Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: The 50 most abundant transcripts from the unfed, virgin adult male Dermacentor variabilis Illumina 1st leg transcriptome.

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Binding Assay, Activity Assay

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: The 50 most abundant transcripts from the unfed, virgin adult male Dermacentor variabilis Illumina 4th leg transcriptome.

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Binding Assay

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Putative transcripts involved in chemoreceptor signal transduction identified exclusively in the Haller’s organ spf transcriptome of unfed, virgin adult male Dermacentor variabilis and their respective tick, nematode and insect matches with the lowest expect value ( e -value). GenBank accession numbers are listed in Appendix A .

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Transduction

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Phylogenetic relationship of transcripts putatively encoding lipocalins (Lip) identified in the Haller’s organ spf (contig 84287) and the Illumina 1st and 4th leg transcriptomes (contigs 42763, 1st legs; contig 466, 4th legs) of unfed, virgin adult male Dermacentor variabilis with lipocalins from Amblyomma triste, Ixodes ricinus, Rhipicephalus microplus and Rattus norvegicus . The phylogenetic tree shows the branch relation of chemosensory lipocalins (red branch) with non-chemosensory lipocalins. Tick putative lipocalins are highlighted with a blue branch color. Acronyms are as follows: first letter of the genus and species ( Amblyomma triste , At; Ixodes ricinus , Ir; Rattus norvegicus , Rn; Rhipicephalus microplus , Rm) followed by the protein name (OBlip or Lip). Putative lipocalin transcripts are boxed. The tree was constructed using Maximum likelihood phylogenetic analysis and bootstrapping set to 500 iterations. Branch values listed are bootstrap percentages (percent confidence), scale set to 20%. A comprehensive list of acronyms and associated GenBank accession numbers are listed in .

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Construct

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Phylogenetic relationship of transcripts putatively encoding G-protein coupled receptors (GPCR) identified exclusively in the Haller’s organ spf transcriptome (contigs 72702, 83622) of unfed, virgin adult male Dermacentor variabilis with their top GenBank BLAST hits (lowest expect value; ) and GPCRs of known clade annotation from Amblyomma americanum , Amblyomma cajennense , Amblyomma triste , Drosophila melanogaster , Ixodes ricinus , Ixodes scapularis , Rhipicephalus microplus , and Rhipicephalus pulchellus . The phylogenetic tree shows four clades, each represented by the following branch colors: blue = clade A; purple = clade C; green = clade D; red = clade B. Acronyms are as follows: first letter of the genus and species ( Amblyomma americanum , Aa; Amblyomma cajennense , Ac; Amblyomma sculptum , As; Amblyomma triste , At; Drosophila melanogaster, Dm; Ixodes ricinus , Ir; Ixodes scapularis , Is; Rhipicephalus microplus , Rm; Rhipicephalus pulchellus , Rp) followed by the protein name (GPCR) and the letter of the associated clade (A, B, and C) or GenBank accession number (JAT99,189.1, EEC06829.1). Putative GPCR transcripts are boxed. The tree was constructed using Maximum likelihood phylogenetic analysis and bootstrapping set to 500 iterations. Branch values listed are bootstrap percentages (percent confidence), scale set to 20%. A comprehensive list of acronyms and associated GenBank accession numbers are listed in .

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Construct

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Phylogenetic relationship of transcripts putatively encoding G-protein α subunits (Gα), one transcript identified in the Haller’s organ spf transcriptome (contig 13937) and transcripts found common in the Illumina 1st and Illumina 4th leg transcriptomes (contigs 14072 and 46297, 1st legs; contigs 2423 and 13329, 4th legs) of unfed, virgin adult male Dermacentor variabilis with Gα subunits of known clade annotation from Caenorhabditis elegans and insects. The phylogenetic tree shows four clades, each represented by the following branch colors: red = Gαi/o clade; green = Gαq clade; purple = Gαq12/13 clade; blue = Gαs clade. Acronyms are as follows: first letter of the genus and species ( Anopheles aquasalis , Aa; Anopheles gambiae , Ag; Drosophila melanogaster , Dm; Caenorhabditis elegans , Ce) followed by the protein name (Gα) and the letter/number of the associated clade. Putative Gα subunit transcripts are boxed. The tree was constructed using Maximum likelihood phylogenetic analysis and bootstrapping set to 500 iterations. Branch values listed are bootstrap percentages (percent confidence), scale set to 20%. A comprehensive list of acronyms and associated GenBank accession numbers are listed in .

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Construct

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Multiple sequence alignment (Clustal Ω) of the deduced amino acid sequence for the putative β-arrestin (contig 1853) identified exclusively in the Haller’s organ spf transcriptome of unfed virgin adult male Dermacentor variabilis versus the Caenorhabditis elegans and Drosophila melanogaster β-arrestins (accession no. CCD67242.1 and AAF32365.1, respectively). Asterisks (*) denote conserved residues, colons (:) indicate conservation between groups of strongly similar properties scoring >0.5 in the Gonnet PAM 250 matrix, and periods (.) indicate conservation between groups of weakly similar properties scoring ≤0.5 on the Gonnet PAM 250 matrix. The solid black bar shows the arrestin amino terminal domain, and the dashed black bar shows the arrestin carboxyl terminal domain. The acronym consists of the first letter of genus and species ( Caenorhabditis elegans , Ce; Drosophila melanogaster , Dm) followed by the protein name (BArr).

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Sequencing

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Putative transcripts involved in chemoreceptor signal modulation/termination and xenobiotic metabolism identified exclusively in the Haller’s organ spf transcriptome of unfed, virgin adult male Dermacentor variabilis and their respective tick, nematode and insect matches with the lowest expect value ( e -value). GenBank accession numbers are listed in Appendix A .

