantation.