Structured Review

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Sequence alignment of the <t>EPSPS</t> 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. <t>NCBI</t> 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.
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Images

1) 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

2) Product Images from "Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code"

Article Title: Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code

Journal: Transcription

doi: 10.1080/21541264.2018.1467718

Pyrococcus furiosis ( Pfu ) aaRS enzymes were searched using NCBI Blast tools for nearest homologs in Pfu . In some cases, Staphylothermus marinus ( Sma ) (archaea) and Escherichia coli ( Eco ) (bacteria) homologs are identified. AlaX is one of a set of tRNA Ala editing enzymes in Pfu .
Figure Legend Snippet: Pyrococcus furiosis ( Pfu ) aaRS enzymes were searched using NCBI Blast tools for nearest homologs in Pfu . In some cases, Staphylothermus marinus ( Sma ) (archaea) and Escherichia coli ( Eco ) (bacteria) homologs are identified. AlaX is one of a set of tRNA Ala editing enzymes in Pfu .

Techniques Used:

3) 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

4) Product Images from "Intestinal peptidases form functional complexes with the neutral amino acid transporter B0AT1"

Article Title: Intestinal peptidases form functional complexes with the neutral amino acid transporter B0AT1

Journal: Biochemical Journal

doi: 10.1042/BJ20120307

Sequence alignments of aminopeptidase family members Potential homologues of mouse APN (P97449) were identified by a NCBI blastp search. Peptide sequences were aligned using COBALT ( http://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?CMD =Web). Highly conserved regions are boxed. In the consensus sequence row, X is any amino acid and B is bulky side chain neutral amino acids. The full-length aligned sequence from E. coli LAP (not shown) was used as the basis for the homology modelling of mouse APN. The three conserved residues in the binding domains of murine APN selected for site-directed mutagenesis are indicated with a vertical line above them, a fourth mutated residue, Tyr 476 , is not shown. AAP1, alanine/arginine aminopeptidase 1; LTA4, leukotriene A-4 hydrolase.
Figure Legend Snippet: Sequence alignments of aminopeptidase family members Potential homologues of mouse APN (P97449) were identified by a NCBI blastp search. Peptide sequences were aligned using COBALT ( http://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?CMD =Web). Highly conserved regions are boxed. In the consensus sequence row, X is any amino acid and B is bulky side chain neutral amino acids. The full-length aligned sequence from E. coli LAP (not shown) was used as the basis for the homology modelling of mouse APN. The three conserved residues in the binding domains of murine APN selected for site-directed mutagenesis are indicated with a vertical line above them, a fourth mutated residue, Tyr 476 , is not shown. AAP1, alanine/arginine aminopeptidase 1; LTA4, leukotriene A-4 hydrolase.

Techniques Used: Sequencing, Binding Assay, Mutagenesis

5) Product Images from "Characterization and Pharmacological Properties of a Novel Multifunctional Kunitz Inhibitor from Erythrina velutina Seeds"

Article Title: Characterization and Pharmacological Properties of a Novel Multifunctional Kunitz Inhibitor from Erythrina velutina Seeds

Journal: PLoS ONE

doi: 10.1371/journal.pone.0063571

EvTI partial primary sequence alignment with sequences of known legume seeds Kunitz-type trypsin inhibitors: E. velutina (EvTI) ; E. caffra (TSI) (gi 157833954) ; E. variegata (ETIb) (gi 262753) ; Psophocarpus tetragonolobus (WBTI) (gi 86450987) ; Bauhinia variegata (BvcTI) (gi 15082208) ; Bauhinia ungulate (gi 32363179) ; Prosopis juliflora (PjTKI) (gi 243387) ; Adenanthera pavonina (ApTKI) (gi 225058). Sequences deposited in the database of NCBI (National Center for Biotechnology Information) were compared using the BLASTp. The alignment was performed using Bio Edit software v 7.0.9.0 through the Clustal W multiple alignment tool.
Figure Legend Snippet: EvTI partial primary sequence alignment with sequences of known legume seeds Kunitz-type trypsin inhibitors: E. velutina (EvTI) ; E. caffra (TSI) (gi 157833954) ; E. variegata (ETIb) (gi 262753) ; Psophocarpus tetragonolobus (WBTI) (gi 86450987) ; Bauhinia variegata (BvcTI) (gi 15082208) ; Bauhinia ungulate (gi 32363179) ; Prosopis juliflora (PjTKI) (gi 243387) ; Adenanthera pavonina (ApTKI) (gi 225058). Sequences deposited in the database of NCBI (National Center for Biotechnology Information) were compared using the BLASTp. The alignment was performed using Bio Edit software v 7.0.9.0 through the Clustal W multiple alignment tool.

