PubMed Health⌕ Search

Biomedical subjects

S Heim

Publications and source records attributed to S Heim.

At least 19 recordsLinked to original sources
PubMed2006

A marginal zone phenotype in follicular lymphoma with t(14;18) is associated with secondary cytogenetic aberrations typical of marginal zone lymphoma.

Marginal zone differentiation of follicular lymphomas (FL), sometimes referred to as monocytoid B-cell differentiation, is a relatively uncommon phenomenon. Recently, this type of differentiation was also linked to secondary cytogenetic aberrations of chromosome 3 in a small number of patients. We have analysed 131 primary nodal FL with t(14;18)(q32;q21) for secondary cytogenetic aberrations previously described as recurrent in marginal zone lymphomas (MZL) to identify their frequency and possible association with morphological evidence of marginal zone differentiation. We searched for trisomy of chromosomes 3, 12, and 18, gains of chromosome arm 3q, deletions of chromosome arm 7p, structural anomalies with break-points in 1q21 and 1p34, as well as the t(1;2)(p22;p12), t(1;14)(p22;q32), t(3;14)(q27;q32), t(6;14)(p21;q32), and t(11;18)(q21;q21) translocations. At least focal morphological evidence of marginal zone differentiation occurred in 35/131 (27%) FL with t(14;18)(q32;q21) as the primary chromosomal abnormality. None of the recurrent balanced translocations characteristic of extranodal MZL were seen secondarily in the nodal FLs with t(14;18)(q32;q21). However, 43/131 (33%) cases had at least one of the above secondary cytogenetic aberrations previously reported as recurrent aberrations in MZL and, when combined, these were significantly more frequent in FL with morphological evidence of marginal zone differentiation (p<0.0001, two-sided Fisher's exact test). Aberrations of chromosome 3 and, in particular, trisomy 3 occurred frequently in FL with marginal zone differentiation (p=0.002 and p<0.0001, respectively, two-sided Fisher's exact test), while chromosome 21, 22, and X chromosome aberrations, which have not been described previously as recurrent in MZL, were also significantly associated with marginal zone differentiation in FL (p=0.002, p=0.037, p=0.039, respectively, two-sided Fisher's exact test).

Cell Differentiation↗
PubMed2006

FISH mapping of i(7q) in acute leukemias and myxoid liposarcoma reveals clustered breakpoints in 7p11.2: implications for formation and pathogenetic outcome of the idic(7)(p11.2).

Isochromosome 7q - i(7q) - is seen in a wide variety of hematologic malignancies and solid tumors, often as a secondary change to a characteristic primary translocation. Despite its high frequency, nothing is known about the formation and the pathogenetic outcome of this abnormality. To address these issues, we performed a detailed fluorescence in situ hybridization (FISH) investigation of four acute lymphoblastic leukemias, one acute myeloid leukemia, and two myxoid liposarcomas with i(7q). Using FISH with bacterial artificial chromosomes (BACs) mapping between 7p12.2 and 7q11.2, the breakpoints (BPs) in all seven cases were shown to cluster to an approximately 340 kb segment at 7p11.2, covered by the overlapping BAC probes RP11-760D2 and RP11-10F11. Thus, the i(7q) should formally be designated idic(7) (p11.2). In one of the cases, FISH with fosmids could narrow down the BP further to an 80-kb sequence delineated by G248P81983A10 and G248P8793H7. No known genes are located in the 340-kb BP cluster region, indicating that the idic(7)(p11.2) does not result in a fusion or deregulation of genes in this segment. The pathogenetically important outcome is thus likely to be an altered gene expression because of copy number changes. The clustering of breakpoints might be due to frequent intrachromosomal duplicons in the BP region.

Acute Disease↗
PubMed2005

Halogenated compounds in a dated sediment core of the Teltow Canal, Berlin: time related sediment contamination.

