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BEI Resources genomic dna
Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic <t>DNA,</t> amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine <t>microbiome</t> composition.
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1) Product Images from "The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization"

Article Title: The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization

Journal: Scientific Reports

doi: 10.1038/s41598-017-11427-2

Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic DNA, amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine microbiome composition.
Figure Legend Snippet: Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic DNA, amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine microbiome composition.

Techniques Used: Generated

2) Product Images from "Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System"

Article Title: Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.00466-17

Limit of detection of B. anthracis assay. (A) Positivity rate for assay cartridges spiked with the indicated numbers of B. anthracis Ames35 genomic DNA equivalents. Ten to 22 reaction mixtures were tested for each concentration shown. (B and C) Positivity rate for blood samples spiked with the indicated numbers of CFU of B. anthracis Sterne (B) and B. anthracis V1B (C). Between 10 and 12 replicates were tested for each concentration. The Gompertz fit curve ( f = a × exp{−exp[−( x − x )]/ b }) and 95% confidence band were generated in SigmaPlot v.13. Cart, filter-based cartridge.
Figure Legend Snippet: Limit of detection of B. anthracis assay. (A) Positivity rate for assay cartridges spiked with the indicated numbers of B. anthracis Ames35 genomic DNA equivalents. Ten to 22 reaction mixtures were tested for each concentration shown. (B and C) Positivity rate for blood samples spiked with the indicated numbers of CFU of B. anthracis Sterne (B) and B. anthracis V1B (C). Between 10 and 12 replicates were tested for each concentration. The Gompertz fit curve ( f = a × exp{−exp[−( x − x )]/ b }) and 95% confidence band were generated in SigmaPlot v.13. Cart, filter-based cartridge.

Techniques Used: Concentration Assay, Generated

3) Product Images from "A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms"

Article Title: A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms

Journal: BMC Microbiology

doi: 10.1186/1471-2180-11-132

Hierarchical clustering of mixed samples demonstrates the resolution capabilities of the UBDA array . This dendogram and heat map illustrates a unique bio-signature pattern obtained from Lactobacillus plantarum , mixed sample (synthetic mixture in a 4:1 ratio of L. plantarum and Streptococcus mitis ), S. mitis , mixed sample (a synthetic mixture of L. plantarum and S. mitis genomic DNA in a ratio of 4:1 with a spike-in of pBluescript plasmid at 50 ng) and pBluescript plasmid. Normalized data from the 9-mer data set were filtered for intensity signals greater than the 20 th percentile. Only intensity signals with a fold change of 5 or greater were included. These 36,059 elements were subjected to hierarchical clustering with Euclidean distance being used as a similarity measure. The signal intensity values were represented on a log 2 scale and range from 8.4 to 13.4.
Figure Legend Snippet: Hierarchical clustering of mixed samples demonstrates the resolution capabilities of the UBDA array . This dendogram and heat map illustrates a unique bio-signature pattern obtained from Lactobacillus plantarum , mixed sample (synthetic mixture in a 4:1 ratio of L. plantarum and Streptococcus mitis ), S. mitis , mixed sample (a synthetic mixture of L. plantarum and S. mitis genomic DNA in a ratio of 4:1 with a spike-in of pBluescript plasmid at 50 ng) and pBluescript plasmid. Normalized data from the 9-mer data set were filtered for intensity signals greater than the 20 th percentile. Only intensity signals with a fold change of 5 or greater were included. These 36,059 elements were subjected to hierarchical clustering with Euclidean distance being used as a similarity measure. The signal intensity values were represented on a log 2 scale and range from 8.4 to 13.4.

Techniques Used: Plasmid Preparation

4) Product Images from "Associations between gut microbial colonization in early life and respiratory outcomes in cystic fibrosis"

Article Title: Associations between gut microbial colonization in early life and respiratory outcomes in cystic fibrosis

Journal: The Journal of pediatrics

doi: 10.1016/j.jpeds.2015.02.049

Comparison of subjects with and without Pseudomonas colonization status in the first six months of life according to microbiome composition using PCA
Figure Legend Snippet: Comparison of subjects with and without Pseudomonas colonization status in the first six months of life according to microbiome composition using PCA

Techniques Used:

Comparison of subjects with and without CF exacerbation in the first six months of life according to microbiome composition using PCA
Figure Legend Snippet: Comparison of subjects with and without CF exacerbation in the first six months of life according to microbiome composition using PCA

Techniques Used:

5) Product Images from "The potential for flower nectar to allow mosquito to mosquito transmission of Francisella tularensis"

Article Title: The potential for flower nectar to allow mosquito to mosquito transmission of Francisella tularensis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0175157

Mosquitoes become colonized with F . tularensis after interacting with flower nectar surrogate. A. Tubes holding a 30% sucrose solution inoculated with F . tularensis were placed within insect chambers for 6 days. As many as six mosquitoes per group were extracted daily, washed with gentamicin to kill surface bacteria, homogenized and plated on media selective for Francisella . Data shown represent the percentage of mosquitoes colonized with F . tularensis LVS (recovery of at least one CFU) on the days indicated and are a combination of three independent experiments. B. DNA was extracted from bacteria isolated from mosquito homogenates plated on media selective for F . tularensis . Only colonies that produced a similar morphology to F . tularensis were selected. The extracted DNA was subjected to PCR using primers specific for mglA of Francisella sp. Agarose gel electrophoresis was used to compare amplicons produced from bacteria isolated from mosquitoes to those generated from bona fide F . tularensis DNA. PCR from only one isolate is shown for simplicity, but all other colonies with similar morphologies produced a similar amplicon band (not shown). PCR reactions lacking Francisella template DNA did not produce amplicons (negative control). C. Cell extracts from isolates were separated by SDS-PAGE and electroblotted onto nitrocellulose. Following blocking, Western blots were probed with an anti-IglC monocolonal antibody. An alkaline-phosphatase anti mouse secondary antibody was used for detection.
Figure Legend Snippet: Mosquitoes become colonized with F . tularensis after interacting with flower nectar surrogate. A. Tubes holding a 30% sucrose solution inoculated with F . tularensis were placed within insect chambers for 6 days. As many as six mosquitoes per group were extracted daily, washed with gentamicin to kill surface bacteria, homogenized and plated on media selective for Francisella . Data shown represent the percentage of mosquitoes colonized with F . tularensis LVS (recovery of at least one CFU) on the days indicated and are a combination of three independent experiments. B. DNA was extracted from bacteria isolated from mosquito homogenates plated on media selective for F . tularensis . Only colonies that produced a similar morphology to F . tularensis were selected. The extracted DNA was subjected to PCR using primers specific for mglA of Francisella sp. Agarose gel electrophoresis was used to compare amplicons produced from bacteria isolated from mosquitoes to those generated from bona fide F . tularensis DNA. PCR from only one isolate is shown for simplicity, but all other colonies with similar morphologies produced a similar amplicon band (not shown). PCR reactions lacking Francisella template DNA did not produce amplicons (negative control). C. Cell extracts from isolates were separated by SDS-PAGE and electroblotted onto nitrocellulose. Following blocking, Western blots were probed with an anti-IglC monocolonal antibody. An alkaline-phosphatase anti mouse secondary antibody was used for detection.

Techniques Used: Isolation, Produced, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Generated, Amplification, Negative Control, SDS Page, Blocking Assay, Western Blot

Mosquitoes transfer F . tularensis from one nectar surrogate source to another. DNA was extracted from bacteria isolated from media selective for F . tularensis . Only colonies that produced a similar morphology to F . tularensis were selected. The extracted DNA was subjected to PCR using primers specific for mglA of Francisella sp. Agarose gel electrophoresis was used to compare amplicons produced from bacteria isolated from nectar surrogate to those generated from bona fide F . tularensis DNA. PCR from only one isolate is shown for simplicity, but all other colonies with similar morphologies produced a similar amplicon band. PCR reactions lacking template DNA did not produce amplicons.
Figure Legend Snippet: Mosquitoes transfer F . tularensis from one nectar surrogate source to another. DNA was extracted from bacteria isolated from media selective for F . tularensis . Only colonies that produced a similar morphology to F . tularensis were selected. The extracted DNA was subjected to PCR using primers specific for mglA of Francisella sp. Agarose gel electrophoresis was used to compare amplicons produced from bacteria isolated from nectar surrogate to those generated from bona fide F . tularensis DNA. PCR from only one isolate is shown for simplicity, but all other colonies with similar morphologies produced a similar amplicon band. PCR reactions lacking template DNA did not produce amplicons.

