Journal: International Journal of Molecular Sciences

Article Title: Chromosome Ordinal Number-Related Genomic Stability Revealed Among Oryza and Other Poaceae Plants

doi: 10.3390/ijms26104778

Figure Lengend Snippet: Loss and retention of genes on chromosomes among the studied species. L. perrieri was used as the reference genome, and a 1 MB sliding window was used to infer the collinear genes (red) and lost genes (light blue) in each chromosome of each species. Red represents retention, and blue represents loss. From the center, the chromosomes in the circle are from O. barthii , O. brachyantha , O. sativa Jing rice, O. glaberrima , O. meridionalis , O. nivara , O. punctata , O. rufipogon, O. glumaepatula , O. sativa Xian rice, S. bicolor , S. italica , and P. americarum . The orange numbers represent chromosome numbers.

Article Snippet: Oryza sativa ssp. Xian (Japonica) (Minghui 63, a Xian rice) [ ] was downloaded from the NCBI (National Center for Biotechnology Information).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Chromosome Ordinal Number-Related Genomic Stability Revealed Among Oryza and Other Poaceae Plants

doi: 10.3390/ijms26104778

Figure Lengend Snippet: Gene loss rates in Oryza plants, with L. perrieri as the reference. The horizontal coordinate represents the 12 chromosomes of the Oryza plant, and the vertical coordinate represents the loss rates. The loss rates of 12 chromosomes of each species in the figure are represented by different colored dots. Note: ( a ) The loss rates of 12 chromosomes of each species. ( b ) The loss rates of 12 chromosomes of subgenome 1. ( c ) The loss rates of 12 chromosomes of subgenome 2.

Article Snippet: Oryza sativa ssp. Xian (Japonica) (Minghui 63, a Xian rice) [ ] was downloaded from the NCBI (National Center for Biotechnology Information).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Chromosome Ordinal Number-Related Genomic Stability Revealed Among Oryza and Other Poaceae Plants

doi: 10.3390/ijms26104778

Figure Lengend Snippet: Phylogenetic relationship and gene loss rates during evolutionary periods. ( a ) Gene loss rate during the differentiation of Oryza plants. A segment of the branch has two numbers, with the top one showing the number of genes lost during the corresponding evolutionary period, and the bottom one showing the gene loss rate during the period. ( b ) The distribution of Ks values between collinear genes after evolutionary rate correction. ( c ) The Ks value of the divergence among species and the estimated divergence time. The abbreviations of the species are represented by the letters in the ordinate. Oa, Ob, Os (Jing), Ol, Om, On, Op, Or, Ou, Os (Xian), Sb, Si, and Pg stand for O. barthii , O. brachyantha , O. sativa Jing rice, O. glaberrima , O. meridionalis , O. nivara , O. punctata , O. rufipogon , O. glumaepatula , O. sativa Xian rice, S. bicolor , S. italica , and P. americarum .

Article Snippet: Oryza sativa ssp. Xian (Japonica) (Minghui 63, a Xian rice) [ ] was downloaded from the NCBI (National Center for Biotechnology Information).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Chromosome Ordinal Number-Related Genomic Stability Revealed Among Oryza and Other Poaceae Plants

doi: 10.3390/ijms26104778

Figure Lengend Snippet: KEGG features of lost genes. ( a ) KEGG features of Oryza sativa Jing rice relative to Oryza rufipogon -specific orthologous genes. ( b ) KEGG features of tandem repeat genes on chromosome 11 of Oryza sativa . ( c ) KEGG features of homologous genes lost in Oryza sativa Jing rice. ( d ) KEGG features of Oryza rufipogon relative to Jing rice-specific orthologous genes. ( e ) KEGG features of lost orthologous genes on chromosome 11 of Jing rice. ( f ) KEGG features of homologous genes lost in Oryza rufipogon .

Article Snippet: Oryza sativa ssp. Xian (Japonica) (Minghui 63, a Xian rice) [ ] was downloaded from the NCBI (National Center for Biotechnology Information).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Chromosome Ordinal Number-Related Genomic Stability Revealed Among Oryza and Other Poaceae Plants

doi: 10.3390/ijms26104778

Figure Lengend Snippet: Evolutionary trajectory of grass chromosomes. The process of evolution from the ancestral chromosomes of grasses to those of rice, sorghum, foxtail millet, and pearl millet was reconstructed. Before the GCT, seven ancestral chromosomes (in different colors) were inferred. The duplicated chromosomes during the GCT were then reduced to 12 due to chromosome fusions and DNA exchanges, whose major structures have been well preserved in Oryza plants. The 12 chromosomes were then reduced in each plant under study. Os, Sb, Si, and Pg stand for O. sativa , S. bicolor , S. italica , and P. americarum .

Article Snippet: Oryza sativa ssp. Xian (Japonica) (Minghui 63, a Xian rice) [ ] was downloaded from the NCBI (National Center for Biotechnology Information).