To study the recent contamination history of DDT (1,1,1-trichloro-2,2-bis(chlorophenyl)ethane) and its metabolites, as well as methoxychlor (1,1,1-trichloro-2,2-bis(p-methoxyphenyl)ethane), chlorfenson (4-chlorophenyl-p-chlorobenzenesulfonate), and further halogenated aromatics, a sediment core was collected from the Teltow Canal in Berlin (Germany). The sampling site is located nearby a former industrial point source, where recently analyses on pre-samples have indicated high concentrations of halogenated organic compounds. The deposition time of the investigated sediments was determined by gamma-spectrometrical dating. Pollution trends of selected contaminants were attributed to a time period between 5 and 10 years. Concentration profiles reflect not only the recent pollution history of these compounds, but also the time-depending effects of the ban, restriction and termination of DDT-production in the German Democratic Republic (GDR). DDT and other chlorinated aromatic compounds were produced onsite until the late 1980s. Maximum values of 133 mg kg(-1) (dry weight) for p,p'-DDD (1,1-dichloro-2,2-bis(chlorophenyl)ethane) and approximately 100 mg kg(-1) (dry weight) for p,p'-DDMS (1-chloro-2,2-bis(chlorophenyl)ethane), main metabolites of the anaerobic degradation of DDT, were determined. The occurrence of all selected contaminants, most of which have been banned more than 10 years ago, demonstrate recent contamination pathways, and the necessity of a continuous long-term monitoring of the affected environment.

Berlin↗
PubMed2004

Assessment of clonal relationships in ipsilateral and bilateral multiple breast carcinomas by comparative genomic hybridisation and hierarchical clustering analysis.

The issue of whether multiple, ipsilateral or bilateral, breast carcinomas represent multiple primary tumours or dissemination of a single carcinomatous process has been difficult to resolve, especially for individual patients. We have addressed the problem by comparative genomic hybridisation analysis of 26 tumours from 12 breast cancer patients with multiple ipsilateral and/or bilateral carcinoma lesions. Genomic imbalances were detected in 25 of the 26 (96%) tumours. Using the genomic imbalances detected in these 26 lesions as well as those previously found by us in an independent series of 35 unifocal breast carcinomas, we compared a probabilistic model for likelihood of independence with unsupervised hierarchical clustering methodologies to determine the clonal relatedness of multiple tumours in breast cancer patients. We conclude that CGH analysis of multiple breast carcinomas followed by unsupervised hierarchical clustering of the genomic imbalances is more reliable than previous criteria to determine the tumours' clonal relationship in individual patients, that most ipsilateral breast carcinomas arise through intramammary spreading of a single breast cancer, and that most patients with bilateral breast carcinomas have two different diseases.

Adult↗
PubMed2004

Assessing DTI data quality using bootstrap analysis.

Diffusion tensor imaging (DTI) is an established method for characterizing and quantifying ultrastructural brain tissue properties. However, DTI-derived variables are affected by various sources of signal uncertainty. The goal of this study was to establish an objective quality measure for DTI based on the nonparametric bootstrap methodology. The confidence intervals (CIs) of white matter (WM) fractional anisotropy (FA) and Clinear were determined by bootstrap analysis and submitted to histogram analysis. The effects of artificial noising and edge-preserving smoothing, as well as enhanced and reduced motion were studied in healthy volunteers. Gender and age effects on data quality as potential confounds in group comparison studies were analyzed. Additional noising showed a detrimental effect on the mean, peak position, and height of the respective CIs at 10% of the original background noise. Inverse changes reflected data improvement induced by edge-preserving smoothing. Motion-dependent impairment was also well depicted by bootstrap-derived parameters. Moreover, there was a significant gender effect, with females displaying less dispersion (attributable to elevated SNR). In conclusion, the bootstrap procedure is a useful tool for assessing DTI data quality. It is sensitive to both noise and motion effects, and may help to exclude confounding effects in group comparisons.

Adult↗
PubMed2004

Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440.

A major challenge in microbiology is the elucidation of the genetic and ecophysiological basis of habitat specificity of microbes. Pseudomonas putida is a paradigm of a ubiquitous metabolically versatile soil bacterium. Strain KT2440, a safety strain that has become a laboratory workhorse worldwide, has been recently sequenced and its genome annotated. By drawing on both published information and on original in silico analysis of its genome, we address here the question of what genomic features of KT2440 could explain or are consistent with its ubiquity, metabolic versatility and adaptability. The genome of KT2440 exhibits combinations of features characteristic of terrestrial, rhizosphere and aquatic bacteria, which thrive in either copiotrophic or oligotrophic habitats, and suggests that P. putida has evolved and acquired functions that equip it to thrive in diverse, often inhospitable environments, either free-living, or in close association with plants. The high diversity of protein families encoded by its genome, the large number and variety of small aralogous families, insertion elements, repetitive extragenic palindromic sequences, as well as the mosaic structure of the genome (with many regions of 'atypical' composition) and the multiplicity of mobile elements, reflect a high functional diversity in P. putida and are indicative of its evolutionary trajectory and adaptation to the diverse habitats in which it thrives. The unusual wealth of determinants for high affinity nutrient acquisition systems, mono- and di-oxygenases, oxido-reductases, ferredoxins and cytochromes, dehydrogenases, sulfur metabolism proteins, for efflux pumps and glutathione-S-transfereases, and for the extensive array of extracytoplasmatic function sigma factors, regulators, and stress response systems, constitute the genomic basis for the exceptional nutritional versatility and opportunism of P. putida , its ubiquity in diverse soil, rhizosphere and aquatic systems, and its renowned tolerance of natural and anthropogenic stresses. This metabolic diversity is also the basis of the impressive evolutionary potential of KT2440, and its utility for the experimental design of novel pathways for the catabolism of organic, particularly aromatic, pollutants, and its potential for bioremediation of soils contaminated with such compounds as well as for its application in the production of high-added value compounds.