Techniques Used: Isolation, Produced, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Generated, Amplification

F . tularensis exhibits limited survival in a sucrose solution, a nectar surrogate. F . tularensis bacteria were incubated in TSBc, 30% sucrose, or water. Bacterial suspensions were incubated at ambient temperature, serial diluted and plated to determine CFU at the indicated time points. Graphed values represent mean CFU ± SE of four combined independent experiments. In some cases, error bars are smaller than the graph symbols. Differences in the average number of F . tularensis LVS recovered (CFU/mL) over the course of the assay were determined by repeated measures two-way ANOVA with Tukey’s multiple comparison test as a post hoc analysis comparing the change in bacterial burden between experimental, positive control, and negative control groups (ANOVA, P
Figure Legend Snippet: F . tularensis exhibits limited survival in a sucrose solution, a nectar surrogate. F . tularensis bacteria were incubated in TSBc, 30% sucrose, or water. Bacterial suspensions were incubated at ambient temperature, serial diluted and plated to determine CFU at the indicated time points. Graphed values represent mean CFU ± SE of four combined independent experiments. In some cases, error bars are smaller than the graph symbols. Differences in the average number of F . tularensis LVS recovered (CFU/mL) over the course of the assay were determined by repeated measures two-way ANOVA with Tukey’s multiple comparison test as a post hoc analysis comparing the change in bacterial burden between experimental, positive control, and negative control groups (ANOVA, P

Techniques Used: Incubation, Positive Control, Negative Control

F . tularensis survives in flower nectar. F . tularensis bacteria were incubated in TSBc, yellow squash nectar, or water. Bacterial suspensions were incubated at 22°C, serial diluted and plated to determine CFU at the indicated time points. Graphed values represent mean CFU ± SE of three combined independent experiments. In some cases, error bars are smaller than the graph symbols. Differences in the average number of F . tularensis LVS recovered (CFU/mL) over the course of the assay were determined by repeated measures two-way ANOVA with Tukey’s multiple comparison test as a post hoc analysis comparing the change in bacterial burden between experimental, positive control, and negative control groups (ANOVA, P
Figure Legend Snippet: F . tularensis survives in flower nectar. F . tularensis bacteria were incubated in TSBc, yellow squash nectar, or water. Bacterial suspensions were incubated at 22°C, serial diluted and plated to determine CFU at the indicated time points. Graphed values represent mean CFU ± SE of three combined independent experiments. In some cases, error bars are smaller than the graph symbols. Differences in the average number of F . tularensis LVS recovered (CFU/mL) over the course of the assay were determined by repeated measures two-way ANOVA with Tukey’s multiple comparison test as a post hoc analysis comparing the change in bacterial burden between experimental, positive control, and negative control groups (ANOVA, P

Techniques Used: Incubation, Positive Control, Negative Control

6) Product Images from "Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System"

Article Title: Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.01126-16

Detection of F. tularensis in the blood of infected macaques. Blood samples from macaques infected with F. tularensis Schu S4 were tested by the cartridge-based F. tularensis assay, a manual qPCR reference F. tularensis assay, and blood culture for the
Figure Legend Snippet: Detection of F. tularensis in the blood of infected macaques. Blood samples from macaques infected with F. tularensis Schu S4 were tested by the cartridge-based F. tularensis assay, a manual qPCR reference F. tularensis assay, and blood culture for the

Techniques Used: Infection, Real-time Polymerase Chain Reaction

Analytical sensitivity of PCR2 versus PCR3 for detecting F. tularensis . (A) Positivity rate for assays spiked with the indicated numbers of F. tularensis subsp. tularensis Schu S4 genomic DNA equivalents. Ten spiked samples were tested for each concentration
Figure Legend Snippet: Analytical sensitivity of PCR2 versus PCR3 for detecting F. tularensis . (A) Positivity rate for assays spiked with the indicated numbers of F. tularensis subsp. tularensis Schu S4 genomic DNA equivalents. Ten spiked samples were tested for each concentration

Techniques Used: Concentration Assay

7) Product Images from "Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound"

Article Title: Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound

Journal: Frontiers in Pharmacology

doi: 10.3389/fphar.2020.00246

Diagrammatic representation of the pbgst-ko plasmids and analysis of potential integration. (A,C) Schematic diagram of the pbgst-ko plasmids (top), the endogenous pbgst locus (center), and the predicted integration (bottom). The plasmids, pbgst-ko 1A (A) and pbgst-ko 1B (B) , contained the tgdhfr / ts selectable marker flanked by the 5′ and 3′ fragments of the pbgst gene. The probe used in Southern blot analysis is shown as dashed lines inside the coding region of the tgdhfr/ts . (B,D) Southern analyses using a tgdhfr/ts specific probe. Parasite chromosomes from two independent transfections were separated by CHEF (B) or FIGE (D) . Hybridization with a tgdhfr/ts specific probe shows no integration of the pbgst-ko 1A plasmid into the pbgst locus (B) . Hybridization with a tgdhfr/ts specific probe shows integration into chromosome 7 and not into the endogenous pbgst locus (chromosome 10, right panel) (D) . (E) Schematic diagram of the plasmids pbgst-ko 2A and pbgst-ko 2B (top), the endogenous pbgst locus (center), and the predicted integration (bottom). The pbgst-ko 2 plasmids contained the hdhfr/yfcu , positive-negative selectable marker under the control of the eef1a promoter. The probe used in Southern blot analysis is shown as dashed lines inside the coding region of hdhfr . (F,G) Southern analyses using an hdhfr specific probe. Hybridization with the hdhfr specific probe shows no integration of the corresponding plasmid (lanes 7–10 in F,G ), pbgst-ko 2A or pbgst-ko 2B , into the pbgst locus (chromosome 10, right arrows) in two independent transfections. As a control, transfection targeting the pbmrp (a dispensable gene) shows a successful integration of the pbmrp-ko plasmid into chromosome 14 ( F , lanes 1 and 2 labeled as T5 S1 pbmrp and T5 S2 pbmrp ; and G , lane 1 labeled as T5 S3 pbmrp ). Diagrams are not drawn to scale. M1, H. wingei chromosome marker; M2, S. cerevisiae chromosome marker; T#S#, transfection number, and sample number.
Figure Legend Snippet: Diagrammatic representation of the pbgst-ko plasmids and analysis of potential integration. (A,C) Schematic diagram of the pbgst-ko plasmids (top), the endogenous pbgst locus (center), and the predicted integration (bottom). The plasmids, pbgst-ko 1A (A) and pbgst-ko 1B (B) , contained the tgdhfr / ts selectable marker flanked by the 5′ and 3′ fragments of the pbgst gene. The probe used in Southern blot analysis is shown as dashed lines inside the coding region of the tgdhfr/ts . (B,D) Southern analyses using a tgdhfr/ts specific probe. Parasite chromosomes from two independent transfections were separated by CHEF (B) or FIGE (D) . Hybridization with a tgdhfr/ts specific probe shows no integration of the pbgst-ko 1A plasmid into the pbgst locus (B) . Hybridization with a tgdhfr/ts specific probe shows integration into chromosome 7 and not into the endogenous pbgst locus (chromosome 10, right panel) (D) . (E) Schematic diagram of the plasmids pbgst-ko 2A and pbgst-ko 2B (top), the endogenous pbgst locus (center), and the predicted integration (bottom). The pbgst-ko 2 plasmids contained the hdhfr/yfcu , positive-negative selectable marker under the control of the eef1a promoter. The probe used in Southern blot analysis is shown as dashed lines inside the coding region of hdhfr . (F,G) Southern analyses using an hdhfr specific probe. Hybridization with the hdhfr specific probe shows no integration of the corresponding plasmid (lanes 7–10 in F,G ), pbgst-ko 2A or pbgst-ko 2B , into the pbgst locus (chromosome 10, right arrows) in two independent transfections. As a control, transfection targeting the pbmrp (a dispensable gene) shows a successful integration of the pbmrp-ko plasmid into chromosome 14 ( F , lanes 1 and 2 labeled as T5 S1 pbmrp and T5 S2 pbmrp ; and G , lane 1 labeled as T5 S3 pbmrp ). Diagrams are not drawn to scale. M1, H. wingei chromosome marker; M2, S. cerevisiae chromosome marker; T#S#, transfection number, and sample number.