Techniques Used: Sequencing, Software

6) Product Images from "Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code"

Article Title: Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code

Journal: Transcription

doi: 10.1080/21541264.2018.1467718

Pyrococcus furiosis ( Pfu ) aaRS enzymes were searched using NCBI Blast tools for nearest homologs in Pfu . In some cases, Staphylothermus marinus ( Sma ) (archaea) and Escherichia coli ( Eco ) (bacteria) homologs are identified. AlaX is one of a set of tRNA Ala editing enzymes in Pfu .
Figure Legend Snippet: Pyrococcus furiosis ( Pfu ) aaRS enzymes were searched using NCBI Blast tools for nearest homologs in Pfu . In some cases, Staphylothermus marinus ( Sma ) (archaea) and Escherichia coli ( Eco ) (bacteria) homologs are identified. AlaX is one of a set of tRNA Ala editing enzymes in Pfu .

Techniques Used:

7) Product Images from "The variome of pneumococcal virulence factors and regulators"

Article Title: The variome of pneumococcal virulence factors and regulators

Journal: BMC Genomics

doi: 10.1186/s12864-017-4376-0

Phylogenetic tree (slanted cladogram) of the pneumococcal genome / strains. By using the online NCBI Tools Genome Tree Report (ncbi.nlm. nih.gov/genome/tree/176 ) and the Tree Viewer 1.17.0 (ncbi.nlm. nih.gov/projects/treeview ), a phylogenetic tree was constructed from the analysis by genomic BLAST of 8290 sequencing projects of pneumococci reported in the NCBI database. The topology of this slanted cladogram showed different pneumococcal lineages, where the selected set of 25 pneumococcal strains can be identified in red as external nodes (the “well-distributed” key features also highlighted in red), evidencing an optimal representation of the pneumococcal population. The overall number of sequenced pneumococcal genomes is provided for each external node. The blue lines depicted those external nodes where fully sequenced and annotated genomes are located
Figure Legend Snippet: Phylogenetic tree (slanted cladogram) of the pneumococcal genome / strains. By using the online NCBI Tools Genome Tree Report (ncbi.nlm. nih.gov/genome/tree/176 ) and the Tree Viewer 1.17.0 (ncbi.nlm. nih.gov/projects/treeview ), a phylogenetic tree was constructed from the analysis by genomic BLAST of 8290 sequencing projects of pneumococci reported in the NCBI database. The topology of this slanted cladogram showed different pneumococcal lineages, where the selected set of 25 pneumococcal strains can be identified in red as external nodes (the “well-distributed” key features also highlighted in red), evidencing an optimal representation of the pneumococcal population. The overall number of sequenced pneumococcal genomes is provided for each external node. The blue lines depicted those external nodes where fully sequenced and annotated genomes are located

Techniques Used: Construct, Sequencing

8) Product Images from "Protein composition of the occlusion bodies of Epinotia aporema granulovirus"

Article Title: Protein composition of the occlusion bodies of Epinotia aporema granulovirus

Journal: PLoS ONE

doi: 10.1371/journal.pone.0207735

Putative fusion protein Epap48-Epap49. (A) Genomic locus containing epap48 (green) and epap49 (blue) genes. The two peptides detected by MS inside the intergenic region are depicted in purple. (B) Genome sequence and translation frame for each gene. Start and stop codons are shown in red (nucleotide numbers are those from NCBI accession number NC_018875).
Figure Legend Snippet: Putative fusion protein Epap48-Epap49. (A) Genomic locus containing epap48 (green) and epap49 (blue) genes. The two peptides detected by MS inside the intergenic region are depicted in purple. (B) Genome sequence and translation frame for each gene. Start and stop codons are shown in red (nucleotide numbers are those from NCBI accession number NC_018875).

Techniques Used: Mass Spectrometry, Sequencing

9) 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

10) Product Images from "Interaction of Infectious Spleen and Kidney Necrosis Virus ORF119L with PINCH Leads to Dominant-Negative Inhibition of Integrin-Linked Kinase and Cardiovascular Defects in Zebrafish"

Article Title: Interaction of Infectious Spleen and Kidney Necrosis Virus ORF119L with PINCH Leads to Dominant-Negative Inhibition of Integrin-Linked Kinase and Cardiovascular Defects in Zebrafish

