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Biomedical subjects

I Sommer

Publications and source records attributed to I Sommer.

At least 19 recordsLinked to original sources
PubMed2004

Predicting protein structure classes from function predictions.

MOTIVATION: We introduce a new approach to using the information contained in sequence-to-function prediction data in order to recognize protein template classes, a critical step in predicting protein structure. The data on which our method is based comprise probabilities of functional categories; for given query sequences these probabilities are obtained by a neural net that has previously been trained on a variety of functionally important features. On a training set of sequences we assess the relevance of individual functional categories for identifying a given structural family. Using a combination of the most relevant categories, the likelihood of a query sequence to belong to a specific family can be estimated. RESULTS: The performance of the method is evaluated using cross-validation. For a fixed structural family and for every sequence, a score is calculated that measures the evidence for family membership. Even for structural families of small size, family members receive significantly higher scores. For some examples, we show that the relevant functional features identified by this method are biologically meaningful. The proposed approach can be used to improve existing sequence-to-structure prediction methods. AVAILABILITY: Matlab code is available on request from the authors. The data are available at http://www.mpisb.mpg.de/~sommer/Fun2Struc/

Algorithms↗
PubMed2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.

SUMMARY: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided. AVAILABILITY: The HNB portal is available at http://www.hnbioinfo.de

Algorithms↗
PubMed2001

Handedness, language lateralisation and anatomical asymmetry in schizophrenia: meta-analysis.

BACKGROUND: Cerebral lateralisation appears to be decreased in schizophrenia. Results of studies investigating this, however, are equivocal. AIMS: To review quantitatively the literature on decreased lateralisation in schizophrenia. METHOD: Meta-analyses were conducted on 19 studies on handedness, 10 dichotic listening studies and 39 studies investigating anatomical asymmetry in schizophrenia. RESULTS: The prevalence of mixed- and left-handedness ('non-right-handedness') was significantly higher in patients with schizophrenia as compared to healthy controls, and also as compared to psychiatric controls. The analysis of dichotic listening studies revealed no significant difference in lateralisation in schizophrenia. However, when analysis was restricted to studies using consonant-vowel or fused word tasks, significantly decreased lateralisation in schizophrenia emerged. Asymmetry of the planum temporale and the Sylvian fissure was significantly decreased in schizophrenia, while asymmetry of the temporal horn of the lateral ventricle was not. CONCLUSION: Strong evidence is provided for decreased cerebral lateralisation in schizophrenia.

Brain↗
PubMed2001

[Malignant humoral hypercalcemia associated with angiotropic large B cell lymphoma].

Angiotropic large B cell lymphoma (angiotropic LCL) or intravascular large cell lymphoma (IVLCL) was diagnosed by liver and bone marrow biopsies and immunohistochemical studies in a 52 year old Caucasian male. IVLCL is a very rare disease characterized by widespread intravascular proliferation of lymphoma cells. Although it most commonly affects the central nervous system or skin and occasionally bone marrow, angiotropic LCL may be present without evidence of localized disease, as seen initially in our patient. To date, only a few cases of intravascular malignant lymphomatosis associated with parathyroid hormone related protein (PTH-rP) induced humoral hypercalcemia have been published. Our extraordinary case was diagnosed mainly by liver biopsy. The neoplastic lymphoid cells stained diffusely and strongly positive with CD-20 (Pan B) and were negative for CD-3 (Pan T) immunostain. The most significant, initial clinical finding was severe, unexplained hypercalcemia (until 18.6 mg/dl). Plasma PTH-rP showed a ten-fold increase at 8 pmol/L (normal value less than 0.8 pmol/L). Very unusual cytogenic abnormalities were found. The patient received the massive third generation combination chemotherapy comprising of Methotrexate, Doxorubicine, Cyclophosphamide, Vincristine, Prednisone and Bleomycin and developed, complete although temporary, clinical, humoral and cytogenetic remission.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2000

The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution.

