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Lars Podsiadlowski - One of the best experts on this subject based on the ideXlab platform.
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multiple rearrangements in mitochondrial genomes of isopoda and phyloGenetic implications
Molecular Phylogenetics and Evolution, 2012Co-Authors: Fabian Kilpert, Christoph Held, Lars PodsiadlowskiAbstract:In this study, we analyse the evolutionary dynamics and phyloGenetic implications of Gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans. The sequence coverage is nearly complete for four of the five newly sequenced species, with only the control region and some tRNA Genes missing, while in Janira maculosa only two thirds of the genome could be determined. Mitochondrial Gene order in isopods seems to be more plastic than that in other crustacean lineages, making all nine known mt Gene orders different. Especially the asellote Janira is characterized by many autapomorphies. The following inferred ancestral isopod mt Gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred Gene Translocation events leading to Gene rearrangements as valuable characters in phyloGenetic analyses. In this first study covering major isopod lineages, potential apomorphies were identified, e.g., a shared relative position of trnR in Valvifera. We also report one of the first findings of homoplasy in mitochondrial Gene order, namely a shared relative position of trnV in unrelated isopod lineages. In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phyloGenetic context.
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The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel Gene order and unusual control region features
BMC Genomics, 2006Co-Authors: Fabian Kilpert, Lars PodsiadlowskiAbstract:Background Sequence data and other characters from mitochondrial genomes (Gene Translocations, secondary structure of RNA molecules) are useful in phyloGenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of Gene Translocation, Gene duplication and Gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. Results The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial Gene order compared to other crustacean species. An overview about mitochondrial Gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4× 10 bp and 3× 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA Genes are putative targets for RNA editing, trnR could not be localized at all. Conclusion Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived Gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis , suggesting that most of the Translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA Genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.
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the complete mitochondrial genome of the common sea slater ligia oceanica crustacea isopoda bears a novel Gene order and unusual control region features
BMC Genomics, 2006Co-Authors: Fabian Kilpert, Lars PodsiadlowskiAbstract:Sequence data and other characters from mitochondrial genomes (Gene Translocations, secondary structure of RNA molecules) are useful in phyloGenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of Gene Translocation, Gene duplication and Gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial Gene order compared to other crustacean species. An overview about mitochondrial Gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4× 10 bp and 3× 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA Genes are putative targets for RNA editing, trnR could not be localized at all. Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived Gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the Translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA Genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.
Fabian Kilpert - One of the best experts on this subject based on the ideXlab platform.
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multiple rearrangements in mitochondrial genomes of isopoda and phyloGenetic implications
Molecular Phylogenetics and Evolution, 2012Co-Authors: Fabian Kilpert, Christoph Held, Lars PodsiadlowskiAbstract:In this study, we analyse the evolutionary dynamics and phyloGenetic implications of Gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans. The sequence coverage is nearly complete for four of the five newly sequenced species, with only the control region and some tRNA Genes missing, while in Janira maculosa only two thirds of the genome could be determined. Mitochondrial Gene order in isopods seems to be more plastic than that in other crustacean lineages, making all nine known mt Gene orders different. Especially the asellote Janira is characterized by many autapomorphies. The following inferred ancestral isopod mt Gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred Gene Translocation events leading to Gene rearrangements as valuable characters in phyloGenetic analyses. In this first study covering major isopod lineages, potential apomorphies were identified, e.g., a shared relative position of trnR in Valvifera. We also report one of the first findings of homoplasy in mitochondrial Gene order, namely a shared relative position of trnV in unrelated isopod lineages. In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phyloGenetic context.
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The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel Gene order and unusual control region features
BMC Genomics, 2006Co-Authors: Fabian Kilpert, Lars PodsiadlowskiAbstract:Background Sequence data and other characters from mitochondrial genomes (Gene Translocations, secondary structure of RNA molecules) are useful in phyloGenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of Gene Translocation, Gene duplication and Gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. Results The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial Gene order compared to other crustacean species. An overview about mitochondrial Gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4× 10 bp and 3× 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA Genes are putative targets for RNA editing, trnR could not be localized at all. Conclusion Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived Gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis , suggesting that most of the Translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA Genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.
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the complete mitochondrial genome of the common sea slater ligia oceanica crustacea isopoda bears a novel Gene order and unusual control region features
BMC Genomics, 2006Co-Authors: Fabian Kilpert, Lars PodsiadlowskiAbstract:Sequence data and other characters from mitochondrial genomes (Gene Translocations, secondary structure of RNA molecules) are useful in phyloGenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of Gene Translocation, Gene duplication and Gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial Gene order compared to other crustacean species. An overview about mitochondrial Gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4× 10 bp and 3× 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA Genes are putative targets for RNA editing, trnR could not be localized at all. Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived Gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the Translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA Genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.