Journal: Journal of Virology

doi: 10.1128/JVI.01955-14

Sequence similarity alignment of ORF119L with the dominant negative form of ILK. (A) Phylogenetic tree analysis of ORF119L orthologues from NCBI zebrafish protein database. These orthologues score highest in levels of identity to ORF119L in the BLAST
Figure Legend Snippet: Sequence similarity alignment of ORF119L with the dominant negative form of ILK. (A) Phylogenetic tree analysis of ORF119L orthologues from NCBI zebrafish protein database. These orthologues score highest in levels of identity to ORF119L in the BLAST

Techniques Used: Sequencing, Dominant Negative Mutation

11) Product Images from "The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria"

Article Title: The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria

Journal: The ISME Journal

doi: 10.1038/ismej.2016.100

Genomic and metagenomic distribution of the cof genes that encode F 420 biosynthesis enzymes. The genes encoding the five known proteins specifically required for F 420 synthesis are shown, namely CofC, CofD, CofE, CofG and CofH, where CofGH represents a fusion protein. ( a ) Distribution of cof genes by phyla in the NCBI Reference Sequence database. ( b ) Distribution of cof genes in 19 publicly available metagenomes by enzyme. ( c ) Distribution of cof genes in 19 publicly available metagenomes by phylum of the closest BLAST hit ( > 60% identity).
Figure Legend Snippet: Genomic and metagenomic distribution of the cof genes that encode F 420 biosynthesis enzymes. The genes encoding the five known proteins specifically required for F 420 synthesis are shown, namely CofC, CofD, CofE, CofG and CofH, where CofGH represents a fusion protein. ( a ) Distribution of cof genes by phyla in the NCBI Reference Sequence database. ( b ) Distribution of cof genes in 19 publicly available metagenomes by enzyme. ( c ) Distribution of cof genes in 19 publicly available metagenomes by phylum of the closest BLAST hit ( > 60% identity).

Techniques Used: Sequencing

12) Product Images from "The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation"

Article Title: The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation

Journal: PLoS ONE

doi: 10.1371/journal.pone.0174754

Relative proportion (%) of phylotypes isolated from the larval gut of insecticide-resistant lines of Spodoptera frugiperda afterr RFLP-PCR analysis and partial sequence (550 pb) of the 16S rDNA. Putative identification obtained after heuristic search of 1350 bp of 16S rDNA against sequences available in the NCBi and EzTaxon-e databases.
Figure Legend Snippet: Relative proportion (%) of phylotypes isolated from the larval gut of insecticide-resistant lines of Spodoptera frugiperda afterr RFLP-PCR analysis and partial sequence (550 pb) of the 16S rDNA. Putative identification obtained after heuristic search of 1350 bp of 16S rDNA against sequences available in the NCBi and EzTaxon-e databases.

Techniques Used: Isolation, Polymerase Chain Reaction, Sequencing

13) 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

14) Product Images from "An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3"

Article Title: An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3

Journal: Scientific Reports

doi: 10.1038/srep44423

Sequence similarity between Geelong’s outbreak parechovirus and related parechovirus sequences. SimPlot analysis was used to calculate and plot the degree of similarity between the Geelong outbreak parechovirus and a panel of parechovirus strain sequences obtained from NCBI. The key to the panel of strain sequences are as follows: AB759206, AB759207, AB759199, AB759204 HPEV3 (Yamagata 2011 lineage – only include coding regions); AB759189, AB7591 HPeV3 (Yamagata 2008 lineage - only include coding regions); GQ183030, GQ183032, GQ183027 HPeV3; GQ183018, GQ183020 HPEV1; KJ659490 HPeV3; KT726985 HPeV1; AJ889918 HPeV3; FJ840477 HPeV1; and DQ315670 HPeV4. Based on information from AB759206 (HPeV3Yamagata 2011 lineage 52 ), the structural/capsid coding region is from nucleotide 701–3013 and the non-structural protein coding region from 3014–7231.
Figure Legend Snippet: Sequence similarity between Geelong’s outbreak parechovirus and related parechovirus sequences. SimPlot analysis was used to calculate and plot the degree of similarity between the Geelong outbreak parechovirus and a panel of parechovirus strain sequences obtained from NCBI. The key to the panel of strain sequences are as follows: AB759206, AB759207, AB759199, AB759204 HPEV3 (Yamagata 2011 lineage – only include coding regions); AB759189, AB7591 HPeV3 (Yamagata 2008 lineage - only include coding regions); GQ183030, GQ183032, GQ183027 HPeV3; GQ183018, GQ183020 HPEV1; KJ659490 HPeV3; KT726985 HPeV1; AJ889918 HPeV3; FJ840477 HPeV1; and DQ315670 HPeV4. Based on information from AB759206 (HPeV3Yamagata 2011 lineage 52 ), the structural/capsid coding region is from nucleotide 701–3013 and the non-structural protein coding region from 3014–7231.

