Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Epsilon-poly-L-lysine: Recent Advances in Biomanufacturing and Applications

doi: 10.3389/fbioe.2021.748976

Figure Lengend Snippet: Domain architectures and catalytic mechanisms of typical non-ribosomal peptide synthase (A) and ε-PL synthetase (in S.albulus , E. festucae and C. variabile ) (B) ( ; ; ; ).

Article Snippet: Among them, Chisso Co. was the most prominent ε-PL manufacturers, which established a production line with an annual output of 1,000 tons, using a mutant strain of Streptomyces albulus ( ).

Techniques:

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Epsilon-poly-L-lysine: Recent Advances in Biomanufacturing and Applications

doi: 10.3389/fbioe.2021.748976

Figure Lengend Snippet: Summary of the cell engineering strategies on ɛ-PL production.

Article Snippet: Among them, Chisso Co. was the most prominent ε-PL manufacturers, which established a production line with an annual output of 1,000 tons, using a mutant strain of Streptomyces albulus ( ).

Techniques: Mutagenesis, Clinical Proteomics, Concentration Assay, Hybridization, Over Expression, Expressing, Clone Assay, Knock-Out, Inhibition, Translocation Assay

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Epsilon-poly-L-lysine: Recent Advances in Biomanufacturing and Applications

doi: 10.3389/fbioe.2021.748976

Figure Lengend Snippet: Possible mechanism for the acid tolerance response by S. albulus M-Z18. Figure modified from . Arg, arginine; Asp, aspartate; L-Lys, L-lysine; C 18:1 , oleic acid; Orn, ornithine; Ala, alanine; Cad, cadaverine; C 14:1 , myristoleic acid; Cit, citrulline; Glu, glutamate; ε-PL, ε-Poly-L-lysine; Sa-fat, saturated fatty acid; Car-PO 4 , carbamoyl phosphate; GABA, γ-aminobutyrate; CFA, cyclopropane fatty acid.

Article Snippet: Among them, Chisso Co. was the most prominent ε-PL manufacturers, which established a production line with an annual output of 1,000 tons, using a mutant strain of Streptomyces albulus ( ).

Techniques: Modification

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Epsilon-poly-L-lysine: Recent Advances in Biomanufacturing and Applications

doi: 10.3389/fbioe.2021.748976

Figure Lengend Snippet: Summary of the process engineering strategies on ɛ-PL production.

Article Snippet: Among them, Chisso Co. was the most prominent ε-PL manufacturers, which established a production line with an annual output of 1,000 tons, using a mutant strain of Streptomyces albulus ( ).

Techniques: Control, Activation Assay, Activity Assay, Concentration Assay, In Situ

Journal: BMC Biology

Article Title: Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

doi: 10.1186/s12915-018-0485-8

Figure Lengend Snippet: Comparative analysis of the dmrt1a and dmrt1bY co-ortholog promoters and presence of Rex1 element sequences in the genomes of selected fish species. a Comparative analysis of the medaka dmrt1 co-ortholog promoter regions. Differences in length for the two promoter regions are caused by Rex1 and Izanagi transposable elements as well as repeats 3 and 4 that were inserted into the dmrt1bY promoter after the duplication event that gave rise to the dmrt1bY gene approximately 10 million years ago . Regions α, β, or γ (brackets [] underlined in red) contain multiple Sox5 binding sites within Rex1 , Izanagi , and repeat 3, respectively, that have been subjected to chromatin immunoprecipitation (ChIP) (see also Additional file : Figure S1). The red star (*) identifies the Dmrt1 binding site described in . b Alignment of the Y-chromosomal Rex1 element together with the 19 remaining Rex1 copies encompassing the sox5 binding site in the medaka genome. Dots indicate conserved nucleotides. Black arrows define primers used for chromatin immunoprecipitation. c Presence of Rex1 element (i) partial sequences, (ii) sequences encompassing the dmrt1bY-nested sox5 binding site, and (iii) sequences encompassing the dmrt1bY-nested sox5 binding site with the intact sox5 binding site in the genomes of medaka ( Oryzias latipes ), tilapia ( Oreochromis niloticus ), zebrafish ( Danio rerio ), cavefish ( Astyanax mexicanus ), cod ( Gadus morhua ), gar ( Lepisosteus oculatus ), stickleback ( Gasterosteus aculeatus ), platy ( Xiphophorus maculatus ), Amazon molly ( Poecilia formosa ), fugu, tetraodon, and coelacanth ( Latimeria chalumnae )

Article Snippet: The Sox5 medaka mutant strain (N541S) has been deposited with the National Bioresource Center ( http://www.nbrp.jp/localeAction.do?lang=en ).

