PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM.

PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator.

A t(4;19) pediatric undifferentiated sarcoma with a novel variant of the CIC-DUX4 fusion transcript.

We report cytogenetic and molecular genetic analysis of a pediatric tumor positive for the CIC-DUX4 fusion. The tumor belongs to a rare, diagnostically challenging subgroup of undifferentiated small round cell sarcomas. A balanced t(4;19)(q35;q13.

SART3-Dependent Accumulation of Incomplete Spliceosomal snRNPs in Cajal Bodies.

Cajal bodies (CBs) are evolutionarily conserved nuclear structures involved in the metabolism of spliceosomal small nuclear ribonucleoprotein particles (snRNPs). CBs are not present in all cell types, and the trigger for their formation is not yet known. Here, we depleted cells of factors required for the final steps of snRNP assembly and assayed for the presence of stalled intermediates in CBs.

The splicing factor U1-70K interacts with the SMN complex and is required for nuclear gem integrity.

The nuclear SMN complex localizes to specific structures called nuclear gems. The loss of gems is a cellular marker for several neurodegenerative diseases. Here, we identify that the U1-snRNP-specific protein U1-70K localizes to nuclear gems, and we show that U1-70K is necessary for gem integrity.

Enzyme-linked electrochemical DNA ligation assay using magnetic beads.

DNA ligases are essential enzymes in all cells and have been proposed as targets for novel antibiotics. Efficient DNA ligase activity assays are thus required for applications in biomedical research. Here we present an enzyme-linked electrochemical assay based on two terminally tagged probes forming a nicked junction upon hybridization with a template DNA.

The C-terminal domain of Brd2 is important for chromatin interaction and regulation of transcription and alternative splicing.

Brd2 is a member of the bromodomain extra terminal (BET) protein family, which consists of four chromatin-interacting proteins that regulate gene expression. Each BET protein contains two N-terminal bromodomains, which recognize acetylated histones, and the C-terminal protein-protein interaction domain. Using a genome-wide screen, we identify 1450 genes whose transcription is regulated by Brd2.

Changes in MYCN expression in human neuroblastoma cell lines following cisplatin treatment may not be related to MYCN copy numbers.

Neuroblastoma is a tumor accounting for approximately 10% of all childhood malignancies and 50% of all childhood cancer-related deaths. MYCN gene copy number variation represents the most important prognostic factor in neuroblastoma. Prognostic significance of MYCN gene expression is more complicated and may depend on other factors such as MYCN gene copy number status.

Burkitt lymphoma (BL): reclassification of 39 lymphomas diagnosed as BL or Burkitt-like lymphoma in the past based on immunohistochemistry and fluorescence in situ hybridization.

Burkitt lymphoma (BL) is a well characterized entity. For atypical findings a term Burkitt-like lymphoma (B-LL) was applied in the past, but the interpretation of the morphological appearances was subjective and poorly reproducible. We used a combined approach (morphology using classical histological staining; immunohistochemistry-IHC; fluorescence in situ hybridization-FISH on interphase nuclei; cytogenetics) to perform a retrospective study on 39 patients diagnosed as BL and B-LL at our department in the years 1982 to 2002.

Cytogenetic and array comparative genomic hybridization analysis of a series of hepatoblastomas.

Hepatoblastoma is the most common primary hepatic tumor in children, and only a limited number of detailed karyotypic analyses have been reported to date. In the present study, cytogenetic abnormalities were identified in nine cases of hepatoblastoma from a single institution. Among characteristic chromosomal changes detected were simple numerical aberrations, structural alterations of chromosomes 1, 2, and 8, and the recurrent unbalanced rearrangements der(4)t(1;4)(q25.

[Clinical relevance of chromosomal aberrations in bone and soft tissue tumors in children and young adults].

Background: We present the results of a cytogenetic and molecular cytogenetic analysis of a series of patients with bone and soft tissue tumors. PATIENTS ANDMETHODS: We analyzed a cohort of 26 patients with Ewing sarcoma/PNET, 15 patients with rhabdomyosarcoma, 5 with synovial sarcoma and one patient with an undifferentiated sarcoma using the cytogenetic and molecular cytogenetic techniques M-FISH and arrayCGH.

Results: We found nonrandom chromosomal structural and numerical changes with diagnostic and prognostic relevance in most patients.

Lipoblastoma in children: an analysis of 5 cases.

Lipoblastoma is a very rare benign tumour that is caused by embryonal fat. The present five cases of lipoblastoma operated on during the years 1996-2005. The localization of the lipoblastomas in our series were very unusual.

A novel variant of SYT-SSX1 fusion gene in a case of spindle cell synovial sarcoma.

