Structured Review

Biotechnology Information ncbi
Whole transcriptome sequence in GPI-AP+ and GPI-AP− granulocytes and differential expression of CXCR2 in various blood cell lineages in PNH (A) Expression levels of mRNAs illustrated in scatter plots. Each point corresponds to one <t>NCBI</t> Reference Sequence (RefSeq) transcript with log10 Fragments per kilobase of transcript per million fragments sequenced (FPKM) values for GPI-AP+ and GPI-AP− granulocytes from PNH patients. A threshold of absolute value (log2 (Y/X)) ≥ 1 and posterior probability of being equally expressed (PPEE) ≤ 0.05 were used to identify differentially expressed RNAs in GPI-AP+ and GPI-AP− granulocytes from PNH. (B) Gene tracks representing <t>RNA-Seq</t> data of the human CXCR2 locus. (C) Top canonical pathways identified by IPA comparing the differentially expressed genes between GPI-AP+ and GPI-AP− granulocytes. (D) Cell surface expression levels of CXCR2, CXCR1 and CSF2RB in GPI-AP+ and GPI-AP− granulocytes from PNH and healthy controls were assessed by flow cytometry (n = 11). Representative histograms are shown. (E) Graphs represent corresponding quantitative analysis of CXCR2 (CXCR1) MFI (geometric mean of fluorescence intensity) on granulocytes from PNH and healthy controls as described in (D). (F) CXCR2 (CXCR1) expression levels were examined in different peripheral blood cell populations (granulocytes, monocytes, T cells, and B cells) from PNH patients (n = 11). Representative histograms are shown. (G) Graphs represent corresponding quantitative analysis of CXCR2 (CXCR1) MFI on blood cells from PNH and healthy controls as described in (F). (H) Confocal imaging analysis validated higher CXCR2 expression in GPI-AP− than GPI-AP+ granulocytes. (I) Flow cytometry analysis of CXCR2 expression in BM HSCs and haematopoietic progenitor cells from PNH and healthy controls (n = 6). Representative histograms are shown. * P < 0.05 by one-way ANOVA and Tukey’s test. FLAER, fluorescein-labelled proaerolysin.
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1) Product Images from "Whole transcriptome sequencing identifies increased CXCR2 expression in PNH granulocytes"

Article Title: Whole transcriptome sequencing identifies increased CXCR2 expression in PNH granulocytes

Journal:

doi: 10.1111/bjh.14502

Whole transcriptome sequence in GPI-AP+ and GPI-AP− granulocytes and differential expression of CXCR2 in various blood cell lineages in PNH (A) Expression levels of mRNAs illustrated in scatter plots. Each point corresponds to one NCBI Reference Sequence (RefSeq) transcript with log10 Fragments per kilobase of transcript per million fragments sequenced (FPKM) values for GPI-AP+ and GPI-AP− granulocytes from PNH patients. A threshold of absolute value (log2 (Y/X)) ≥ 1 and posterior probability of being equally expressed (PPEE) ≤ 0.05 were used to identify differentially expressed RNAs in GPI-AP+ and GPI-AP− granulocytes from PNH. (B) Gene tracks representing RNA-Seq data of the human CXCR2 locus. (C) Top canonical pathways identified by IPA comparing the differentially expressed genes between GPI-AP+ and GPI-AP− granulocytes. (D) Cell surface expression levels of CXCR2, CXCR1 and CSF2RB in GPI-AP+ and GPI-AP− granulocytes from PNH and healthy controls were assessed by flow cytometry (n = 11). Representative histograms are shown. (E) Graphs represent corresponding quantitative analysis of CXCR2 (CXCR1) MFI (geometric mean of fluorescence intensity) on granulocytes from PNH and healthy controls as described in (D). (F) CXCR2 (CXCR1) expression levels were examined in different peripheral blood cell populations (granulocytes, monocytes, T cells, and B cells) from PNH patients (n = 11). Representative histograms are shown. (G) Graphs represent corresponding quantitative analysis of CXCR2 (CXCR1) MFI on blood cells from PNH and healthy controls as described in (F). (H) Confocal imaging analysis validated higher CXCR2 expression in GPI-AP− than GPI-AP+ granulocytes. (I) Flow cytometry analysis of CXCR2 expression in BM HSCs and haematopoietic progenitor cells from PNH and healthy controls (n = 6). Representative histograms are shown. * P < 0.05 by one-way ANOVA and Tukey’s test. FLAER, fluorescein-labelled proaerolysin.
Figure Legend Snippet: Whole transcriptome sequence in GPI-AP+ and GPI-AP− granulocytes and differential expression of CXCR2 in various blood cell lineages in PNH (A) Expression levels of mRNAs illustrated in scatter plots. Each point corresponds to one NCBI Reference Sequence (RefSeq) transcript with log10 Fragments per kilobase of transcript per million fragments sequenced (FPKM) values for GPI-AP+ and GPI-AP− granulocytes from PNH patients. A threshold of absolute value (log2 (Y/X)) ≥ 1 and posterior probability of being equally expressed (PPEE) ≤ 0.05 were used to identify differentially expressed RNAs in GPI-AP+ and GPI-AP− granulocytes from PNH. (B) Gene tracks representing RNA-Seq data of the human CXCR2 locus. (C) Top canonical pathways identified by IPA comparing the differentially expressed genes between GPI-AP+ and GPI-AP− granulocytes. (D) Cell surface expression levels of CXCR2, CXCR1 and CSF2RB in GPI-AP+ and GPI-AP− granulocytes from PNH and healthy controls were assessed by flow cytometry (n = 11). Representative histograms are shown. (E) Graphs represent corresponding quantitative analysis of CXCR2 (CXCR1) MFI (geometric mean of fluorescence intensity) on granulocytes from PNH and healthy controls as described in (D). (F) CXCR2 (CXCR1) expression levels were examined in different peripheral blood cell populations (granulocytes, monocytes, T cells, and B cells) from PNH patients (n = 11). Representative histograms are shown. (G) Graphs represent corresponding quantitative analysis of CXCR2 (CXCR1) MFI on blood cells from PNH and healthy controls as described in (F). (H) Confocal imaging analysis validated higher CXCR2 expression in GPI-AP− than GPI-AP+ granulocytes. (I) Flow cytometry analysis of CXCR2 expression in BM HSCs and haematopoietic progenitor cells from PNH and healthy controls (n = 6). Representative histograms are shown. * P < 0.05 by one-way ANOVA and Tukey’s test. FLAER, fluorescein-labelled proaerolysin.

Techniques Used: Sequencing, Expressing, RNA Sequencing Assay, Indirect Immunoperoxidase Assay, Flow Cytometry, Cytometry, Fluorescence, Imaging

2) Product Images from "Identification and characterization of a salt stress-inducible zinc finger protein from Festuca arundinacea"

Article Title: Identification and characterization of a salt stress-inducible zinc finger protein from Festuca arundinacea

Journal: BMC Research Notes

doi: 10.1186/1756-0500-5-66

Phylogenetic tree of FaZnF and related genes . The top BLAST hits from each genera obtained when FaZnF was used for BLAST analysis at NCBI [ 49 ]. Also included is
Figure Legend Snippet: Phylogenetic tree of FaZnF and related genes . The top BLAST hits from each genera obtained when FaZnF was used for BLAST analysis at NCBI [ 49 ]. Also included is "TA567_4606_Festuca" which was the top BLAST hit when TIGR Plant Transcript Assembly http://plantta.jcvi.org/search.shtml was queried with FaZnF [ 50 ]. This transcript assembly contained ESTs from a heat stressed cDNA subtraction library from tall fescue [ 80 ] and was most closely related to FaZnF . The scale bar represents .09 nucleotide substitutions per site, or 9 nucleotide differences per 100 nucleotides.

Techniques Used:

Phylogenetic tree of FaZnF and related proteins . The top BLAST hits from different genera (only the top hit from each genera is included) obtained when FaZnF was used for a protein BLAST analysis at NCBI [ 50 ]. The protein most closely related to FaZnF is a predicted protein from Hordeum vulgare which was identified in a subtraction cDNA library from seedling shoot and root treated with ABA. The scale bar represents .08 amino acid substitutions per site, or 8 amino acid differences per 100 amino acids.
Figure Legend Snippet: Phylogenetic tree of FaZnF and related proteins . The top BLAST hits from different genera (only the top hit from each genera is included) obtained when FaZnF was used for a protein BLAST analysis at NCBI [ 50 ]. The protein most closely related to FaZnF is a predicted protein from Hordeum vulgare which was identified in a subtraction cDNA library from seedling shoot and root treated with ABA. The scale bar represents .08 amino acid substitutions per site, or 8 amino acid differences per 100 amino acids.

Techniques Used: cDNA Library Assay

3) Product Images from "Enterobacterial Small Mobile Sequences Carry Open Reading Frames and are Found Intragenically--Evolutionary Implications for Formation of New Peptides"

Article Title: Enterobacterial Small Mobile Sequences Carry Open Reading Frames and are Found Intragenically--Evolutionary Implications for Formation of New Peptides

Journal: Gene Regulation and Systems Biology

doi:

Amino acid sequence of YP_0349 and domain LbetaH (Left-Handed Parallel beta-Helix) location. The RU spans the first half of the peptide chain is shown. A number of bacterial transferases display the LbetaH motif with tandem hexapeptide repeats ( Raetz and Rod-erick, 1995 ). Part of the drawing is from the NCBI web site: http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi
Figure Legend Snippet: Amino acid sequence of YP_0349 and domain LbetaH (Left-Handed Parallel beta-Helix) location. The RU spans the first half of the peptide chain is shown. A number of bacterial transferases display the LbetaH motif with tandem hexapeptide repeats ( Raetz and Rod-erick, 1995 ). Part of the drawing is from the NCBI web site: http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi

Techniques Used: Sequencing

Diagrammatic representation of ECA3499 amino acid chain showing the amidase conserved domain ( Geer et al 2002 ) (as shown on the NCBI web site: http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi ). The region of the peptide chain containing the RU-1-like sequence (positions 463–496) is also shown.
Figure Legend Snippet: Diagrammatic representation of ECA3499 amino acid chain showing the amidase conserved domain ( Geer et al 2002 ) (as shown on the NCBI web site: http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi ). The region of the peptide chain containing the RU-1-like sequence (positions 463–496) is also shown.

Techniques Used: Sequencing

4) Product Images from "Survey of the bacteriophage phoH gene in wetland sediments in northeast China"

Article Title: Survey of the bacteriophage phoH gene in wetland sediments in northeast China

Journal: Scientific Reports

doi: 10.1038/s41598-018-37508-4

Neighbor-joining phylogenetic tree constructed with phoH sequences obtained in wetland sediments and their closest relatives retrieved from GenBank at the amino acid level. Numbers in parentheses are the accession numbers of phoH sequences in the NCBI website. The phoH sequences from bacteria and viruses (phages) are shown in normal gray letters and bold black letters, respectively. The bootstrap support values
Figure Legend Snippet: Neighbor-joining phylogenetic tree constructed with phoH sequences obtained in wetland sediments and their closest relatives retrieved from GenBank at the amino acid level. Numbers in parentheses are the accession numbers of phoH sequences in the NCBI website. The phoH sequences from bacteria and viruses (phages) are shown in normal gray letters and bold black letters, respectively. The bootstrap support values

Techniques Used: Construct

Neighbor-joining phylogenetic tree constructed with phage phoH sequences obtained in wetland sediments and the phoH sequences of cultured bacteria, phages and eukaryotic viruses at the amino acid level. The phoH sequences from cultured phages of Synechococcus , Prochlorococcus and heterotrophic bacteria are shown in bold black letters, while the phoH sequences from cultured bacteria are shown in normal black letters. Numbers in parentheses are the accession numbers of phoH sequences in the NCBI website. Bootstrap support values
Figure Legend Snippet: Neighbor-joining phylogenetic tree constructed with phage phoH sequences obtained in wetland sediments and the phoH sequences of cultured bacteria, phages and eukaryotic viruses at the amino acid level. The phoH sequences from cultured phages of Synechococcus , Prochlorococcus and heterotrophic bacteria are shown in bold black letters, while the phoH sequences from cultured bacteria are shown in normal black letters. Numbers in parentheses are the accession numbers of phoH sequences in the NCBI website. Bootstrap support values

Techniques Used: Construct, Cell Culture

5) Product Images from "An intragenic approach to confer glyphosate resistance in chile (Capsicum annuum) by introducing an in vitro mutagenized chile EPSPS gene encoding for a glyphosate resistant EPSPS protein"

Article Title: An intragenic approach to confer glyphosate resistance in chile (Capsicum annuum) by introducing an in vitro mutagenized chile EPSPS gene encoding for a glyphosate resistant EPSPS protein

Journal: PLoS ONE

doi: 10.1371/journal.pone.0194666

Sequence alignment of the EPSPS proteins from the Solanaceae family. EPSPS amino acid sequences from Capsicum annuum , Nicotiana attenuata , Nicotiana sylvestris , Nicotiana tabcum , Nicotiana tomentosiformis , Petunia hybrida , Solanum lycopersicum , Solanum pennellii and Solanum tuberosum were compared to the sequences of Zea mays EPSPS and the EPSPS mutant from Eleusine indica by multiple protein alignment. NCBI accession nos. for the protein sequences are indicated. Sequence numbers correspond to their position in the Capsicum annuum EPSPS. Only a partial view of the alignment that corresponds to the substrate binding region is shown. Dots represent conserved amino acids and dashes represent deletions. Amino acid residues involved in binding of the phospho enol pyruvate are marked with asterisks [ 10 ]. The amino acids 179 and 183, replaced by site-directed mutagenesis are indicated.
Figure Legend Snippet: Sequence alignment of the EPSPS proteins from the Solanaceae family. EPSPS amino acid sequences from Capsicum annuum , Nicotiana attenuata , Nicotiana sylvestris , Nicotiana tabcum , Nicotiana tomentosiformis , Petunia hybrida , Solanum lycopersicum , Solanum pennellii and Solanum tuberosum were compared to the sequences of Zea mays EPSPS and the EPSPS mutant from Eleusine indica by multiple protein alignment. NCBI accession nos. for the protein sequences are indicated. Sequence numbers correspond to their position in the Capsicum annuum EPSPS. Only a partial view of the alignment that corresponds to the substrate binding region is shown. Dots represent conserved amino acids and dashes represent deletions. Amino acid residues involved in binding of the phospho enol pyruvate are marked with asterisks [ 10 ]. The amino acids 179 and 183, replaced by site-directed mutagenesis are indicated.