Techniques: Binding Assay, Chromatin Immunoprecipitation

Journal: BMC Biology

Article Title: Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

doi: 10.1186/s12915-018-0485-8

Figure Lengend Snippet: Analysis of Sox5 binding to the dmrt1bY promoter and regulation of dmrt1bY promoter activity upon modulation of Sox5 expression. a Chromatin immunoprecipitation (ChIP) of Sox5 binding to regions α, β, or γ of the dmrt1bY proximal promoter. Transient transfection of a flagged and tagged version of Sox5 into either medaka spermatogonial or fibroblast cell lines and subsequent immunoprecipitation (FLAG antibody) followed by the quantitative real-time polymerase chain reaction. Results are presented as enrichment compared to the input and correspond to three independent immunoprecipitations for each region (α, β, or γ). Statistical significance was assessed with the Wilcoxon–Mann–Whitney test ( N = 3). b1–b4 Analysis of dmrt1bY proximal promoter activity after Sox5 transient transfection into the medaka spermatogonial cell line (Sg3). Deletions of the 5′ dmrt1bY promoter were generated: b1 α region, b2 α and β regions, b3, b4 α, β, and γ regions. Transcriptional activity was quantified in the absence (control, -Sox5) or presence (+Sox5) of Sox5. Statistical significance was assessed with the Wilcoxon–Mann–Whitney test ( N = 4). c Detailed analysis of the transcriptional activity of the alpha (α), alpha-mutant (α-MUT), and beta (β) fragments. Statistical significance was assessed with the Wilcoxon–Mann–Whitney test ( N = 4). * p value ≤ 0.05, ** p value ≤ 0.01. ns non-significant, OLF Oryzias latipes fibroblast, Sg3 Oryzias latipes spermatogonial cell

Article Snippet: The Sox5 medaka mutant strain (N541S) has been deposited with the National Bioresource Center ( http://www.nbrp.jp/localeAction.do?lang=en ).

Techniques: Binding Assay, Activity Assay, Expressing, Chromatin Immunoprecipitation, Transfection, Immunoprecipitation, Real-time Polymerase Chain Reaction, MANN-WHITNEY, Generated, Control, Mutagenesis

Journal: BMC Biology

Article Title: Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

doi: 10.1186/s12915-018-0485-8

Figure Lengend Snippet: Effects of Sox5 modulation on dmrt1bY gene expression. Analysis of dmrtbY a transcriptional regulation after sox5 transient transfection in either spermatogonial or fibroblast medaka cell lines at 24 or 48 h post-transfection. Dataset results of four independent transfections. Statistical significance was assessed with the Wilcoxon–Mann–Whitney test ( N = 4; * p value ≤ 0.05, ** p value ≤ 0.01). b Overexpression of sox5 was stimulated in fish eggs. The expression of dmrt1bY and germ-cell markers ( nanos2 , nanos3 , dead-end , vasa , tra2a , and piwi ) were monitored at stage 18 of development and compared to wild-type fish embryos. Dataset results of three independent transfections. Statistical significance was assessed with the t -test ( N = 3 and each replicate is a pool of 25 eggs; * p value ≤ 0.05, ** p value ≤ 0.01). ns non-significant, OLF Oryzias latipes fibroblast, Sg3 Oryzias latipes spermatogonial cell

Article Snippet: The Sox5 medaka mutant strain (N541S) has been deposited with the National Bioresource Center ( http://www.nbrp.jp/localeAction.do?lang=en ).

Techniques: Gene Expression, Transfection, MANN-WHITNEY, Over Expression, Expressing

Journal: BMC Biology

Article Title: Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

doi: 10.1186/s12915-018-0485-8

Figure Lengend Snippet: Expression of medaka sox5 during embryogenesis. a to c and e to g Medaka sox5 expression investigated by whole-mount in situ hybridization or d , h , and i fluorescence using a transgenic reporter line for which a 3288-bp sox5 promoter fragment drives the expression of mCherry. a-c Between stages 18 and 22, sox5 mRNA localizes predominantly in the head and tail bud regions of the embryos. c,d At stage 22, additional expression is detected in the lateral plate mesoderm of the embryos (arrows). e – g' From stage 24 onward, sox5 expression spans over the dorsal neural tube and pre-migratory neural crest cells (arrowheads). g,g' At stage 29, sox5 expression is also seen in ventral migrating neural crest cells (arrowheads). h and i Fluorescent sox5 expression is monitored in the neural tube and neural crest cells of hatching embryos (stages 38/39). h For comparison, patched2 highlights the notochord at stage 39

Article Snippet: The Sox5 medaka mutant strain (N541S) has been deposited with the National Bioresource Center ( http://www.nbrp.jp/localeAction.do?lang=en ).

Techniques: Expressing, In Situ Hybridization, Fluorescence, Transgenic Assay, Comparison

Journal: BMC Biology

Article Title: Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

doi: 10.1186/s12915-018-0485-8

Figure Lengend Snippet: Comparative analysis of sox5 and dmrt1bY expression dynamics during gonadal primordium formation. Expression of sox5 compared to dmrt1by in a double transgenic fluorescent reporter line. a – c During early gonadal formation, sox5 is first detected in the somatic tissues surrounding the germ cells at stages 26 to 28. At the same time, dmrt1bY is expressed in germ cells. d – i By stages 33 to 34, sox5 expression becomes restricted to the germ cells. dmrt1bY is also expressed in the germ cells at those specific stages of development. Variations within the respective levels of sox5 and dmrt1bY expression are clearly observable ( d compared to e and f and g compared to h and i ). j , k Around hatching (stages 38/39), the expression of sox5 strengthens in all germ cells while parallel dmrt1bY expression quickly switches from germ cells only to somatic germ-cell-surrounding cells only. l In vivo visualization of the dynamics of expression localization of sox5 and dmrt1bY during male gonadal primordium development. The expression of sox5 and dmrt1bY is highly dynamic during primordium gonadal formation, switching from somatic to germ cells and vice versa, respectively, from stage 26 until hatching. Being mutual repressors of each other, a seesaw of expression is observed, finally finely restricting dmrt1bY expression in the somatic part of the primordium gonad. Blue and red represent cellular expression localizations only and should not been interpreted as expression levels

