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Data for: The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders
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Data for "Transcriptional Diversification in a Human-Adapting Zoonotic Pathogen Drives Niche-Specific Evolution"
<div> <p>This repository contains the data and codes for reproducing results and figures in the associated manuscript:</p> <p>Transcriptional Diversification in a Human-Adapting Zoonotic Pathogen Drives Niche-Specific Evolution</p> </div>
Data from: Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size
In vitro and in vivo evolution experiments on Escherichia coli revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of E. coli in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant E. coli clone ED1a belonging to B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed amutation rate of 6.90x10-7 per base per year of the chromosome for E. coli ED1a in healthy human gut. We observed a very limited genomic diversity, and could not detect any evidence of selection contrary to what is observed in experimental evolution over similar length of time. We therefore suggest that ED1a being well adapted to the healthy human gut evolves mostly neutrally with a low effective population size (Ne ≈ 500 – 1700).
Figure 9 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 9 - Image of Haematoloechus similis;a. Drawing of cercaria structureb. Cercaria without stainingc. Sporocyst stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: s – stylet, os – oral sucker, p – pharynx, pg – penetration gland, vs – ventral sucker, eb – excretory bladder, ta – tail, spo: sporocyst, c – cercaria, b – body, sp – spine (scale a, b = 50 µm, c = 50 µm).
Figure 8 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 8 - Image of Loxogenoides bicolor;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Sporocyst stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: s – stylet, os – oral sucker, vi – vigulate gland, p – pharynx, pg – penetration gland, vs – ventral sucker, eb – excretory bladder, ta – tail, spo: sporocyst, c – cercaria, b – body, sp – spine (scale a, b = 50 µm, c = 20 µm).
Figure 6 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 6 - Image of Centrocestus formosanus;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Redia stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, es – eye spot, p – pharynx, pg – penetration gland, vs – ventral sucker, eb – excretory bladder, ta – tail, df – dorsal finfold, ti – tip, re – redia, c – cercaria, b – body, sp – spine (scale a, b = 100 µm, c = 10 µm).
Figure 5 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 5 - Image of Stictodora tridactyla;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Redia stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, ep – esophagus, es – eye spot, p – pharynx, pg – penetration gland, vs – ventral sucker, eb – excretory bladder, lf – lateral finfold, ta – tail, df – dorsal finfold, re – redia, c – cercaria, b – body, sp – spine, sh – sensory hair (scale a, b = 100 µm, c = 10 µm).
Figure 4 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 4 - Image of Haplorchis taichui;a. Drawing of cercaria structureb. Cercaria without stainingc. Redia without stainingd.–g. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, es – eye spot, p – pharynx, pg – penetration gland, gi – genital primordial, eb – excretory bladder, lf – lateral finfold, ta – tail, df – dorsal finfold, re – redia, c – cercaria, sp – spine (scale a, b = 100 µm, c = 20 µm).
Figure 3 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 3 - Image of Haplorchis pumilio;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Redia stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, es – eye spot, p – pharynx, pg – penetration gland, vs – ventral sucker, eb – excretory bladder, lf – lateral finfold, ta – tail, df – dorsal finfold, re – redia, c – cercaria, b – body, sp – spine, sh – sensory hair (scale a, b = 100 µm, c = 10 µm).
Figure 20 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 20 - Image of Podocotyle (Podocotyle) lepomis;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Sporocyst stained with 0.5% neutral redd.–f. Images of Scanning ElectronmicroscopeAbbreviations: s – stylet, os – oral sucker, p – pharynx, penetration gland, vs – ventral sucker, eb – excretory bladder, ta – tail, ad – adhesive organ, spo – sporocyst, c – cercaria (scale a, b = 100 µm, c = 10 µm).
Figure 7 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 7 - Image of Acanthatrium hitaense;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Sporocyst stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: s – stylet, os – oral sucker, vi – vigulate gland, p – pharynx, pg – penetration gland, vs – ventral sucker, eb – excretory bladder, ta – tail, ti – tip, spo: sporocyst, c – cercaria, b – body, sp – spine (scale a, b = 25 µm, c = 50 µm).