Techniques Used: Sequencing

15) Product Images from "mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species"

Article Title: mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

Journal: Microbial Genomics

doi: 10.1099/mgen.0.000224

Workflow to create the plasmid models for Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli . (a) For E. faecium , 62 Illumina-sequenced strains were selected for ONT sequencing and Unicycler was used to extend the number of complete genomes available for this species. For E. coli and K. pneumoniae , we downloaded complete genomes with plasmids associated from the Assembly Entrez NCBI database. (b) For E. coli and K. pneumoniae , we simulated reads with 50× coverage and no error rate using wgsim. (c) Illumina simulated and non-simulated reads were de novo assembled using SPAdes. (d) We mapped short-read contigs against complete genome sequences to define a reliable dataset of short-read contigs as plasmid or chromosome derived. (e) For each bacterial species, five machine-learning classifiers were trained (10-fold cross-validation) and compared using a specific bacterial species training and test set. (f) SVM models were implemented in mlplasmids and used to predict plasmid- and chromosome-derived sequences in isolates with only short-read WGS data available. The complete workflow is available from https://gitlab.com/sirarredondo/analysis_mlplasmids .
Figure Legend Snippet: Workflow to create the plasmid models for Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli . (a) For E. faecium , 62 Illumina-sequenced strains were selected for ONT sequencing and Unicycler was used to extend the number of complete genomes available for this species. For E. coli and K. pneumoniae , we downloaded complete genomes with plasmids associated from the Assembly Entrez NCBI database. (b) For E. coli and K. pneumoniae , we simulated reads with 50× coverage and no error rate using wgsim. (c) Illumina simulated and non-simulated reads were de novo assembled using SPAdes. (d) We mapped short-read contigs against complete genome sequences to define a reliable dataset of short-read contigs as plasmid or chromosome derived. (e) For each bacterial species, five machine-learning classifiers were trained (10-fold cross-validation) and compared using a specific bacterial species training and test set. (f) SVM models were implemented in mlplasmids and used to predict plasmid- and chromosome-derived sequences in isolates with only short-read WGS data available. The complete workflow is available from https://gitlab.com/sirarredondo/analysis_mlplasmids .

Techniques Used: Plasmid Preparation, Sequencing, Derivative Assay

16) 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

17) Product Images from "Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation"

Article Title: Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx1031

A view of the graphical display accessed from the report page of CCDS3542.1 ( https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS DATA=CCDS3542 ORGANISM=0 BUILDS=CURRENTBUILDS ) using the purple ‘S’ icon. ( A ) Transcripts and proteins from NCBI Annotation Release 108. ( B ) Transcripts and proteins from Ensembl Release 85. The green bar indicates the gene; transcripts are shown in purple and proteins are shown in red color. Positioning the cursor over any of these objects (gene, transcript or protein) opens a tool tip which includes additional information and links. Proteins in the NCBI annotation display that are in the CCDS set include a link to the CCDS ID in the tool tip. The gray box to the right (indicated by vertical arrow) is the tool tip corresponding to the protein accession NP_002514.1. Differences between any two objects can also be revealed as vertical lines (indicated by horizontal arrows) when the objects (NM_002523.2 and ENST00000265634 in the figure) are selected using the ‘Control’ or ‘Command’ button on the keyboard.
Figure Legend Snippet: A view of the graphical display accessed from the report page of CCDS3542.1 ( https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS DATA=CCDS3542 ORGANISM=0 BUILDS=CURRENTBUILDS ) using the purple ‘S’ icon. ( A ) Transcripts and proteins from NCBI Annotation Release 108. ( B ) Transcripts and proteins from Ensembl Release 85. The green bar indicates the gene; transcripts are shown in purple and proteins are shown in red color. Positioning the cursor over any of these objects (gene, transcript or protein) opens a tool tip which includes additional information and links. Proteins in the NCBI annotation display that are in the CCDS set include a link to the CCDS ID in the tool tip. The gray box to the right (indicated by vertical arrow) is the tool tip corresponding to the protein accession NP_002514.1. Differences between any two objects can also be revealed as vertical lines (indicated by horizontal arrows) when the objects (NM_002523.2 and ENST00000265634 in the figure) are selected using the ‘Control’ or ‘Command’ button on the keyboard.

Techniques Used: Polyacrylamide Gel Electrophoresis

18) 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 ]. 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 ]. 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 ). 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 ). NCBI accession nos. for the solanaceous EPSPS nucleotide sequences are indicated.