Techniques Used: Marker, Southern Blot, Transfection, Hybridization, Plasmid Preparation, Labeling

8) Product Images from "High rates of parasite recrudescence following intermittent preventive treatment with sulphadoxine-pyrimethamine during pregnancy in Benin"

Article Title: High rates of parasite recrudescence following intermittent preventive treatment with sulphadoxine-pyrimethamine during pregnancy in Benin

Journal: Malaria Journal

doi: 10.1186/1475-2875-12-195

Prevalence rates of recurrent infections. Plasmodium parasites were counted against 200 leukocytes with a 100 × objective lens under oil immersion. Each qPCR reaction mixture contained 5 μL DNA template in a final volume of 20 μL, 10 μL of Master Mix (Applied Biosystem), both the genus-specific and P. falciparum specific primers and probes detection system (Plasmo/Pf) as described [ 24 ]. Panel A : Prevalence rates of recurrent infections assessed by microscopy (BS) and PCR. Data are shown as pooled (covering the two months following treatment) or split into first and second month (days 7–30 or 31–60). Panel B : Prevalence rates of recurrent infections assessed by PCR according to the IPTp dose received. Data are shown as pooled (covering the two months following treatment) or split into first and second month (days seven-30 or 31–60).
Figure Legend Snippet: Prevalence rates of recurrent infections. Plasmodium parasites were counted against 200 leukocytes with a 100 × objective lens under oil immersion. Each qPCR reaction mixture contained 5 μL DNA template in a final volume of 20 μL, 10 μL of Master Mix (Applied Biosystem), both the genus-specific and P. falciparum specific primers and probes detection system (Plasmo/Pf) as described [ 24 ]. Panel A : Prevalence rates of recurrent infections assessed by microscopy (BS) and PCR. Data are shown as pooled (covering the two months following treatment) or split into first and second month (days 7–30 or 31–60). Panel B : Prevalence rates of recurrent infections assessed by PCR according to the IPTp dose received. Data are shown as pooled (covering the two months following treatment) or split into first and second month (days seven-30 or 31–60).

Techniques Used: Real-time Polymerase Chain Reaction, Microscopy, Polymerase Chain Reaction

9) Product Images from "Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum"

Article Title: Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum

Journal: Microbial Cell Factories

doi: 10.1186/s12934-018-0880-4

Phylogenetic tree of bacterial tannases. Tree showing evolutionary relationships between all bacterial tannases genetically identified to date. The numbers indicate branches lengths. F. nucleatum subsp. polymorphum TanB Fnp is indicated in blue
Figure Legend Snippet: Phylogenetic tree of bacterial tannases. Tree showing evolutionary relationships between all bacterial tannases genetically identified to date. The numbers indicate branches lengths. F. nucleatum subsp. polymorphum TanB Fnp is indicated in blue

Techniques Used:

Purification of recombinant F. nucleatum subsp. polymorphum tannase TanB Fnp . a SDS-PAGE analysis of TanB Fnp fractions obtained before and after His-affinity resin chromatography. b UV absorbance of different fractions obtained after gel filtration chromatography. c SDS-PAGE analysis of fractions obtained after gel filtration chromatography
Figure Legend Snippet: Purification of recombinant F. nucleatum subsp. polymorphum tannase TanB Fnp . a SDS-PAGE analysis of TanB Fnp fractions obtained before and after His-affinity resin chromatography. b UV absorbance of different fractions obtained after gel filtration chromatography. c SDS-PAGE analysis of fractions obtained after gel filtration chromatography

Techniques Used: Purification, Recombinant, SDS Page, Chromatography, Filtration

10) Product Images from "Rapid Focused Sequencing: A Multiplexed Assay for Simultaneous Detection and Strain Typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis"

Article Title: Rapid Focused Sequencing: A Multiplexed Assay for Simultaneous Detection and Strain Typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0056093

30-plex PCR profiles generated from select biothreat agents Ba, Ft , and Yp . Electropherogram obtained from 100 copies of Ba strain Sterne (A); from 1000 copies of Ft subsp. tularensis WY96 (B); and from 100 copies of Yp bv. mediavalis strain KIM10v (C). Note that 1000 copies of Ft DNA are required to detect two of the FAM-labeled targets ( acp A and spe A) due to their high AT content resulting in reduced PCR efficiency.
Figure Legend Snippet: 30-plex PCR profiles generated from select biothreat agents Ba, Ft , and Yp . Electropherogram obtained from 100 copies of Ba strain Sterne (A); from 1000 copies of Ft subsp. tularensis WY96 (B); and from 100 copies of Yp bv. mediavalis strain KIM10v (C). Note that 1000 copies of Ft DNA are required to detect two of the FAM-labeled targets ( acp A and spe A) due to their high AT content resulting in reduced PCR efficiency.

Techniques Used: Polymerase Chain Reaction, Generated, Labeling

10-plex PCR profiles generated from representative Ft strains (left panel) and Yp and Yp NN strains (right panel). The FAM (blue), TMR (black) and ROX (red) labeled products are aligned to emphasize the variant and non-variant fragment sizes observed across these strains. Six of ten fragments ( acp A, pep O, mig R, fop A, tul 4-FTT0900, and igl C) in the 10-plex Ft panel are invariable in length between strains subsp. tularensis SchuS4 and WY96, and subsp. holarctica 14LVS and 425. In Yp 10-plex panel, size variability is observed primarily in 4 loci ( glp D, ail, arg S-YPO2047 and YPO1976). Both Ft 10-plex and Yp 10-plex panels do not have any JOE-labeled (green) primers. For each reaction, 100 genome equivalents of each strain were used as template to PCR.
Figure Legend Snippet: 10-plex PCR profiles generated from representative Ft strains (left panel) and Yp and Yp NN strains (right panel). The FAM (blue), TMR (black) and ROX (red) labeled products are aligned to emphasize the variant and non-variant fragment sizes observed across these strains. Six of ten fragments ( acp A, pep O, mig R, fop A, tul 4-FTT0900, and igl C) in the 10-plex Ft panel are invariable in length between strains subsp. tularensis SchuS4 and WY96, and subsp. holarctica 14LVS and 425. In Yp 10-plex panel, size variability is observed primarily in 4 loci ( glp D, ail, arg S-YPO2047 and YPO1976). Both Ft 10-plex and Yp 10-plex panels do not have any JOE-labeled (green) primers. For each reaction, 100 genome equivalents of each strain were used as template to PCR.

Techniques Used: Polymerase Chain Reaction, Generated, Labeling, Variant Assay

11) Product Images from "A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms"

Article Title: A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms

Journal: BMC Microbiology

doi: 10.1186/1471-2180-11-132

Hierarchical clustering of mixed samples demonstrates the resolution capabilities of the UBDA array . This dendogram and heat map illustrates a unique bio-signature pattern obtained from Lactobacillus plantarum , mixed sample (synthetic mixture in a 4:1 ratio of L. plantarum and Streptococcus mitis ), S. mitis , mixed sample (a synthetic mixture of L. plantarum and S. mitis genomic DNA in a ratio of 4:1 with a spike-in of pBluescript plasmid at 50 ng) and pBluescript plasmid. Normalized data from the 9-mer data set were filtered for intensity signals greater than the 20 th percentile. Only intensity signals with a fold change of 5 or greater were included. These 36,059 elements were subjected to hierarchical clustering with Euclidean distance being used as a similarity measure. The signal intensity values were represented on a log 2 scale and range from 8.4 to 13.4.
Figure Legend Snippet: Hierarchical clustering of mixed samples demonstrates the resolution capabilities of the UBDA array . This dendogram and heat map illustrates a unique bio-signature pattern obtained from Lactobacillus plantarum , mixed sample (synthetic mixture in a 4:1 ratio of L. plantarum and Streptococcus mitis ), S. mitis , mixed sample (a synthetic mixture of L. plantarum and S. mitis genomic DNA in a ratio of 4:1 with a spike-in of pBluescript plasmid at 50 ng) and pBluescript plasmid. Normalized data from the 9-mer data set were filtered for intensity signals greater than the 20 th percentile. Only intensity signals with a fold change of 5 or greater were included. These 36,059 elements were subjected to hierarchical clustering with Euclidean distance being used as a similarity measure. The signal intensity values were represented on a log 2 scale and range from 8.4 to 13.4.