Techniques Used: Sequencing, Mutagenesis, Binding Assay

Nucleotide sequence alignment tree of EPSPS from plants in the Solanaceae family. EPSPS cDNA sequences from Capsicum annuum , Nicotiana attenuata , Nicotiana sylvestris , Nicotiana tabcum , Nicotiana tomentosiformis , Petunia hybrida , Solanum lycopersicum , Solanum pennellii and Solanum tuberosum were subjected to multiple alignment. The Neighbor-joining consensus tree clustered the EPSPS sequences in two groups EPSPS1 and EPSPS2 . The numbers on the branches represent the percent bootstrap support for 1000 replicates. The tree was rooted with EPSPS sequences from plants in the Asterids clade (shown at https://doi.org/10.6084/m9.figshare.5995309.v1 ). NCBI accession nos. for the solanaceous EPSPS nucleotide sequences are indicated.
Figure Legend Snippet: Nucleotide sequence alignment tree of EPSPS from plants in the Solanaceae family. EPSPS cDNA sequences from Capsicum annuum , Nicotiana attenuata , Nicotiana sylvestris , Nicotiana tabcum , Nicotiana tomentosiformis , Petunia hybrida , Solanum lycopersicum , Solanum pennellii and Solanum tuberosum were subjected to multiple alignment. The Neighbor-joining consensus tree clustered the EPSPS sequences in two groups EPSPS1 and EPSPS2 . The numbers on the branches represent the percent bootstrap support for 1000 replicates. The tree was rooted with EPSPS sequences from plants in the Asterids clade (shown at https://doi.org/10.6084/m9.figshare.5995309.v1 ). NCBI accession nos. for the solanaceous EPSPS nucleotide sequences are indicated.

Techniques Used: Sequencing

6) Product Images from "Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection"

Article Title: Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1005325

Phylogenetic analysis of HPgV-2 relative to other pegiviruses and hepaciviruses. (A) Pairwise amino acid identity plots comparing HPgV-2 (UC0125.US) with other representative pegiviruses (red) and hepaciviruses (blue). The sliding window size is 50 nt. (B) Phylogenetic trees of the NS3 (left) and NS5B (right) proteins were constructed for 10 newly sequenced HPgV-2 strains (boldface red), representative hepaciviruses, and all fully sequenced pegiviruses in the NCBI nt database except for members of the simian pegivirus clade, for which 5 representative strains are shown (triangle). Each tree is rooted with yellow fever virus (YFV) as an outgroup.
Figure Legend Snippet: Phylogenetic analysis of HPgV-2 relative to other pegiviruses and hepaciviruses. (A) Pairwise amino acid identity plots comparing HPgV-2 (UC0125.US) with other representative pegiviruses (red) and hepaciviruses (blue). The sliding window size is 50 nt. (B) Phylogenetic trees of the NS3 (left) and NS5B (right) proteins were constructed for 10 newly sequenced HPgV-2 strains (boldface red), representative hepaciviruses, and all fully sequenced pegiviruses in the NCBI nt database except for members of the simian pegivirus clade, for which 5 representative strains are shown (triangle). Each tree is rooted with yellow fever virus (YFV) as an outgroup.

Techniques Used: Construct

7) Product Images from "Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases"

Article Title: Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.03353

Structural groups of Ni-CODHs. The representative protein sequences of each structural group of Ni-CODHs and HCPs are represented by multiple sequence alignments. The alignment of the N- and C-terminal extensions and the insertions was manually modified for representation. The number of proteins in each structural group is shown in parentheses. The Cys residues of the metal clusters and catalytic residues are highlighted by different color backgrounds as follows: green , D-cluster; blue , B-cluster; magenta , C-cluster; yellow , E- and F-clusters; cyan , acid-base catalysts; and red , putative novel clusters. The His residues in the His-rich regions of structural groups B-1 and B-4 are shown in blue letters , and the Glu residues at the equivalent position of Glu494 in the catalytic hybrid cluster of D. vulgaris HCP are shown in yellow letters ( Aragão et al., 2008 ). The NCBI accession numbers of the representative sequences are as follows: A-1, WP_011305243 ; A-2, WP_010878596 ; A-3, OGW06734 ; A-4, OIP92259 ; A-5, ODS42986 ; A-6, OIP30420 ; B-1, WP_026514536 ; B-2, WP_015485077 ; B-3, WP_012645460 ; B-4, WP_011393470 ; C-1, WP_039226206 ; C-2, WP_013237576 ; C-3, WP_010870233 ; C-4, WP_044921150 ; D-1, WP_011342982 ; D-2, WP_015926279 ; D-3, WP_079933214 ; D-4, WP_096205957 ; E-1, WP_012571978 ; E-2, WP_010939375 ; E-3, WP_088535808 ; F-1, WP_011343033 ; F-2, WP_011389181 ; G-1, OGP75751 ; and HCP, WP_010939296 .
Figure Legend Snippet: Structural groups of Ni-CODHs. The representative protein sequences of each structural group of Ni-CODHs and HCPs are represented by multiple sequence alignments. The alignment of the N- and C-terminal extensions and the insertions was manually modified for representation. The number of proteins in each structural group is shown in parentheses. The Cys residues of the metal clusters and catalytic residues are highlighted by different color backgrounds as follows: green , D-cluster; blue , B-cluster; magenta , C-cluster; yellow , E- and F-clusters; cyan , acid-base catalysts; and red , putative novel clusters. The His residues in the His-rich regions of structural groups B-1 and B-4 are shown in blue letters , and the Glu residues at the equivalent position of Glu494 in the catalytic hybrid cluster of D. vulgaris HCP are shown in yellow letters ( Aragão et al., 2008 ). The NCBI accession numbers of the representative sequences are as follows: A-1, WP_011305243 ; A-2, WP_010878596 ; A-3, OGW06734 ; A-4, OIP92259 ; A-5, ODS42986 ; A-6, OIP30420 ; B-1, WP_026514536 ; B-2, WP_015485077 ; B-3, WP_012645460 ; B-4, WP_011393470 ; C-1, WP_039226206 ; C-2, WP_013237576 ; C-3, WP_010870233 ; C-4, WP_044921150 ; D-1, WP_011342982 ; D-2, WP_015926279 ; D-3, WP_079933214 ; D-4, WP_096205957 ; E-1, WP_012571978 ; E-2, WP_010939375 ; E-3, WP_088535808 ; F-1, WP_011343033 ; F-2, WP_011389181 ; G-1, OGP75751 ; and HCP, WP_010939296 .

Techniques Used: Sequencing, Modification

Structural and phylogenetic relationships of the catalytic sites between structural group D-1 Ni-CODHs and HCPs. (A) The predicted structure of the catalytic site of C. hydrogenoformans CooSV (structural group D-2; NCBI protein accession number: WP_011342982 ). (B) The structure of the catalytic site of D. vulgaris HCP (PDB ID: 1W9M). (C) The structure of the catalytic site of C. hydrogenoformans CooSII (structural group F-1; PDB ID: 4UDX). The residues forming the catalytic sites are represented in stick forms and colored as follows (related to Figure 2 ): magenta , the C-clusters and hybrid cluster; cyan , acid–base catalysts; and yellow , the Glu residue unique to the hybrid cluster of HCPs and the corresponding residues of C. hydrogenoformans CooSV and CooSII. The Ni, Fe, S, and O atoms of the metal clusters are colored in green, brown, yellow , and red , respectively. The C and O atoms of CO 2 are colored in white and red , respectively. (D) The phylogenetic tree of the HCP family from the Pfam seed dataset (PF03063) ( Finn et al., 2016 ). The branches of C. hydrogenoformans CooSII and CooSV and D. vulgaris HCP are indicated by red arrows .
Figure Legend Snippet: Structural and phylogenetic relationships of the catalytic sites between structural group D-1 Ni-CODHs and HCPs. (A) The predicted structure of the catalytic site of C. hydrogenoformans CooSV (structural group D-2; NCBI protein accession number: WP_011342982 ). (B) The structure of the catalytic site of D. vulgaris HCP (PDB ID: 1W9M). (C) The structure of the catalytic site of C. hydrogenoformans CooSII (structural group F-1; PDB ID: 4UDX). The residues forming the catalytic sites are represented in stick forms and colored as follows (related to Figure 2 ): magenta , the C-clusters and hybrid cluster; cyan , acid–base catalysts; and yellow , the Glu residue unique to the hybrid cluster of HCPs and the corresponding residues of C. hydrogenoformans CooSV and CooSII. The Ni, Fe, S, and O atoms of the metal clusters are colored in green, brown, yellow , and red , respectively. The C and O atoms of CO 2 are colored in white and red , respectively. (D) The phylogenetic tree of the HCP family from the Pfam seed dataset (PF03063) ( Finn et al., 2016 ). The branches of C. hydrogenoformans CooSII and CooSV and D. vulgaris HCP are indicated by red arrows .

Techniques Used:

8) Product Images from "The Armadillo (Dasypus novemcinctus): A Witness but Not a Functional Example for the Emergence of the Butyrophilin 3/Vγ9Vδ2 System in Placental Mammals"

Article Title: The Armadillo (Dasypus novemcinctus): A Witness but Not a Functional Example for the Emergence of the Butyrophilin 3/Vγ9Vδ2 System in Placental Mammals

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2018.00265

Genomic organization of armadillo Butyrophilin 3 ( BTN3 ) homologous regions BTN3-V, BTN3-C , and B30.2 show similarities to human, alpaca, and dolphin BTN3 loci. The human BTN3A3 locus (A) was determined by National Center for Biotechnology Information (NCBI) megablast of BTN3A3 (GenBank: ) to Human G + T database (GenBank/Assembly: ). The alpaca BTN3 -like locus (B) was mapped using NCBI blastn of the predicted alpaca BTN3A3 to Vicugna pacos wgs database. Dolphin BTN3 -like loci (C,D) were identified using NCBI blastn of the predicted dolphin BTN3A3 to Tursiops truncatus wgs. Armadillo BTN3 homologous regions (E–G) were identified by NCBI blastn of human BTN3A3 to Dasypus novemcinctus whole genome shotgun contigs database (taxid: 9361). Exons are represented by boxes: translatable (solid black), non-translatable (striped black), missing (solid white) found by intron homologies (solid gray). The size of the exon, location in assembly/contig, and nucleotide identity of the regions to human BTN3A3 are indicated in bold. Intron lengths were calculated based on location in contigs and putative deletions are shown by dashed lines and “d”. Stop codons are indicated by “s” at the approximate location in the gene (*location of the proposed juxtamembrane motif important for PAg recognition ; **location of the putative ATG at nt 1982).
Figure Legend Snippet: Genomic organization of armadillo Butyrophilin 3 ( BTN3 ) homologous regions BTN3-V, BTN3-C , and B30.2 show similarities to human, alpaca, and dolphin BTN3 loci. The human BTN3A3 locus (A) was determined by National Center for Biotechnology Information (NCBI) megablast of BTN3A3 (GenBank: ) to Human G + T database (GenBank/Assembly: ). The alpaca BTN3 -like locus (B) was mapped using NCBI blastn of the predicted alpaca BTN3A3 to Vicugna pacos wgs database. Dolphin BTN3 -like loci (C,D) were identified using NCBI blastn of the predicted dolphin BTN3A3 to Tursiops truncatus wgs. Armadillo BTN3 homologous regions (E–G) were identified by NCBI blastn of human BTN3A3 to Dasypus novemcinctus whole genome shotgun contigs database (taxid: 9361). Exons are represented by boxes: translatable (solid black), non-translatable (striped black), missing (solid white) found by intron homologies (solid gray). The size of the exon, location in assembly/contig, and nucleotide identity of the regions to human BTN3A3 are indicated in bold. Intron lengths were calculated based on location in contigs and putative deletions are shown by dashed lines and “d”. Stop codons are indicated by “s” at the approximate location in the gene (*location of the proposed juxtamembrane motif important for PAg recognition ; **location of the putative ATG at nt 1982).