Techniques Used: Sequencing

19) Product Images from "Chloroplast genomes: diversity, evolution, and applications in genetic engineering"

Article Title: Chloroplast genomes: diversity, evolution, and applications in genetic engineering

Journal: Genome Biology

doi: 10.1186/s13059-016-1004-2

Chloroplast genome structure and gene expression across tracheophytes. These 658 chloroplast genomes were downloaded from NCBI Organelle Resources. The X-axis indicates the taxonomy of the chloroplast genome species following the Angiosperm Phylogeny Group III system and NCBI taxonomy. The bar width represents 100 species. The Y-axis shows the chloroplast genes, which were classified by different chloroplast regions. Gray boxes indicate absence of genes. Red boxes indicate stop codons in genes. Blue boxes indicate unknown nucleotides ( N ) in genes. IR inverted repeat, LSC large single-copy region, SSC small single-copy region
Figure Legend Snippet: Chloroplast genome structure and gene expression across tracheophytes. These 658 chloroplast genomes were downloaded from NCBI Organelle Resources. The X-axis indicates the taxonomy of the chloroplast genome species following the Angiosperm Phylogeny Group III system and NCBI taxonomy. The bar width represents 100 species. The Y-axis shows the chloroplast genes, which were classified by different chloroplast regions. Gray boxes indicate absence of genes. Red boxes indicate stop codons in genes. Blue boxes indicate unknown nucleotides ( N ) in genes. IR inverted repeat, LSC large single-copy region, SSC small single-copy region

Techniques Used: Expressing

20) Product Images from "Evolutionary and network analysis of virus sequences from infants infected with an Australian recombinant strain of human parechovirus type 3"

Article Title: Evolutionary and network analysis of virus sequences from infants infected with an Australian recombinant strain of human parechovirus type 3

Journal: Scientific Reports

doi: 10.1038/s41598-017-04145-2

Maximum Likelihood (ML) phylogenetic tree based on the capsid encoding region from nucleotide 701–3013 of the 18 Australian HPeV3 sequences together with the closest related Yamagata 2011 virus sequences. Sequences were aligned using Clustal W and phylogenetic analysis was conducted using MEGA 6 and the Maximum Likelihood (ML) method based on the Tamura-Nei model 51 . The tree with the highest log likelihood is shown. Bootstrap test involved 1000 replicates to determine reliability of the inferred tree. The numbers at nodes represent bootstrap values. Branch lengths are scaled according to the numbers of nucleotide substitutions per site. Details of the samples are given in Table 1 and in the text. Samples 759204, 759205 and 759207 are the closest related Yamagata 2011 lineage virus sequences and taken from NCBI with the corresponding accession numbers: AB759204, AB759205, AB759207. Based on information from AB759206 (HPeV3 Yamagata 2011 lineage 39 ), the structural/capsid coding region is from nucleotide 701–3013 and the nonstructural protein coding region from 3014–7231 and inferred from that the 5′-UTR spans nucleotide 1-700 and the 3′-UTR from 7232–7334 including 12 As of the poly-A tail. A) Midpoint rooted tree and B) rooted on the closest related non-Australian sequence, AB759204.
Figure Legend Snippet: Maximum Likelihood (ML) phylogenetic tree based on the capsid encoding region from nucleotide 701–3013 of the 18 Australian HPeV3 sequences together with the closest related Yamagata 2011 virus sequences. Sequences were aligned using Clustal W and phylogenetic analysis was conducted using MEGA 6 and the Maximum Likelihood (ML) method based on the Tamura-Nei model 51 . The tree with the highest log likelihood is shown. Bootstrap test involved 1000 replicates to determine reliability of the inferred tree. The numbers at nodes represent bootstrap values. Branch lengths are scaled according to the numbers of nucleotide substitutions per site. Details of the samples are given in Table 1 and in the text. Samples 759204, 759205 and 759207 are the closest related Yamagata 2011 lineage virus sequences and taken from NCBI with the corresponding accession numbers: AB759204, AB759205, AB759207. Based on information from AB759206 (HPeV3 Yamagata 2011 lineage 39 ), the structural/capsid coding region is from nucleotide 701–3013 and the nonstructural protein coding region from 3014–7231 and inferred from that the 5′-UTR spans nucleotide 1-700 and the 3′-UTR from 7232–7334 including 12 As of the poly-A tail. A) Midpoint rooted tree and B) rooted on the closest related non-Australian sequence, AB759204.