The Escherichia coli 23 S and 5 S rRNA molecules have been fitted helix by helix to a cryo-electron microscopic (EM) reconstruction of the 50 S ribosomal subunit, using an unfiltered version of the recently published 50 S reconstruction at 7.5 A resolution. At this resolution, the EM density shows a well-defined network of fine structural elements, in which the major and minor grooves of the rRNA helices can be discerned at many locations. The 3D folding of the rRNA molecules within this EM density is constrained by their well-established secondary structures, and further constraints are provided by intra and inter-rRNA crosslinking data, as well as by tertiary interactions and pseudoknots. RNA-protein cross-link and foot-print sites on the 23 S and 5 S rRNA were used to position the rRNA elements concerned in relation to the known arrangement of the ribosomal proteins as determined by immuno-electron microscopy. The published X-ray or NMR structures of seven 50 S ribosomal proteins or RNA-protein complexes were incorporated into the EM density. The 3D locations of cross-link and foot-print sites to the 23 S rRNA from tRNA bound to the ribosomal A, P or E sites were correlated with the positions of the tRNA molecules directly observed in earlier reconstructions of the 70 S ribosome at 13 A or 20 A. Similarly, the positions of cross-link sites within the peptidyl transferase ring of the 23 S rRNA from the aminoacyl residue of tRNA were correlated with the locations of the CCA ends of the A and P site tRNA. Sites on the 23 S rRNA that are cross-linked to the N termini of peptides of different lengths were all found to lie within or close to the internal tunnel connecting the peptidyl transferase region with the presumed peptide exit site on the solvent side of the 50 S subunit. The post-transcriptionally modified bases in the 23 S rRNA form a cluster close to the peptidyl transferase area. The minimum conserved core elements of the secondary structure of the 23 S rRNA form a compact block within the 3D structure and, conversely, the points corresponding to the locations of expansion segments in 28 S rRNA all lie on the outside of the structure.

Base Sequence↗
PubMed1996

Monoclonal antibody O10 defines a conformationally sensitive cell-surface epitope of proteolipid protein (PLP): evidence that PLP misfolding underlies dysmyelination in mutant mice.

Mutations in the gene for proteolipid protein (PLP) have been associated with CNS dysmyelination and abnormal oligodendrocyte death in spontaneous mouse mutants and in Pelizaeus-Merzbacher disease; however, the effect of mutations on PLP structure and function are little understood. We have identified a monoclonal antibody directed against a novel cell surface epitope of PLP, termed O10. By immunofluorescence analysis, COS-7 cells transiently transfected to express PLP (or its isoform DM20) can be stained with antibody O10 and another antibody (A431) directed against the C terminus of PLP/DM20. The subcellular distribution of immunofluorescence labels for the two antibodies is not identical, suggesting that the O10 epitope is acquired post-translationally. When PLP/DM20 from jimpy, jimpymsd, and rumpshaker mutant mice is expressed in COS-7 cells and compared with wild-type PLP/DM20, none of the mutant isoforms displays the O10 epitope, whereas the C-terminal epitope is detected. Because the O10 but not the A431 epitope is also sensitive to SDS and reducing agents, this strongly suggests abnormal protein folding in the PLP mutants. PLP from jimpymsd mice is obviously misfolded, because the amino acid substitution (Ala242 --> Val) is located within a transmembrane domain to which the O10 antibody does not bind. We propose that the O10 epitope emerges as the full length protein reaches a functional tertiary structure and that the absence of this epitope marks a structural defect of PLP that leads to dysmyelination.

Animals↗
PubMed1996

Evidence that some oligodendrocyte progenitors in the developing optic pathway express the plp gene.

DM-20, a product of the proteolipid protein (plp) gene, has been demonstrated in the spinal cord of the mouse embryo as early as embryonic day 12 (E12) in certain cells, some of which are identifiable as oligodendrocyte progenitors. The present work uses optic pathways of rat and mouse as well-characterized systems for the study of gliogenesis. plp gene expression was monitored with a combination of reverse transcriptase polymerase chain reaction, in situ hybridization, and immunostaining with antibodies to different PLP peptide sequences, combined with O-2A lineage markers. In tissue sections, hybridizing cells were detected initially in the proximal optic tracts between E18 and birth and thereafter progressively in the chiasm and optic nerves. Small unbranched cells expressing DM-20 but not myelin basic protein (MBP) and probably representing progenitors were detectable by immunostaining in similar locations. With increasing postnatal ages, cells representing maturing oligodendrocytes which co-label for PLP and MBP are present in the optic pathways. In vitro analysis of freshly dissociated cells from premyelinated optic nerve demonstrated that the plp gene is expressed in some O-2A progenitor cells as well as mature oligodendrocytes. We also present evidence that increase in expression of the plp gene along the O-2A lineage differentiation is not progressive but that downregulation at the proligodendroblast (O4+/O1-) stage probably occurs. We suggest that progenitors express the dm-20 isoform while oligodendrocytes express predominantly the plp isoform. Not all progenitors express the plp gene at the times studied, indicating that the presence of DM-20 is either transitory in individual cells or that only a sub-population is involved. The function of DM-20 at this early stage of the oligodendrocyte lineage has yet to be determined.