Techniques Used:

9) Product Images from "Advances in understanding – genetic basis of intellectual disability"

Article Title: Advances in understanding – genetic basis of intellectual disability

Journal: F1000Research

doi: 10.12688/f1000research.7134.1

Mapping of the intellectual disability genes on the human karyogram (G-banded) using the Genome Decoration page at National Center for Biotechnology Information. See website at http://www.ncbi.nlm.nih.gov/genome/tools/gdp . Please note that genes causing ID tend to concentrate in G-negative bands, like all other genes. CI, cognitive impairment; DD, developmental delay; ID, intellectual disability; MR, mental retardation.
Figure Legend Snippet: Mapping of the intellectual disability genes on the human karyogram (G-banded) using the Genome Decoration page at National Center for Biotechnology Information. See website at http://www.ncbi.nlm.nih.gov/genome/tools/gdp . Please note that genes causing ID tend to concentrate in G-negative bands, like all other genes. CI, cognitive impairment; DD, developmental delay; ID, intellectual disability; MR, mental retardation.

Techniques Used: Polyacrylamide Gel Electrophoresis

10) Product Images from "Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins"

Article Title: Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins

Journal: PLoS Biology

doi: 10.1371/journal.pbio.2004204

Identification and characterisation of lincRNA Ginir from mouse melanoma cells. (A and B) The 5′ and 3′ ends of the 557-base Ginir transcript were extended using RACE. PCRs were performed with AP1 and AP2 and Ginir-specific primers G1F and G4R for 3′ RACE and primers G1R and G4F for 5′ RACE (A). For nested PCR, primary PCR products were used as templates. Primer sequences are enlisted in S4 Table included in the Materials and methods section. The 5′–3′ RACE was followed by Southern hybridisation with Ginir sequence–specific probes (B). (C) Schematic representation of Ginir (NCBI Acc. No: EF649772.1) on mouse chromosome X (ChrX: 61982243–61982854) was acquired using the UCSC genome browser ( http://genome.ucsc.edu/cgi-bin/hgBlat ) and GRCm38/mm10 Assembly. The bottom region shows ESTs and repeat elements spanning the Ginir locus. (D) The genomic region showing location of LDOC1 and MAGE genes spanning the contig bearing Ginir ( www.ensembl.org ). (E) Schematic representation of Ginir genomic sequence homology between mouse and rat species acquired using ENSEMBL ( www.ensembl.org ). AP1, adapter primer 1; AP2, adapter primer 2; EST, expressed sequence tag; Ginir, Genomic Instability Inducing RNA; LDOC1, LDOC1, Leucine Zipper down-regulated in cancer-1; lincRNA, long intergenic noncoding RNA; MAGE, the melanoma antigen gene; NCBI, National Center for Biotechnology Information; PCR, polymerase chain reaction; RACE, rapid amplification of cDNA ends; UCSC, University of California, Santa Cruz.
Figure Legend Snippet: Identification and characterisation of lincRNA Ginir from mouse melanoma cells. (A and B) The 5′ and 3′ ends of the 557-base Ginir transcript were extended using RACE. PCRs were performed with AP1 and AP2 and Ginir-specific primers G1F and G4R for 3′ RACE and primers G1R and G4F for 5′ RACE (A). For nested PCR, primary PCR products were used as templates. Primer sequences are enlisted in S4 Table included in the Materials and methods section. The 5′–3′ RACE was followed by Southern hybridisation with Ginir sequence–specific probes (B). (C) Schematic representation of Ginir (NCBI Acc. No: EF649772.1) on mouse chromosome X (ChrX: 61982243–61982854) was acquired using the UCSC genome browser ( http://genome.ucsc.edu/cgi-bin/hgBlat ) and GRCm38/mm10 Assembly. The bottom region shows ESTs and repeat elements spanning the Ginir locus. (D) The genomic region showing location of LDOC1 and MAGE genes spanning the contig bearing Ginir ( www.ensembl.org ). (E) Schematic representation of Ginir genomic sequence homology between mouse and rat species acquired using ENSEMBL ( www.ensembl.org ). AP1, adapter primer 1; AP2, adapter primer 2; EST, expressed sequence tag; Ginir, Genomic Instability Inducing RNA; LDOC1, LDOC1, Leucine Zipper down-regulated in cancer-1; lincRNA, long intergenic noncoding RNA; MAGE, the melanoma antigen gene; NCBI, National Center for Biotechnology Information; PCR, polymerase chain reaction; RACE, rapid amplification of cDNA ends; UCSC, University of California, Santa Cruz.

Techniques Used: Nested PCR, Polymerase Chain Reaction, Hybridization, Sequencing, Rapid Amplification of cDNA Ends

11) Product Images from "Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites. Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites"

Article Title: Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites. Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites

Journal: MicrobiologyOpen

doi: 10.1002/mbo3.490

Relative abundance of ARHD sequences in each site based on the functional classification against the NCBI RefSeq database by BLAST
Figure Legend Snippet: Relative abundance of ARHD sequences in each site based on the functional classification against the NCBI RefSeq database by BLAST

Techniques Used: Functional Assay

Distribution of genera in each site based on the relative abundance of ARHD sequences annotated against the NCBI RefSeq database by BLAST
Figure Legend Snippet: Distribution of genera in each site based on the relative abundance of ARHD sequences annotated against the NCBI RefSeq database by BLAST

Techniques Used:

12) Product Images from "The variable quality of metadata about biological samples used in biomedical experiments"

Article Title: The variable quality of metadata about biological samples used in biomedical experiments

Journal: Scientific Data

doi: 10.1038/sdata.2019.21

Metadata submissions to NCBI BioSample from 2009–2017. The columns represent the total number of metadata record submissions to NCBI BioSample in a year, split between Generic and non-Generic records. The Non-Generic metadata records column contains data labels with the absolute number of records. Generic records make up nearly all the submissions in the early years of BioSample, and the bulk of the submissions even in recent years.
Figure Legend Snippet: Metadata submissions to NCBI BioSample from 2009–2017. The columns represent the total number of metadata record submissions to NCBI BioSample in a year, split between Generic and non-Generic records. The Non-Generic metadata records column contains data labels with the absolute number of records. Generic records make up nearly all the submissions in the early years of BioSample, and the bulk of the submissions even in recent years.

Techniques Used:

Mention of metadata packages in NCBI BioSample. The chart shows the package names followed by the number (and percentage) of metadata records that use that package. The Generic package does not specify any required or optional attributes.
Figure Legend Snippet: Mention of metadata packages in NCBI BioSample. The chart shows the package names followed by the number (and percentage) of metadata records that use that package. The Generic package does not specify any required or optional attributes.

Techniques Used:

Quality of attributes in packaged metadata records in NCBI BioSample. The columns represent the metadata attribute types. Each column shows the number and percentage of metadata attributes whose values are either well-specified or invalid.
Figure Legend Snippet: Quality of attributes in packaged metadata records in NCBI BioSample. The columns represent the metadata attribute types. Each column shows the number and percentage of metadata attributes whose values are either well-specified or invalid.

Techniques Used:

Quality of dictionary attributes in NCBI BioSample according to their type. The columns show the number and percentage of attributes whose values are well-specified or invalid.
Figure Legend Snippet: Quality of dictionary attributes in NCBI BioSample according to their type. The columns show the number and percentage of attributes whose values are well-specified or invalid.

Techniques Used:

Example metadata record from the NCBI BioSample. An NCBI BioSample metadata record has a title, potentially multiple identifiers associated with it, an organism, a package specification (explained in Section 2.1), multiple attributes in the form of name-value pairs, a description with keywords associated with it, information about the record submitter, and finally accession details.
Figure Legend Snippet: Example metadata record from the NCBI BioSample. An NCBI BioSample metadata record has a title, potentially multiple identifiers associated with it, an organism, a package specification (explained in Section 2.1), multiple attributes in the form of name-value pairs, a description with keywords associated with it, information about the record submitter, and finally accession details.

Techniques Used:

13) Product Images from "siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake"

Article Title: siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake

Journal: Genome Biology

doi: 10.1186/gb-2007-8-7-r142

Diced-siRNA screen of the human signaling proteome identifies regulators of transferrin uptake. (a) Selected d-siRNAs include proteins with known signaling related domains (as named and annotated in the NCBI CDD database of 20 July 2005 [29]. Related domains were pooled in the same category bin). Transmembrane receptors and transcription factors were excluded. (b) Examples of signaling pathways and numbers of their components represented in the selected signaling proteome set. (c) Measured transferrin uptake values (F) from the human signaling proteome screen. Data sorted in ascending order. (d) Method to calculate hit probabilities by CAsH analysis. The histogram of the screen data (light blue) is compared to the stochastic noise distribution (red). CAsH values correspond to the estimated fraction of hits for each F score. (e) Regions within mRNAs selected to design the two independent d-siRNA pools. Seq1 corresponds to the region chosen to synthesize the initial batches of d-siRNAs, Seq2 to the region chosen to synthesize the second, independent batch. (f) Transferrin uptake regulators identified by two independent d-siRNA pools. (g) Genes increasing or decreasing transferrin uptake in HeLa cells.
Figure Legend Snippet: Diced-siRNA screen of the human signaling proteome identifies regulators of transferrin uptake. (a) Selected d-siRNAs include proteins with known signaling related domains (as named and annotated in the NCBI CDD database of 20 July 2005 [29]. Related domains were pooled in the same category bin). Transmembrane receptors and transcription factors were excluded. (b) Examples of signaling pathways and numbers of their components represented in the selected signaling proteome set. (c) Measured transferrin uptake values (F) from the human signaling proteome screen. Data sorted in ascending order. (d) Method to calculate hit probabilities by CAsH analysis. The histogram of the screen data (light blue) is compared to the stochastic noise distribution (red). CAsH values correspond to the estimated fraction of hits for each F score. (e) Regions within mRNAs selected to design the two independent d-siRNA pools. Seq1 corresponds to the region chosen to synthesize the initial batches of d-siRNAs, Seq2 to the region chosen to synthesize the second, independent batch. (f) Transferrin uptake regulators identified by two independent d-siRNA pools. (g) Genes increasing or decreasing transferrin uptake in HeLa cells.

Techniques Used:

14) Product Images from "OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders"

Article Title: OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

Journal: Nucleic Acids Research

doi: 10.1093/nar/gku1205

OMIM entry for protein O-mannosyltransferase 1 (607423). Arrows call attention to the following: the unique MIM number 607423 with an asterisk prefix denoting a gene. Approved gene symbol obtained directly from the Human Gene Nomenclature Committee data. Cytogenetic location and Genomic coordinates obtained from NCBI. Gene–phenotype relationships table showing allelic disorders, their MIM numbers, and the phenotype mapping key. The Table of Contents (TOC) facilitates navigation within the OMIM entry, and external resource links specific for the gene are topically organized and listed below the TOC.
Figure Legend Snippet: OMIM entry for protein O-mannosyltransferase 1 (607423). Arrows call attention to the following: the unique MIM number 607423 with an asterisk prefix denoting a gene. Approved gene symbol obtained directly from the Human Gene Nomenclature Committee data. Cytogenetic location and Genomic coordinates obtained from NCBI. Gene–phenotype relationships table showing allelic disorders, their MIM numbers, and the phenotype mapping key. The Table of Contents (TOC) facilitates navigation within the OMIM entry, and external resource links specific for the gene are topically organized and listed below the TOC.

Techniques Used:

15) Product Images from "Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses"

Article Title: Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

Journal: PLoS ONE

doi: 10.1371/journal.pone.0104579

Comparison of consensus sequences calculated from alignments of Illumina MiSeq short-read data to a nearly identical reference with four reference-guided assemblers. Genomic DNA from the Listeriosis Reference Service for Canada's (LRS) Listeria monocytogenes strain 08-5578 subculture was indexed and sequenced twelve times. The resulting reads were aligned with four reference-guided assemblers (BWA, MOSAIK, Novoalign, and SMALT) using an L. monocytogenes strain 08-5578 chromosome sequence obtained from the National Center for Biotechnology Information (NCBI) archive as a reference. The NCBI strain 08-5578 chromosome sequence differs from the LRS strain 08-5578 chromosome sequence at three nucleotide positions. The numbers of false positive sites (a), true positive sites (b), ambiguous sites (c), and gaps (d) present in the resulting consensus sequences relative to the calculated coverage of each assembly are shown. Lines were calculated with power regression and smoothed using a Catmull-Rom Spline.
Figure Legend Snippet: Comparison of consensus sequences calculated from alignments of Illumina MiSeq short-read data to a nearly identical reference with four reference-guided assemblers. Genomic DNA from the Listeriosis Reference Service for Canada's (LRS) Listeria monocytogenes strain 08-5578 subculture was indexed and sequenced twelve times. The resulting reads were aligned with four reference-guided assemblers (BWA, MOSAIK, Novoalign, and SMALT) using an L. monocytogenes strain 08-5578 chromosome sequence obtained from the National Center for Biotechnology Information (NCBI) archive as a reference. The NCBI strain 08-5578 chromosome sequence differs from the LRS strain 08-5578 chromosome sequence at three nucleotide positions. The numbers of false positive sites (a), true positive sites (b), ambiguous sites (c), and gaps (d) present in the resulting consensus sequences relative to the calculated coverage of each assembly are shown. Lines were calculated with power regression and smoothed using a Catmull-Rom Spline.