Techniques Used: Plasmid Preparation

12) Product Images from "Rapid Focused Sequencing: A Multiplexed Assay for Simultaneous Detection and Strain Typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis"

Article Title: Rapid Focused Sequencing: A Multiplexed Assay for Simultaneous Detection and Strain Typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0056093

30-plex PCR profiles generated from select biothreat agents Ba, Ft , and Yp . Electropherogram obtained from 100 copies of Ba strain Sterne (A); from 1000 copies of Ft subsp. tularensis WY96 (B); and from 100 copies of Yp bv. mediavalis strain KIM10v (C). Note that 1000 copies of Ft DNA are required to detect two of the FAM-labeled targets ( acp A and spe A) due to their high AT content resulting in reduced PCR efficiency.
Figure Legend Snippet: 30-plex PCR profiles generated from select biothreat agents Ba, Ft , and Yp . Electropherogram obtained from 100 copies of Ba strain Sterne (A); from 1000 copies of Ft subsp. tularensis WY96 (B); and from 100 copies of Yp bv. mediavalis strain KIM10v (C). Note that 1000 copies of Ft DNA are required to detect two of the FAM-labeled targets ( acp A and spe A) due to their high AT content resulting in reduced PCR efficiency.

Techniques Used: Polymerase Chain Reaction, Generated, Labeling

13) Product Images from "Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System"

Article Title: Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.00466-17

Limit of detection of B. anthracis assay. (A) Positivity rate for assay cartridges spiked with the indicated numbers of B. anthracis Ames35 genomic DNA equivalents. Ten to 22 reaction mixtures were tested for each concentration shown. (B and C) Positivity rate for blood samples spiked with the indicated numbers of CFU of B. anthracis Sterne (B) and B. anthracis V1B (C). Between 10 and 12 replicates were tested for each concentration. The Gompertz fit curve ( f = a × exp{−exp[−( x − x )]/ b }) and 95% confidence band were generated in SigmaPlot v.13. Cart, filter-based cartridge.
Figure Legend Snippet: Limit of detection of B. anthracis assay. (A) Positivity rate for assay cartridges spiked with the indicated numbers of B. anthracis Ames35 genomic DNA equivalents. Ten to 22 reaction mixtures were tested for each concentration shown. (B and C) Positivity rate for blood samples spiked with the indicated numbers of CFU of B. anthracis Sterne (B) and B. anthracis V1B (C). Between 10 and 12 replicates were tested for each concentration. The Gompertz fit curve ( f = a × exp{−exp[−( x − x )]/ b }) and 95% confidence band were generated in SigmaPlot v.13. Cart, filter-based cartridge.

Techniques Used: Concentration Assay, Generated

14) Product Images from "A High-Efficiency Superhydrophobic Plasma Separator"

Article Title: A High-Efficiency Superhydrophobic Plasma Separator

Journal: Lab on a chip

doi: 10.1039/c5lc01235j

A sequence of images illustrating the plasma separation process. (A) A 200 μL of blood sample spiked with S. mansoni DNA was loaded into the superhydrophobic plasma separator. (B) When the top cover was closed, the blood was sandwiched between
Figure Legend Snippet: A sequence of images illustrating the plasma separation process. (A) A 200 μL of blood sample spiked with S. mansoni DNA was loaded into the superhydrophobic plasma separator. (B) When the top cover was closed, the blood was sandwiched between

Techniques Used: Sequencing

(A) Recovery efficiency of S. mansoni genomic DNA on our plasma separator at various concentrations. (B) Endpoint, fluorescence images of intercalating dye in three amplification chambers, target DNA amount in each chamber is 10 fg, 1 fg and 0 fg (negative
Figure Legend Snippet: (A) Recovery efficiency of S. mansoni genomic DNA on our plasma separator at various concentrations. (B) Endpoint, fluorescence images of intercalating dye in three amplification chambers, target DNA amount in each chamber is 10 fg, 1 fg and 0 fg (negative

Techniques Used: Fluorescence, Amplification

15) Product Images from "Schistosoma species detection by environmental DNA assays in African freshwaters"

Article Title: Schistosoma species detection by environmental DNA assays in African freshwaters

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0008129

Locations of eDNA sampling sites in the Mbeya Region of Tanzania in 2018. In total eight sites were surveyed, labelled A-H. The key results from eDNA survey (helix symbol), host snail survey (snail symbol) and test for the presence of schistosomes in snail tissue (cercariae symbol) are given for S . haematobium (H) and S . mansoni (M) assays, with + indicating the site was positive, while a dot indicates no detection was made. Map drawn using the following open source software and data: DIVA-GIS7.5 ( https://www.diva-gis.org ); Africa river network (15 sec resolution), African drainage basin (15sec resolution) and African Digital Elevation Model data (30 sec resolution) from HydroSHEDS ( https://www.hydrosheds.org ); African Water Bodies shapefile from RCMRD GeoPortal ( http://geoportal.rcmrd.org ).
Figure Legend Snippet: Locations of eDNA sampling sites in the Mbeya Region of Tanzania in 2018. In total eight sites were surveyed, labelled A-H. The key results from eDNA survey (helix symbol), host snail survey (snail symbol) and test for the presence of schistosomes in snail tissue (cercariae symbol) are given for S . haematobium (H) and S . mansoni (M) assays, with + indicating the site was positive, while a dot indicates no detection was made. Map drawn using the following open source software and data: DIVA-GIS7.5 ( https://www.diva-gis.org ); Africa river network (15 sec resolution), African drainage basin (15sec resolution) and African Digital Elevation Model data (30 sec resolution) from HydroSHEDS ( https://www.hydrosheds.org ); African Water Bodies shapefile from RCMRD GeoPortal ( http://geoportal.rcmrd.org ).

Techniques Used: Sampling, Software

Maximum likelihood phylogenetic reconstruction of the mtDNA 16S sequences used for the establishing the specificity of the assays designed for S . haematobium , S . mansoni and S . japonicum . Numbers above branches represent the branch support (proportion of 100 bootstrap replicates.
Figure Legend Snippet: Maximum likelihood phylogenetic reconstruction of the mtDNA 16S sequences used for the establishing the specificity of the assays designed for S . haematobium , S . mansoni and S . japonicum . Numbers above branches represent the branch support (proportion of 100 bootstrap replicates.

Techniques Used:

Probability of qPCR amplification of DNA standards of concentrations ranging from 1 copy/μl to 1,000,000 copies/μl. a) S . mansoni assay–probability of amplification in any one qPCR across all standard templates tested. b) S . mansoni assay–probability of amplification in any one standard template that is subject to triplicate qPCR, c) S . haematobium assay–probability of amplification in any one qPCR across all standard templates tested, d) S . haematobium assay–probability of amplification in any one standard template that is subject to triplicate qPCR. Lines represent logistic models of the form y = a / (1 + b *e (- cx ) ). a) a = 1.002, b = 27.303, c = 3.826. b) a = 1.000, b = 7.501, c = 4.786. c) a = 1.004, b = 1.009, c = 1.415. b) a = 1.004, b = 0.342, c = 1.399. All models r > 0.995. Grey shading indicates 95% confidence intervals.
Figure Legend Snippet: Probability of qPCR amplification of DNA standards of concentrations ranging from 1 copy/μl to 1,000,000 copies/μl. a) S . mansoni assay–probability of amplification in any one qPCR across all standard templates tested. b) S . mansoni assay–probability of amplification in any one standard template that is subject to triplicate qPCR, c) S . haematobium assay–probability of amplification in any one qPCR across all standard templates tested, d) S . haematobium assay–probability of amplification in any one standard template that is subject to triplicate qPCR. Lines represent logistic models of the form y = a / (1 + b *e (- cx ) ). a) a = 1.002, b = 27.303, c = 3.826. b) a = 1.000, b = 7.501, c = 4.786. c) a = 1.004, b = 1.009, c = 1.415. b) a = 1.004, b = 0.342, c = 1.399. All models r > 0.995. Grey shading indicates 95% confidence intervals.