Animals↗
PubMed1995

Role of the cytoskeleton in the reaction of fibroblasts to multiple grooved substrata.

The role of the cytoskeleton and cell attachments in the alignment of baby hamster kidney fibroblasts to ridge and groove substratum topography was investigated using confocal scanning microscopy. This was carried out with normal cells and cells treated with the cytoskeleton modifiers cytochalasin D, colcemid, and taxol. Actin was localised with fluorescent phalloidin. Tubulin, vinculin, and intracellular adhesion molecule-1 were visualised by indirect immunofluorescence. The spreading, elongation, and orientation of the cells after 24 h of culture in these conditions were measured on grooves of 5, 10, and 25 microns width and 0.5, 1, 2, and 5 microns depth. We have also observed events over the first 30 min of cell attachment. Five minutes after cell attachment, F-actin condensations were seen close to the intersection of groove wall and ridge top, that is, at a topographic discontinuity. The condensations were often at right angles to the groove edge and showed a periodicity of 0.6 microns. Vinculin arrangement at the early stages of cell spreading was similar to that of actin. Organisation of the microtubule system followed later, becoming obvious at about 30 min after cell plating. The Curtis and Clark theory (that cells react to topography primarily at lines of discontinuity in the substratum by actin nucleation) is supported by these results. The use of cytoskeletal poisons did not entirely abolish cell reaction to grooves. Colcemid increased cell spreading and reduced cell orientation and elongation. Cytochalasin D reduced cell spreading, orientation, and elongation. Taxol reduced cell elongation but did not affect cell spreading and orientation. We conclude that the aggregation of actin along groove/ridge boundaries is a primary driving event in determining fibroblast orientation on microgrooved substrata.

Animals↗
PubMed1995

O-2A progenitors of the mouse optic nerve exhibit a developmental pattern of antigen expression different from the rat.

In a previous study we demonstrated that differentiation and development of mouse oligodendrocytes is similar to that of the rat after the stage at which O4 is acquired. In this present study we compare directly the early differentiation of oligodendrocytes in the mouse and rat post natal optic nerve and show that the two species differ at the O-2A progenitor and proligodendroblast stages. Mouse progenitors show a variety of morphologies compared to the typical bipolar appearance in the rat. Many murine cells fail to immunolabel with A2B5, GD3, O4, and RmAb, classical markers for rat progenitors, proligodendroblasts, and immature oligodendrocytes. We find that these "unlabeled" cells stain for GAP-43 and that expression of GAP-43 overlaps A2B5 and GD3 in the earlier progenitors and O4, RmAb, and O1 in the later proligodendroblasts and immature oligodendrocytes. Our data suggest that in the development of the mouse O-2A progenitor cells there is a developmental discontinuity between the earlier markers such as A2B5 and GD3 and the later marker O4, which can be filled by GAP-43. We therefore consider that GAP-43 could be used in the mouse, in addition to the classical O-2A markers, for the study of the early oligodendrocyte lineage as it labels an otherwise undetectable O-2A population.

Animals↗
PubMed1993

Principal cells of the rat medial nucleus of the trapezoid body: an intracellular in vivo study of their physiology and morphology.

