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    ATCC genome sequenced t denticola atcc 35405t strain
    Genome Sequenced T Denticola Atcc 35405t Strain, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher steponeplus real time pcr system
    Steponeplus Real Time Pcr System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 52235 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Applied Maths bionumerics v6
    Bionumerics V6, supplied by Applied Maths, used in various techniques. Bioz Stars score: 85/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc germplasm accessions
    Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all <t>germplasm</t> accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.
    Germplasm Accessions, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 139 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    GenScript tcauk1
    Analysis of <t>TcAUK1</t> overexpressing epimastigotes. (A) Isolated DNA from pTREX and pTREX-TcAUK1 epimastigotes was treated with different restriction endonucleases and analyzed by Southern blot to confirm the extra copy of TcAUK1 in the genome of transgenic cells. (B) Immunoblot against TcAUK1 protein in pTREX and pTREX-TcAUK1 cells extracts. The β-Tubulin protein was used as loading control. (C) pTREX and clonal pTREX-TcAUK1 epimastigotes were cultivated and monitored for cell growth every day. Cell number was plotted in a logarithmic scale and the presented data is a mean ± s.d. of three independent cell cultures. Cells duplication time in each independent culture was calculated and a Paired T test (p
    Tcauk1, supplied by GenScript, used in various techniques. Bioz Stars score: 93/100, based on 101 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

    Journal: Molecular Ecology

    Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

    doi: 10.1111/mec.13138

    Figure Lengend Snippet: Parsimony tree of 15 996 soybean accessions with high confidence data at all single nucleotide polymorphisms (SNPs) in the S2 linkage disequilibrium block surrounding Rhg1 . The four terminal branches containing all germplasm accessions described elsewhere in the manuscript are labelled, together with the number of accessions carrying the same combination of SNPs.

    Article Snippet: The germplasm accessions in the WGS data are as follows: three single-copy germplasm accessions (Williams 82, PI 427136, & PI 518751), one 2 copy (PI 438489 B), three 3 copy (PI 467327, Peking, & PI 89772), one 4 copy (PI 89008), three 6 copy (PI 87631-1, PI 461509, & PI 467332), two 7 copy (PI 92720 & Cloud), one 9 copy (PI 88788) and four 10 copy (PI 209332, LD10-30036, LD09-15087a, & LD00-3309).

    Techniques: Blocking Assay

    Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

    Journal: Molecular Ecology

    Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

    doi: 10.1111/mec.13138

    Figure Lengend Snippet: Signatures of selection at the Rhg1 locus. (a) Nucleotide diversity (π and θ), Tajima's D and linkage disequilibrium were measured in the 1.5-Mbp region across the locus in 19 548 accessions (18 383 Glycine max 1165 Glycine soja ). The mean and 75th and 95th percentiles of whole-genome Tajima's D are marked by horizontal lines in corresponding graphs. (b) F ST was calculated for lines with experimentally determined copy number (46 single copy vs. 48 multiple copy). Direction of telomere = ‘tel’. The mean and 95th percentile of whole-genome F ST are marked by horizontal lines. Red marks indicates statistical significance. (c) F ST between geographic subpopulations. One hundred and thirty-five single nucleotide polymorphisms were used to compare: Top graph, between 3311 germplasm accessions from Korea and 3855 from China; centre, between 3311 from Korea and 2466 from Japan; bottom, between 3855 from China and 2466 from Japan. The mean and 95th percentile values of whole-genome F ST are marked by a horizontal line in the corresponding graphs.

    Article Snippet: The germplasm accessions in the WGS data are as follows: three single-copy germplasm accessions (Williams 82, PI 427136, & PI 518751), one 2 copy (PI 438489 B), three 3 copy (PI 467327, Peking, & PI 89772), one 4 copy (PI 89008), three 6 copy (PI 87631-1, PI 461509, & PI 467332), two 7 copy (PI 92720 & Cloud), one 9 copy (PI 88788) and four 10 copy (PI 209332, LD10-30036, LD09-15087a, & LD00-3309).