Article Snippet: The Sox5 medaka mutant strain (N541S) has been deposited with the National Bioresource Center ( http://www.nbrp.jp/localeAction.do?lang=en ).

Techniques: Expressing, Transgenic Assay, In Vivo

Journal: BMC Biology

Article Title: Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

doi: 10.1186/s12915-018-0485-8

Figure Lengend Snippet: Expression of sox5 in adult gonads. a – d In adult testes, sox5 fluorescence is restricted to the cells located between the lobules where the germ and Sertoli cells lie. a , b In double transgenic reporter fish, fluorescence of sox5 and dmrt1bY (marking the Sertoli cells) is distinct. c, d The interlobular expression of sox5 co-localizes with 11-β-hydroxylase, a marker of Leydig cells. e – j Expression of sox5 is also detected in another discrete population of cells between but always close to the germinal lobules. h - j Small in size, these sox5 -positive cells also express vasa , a specific marker of germ cells. k – n The sox5- and vasa-positive cells do not express dmrt1bY . o – q In adult ovaries, only extremely few sox5 positive cells are detected.

Article Snippet: The Sox5 medaka mutant strain (N541S) has been deposited with the National Bioresource Center ( http://www.nbrp.jp/localeAction.do?lang=en ).

Techniques: Expressing, Fluorescence, Transgenic Assay, Marker

Journal: BMC Biology

Article Title: Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

doi: 10.1186/s12915-018-0485-8

Figure Lengend Snippet: Regulation of PGC numbers by Sox5. a , b As early as stage 22, a drastic reduction of the germ-cell number ( vasa in situ hybridization) is observed in sox5 -/- mutants compared to wild-type embryos. c For conditional knock-in and rescue of the sox5 -/- mutant fish, a transgenic line expressing sox5 was produced. See “ ” for details. d , e In vivo visualization of the effective recombination and expression of sox5 is apparent after a switch from red cytoplasmic to green nuclear-localized fluorescence. After Cre recombinase injection at the one-cell stage, an almost total recombination is observed, leading to the expression of the sox5 transcript as monitored by green fluorescence. Stars indicate auto-fluorescent pigment cells and arrows indicate recombined germ cells. f Germ-cell numbers in sox5 mutant medaka after in vivo recombination and expression of sox5 . Of note, for that specific experiment, embryos were additionally injected with a GFP-Nanos 3′ untranslated region (UTR) mRNA construct allowing effective PGC monitoring. Statistical significance was assessed with the Wilcoxon–Mann–Whitney test ( N = 30, 28, and 42 for Sox5 -/- , Sox5 -/- recombined, and wild-type embryos, respectively; * p value ≤ 0.05, ** p value ≤ 0.01). GFP green fluorescent protein, ns non-significant, PGC primordial germ cell

Article Snippet: The Sox5 medaka mutant strain (N541S) has been deposited with the National Bioresource Center ( http://www.nbrp.jp/localeAction.do?lang=en ).

Techniques: In Situ Hybridization, Knock-In, Mutagenesis, Transgenic Assay, Expressing, Produced, In Vivo, Fluorescence, Injection, Construct, MANN-WHITNEY

Journal: BMC Biology

Article Title: Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

doi: 10.1186/s12915-018-0485-8

Figure Lengend Snippet: Phenotypic versus genotypic sex of sox5-/- mutants and regulation of the dmrt1 co-orthologs and a set of germ-cell markers in sox5-/- mutant embryos. a Phenotypic versus genotypic sex of sox5 -/- mutant fish. Complete XX female-to-male sex reversion was obtained. b Sexual phenotype of the adult medaka. Wild-type XX females have a triangular-shaped anal fin as well as fused dorsal fin rays. Wild-type XY males have a parallelogram-shaped anal fin as well as split dorsal fin rays. c Regulation of the expression of dmrt1bY and other germ-cell markers ( nanos2 , nanos3 , dead-end , vasa , tra2a , and piwi ) in sox5 -/- mutants compared to wild-type embryos at different stages of development (stages 28, 32, and 39). Dataset results of three different batches of eggs obtained from different couples. Statistical significance was assessed with the t -test ( N = 3 and each replicate is a pool of 25 eggs; * p value ≤ 0.05, ** p value ≤ 0.01). ns non-significant

Article Snippet: The Sox5 medaka mutant strain (N541S) has been deposited with the National Bioresource Center ( http://www.nbrp.jp/localeAction.do?lang=en ).

Techniques: Mutagenesis, Expressing