The medial nucleus of the trapezoid body (MNTB) is one of several principal nuclei in the superior olivary complex (SOC) of mammals. It is classically thought to function as a relay station between the contralateral ventral cochlear nucleus and the lateral superior olive (LSO), playing a role among those brainstem nuclei that are involved in binaural hearing. In order to characterise the physiology and morphology at the cellular level of the major neuronal component of the MNTB, the principal cells, we have analysed these neurons in rats in vivo using intracellular recordings and horseradish peroxidase-labelling. Our data demonstrate that MNTB principal cells, when being stimulated acoustically via the contralateral ear, show a phasic-tonic response with an onset latency of 3.5 ms and a suppression of their spontaneous activity following stimulus offset. These neurons have an axonal morphology whose complexity has not yet been described. All cells (n = 10) projected exclusively ipsilaterally and had terminal axonal arbors in a variety of auditory brainstem nuclei. At least two and maximally seven auditory targets were innervated by an individual cell. Each cell projected into the LSO and the superior paraolivary nucleus (SPN). Additional projections that were intrinsic to the SOC were often observed in the lateral nucleus of the trapezoid body and in periolivary regions, with only one cell projecting into the medial superior olive. Most, if not all, MNTB principal cells also had projections that were extrinsic to the SOC, as their axons ascended into the lateral lemniscus. In two neurons the ascending axon formed terminal arbors in the ventral nucleus of the lateral lemniscus, and the dorsal nucleus of the lateral lemniscus could be identified as a target of one neuron. The location of the cell bodies of the MNTB principal cells correlated with the neurons' best frequencies, thereby demonstrating a tonotopic organisation of the MNTB, with high frequencies being represented medially and low frequencies laterally. The axonal projections into the LSO and the SPN were also tonotopically organised and the alignment of the tonotopically organised and the alignment of the tonotopic axes was similar to that in the MNTB. Our results confirm previous data from other species and suggest that MNTB principal cells have a great amount of physiological and morphological similarities across mammalian species. Furthermore, the complexity of the axonal projections indicates that these neurons play a role in auditory information processing which goes far beyond their previously described classical role.

Acoustic Stimulation↗
PubMed1993

Characterization of cDNA clones encoding a major microneme antigen of Sarcocystis muris (Apicomplexa) cyst merozoites.

Two monoclonal antibodies directed against a microneme antigen of Sarcocystis muris cyst merozoites (16/17 kDa band doublet) were used to isolate cDNA clones from a lambda ZAP expression library. Restriction analysis revealed that the inserts were highly similar, with sizes ranging between 1.8 and 2.3 kb. In addition, a full-length cDNA insert of 2.6 kb was obtained by hybridization screening. On Northern blots, a single mRNA species of 2.7 kb was detected by a cDNA-derived probe. Southern blot hybridization suggests that the gene is present as a single copy. The nucleotide sequence of the full-length clone contains a single reading frame with a coding capacity of 26.5 kDa. The hypothetical polypeptide consists of a putative N-terminal signal peptide followed by a hydrophilic domain of unknown function, and the mature protein sequence. After purifying the 16/17 kDa antigen from cyst merozoites, a partial N-terminal amino acid sequence was obtained. Thus, the identity of the cDNA sequence was confirmed. The deduced sequence of the mature protein is predominantly hydrophilic and rich in cysteine (8.7%). Database searching suggested weak homologies of the hypothetical polypeptide to plasma kallikrein, tenascin and blood coagulation factors.

Amino Acid Sequence↗
PubMed1992

[Remission of acute promyelocytic leukemia after all-trans-retinoic acid].

This is the first report in Israel of the successful treatment of acute promyelocytic leukemia (APL; M3) with an active metabolite of vitamin A. In a 42-year-old woman with APL all-trans-retinoic acid (ATRA; tretinoin), 45 mg/m2/day was given per os for 90 days. APL is associated with a distinct cytogenetic abnormality: translocation of a portion of the long arm chromosome 17 onto the long arm chromosome 15t (15; 17) with a breakpoint on chromosome 17 in the region of the retinoic acid receptor-alpha (RAR-alpha), playing a crucial role in the leukemogenesis of APL. In man, the drug induces myeloid and mainly promyelocytic leukemic cells to differentiate, without the development of bone marrow hypoplasia. In our patient it caused complete remission and the disappearance of intravascular disseminated coagulation. The only side-effects were a transient macular rash, gastrointestinal symptoms and mild hypertriglyceridemia. Other principal adverse effects reported in the literature are relatively not very serious and consist of dryness of the skin, occasional headaches and intracranial hypertension, nasal congestion, lymphadenopathy, respiratory distress with infiltrates in the lung, bone pain and increased hepatic aminotransferase. A hyperleukocytosis syndrome seems to be more problematic. ATRA appears to be superior to conventional chemotherapeutic regimens. It is safe and highly effective in inducing clinical, morphologic and karyotypic remission with a marked decrease in the expression of the abnormal RAR-message in APL. There is a possible molecular link between the pathogenesis and treatment of this severe and often fatal coagulopathic disease. This therapy of course does not eradicate the leukemic clone, and consolidation chemotherapy or bone marrow transplantation is necessary.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1992

Glyphosate tolerance of cultured Corydalis sempervirens cells is acquired by an increased rate of transcription of 5-enolpyruvylshikimate 3-phosphate synthase as well as by a reduced turnover of the enzyme.