Techniques Used: Sequencing

Comparison of consensus sequences calculated from alignments of Illumina MiSeq short-read data to a non-identical reference with four reference-guided assemblers. Genomic DNA from the Listeriosis Reference Service for Canada's (LRS) Listeria monocytogenes strain 08-5578 subculture was sequenced and indexed twelve times. The resulting reads were aligned with four reference-guided assemblers (BWA, MOSAIK, Novoalign, and SMALT) using an L. monocytogenes strain EGD-e chromosome sequence obtained from the National Center for Biotechnology Information (NCBI) archive as a reference. The NCBI strain EGD-e chromosome sequence differs from the LRS strain 08-5578 chromosome sequence at 25,347 nucleotide positions. The numbers of false positive sites (a), true positive sites (b), ambiguous sites (c), and gaps (d) present in the resulting consensus sequences relative to the calculated coverage of each assembly are shown. Lines were calculated with power regression and smoothed using a Catmull-Rom Spline.
Figure Legend Snippet: Comparison of consensus sequences calculated from alignments of Illumina MiSeq short-read data to a non-identical reference with four reference-guided assemblers. Genomic DNA from the Listeriosis Reference Service for Canada's (LRS) Listeria monocytogenes strain 08-5578 subculture was sequenced and indexed twelve times. The resulting reads were aligned with four reference-guided assemblers (BWA, MOSAIK, Novoalign, and SMALT) using an L. monocytogenes strain EGD-e chromosome sequence obtained from the National Center for Biotechnology Information (NCBI) archive as a reference. The NCBI strain EGD-e chromosome sequence differs from the LRS strain 08-5578 chromosome sequence at 25,347 nucleotide positions. The numbers of false positive sites (a), true positive sites (b), ambiguous sites (c), and gaps (d) present in the resulting consensus sequences relative to the calculated coverage of each assembly are shown. Lines were calculated with power regression and smoothed using a Catmull-Rom Spline.

Techniques Used: Sequencing

16) Product Images from "rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development"

Article Title: rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

Journal: Nucleic Acids Research

doi: 10.1093/nar/gku1201

Screen shot of a ‘Browse Taxonomy’ search result for the family Acetobacteraceae using NCBI taxonomy. Statistics for 16S gene counts of all 18 records are shown in the upper-left table. The distribution of 16S counts among the records is shown in the histogram to the right. Summary data for the individual records are shown in the larger table below. Record ids that are prefixed with ‘ rrn DBv3-’ were sourced from rrn DB v3.1.227. The other record ids are KEGG accessions. Data source organism names have been given higher visibility than NCBI names because they more often include strain designations. Viewing an NCBI name requires a mouse-hover over the table cell as shown for record rrn DBv3-1403. RDP taxonomy displayed in this table is limited to genus assignment. Each data source record id is hyperlinked to its corresponding record-detail web page. The records can be reordered by clicking on most column headers.
Figure Legend Snippet: Screen shot of a ‘Browse Taxonomy’ search result for the family Acetobacteraceae using NCBI taxonomy. Statistics for 16S gene counts of all 18 records are shown in the upper-left table. The distribution of 16S counts among the records is shown in the histogram to the right. Summary data for the individual records are shown in the larger table below. Record ids that are prefixed with ‘ rrn DBv3-’ were sourced from rrn DB v3.1.227. The other record ids are KEGG accessions. Data source organism names have been given higher visibility than NCBI names because they more often include strain designations. Viewing an NCBI name requires a mouse-hover over the table cell as shown for record rrn DBv3-1403. RDP taxonomy displayed in this table is limited to genus assignment. Each data source record id is hyperlinked to its corresponding record-detail web page. The records can be reordered by clicking on most column headers.

Techniques Used: Polyacrylamide Gel Electrophoresis

17) Product Images from "Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins"

Article Title: Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins

Journal: BMC Immunology

doi: 10.1186/s12865-016-0154-z

MHCI can bind directly to PDZ domains in vitro. a Schematic showing the exons that encode the classical MHCI H2-K b . A signal sequence (S) is followed by exons encoding the three extracellular alpha domains, a single exon encoding the transmembrane domain, and three exons (6, 7, and 8) encoding the intracellular domain (not drawn to scale). Bottom, amino acid sequence of exons 6, 7, and 8 in H2-K b . Putative PDZ ligand motifs are underlined. Exon 6 encodes the overlapping ligand motifs GDYA, DYAL, and YALA, exon 7 encodes the overlapping ligand motifs TSDL and DLSL, and exon 8 encodes the C-terminal motif HSLA. Only the overlapping motifs DCKV and KVMV span an exon/intron boundary. Notably, KVMV is also among the least conserved putative PDZ ligand motifs in H2-K b , since it is not detected in this position in any other mouse MHCI. Intronic structure, NCBI. Adapted from [ 15 ]. b Schematic of in vitro binding assay. Different recombinant PDZ domain peptides are bound to each membrane spot, and the membrane is panned with GST-tagged recombinant cytoplasmic domains from specific MHCI proteins. A direct interaction between the cytoplasmic domain of MHCI and a given PDZ domain will be apparent as a black spot after visualization of bound anti-GST antibodies. c The cytoplasmic domain of the classical MHCI H2-K b can bind directly to PDZ1 and to a lesser extent PDZ4+5 of MAGI-1, but not to PDZs 2 or 3 of the same protein. See Additional file 4 : Figure S4B D for validation of the identity of H2-K peptides, and S4E-F for titration of H2-K b binding. d The cytoplasmic domain of the classical MHCI H2-K b does not bind to PDZ1+2 (expressed together) or PDZ 3 of SAP97. e MAGI-1 binding by recombinant cytoplasmic domains derived from different classical and nonclassical MHCI proteins. Notably, the ability to bind to PDZ1 of MAGI-1 correlates with the presence of a class 1 PDZ ligand motif, which is present in H2-K b and H2-T22, but not H2-D or H2-T23 (see f ). f Amino acid sequences of the cytoplasmic domains of mouse and human MHCIs, aligned in ClustalW. Highlighted, putative class 1 PDZ ligand motifs (consensus [X – S/T – X – V/L]) that match MAGI-1 PDZ1’s binding preferences [ 80 – 82 ]. g Competition assays show that preincubation of column-bound MAGI-1 PDZ1 with cytoplasmic peptides derived from H2-T22, which can bind, but not H2-D, which cannot, precludes subsequent binding by peptides derived from H2-K. Left , pure H2-K not applied to a column; “none”, preincubation in buffer alone. H2-K was detected using an antibody against the cytoplasmic domain of H2-K (see Methods ). Bottom , anti-His antibody shows eluted MAGI-1 peptide ( arrow ). h A point mutation in the lone class 1 PDZ ligand motif, TSDL, in the cytoplasmic domain of H2-K b attenuates binding to MAGI-1 PDZ1. The location of the mutated residue (T329) is shown in ( a )
Figure Legend Snippet: MHCI can bind directly to PDZ domains in vitro. a Schematic showing the exons that encode the classical MHCI H2-K b . A signal sequence (S) is followed by exons encoding the three extracellular alpha domains, a single exon encoding the transmembrane domain, and three exons (6, 7, and 8) encoding the intracellular domain (not drawn to scale). Bottom, amino acid sequence of exons 6, 7, and 8 in H2-K b . Putative PDZ ligand motifs are underlined. Exon 6 encodes the overlapping ligand motifs GDYA, DYAL, and YALA, exon 7 encodes the overlapping ligand motifs TSDL and DLSL, and exon 8 encodes the C-terminal motif HSLA. Only the overlapping motifs DCKV and KVMV span an exon/intron boundary. Notably, KVMV is also among the least conserved putative PDZ ligand motifs in H2-K b , since it is not detected in this position in any other mouse MHCI. Intronic structure, NCBI. Adapted from [ 15 ]. b Schematic of in vitro binding assay. Different recombinant PDZ domain peptides are bound to each membrane spot, and the membrane is panned with GST-tagged recombinant cytoplasmic domains from specific MHCI proteins. A direct interaction between the cytoplasmic domain of MHCI and a given PDZ domain will be apparent as a black spot after visualization of bound anti-GST antibodies. c The cytoplasmic domain of the classical MHCI H2-K b can bind directly to PDZ1 and to a lesser extent PDZ4+5 of MAGI-1, but not to PDZs 2 or 3 of the same protein. See Additional file 4 : Figure S4B D for validation of the identity of H2-K peptides, and S4E-F for titration of H2-K b binding. d The cytoplasmic domain of the classical MHCI H2-K b does not bind to PDZ1+2 (expressed together) or PDZ 3 of SAP97. e MAGI-1 binding by recombinant cytoplasmic domains derived from different classical and nonclassical MHCI proteins. Notably, the ability to bind to PDZ1 of MAGI-1 correlates with the presence of a class 1 PDZ ligand motif, which is present in H2-K b and H2-T22, but not H2-D or H2-T23 (see f ). f Amino acid sequences of the cytoplasmic domains of mouse and human MHCIs, aligned in ClustalW. Highlighted, putative class 1 PDZ ligand motifs (consensus [X – S/T – X – V/L]) that match MAGI-1 PDZ1’s binding preferences [ 80 – 82 ]. g Competition assays show that preincubation of column-bound MAGI-1 PDZ1 with cytoplasmic peptides derived from H2-T22, which can bind, but not H2-D, which cannot, precludes subsequent binding by peptides derived from H2-K. Left , pure H2-K not applied to a column; “none”, preincubation in buffer alone. H2-K was detected using an antibody against the cytoplasmic domain of H2-K (see Methods ). Bottom , anti-His antibody shows eluted MAGI-1 peptide ( arrow ). h A point mutation in the lone class 1 PDZ ligand motif, TSDL, in the cytoplasmic domain of H2-K b attenuates binding to MAGI-1 PDZ1. The location of the mutated residue (T329) is shown in ( a )

Techniques Used: In Vitro, Sequencing, Binding Assay, Recombinant, Titration, Derivative Assay, Mutagenesis

MHCI gene family, and conservation of PDZ ligand motifs in MHCI cytoplasmic domains. a Greatly simplified schematic of the MHCI genomic region in humans (HLA, on chromosome 6, top ) and mice (H2, on chromosome 17, bottom ), showing the relative positions of the classical ( black boxes ) and non-classical ( white boxes ) MHCI genes or gene families. Multi-member gene clusters are indicated by breaks in the chromosome. Numerous genes and pseudogenes have been omitted for clarity, and distances are not to scale. Centromeric is to the left. Adapted from [ 62 ]. b Logo showing conservation of amino acids within closest-match homologues of the human classical MHCI HLA-A. The height of each letter corresponds to the extent of conservation across species. Color code: ST, orange ; YFWCMVILA, green ; DE, red ; all others black. Below, individual source sequences. Putative PDZ ligand motifs are in red. Previously noted conserved serine and tyrosine residues that can be phosphorylated in some species (underlined in bold in b and c ; see text) are embedded in PDZ ligand motifs in several MHCI proteins. Similar alignments have been performed previously (e.g., [ 15 ]). * = conserved; : = semi-conserved; . = similar. c Aligned amino acid sequences of the cytoplasmic domains of human MHCI proteins, with putative PDZ ligand motifs highlighted (class 1PDZ ligand, orange; class 2, blue; class 3, purple). Consensus motifs: class 1 PDZ, S/T-X-Y/F/W/C/M/V/I/L/A; class 2 PDZ, ΦXΦ (Y/F/W/C/M/V/I/L/A-X-Y/F/W/C/M/V/I/L/A); class 3 PDZ, D/E-X-Y/F/W/C/M/V/I/L/A [ 49 ]. Human reference sequences obtained from NCBI, alignments performed using T-Coffee [ 34 ]. d Conservation of PDZ ligands across human HLA genes from c , despite non-conservative substitutions. In two cases, a class 1 ligand motif is converted to class 2 by the substitution (2), but remains a putative PDZ ligand. Color code as in ( b )
Figure Legend Snippet: MHCI gene family, and conservation of PDZ ligand motifs in MHCI cytoplasmic domains. a Greatly simplified schematic of the MHCI genomic region in humans (HLA, on chromosome 6, top ) and mice (H2, on chromosome 17, bottom ), showing the relative positions of the classical ( black boxes ) and non-classical ( white boxes ) MHCI genes or gene families. Multi-member gene clusters are indicated by breaks in the chromosome. Numerous genes and pseudogenes have been omitted for clarity, and distances are not to scale. Centromeric is to the left. Adapted from [ 62 ]. b Logo showing conservation of amino acids within closest-match homologues of the human classical MHCI HLA-A. The height of each letter corresponds to the extent of conservation across species. Color code: ST, orange ; YFWCMVILA, green ; DE, red ; all others black. Below, individual source sequences. Putative PDZ ligand motifs are in red. Previously noted conserved serine and tyrosine residues that can be phosphorylated in some species (underlined in bold in b and c ; see text) are embedded in PDZ ligand motifs in several MHCI proteins. Similar alignments have been performed previously (e.g., [ 15 ]). * = conserved; : = semi-conserved; . = similar. c Aligned amino acid sequences of the cytoplasmic domains of human MHCI proteins, with putative PDZ ligand motifs highlighted (class 1PDZ ligand, orange; class 2, blue; class 3, purple). Consensus motifs: class 1 PDZ, S/T-X-Y/F/W/C/M/V/I/L/A; class 2 PDZ, ΦXΦ (Y/F/W/C/M/V/I/L/A-X-Y/F/W/C/M/V/I/L/A); class 3 PDZ, D/E-X-Y/F/W/C/M/V/I/L/A [ 49 ]. Human reference sequences obtained from NCBI, alignments performed using T-Coffee [ 34 ]. d Conservation of PDZ ligands across human HLA genes from c , despite non-conservative substitutions. In two cases, a class 1 ligand motif is converted to class 2 by the substitution (2), but remains a putative PDZ ligand. Color code as in ( b )