Figure 2 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 2 - Shell Morphology of Melanoides tuberculata in Thailand;a. Sri Satchanalai Stream, Sri Satchanalai National Park, Sri Satchanalai District, Sukhothai Province (SUT0109009)b. Lam Takhong Stream, Khao Yai National Park, Pak Chong District, Nakhon, Ratchasima Province (SUT0109020)c. Rice Field at Nong Kra Done, Muang District, Nakhon Pathom Province (SUT0109062)d. Pond in Silpakorn University, Muang District, Nakhon Pathom Province (SUT0109063)e. Bang Ta-nai Canal, Pak Kred District, Nontaburi Province (SUT0109065)f. Huay Nuang Stream, Suanphueng District, Ratchaburi Province (SUT0109108)Scale bar = 1.0 mm.
Figure 18 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 18 - Image of Gastrothylax crumenifer;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Redia stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, p – pharynx, es – eye spot, vs – ventral sucker, ga – genital atrium, in – intestine, vs – ventral sucker, ta – tail, re – redia, c – cercaria (scale a, b = 100 µm, c = 10 µm).
Figure 19 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 19 - Image of Cercaria caribbea LXVIII;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Sporocyst stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, p – pharynx, vs – ventral sucker eb – excretory bladder, ta – tail, spo – sporocyst (scale a, b = 100 µm, c = 10 µm).
Figure 16 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 16 - Image of Mesostephanus appendiculatus;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Sporocyst stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, p – pharynx, in – intestine, vs – ventral sucker, eb – excretory bladder, ta – tail, fu – furca, ff – furcal finfold b – body, sp – spine, ex – excretory pore, spo – sporocyst, c – cercaria (scale a, b = 100 µm, c = 20 µm).
Figure 15 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 15 - Image of Apatemon gracilis;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Sporocyst stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, p – pharynx, es – eye spot, vs – ventral sucker, in – intestine, pg – penetration gland, eb – excretory bladder, ta – tail, cb – caudal body, fu – furca, b – body, sp – spine, spo – sporocyst, c – cercaria (scale a, b = 100 µm, c = 20 µm).
Figure 14 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 14 - Image of Transversotrema laruei;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Redia stained with 0.5% neutral redd.–f. Images of Scanning ElectronmicroscopeAbbreviations: gp – genital pore, es – eye spot, m – mouth, ov – ovary, vs – ventral sucker, te – testes, eb – excretory bladder, i – intestine, ap – appendages, ta – tail, fu – furca, p – pharynx, re – redia, c – cercaria (scale a, b = 100 µm, c = 20 µm).
Figure 17 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 17 - Image of Echinochasmus pelecani;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Redia stained with 0.5% neutral redd.–g. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, cs – collar spine, p – pharynx, in – intestine, vs – ventral sucker, mct – main collecting tube, ta – tail, re – redia, c – cercaria (scale a, b = 50 µm, c = 10 µm).
Figure 13 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 13 - Image of Alaria mustelae;a. Drawing of cercaria structureb. Cercaria stained with 0.5% neutral redc. Sporocyst stained with 0.5% neutral redd.–f. Images of Scanning ElectronmicroscopeAbbreviations: os – oral sucker, p – pharynx, es – eye spot, ep – esophagus, vs – ventral sucker, in – intestine, pg – penetration gland, eb – excretory bladder, ta – tail, fu – furca, spo: sporocyst, c – cercaria (scale a, b = 50 µm, c = 10 µm).
Figure 12 from: Krailas D, Namchote S, Koonchornboon T, Dechruksa W, Boonmekam D (2014) Trematodes obtained from the thiarid freshwater snail Melanoides tuberculata (Müller, 1774) as vector of human infections in Thailand. Zoosystematics and Evolution 90(1): 57-86. https://doi.org/10.3897/zse.90.7306
Figure 12 - Image of Cardicola alseae;a. Drawing of cercaria structureb. Cercaria stained with Semichon's acetic carmine & fast greenc. Sporocyst stained with 0.5% neutral redd.–f. Images of Scanning ElectronmicroscopeAbbreviations: dm – dorso-median finfold, pg – penetration gland, eb – excretory bladder, an – anterior organ, ta – tail, cb – caudal body, sp – spine, fu – furca, spo: sporocyst, c – cercaria (scale a, b = 50 µm, c = 20 µm).
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