Adaptation, Physiological↗
PubMed2003

Proteome reference map of Pseudomonas putida strain KT2440 for genome expression profiling: distinct responses of KT2440 and Pseudomonas aeruginosa strain PAO1 to iron deprivation and a new form of superoxide dismutase.

The genome sequence of Pseudomonas putida strain KT2440, a nutritionally versatile, saprophytic and plant root-colonizing Gram-negative soil bacterium, was recently determined by K. E. Nelson et al. (2002, Environ Microbiol 4: 799-808). Here, we present a two-dimensional gel protein reference map of KT2440 cells grown in mineral salts medium with glucose as carbon source. Proteins were identified by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) analysis, in conjunction with an in-house database developed from the genome sequence of KT2440, and approximately 200 two-dimensional gel spots were assigned. The map was used to assess the genomic response of KT2440 to iron limitation stress and to compare this response with that of the closely related facultative human pathogen Pseudomonas aeruginosa strain PAO1. The synthesis of about 25 proteins was affected in both strains, including four prominent upregulated ferric uptake regulator (Fur) protein-dependent proteins, but there were also striking differences in their proteome responses, for example in the expression of superoxide dismutases (Sod), which may indicate important roles of iron-responsive functions in the adaptation of these two bacteria to different lifestyles. The Sod enzyme of KT2440 was shown to be a novel heterodimer of the SodA and SodB polypeptides.

Adaptation, Biological↗
PubMed2002

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.

Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.

Bacterial Proteins↗
PubMed2002

M-FISH cytogenetic analysis of non-Hodgkin lymphomas with t(14;18)(q32;q21) and add(1)(p36) as a secondary abnormality shows that the extra material often comes from chromosome arm 17q.

The most common translocation in non-Hodgkin lymphomas (NHL) is a t(14;18)(q32;q21) recombining the immunoglobulin heavy-chain gene (IGH) on chromosome 14 with the B cell leukemia/lymphoma 2 (BCL2) gene on chromosome 18. Although NHLs carrying a t(14;18) typically begin as low-grade, follicular lymphomas, they have a tendency towards transformation to more aggressive disease, something that is accompanied, presumably caused, by the acquisition of secondary chromosomal changes. One such common change is add(1)(p36), in which material of unknown origin is added to the tip of the short arm of chromosome 1. We used multicolor fluorescence in situ hybridization (M-FISH), a new FISH-based screening technique, to better characterize the rearrangement. Whenever doubt persisted after M-FISH, hybridization with chromosome-specific probes was also performed. In 5 out of 14 informative cases, the extra material on 1p36 could be shown to have come from 17q, more specifically 17q11-21 --> qter, whereas it came from 6p and 11q in two cases each and from 3p, 8p, 8q, 9q, and 12p in one case each. It appears, therefore, that der(1)t(1;17)(p36;q11-21) is a common secondary aberration in NHLs with t(14;18) as the primary abnormality, accounting for about one-third of all add(1)(p36) chromosomes seen in this cytogenetic subset.

Chromosome Aberrations↗
PubMed2002

Characterization of supernumerary rings and giant marker chromosomes in well-differentiated lipomatous tumors by a combination of G-banding, CGH, M-FISH, and chromosome- and locus-specific FISH.