Techniques Used: Sequencing

Related Articles

Selection:

Article Title: The variome of pneumococcal virulence factors and regulators
Article Snippet: .. Definition of the study population set and determination of the optimal representation of the entire population of pneumococci The search and selection of the Streptococcus pneumoniae strains for the analysis in this study was done using the microbial database of the “National Center for Biotechnology Information ” NCBI ( http://www.ncbi.nlm.nih.gov/genome ) [ ]. ..

Mass Spectrometry:

Article Title: Protein composition of the occlusion bodies of Epinotia aporema granulovirus
Article Snippet: .. Analysis of MS data Q Exactive raw data was processed using Proteome DiscovererTM software (version 2.1.1.21, Thermo Scientific) and searched against EpapGV protein database downloaded from NCBI (accession number NC_018875, National Center for Biotechnology Information; www.ncbi.nlm.nih.gov ) digested with trypsin with a maximum of one missed cleavage per peptide. .. Proteome DiscovererTM searches were performed with a precursor mass tolerance of 10 ppm and product ion tolerance of 0.05 Da.

Construct:

Article Title: Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code
Article Snippet: .. To construct the pathway for aaRS evolution, NCBI (National Center for Biotechnology Information) Blast tools were used with relaxed search metrics to identify the closest apparent relationships between aaRS proteins. ..

CTL Assay:

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

Generated:

Article Title: Characterization and Pharmacological Properties of a Novel Multifunctional Kunitz Inhibitor from Erythrina velutina Seeds
Article Snippet: .. In silico alignment analyses The peptide sequences generated were examined and compared to Kunitz-type inhibitor sequences deposited in the NCBI (National Center for Biotechnology Information, www. ncbi.nlm.nih.gov) database using the BLASTp serch tool . .. EvTI sequences that showed highest identities with other inhibitors were aligned by using the BioEdit computer program v. 7.0.9.0 with the ClustalW multiple alignment tool .

In Silico:

Article Title: Characterization and Pharmacological Properties of a Novel Multifunctional Kunitz Inhibitor from Erythrina velutina Seeds
Article Snippet: .. In silico alignment analyses The peptide sequences generated were examined and compared to Kunitz-type inhibitor sequences deposited in the NCBI (National Center for Biotechnology Information, www. ncbi.nlm.nih.gov) database using the BLASTp serch tool . .. EvTI sequences that showed highest identities with other inhibitors were aligned by using the BioEdit computer program v. 7.0.9.0 with the ClustalW multiple alignment tool .

Polyacrylamide Gel Electrophoresis:

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

Sequencing:

Article Title: Intestinal peptidases form functional complexes with the neutral amino acid transporter B0AT1
Article Snippet: .. Identification of proteins homologous to mouse APN was conducted using the NCBI (National Centre for Biotechnology Information)'s BlastP protein sequence search and alignment tool ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ). ..

SDS Page:

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

Software:

Article Title: Protein composition of the occlusion bodies of Epinotia aporema granulovirus
Article Snippet: .. Analysis of MS data Q Exactive raw data was processed using Proteome DiscovererTM software (version 2.1.1.21, Thermo Scientific) and searched against EpapGV protein database downloaded from NCBI (accession number NC_018875, National Center for Biotechnology Information; www.ncbi.nlm.nih.gov ) digested with trypsin with a maximum of one missed cleavage per peptide. .. Proteome DiscovererTM searches were performed with a precursor mass tolerance of 10 ppm and product ion tolerance of 0.05 Da.

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    Biotechnology Information biotechnology information ncbi
    Distribution of BTLs from embryophites in six groups. Heat map representation of the number of BTLs from the 29 species in each one of the six groups by a gray scale. The species tree displayed to the left is adapted from the National Center of Biotechnology Information <t>(NCBI)</t> taxonomy server ( <t>http://www.ncbi.nlm.nih.gov/Taxonomy</t> ). The total number of genes in each group is shown at the bottom (the catalog of the 396 BTLs in 6 groups in displayed in Table S4 ). The species tree is the same as in Figure 2 . Novel sequence LOGOs mapped to regions III and V on each group are displayed below the heat map; the occurrence for each of these LOGOs is more than 5%.
    Biotechnology Information Ncbi, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 94/100, based on 1511 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Biotechnology Information protein information resource ncbi national center
    The cross-reference among different types of gene identifiers is improved by the DAVID Gene Concept. A. As global examples, four popular types of protein identifiers <t>(PIR</t> ID, UniProt Accession, RefSeq Protein, and GenPept Accession) are only cross-referenced partially by <t>NCBI</t> Entrez Gene (EG), UniProt UniRef100 (UP), and PIR NRef100 (NF). B. The DAVID Gene Concept, a single-linkage algorithm, iteratively agglomerates all types of gene IDs, belonging to the same gene entry, for example, ubiquitin specific peptidase 8 (USP8) , into one DAVID gene cluster (ID 2859041). Such integration makes the cross-reference of different types of gene IDs more comprehensive than that in each of the original databases, particularly for the IDs across NCBI and UniProt systems.
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    Image Search Results


    Distribution of BTLs from embryophites in six groups. Heat map representation of the number of BTLs from the 29 species in each one of the six groups by a gray scale. The species tree displayed to the left is adapted from the National Center of Biotechnology Information (NCBI) taxonomy server ( http://www.ncbi.nlm.nih.gov/Taxonomy ). The total number of genes in each group is shown at the bottom (the catalog of the 396 BTLs in 6 groups in displayed in Table S4 ). The species tree is the same as in Figure 2 . Novel sequence LOGOs mapped to regions III and V on each group are displayed below the heat map; the occurrence for each of these LOGOs is more than 5%.

    Journal: PLoS ONE

    Article Title: Expansion and Diversification of BTL Ring-H2 Ubiquitin Ligases in Angiosperms: Putative Rabring7/BCA2 Orthologs

    doi: 10.1371/journal.pone.0072729

    Figure Lengend Snippet: Distribution of BTLs from embryophites in six groups. Heat map representation of the number of BTLs from the 29 species in each one of the six groups by a gray scale. The species tree displayed to the left is adapted from the National Center of Biotechnology Information (NCBI) taxonomy server ( http://www.ncbi.nlm.nih.gov/Taxonomy ). The total number of genes in each group is shown at the bottom (the catalog of the 396 BTLs in 6 groups in displayed in Table S4 ). The species tree is the same as in Figure 2 . Novel sequence LOGOs mapped to regions III and V on each group are displayed below the heat map; the occurrence for each of these LOGOs is more than 5%.

    Article Snippet: The phylogenies for Rabring7/BCA2/BTLs, obtained with NJ, ML, and MP, were assessed to compare their agree with conventional taxonomic classification in Order, Family and Genera; got from the National Center of Biotechnology Information (NCBI) taxonomy server http://www.ncbi.nlm.nih.gov/Taxonomy .

    Techniques: Sequencing

    Number of retrieved Rabring7/BCA2/BTLs in eukaryotes. The phylogenetic relationship between thirty-three viridiplantae, forty-one animal, eighteen fungal, and fifteen protist genomes is displayed in a circle. Relationships were adapted from the National Center of Biotechnology Information (NCBI) taxonomy server ( http://www.ncbi.nlm.nih.gov/Taxonomy ). The color code for major group f organisms is shown at the bottom. The species abbreviations are listed in Table S1 and the genes are listed in Tables S2 and S4 .

    Journal: PLoS ONE

    Article Title: Expansion and Diversification of BTL Ring-H2 Ubiquitin Ligases in Angiosperms: Putative Rabring7/BCA2 Orthologs

    doi: 10.1371/journal.pone.0072729

    Figure Lengend Snippet: Number of retrieved Rabring7/BCA2/BTLs in eukaryotes. The phylogenetic relationship between thirty-three viridiplantae, forty-one animal, eighteen fungal, and fifteen protist genomes is displayed in a circle. Relationships were adapted from the National Center of Biotechnology Information (NCBI) taxonomy server ( http://www.ncbi.nlm.nih.gov/Taxonomy ). The color code for major group f organisms is shown at the bottom. The species abbreviations are listed in Table S1 and the genes are listed in Tables S2 and S4 .

    Article Snippet: The phylogenies for Rabring7/BCA2/BTLs, obtained with NJ, ML, and MP, were assessed to compare their agree with conventional taxonomic classification in Order, Family and Genera; got from the National Center of Biotechnology Information (NCBI) taxonomy server http://www.ncbi.nlm.nih.gov/Taxonomy .

    Techniques:

    Functional categories and their corresponding percentages in the GCMN proteome. Molecular function ( A ), biological process ( B ), and clusters of orthologous groups (COG) ( C ) were analyzed using the online bioinformatic tools PANTHER ( http://www.pantherdb.org/ ) and COGnitor provided by the NCBI database ( http://www.ncbi.nlm.nih.gov/COG/old/xognitor.html ).

    Journal: Proteome Science

    Article Title: Human giant congenital melanocytic nevus exhibits potential proteomic alterations leading to melanotumorigenesis

    doi: 10.1186/1477-5956-10-50

    Figure Lengend Snippet: Functional categories and their corresponding percentages in the GCMN proteome. Molecular function ( A ), biological process ( B ), and clusters of orthologous groups (COG) ( C ) were analyzed using the online bioinformatic tools PANTHER ( http://www.pantherdb.org/ ) and COGnitor provided by the NCBI database ( http://www.ncbi.nlm.nih.gov/COG/old/xognitor.html ).