    Techniques: Selection

    Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

    Journal: Molecular Ecology

    Article Title: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

    doi: 10.1111/mec.13138

    Figure Lengend Snippet: Diversity, linkage disequilibrium (LD) and sequence analysis of the region surrounding the Rhg1 locus. (a) Nucleotide diversity within 38 protein-coding genes surrounding Rhg1 in eighteen germplasm accessions (with 1–10 copies at Rhg1 ) is displayed in the uppermost graph. Those accessions with three copies (centre graph) and nine and ten copies (bottom graph) were also analysed separately. The average nucleotide diversity (π; 0.00053) of all coding regions in Glycine max is marked by a horizontal line. (b) LD plot using the r 2 metric for the 400-kb region surrounding the Rhg1 locus. The same 18 accessions were used. Regions S1, S2 and S3 represent three linkage blocks used in further analysis. tel: telomere. (c) Phylogenetic trees derived from parsimony analysis of the three LD blocks. The tree for the region of linkage block S2 that contains Rhg1 is consistent with the analysis of the repeat sequence (Fig. 2 ). The copy number of each accession is in parentheses. The consensus trees were created after collapsing branches with bootstrap values

    Article Snippet: The germplasm accessions in the WGS data are as follows: three single-copy germplasm accessions (Williams 82, PI 427136, & PI 518751), one 2 copy (PI 438489 B), three 3 copy (PI 467327, Peking, & PI 89772), one 4 copy (PI 89008), three 6 copy (PI 87631-1, PI 461509, & PI 467332), two 7 copy (PI 92720 & Cloud), one 9 copy (PI 88788) and four 10 copy (PI 209332, LD10-30036, LD09-15087a, & LD00-3309).

    Techniques: Sequencing, Derivative Assay, Blocking Assay

    Analysis of TcAUK1 overexpressing epimastigotes. (A) Isolated DNA from pTREX and pTREX-TcAUK1 epimastigotes was treated with different restriction endonucleases and analyzed by Southern blot to confirm the extra copy of TcAUK1 in the genome of transgenic cells. (B) Immunoblot against TcAUK1 protein in pTREX and pTREX-TcAUK1 cells extracts. The β-Tubulin protein was used as loading control. (C) pTREX and clonal pTREX-TcAUK1 epimastigotes were cultivated and monitored for cell growth every day. Cell number was plotted in a logarithmic scale and the presented data is a mean ± s.d. of three independent cell cultures. Cells duplication time in each independent culture was calculated and a Paired T test (p

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Aurora kinase protein family in Trypanosoma cruzi: Novel role of an AUK-B homologue in kinetoplast replication

    doi: 10.1371/journal.pntd.0007256

    Figure Lengend Snippet: Analysis of TcAUK1 overexpressing epimastigotes. (A) Isolated DNA from pTREX and pTREX-TcAUK1 epimastigotes was treated with different restriction endonucleases and analyzed by Southern blot to confirm the extra copy of TcAUK1 in the genome of transgenic cells. (B) Immunoblot against TcAUK1 protein in pTREX and pTREX-TcAUK1 cells extracts. The β-Tubulin protein was used as loading control. (C) pTREX and clonal pTREX-TcAUK1 epimastigotes were cultivated and monitored for cell growth every day. Cell number was plotted in a logarithmic scale and the presented data is a mean ± s.d. of three independent cell cultures. Cells duplication time in each independent culture was calculated and a Paired T test (p

    Article Snippet: A detailed analysis of the information found in the database suggests that the CDS retrieved for TcAUK1 and TcAUK2 correspond to allelic variants of single copy genes.

    Techniques: Isolation, Southern Blot, Transgenic Assay

    TcAUK1 localization in epimastigote forms. (A) Epimastigote forms were cell cycle synchronized with HU and the indicated cell cycle phases confirmed by flow cytometry. TcAUK1 (rabbit antiserum to TcAUK1) and nucleus/kinetoplast (DAPI). (B) TcAUK1 coding sequence was cloned into pTEXeGFP expression vector and epimastigotes were transfected. Shortly after transfection (24–48 hs), the localization of the fusion protein was evaluated by fluorescence microscopy.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Aurora kinase protein family in Trypanosoma cruzi: Novel role of an AUK-B homologue in kinetoplast replication

    doi: 10.1371/journal.pntd.0007256

    Figure Lengend Snippet: TcAUK1 localization in epimastigote forms. (A) Epimastigote forms were cell cycle synchronized with HU and the indicated cell cycle phases confirmed by flow cytometry. TcAUK1 (rabbit antiserum to TcAUK1) and nucleus/kinetoplast (DAPI). (B) TcAUK1 coding sequence was cloned into pTEXeGFP expression vector and epimastigotes were transfected. Shortly after transfection (24–48 hs), the localization of the fusion protein was evaluated by fluorescence microscopy.

