The Experts below are selected from a list of 6561 Experts worldwide ranked by ideXlab platform
Lars Podsiadlowski - One of the best experts on this subject based on the ideXlab platform.
-
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.
-
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.
-
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.
Qijun Chen - One of the best experts on this subject based on the ideXlab platform.
-
comparative itraq based quantitative proteomic analysis of the chinese grass shrimp palaemonetes sinensis infected with the Isopod parasite tachaea chinensis
Parasites & Vectors, 2019Co-Authors: Yingdong Li, Weibin Xu, Xin Li, Yingying Zhao, Jing Dong, Qijun ChenAbstract:Although parasitic Isopods can negatively affect the reproduction and ingestion of several commercially important crustaceans, little is known regarding the mechanisms that underlie these effects. In the present study, the iTRAQ (isobaric tags for relative and absolute quantification) approach was applied to identify differentially expressed proteins in the Chinese grass shrimp Palaemonetes sinensis infected with the parasitic Isopod Tachaea chinensis. On the basis of our analysis, we identified 1262 proteins from a total of 4292 peptides. There was a significant difference in the expression of 182 proteins between the control and infected groups, among which 69 were upregulated and 113 were downregulated after T. chinensis infection. The differentially expressed proteins revealed that parasitism may inhibit the immune response, thereby increasing host vulnerability to additional lethal infection. Furthermore, T. chinensis may secrete anticoagulants to inhibit hemolymph clotting. Moreover, the Isopod parasite placed a heavy metabolic burden on the host, particularly with respect to glucose metabolism. Our study is the first to use the iTRAQ-based proteomic approach to analyze the effects of an Isopod parasite on its host. The results we obtained using this approach will make a valuable contribution to understanding the molecular mechanisms underlying Isopod parasitism on crustaceans.
-
comparative transcriptome analysis of chinese grass shrimp palaemonetes sinensis infected with Isopod parasite tachaea chinensis
Fish & Shellfish Immunology, 2018Co-Authors: Yingdong Li, Weibin Xu, Xiaodong Li, Xin Li, Hongbo Jiang, Qijun ChenAbstract:Abstract Parasitic Isopods negatively affect reproduction and ingestion in several commercially important crustaceans; however, little is known about such parasite–host interactions. Therefore, we performed high-throughput sequencing of cDNA samples from Chinese grass shrimp Palaemonetes sinensis infected by parasitic Isopod Tachaea chinensis and a non-infected control. We randomly assembled 46,858,882 and 41,110,746 clean reads from the parasitized and control groups, respectively. From these, we identified 1323 differentially expressed genes (DEGs) (p
Fabian Kilpert - One of the best experts on this subject based on the ideXlab platform.
-
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.
-
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.
-
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.
Yingdong Li - One of the best experts on this subject based on the ideXlab platform.
-
comparative itraq based quantitative proteomic analysis of the chinese grass shrimp palaemonetes sinensis infected with the Isopod parasite tachaea chinensis
Parasites & Vectors, 2019Co-Authors: Yingdong Li, Weibin Xu, Xin Li, Yingying Zhao, Jing Dong, Qijun ChenAbstract:Although parasitic Isopods can negatively affect the reproduction and ingestion of several commercially important crustaceans, little is known regarding the mechanisms that underlie these effects. In the present study, the iTRAQ (isobaric tags for relative and absolute quantification) approach was applied to identify differentially expressed proteins in the Chinese grass shrimp Palaemonetes sinensis infected with the parasitic Isopod Tachaea chinensis. On the basis of our analysis, we identified 1262 proteins from a total of 4292 peptides. There was a significant difference in the expression of 182 proteins between the control and infected groups, among which 69 were upregulated and 113 were downregulated after T. chinensis infection. The differentially expressed proteins revealed that parasitism may inhibit the immune response, thereby increasing host vulnerability to additional lethal infection. Furthermore, T. chinensis may secrete anticoagulants to inhibit hemolymph clotting. Moreover, the Isopod parasite placed a heavy metabolic burden on the host, particularly with respect to glucose metabolism. Our study is the first to use the iTRAQ-based proteomic approach to analyze the effects of an Isopod parasite on its host. The results we obtained using this approach will make a valuable contribution to understanding the molecular mechanisms underlying Isopod parasitism on crustaceans.