    Article Snippet: Bioinformatics analysis A systemic bioinformatics analysis of the GCMN proteome was conducted using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING 8.3) [ ], the Protein Analysis Through Evolutionary Relationships classification system (PANTHER 7.0) [ ], the National Center for Biotechnology Information (NCBI) COG database [ ], Cytoscape, and ClueGO [ ].

    Techniques: Functional Assay

    Gene structures and isoforms for the human and mouse LIPH genes. Derived from AceView website http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/ (Thierry-Mieg and Thierry-Mieg 2006 ); the major isoform variants are shown with capped 5′- and 3′-ends for the predicted mRNA sequences; introns and coding exons are shown; miRNA binding sites were identified for the LIPH genes (shown as stars ); the direction for transcription is shown; 3′-UTR 3′-untranslated region; a scale is shown in base pairs (bps); coding exons are in pink ; untranslated 5′- and 3′-regions are shown as open rectangles

    Journal: 3 Biotech

    Article Title: Comparative structures and evolution of vertebrate lipase H (LIPH) genes and proteins: a relative of the phospholipase A1 gene families

    doi: 10.1007/s13205-012-0087-z

    Figure Lengend Snippet: Gene structures and isoforms for the human and mouse LIPH genes. Derived from AceView website http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/ (Thierry-Mieg and Thierry-Mieg 2006 ); the major isoform variants are shown with capped 5′- and 3′-ends for the predicted mRNA sequences; introns and coding exons are shown; miRNA binding sites were identified for the LIPH genes (shown as stars ); the direction for transcription is shown; 3′-UTR 3′-untranslated region; a scale is shown in base pairs (bps); coding exons are in pink ; untranslated 5′- and 3′-regions are shown as open rectangles

    Article Snippet: Vertebrate LIPH gene and protein identification Basic local alignment search tool (BLAST) studies were undertaken using web tools from the National Center for Biotechnology Information (NCBI) ( http://www.blast.ncbi.nlm.nih.gov/Blast.cgi ) (Altschul et al. ).

    Techniques: Derivative Assay, Binding Assay

    The cross-reference among different types of gene identifiers is improved by the DAVID Gene Concept. A. As global examples, four popular types of protein identifiers (PIR ID, UniProt Accession, RefSeq Protein, and GenPept Accession) are only cross-referenced partially by NCBI Entrez Gene (EG), UniProt UniRef100 (UP), and PIR NRef100 (NF). B. The DAVID Gene Concept, a single-linkage algorithm, iteratively agglomerates all types of gene IDs, belonging to the same gene entry, for example, ubiquitin specific peptidase 8 (USP8) , into one DAVID gene cluster (ID 2859041). Such integration makes the cross-reference of different types of gene IDs more comprehensive than that in each of the original databases, particularly for the IDs across NCBI and UniProt systems.

    Journal: BMC Bioinformatics

    Article Title: DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

    doi: 10.1186/1471-2105-8-426

    Figure Lengend Snippet: The cross-reference among different types of gene identifiers is improved by the DAVID Gene Concept. A. As global examples, four popular types of protein identifiers (PIR ID, UniProt Accession, RefSeq Protein, and GenPept Accession) are only cross-referenced partially by NCBI Entrez Gene (EG), UniProt UniRef100 (UP), and PIR NRef100 (NF). B. The DAVID Gene Concept, a single-linkage algorithm, iteratively agglomerates all types of gene IDs, belonging to the same gene entry, for example, ubiquitin specific peptidase 8 (USP8) , into one DAVID gene cluster (ID 2859041). Such integration makes the cross-reference of different types of gene IDs more comprehensive than that in each of the original databases, particularly for the IDs across NCBI and UniProt systems.

    Article Snippet: Abbreviations DAVID: Database for Annotation, Visualization and Integrated Discovery PIR: Protein Information Resource NCBI: National Center for Biotechnology Information BLAST: Basic Local Alignment Search Tool EMBL: European Molecular Biology Laboratory DDBJ: DNA Data Bank of Japan RefSeq: Reference Sequence GO: Gene Ontology SMART: Simple Modular Architecture Research Tool DID: DAVID Identifier EG: Entrez Gene UP: UniProt-UniRef NF: PIR-NRef OMIM: Online Mendelian Inheritance in Man Pfam: Protein Family LIB: Laboratory of Immunopathogenesis and Bioinformatics

    Techniques: