3404 genomes  (ATCC)

Journal: Mycoses

Article Title: Integrated Genomic and Phenotypic Analyses Reveal Convergent Resistance Patterns in Clinical Candida tropicalis Isolates

doi: 10.1111/myc.70181

Figure Lengend Snippet: SNP‐based phylogenetic tree of hospital isolates and the ATCC control reference genome, C. tropicalis MYA‐3404.

Article Snippet: SNPs of the ATCC C. tropicalis MYA‐3404 genomes were compared to the SNPs of the isolates by using the snippy multicommand (snippy‐base application v4.5.0) [ ] that generates a core genome multiple alignment against a common reference.

Techniques: Control

Journal: Mycoses

Article Title: Integrated Genomic and Phenotypic Analyses Reveal Convergent Resistance Patterns in Clinical Candida tropicalis Isolates

doi: 10.1111/myc.70181

Figure Lengend Snippet: Quantification of ergosterol content. The black bar represents the control strain C. tropicalis MYA‐3404, that is sensitive to antifungal agents. The grey bars represent the hospital isolates. Statistical significance was calculated using One‐way ANOVA ( p < 0.0001) coupled to Dunnett's multiple comparisons test: Control versus 46: p = 0.4182; Control versus 47: p = 0.0009; Control versus 50: p < 0.0001; Control versus 52: p < 0.0001; Control versus 53: p < 0.0001; Control versus 54: p = 0.9957; Control versus 57: p = 0.0066; Control versus 58: p = 0.0838; Control versus 60: p = 0.0051; Control versus 61: p = 0.9997; Control versus 62: p = 0.0004; Control versus 63: p = 0.0003; Control versus 65: p = 0.0032; Control versus 66: p = 0.2012.

Article Snippet: SNPs of the ATCC C. tropicalis MYA‐3404 genomes were compared to the SNPs of the isolates by using the snippy multicommand (snippy‐base application v4.5.0) [ ] that generates a core genome multiple alignment against a common reference.

Techniques: Control

Journal: Mycoses

Article Title: Integrated Genomic and Phenotypic Analyses Reveal Convergent Resistance Patterns in Clinical Candida tropicalis Isolates

doi: 10.1111/myc.70181

Figure Lengend Snippet: Adhesion to human cells. The black bar represents the control strain C. tropicalis MYA‐3404, that is sensitive to antifungal agents. The grey bars represent the hospital isolates. Statistical significance was calculated using One‐way ANOVA ( p < 0.0001) coupled to Dunnett's multiple comparisons test: Control versus 46: p = 0.0001; Control versus 47: p = 0.0283; Control versus 50: p = 0.9997; Control versus 52: p = 0.9341; Control versus 53: p = 0.002; Control versus 54: p = 0.9999; Control versus 57: p > 0.9999; Control versus 58: p = 0.1689; Control versus 60: p = 0.0016; Control versus 61: p = 0.8017; Control versus 62: p = 0.0027; Control versus 63: p = 0.0035; Control versus 65: p = 0.9653; Control versus 66: p = 0.6953.

Article Snippet: SNPs of the ATCC C. tropicalis MYA‐3404 genomes were compared to the SNPs of the isolates by using the snippy multicommand (snippy‐base application v4.5.0) [ ] that generates a core genome multiple alignment against a common reference.

Techniques: Control

Journal: Mycoses

Article Title: Integrated Genomic and Phenotypic Analyses Reveal Convergent Resistance Patterns in Clinical Candida tropicalis Isolates

doi: 10.1111/myc.70181

Figure Lengend Snippet: Biofilm formation. The black bar represents the control strain C. tropicalis MYA‐3404, that is sensitive to antifungal agents. The grey bars represent the hospital isolates. Statistical significance was calculated using one‐way ANOVA ( p < 0.0001) coupled to Dunnett's multiple comparisons test: Control versus 46: p = 0.0001; Control versus 47: p < 0.0001; Control versus 50: p < 0.0001; Control versus 52: p = 0.0588; Control versus 53: p = 0.0221; Control versus 54: p < 0.0001; Control versus 57: p = 0.9993; Control versus 58: p = 0.0644; Control versus 60: p = 0.5937; Control versus 61: p < 0.0001; Control versus 62: p = 0.1254; Control versus 63: p = 0.0971; Control versus 65: p = 0.5359; Control versus 66: p < 0.0001.