Jessica L Davis - One of the best experts on this subject based on the ideXlab platform.
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ewsr1 nfatc2 Gene fusion in a soft tissue tumor with epithelioid round cell morphology and abundant stroma a case report and review of the literature
Human Pathology, 2018Co-Authors: Jarish N Cohen, Amit J Sabnis, Gregor Krings, Andrew E Horvai, Jessica L DavisAbstract:Summary Mesenchymal round cell tumors are a diverse group of neoplasms defined by primitive, often high-grade cytomorphology. The most common molecular alterations detected in these tumors are Gene rearrangements involving EWSR1 to one of many fusion partners. Rare EWSR1-NFATC2 Gene rearrangements, corresponding to a t(20;22) Gene Translocation, have been described in mesenchymal tumors with clear round cell morphology and a predilection for the skeleton. We present a case of a tumor harboring the EWSR1-NFATC2 Gene fusion arising in the subcutaneous tissue of a young woman. The tumor exhibited corded and trabecular architecture of epithelioid cells within abundant myxoid and fibrous stroma. The cells showed strong immunoreactivity for NKX2.2, variable CD99, keratin, and EMA, but were negative for S100 and myoepithelial markers. Importantly, similar to previously reported cases the clinical course was more indolent than that of Ewing sarcoma. This case highlights the distinctive clinicopathologic characteristics of EWSR1-NFATC2 Gene fusion-associated neoplasms that distinguish them from Ewing sarcoma.
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ewsr1 nfatc2 Gene fusion in a soft tissue tumor with epithelioid round cell morphology and abundant stroma a case report and review of the literature
Human Pathology, 2018Co-Authors: Jarish N Cohen, Amit J Sabnis, Gregor Krings, Andrew E Horvai, Soojin Cho, Jessica L DavisAbstract:Mesenchymal round cell tumors are a diverse group of neoplasms defined by primitive, often high-grade cytomorphology. The most common molecular alterations detected in these tumors are Gene rearrangements involving EWSR1 to one of many fusion partners. Rare EWSR1-NFATC2 Gene rearrangements, corresponding to a t(20;22) Gene Translocation, have been described in mesenchymal tumors with clear round cell morphology and a predilection for the skeleton. We present a case of a tumor harboring the EWSR1-NFATC2 Gene fusion arising in the subcutaneous tissue of a young woman. The tumor exhibited corded and trabecular architecture of epithelioid cells within abundant myxoid and fibrous stroma. The cells showed strong immunoreactivity for NKX2.2, variable CD99, keratin, and epithelial membrane antigen, but were negative for S100 and myoepithelial markers. Importantly, similar to previously reported cases, the clinical course was more indolent than that of Ewing sarcoma. This case highlights the distinctive clinicopathological characteristics of EWSR1-NFATC2 Gene fusion-associated neoplasms that distinguish them from Ewing sarcoma.
John K C Chan - One of the best experts on this subject based on the ideXlab platform.
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angiomatoid fibrous histiocytoma unusual sites and unusual morphology
Modern Pathology, 2011Co-Authors: Gang Chen, Andrew L Folpe, Thomas V Colby, Kesavan Sittampalam, Martine Patey, Ming Guang Chen, John K C ChanAbstract:Angiomatoid fibrous histiocytoma is a soft tissue neoplasm of low malignant potential, typically occurring in the superficial soft tissues of the extremities in children and young adults. Occurrence outside somatic soft tissues is most uncommon. This report describes eight such cases, involving the lung (three cases), mediastinum (one case), vulva (two cases), retroperitoneum (one case) and ovary (one case), with the latter three locations being hitherto unreported sites of occurrence. Patients had a median age of 48 years, and presented with symptoms related to the mass lesion (five cases) or were incidentally found to harbor a tumor (three cases). Besides the typical histological features such as an outer shell of lymphoid tissue, multinodular aggregates of dendritic-like tumor cells, blood-filled spaces and abundant admixed plasma cells, unusual features were found focally in some cases, including clear cells, rhabdomyoblast-like cells, pulmonary edema-like pattern and tumor cell cords lying in a myxoid stroma. Immunoreactivity for the epithelial membrane antigen, desmin, smooth-muscle actin, CD68 and CD99 was found in 100, 63, 43, 100 and 100% of cases, respectively. Molecular studies provided support for the diagnosis in all seven tested cases-EWS Gene Translocation in six cases (partner Gene being CREB1 in three and ATF1 in two in which information was available) and FUS Gene Translocation in one case. Comparison of the reported cases of extrasomatic angiomatoid fibrous histiocytoma with their somatic soft tissue counterparts showed a number of differences: higher mean age, slight male predominance (particularly for bone lesions), larger tumors, higher frequency of systemic symptoms, higher recurrence rate, myxoid change being more common and a much higher frequency of EWS/ATF1 Gene fusion.