-
comparative transcriptome analysis of chinese grass shrimp palaemonetes sinensis infected with Isopod parasite tachaea chinensis
Fish & Shellfish Immunology, 2018Co-Authors: Yingdong Li, Weibin Xu, Xiaodong Li, Xin Li, Hongbo Jiang, Qijun ChenAbstract:Abstract Parasitic Isopods negatively affect reproduction and ingestion in several commercially important crustaceans; however, little is known about such parasite–host interactions. Therefore, we performed high-throughput sequencing of cDNA samples from Chinese grass shrimp Palaemonetes sinensis infected by parasitic Isopod Tachaea chinensis and a non-infected control. We randomly assembled 46,858,882 and 41,110,746 clean reads from the parasitized and control groups, respectively. From these, we identified 1323 differentially expressed genes (DEGs) (p
Amadeu M V M Soares - One of the best experts on this subject based on the ideXlab platform.
-
ceo2 nanoparticles induce no changes in phenanthrene toxicity to the soil organisms porcellionides pruinosus and folsomia candida
Ecotoxicology and Environmental Safety, 2015Co-Authors: Paula S Tourinho, Susana Loureiro, Amadeu M V M Soares, Pauline L Waalewijnkool, Irene Zantkuijl, Kerstin Jurkschat, Claus Svendsen, Cornelis A M Van GestelAbstract:Cerium oxide nanoparticles (CeO2 NPs) are used as diesel fuel additives to catalyze oxidation. Phenanthrene is a major component of diesel exhaust particles and one of the most common pollutants in the environment. This study aimed at determining the effect of CeO2 NPs on the toxicity of phenanthrene in Lufa 2.2 standard soil for the Isopod Porcellionides pruinosus and the springtail Folsomia candida. Toxicity tests were performed in the presence of CeO2 concentrations of 10, 100 or 1000 mg Ce/kg dry soil and compared with results in the absence of CeO2 NPs. CeO2 NPs had no adverse effects on Isopod survival and growth or springtail survival and reproduction. For the Isopods, LC50s for the effect of phenanthrene ranged from 110 to 143 mg/kg dry soil, and EC50s from 17.6 to 31.6 mg/kg dry soil. For the springtails, LC50s ranged between 61.5 and 88.3 mg/kg dry soil and EC50s from 52.2 to 76.7 mg/kg dry soil. From this study it may be concluded that CeO2 NPs have a low toxicity and do not affect toxicity of phenanthrene to Isopods and springtails.
-
influence of soil ph on the toxicity of zinc oxide nanoparticles to the terrestrial Isopod porcellionides pruinosus
Environmental Toxicology and Chemistry, 2013Co-Authors: Paula S Tourinho, Amadeu M V M Soares, Cornelis A M Van Gestel, Stephen Lofts, Susana LoureiroAbstract:The effects of soil pH on the toxicity of ZnO nanoparticles (NPs) to the terrestrial Isopod Porcellionides pruinosus were evaluated. Isopods were exposed to a natural soil amended with CaCO3 to reach 3 different pHCaCl2 levels (4.5, 6.2, and 7.3) and to standard LUFA 2.2 soil (pH 5.5) spiked with ZnO NPs (30 nm), non-nano ZnO (200 nm), and ionic Zn as ZnCl2. Toxicity was expressed based on total Zn concentration in soil, as well as total Zn and free Zn2+ ion concentrations in porewater. Compared with ZnO-spiked soils, the ZnCl2-spiked soils had lower pH and higher porewater Ca2+ and Zn levels. Isopod survival did not differ between Zn forms and soils, but survival was higher for Isopods exposed to ZnO NPs at pH 4.5. Median effect concentrations (EC50s) for biomass change showed similar trends for all Zn forms in all soils, with higher values at intermediate pH. Median lethal concentration (LC50) and EC50 values based on porewater Zn or free Zn ion concentrations were much lower for ZnO than for ionic zinc. Zn body concentrations increased in a dose-related manner, but no effect of soil pH was found. It is suggested not only that dissolved or free Zn in porewater contributed to uptake and toxicity, but also that oral uptake (i.e., ingestion of soil particles) could be an important additional route of exposure. Environ Toxicol Chem 2013;32:2808–2815. © 2013 SETAC
-
feeding behaviour of the terrestrial Isopod porcellionides pruinosus brandt 1833 crustacea Isopoda in response to changes in food quality and contamination