Cell cultures of Corydalis sempervirens, tolerant to the herbicide glyphosate, have a 30-40-fold increased level of the herbicide's target enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, a ten-fold enhanced level of the corresponding mRNA but no amplification of the gene (Holländer-Czytko et al., Plant Mol Biol 11 (1988) 215-220). The increase at the transcriptional level is due to a higher rate of transcription of the gene, which was observed in run-off transcription assays with isolated nuclei. The further amplification at the protein level is the result of stabilization of the enzyme by the herbicide. In the presence of glyphosate the half-life of EPSP synthase was doubled leading to higher levels of both protein and enzyme activity. Overproduction of the enzyme in adapted cultures is stable at the transcriptional level, as cells from adapted cultures grown in the absence of glyphosate for three years still display an about ten-fold higher enzyme activity and transcript level than non-adapted cultures.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗
PubMed1992

A comparison of sporozoite and cyst merozoite surface proteins of Sarcocystis.

Surface labeling of Sarcocystis muris and S. suicanis sporozoites with N-hydroxysuccinimide biotin led to the detection of major membrane proteins with relative molecular weights of 29 and 30 kDa, respectively. Immunoblots of Sarcocystis sporozoite proteins probed with sera from infected hosts or with polyclonal monospecific antibodies generated against membrane antigens of cyst merozoites (noncorresponding stages) showed cross-reactivity between the two developmental stages (cyst merozoites and sporozoites) as well as between the species S. muris and S. suicanis. Two-dimensional gel electrophoresis resulted in the identification of isoforms of the sporozoite membrane antigens, with isoelectric points ranging from pH 4.7 to pH 6.4 for S. muris and from pH 4.7 to pH 5.2 for S. suicanis. The molecular masses, the charge heterogeneity, and the immunological reactivity of the surface proteins of Sarcocystis sporozoites were similar to those of cyst merozoites of both species.

Animals↗
PubMed1992

Cloning and expression in Escherichia coli of cDNAs encoding a 31-kilodalton surface antigen of Sarcocystis muris.

Using polyadenylated RNA isolated from Sarcocystis muris cyst merozoites, we have constructed a cDNA library in the expression vector lambda ZAP. Immunoscreening with monoclonal and polyclonal antibodies directed against a 31-kDa surface antigen of S. muris [1] yielded a number of clones with insert sizes ranging between 1.1 kb and 1.3 kb. An additional clone with an insert length of 1.55 kb was isolated by screening with a labeled DNA probe derived from one of the cDNA clones. The cDNA sequence was found to contain an open reading frame specifying a polypeptide of 280 amino acids with a predicted size of 29.7 kDa. The deduced amino acid sequence is rich in serine and threonine (22%) and harbors a hypothetical N-terminal signal peptide sequence as well as a C-terminal glycosyl phosphatidylinositol anchor attachment site. The predicted amino acid sequence has been confirmed by peptide sequencing and an analysis of the overall amino acid composition of the 31-kDa protein. A recombinant protein was obtained which was recognized by the polyclonal antibodies directed against the 31-kDa antigen. Antiserum raised against the purified fusion protein specifically reacted with a 31-kDa protein from S. muris cystozoites. Southern blot analysis indicated that the corresponding gene exists as a single copy within the S. muris genome.

Amino Acid Sequence↗
PubMed1991

Biochemical and immunological characterization of major surface antigens of Sarcocystis muris and S. suicanis cyst merozoites.

Surface proteins of Sarcocystis cyst merozoites were labeled by biotinylation or radioiodination and identified on Western blots after sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The major labeled proteins of S. muris and S. suicanis have relative molecular masses of 31 and 33 kDa, respectively. Immunoblots performed with the 31-kDa protein and sera of experimentally infected mice or with monoclonal antibodies to S. muris revealed that this protein is immunogenic. Indirect fluorescent antibody tests (IFAT) executed using Sarcocystis cyst merozoites and polyclonal monospecific antibodies obtained from rabbits immunized with homogeneous major surface antigens gave additional evidence for the localization of the identified antigens in the pellicle. Analysis of S. muris and S. suicanis proteins by two-dimensional gel electrophoresis revealed multiple isoelectric forms.

Animals↗