Article Snippet: SNPs of the ATCC C. tropicalis MYA‐3404 genomes were compared to the SNPs of the isolates by using the snippy multicommand (snippy‐base application v4.5.0) [ ] that generates a core genome multiple alignment against a common reference.

Techniques: Control

Journal: Mycoses

Article Title: Integrated Genomic and Phenotypic Analyses Reveal Convergent Resistance Patterns in Clinical Candida tropicalis Isolates

doi: 10.1111/myc.70181

Figure Lengend Snippet: Quantification of chitin content. The black bar represents the control strain C. tropicalis MYA‐3404, that is sensitive to antifungal agents. The grey bars represent the hospital isolates. Statistical significance was calculated using One‐way ANOVA ( p < 0.0001) coupled to Dunnett's multiple comparisons test: Control versus 46: p = 0.1409; Control versus 47: p = 0.9911; Control versus 50: p = 0.9996; Control versus 52: p = 0.0012; Control versus 53: p = 0.408; Control versus 54: p = 0.408; Control versus 57: p = 0.0034; Control versus 58: p = 0.0024; Control versus 60: p < 0.0001; Control versus 61: p = 0.0007; Control versus 62: p = 0.0005; Control versus 63: p < 0.0001; Control versus 65: p = 0.0403; Control versus 66: p < 0.0001.

Article Snippet: SNPs of the ATCC C. tropicalis MYA‐3404 genomes were compared to the SNPs of the isolates by using the snippy multicommand (snippy‐base application v4.5.0) [ ] that generates a core genome multiple alignment against a common reference.

Techniques: Control

Journal: BMC Developmental Biology

Article Title: Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration

doi: 10.1186/1471-213X-11-70

Figure Lengend Snippet: The Xenopus tropicalis tadpole has the capacity to regenerate its tail . ( A ) Schematic diagram of the tissues located in the Xenopus tropicalis tadpole tail. ( B ) Transverse section of tadpole tail visualized with toluidine blue. ( C-E ) An amputated tail (C), uncut tail (D), and regenerated tail 7 days after amputation (E). ( F-H ) Immunostaining against skeletal muscle (12/101; F), neurons (acetylated tubulin; G), and vasculature (mTie-2::eGFP transgene; H). ( I-O ) A regenerated tail at one month post-amputation (I). Immunostaining showing skeletal muscle (12/101; J, K), neurons (acetylated tubulin; L, M), and vasculature (mTieGFP transgene; N, O) in non-cut and regenerated tails 28 days post amputation. Green arrowhead depicts amputation site; red arrowhead shows parallel axonal tract; orange arrowheads shows parallel blood vessels. Red scale bar is 1000 μm.

Article Snippet: We examined gene expression using the Xenopus tropicalis Affymetrix genome array during three phases of regeneration, uncovering more than 1,000 genes that are significantly modulated during tail regeneration.

Techniques: Immunostaining

Journal: BMC Developmental Biology

Article Title: Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration

doi: 10.1186/1471-213X-11-70

Figure Lengend Snippet: Array analysis of X. tropicalis tail regeneration . ( A ) The schematic diagrams of the early, intermediate, and late stages of tail regeneration. The circled areas depict the portion of tissue, and hence the RNA, collected and used for array analysis. ( B ) Shows the similarities of the eight arrays (four array time points in duplicate) using principal component analysis (PCA) mapping.

Article Snippet: We examined gene expression using the Xenopus tropicalis Affymetrix genome array during three phases of regeneration, uncovering more than 1,000 genes that are significantly modulated during tail regeneration.

Techniques:

Journal: BMC Developmental Biology

Article Title: Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration

doi: 10.1186/1471-213X-11-70

Figure Lengend Snippet: Analysis X.tropicalis array

Article Snippet: We examined gene expression using the Xenopus tropicalis Affymetrix genome array during three phases of regeneration, uncovering more than 1,000 genes that are significantly modulated during tail regeneration.

Techniques: Expressing

Journal: BMC Developmental Biology

Article Title: Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration

doi: 10.1186/1471-213X-11-70

Figure Lengend Snippet: RT-qPCR Primer and Probe Sequences

Article Snippet: We examined gene expression using the Xenopus tropicalis Affymetrix genome array during three phases of regeneration, uncovering more than 1,000 genes that are significantly modulated during tail regeneration.

Techniques: Sequencing