Techniques Used: Mouse Assay

18) Product Images from "INFLAMMASOMES ARE DIFFERENTIALLY EXPRESSED IN CARDIOVASCUALR AND OTHER TISSUES"

Article Title: INFLAMMASOMES ARE DIFFERENTIALLY EXPRESSED IN CARDIOVASCUALR AND OTHER TISSUES

Journal: International journal of immunopathology and pharmacology

doi: 10.1177/039463200902200208

The gene expression profiles of TLRs, NLRs, other inflammasome components, proinflammatory caspases and caspase-1 cleaved cytokines A. Data presenting format. As an example, the gene expression profiles of house-keeping gene Rho GDP dissociation inhibitor (GDI) alpha in the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues are presented, with the tissue names shown in the bottom of the figure. The gene expression data were normalized by the β-actin expression data from the same tissue, which are presented in the left Y-axis. The expression ratios among tissues were generated by normalizing the arbitrary units of the gene in the tissue with the median levels of the arbitrary units of the gene in all the tissues, which are presented in the right Y-axis. In order to define confidential intervals for statistically higher expression levels of given genes, we calculated the confidential intervals of tissue expression [the mean X + 2 × standard deviations (SD) = 2.62] for three common house keeping genes including Rho GDP dissociation inhibitor alpha (ARHGDIA, Hs.159161), glyceraldehyde-3-phosphate dehydrogenase (GAPDH, Hs.544577) and ribosomal protein S27a (RPS27A, Hs.311640). The expression variations of given genes in tissues, when they were larger than 2.62 folds, were defined as the high expression levels with statistical significance (the right Y-axis). B. The expression profiles of TLRs. The X-axis indicates the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues with the order the same as that shown in Fig. 2A. C. The expression profiles of NLRs. The X-axis indicates the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues with the order the same as that shown in Fig. 2A. D. The expression profiles of other inflammasome components. The X-axis indicates the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues with the order the same as that shown in Fig. 2A. E. The expression profiles of proinflammatory caspases. The X-axis indicates the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues with the order the same as that shown in Fig. 2A. The follows are the human gene ID numbers in the NCBI/UniGene database: β-actin, Hs.520640; TLR1, Hs.654532; TLR2, Hs.519033; TLR3, Hs.657724; TLR4, Hs.174312; TLR5, Hs.604542; TLR6, Hs.662185; TLR7, Hs.659215; TLR8, Hs.660543; TLR9, Hs.87968; TLR10, Hs.120551; NOD1, Hs.405153; NOD2, Hs.592072; NOD3 (NLRC3), Hs.592091; NOD4 (NLRC5), Hs.528836; NALP1 (NLRP1), Hs. 652273; NALP2 (NLRP2), Hs.369279; NALP3 (NLRP3), Hs.159483; NALP4 (NLRP4), Hs.631533; NALP5 (NLRP5), Hs.356872 (no expression data available in the tissues examined); NALP6 (NLRP6), Hs.352611; NALP7 (NLRP7), Hs.351118; NALP8 (NLRP8), Hs.446925 (no tissue expression data available); NALP9 (NLRP9), Hs.661568; NALP10 (NLRP10), HS.449636; NALP11 (NLRP11), Hs.375039; NALP12 (NLRP12), Hs.631573; NALP13 (NLRP13), Hs.446924 (no tissue expression data available); NALP14 (NLRP14), Hs.449637; NAIP, Hs.654500; IPAF (NLRC4), Hs.574741; Cardinal (CARD8), Hs.446146; COP1 (CARD16), Hs.348365; PYCARD (ASC), Hs.499094; Caspase-1 (CAS1), Hs.2490; Caspase-4 (CAS4), Hs.138378; Caspase-5 (CAS5), Hs.213327; Caspase-12 (CAS12), Hs.476989; IL-1β, Hs.126256; IL-18, Hs.83077; and IL-33, Hs.348390.
Figure Legend Snippet: The gene expression profiles of TLRs, NLRs, other inflammasome components, proinflammatory caspases and caspase-1 cleaved cytokines A. Data presenting format. As an example, the gene expression profiles of house-keeping gene Rho GDP dissociation inhibitor (GDI) alpha in the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues are presented, with the tissue names shown in the bottom of the figure. The gene expression data were normalized by the β-actin expression data from the same tissue, which are presented in the left Y-axis. The expression ratios among tissues were generated by normalizing the arbitrary units of the gene in the tissue with the median levels of the arbitrary units of the gene in all the tissues, which are presented in the right Y-axis. In order to define confidential intervals for statistically higher expression levels of given genes, we calculated the confidential intervals of tissue expression [the mean X + 2 × standard deviations (SD) = 2.62] for three common house keeping genes including Rho GDP dissociation inhibitor alpha (ARHGDIA, Hs.159161), glyceraldehyde-3-phosphate dehydrogenase (GAPDH, Hs.544577) and ribosomal protein S27a (RPS27A, Hs.311640). The expression variations of given genes in tissues, when they were larger than 2.62 folds, were defined as the high expression levels with statistical significance (the right Y-axis). B. The expression profiles of TLRs. The X-axis indicates the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues with the order the same as that shown in Fig. 2A. C. The expression profiles of NLRs. The X-axis indicates the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues with the order the same as that shown in Fig. 2A. D. The expression profiles of other inflammasome components. The X-axis indicates the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues with the order the same as that shown in Fig. 2A. E. The expression profiles of proinflammatory caspases. The X-axis indicates the eleven tissues including vascular tissue, blood, heart, trachea and immune system tissues with the order the same as that shown in Fig. 2A. The follows are the human gene ID numbers in the NCBI/UniGene database: β-actin, Hs.520640; TLR1, Hs.654532; TLR2, Hs.519033; TLR3, Hs.657724; TLR4, Hs.174312; TLR5, Hs.604542; TLR6, Hs.662185; TLR7, Hs.659215; TLR8, Hs.660543; TLR9, Hs.87968; TLR10, Hs.120551; NOD1, Hs.405153; NOD2, Hs.592072; NOD3 (NLRC3), Hs.592091; NOD4 (NLRC5), Hs.528836; NALP1 (NLRP1), Hs. 652273; NALP2 (NLRP2), Hs.369279; NALP3 (NLRP3), Hs.159483; NALP4 (NLRP4), Hs.631533; NALP5 (NLRP5), Hs.356872 (no expression data available in the tissues examined); NALP6 (NLRP6), Hs.352611; NALP7 (NLRP7), Hs.351118; NALP8 (NLRP8), Hs.446925 (no tissue expression data available); NALP9 (NLRP9), Hs.661568; NALP10 (NLRP10), HS.449636; NALP11 (NLRP11), Hs.375039; NALP12 (NLRP12), Hs.631573; NALP13 (NLRP13), Hs.446924 (no tissue expression data available); NALP14 (NLRP14), Hs.449637; NAIP, Hs.654500; IPAF (NLRC4), Hs.574741; Cardinal (CARD8), Hs.446146; COP1 (CARD16), Hs.348365; PYCARD (ASC), Hs.499094; Caspase-1 (CAS1), Hs.2490; Caspase-4 (CAS4), Hs.138378; Caspase-5 (CAS5), Hs.213327; Caspase-12 (CAS12), Hs.476989; IL-1β, Hs.126256; IL-18, Hs.83077; and IL-33, Hs.348390.

Techniques Used: Expressing, Generated

The flow chart of database mining analysis of gene expression profiles using NCBI/UniGene database.
Figure Legend Snippet: The flow chart of database mining analysis of gene expression profiles using NCBI/UniGene database.

Techniques Used: Flow Cytometry, Expressing

19) Product Images from "Roseburia intestinalis inhibits interleukin-17 excretion and promotes regulatory T cells differentiation in colitis"

Article Title: Roseburia intestinalis inhibits interleukin-17 excretion and promotes regulatory T cells differentiation in colitis

Journal: Molecular Medicine Reports

doi: 10.3892/mmr.2018.8833

IL-17 expression in human specimens, and in mouse serum and colon tissue. Relative expression of IL-17 mRNA in HC, UC and CD tissues, based on data obtained from the NCBI's GEO database (A) GSE59071 and (B) GSE9452). (C) IL-17 concentrations in mouse serum. (D) Representative immunohistochemical staining of IL-17 in mouse colon mucosa. The upper and lower panels are magnification, ×200 and ×400, respectively. *P
Figure Legend Snippet: IL-17 expression in human specimens, and in mouse serum and colon tissue. Relative expression of IL-17 mRNA in HC, UC and CD tissues, based on data obtained from the NCBI's GEO database (A) GSE59071 and (B) GSE9452). (C) IL-17 concentrations in mouse serum. (D) Representative immunohistochemical staining of IL-17 in mouse colon mucosa. The upper and lower panels are magnification, ×200 and ×400, respectively. *P

Techniques Used: Expressing, Immunohistochemistry, Staining

20) Product Images from "Molecular Cloning and Characterization of Novel Phytocystatin Gene from Turmeric, Curcuma longa"

Article Title: Molecular Cloning and Characterization of Novel Phytocystatin Gene from Turmeric, Curcuma longa

Journal: BioMed Research International

doi: 10.1155/2014/973790

Multiple alignments of the deduced amino acids of the full-length sequence of CypCl (indicated with black arrow) with other phytocystatin sequences from other plants obtained from the GenBank database in the NCBI website. They were Amaranthus hypochondiacus (ABG89856.1), Theobroma cacao (EOY19584.1), Ricinus communis (CAA89697.1), Ipomoea batatas (AAD13812.1), Solanum lycopersium (AAF23126.1), Petunia x hybrida (AAU81597.1), Sesamum indicum (AAK15090.1), Cucumis sativus (XP_004165517.1), Oryza sativa japonica group (Os01g0270100), Elaeis guineensis (ACF06548.1), Oryza sativa (AAL30830.1), Sorghum bicolour (CAA60634.1), Zea mays (NP001105295.1), Triticum aestivum x Secale cereal (ADP50760.1), Pelargonium x hortorum (ABG81097.1), Jatropha curcas (ADB02894.1), Ananas comosus (AAQ07259.1), Arabidopsis thaliana 1 (NP19675.1), Colocasia esculenta (AAM88397.1), Vitis cinerea var. helleri x Vitis riparia (ADD51191.1), Brassica rapa (ABK78689.1), Fragaria x ananassa (CAH60163.1), and Glycine max (NP001237734.1).
Figure Legend Snippet: Multiple alignments of the deduced amino acids of the full-length sequence of CypCl (indicated with black arrow) with other phytocystatin sequences from other plants obtained from the GenBank database in the NCBI website. They were Amaranthus hypochondiacus (ABG89856.1), Theobroma cacao (EOY19584.1), Ricinus communis (CAA89697.1), Ipomoea batatas (AAD13812.1), Solanum lycopersium (AAF23126.1), Petunia x hybrida (AAU81597.1), Sesamum indicum (AAK15090.1), Cucumis sativus (XP_004165517.1), Oryza sativa japonica group (Os01g0270100), Elaeis guineensis (ACF06548.1), Oryza sativa (AAL30830.1), Sorghum bicolour (CAA60634.1), Zea mays (NP001105295.1), Triticum aestivum x Secale cereal (ADP50760.1), Pelargonium x hortorum (ABG81097.1), Jatropha curcas (ADB02894.1), Ananas comosus (AAQ07259.1), Arabidopsis thaliana 1 (NP19675.1), Colocasia esculenta (AAM88397.1), Vitis cinerea var. helleri x Vitis riparia (ADD51191.1), Brassica rapa (ABK78689.1), Fragaria x ananassa (CAH60163.1), and Glycine max (NP001237734.1).

Techniques Used: Sequencing

Related Articles

Clone Assay:

Article Title: Interleukin (IL)-2 Is a Key Regulator of T Helper 1 and T Helper 2 Cytokine Expression in Fish: Functional Characterization of Two Divergent IL2 Paralogs in Salmonids
Article Snippet: Paragraph title: Cloning of Salmonid IL2B cDNA in Atlantic Salmon and Rainbow Trout ... BLAST ( ) search using know salmonid and other fish IL2 at the National Center for Biotechnology Information (NCBI) identified a salmon WGS contig (acc. no. AGKD04000795) that could encode for a second IL2 (termed IL2B thereafter).