Supernumerary ring chromosomes and/or giant marker chromosomes are often seen in soft-tissue tumors of low-grade or borderline malignancy, such as well-differentiated liposarcomas or atypical lipomas. Classic cytogenetic banding techniques have proved insufficient to identify the genomic composition and structure of such rings and markers, but fluorescent in situ hybridization (FISH) studies have shown that they consist mainly of amplified material from chromosome 12, more specifically from bands 12q13-->q15. We have used the new FISH-based screening techniques comparative genomic hybridization (CGH) and multicolor-FISH (M-FISH) in combination with G-banding and analysis by chromosome- and locus-specific fluorescent in situ probes to examine in detail the karyotypic characteristics of 22 lipomatous tumors, most of them classified histologically as well-differentiated liposarcomas, selected because they had been shown to harbor rings and/or marker chromosomes. M-FISH, in contrast to G- banding, was found to be informative with regard to the chromosomal origin of the rings and other markers present, whereas CGH and hybridizations with locus-specific probes helped identify which subchromosomal regions were involved. We found that chromosome bands 12q15-->q21 were always gained, with 12q15-->q21 being amplified (i.e., a green-to-red ratio >2 by CGH) in 14 of 22 tumors. In three tumors, two distinct but close amplicons in 12q could be identified, corresponding to bands 12q13-->q15 and 12q21. The genomic segment 1q21-->q23 was gained in 12 cases, reaching the level of amplification in seven. Bands 6q24 and 7p15, whose pathogenetic involvement in liposarcomas has not been reported previously, were gained in three cases each. In addition, the rings and giant markers often contained interspersed sequences from several other chromosomes that did not give an equally clear impression of being nonrandomly involved.

Biomarkers, Tumor↗
PubMed2001

Identification of cytogenetic subgroups and karyotypic pathways in transitional cell carcinoma.

The clinical course in urinary bladder cancer is difficult or impossible to predict based on conventional disease parameters. It is a reasonable hypothesis that the genetic aberrations acquired by the tumor cells, being instrumental in bringing about the disease in the first place, may also hold the key to more reliable prognostication. However, though 200 transitional cell carcinomas (TCC), the most common bladder cancer in the Western world, with clonal chromosomal abnormalities have been reported, our knowledge about the karyotypic characteristics of these tumors remains insufficient. The aberration pattern is clearly nonrandom, but no completely specific primary or secondary karyotypic abnormality has been identified, and the chronological order in which the aberrations appear during disease progression is not well known. The high degree of karyotypic complexity in epithelial tumors like TCC is one reason why our picture of the sequential order of cytogenetic evolution is unclear. To overcome some of these difficulties we have used several statistical methods that allow analysis and interpretation of the relationship between cytogenetic aberrations in TCC. We show that there exists a temporal order with respect to the appearance of chromosomal imbalances and that this order is highly correlated with tumor stage and grade. Analyzing changes in the distribution of imbalances per tumor in G1, G2, and G3 tumors, we suggest that progression involves the acquisition of cytogenetically detectable and submicroscopic genetic changes at comparable frequencies. By means of computer simulations, we show that the imbalances -9, +7, and 1q+ appear earlier than expected from random events and that -6q, -5q, -18, +5p, -22p, and -15 appear later than expected. Using principal component analysis, we identify two cytogenetic pathways in TCC, one initiated by -9 and followed by -11p and 1q+, the other initiated by +7 and followed by 8p- and +8q. The -9 pathway was correlated with stage Ta-T2 tumors, whereas the +7 pathway was correlated with stage T1-T3 tumors, i.e., +7 tumors appeared to be more aggressive. Although these pathways are well separated at earlier stages, they later converge to contain a common set of imbalances.

Carcinoma, Transitional Cell↗
PubMed2001

Functional asymmetry in schizophrenic patients during auditory speech processing.

In two experiments, functional laterality and interhemispheric transfer was investigated in schizophrenic patients (n=14) and healthy controls (n=17). In Experiment 1, words and pseudowords were presented either to the left or right ear (monaural condition) or simultaneously to both ears (binaural condition). In Experiment 2, subjects had to discriminate two tones differing in frequency during monaural and binaural stimulation. Healthy controls showed a right ear advantage (REA) for word stimuli, indicating left-hemispheric superiority for word processing. The same lateralization pattern was found in schizophrenic patients, indicating unimpaired functional lateralization of auditory language processing. In both groups, no REA was found for pseudowords resulting in significant WordnessxEar interactions. When presented binaurally, auditory processing of words and pseudowords did not differ significantly from any of the two monaural conditions. Tone discrimination did not lead to any ear asymmetry. The results show normal patterns of functional asymmetry during auditory language processing and tone discrimination in schizophrenic patients.

