Journal: PLoS ONE

Article Title: Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

doi: 10.1371/journal.pone.0038499

Figure Lengend Snippet: Workflow of the sequences analysis, from raw data to assignment.

Article Snippet: The aforementioned databases were scanned using the BlastN and BlastX algorithms provided by Paracel Blast (Striking Development), a software capable of executing searches on multiple non-shared-memory processors simultaneously.

Techniques: Sequencing

Journal: Wound Repair and Regeneration

Article Title: A multimodel regime for evaluating effectiveness of antimicrobial wound care products in microbial biofilms

doi: 10.1111/wrr.12806

Figure Lengend Snippet: Log CFU/biofilm values of LMBM multispecies biofilm containing SA, S. aureus HCMC 6‐1, EF, E. faecium 700 221, and PA, P. aeruginosa PAO1. Treatments that share the same letter are not significantly different ( P < .05)

Article Snippet: Leading wound gel products representing the most commonly used antimicrobials or presenting claims affecting biofilm were evaluated for effectiveness in microbial biofilms: BlastX Antimicrobial Wound Gel (Next Science LLC, Jacksonville, Florida) containing benzalkonium chloride (BAC), Iodosorb Cadexomer Iodine Gel (Smith & Nephew Medical Ltd, Hull, England) containing cadexomer iodine (CI), Prontosan Wound Gel X (BBraun Medical, Inc., Melsunge, Germany) containing polyhexamethylene biguanide (PHMB), Octenilin Wound Gel (Schülke & Mayr GmbH, Norderstedt, Germany) containing octenidine (OCT), SilvaSorb Silver Antimicrobial Wound Gel (Medline Industries, Inc., Mundelein, IL) containing silver (AG), Anasept Antimicrobial Skin & Wound Gel (Anacapa Technologies, Inc., San Dimas, CA) containing hypochlorous acid (HCA), and PluroGel Burn and Wound Dressing (Medline Industries, Inc., Northfield, Illinois) containing poloxamer 188, a nonionic surfactant (POL).

Techniques:

Journal: Wound Repair and Regeneration

Article Title: A multimodel regime for evaluating effectiveness of antimicrobial wound care products in microbial biofilms

doi: 10.1111/wrr.12806

Figure Lengend Snippet: Log CFU/biofilm values of MKL multispecies biofilm containing SA ‐ S. aureus HCMC 6‐1, PA, P. aeruginosa PAO1, and CA, Candida albicans SC3514. Treatments that share the same letter are not significantly different ( P < .05)

Article Snippet: Leading wound gel products representing the most commonly used antimicrobials or presenting claims affecting biofilm were evaluated for effectiveness in microbial biofilms: BlastX Antimicrobial Wound Gel (Next Science LLC, Jacksonville, Florida) containing benzalkonium chloride (BAC), Iodosorb Cadexomer Iodine Gel (Smith & Nephew Medical Ltd, Hull, England) containing cadexomer iodine (CI), Prontosan Wound Gel X (BBraun Medical, Inc., Melsunge, Germany) containing polyhexamethylene biguanide (PHMB), Octenilin Wound Gel (Schülke & Mayr GmbH, Norderstedt, Germany) containing octenidine (OCT), SilvaSorb Silver Antimicrobial Wound Gel (Medline Industries, Inc., Mundelein, IL) containing silver (AG), Anasept Antimicrobial Skin & Wound Gel (Anacapa Technologies, Inc., San Dimas, CA) containing hypochlorous acid (HCA), and PluroGel Burn and Wound Dressing (Medline Industries, Inc., Northfield, Illinois) containing poloxamer 188, a nonionic surfactant (POL).

Techniques:

Journal: Wound Repair and Regeneration

Article Title: A multimodel regime for evaluating effectiveness of antimicrobial wound care products in microbial biofilms

doi: 10.1111/wrr.12806

Figure Lengend Snippet: Log CFU/excision values of SA— S. aureus Xen29 biofilms in nude mice. For 2×, treatments were applied at T0 and T24 hours, then recovered at 48 hours. For 1×, treatments were applied at T0, then recovered at 48 hours. *Treatments are significantly different from untreated control ( P < .05)

Article Snippet: Leading wound gel products representing the most commonly used antimicrobials or presenting claims affecting biofilm were evaluated for effectiveness in microbial biofilms: BlastX Antimicrobial Wound Gel (Next Science LLC, Jacksonville, Florida) containing benzalkonium chloride (BAC), Iodosorb Cadexomer Iodine Gel (Smith & Nephew Medical Ltd, Hull, England) containing cadexomer iodine (CI), Prontosan Wound Gel X (BBraun Medical, Inc., Melsunge, Germany) containing polyhexamethylene biguanide (PHMB), Octenilin Wound Gel (Schülke & Mayr GmbH, Norderstedt, Germany) containing octenidine (OCT), SilvaSorb Silver Antimicrobial Wound Gel (Medline Industries, Inc., Mundelein, IL) containing silver (AG), Anasept Antimicrobial Skin & Wound Gel (Anacapa Technologies, Inc., San Dimas, CA) containing hypochlorous acid (HCA), and PluroGel Burn and Wound Dressing (Medline Industries, Inc., Northfield, Illinois) containing poloxamer 188, a nonionic surfactant (POL).

Techniques: Control

Journal: BMC Genomics

Article Title: Comparative analysis of expressed sequence tags from three castes and two life stages of the termite Reticulitermes flavipes

doi: 10.1186/1471-2164-11-463

Figure Lengend Snippet: In silico analysis of transcript bias in contigs formed from all sequences in each library, the ten highest R-values were analyzed using BLASTX (e-value ≤1E -10 ).

Article Snippet: Both singletons and contigs were assigned putative functions using a batch BLASTX reference search from the non-redundant protein database using BlastStation (v2.61, TMSoftware, Arcadia, CA), with an e-value ≤1e -10 .

Techniques: In Silico

Journal: BMC Genomics

Article Title: Comparative analysis of expressed sequence tags from three castes and two life stages of the termite Reticulitermes flavipes

doi: 10.1186/1471-2164-11-463

Figure Lengend Snippet: In silico analysis and predicted protein function of 10 contigs with the highest R-value with no putative role assigned by a BLASTX search.

Article Snippet: Both singletons and contigs were assigned putative functions using a batch BLASTX reference search from the non-redundant protein database using BlastStation (v2.61, TMSoftware, Arcadia, CA), with an e-value ≤1e -10 .

Techniques: In Silico, Activity Assay

Journal:

Article Title: Computational Inference of Homologous Gene Structures in the Human Genome

doi: 10.1101/gr.175701

Figure Lengend Snippet: Examples of GenomeScan predictions. GenomeScan was run with GenomeScript, using similarity to available mouse proteins from GenPept Release 118 (June 2000). Two examples are shown. Exons and genes on the forward strand are shown above the sequence line; reverse strand exons and genes are shown below the sequence line. BLASTX hits with P < 0.05 are shown as green blocks above or below the sequence line, according to the reading frame/strand indicated by BLAST. (A) GenBank locus HUMBRCA1 (accession no. L78833). (B) GenBank locus HSU52111 (accession no. U52111). Only the first 140 kbp (of 153 kbp) of the sequence is shown for clarity. The extra predicted exons upstream of PLEXR and SK and the extra predicted gene at ∼118 kb are supported by several human ESTs (accession nos. AW663636, AA514687, AW071821, and others).

Article Snippet: Comparing the GenomeScan output to that of BLASTX and GENSCAN , in many cases it is clear that BLASTX is helping GenomeScan to identify exons missed by GENSCAN in the expected way (e.g., the first five exons of BRCA1 ).

Techniques: Sequencing

Journal:

Article Title: Computational Inference of Homologous Gene Structures in the Human Genome

doi: 10.1101/gr.175701

Figure Lengend Snippet: Exon- and nucleotide-level accuracy of similarity-based gene-prediction programs as a function of protein similarity. (A) Exon-level sensitivity (ESn: percent of exons predicted exactly) and (B) exon-level specificity (ESp: percent of predicted exons exactly correct) were calculated for subsets of the SingleGene dataset and grouped according to the level of BLASTP similarity (in the context of a database search) between the encoded protein and the protein used in the prediction for GenomeScan, Procrustes, and GeneWise as described by Guigó et al. 2000). The definitions of the subsets and number of genes per subset were as follows: 10−5 > P >10−10 (90); 10−10 > P > 10−20 (103); 10−20 > P >10−30 (102); 10−30 > P > 10−40 (97); 10−40 > P >10−60 (114); 10−60 > P > 10−80 (97); 10−80 > P > 10−120 (97); and P < 10−120 (72). For example, 114 of the 175 sequences in the SingleGene dataset had a homolog with BLAST P-value in the range 10−60< P < 10−40. For sequences in this subset, GenomeScan was run using the results of a BLASTX run of the genomic sequence against the top hit in the nonredundant protein database that had sequence similarity in the desired range (10−40 > P > 10−60). GeneWise and Procrustes data, run using the same peptides as input, are from Guigó et al. (2000). (C) Nucleotide-level sensitivity (NSn: percent of coding nucleotides predicted correctly) and (D) nucleotide-level specificity (NSp: percent of predicted coding nucleotides that are correct). Accuracy statistics on the SingleGene dataset as a whole for the ab initio gene-prediction methods GENSCAN, HMMGene 1.1, and GRAIL 3.1, respectively, were as follows: ESn (0.79, 0.75, 0.47); ESp (0.77, 0.68, 0.61); NSn (0.93, 0.86, 0.68): NSp (0.91, 0.74, 0.94).

Article Snippet: Comparing the GenomeScan output to that of BLASTX and GENSCAN , in many cases it is clear that BLASTX is helping GenomeScan to identify exons missed by GENSCAN in the expected way (e.g., the first five exons of BRCA1 ).

Techniques: Sequencing