Article Title: Two novel mitoviruses from a Canadian isolate of the Dutch elm pathogen Ophiostoma novo-ulmi (93-1224)
Article Snippet: There are twenty-five fully characterized species of genus Mitovirus listed in the National Center for Biotechnology Information (NCBI) Genome database, seven of which are found in the fungal genus Ophiostoma . .. Population genetic studies of the pathogen at the western Canadian disease front demonstrated that there was little diversity in the O. novo-ulmi isolates surveyed.

Article Title: Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence
Article Snippet: BLAST similarity analysis [ ] of the nucleotide sequences of the assemblies (contigs and singlets) against the mRNA sequences of RefSeq (release 49; 13 September 2011) at the National Center for Biotechnology Information (NCBI) [ ] revealed that the cDNA sequences corresponded to 13,691 unique human genes (Table ). .. BLAST similarity analysis [ ] of the nucleotide sequences of the assemblies (contigs and singlets) against the mRNA sequences of RefSeq (release 49; 13 September 2011) at the National Center for Biotechnology Information (NCBI) [ ] revealed that the cDNA sequences corresponded to 13,691 unique human genes (Table ).

Functional Assay:

Article Title: Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist
Article Snippet: Paragraph title: Comparative Phylogenetic and Functional Analysis of Effector Genes. ... To identify the source of its closest relative, each effector gene was aligned (BLASTn) against the National Center for Biotechnology Information (NCBI) reference genome dataset, including 1,512 complete genomes from commensal bacteria species.

Article Title: Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence
Article Snippet: BLAST similarity analysis [ ] of the nucleotide sequences of the assemblies (contigs and singlets) against the mRNA sequences of RefSeq (release 49; 13 September 2011) at the National Center for Biotechnology Information (NCBI) [ ] revealed that the cDNA sequences corresponded to 13,691 unique human genes (Table ). .. Ideally, almost all of the clones in the full-length-enriched cDNA libraries would contain entire coding sequences (CDSs).

Amplification:

Article Title: Interleukin (IL)-2 Is a Key Regulator of T Helper 1 and T Helper 2 Cytokine Expression in Fish: Functional Characterization of Two Divergent IL2 Paralogs in Salmonids
Article Snippet: BLAST ( ) search using know salmonid and other fish IL2 at the National Center for Biotechnology Information (NCBI) identified a salmon WGS contig (acc. no. AGKD04000795) that could encode for a second IL2 (termed IL2B thereafter). .. A 0.9 kb 3′-RACE product was obtained, cloned, sequenced, and encoded the salmon IL-2B (acc. no. HE805272).

Article Title: The Armadillo (Dasypus novemcinctus): A Witness but Not a Functional Example for the Emergence of the Butyrophilin 3/Vγ9Vδ2 System in Placental Mammals
Article Snippet: Dasypus novemcinctus (taxid 9361) whole genomic shotgun sequences (wgs) were taken from the National Center for Biotechnology Information (NCBI) databases (BioProject: PRJNA12594/PRJNA196486; BioSample: SAMN02953623; GenBank: gb|AAGV00000000.3). .. Dasypus novemcinctus (taxid 9361) whole genomic shotgun sequences (wgs) were taken from the National Center for Biotechnology Information (NCBI) databases (BioProject: PRJNA12594/PRJNA196486; BioSample: SAMN02953623; GenBank: gb|AAGV00000000.3).

Expressing:

Article Title: MicroRNA-155, induced by FOXP3 through transcriptional repression of BRCA1, is associated with tumor initiation in human breast cancer
Article Snippet: In the present study, we investigated a) the clinical relevance of miR-155 in both tumor cells and in circulation during tumor initiation and progression, b) the transcriptional regulation of miR-155, and c) the origin of circulating miR-155 in patients with breast cancer. .. To assess the clinical relevance of miR-155 in human primary breast cancers, the expression profile of miR-155 was characterized by bioinformatics analysis of public datasets from a) the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) and b) the National Cancer Institute (NCI) The Cancer Genome Atlas (TCGA). .. As determined by analysis of the NCBI GEO data, expression of miR-155 was more than 5-fold higher in ductal carcinoma in situ (DCIS) and intraductal (IDC) tumors than in normal breast tissues (Figure ).

Article Title: Chemokine Network and Overall Survival in TP53 Wild-Type and Mutant Ovarian Cancer
Article Snippet: Here, we investigated the chemokine network in different subtypes of human EOC, focusing on whether there is association in TP53 status and chemokine network and how this correlates with OC survival. .. Data analysis was performed on publicly available microarray data-sets that were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) ( http://www.ncbi.nlm.nih.gov/geo/ ) database under accession numbers GSE6008 and GSE63885. .. For GSE6008, RNA expression data were from 99 individual OC cases (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovarian samples.

Article Title: Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist
Article Snippet: To identify the source of its closest relative, each effector gene was aligned (BLASTn) against the National Center for Biotechnology Information (NCBI) reference genome dataset, including 1,512 complete genomes from commensal bacteria species. .. The most closely related sequences identified for each Cbeg derived from just two phyla, either Bacteroidetes (23 of 26 genes) or Firmicutes (3 of 26 genes).

Mutagenesis:

Article Title: Chemokine Network and Overall Survival in TP53 Wild-Type and Mutant Ovarian Cancer
Article Snippet: Data analysis was performed on publicly available microarray data-sets that were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) ( http://www.ncbi.nlm.nih.gov/geo/ ) database under accession numbers GSE6008 and GSE63885. .. For GSE6008, RNA expression data were from 99 individual OC cases (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovarian samples.

Genomic Sequencing:

Article Title: Comparative Studies of Vertebrate Beta Integrin Genes and Proteins: Ancient Genes in Vertebrate Evolution
Article Snippet: BLAST (Basic Local Alignment Search Tool) studies were undertaken using web tools from the National Center for Biotechnology Information (NCBI) ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ) [ ]. .. This procedure produced multiple BLAST ‘hits’ for each of the protein databases which were individually examined and retained in FASTA format, and a record kept of the sequences for predicted mRNAs and encoded ITB-like proteins.

Sequencing:

Article Title: Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study
Article Snippet: 2 × 300 bp paired-end sequencing was performed on an Illumina MiSeq (Illumina, San Diego, CA, United States) using Nextera XT libraries and the MiSeq Reagent Kit v3 600 cycles (Illumina). .. Raw sequencing data has been deposited in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA473796 . .. Paired-end read data for 72 reference strains for serotypes isolated in this study were downloaded from the NCBI-SRA.

Article Title: The Armadillo (Dasypus novemcinctus): A Witness but Not a Functional Example for the Emergence of the Butyrophilin 3/Vγ9Vδ2 System in Placental Mammals
Article Snippet: Dasypus novemcinctus (taxid 9361) whole genomic shotgun sequences (wgs) were taken from the National Center for Biotechnology Information (NCBI) databases (BioProject: PRJNA12594/PRJNA196486; BioSample: SAMN02953623; GenBank: gb|AAGV00000000.3). .. Dasypus novemcinctus (taxid 9361) whole genomic shotgun sequences (wgs) were taken from the National Center for Biotechnology Information (NCBI) databases (BioProject: PRJNA12594/PRJNA196486; BioSample: SAMN02953623; GenBank: gb|AAGV00000000.3).

Article Title: Functional Divergence in Teleost Cardiac Troponin Paralogs Guides Variation in the Interaction of TnI Switch Region with TnC
Article Snippet: All available full-length sequences for Actinopterygii (ray-finned fishes) were collected from the National Center for Biotechnology Information (NCBI) GenBank and Ensembl ( http://www.ensembl.org/index.html ) ( supplementary table S1 , Supplementary Material online ). .. All available full-length sequences for Actinopterygii (ray-finned fishes) were collected from the National Center for Biotechnology Information (NCBI) GenBank and Ensembl ( http://www.ensembl.org/index.html ) ( supplementary table S1 , Supplementary Material online ).

Article Title: Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses
Article Snippet: Here, ambiguously called sites were considered to be artefacts of genome sequencing and assembly, rather than indicators of heterogeneity, as L. monocytogenes genomes are highly conserved with low evolutionary rates . .. In total, ten sets of simulated reads were generated at 50-fold coverage using the 08-5578 chromosomal DNA sequence (NC_013766.1) available from the National Center for Biotechnology Information (NCBI) archive as a template. .. In order to mimic the use of reference sequences of varying genetic distances, the NCBI 08-5578 chromosome sequence was altered by randomly introducing 101 –105 variants in silico , generating five reference sequences that are approximately 0.00032–3.2% distant at the nucleotide level from the unaltered 08-5578 chromosome sequence.

Article Title: Comparative Studies of Vertebrate Beta Integrin Genes and Proteins: Ancient Genes in Vertebrate Evolution
Article Snippet: BLAST (Basic Local Alignment Search Tool) studies were undertaken using web tools from the National Center for Biotechnology Information (NCBI) ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ) [ ]. .. BLAST (Basic Local Alignment Search Tool) studies were undertaken using web tools from the National Center for Biotechnology Information (NCBI) ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ) [ ].

Article Title: Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases
Article Snippet: Our findings suggest that Ni-CODHs are more diverse in their structures and functions than previously reported. .. The amino acid sequences corresponding to Ni-CODHs were obtained from the National Center for Biotechnology Information (NCBI) non-redundant protein sequence database ( ) (as of January 4, 2018) through a BLASTp search ( ) using C. hydrogenoformans CooSII (WP_011343033) and the M. barkeri ACS α subunit (WP_011305243) as queries. .. Overlapping hits were excluded to construct the non-redundant dataset.

Mouse Assay:

Article Title: Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins
Article Snippet: Similarly, in mice, there are three classical MHCI genes and several non-classical MHCI genes (Fig. ). .. Full length amino acid sequences for seven human MHCIs and MHCI-like proteins and 18 mouse MHCI proteins were obtained from NCBI (National Center for Biotechnology Information), and the cytoplasmic domains were identified using splicing information, and aligned within species using T-Coffee [ ].

Produced:

Article Title: Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses
Article Snippet: In total, ten sets of simulated reads were generated at 50-fold coverage using the 08-5578 chromosomal DNA sequence (NC_013766.1) available from the National Center for Biotechnology Information (NCBI) archive as a template. .. Comparison of the resulting consensus sequences with the reference sequences revealed that, when only ten nucleotide variants were present, all SNPs were detected in every sequence regardless of which assembler was used ( and ).

Article Title: Comparative Studies of Vertebrate Beta Integrin Genes and Proteins: Ancient Genes in Vertebrate Evolution
Article Snippet: BLAST (Basic Local Alignment Search Tool) studies were undertaken using web tools from the National Center for Biotechnology Information (NCBI) ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ) [ ]. .. Non-redundant protein sequence databases for several vertebrate genomes were examined using the blastp algorithm, including human (Homo sapiens ) [ ]; horse (Equus caballus ) [ ]; mouse (Mus musculus ) [ ]; opossum (Monodelphis domestica ) [ ]; chicken (Gallus gallus ) [ ]; frog (Xenopus tropicalis ) ( http://genome.jgi-psf.org/Xentr3/Xentr3.home.html ); zebrafish (Danio rerio ) ( http://www.sanger.ac.uk/Projects/D_rerio/ ); and nematode (Caenorhabditis elegans ) ( http://genome.ucsc.edu/ ).

Microarray:

Article Title: Chemokine Network and Overall Survival in TP53 Wild-Type and Mutant Ovarian Cancer
Article Snippet: Here, we investigated the chemokine network in different subtypes of human EOC, focusing on whether there is association in TP53 status and chemokine network and how this correlates with OC survival. .. Data analysis was performed on publicly available microarray data-sets that were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) ( http://www.ncbi.nlm.nih.gov/geo/ ) database under accession numbers GSE6008 and GSE63885. .. For GSE6008, RNA expression data were from 99 individual OC cases (37 endometrioid, 41 serous, 13 mucinous, and 8 clear cell carcinomas) and 4 individual normal ovarian samples.

Generated:

Article Title: Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses
Article Snippet: Here, ambiguously called sites were considered to be artefacts of genome sequencing and assembly, rather than indicators of heterogeneity, as L. monocytogenes genomes are highly conserved with low evolutionary rates . .. In total, ten sets of simulated reads were generated at 50-fold coverage using the 08-5578 chromosomal DNA sequence (NC_013766.1) available from the National Center for Biotechnology Information (NCBI) archive as a template. .. In order to mimic the use of reference sequences of varying genetic distances, the NCBI 08-5578 chromosome sequence was altered by randomly introducing 101 –105 variants in silico , generating five reference sequences that are approximately 0.00032–3.2% distant at the nucleotide level from the unaltered 08-5578 chromosome sequence.

Article Title: Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence
Article Snippet: Paragraph title: Genes and chromosomal locations corresponding to assemblies generated from pig ESTs ... BLAST similarity analysis [ ] of the nucleotide sequences of the assemblies (contigs and singlets) against the mRNA sequences of RefSeq (release 49; 13 September 2011) at the National Center for Biotechnology Information (NCBI) [ ] revealed that the cDNA sequences corresponded to 13,691 unique human genes (Table ).

Gas Chromatography:

Article Title: Quality control of next-generation sequencing data without a reference
Article Snippet: The proportion of G and C bases (GC content) and the read coverage for each contig in the draft assembly of this mixed dataset were calculated using the TAGC plot pipeline (available at https://github.com/sujaikumar/assemblage ; Kumar and Blaxter, ; Kumar et al., ). .. To identify potential contaminants de novo , contigs or a subset of contigs from the assemblies of the genomic data were compared to the National Center for Biotechnology Information (NCBI) non-redundant nucleotide database (nt) using megablast program in BLAST (ncbi-blast-2.2.28+) (Altschul et al., ).

Derivative Assay:

Article Title: Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist
Article Snippet: To identify the source of its closest relative, each effector gene was aligned (BLASTn) against the National Center for Biotechnology Information (NCBI) reference genome dataset, including 1,512 complete genomes from commensal bacteria species. .. To identify the source of its closest relative, each effector gene was aligned (BLASTn) against the National Center for Biotechnology Information (NCBI) reference genome dataset, including 1,512 complete genomes from commensal bacteria species.

Article Title: Comparative Studies of Vertebrate Beta Integrin Genes and Proteins: Ancient Genes in Vertebrate Evolution
Article Snippet: BLAST (Basic Local Alignment Search Tool) studies were undertaken using web tools from the National Center for Biotechnology Information (NCBI) ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ) [ ]. .. This procedure produced multiple BLAST ‘hits’ for each of the protein databases which were individually examined and retained in FASTA format, and a record kept of the sequences for predicted mRNAs and encoded ITB-like proteins.

Polyacrylamide Gel Electrophoresis:

Article Title: Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins
Article Snippet: Aggregate search results for each sample were imported into Scaffold software (v. 4.4.8 Proteome Software, Portland, OR), for consolidation and visualization. .. C-terminus, carboxy terminus; CTL, cytotoxic T lymphocyte; GST, glutathione S-transferase; HLA, human leukocyte antigen; HRP, horseradish peroxidase; MHCI, major histocompatibility complex class I; NCBI, National Center for Biotechnology Information; NMDA, N -methyl D -aspartate; PDZ, PSD-95/discs large/zonula occludens-1; PVDF, polyvinylidene fluoride; RT, room temperature; SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis; TBS, tris-buffered saline; TBST, tris-buffered saline + Tween 20 .. Additional file 1: Figure S1.

DNA Purification:

Article Title: Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study
Article Snippet: Genomic DNA was extracted from pure cultures using the MasterPure DNA Purification Kit (Epicentre, Madison, WI, United States) or the DNeasy Blood and Tissue Kits (Qiagen). .. Raw sequencing data has been deposited in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) under BioProject PRJNA473796 .

cDNA Library Assay:

Article Title: Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence
Article Snippet: BLAST similarity analysis [ ] of the nucleotide sequences of the assemblies (contigs and singlets) against the mRNA sequences of RefSeq (release 49; 13 September 2011) at the National Center for Biotechnology Information (NCBI) [ ] revealed that the cDNA sequences corresponded to 13,691 unique human genes (Table ). .. Ideally, almost all of the clones in the full-length-enriched cDNA libraries would contain entire coding sequences (CDSs).

Western Blot:

Article Title: Two novel mitoviruses from a Canadian isolate of the Dutch elm pathogen Ophiostoma novo-ulmi (93-1224)
Article Snippet: There are twenty-five fully characterized species of genus Mitovirus listed in the National Center for Biotechnology Information (NCBI) Genome database, seven of which are found in the fungal genus Ophiostoma . .. Population genetic studies of the pathogen at the western Canadian disease front demonstrated that there was little diversity in the O. novo-ulmi isolates surveyed.

CTL Assay:

Article Title: Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins
Article Snippet: Aggregate search results for each sample were imported into Scaffold software (v. 4.4.8 Proteome Software, Portland, OR), for consolidation and visualization. .. C-terminus, carboxy terminus; CTL, cytotoxic T lymphocyte; GST, glutathione S-transferase; HLA, human leukocyte antigen; HRP, horseradish peroxidase; MHCI, major histocompatibility complex class I; NCBI, National Center for Biotechnology Information; NMDA, N -methyl D -aspartate; PDZ, PSD-95/discs large/zonula occludens-1; PVDF, polyvinylidene fluoride; RT, room temperature; SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis; TBS, tris-buffered saline; TBST, tris-buffered saline + Tween 20 .. Additional file 1: Figure S1.

Fluorescence In Situ Hybridization:

Article Title: Interleukin (IL)-2 Is a Key Regulator of T Helper 1 and T Helper 2 Cytokine Expression in Fish: Functional Characterization of Two Divergent IL2 Paralogs in Salmonids
Article Snippet: The IL2B cloning was performed in 2011 when no trout whole genome shotgun sequences (WGS) were available. .. BLAST ( ) search using know salmonid and other fish IL2 at the National Center for Biotechnology Information (NCBI) identified a salmon WGS contig (acc. no. AGKD04000795) that could encode for a second IL2 (termed IL2B thereafter). .. Exons were predicted and primers were designed to the 5′-untranslated region (UTR) (sIL2BF1–2, Table S1 in Supplementary Material) and used for 3′-RACE (rapid amplification of cDNA ends) using salmon SMART cDNA prepared from PMA and CI stimulated blood samples, as described previously ( ).

other:

Article Title: The variable quality of metadata about biological samples used in biomedical experiments
Article Snippet: The metadata under analysis are stored in two well-known databases: BioSample—a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples—a repository managed by the European Bioinformatics Institute (EBI).

Article Title: Fungal Lactamases: Their Occurrence and Function
Article Snippet: As of March 1, 2017, there were 1,096,469 manually and computationally annotated β-lactamase encoding genes reported in the National Center for Biotechnology Information (NCBI) protein database across all kingdoms of life.

Article Title: PubChem BioAssay: 2017 update
Article Snippet: PubChem BioAssay ( – ) is an open access database hosted by the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH).

Article Title: Re-emergence of H3N2 strains carrying potential neutralizing mutations at the N-linked glycosylation site at the hemagglutinin head, post the 2009 H1N1 pandemic
Article Snippet: To elucidate the annual epidemics of seasonal influenza virus after the 2009 pandemic, we referred to the websites of National Institute of Infectious Diseases in Japan ( http://www.nih.go.jp/niid/en/ ) and the Influenza Virus Resource of the National Center for Biotechnology Information (NCBI) ( http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html ) [ ].

Article Title: An intragenic approach to confer glyphosate resistance in chile (Capsicum annuum) by introducing an in vitro mutagenized chile EPSPS gene encoding for a glyphosate resistant EPSPS protein
Article Snippet: EPSPS nucleotide sequences were retrieved from the NCBI (National Center for Biotechnology Information) database by BLAST search using the Capsicum annuum EPSPS cDNA as query.

SDS Page:

Article Title: Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins
Article Snippet: Aggregate search results for each sample were imported into Scaffold software (v. 4.4.8 Proteome Software, Portland, OR), for consolidation and visualization. .. C-terminus, carboxy terminus; CTL, cytotoxic T lymphocyte; GST, glutathione S-transferase; HLA, human leukocyte antigen; HRP, horseradish peroxidase; MHCI, major histocompatibility complex class I; NCBI, National Center for Biotechnology Information; NMDA, N -methyl D -aspartate; PDZ, PSD-95/discs large/zonula occludens-1; PVDF, polyvinylidene fluoride; RT, room temperature; SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis; TBS, tris-buffered saline; TBST, tris-buffered saline + Tween 20 .. Additional file 1: Figure S1.

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    Biotechnology Information ncbi
    Metadata submissions to <t>NCBI</t> <t>BioSample</t> from 2009–2017. The columns represent the total number of metadata record submissions to NCBI BioSample in a year, split between Generic and non-Generic records. The Non-Generic metadata records column contains data labels with the absolute number of records. Generic records make up nearly all the submissions in the early years of BioSample, and the bulk of the submissions even in recent years.
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    Metadata submissions to NCBI BioSample from 2009–2017. The columns represent the total number of metadata record submissions to NCBI BioSample in a year, split between Generic and non-Generic records. The Non-Generic metadata records column contains data labels with the absolute number of records. Generic records make up nearly all the submissions in the early years of BioSample, and the bulk of the submissions even in recent years.

    Journal: Scientific Data

    Article Title: The variable quality of metadata about biological samples used in biomedical experiments

    doi: 10.1038/sdata.2019.21

    Figure Lengend Snippet: Metadata submissions to NCBI BioSample from 2009–2017. The columns represent the total number of metadata record submissions to NCBI BioSample in a year, split between Generic and non-Generic records. The Non-Generic metadata records column contains data labels with the absolute number of records. Generic records make up nearly all the submissions in the early years of BioSample, and the bulk of the submissions even in recent years.

    Article Snippet: The metadata under analysis are stored in two well-known databases: BioSample—a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples—a repository managed by the European Bioinformatics Institute (EBI).

    Techniques:

    Mention of metadata packages in NCBI BioSample. The chart shows the package names followed by the number (and percentage) of metadata records that use that package. The Generic package does not specify any required or optional attributes.

    Journal: Scientific Data

    Article Title: The variable quality of metadata about biological samples used in biomedical experiments

    doi: 10.1038/sdata.2019.21

    Figure Lengend Snippet: Mention of metadata packages in NCBI BioSample. The chart shows the package names followed by the number (and percentage) of metadata records that use that package. The Generic package does not specify any required or optional attributes.

    Article Snippet: The metadata under analysis are stored in two well-known databases: BioSample—a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples—a repository managed by the European Bioinformatics Institute (EBI).

    Techniques:

    Quality of attributes in packaged metadata records in NCBI BioSample. The columns represent the metadata attribute types. Each column shows the number and percentage of metadata attributes whose values are either well-specified or invalid.

    Journal: Scientific Data

    Article Title: The variable quality of metadata about biological samples used in biomedical experiments

    doi: 10.1038/sdata.2019.21

    Figure Lengend Snippet: Quality of attributes in packaged metadata records in NCBI BioSample. The columns represent the metadata attribute types. Each column shows the number and percentage of metadata attributes whose values are either well-specified or invalid.

    Article Snippet: The metadata under analysis are stored in two well-known databases: BioSample—a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples—a repository managed by the European Bioinformatics Institute (EBI).

    Techniques:

    Quality of dictionary attributes in NCBI BioSample according to their type. The columns show the number and percentage of attributes whose values are well-specified or invalid.

    Journal: Scientific Data

    Article Title: The variable quality of metadata about biological samples used in biomedical experiments

    doi: 10.1038/sdata.2019.21

    Figure Lengend Snippet: Quality of dictionary attributes in NCBI BioSample according to their type. The columns show the number and percentage of attributes whose values are well-specified or invalid.

    Article Snippet: The metadata under analysis are stored in two well-known databases: BioSample—a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples—a repository managed by the European Bioinformatics Institute (EBI).

    Techniques:

    Example metadata record from the NCBI BioSample. An NCBI BioSample metadata record has a title, potentially multiple identifiers associated with it, an organism, a package specification (explained in Section 2.1), multiple attributes in the form of name-value pairs, a description with keywords associated with it, information about the record submitter, and finally accession details.

    Journal: Scientific Data

    Article Title: The variable quality of metadata about biological samples used in biomedical experiments

    doi: 10.1038/sdata.2019.21

    Figure Lengend Snippet: Example metadata record from the NCBI BioSample. An NCBI BioSample metadata record has a title, potentially multiple identifiers associated with it, an organism, a package specification (explained in Section 2.1), multiple attributes in the form of name-value pairs, a description with keywords associated with it, information about the record submitter, and finally accession details.

    Article Snippet: The metadata under analysis are stored in two well-known databases: BioSample—a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples—a repository managed by the European Bioinformatics Institute (EBI).

    Techniques:

    Expression of miR-155 in human normal breast and breast cancer samples (A-C) Data analyses were performed using the datasets from NCBI GEO database. Quantification of miR-155 expression (A) in samples of normal breast and DCIS and invasive ductal carcinoma, (B) in normal breast and non-basal and basal-like breast cancer samples, and (C) in localized and brain metastatic breast cancer samples. Data analyses were performed using datasets from the NCI TCGA database. Quantification of miR-155 or MIR155HG expression was accomplished (D) for normal breast and breast lobular carcinoma and ductal carcinoma samples, (E) for breast cancer samples with different stages, (F) for breast cancer samples with ER/PR/HER2 status, and (G) for non-TNBC and TNBC samples. All data are presented as the means and SD or as the medians and interquartile ranges. * p

    Journal: Oncotarget

    Article Title: MicroRNA-155, induced by FOXP3 through transcriptional repression of BRCA1, is associated with tumor initiation in human breast cancer

    doi: 10.18632/oncotarget.17816

    Figure Lengend Snippet: Expression of miR-155 in human normal breast and breast cancer samples (A-C) Data analyses were performed using the datasets from NCBI GEO database. Quantification of miR-155 expression (A) in samples of normal breast and DCIS and invasive ductal carcinoma, (B) in normal breast and non-basal and basal-like breast cancer samples, and (C) in localized and brain metastatic breast cancer samples. Data analyses were performed using datasets from the NCI TCGA database. Quantification of miR-155 or MIR155HG expression was accomplished (D) for normal breast and breast lobular carcinoma and ductal carcinoma samples, (E) for breast cancer samples with different stages, (F) for breast cancer samples with ER/PR/HER2 status, and (G) for non-TNBC and TNBC samples. All data are presented as the means and SD or as the medians and interquartile ranges. * p

    Article Snippet: To assess the clinical relevance of miR-155 in human primary breast cancers, the expression profile of miR-155 was characterized by bioinformatics analysis of public datasets from a) the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) and b) the National Cancer Institute (NCI) The Cancer Genome Atlas (TCGA).