Adult↗
PubMed2001

Complications of meningococcal disease in college students.

A retrospective study was conducted to provide a description of the risk, complications, fatality, and sequelae associated with invasive meningococcal disease in college students admitted in the Allegheny county (Pennsylvania) hospital system from January 1990 to May 1999.

Adult↗
PubMed2001

Characterization of chromosomal abnormalities in uroepithelial carcinomas by G-banding, spectral karyotyping and FISH analysis.

Chromosome analysis by G-banding, spectral karyotyping (SKY) and fluorescence in situ hybridization (FISH) was performed on 24 short-term cultured transitional cell bladder carcinomas and 5 cell lines established from bladder carcinomas. Except for one tumor with an apparently normal chromosomal constitution, clonal chromosome abnormalities were detected in all examined cases by the combined approach. The application of SKY and FISH techniques improved the karyotypic descriptions, originally based on G-banding only, by identifying 32 additional numerical changes, by establishing the chromosomal origin of 27 markers and 2 ring chromosomes, by redefining 53 aberrations and by detecting 15 hidden chromosomal rearrangements. No recurrent translocation, however, was detected. The most prominent karyotypic feature was thus the occurrence of deletions and losses of whole chromosome copies indicating the importance of tumor suppressor genes in transitional cell carcinoma pathogenesis. Invasive carcinomas were karyotypically more complex than were low grade superficial tumors. Specific losses of material from chromosome 9 and from chromosome arms 11p and 8p, and gains of 8q and 1q seem to be early changes appearing in superficial tumors, whereas losses from 4p and 17p and the formation of an isochromosome for 5p were associated with more aggressive tumor phenotypes.

Aged↗
PubMed2001

Assessments of clonal composition of colorectal adenomas by FISH analysis of chromosomes 1, 7, 13 and 20.

Chromosome banding analysis has shown that numerical aberrations, in particular gains of chromosomes 7, 13 and 20, are common in colorectal adenomas but cannot provide reliable information on the size of the abnormal clones in vivo. We examined interphase nuclei from 70 colorectal adenomas, of which 64 had been previously karyotyped, using fluorescence in situ hybridization (FISH) with probes for the pericentromeric regions of chromosomes 1, 7, 13 and 20. Gain of chromosome 7 was seen in 34% of the analyzed adenomas, +13 was seen in 44% and trisomy 20 was found in 32% of the adenomas, verifying that the trisomies are in vivo phenomena. The median proportion of cells with trisomy was larger than 50%. A comparison with the G-banding analysis showed a good correlation between the results yielded by the 2 methods. Based on the clonal size and karyotypic findings, a likely order of events during clonal evolution could be ascribed to each case. More than 1 numerical aberration was detected by FISH analysis in 16 adenomas. In 6 adenomas, a clone with only trisomy 7 was present alongside a clone with additional gain(s) of chromosomes 13 and/or 20. Seven cases had gain of chromosome 13 and/or gain of chromosome 20 in the largest clone, suggesting that a clone with either of these changes was present before the changes in chromosome 7 copy number took place. On the basis of the results of this combined meta- and interphase cytogenetic study, we conclude that gains of chromosomes 7, 13 and 20 are common in colorectal adenomas and that the trisomies usually are present in a large proportion of the cells. They seem to be primary chromosome aberrations in some adenomas, whereas in others they arise secondarily as part of the clonal evolution. Although the first gain usually is of chromosome 7, it is evident that it is the end result of the chromosomal aberrations, not the exact sequence in which they occur, that determines the pathogenetic consequences.

Adenoma↗
PubMed2001

Auditory temporal processing deficit in dyslexia is associated with enhanced sensitivity in the visual modality.

Developmental dyslexia has been associated with a deficit in temporal processing, but it is controversial whether the postulated deficit is pansensory or limited to the auditory modality. We present psychophysical assessment data of auditory and visual temporal processing abilities in children with dyslexia. While none of the dyslexic children displayed temporal processing abnormalities in the visual sensory modality, dyslexics with poor auditory temporal scores reached high-level visual performance. Our results do not confirm the hypothesis of a general temporal processing deficit for dyslexia but suggest that limitations in auditory temporal processing might be compensated for by a well-functioning visual sensory modality.

Adaptation, Physiological↗