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Phylogenetic relationship of transcripts putatively encoding cytochrome P450s (CYP or P450; contigs 1691, 6898, 14383 and 69591) identified in the Haller’s organ spf transcriptome of unfed, virgin adult male Dermacentor variabilis with P450s of known clan annotation from Ixodes scapularis (Is). The phylogenetic tree shows four P450 clades, each represented by a branch color as follows: green = CYP2 clade; red = CYP3 clade; blue = CYP4 clade; purple = mitochondrial CYP or CYPmit clade. Acronyms consist of the first letter of the genus and species (Is) followed by the protein name (CYP) and the number or abbreviation (mit = mitochondrial) of the associated clade. Putative P450s transcripts are boxed. The tree was constructed using Maximum likelihood phylogenetic analysis and bootstrapping set to 500 iterations. Branch values listed are bootstrap percentages (percent confidence), scale set to 20%. A comprehensive list of acronyms and associated GenBank accession numbers are listed in .

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Construct

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Phylogenetic relationship of transcripts putatively encoding glutathione S-transferases (GST; contigs 4931 and 12057) identified in the Haller’s organ spf transcriptome of unfed, virgin adult male Dermacentor variabilis with GSTs of known clade annotation from Ixodes scapularis (Is) . The phylogenetic tree shows 5 GST clades, each represented by a different branch color as follows: red = epsilon GST clade; blue = delta GST clade; green = mu GST clade; purple = omega GST clade; yellow = zeta GST clade. Acronyms consist of the first letter of the genus and species (Is), followed by protein name (GST) and the first letter of the associated clade (delta, D; epsilon, E; omega, O; mu, M; zeta, Z); acronyms are numbered 1, 2 and 3 to differentiate distinct sequences. Putative GST transcripts are boxed. The tree was constructed using Maximum likelihood phylogenetic analysis and bootstrapping set to 500 iterations. Branch values listed are bootstrap percentages (percent confidence), scale set to 20%. A comprehensive list of acronyms and associated GenBank accession numbers are listed in .

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Construct

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Observed behavior in response to the removal of either the 1st or 4th pairs of legs in unfed, virgin adult D. variabilis . ( A ) Time to rabbit ( Oryctolagus cuniculus ) and attachment by tick. Replicates of 4, with a mixed population of 15 female and 15 male ticks; ( B ) Petri dish assay two choice repellency assay. Replicates of 3 and 6 were conducted for the control and treatment, respectively, with a mixed population of 4 female and 4 male ticks; ( C ) Relative mRNA expression (Δ C t) of the chemosensory proteins β-arrestin, G-protein α o subunit (Gαo) and G-protein coupled receptor (GPCR) in unfed versus fully blood fed adult female and male D. variabilis after normalization to expression levels of glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Replicates of 5, using 2ng cDNA, 10 μL reactions. Statistical analyses were performed using an ANOVA (analysis of variance statistical model) and a Sidak’s multiple comparison test (* p < 0.05; error bars = ±1 SEM, standard error of the mean).

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques: Petri Dish Assay, Control, Expressing, Comparison

Journal: International Journal of Molecular Sciences

Article Title: Tick Haller’s Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects

doi: 10.3390/ijms18071563

Figure Lengend Snippet: Comprehensive list of the acronyms presented in alignments and phylogenetic trees, with the identifying species and GenBank accession numbers, and proteins used during tBLASTn searches of the Illumina 1st and 4th leg BLAST databases.

Article Snippet: Lastly, using the NCBI BLAST+ toolkit and the “makeBLASTdb” UNIX coding, the Illumina 1st leg transcriptome fasta file was used to create a BLASTable database.

Techniques:

Journal: PLOS ONE

Article Title: Learning important common data elements from shared study data: The All of Us program analysis

doi: 10.1371/journal.pone.0283601

Figure Lengend Snippet: Subset of CRF elements (ordered by descending event count).

Article Snippet: Are you covered by health insurance or some other kind of health care plan [PhenX] , LOINC , 931119 , Yes , LOINC , 554459 , 59.5%.

Techniques: Isolation

Journal: PLOS ONE

Article Title: Learning important common data elements from shared study data: The All of Us program analysis

doi: 10.1371/journal.pone.0283601

Figure Lengend Snippet: Initiative CDEs answered by more than 99.9% of participants.

Article Snippet: Are you covered by health insurance or some other kind of health care plan [PhenX] , LOINC , 931119 , Yes , LOINC , 554459 , 59.5%.

Techniques:

Journal: PLOS ONE

Article Title: Learning important common data elements from shared study data: The All of Us program analysis

doi: 10.1371/journal.pone.0283601

Figure Lengend Snippet: Examples of CRF element-value combinations.

Article Snippet: Are you covered by health insurance or some other kind of health care plan [PhenX] , LOINC , 931119 , Yes , LOINC , 554459 , 59.5%.

Techniques:

Journal: PLOS ONE

Article Title: Learning important common data elements from shared study data: The All of Us program analysis

doi: 10.1371/journal.pone.0283601

Figure Lengend Snippet: Elements included in both EHR and CRF data.

Article Snippet: Are you covered by health insurance or some other kind of health care plan [PhenX] , LOINC , 931119 , Yes , LOINC , 554459 , 59.5%.

Techniques:

Journal: Journal of Imaging

Article Title: A Soft Coprocessor Approach for Developing Image and Video Processing Applications on FPGAs

doi: 10.3390/jimaging8020042

Figure Lengend Snippet: From text-based DFG to hardware platform through Xilinx SDK.

Article Snippet: This code is for the Xilinx SDK after the hardware platform has already been defined and synthesized.

Techniques: