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Falk Hildebrand - One of the best experts on this subject based on the ideXlab platform.
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evidence of selection upon genomic gc content in bacteria
PLOS Genetics, 2010Co-Authors: Falk Hildebrand, Axel Meyer, Adam EyrewalkerAbstract:The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%. This variation is generally ascribed to differences in the pattern of mutation between bacteria. Here we test this hypothesis by examining patterns of synonymous polymorphism using datasets from 149 bacterial species. We find a large excess of synonymous GC→AT mutations over AT→GC mutations segregating in all but the most AT-rich bacteria, across a broad range of phylogenetically diverse species. We show that the excess of GC→AT mutations is inconsistent with mutation bias, since it would imply that most GC-rich bacteria are declining in GC-content; such a pattern would be unsustainable. We also show that the patterns are probably not due to translational selection or biased gene conversion, because optimal codons tend to be AT-rich, and the excess of GC→AT SNPs is observed in datasets with no evidence of recombination. We therefore conclude that there is selection to increase synonymous GC-content in many species. Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria.
Sandoval C. Nieves - One of the best experts on this subject based on the ideXlab platform.
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Patogenicidad de una cepa de Yersinia ruckeri de un brote de yersiniosis en truchas arcoíris (Oncorhynchus mykiss) de Huaraz, Perú
'Universidad Nacional Mayor de San Marcos Vicerectorado de Investigacion', 2019Co-Authors: Mesías V. Fernando, Vargas L. Mario, Cueva Q. Alexander, Manchego S. Alberto, Sandoval C. NievesAbstract:The objectives of this study were to determine the pathogenicity of a strain of Yersinia ruckeri, from an outbreak of yersiniosis in Huaraz and to characterize histopathological lesions in various organs of rainbow trout fingerlings (Oncorhynchus mykiss). One hundred fingerlings with an average weight of 7.25 g were used, divided into 5 groups of 20 individuals (four experimental and one control), kept in 30 L ponds. Experimental groups were inoculated via i.m. with 0.1 ml of the bacterial strain in concentrations of 1x104/ml (G1), 4x104/ml (G2), 1x108/ml (G3) and 4x108/ml (G4), and the control group with PBS. Clinical signs, external and internal lesions, morbidity and mortality were recorded for 12 days post-inoculation. Samples of liver, intestine, spleen, kidney, muscle and gills were collected for histopathological analysis. All fish inoculated with Y. ruckeri showed signs and lesions compatible with yersiniosis. Most of individuals had inappetence and melanosis, as well as splenomegaly, mucous content in the intestine and intestinal congestion. Mortalities were 65 and 60% for G1 and G2, respectively and 100% for G3 and G4. Fat degeneration was found in liver, necrosis in intestine and muscle, presence of melanomacrophages and congestion in spleen and kidney, hyperplasia and fusion of lamellae in gills. Results indicate that Y. ruckeri strain from Huaraz is highly pathogenic.El presente estudio tuvo como objetivos determinar la patogenicidad de una cepa de Yersinia ruckeri, procedente de un brote de yersiniosis en Huaraz y caracterizar las lesiones histopatológicas en diversos órganos de alevines de trucha arcoíris (Oncorhynchus mykiss). Se utilizaron 100 alevines con peso promedio de 7.25 g, divididos en 5 grupos de 20 individuos (cuatro experimentales y un control), mantenidos en estanques de 30 L. Los grupos experimentales fueron inoculados vía i.m. con 0.1 ml de la cepa bacteriana en concentraciones de 1x104/ml (G1), 4x104/ml (G2), 1x108/ml (G3) y 4x108/ml (G4). y el grupo control con PBS. Los signos clínicos, lesiones externas e internas, morbilidad y mortalidad se registraron durante 12 días pos-inoculación. Se colectaron muestras de hígado, intestino, bazo, riñón, músculo y branquias para el análisis histopatológico. Todos los peces inoculados con Y. ruckeri presentaron signos y lesiones compatibles con yersiniosis; registrándose mayormente inapetencia y melanosis, así como esplenomegalia, contenido mucoso en intestino y congestión intestinal. Las mortalidades fueron del 65 y 60% para G1 y G2, respectivamente, y de 100% para G3 y G4. A nivel histopatológico, se halló degeneración grasa en hígado, necrosis en intestino y músculo, presencia de melanomacrófagos y congestión en bazo y riñón, hiperplasia y fusión de lamelas en branquias. Los resultados indican que la cepa de Y. ruckeri procedente de Huaraz es altamente patógena
Ali Dadkhodaie - One of the best experts on this subject based on the ideXlab platform.
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dissection of genotype environment interactions for mucilage and seed yield in plantago species application of ammi and gge biplot analyses
PLOS ONE, 2018Co-Authors: Zolfaghar Shahriari, Bahram Heidari, Ali DadkhodaieAbstract:Genotype × environment interaction (GEI) is an important aspect of both plant breeding and the successful introduction of new cultivars. In the present study, additive main effects and multiplicative interactions (AMMI) and genotype (G) main effects and genotype (G) × environment (E) interaction (GGE) biplot analyses were used to identify stable genotypes and to dissect GEI in Plantago. In total, 10 managed field trials were considered as environments to analyze GEI in thirty genotypes belonging to eight Plantago species. Genotypes were evaluated in a drought stress treatment and in normal irrigation conditions at two locations in Shiraz (Bajgah) for three years (2013-2014- 2015) and Kooshkak (Marvdasht, Fars, Iran) for two years (2014–2015). Three traits, seed yield and mucilage yield and content, were measured at each experimental site and in natural Plantago habitats. AMMI2 biplot analyses identified genotypes from several species with higher stability for seed yield and other genotypes with stable mucilage content and yield. P. lanceolata (G26), P. officinalis (G10), P. ovata (G14), P. ampleexcaulis (G11) and P. major (G4) had higher stability for seed yield. For mucilage yield, G21, G18 and G20 (P. psyllium), G1, G2 and G4 (P. major), G9 and G10 (P. officinalis) and P. lanceolata were identified as stable. G13 (P. ovata), G5 and G6 (P. major) and G30 (P. lagopus) had higher stability for mucilage content. No one genotype was found to have high levels of stability for more than one trait but some species had more than one genotype exhibiting stable trait performance. Based on trait variation, GGE biplot analysis identified two representative environments, one for seed yield and one for mucilage yield and content, with good discriminating ability. The identification of stable genotypes and representative environments should assist the breeding of new Plantago cultivars.
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Dissection of genotype × environment interactions for mucilage and seed yield in Plantago species: Application of AMMI and GGE biplot analyses
2018Co-Authors: Zolfaghar Shahriari, Bahram Heidari, Ali DadkhodaieAbstract:Genotype × environment interaction (GEI) is an important aspect of both plant breeding and the successful introduction of new cultivars. In the present study, additive main effects and multiplicative interactions (AMMI) and genotype (G) main effects and genotype (G) × environment (E) interaction (GGE) biplot analyses were used to identify stable genotypes and to dissect GEI in Plantago. In total, 10 managed field trials were considered as environments to analyze GEI in thirty genotypes belonging to eight Plantago species. Genotypes were evaluated in a drought stress treatment and in normal irrigation conditions at two locations in Shiraz (Bajgah) for three years (2013-2014- 2015) and Kooshkak (Marvdasht, Fars, Iran) for two years (2014–2015). Three traits, seed yield and mucilage yield and content, were measured at each experimental site and in natural Plantago habitats. AMMI2 biplot analyses identified genotypes from several species with higher stability for seed yield and other genotypes with stable mucilage content and yield. P. lanceolata (G26), P. officinalis (G10), P. ovata (G14), P. ampleexcaulis (G11) and P. major (G4) had higher stability for seed yield. For mucilage yield, G21, G18 and G20 (P. psyllium), G1, G2 and G4 (P. major), G9 and G10 (P. officinalis) and P. lanceolata were identified as stable. G13 (P. ovata), G5 and G6 (P. major) and G30 (P. lagopus) had higher stability for mucilage content. No one genotype was found to have high levels of stability for more than one trait but some species had more than one genotype exhibiting stable trait performance. Based on trait variation, GGE biplot analysis identified two representative environments, one for seed yield and one for mucilage yield and content, with good discriminating ability. The identification of stable genotypes and representative environments should assist the breeding of new Plantago cultivars.
Jiangwei Yan - One of the best experts on this subject based on the ideXlab platform.
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gc content variability of eubacteria is governed by the pol iii α subunit
Biochemical and Biophysical Research Communications, 2007Co-Authors: Xiaoqian Zhao, Zhang Zhang, Jiangwei YanAbstract:Abstract Eubacterial genomes have highly variable GC content (0.17–0.75) and the primary mechanism of such variability remains unknown. The place to look for is what actually catalyzes the synthesis of DNA, where DNA polymerase III is at the center stage, particularly one of its 10 subunits—the α subunit. According to the dimeric combination of α subunits, GC contents of eubacterial genomes were partitioned into three groups with distinct GC content variation spectra: dnaE1 (full-spectrum), dnaE2/dnaE1 (high-GC), and polC/dnaE3 (low-GC). Therefore, genomic GC content variability is believed to be governed primarily by the α subunit grouping of DNA polymerase III; it is of essence in genome composition analysis to take full account of such a grouping principle. Since horizontal gene transfer is very frequent among bacterial genomes, exceptions of the grouping scheme, a few percents of the total, are readily identifiable and should be excluded from in-depth analyses on nucleotide compositions.
Adam Eyrewalker - One of the best experts on this subject based on the ideXlab platform.
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evidence of selection upon genomic gc content in bacteria
PLOS Genetics, 2010Co-Authors: Falk Hildebrand, Axel Meyer, Adam EyrewalkerAbstract:The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%. This variation is generally ascribed to differences in the pattern of mutation between bacteria. Here we test this hypothesis by examining patterns of synonymous polymorphism using datasets from 149 bacterial species. We find a large excess of synonymous GC→AT mutations over AT→GC mutations segregating in all but the most AT-rich bacteria, across a broad range of phylogenetically diverse species. We show that the excess of GC→AT mutations is inconsistent with mutation bias, since it would imply that most GC-rich bacteria are declining in GC-content; such a pattern would be unsustainable. We also show that the patterns are probably not due to translational selection or biased gene conversion, because optimal codons tend to be AT-rich, and the excess of GC→AT SNPs is observed in datasets with no evidence of recombination. We therefore conclude that there is selection to increase synonymous GC-content in many species. Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria.