Science of The Total Environment, 2006Co-Authors: Susana Loureiro, Alexandra Sampaio, A D Brandao, Antonio J A Nogueira, Amadeu M V M SoaresAbstract:Soil decomposition is mainly dependent on the nature and characteristics of organic matter within the soil, the environmental conditions and the activity of microorganisms and soil fauna. Isopods play an important role in decomposition through litter fragmentation and stimulating and/or ingesting fungi and bacteria. The aim of this study was to jointly evaluate the effect of different food types and the effect of heavy metal contamination of those foods through Isopod feeding performance assays. These studies used the terrestrial Isopod Porcellionides pruinosus. After feeding with different leaf types for the study on feeding performance, alder leaves were chosen for the contamination experiments. Feeding parameters like consumption, assimilation, egestion and growth ratios were calculated and compared among treatments and food type. Lower quality food decreased Isopods performance. Exotic food types were shown to be less preferred than alder or oak leaves. Contaminated food also resulted in a decrease in performance among the feeding parameters studies, although Isopods can tolerate in certain cases high amounts of heavy metals. For this reason it is possible that in future this crustacean can be used as bioindicators of soil contamination or in the evaluation of contaminated sites or remediation processes.
-
assimilation efficiency and toxicokinetics of 14c lindane in the terrestrial Isopod porcellionides pruinosus the role of Isopods in degradation of persistent soil pollutants
Ecotoxicology, 2002Co-Authors: Susana Loureiro, Antonio J A Nogueira, Jose Paulo Sousa, Amadeu M V M SoaresAbstract:An achievable way to evaluate the bioavailability of a certain toxic in the environment is to measure the concentration inside soil organisms. Non-target saprotrophic organisms like Isopods are often exposed to agrochemicals or other kind of persistent chemicals. In this study the Isopod Porcellionides pruinosus was exposed to a constant concentration of Lindane (γ-HCH) via food. Using toxicokinetic models the bioaccumulation and fate of the pesticide by Isopods was assessed and compared with previous studies, where an unexpected decrease in γ-HCH concentration was observed. Animal body burdens showed higher values, and a lower assimilation rate constant, although the elimination rate constant was twice the value previously observed. It was also observed that a significant amount of γ-HCH had an unknown fate. To discover its possible destiny, a factorial experiment was carried out using two types of CO2 traps and contaminated leaves in the presence and absence of Isopods. It was concluded that Isopod activity might have been responsible for a more rapid biotransformation of γ-HCH in leaves, since the amount of the pesticide is reduced in their presence.
-
effect of endosulfan and parathion on energy reserves and physiological parameters of the terrestrial Isopod porcellio dilatatus
Ecotoxicology and Environmental Safety, 2001Co-Authors: Sonia M Ribeiro, Antonio J A Nogueira, Jose Paulo Sousa, Amadeu M V M SoaresAbstract:The in vivo effects of parathion and endosulfan on the Isopod Porcellio dilatatus were investigated. Feeding parameters (food consumption and assimilation rates), growth, and energy reserves (glycogen, lipid, and protein contents) of pesticide-exposed Isopods were compared with those of control animals. Isopods were exposed to a wide range of concentrations of parathion or endosulfan (0.1, 1, 10, 25, 50, 100, 250, and 500 μg/g of food) for 21 days. The route of uptake of the pesticides was through the diet (alder leaves). Results revealed that parathion induces a significant depression of glycogen, lipid, and protein contents. However, no significant effect was observed on either feeding parameters or growth. Animals fed endosulfan-contaminated food had smaller amounts of glycogen and lipid than control animals, while protein levels were similar in all treatments. Endosulfan also induced a significant decrease in food consumption and assimilation rates at the highest concentrations tested. Growth rate was also significantly affected by endosulfan. These results suggest that the Isopod P. dilatatus is a suitable species for use in toxicity tests and that energy reserves could be used as effect criteria in both laboratory and field studies.