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angiomatoid fibrous histiocytoma first report of primary pulmonary origin
The American Journal of Surgical Pathology, 2009Co-Authors: Li Ren, Shuangping Guo, Xiaoge Zhou, John K C ChanAbstract:Angiomatoid fibrous histiocytoma is an uncommon soft tissue tumor most frequently affecting the deep dermis and subcutis of the extremities in children and young adults. We report the first case presenting as a primary pulmonary tumor in a 46-year-old man. Histologically, the tumor was composed of multiple cellular nodules surrounded by a fibrous pseudocapsule and peritumoral lymphoplasmacytic infiltrates. The nodules were composed of histiocytoid cells with a diffuse, whorled, or vague storiform pattern, with the intervening areas densely packed with plasma cells and lymphocytes. The tumor cells were immunoreactive for epithelial membrane antigen, and focally desmin, CD68, and CD163. Fluorescence in-situ hybridization revealed EWS Gene Translocation, which was further confirmed on polymerase chain reaction to result from EWS/ATF1 Gene fusion. It is important to recognize that angiomatoid fibrous histiocytoma can occur in the lung because its histologic features are rather nondescript and thus can be mistaken for other tumors such as meningioma, inflammatory myofibroblastic tumor, and follicular dendritic cell sarcoma.
Jarish N Cohen - One of the best experts on this subject based on the ideXlab platform.
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ewsr1 nfatc2 Gene fusion in a soft tissue tumor with epithelioid round cell morphology and abundant stroma a case report and review of the literature
Human Pathology, 2018Co-Authors: Jarish N Cohen, Amit J Sabnis, Gregor Krings, Andrew E Horvai, Jessica L DavisAbstract:Summary Mesenchymal round cell tumors are a diverse group of neoplasms defined by primitive, often high-grade cytomorphology. The most common molecular alterations detected in these tumors are Gene rearrangements involving EWSR1 to one of many fusion partners. Rare EWSR1-NFATC2 Gene rearrangements, corresponding to a t(20;22) Gene Translocation, have been described in mesenchymal tumors with clear round cell morphology and a predilection for the skeleton. We present a case of a tumor harboring the EWSR1-NFATC2 Gene fusion arising in the subcutaneous tissue of a young woman. The tumor exhibited corded and trabecular architecture of epithelioid cells within abundant myxoid and fibrous stroma. The cells showed strong immunoreactivity for NKX2.2, variable CD99, keratin, and EMA, but were negative for S100 and myoepithelial markers. Importantly, similar to previously reported cases the clinical course was more indolent than that of Ewing sarcoma. This case highlights the distinctive clinicopathologic characteristics of EWSR1-NFATC2 Gene fusion-associated neoplasms that distinguish them from Ewing sarcoma.
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ewsr1 nfatc2 Gene fusion in a soft tissue tumor with epithelioid round cell morphology and abundant stroma a case report and review of the literature
Human Pathology, 2018Co-Authors: Jarish N Cohen, Amit J Sabnis, Gregor Krings, Andrew E Horvai, Soojin Cho, Jessica L DavisAbstract:Mesenchymal round cell tumors are a diverse group of neoplasms defined by primitive, often high-grade cytomorphology. The most common molecular alterations detected in these tumors are Gene rearrangements involving EWSR1 to one of many fusion partners. Rare EWSR1-NFATC2 Gene rearrangements, corresponding to a t(20;22) Gene Translocation, have been described in mesenchymal tumors with clear round cell morphology and a predilection for the skeleton. We present a case of a tumor harboring the EWSR1-NFATC2 Gene fusion arising in the subcutaneous tissue of a young woman. The tumor exhibited corded and trabecular architecture of epithelioid cells within abundant myxoid and fibrous stroma. The cells showed strong immunoreactivity for NKX2.2, variable CD99, keratin, and epithelial membrane antigen, but were negative for S100 and myoepithelial markers. Importantly, similar to previously reported cases, the clinical course was more indolent than that of Ewing sarcoma. This case highlights the distinctive clinicopathological characteristics of EWSR1-NFATC2 Gene fusion-associated neoplasms that distinguish them from Ewing sarcoma.