Techniques:

Journal: Journal of Pineal Research

Article Title: IAT4 , a New Indolamine N ‐Acetyltransferase in Saccharomyces cerevisiae Involved in Melatonin Biosynthesis

doi: 10.1111/jpi.70053

Figure Lengend Snippet: Illustration of the biosynthetic pathway of melatonin from tryptophan for different organisms. 5‐OHTrp, 5‐hydroxytryptophan; 5‐MT, 5‐methoxytryptamine; l ‐Trp, tryptophan; NAcSer, N ‐acetylserotonin. Enzymes represented are AADC, aromatic amino acid decarboxylase; AANAT, aromatic amino acid N ‐acetyltransferase; ASMT, N ‐acetylserotonin methyltransferase; COMT, caffeic acid O ‐methyltransferase; SNAT, serotonin N ‐acetyltransferase; T5H, tryptamine 5‐hydroxylase; TDC, tryptophan decarboxylase; TPH, tryptophan hydroxylase. Colours refer to the pathway and enzymes usually employed by each organism. Orange refers to mammalian pathway, green for plants, and blue for yeast.

Article Snippet: The construction of this strain was described by Planells‐Cárcel et al. [ ] and it was as follows: the sequences of the TDC gene from Clostridium sporogenes ( Cs TDC) and T5H from Oryza sativa ( Os T5H) were chemically synthesised by Twist Bioscience (California, USA) and optimised for the use of codons from S. cerevisiae .

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Journal: Microbial Biotechnology

Article Title: Metabolic Engineering of a Serotonin Overproducing Saccharomyces cerevisiae Strain

doi: 10.1111/1751-7915.70140

Figure Lengend Snippet: Illustrative scheme of aromatic amino acid metabolism from sugar catabolism in S. cerevisiae . Tryptophan is produced from the precursors phosphoenolpyruvate and D‐erythrose 4‐phosphate, from glycolysis and the pentose phosphate pathway respectively, via the shikimic acid pathway. The last part of the diagram represents the pathway we have constructed for the production of serotonin from tryptophan. The enzymes shown are tryptophan decarboxylase (TDC) from C. sporogenes and tryptamine 5‐hydroxylase (T5H) from O. sativa , represented by their AlphaFold structural models.

Article Snippet: The sequences of the TDC gene from Clostridium sporogenes ( Cs TDC) and T5H from Oryza sativa ( Os T5H) were chemically synthesised by Twist Bioscience (California, USA) and optimised for the use of codons from S. cerevisiae (Table ).

Techniques: Produced, Construct

Journal: Microbial Biotechnology

Article Title: Metabolic Engineering of a Serotonin Overproducing Saccharomyces cerevisiae Strain

doi: 10.1111/1751-7915.70140

Figure Lengend Snippet: Effect of expressing Cs TDC, Os T5H and ARO4 * in BY4743 on serotonin production. Table below the graph list heterologous genes present in the different strains. BS3 overexpresses the Cs TDC and Os T5H genes, BS4 overexpresses Cs TDC, Os T5H and ARO4 *, wild type BY4743 was used as a control. Strains were cultivated for 72 h in SD 80 medium with 300 mg/L of nitrogen in the form of ammonium sulphate and L‐TRP mixture (light blue) or ammonium sulphate exclusively (dark blue). Standard deviations from the values of three biological replicates are represented by error bars. The serotonin titres produced by the different strains and the two media were compared using one‐way ANOVA and Tukey's test for a p ‐value < 0.05. Shared letters indicate no significant difference in serotonin titres.

Article Snippet: The sequences of the TDC gene from Clostridium sporogenes ( Cs TDC) and T5H from Oryza sativa ( Os T5H) were chemically synthesised by Twist Bioscience (California, USA) and optimised for the use of codons from S. cerevisiae (Table ).

Techniques: Expressing, Control, Produced

Journal: Microbial Biotechnology

Article Title: Metabolic Engineering of a Serotonin Overproducing Saccharomyces cerevisiae Strain

doi: 10.1111/1751-7915.70140

Figure Lengend Snippet: Schematic of tryptophan‐derived metabolic pathways and serotonin production for the study of potential bottlenecks. The strains evaluated are BY4743 (control strain), BS3 strain (harbouring Cs TDC and Os T5H genes for serotonin production) and BS4 strain (BS3 strain background plus ARO4 * gene). Each compound concentration (μM) is showed in a graphic represented by mean and standard deviation. One‐way ANOVA was performance for each compound to show significant differences between strains. The limit of detection (LOD) for each metabolite is given in brackets: Anthranilic acid (10 nM), Tyrosine (2 nM), Phenylalanine (80 nM), Tryptophan (40 nM), Tryptamine (2.5 nM), 5‐hydroxytryptophan (2 nM), Serotonin (10 nM), acetylserotonin (2 nM), 5‐methoxytryptamine (2 nM), Melatonin (5 nM), N‐Formylkynurenine (2 nM), Kynurenine (2 nM), Kynurenic acid (2 nM), Hydroxyanthranilic acid (40 nM), Xanthurenic acid (2 nM), 3‐hydroxykynurenine (2 nM). ns, no significant. * p ‐value < 0.05; ** p ‐value < 0.01; *** p ‐value < 0.001. ns = not significant.

Article Snippet: The sequences of the TDC gene from Clostridium sporogenes ( Cs TDC) and T5H from Oryza sativa ( Os T5H) were chemically synthesised by Twist Bioscience (California, USA) and optimised for the use of codons from S. cerevisiae (Table ).

Techniques: Derivative Assay, Control, Concentration Assay, Standard Deviation