Techniques Used: Real-time Polymerase Chain Reaction, Amplification

16) Product Images from "Schistosoma species detection by environmental DNA assays in African freshwaters"

Article Title: Schistosoma species detection by environmental DNA assays in African freshwaters

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0008129

Maximum likelihood phylogenetic reconstruction of the mtDNA 16S sequences used for the establishing the specificity of the assays designed for S . haematobium , S . mansoni and S . japonicum . Numbers above branches represent the branch support (proportion of 100 bootstrap replicates.
Figure Legend Snippet: Maximum likelihood phylogenetic reconstruction of the mtDNA 16S sequences used for the establishing the specificity of the assays designed for S . haematobium , S . mansoni and S . japonicum . Numbers above branches represent the branch support (proportion of 100 bootstrap replicates.

Techniques Used:

17) Product Images from "Caught in Action: Selecting Peptide Aptamers Against Intrinsically Disordered Proteins in Live Cells"

Article Title: Caught in Action: Selecting Peptide Aptamers Against Intrinsically Disordered Proteins in Live Cells

Journal: Scientific Reports

doi: 10.1038/srep09402

PA-1, but not PA-3 or PA-7, rescues proteasome substrate FabD from degradation and inhibits the growth of BCG. (a) Diagram of the expression shuttle vector, pVV16, used in the BCG assay. The plasmid contains an E. coli origin derived from pUC19, a mycobacterial origin derived from pAL5000 46 , and a constitutively active BCG hsp60 promoter. (b) BCG-FLAG-FabD was transformed with pVV16-PA-1, -PA-3, and -PA-7 to examine the steady-state level of FLAG-tagged FabD in untreated cells. As a control, BCG was incubated with and without 50 μM Btz. Anti-groEL2 was used as a loading control. (c) BCG plates after 3 weeks of growth show a 100-fold reduction in colonies due to expression of PA-1. (d) Inhibition of BCG growth under conditions that reduce proteasome function. 50 μM Btz, GL5, and DETA- NO were used as indicated. Error bars represent standard deviations and asterisks indicate p- values
Figure Legend Snippet: PA-1, but not PA-3 or PA-7, rescues proteasome substrate FabD from degradation and inhibits the growth of BCG. (a) Diagram of the expression shuttle vector, pVV16, used in the BCG assay. The plasmid contains an E. coli origin derived from pUC19, a mycobacterial origin derived from pAL5000 46 , and a constitutively active BCG hsp60 promoter. (b) BCG-FLAG-FabD was transformed with pVV16-PA-1, -PA-3, and -PA-7 to examine the steady-state level of FLAG-tagged FabD in untreated cells. As a control, BCG was incubated with and without 50 μM Btz. Anti-groEL2 was used as a loading control. (c) BCG plates after 3 weeks of growth show a 100-fold reduction in colonies due to expression of PA-1. (d) Inhibition of BCG growth under conditions that reduce proteasome function. 50 μM Btz, GL5, and DETA- NO were used as indicated. Error bars represent standard deviations and asterisks indicate p- values

Techniques Used: Expressing, Plasmid Preparation, Derivative Assay, Transformation Assay, Incubation, Inhibition

18) Product Images from "Rapid Focused Sequencing: A Multiplexed Assay for Simultaneous Detection and Strain Typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis"

Article Title: Rapid Focused Sequencing: A Multiplexed Assay for Simultaneous Detection and Strain Typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0056093

10-plex PCR profiles generated from representative Ft strains (left panel) and Yp and Yp NN strains (right panel). The FAM (blue), TMR (black) and ROX (red) labeled products are aligned to emphasize the variant and non-variant fragment sizes observed across these strains. Six of ten fragments ( acp A, pep O, mig R, fop A, tul 4-FTT0900, and igl C) in the 10-plex Ft panel are invariable in length between strains subsp. tularensis SchuS4 and WY96, and subsp. holarctica 14LVS and 425. In Yp 10-plex panel, size variability is observed primarily in 4 loci ( glp D, ail, arg S-YPO2047 and YPO1976). Both Ft 10-plex and Yp 10-plex panels do not have any JOE-labeled (green) primers. For each reaction, 100 genome equivalents of each strain were used as template to PCR.
Figure Legend Snippet: 10-plex PCR profiles generated from representative Ft strains (left panel) and Yp and Yp NN strains (right panel). The FAM (blue), TMR (black) and ROX (red) labeled products are aligned to emphasize the variant and non-variant fragment sizes observed across these strains. Six of ten fragments ( acp A, pep O, mig R, fop A, tul 4-FTT0900, and igl C) in the 10-plex Ft panel are invariable in length between strains subsp. tularensis SchuS4 and WY96, and subsp. holarctica 14LVS and 425. In Yp 10-plex panel, size variability is observed primarily in 4 loci ( glp D, ail, arg S-YPO2047 and YPO1976). Both Ft 10-plex and Yp 10-plex panels do not have any JOE-labeled (green) primers. For each reaction, 100 genome equivalents of each strain were used as template to PCR.

Techniques Used: Polymerase Chain Reaction, Generated, Labeling, Variant Assay

19) Product Images from "Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System"

Article Title: Rapid Detection of Bacillus anthracis Bloodstream Infections by Use of a Novel Assay in the GeneXpert System

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.00466-17

Limit of detection of B. anthracis assay. (A) Positivity rate for assay cartridges spiked with the indicated numbers of B. anthracis Ames35 genomic DNA equivalents. Ten to 22 reaction mixtures were tested for each concentration shown. (B and C) Positivity rate for blood samples spiked with the indicated numbers of CFU of B. anthracis Sterne (B) and B. anthracis V1B (C). Between 10 and 12 replicates were tested for each concentration. The Gompertz fit curve ( f = a × exp{−exp[−( x − x )]/ b }) and 95% confidence band were generated in SigmaPlot v.13. Cart, filter-based cartridge.
Figure Legend Snippet: Limit of detection of B. anthracis assay. (A) Positivity rate for assay cartridges spiked with the indicated numbers of B. anthracis Ames35 genomic DNA equivalents. Ten to 22 reaction mixtures were tested for each concentration shown. (B and C) Positivity rate for blood samples spiked with the indicated numbers of CFU of B. anthracis Sterne (B) and B. anthracis V1B (C). Between 10 and 12 replicates were tested for each concentration. The Gompertz fit curve ( f = a × exp{−exp[−( x − x )]/ b }) and 95% confidence band were generated in SigmaPlot v.13. Cart, filter-based cartridge.

Techniques Used: Concentration Assay, Generated

20) Product Images from "A Loop-Mediated Isothermal Amplification (LAMP) Assay for Early Detection of Schistosoma mansoni in Stool Samples: A Diagnostic Approach in a Murine Model"

Article Title: A Loop-Mediated Isothermal Amplification (LAMP) Assay for Early Detection of Schistosoma mansoni in Stool Samples: A Diagnostic Approach in a Murine Model

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0003126

PCR verification, detection limit and specificity using outer primers F3 and B3. (A) PCR verification of expected 206 bp target length amplicon. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sm, S. mansoni DNA (1 ng); lane N, negative control (no DNA template). (B) Detection limit of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sm: S. mansoni DNA (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions of S. mansoni DNA; lane N, negative control (no DNA template). (C) Specificity of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm, Sh, Sj, Si, Fh, Dd, Hd, Cd, Ll, Bp, As, Ts, Tt, Eg, Cp, Gd, Eh, S. mansoni , S. haematobium , S. japonicum , S. intercalatum , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Cryptosporidium parvum , Giardia intestinalis and Entamoeba histolytica DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template).
Figure Legend Snippet: PCR verification, detection limit and specificity using outer primers F3 and B3. (A) PCR verification of expected 206 bp target length amplicon. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sm, S. mansoni DNA (1 ng); lane N, negative control (no DNA template). (B) Detection limit of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sm: S. mansoni DNA (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions of S. mansoni DNA; lane N, negative control (no DNA template). (C) Specificity of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm, Sh, Sj, Si, Fh, Dd, Hd, Cd, Ll, Bp, As, Ts, Tt, Eg, Cp, Gd, Eh, S. mansoni , S. haematobium , S. japonicum , S. intercalatum , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Cryptosporidium parvum , Giardia intestinalis and Entamoeba histolytica DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template).

Techniques Used: Polymerase Chain Reaction, Amplification, Molecular Weight, Marker, Negative Control

Specificity and sensitivity assessment of the LAMP assay for S. mansoni . (A) Specificity assessment performed with SmMIT-LAMP is shown. Identical results were obtained using Loopamp DNA amplification Kit . A ladder of multiple bands of different sizes could be only observed in S. mansoni DNA sample. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm, Sh, Sj, Si, Fh, Dd, Hd, Cd, Ll, Bp, As, Ts, Tt, Eg, Cp, Gd, Eh, S. mansoni , S. haematobium , S. japonicum , S. intercalatum , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Cryptosporidium parvum , Giardia intestinalis and Entamoeba histolytica DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template). (B) Sensitivity assessment performed with the Loopamp DNA amplification kit at 63°C for 1 h using serial dilutions of S. mansoni genomic DNA by the addition of SYBR Green I (up) or by visualization on agarose gel (down). (C) Sensitivity assessment performed with SmMIT-LAMP at 63°C for 1 h using serial dilutions of S. mansoni genomic DNA by the addition of SYBR Green I (up) or by visualization on agarose gel (down). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm: genomic DNA from S. mansoni (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions; lanes N: negative controls (no DNA template).
Figure Legend Snippet: Specificity and sensitivity assessment of the LAMP assay for S. mansoni . (A) Specificity assessment performed with SmMIT-LAMP is shown. Identical results were obtained using Loopamp DNA amplification Kit . A ladder of multiple bands of different sizes could be only observed in S. mansoni DNA sample. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm, Sh, Sj, Si, Fh, Dd, Hd, Cd, Ll, Bp, As, Ts, Tt, Eg, Cp, Gd, Eh, S. mansoni , S. haematobium , S. japonicum , S. intercalatum , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Cryptosporidium parvum , Giardia intestinalis and Entamoeba histolytica DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template). (B) Sensitivity assessment performed with the Loopamp DNA amplification kit at 63°C for 1 h using serial dilutions of S. mansoni genomic DNA by the addition of SYBR Green I (up) or by visualization on agarose gel (down). (C) Sensitivity assessment performed with SmMIT-LAMP at 63°C for 1 h using serial dilutions of S. mansoni genomic DNA by the addition of SYBR Green I (up) or by visualization on agarose gel (down). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm: genomic DNA from S. mansoni (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions; lanes N: negative controls (no DNA template).

Techniques Used: Lamp Assay, Amplification, Molecular Weight, Marker, Negative Control, SYBR Green Assay, Agarose Gel Electrophoresis

21) Product Images from "Transcription Factor Redundancy Ensures Induction of the Antiviral State *"

Article Title: Transcription Factor Redundancy Ensures Induction of the Antiviral State *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M110.165936

Affymetrix analysis of STAT1-independent IRF7-induced genes. A , Western blot and binding analysis of 2FTGH and U3A extracts from mock or IFNβ-treated cells exogenously expressing the indicated combinations of GFP, IRF7, and IKKϵ. EMSA
Figure Legend Snippet: Affymetrix analysis of STAT1-independent IRF7-induced genes. A , Western blot and binding analysis of 2FTGH and U3A extracts from mock or IFNβ-treated cells exogenously expressing the indicated combinations of GFP, IRF7, and IKKϵ. EMSA

Techniques Used: Western Blot, Binding Assay, Expressing

ISRE-specific expression of virus-inducible genes. A , U3A cells stably expressing GFP, IRF7, or STAT1 were treated with IFNβ or infected at an MOI of 5 with an influenza A virus mutant harboring two amino acid changes in the NS1 protein (Flu-NS1mut).
Figure Legend Snippet: ISRE-specific expression of virus-inducible genes. A , U3A cells stably expressing GFP, IRF7, or STAT1 were treated with IFNβ or infected at an MOI of 5 with an influenza A virus mutant harboring two amino acid changes in the NS1 protein (Flu-NS1mut).

Techniques Used: Expressing, Stable Transfection, Infection, Mutagenesis

IRF3-, IRF7-, and ISGF3-specific binding of human ISREs. EMSAs were performed with extracts from fibroblasts exogenously expressing IRF3, IRF7, or ISGF3 in addition to IKKϵ or IFNβ. EMSA probe sequences are depicted below each corresponding
Figure Legend Snippet: IRF3-, IRF7-, and ISGF3-specific binding of human ISREs. EMSAs were performed with extracts from fibroblasts exogenously expressing IRF3, IRF7, or ISGF3 in addition to IKKϵ or IFNβ. EMSA probe sequences are depicted below each corresponding

Techniques Used: Binding Assay, Expressing

Systematic analysis of DNA binding of IRF7 and ISGF3. A–P , EMSAs were performed with extracts derived from fibroblasts exogenously expressing IRF7 and IKKϵ or the components of ISGF3 in the presence of IFNβ or IKKϵ. Respective
Figure Legend Snippet: Systematic analysis of DNA binding of IRF7 and ISGF3. A–P , EMSAs were performed with extracts derived from fibroblasts exogenously expressing IRF7 and IKKϵ or the components of ISGF3 in the presence of IFNβ or IKKϵ. Respective

Techniques Used: Binding Assay, Derivative Assay, Expressing

22) Product Images from "Detection of duo-schistosome infection from filtered urine samples from school children in Zambia after MDA"

Article Title: Detection of duo-schistosome infection from filtered urine samples from school children in Zambia after MDA

Journal: PLoS ONE

doi: 10.1371/journal.pone.0189400

Detection of dual infection (both S . mansoni and S . haematobium ) by species-specific repeat DNA amplification from single urine sample. The dual infection for both species is categorized into two different age groups (Group A: 7–12 years and Group B: 13–15 years) and for both female and male participants.
Figure Legend Snippet: Detection of dual infection (both S . mansoni and S . haematobium ) by species-specific repeat DNA amplification from single urine sample. The dual infection for both species is categorized into two different age groups (Group A: 7–12 years and Group B: 13–15 years) and for both female and male participants.

Techniques Used: Infection, Amplification

23) Product Images from "Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population"

Article Title: Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.02533

Global taxonomic pattern of bacterial (A) and Fungal (B) diversity for the dominant taxa in the three body sites examined. We have only shown here patient samples with > 1000 reads in both the 16S and ITS datasets simultaneously to maintain the same patients in both analyses.
Figure Legend Snippet: Global taxonomic pattern of bacterial (A) and Fungal (B) diversity for the dominant taxa in the three body sites examined. We have only shown here patient samples with > 1000 reads in both the 16S and ITS datasets simultaneously to maintain the same patients in both analyses.