    Article Snippet: A detailed analysis of the information found in the database suggests that the CDS retrieved for TcAUK1 and TcAUK2 correspond to allelic variants of single copy genes.

    Techniques: Flow Cytometry, Cytometry, Sequencing, Clone Assay, Expressing, Plasmid Preparation, Transfection, Fluorescence, Microscopy

    Expression of TcAUKs genes. (A) RT-PCR of the three TcAUKs and Actin (housekeeping control) in epimastigotes (E), trypomastigotes (T) and amastigotes (A) of T . cruzi . (-): PCR negative control. I and II indicate the specific amplification products of similar length obtained for TcAUK3 (B) Nucleotide sequence of the 5´ Untranslated Region of each TcAUK mRNA. The Spliced Leader sequence and the starting ATG codon followed by the initial sequence of the genes (CDS) are indicated. I and II reference to the bands indicated in (A). Underlined in TcAUK3 is the region of the 5´ UTR absent in one of the two amplification products. (C) Immunoblot of TcAUK1 in total cell extracts from Epimastigotes (E), Trypomastigotes (T) and Amastigotes (A).

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Aurora kinase protein family in Trypanosoma cruzi: Novel role of an AUK-B homologue in kinetoplast replication

    doi: 10.1371/journal.pntd.0007256

    Figure Lengend Snippet: Expression of TcAUKs genes. (A) RT-PCR of the three TcAUKs and Actin (housekeeping control) in epimastigotes (E), trypomastigotes (T) and amastigotes (A) of T . cruzi . (-): PCR negative control. I and II indicate the specific amplification products of similar length obtained for TcAUK3 (B) Nucleotide sequence of the 5´ Untranslated Region of each TcAUK mRNA. The Spliced Leader sequence and the starting ATG codon followed by the initial sequence of the genes (CDS) are indicated. I and II reference to the bands indicated in (A). Underlined in TcAUK3 is the region of the 5´ UTR absent in one of the two amplification products. (C) Immunoblot of TcAUK1 in total cell extracts from Epimastigotes (E), Trypomastigotes (T) and Amastigotes (A).

    Article Snippet: A detailed analysis of the information found in the database suggests that the CDS retrieved for TcAUK1 and TcAUK2 correspond to allelic variants of single copy genes.

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Negative Control, Amplification, Sequencing

    TcAUK1 localization in the different forms of T . cruzi . (A) Epimastigote forms at different points of the cell cycle (1F1K1N, 2F2K1N, 2F2K2N) were co-immunostained with rabbit antiserum to TcAUK1 and mouse KMX-1 for TcAUK1 and mitotic spindle, respectively. Yellow arrowhead indicates cells where the nuclei have not segregated yet, and white arrowhead points cells where both nuclei are segregating and (B) Amastigote and Trypomastigote forms isolated from culture supernatants were immunostained with rabbit antiserum to TcAUK1. (C) Infected Vero cells were stained with rhodamine-conjugated phalloidin for actin filaments and intracellular parasites were immunostained with rabbit antiserum to TcAUK1. In all cases, to dye DNA structures–nucleus (n or N) and kinetoplast (k)–cells were counterstained with DAPI. White squares point the magnified regions.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Aurora kinase protein family in Trypanosoma cruzi: Novel role of an AUK-B homologue in kinetoplast replication

    doi: 10.1371/journal.pntd.0007256

    Figure Lengend Snippet: TcAUK1 localization in the different forms of T . cruzi . (A) Epimastigote forms at different points of the cell cycle (1F1K1N, 2F2K1N, 2F2K2N) were co-immunostained with rabbit antiserum to TcAUK1 and mouse KMX-1 for TcAUK1 and mitotic spindle, respectively. Yellow arrowhead indicates cells where the nuclei have not segregated yet, and white arrowhead points cells where both nuclei are segregating and (B) Amastigote and Trypomastigote forms isolated from culture supernatants were immunostained with rabbit antiserum to TcAUK1. (C) Infected Vero cells were stained with rhodamine-conjugated phalloidin for actin filaments and intracellular parasites were immunostained with rabbit antiserum to TcAUK1. In all cases, to dye DNA structures–nucleus (n or N) and kinetoplast (k)–cells were counterstained with DAPI. White squares point the magnified regions.

    Article Snippet: A detailed analysis of the information found in the database suggests that the CDS retrieved for TcAUK1 and TcAUK2 correspond to allelic variants of single copy genes.

    Techniques: Isolation, Infection, Staining

    Effect of TcAUK1 overexpression on cell cycle progression in epimastigotes. (A) Mitotic progression of pTREX and pTREX-TcAUK1 synchronized cells was monitored by flow cytometry, measuring DNA content every 30 min between hours 11 to 14 post-releasing. (B) Mitotic spindle dynamics and DNA structure duplication (nucleus and kinetoplast) in WT cells were observed by immunostaining with mouse KMX-1 monoclonal antibody and DAPI dye, respectively. In the schematic representation of the events captured by microscopy: green is the mitotic spindle, blue the nucleus and dark blue the kinetoplast; NF means new flagellum and FP is flagellar pocket. (C) Graphical representation of cells with different number of flagellum (F), nucleus (N) and kinetoplast (K) in synchronized control (pTREX) and overexpression cells (pTREX-TcAUK1) at different time points after realizing (11 to 14 hs). Data are presented as the percentage of over 200 cells counted. (D) Mitotic spindle assembling (yellow arrows) and flagellum duplication in TcAUK1 overexpressing cells by immunostaining with mouse monoclonal KMX-1 antibody. Cell’s nucleus and kinetoplast (red arrows) were counterstained with DAPI.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Aurora kinase protein family in Trypanosoma cruzi: Novel role of an AUK-B homologue in kinetoplast replication

    doi: 10.1371/journal.pntd.0007256

    Figure Lengend Snippet: Effect of TcAUK1 overexpression on cell cycle progression in epimastigotes. (A) Mitotic progression of pTREX and pTREX-TcAUK1 synchronized cells was monitored by flow cytometry, measuring DNA content every 30 min between hours 11 to 14 post-releasing. (B) Mitotic spindle dynamics and DNA structure duplication (nucleus and kinetoplast) in WT cells were observed by immunostaining with mouse KMX-1 monoclonal antibody and DAPI dye, respectively. In the schematic representation of the events captured by microscopy: green is the mitotic spindle, blue the nucleus and dark blue the kinetoplast; NF means new flagellum and FP is flagellar pocket. (C) Graphical representation of cells with different number of flagellum (F), nucleus (N) and kinetoplast (K) in synchronized control (pTREX) and overexpression cells (pTREX-TcAUK1) at different time points after realizing (11 to 14 hs). Data are presented as the percentage of over 200 cells counted. (D) Mitotic spindle assembling (yellow arrows) and flagellum duplication in TcAUK1 overexpressing cells by immunostaining with mouse monoclonal KMX-1 antibody. Cell’s nucleus and kinetoplast (red arrows) were counterstained with DAPI.

    Article Snippet: A detailed analysis of the information found in the database suggests that the CDS retrieved for TcAUK1 and TcAUK2 correspond to allelic variants of single copy genes.

    Techniques: Over Expression, Flow Cytometry, Cytometry, Immunostaining, Microscopy

    TcAUK1 localization in synchronized overexpressing epimastigotes. TcAUK1 overexpressing epimastigotes, at different phases of cell cycle, were stained for mitotic spindle (mouse monoclonal KMX-1 antibody), TcAUK1 (rabbit antiserum to TcAUK1) and nucleus/kinetoplast (DAPI).

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Aurora kinase protein family in Trypanosoma cruzi: Novel role of an AUK-B homologue in kinetoplast replication

    doi: 10.1371/journal.pntd.0007256

    Figure Lengend Snippet: TcAUK1 localization in synchronized overexpressing epimastigotes. TcAUK1 overexpressing epimastigotes, at different phases of cell cycle, were stained for mitotic spindle (mouse monoclonal KMX-1 antibody), TcAUK1 (rabbit antiserum to TcAUK1) and nucleus/kinetoplast (DAPI).

    Article Snippet: A detailed analysis of the information found in the database suggests that the CDS retrieved for TcAUK1 and TcAUK2 correspond to allelic variants of single copy genes.

    Techniques: Staining