Synovial sarcoma (SS) is a rare soft-tissue tumor that affects children and young adults. It is characterized by chromosomal translocation t(X;18)(p11.2;q11.

Teratoma in an adolescent with malignant transformation into embryonal rhabdomyosarcoma: case report.

Background: The somatic type tumors are occasionally found in nonseminomatous germ cell tumors in men. These malignancies are presumed to arise from malignant transformation (MT) of teratoma or by differentiation of totipotential germ cell.

Observation: A case of MT of germ cell tumor in 17-year-old male into embryonal rhabdomyosarcoma is described.

Primary mediastinal (thymic) large B-cell lymphoma with a der(14)t(8;14)(q24;q32) and a translocation of MYC to the derivative chromosome 14 with a deleted IgH locus.

We report a case of primary mediastinal (thymic) large B-cell lymphoma (PMBL) with an initial karyotype containing numerical chromosomal aberrations: +X, +9, +12, +21, and a novel translocation t(2;11)(q?31; q23 approximately 24) with a duplication of the derivative chromosome 11. Subsequent multicolor fluorescence in situ hybridization (M-FISH) analysis revealed a der(14)t(8;14)(q24;q32). Further analysis using fluorescence in situ hybridization (FISH) with locus-specific probes revealed loss of the entire IgH locus from the der(14)t(8;14) and relocation of MYC to this derivative chromosome 14.

[Anaplastic large-cell lymphoma: review].

Anaplastic large cell lymphomas (ALCLs) represent a heterogeneous group of malignant lymphoproliferative diseases. Most of the cases are of T-cell line with a loss of cell surface receptors but with a production of cytotoxic cytoplasmatic granules--immunohistochemically (IHC) positive perforin, granzyme B, and TIA-1. The diagnostics of ALCL is based on morphological findings and results of IHC, which further stratify ALCLs to basic immunophenotypes according to ALK (anaplastic lymphoma kinase) protein expression--ALCL CD30+ ALK+ and ALCL CD30+ ALK+.

Malignant peripheral primitive neuroectodermal tumor of the kidney.

Ewing family of tumors is a group of highly aggressive neoplasias that occur most commonly in the first two decades of life. These tumors are most frequently localized in bones, less frequently in soft tissues. They usually appear as undifferentiated small round-cell tumors.

[Detection of minimal residual disease in Ewing's sarcoma using RT-PCR].

Background: More than 90% of Ewing's sarcomas (ES) contain a fusion of the EWS and FLI-1 genes, due to the t(11;22)(q23;q12) translocation. At the molecular level, the EWS-FLI-1 rearrangement shows great diversity. Specifically, many different combinations of exons from EWS-FLI-1 encode in-frame fusion transcripts and result in differences in length and composition of the chimeric protein, which function as an oncogenic aberrant transcription factor.

Gene aberrations in childhood brain tumors.

We present the results of the examination of prognostic markers in 40 children suffering from brain tumors. Prognostic markers such as amplification of the N-myc and c-myc, deletion of the 17p, and DNA ploidy are indispensable factors for the determination of diagnosis. An increased number of c-myc gene copies was found in malignant brain tumors, especially embryonal, more often than reported in the literature.

Environmental genotoxicity monitoring using Salmonella typhimurium strains as indicator system.

Screening for mutagens in environmental complex mixtures is gradually accepted as a routine methodology in the monitoring processes. Examination of 70 drinking water samples showed that the variations in the degree of mutagenicity was dependent on the location of the water source and the type of drinking water tested. Analogous screening for mutagens in river and waste waters may help better assess the potential genotoxic hazard from various types of industrial technology.

Enzyme synthesis of L-tryptophan.

Enzyme synthesis of tryptophan from indole, pyruvate and ammonium salts was studied using Escherichia coli cells exhibiting a significant tryptophanase activity. In addition to the effect of cultivation medium composition and cultivation conditions, factors affecting the course of the conversion were investigated. Production of 32.

Simultaneous induction of three catabolic enzymes in Escherichia coli.

During a simultaneous induction of three enzymes which are subject to catabolite repression (beta-galactosidase, tryptophanase and amylomaltase, or beta-galactosidase, tryptophanase and D-serine deaminase) in a batch culture, the rates of synthesis of beta-galactosidase and tryptophanase decreases, while the rates of synthesis of amylomaltase and D-serine deaminase remain unaffected. The addition of cAMP brings about a considerable increase of the rate of synthesis of D-serine deaminase and a partial synthesis rate increase of beta-galactosidase whihle the synthesis rate of tryptophanase remains lowered and the synthesis rate of amylomaltase remains unaffected. In a continuous culture beta-galactosidase, tryptophanase and D-serine deaminase are synthesized simultaneously at a maximum rate without mutual influence.