Techniques Used:

24) Product Images from "Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum"

Article Title: Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum

Journal: Microbial Cell Factories

doi: 10.1186/s12934-018-0880-4

Phylogenetic tree of bacterial tannases. Tree showing evolutionary relationships between all bacterial tannases genetically identified to date. The numbers indicate branches lengths. F. nucleatum subsp. polymorphum TanB Fnp is indicated in blue
Figure Legend Snippet: Phylogenetic tree of bacterial tannases. Tree showing evolutionary relationships between all bacterial tannases genetically identified to date. The numbers indicate branches lengths. F. nucleatum subsp. polymorphum TanB Fnp is indicated in blue

Techniques Used:

Purification of recombinant F. nucleatum subsp. polymorphum tannase TanB Fnp . a SDS-PAGE analysis of TanB Fnp fractions obtained before and after His-affinity resin chromatography. b UV absorbance of different fractions obtained after gel filtration chromatography. c SDS-PAGE analysis of fractions obtained after gel filtration chromatography
Figure Legend Snippet: Purification of recombinant F. nucleatum subsp. polymorphum tannase TanB Fnp . a SDS-PAGE analysis of TanB Fnp fractions obtained before and after His-affinity resin chromatography. b UV absorbance of different fractions obtained after gel filtration chromatography. c SDS-PAGE analysis of fractions obtained after gel filtration chromatography

Techniques Used: Purification, Recombinant, SDS Page, Chromatography, Filtration

25) Product Images from "Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System"

Article Title: Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.01126-16

Assay performance in dynamic range testing in cartridge-based PCR assay. (A and B) Real-time PCR curves for the cartridge-based assay over the range of F. tularensis LVS spiked into human (A) and macaque blood (B). (C and D) Cycle threshold (C) and endpoint
Figure Legend Snippet: Assay performance in dynamic range testing in cartridge-based PCR assay. (A and B) Real-time PCR curves for the cartridge-based assay over the range of F. tularensis LVS spiked into human (A) and macaque blood (B). (C and D) Cycle threshold (C) and endpoint

Techniques Used: Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

Detection of F. tularensis in the blood of infected macaques. Blood samples from macaques infected with F. tularensis Schu S4 were tested by the cartridge-based F. tularensis assay, a manual qPCR reference F. tularensis assay, and blood culture for the
Figure Legend Snippet: Detection of F. tularensis in the blood of infected macaques. Blood samples from macaques infected with F. tularensis Schu S4 were tested by the cartridge-based F. tularensis assay, a manual qPCR reference F. tularensis assay, and blood culture for the

Techniques Used: Infection, Real-time Polymerase Chain Reaction

Three-step double-nested-PCR approach to detect F. tularensis . A first PCR (PCR1) amplifies an outer 138-bp amplicon, and this is followed by a second (PCR2) nested amplification to create an 80-bp amplicon. Finally, a third heminested-PCR (PCR3) creates
Figure Legend Snippet: Three-step double-nested-PCR approach to detect F. tularensis . A first PCR (PCR1) amplifies an outer 138-bp amplicon, and this is followed by a second (PCR2) nested amplification to create an 80-bp amplicon. Finally, a third heminested-PCR (PCR3) creates

Techniques Used: Nested PCR, Polymerase Chain Reaction, Amplification

Analytical sensitivity of PCR2 versus PCR3 for detecting F. tularensis . (A) Positivity rate for assays spiked with the indicated numbers of F. tularensis subsp. tularensis Schu S4 genomic DNA equivalents. Ten spiked samples were tested for each concentration
Figure Legend Snippet: Analytical sensitivity of PCR2 versus PCR3 for detecting F. tularensis . (A) Positivity rate for assays spiked with the indicated numbers of F. tularensis subsp. tularensis Schu S4 genomic DNA equivalents. Ten spiked samples were tested for each concentration

Techniques Used: Concentration Assay

26) Product Images from "Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound"

Article Title: Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound

Journal: Frontiers in Pharmacology

doi: 10.3389/fphar.2020.00246

Diagrammatic representation of the pbgst-ko plasmids and analysis of potential integration. (A,C) Schematic diagram of the pbgst-ko plasmids (top), the endogenous pbgst locus (center), and the predicted integration (bottom). The plasmids, pbgst-ko 1A (A) and pbgst-ko 1B (B) , contained the tgdhfr / ts selectable marker flanked by the 5′ and 3′ fragments of the pbgst gene. The probe used in Southern blot analysis is shown as dashed lines inside the coding region of the tgdhfr/ts . (B,D) Southern analyses using a tgdhfr/ts specific probe. Parasite chromosomes from two independent transfections were separated by CHEF (B) or FIGE (D) . Hybridization with a tgdhfr/ts specific probe shows no integration of the pbgst-ko 1A plasmid into the pbgst locus (B) . Hybridization with a tgdhfr/ts specific probe shows integration into chromosome 7 and not into the endogenous pbgst locus (chromosome 10, right panel) (D) . (E) Schematic diagram of the plasmids pbgst-ko 2A and pbgst-ko 2B (top), the endogenous pbgst locus (center), and the predicted integration (bottom). The pbgst-ko 2 plasmids contained the hdhfr/yfcu , positive-negative selectable marker under the control of the eef1a promoter. The probe used in Southern blot analysis is shown as dashed lines inside the coding region of hdhfr . (F,G) Southern analyses using an hdhfr specific probe. Hybridization with the hdhfr specific probe shows no integration of the corresponding plasmid (lanes 7–10 in F,G ), pbgst-ko 2A or pbgst-ko 2B , into the pbgst locus (chromosome 10, right arrows) in two independent transfections. As a control, transfection targeting the pbmrp (a dispensable gene) shows a successful integration of the pbmrp-ko plasmid into chromosome 14 ( F , lanes 1 and 2 labeled as T5 S1 pbmrp and T5 S2 pbmrp ; and G , lane 1 labeled as T5 S3 pbmrp ). Diagrams are not drawn to scale. M1, H. wingei chromosome marker; M2, S. cerevisiae chromosome marker; T#S#, transfection number, and sample number.
Figure Legend Snippet: Diagrammatic representation of the pbgst-ko plasmids and analysis of potential integration. (A,C) Schematic diagram of the pbgst-ko plasmids (top), the endogenous pbgst locus (center), and the predicted integration (bottom). The plasmids, pbgst-ko 1A (A) and pbgst-ko 1B (B) , contained the tgdhfr / ts selectable marker flanked by the 5′ and 3′ fragments of the pbgst gene. The probe used in Southern blot analysis is shown as dashed lines inside the coding region of the tgdhfr/ts . (B,D) Southern analyses using a tgdhfr/ts specific probe. Parasite chromosomes from two independent transfections were separated by CHEF (B) or FIGE (D) . Hybridization with a tgdhfr/ts specific probe shows no integration of the pbgst-ko 1A plasmid into the pbgst locus (B) . Hybridization with a tgdhfr/ts specific probe shows integration into chromosome 7 and not into the endogenous pbgst locus (chromosome 10, right panel) (D) . (E) Schematic diagram of the plasmids pbgst-ko 2A and pbgst-ko 2B (top), the endogenous pbgst locus (center), and the predicted integration (bottom). The pbgst-ko 2 plasmids contained the hdhfr/yfcu , positive-negative selectable marker under the control of the eef1a promoter. The probe used in Southern blot analysis is shown as dashed lines inside the coding region of hdhfr . (F,G) Southern analyses using an hdhfr specific probe. Hybridization with the hdhfr specific probe shows no integration of the corresponding plasmid (lanes 7–10 in F,G ), pbgst-ko 2A or pbgst-ko 2B , into the pbgst locus (chromosome 10, right arrows) in two independent transfections. As a control, transfection targeting the pbmrp (a dispensable gene) shows a successful integration of the pbmrp-ko plasmid into chromosome 14 ( F , lanes 1 and 2 labeled as T5 S1 pbmrp and T5 S2 pbmrp ; and G , lane 1 labeled as T5 S3 pbmrp ). Diagrams are not drawn to scale. M1, H. wingei chromosome marker; M2, S. cerevisiae chromosome marker; T#S#, transfection number, and sample number.

