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Gene Arrangement (gene + arrangement)

Distribution by Scientific Domains
Life Sciences60%
Medical Sciences40%

Selected Abstracts

Organization of butyrate synthetic genes in human colonic bacteria: phylogenetic conservation and horizontal gene transfer

FEMS MICROBIOLOGY LETTERS, Issue 2 2007
Petra Louis
Abstract Butyrate producers constitute an important bacterial group in the human large intestine. Butyryl-CoA is formed from two molecules of acetyl-CoA in a process resembling ,-oxidation in reverse. Three different arrangements of the six genes coding for this pathway have been found in low mol% G+C-content Gram-positive human colonic bacteria using DNA sequencing and degenerate PCR. Gene arrangements were strongly conserved within phylogenetic groups defined by 16S rRNA gene sequence relationships. In the case of one of the genes, encoding ,-hydroxybutyryl-CoA dehydrogenase, however, sequence relationships were strongly suggestive of horizontal gene transfer between lineages. The newly identified gene for butyryl-CoA CoA-transferase, which performs the final step in butyrate formation in most known human colonic bacteria, was not closely linked to these central pathway genes. [source]

SEASONAL CYCLES OF ALLOZYME-BY-CHROMOSOMAL-INVERSION GAMETIC DISEQUILIBRIUM IN DROSOPHILA SUBOBSCURA

EVOLUTION, Issue 4 2003
Francisco Rodríguez-Trelles
Abstract Allozyme loci are frequently found non randomly associated to the chromosomal inversions in which they are included in Drosophila. Two opposite views compete to explain strong allozyme-by-inversion gametic disequilibria: they result from natural selection or, conversely, merely represent remnants of associations accidentally established at the origin of inversions. Empirical efforts aimed at deciding between adaptive and historical scenarios have focused on the spatial distribution of disequilibria. Yet, the evolutionary significance of these associations remains uncertain. I report here the results of a time-series analysis of the seasonal variation of alleles at six allozyme loci (Acph, Lap, Pept-1, Ao, Mpi, and Xdh) in connection with the O chromosomal polymorphisms of D. subobscura. The findings were: (1) in the segment I of the O chromosome, Lap and Pept-1 allozymes changed seasonally in a cyclical fashion within the ST gene arrangement, but they changed erratically within the 3+4 gene configuration; (2) the frequencies of Lap111 and Pept-10,40 within ST dropped to their lowest values in early and late summer, respectively, when the seasonal level of the ST arrangement is lowest. Furthermore, Lap1,11 and Pept-10,40 covary with ST only within these seasons, yet in a fashion inconsistent with these alleles having a major influence on the dynamics of the inversion; (3) seasonal cycling of alleles within inversions were not detected at Acph, Ao, Mpi, and Xdh, yet these loci are nearly monomorphic at the study population, and/or their sampled series were shorter than those for Lap and Pept-1; and (4) simply monitoring allozyme frequencies separately for each inversion proved to be superior, for evidencing the seasonal cycles of the disequilibria, to the use of the D' coefficient of association. Observed seasonal cycles of allozymes within inversions likely reflect natural selection. [source]

Subcutaneous Panniculitis-Like T Cell Lymphoma Developing in a Patient with Chronic B-Cell Lympocytic Leukemia

JOURNAL OF CUTANEOUS PATHOLOGY, Issue 1 2005
L Shahabi
Subcutaneous panniculitis-like T-cell lymphoma (SPTCL) is an unusual peripheral lymphoma most typically presenting with a cytotoxic (CD8-positive, TIA-1-positive) immunophenotype. SPTCLs may have an indolent or highly aggressive clinical course. Histologically, SPTCL may be notoriously difficult to diagnosis. Cases of SPTCL with a deceptively benign appearance similar to that of subcutaneous lupus erythematosus have been described. SPTCL associated with a concomitant systemic leukemia/lymphoma has not been documented in the literature. We report a case of SPTCL arising in a 65-year-old female with a well-established history of B-cell lymphocytic leukemia (BCLL). She presented with two months of recurrent fever and painless erythematous nodules on bilateral lower extremities that were clinically felt to be erythema nodosum. Initial biopsies demonstrated a polymorphous lobular infiltrate with neutrophils, karyorrhexis and lipomembranous change. An excisional biopsy demonstrated an atypical lymphoid population that expressed CD8 and TIA1. PCR analysis confirmed T-cell receptor gene arrangement. The patient was treated with systemic chemotherapy with resolution of her symptoms and complete remission. This is the first well documented case of SPTCL occurring in a patient with long standing B-CLL, and highlights the difficulty of establishing an unequivocal diagnosis of SPTCL. [source]

Rearrangement of immunoglobulin heavy and light chains and VH family in thyroid and salivary gland lymphomas

PATHOLOGY INTERNATIONAL, Issue 12 2002
Kei Kato
It is often difficult to differentiate extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) from non-neoplastic inflammatory conditions. Demonstration of clonal lymphoid proliferation by molecular procedures is important for accurate diagnosis. We examined the clonal population of B-cell lymphomas in nine cases of thyroid and two cases of salivary gland B-cell lymphoma using semi-nested polymerase chain reaction (PCR)-based assay for IgH gene arrangement and reverse transcription (RT)-PCR single-strand conformation polymorphism (SSCP) for the detection of IgL gene rearrangement. Clonality was evident in nine out of 11 cases of B-cell lymphomas examined by PCR, and in six of eight cases by RT-PCR SSCP. In addition, analysis of VH families was performed in eight cases. Although VH3 family was frequently used, each case demonstrated the VH4, VH5 or VH6 family. It is possible that the normal counterpart of thyroid or salivary gland lymphoma might be different from peripheral blood B lymphocytes, which usually use VH3 family. Our results indicate that although no clonality was noted in one case by both PCR and SSCP, these molecular methods are useful as supplementary diagnostic tests for both thyroid and salivary gland lymphomas. [source]

The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2005
MASAKI MIYA
In a previous study based on 100 whole mitochondrial genome (mitogenome) sequences, we sought to provide a new perspective on the ordinal relationships of higher ray-finned fish (Actinopterygii). The study left unexplored the phylogenetic ,position, of, toadfishes, (order, Batrachoidiformes),, as, data, were, unavailable, owing, to, technical, difficulties. In the present study, we successfully determined mitogenomic sequences for two toadfish species (Batrachomoeus trispinosus and Porichthys myriaster) and found that the difficulties resulted from unusual gene arrangements and associated repetitive non-coding sequences. Unambiguously aligned, concatenated mitogenomic sequences (13 461 bp) from 102 higher actinopterygians (excluding the ND6 gene and control region) were divided into five partitions (1st, 2nd and 3rd codon positions of the protein-coding genes, tRNA genes and rRNA genes) and partitioned Bayesian analyses were conducted. The resultant phylogenies strongly suggest that the toadfishes are not members of relatively primitive higher actinopterygians (Paracanthopterygii), but belong to a crown group of actinopterygians (Percomorpha), as was demonstrated for ophidiiform eels (Ophidiiformes) and anglerfishes (Lophiiformes) in the previous study. We propose revised limits of major unranked categories for higher actinopterygians and a new name (Berycomorpha) for a clade comprising two reciprocally paraphyletic orders (Beryciformes and Stephanoberyciformes) based on the present mitogenomic phylogenies. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85, 289,306. [source]