    Techniques: Expressing

    FOXP3-BRCA1-miR-155 axis in human breast cancer cells (A) The relative expression levels of BRCA1 and TP63 in FOXP3 Tet-off MCF7 cells with or without Dox. The expression of genes in cells with Dox is a reference, 1.0. (B) The expression of miR-155 in FOXP3 Tet-off MCF7 cells before and after BRCA1 silencing. Top panels: Representative Western blots showing BRCA1 expression after transfection with BRCA1 siRNAs or scramble control in the cells. Bottom graphs: Quantification of miR-155 expression as a percentage of RNU6B expression after transfection in the cells. The expression of miR-155 in cells with Dox as a reference, 1.0. Scr, scramble; siR, siRNA. (C) Quantification of miR-155 expression after BRCA1 siRNA silencing in MCF10A cells (data from a NCBI GEO dataset). siBRCA1 , BRCA1 siRNA. (D) Heat map depiction of alterations in miR-155 target gene expression in FOXP3 Tet-off MCF7 cells was generated from Affymetrix Human U133 plus 2.0 microarrays (EMBL-EBI, accession number E-MTAB-73). (E) Expression levels of BRCA1 , miR-155, and RAD51 as a percentage of GAPDH or RNU6B expression in FOXP3 Tet-off MCF7 cells with or without Dox. (F) Schematic representation of the FOXP3-BRCA1-miR-155 axis in human breast cancer cells. All data are presented as the means and SD of triplicates. * p

    Journal: Oncotarget

    Article Title: MicroRNA-155, induced by FOXP3 through transcriptional repression of BRCA1, is associated with tumor initiation in human breast cancer

    doi: 10.18632/oncotarget.17816

    Figure Lengend Snippet: FOXP3-BRCA1-miR-155 axis in human breast cancer cells (A) The relative expression levels of BRCA1 and TP63 in FOXP3 Tet-off MCF7 cells with or without Dox. The expression of genes in cells with Dox is a reference, 1.0. (B) The expression of miR-155 in FOXP3 Tet-off MCF7 cells before and after BRCA1 silencing. Top panels: Representative Western blots showing BRCA1 expression after transfection with BRCA1 siRNAs or scramble control in the cells. Bottom graphs: Quantification of miR-155 expression as a percentage of RNU6B expression after transfection in the cells. The expression of miR-155 in cells with Dox as a reference, 1.0. Scr, scramble; siR, siRNA. (C) Quantification of miR-155 expression after BRCA1 siRNA silencing in MCF10A cells (data from a NCBI GEO dataset). siBRCA1 , BRCA1 siRNA. (D) Heat map depiction of alterations in miR-155 target gene expression in FOXP3 Tet-off MCF7 cells was generated from Affymetrix Human U133 plus 2.0 microarrays (EMBL-EBI, accession number E-MTAB-73). (E) Expression levels of BRCA1 , miR-155, and RAD51 as a percentage of GAPDH or RNU6B expression in FOXP3 Tet-off MCF7 cells with or without Dox. (F) Schematic representation of the FOXP3-BRCA1-miR-155 axis in human breast cancer cells. All data are presented as the means and SD of triplicates. * p

    Article Snippet: To assess the clinical relevance of miR-155 in human primary breast cancers, the expression profile of miR-155 was characterized by bioinformatics analysis of public datasets from a) the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) and b) the National Cancer Institute (NCI) The Cancer Genome Atlas (TCGA).

    Techniques: Expressing, Western Blot, Transfection, Generated

    Phylogenetic placement of predicted Fusarium verticillioides lactamase genes based on amino acid sequence alignment. This cartoon summarizes the phylogenetic pattern of lactamase genes with intact core motifs in F. verticillioides . Each query lactamase amino acid sequence was searched for its top 50 homologs using BLASTP in NCBI. Neighbor-joining trees using the Jukes–Cantor genetic distance model were constructed by Geneious Tree Builder (Ver. 8.1) for each individual homology search. All tree topographies complied with the configuration such that each F. verticillioides lactamase fell into one of three positions marked as A, B, and C. Collapsed clades are shown as triangles.

    Journal: Frontiers in Microbiology

    Article Title: Fungal Lactamases: Their Occurrence and Function

    doi: 10.3389/fmicb.2017.01775

    Figure Lengend Snippet: Phylogenetic placement of predicted Fusarium verticillioides lactamase genes based on amino acid sequence alignment. This cartoon summarizes the phylogenetic pattern of lactamase genes with intact core motifs in F. verticillioides . Each query lactamase amino acid sequence was searched for its top 50 homologs using BLASTP in NCBI. Neighbor-joining trees using the Jukes–Cantor genetic distance model were constructed by Geneious Tree Builder (Ver. 8.1) for each individual homology search. All tree topographies complied with the configuration such that each F. verticillioides lactamase fell into one of three positions marked as A, B, and C. Collapsed clades are shown as triangles.

    Article Snippet: As of March 1, 2017, there were 1,096,469 manually and computationally annotated β-lactamase encoding genes reported in the National Center for Biotechnology Information (NCBI) protein database across all kingdoms of life.

    Techniques: Sequencing, Construct

    Sunburst visualization of β-lactamase gene distribution by major taxon. Each node of the taxonomic hierarchy is represented as a separate arc, arranged radially with the domains at the center and the phyla arrayed around the outermost ring. The area of each arc is proportional to the number of β-lactamases reported in the NCBI protein database. I, M, and O refer to inner, middle, and outer arcs. The frequency of Fusarium lactamases among the Ascomycota is denoted in bar chart form.

    Journal: Frontiers in Microbiology

    Article Title: Fungal Lactamases: Their Occurrence and Function

    doi: 10.3389/fmicb.2017.01775

    Figure Lengend Snippet: Sunburst visualization of β-lactamase gene distribution by major taxon. Each node of the taxonomic hierarchy is represented as a separate arc, arranged radially with the domains at the center and the phyla arrayed around the outermost ring. The area of each arc is proportional to the number of β-lactamases reported in the NCBI protein database. I, M, and O refer to inner, middle, and outer arcs. The frequency of Fusarium lactamases among the Ascomycota is denoted in bar chart form.

    Article Snippet: As of March 1, 2017, there were 1,096,469 manually and computationally annotated β-lactamase encoding genes reported in the National Center for Biotechnology Information (NCBI) protein database across all kingdoms of life.

    Techniques:

    Lactamase genes are abundant within some fungi. The number of annotated ORFs possessing a lactamase domain is shown for the top 40 fungi among all annotated fungal species identified from the NCBI Protein Database. Species are ranked by the abundance of lactamases. Fungi known to be soil-borne are displayed with red bars, those not clearly cited in literature as soil-borne fungi are in blue, and yeast along with selected obligate plant pathogens are in gray. Numbers of Fusarium lactamases are highlighted in yellow.

    Journal: Frontiers in Microbiology

    Article Title: Fungal Lactamases: Their Occurrence and Function

    doi: 10.3389/fmicb.2017.01775

    Figure Lengend Snippet: Lactamase genes are abundant within some fungi. The number of annotated ORFs possessing a lactamase domain is shown for the top 40 fungi among all annotated fungal species identified from the NCBI Protein Database. Species are ranked by the abundance of lactamases. Fungi known to be soil-borne are displayed with red bars, those not clearly cited in literature as soil-borne fungi are in blue, and yeast along with selected obligate plant pathogens are in gray. Numbers of Fusarium lactamases are highlighted in yellow.

    Article Snippet: As of March 1, 2017, there were 1,096,469 manually and computationally annotated β-lactamase encoding genes reported in the National Center for Biotechnology Information (NCBI) protein database across all kingdoms of life.

    Techniques:

    Chemokine and chemokine receptor signatures in EOC subtypes. Heatmap of chemokine expression profiles in EOC subtypes, including clear cell (n=8, yellow), endometrioid (n=37, blue), mucinous (n=13, green), and serous (n=41, red), and normal ovarian samples (n=4, black) from the NCBI GEO ( http://www.ncbi.nlm.nih.gov/geo/ ) database (GSE6008) using Gitools 2.3.1. Bold yellow, green and black letters indicate dominant chemokines in clear cell, mucinous and normal samples, respectively. The right panel indicates statistical analysis of chemokine expression intensities using ANOVA and Tukey's pairwise comparisons.

    Journal: Immune Network

    Article Title: Chemokine Network and Overall Survival in TP53 Wild-Type and Mutant Ovarian Cancer

    doi: 10.4110/in.2018.18.e29

    Figure Lengend Snippet: Chemokine and chemokine receptor signatures in EOC subtypes. Heatmap of chemokine expression profiles in EOC subtypes, including clear cell (n=8, yellow), endometrioid (n=37, blue), mucinous (n=13, green), and serous (n=41, red), and normal ovarian samples (n=4, black) from the NCBI GEO ( http://www.ncbi.nlm.nih.gov/geo/ ) database (GSE6008) using Gitools 2.3.1. Bold yellow, green and black letters indicate dominant chemokines in clear cell, mucinous and normal samples, respectively. The right panel indicates statistical analysis of chemokine expression intensities using ANOVA and Tukey's pairwise comparisons.

    Article Snippet: Data analysis was performed on publicly available microarray data-sets that were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) ( http://www.ncbi.nlm.nih.gov/geo/ ) database under accession numbers GSE6008 and GSE63885.

    Techniques: Expressing

    Chemokine and chemokine receptor signatures in TP53 WT and TP53 m endometrioid OC. (A) Heatmap of chemokine and chemokine receptor expression profiles in TP53 WT (n=22) and TP53 m (n=15) endometrioid OC from NCBI GEO ( http://www.ncbi.nlm.nih.gov/geo/ ) database (GSE6008) using Gitools 2.3.1. Blue letter indicates the dominant chemokine in TP53 WT endometrioid OC. Right panel indicates statistical analysis of chemokine expression intensities using Student's t -test. (B) Kaplan-Meier plots for OS and PFS based on expression levels of CXCL14 in endometrioid OC patients from GEO and TCGA (probes; Affymetrix HG-U133A, HG-U133A 2.0, and HG-U133 Plus 2.0 microarrays). Black and red letters indicate low and high expression of CXCL14, respectively.

    Journal: Immune Network

    Article Title: Chemokine Network and Overall Survival in TP53 Wild-Type and Mutant Ovarian Cancer

    doi: 10.4110/in.2018.18.e29

    Figure Lengend Snippet: Chemokine and chemokine receptor signatures in TP53 WT and TP53 m endometrioid OC. (A) Heatmap of chemokine and chemokine receptor expression profiles in TP53 WT (n=22) and TP53 m (n=15) endometrioid OC from NCBI GEO ( http://www.ncbi.nlm.nih.gov/geo/ ) database (GSE6008) using Gitools 2.3.1. Blue letter indicates the dominant chemokine in TP53 WT endometrioid OC. Right panel indicates statistical analysis of chemokine expression intensities using Student's t -test. (B) Kaplan-Meier plots for OS and PFS based on expression levels of CXCL14 in endometrioid OC patients from GEO and TCGA (probes; Affymetrix HG-U133A, HG-U133A 2.0, and HG-U133 Plus 2.0 microarrays). Black and red letters indicate low and high expression of CXCL14, respectively.

    Article Snippet: Data analysis was performed on publicly available microarray data-sets that were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) ( http://www.ncbi.nlm.nih.gov/geo/ ) database under accession numbers GSE6008 and GSE63885.

    Techniques: Expressing

    Chemokine and chemokine receptor signatures in TP53 WT and TP53 m serous OC. (A) Heatmap of chemokine and chemokine receptor expression profiles in TP53 WT (n=9) and TP53 m (n=62) serous EOC from NCBI GEO ( http://www.ncbi.nlm.nih.gov/geo/ ) database (GSE63885) using Gitools 2.3.1. Red letters indicate dominant chemokines in TP53 m serous OC. Right panel indicates statistical analysis of chemokine expression intensities using Student's t -test.

    Journal: Immune Network

    Article Title: Chemokine Network and Overall Survival in TP53 Wild-Type and Mutant Ovarian Cancer

    doi: 10.4110/in.2018.18.e29

    Figure Lengend Snippet: Chemokine and chemokine receptor signatures in TP53 WT and TP53 m serous OC. (A) Heatmap of chemokine and chemokine receptor expression profiles in TP53 WT (n=9) and TP53 m (n=62) serous EOC from NCBI GEO ( http://www.ncbi.nlm.nih.gov/geo/ ) database (GSE63885) using Gitools 2.3.1. Red letters indicate dominant chemokines in TP53 m serous OC. Right panel indicates statistical analysis of chemokine expression intensities using Student's t -test.

    Article Snippet: Data analysis was performed on publicly available microarray data-sets that were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) ( http://www.ncbi.nlm.nih.gov/geo/ ) database under accession numbers GSE6008 and GSE63885.

    Techniques: Expressing