Techniques Used: Marker, Southern Blot, Transfection, Hybridization, Plasmid Preparation, Labeling

27) Product Images from "A Loop-Mediated Isothermal Amplification (LAMP) Assay for Early Detection of Schistosoma mansoni in Stool Samples: A Diagnostic Approach in a Murine Model"

Article Title: A Loop-Mediated Isothermal Amplification (LAMP) Assay for Early Detection of Schistosoma mansoni in Stool Samples: A Diagnostic Approach in a Murine Model

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0003126

PCR verification, detection limit and specificity using outer primers F3 and B3. (A) PCR verification of expected 206 bp target length amplicon. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sm, S. mansoni DNA (1 ng); lane N, negative control (no DNA template). (B) Detection limit of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sm: S. mansoni DNA (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions of S. mansoni DNA; lane N, negative control (no DNA template). (C) Specificity of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm, Sh, Sj, Si, Fh, Dd, Hd, Cd, Ll, Bp, As, Ts, Tt, Eg, Cp, Gd, Eh, S. mansoni , S. haematobium , S. japonicum , S. intercalatum , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Cryptosporidium parvum , Giardia intestinalis and Entamoeba histolytica DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template).
Figure Legend Snippet: PCR verification, detection limit and specificity using outer primers F3 and B3. (A) PCR verification of expected 206 bp target length amplicon. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sm, S. mansoni DNA (1 ng); lane N, negative control (no DNA template). (B) Detection limit of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sm: S. mansoni DNA (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions of S. mansoni DNA; lane N, negative control (no DNA template). (C) Specificity of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm, Sh, Sj, Si, Fh, Dd, Hd, Cd, Ll, Bp, As, Ts, Tt, Eg, Cp, Gd, Eh, S. mansoni , S. haematobium , S. japonicum , S. intercalatum , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Cryptosporidium parvum , Giardia intestinalis and Entamoeba histolytica DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template).

Techniques Used: Polymerase Chain Reaction, Amplification, Molecular Weight, Marker, Negative Control

Specificity and sensitivity assessment of the LAMP assay for S. mansoni . (A) Specificity assessment performed with SmMIT-LAMP is shown. Identical results were obtained using Loopamp DNA amplification Kit . A ladder of multiple bands of different sizes could be only observed in S. mansoni DNA sample. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm, Sh, Sj, Si, Fh, Dd, Hd, Cd, Ll, Bp, As, Ts, Tt, Eg, Cp, Gd, Eh, S. mansoni , S. haematobium , S. japonicum , S. intercalatum , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Cryptosporidium parvum , Giardia intestinalis and Entamoeba histolytica DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template). (B) Sensitivity assessment performed with the Loopamp DNA amplification kit at 63°C for 1 h using serial dilutions of S. mansoni genomic DNA by the addition of SYBR Green I (up) or by visualization on agarose gel (down). (C) Sensitivity assessment performed with SmMIT-LAMP at 63°C for 1 h using serial dilutions of S. mansoni genomic DNA by the addition of SYBR Green I (up) or by visualization on agarose gel (down). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm: genomic DNA from S. mansoni (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions; lanes N: negative controls (no DNA template).
Figure Legend Snippet: Specificity and sensitivity assessment of the LAMP assay for S. mansoni . (A) Specificity assessment performed with SmMIT-LAMP is shown. Identical results were obtained using Loopamp DNA amplification Kit . A ladder of multiple bands of different sizes could be only observed in S. mansoni DNA sample. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm, Sh, Sj, Si, Fh, Dd, Hd, Cd, Ll, Bp, As, Ts, Tt, Eg, Cp, Gd, Eh, S. mansoni , S. haematobium , S. japonicum , S. intercalatum , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Cryptosporidium parvum , Giardia intestinalis and Entamoeba histolytica DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template). (B) Sensitivity assessment performed with the Loopamp DNA amplification kit at 63°C for 1 h using serial dilutions of S. mansoni genomic DNA by the addition of SYBR Green I (up) or by visualization on agarose gel (down). (C) Sensitivity assessment performed with SmMIT-LAMP at 63°C for 1 h using serial dilutions of S. mansoni genomic DNA by the addition of SYBR Green I (up) or by visualization on agarose gel (down). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sm: genomic DNA from S. mansoni (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions; lanes N: negative controls (no DNA template).

Techniques Used: Lamp Assay, Amplification, Molecular Weight, Marker, Negative Control, SYBR Green Assay, Agarose Gel Electrophoresis

28) Product Images from "Red Clover Aryl Hydrocarbon Receptor (AhR) and Estrogen Receptor (ER) Agonists Enhance Genotoxic Estrogen Metabolism"

Article Title: Red Clover Aryl Hydrocarbon Receptor (AhR) and Estrogen Receptor (ER) Agonists Enhance Genotoxic Estrogen Metabolism

Journal: Chemical Research in Toxicology

doi: 10.1021/acs.chemrestox.7b00237

XRE-luciferase reporter activity analyzed after 24 h treatment with isoflavones (10 μM), BA, FN, GN, and DZ, in (A) HC-04 cells and (B) in MCF-7 cells. ICI 182,780 (1 μM) was added 2 h before treatment with compounds, and cells were incubated for an additional 24 h before analysis of XRE-luciferase reporter activity.
Figure Legend Snippet: XRE-luciferase reporter activity analyzed after 24 h treatment with isoflavones (10 μM), BA, FN, GN, and DZ, in (A) HC-04 cells and (B) in MCF-7 cells. ICI 182,780 (1 μM) was added 2 h before treatment with compounds, and cells were incubated for an additional 24 h before analysis of XRE-luciferase reporter activity.

Techniques Used: Luciferase, Activity Assay, Incubation

29) Product Images from "Flagellin Encoded in Gene-Based Vector Vaccines Is a Route-Dependent Immune Adjuvant"

Article Title: Flagellin Encoded in Gene-Based Vector Vaccines Is a Route-Dependent Immune Adjuvant

Journal: PLoS ONE

doi: 10.1371/journal.pone.0148701

Co-priming with flagellin enhanced Ag85B-specific CD4+ and CD8+ T cell responses following DNA immunization. Mice were immunized twice via the IM route with DNA vaccine encoding Ag85B and/or flagellin as shown in Table 1 . At week 3 post-immunization, CD4+ T cell responses in spleen (A) and lung (B) were assayed by IFN-γ ELISpot. Data shown are mean of SFCs ± SEM per group, (* p
Figure Legend Snippet: Co-priming with flagellin enhanced Ag85B-specific CD4+ and CD8+ T cell responses following DNA immunization. Mice were immunized twice via the IM route with DNA vaccine encoding Ag85B and/or flagellin as shown in Table 1 . At week 3 post-immunization, CD4+ T cell responses in spleen (A) and lung (B) were assayed by IFN-γ ELISpot. Data shown are mean of SFCs ± SEM per group, (* p

Techniques Used: Mouse Assay, Enzyme-linked Immunospot

Enhancement of pulmonary mucosal and circulating Ag85B-specific CD4+ and CD8+ T cell responses when flagellin was co-expressed in the priming phase of mucosal prime-boost immunization. Mice were primed twice with DNA vaccine via the IM route and boosted IN with Ad vaccine encoding Ag85B and/or flagellin 3 weeks later as shown in Table 1 . At week 3 post-boosting, CD4+ and CD8+ T cell responses in spleen (A D respectively), lung-associated lymph nodes (B E respectively), and peripheral lung tissues (C F respectively),were assayed by IFN-γ ELISpot. Data shown are mean of SFCs ± SEM, (* p
Figure Legend Snippet: Enhancement of pulmonary mucosal and circulating Ag85B-specific CD4+ and CD8+ T cell responses when flagellin was co-expressed in the priming phase of mucosal prime-boost immunization. Mice were primed twice with DNA vaccine via the IM route and boosted IN with Ad vaccine encoding Ag85B and/or flagellin 3 weeks later as shown in Table 1 . At week 3 post-boosting, CD4+ and CD8+ T cell responses in spleen (A D respectively), lung-associated lymph nodes (B E respectively), and peripheral lung tissues (C F respectively),were assayed by IFN-γ ELISpot. Data shown are mean of SFCs ± SEM, (* p

Techniques Used: Mouse Assay, Enzyme-linked Immunospot

DNA and adenovirus vaccine vectors encoding Ag85B and expression of biologically-active flagellin. (A) Supernatants from DNA-transfected or Ad-infected 293A cells were tested for expression of flagellin by Western blot, lane 1 DNA-FliC, lane 2 DNA-85B-FliC, lane 3 DNA-control, lane 4 Ad-FliC, lane 5 mock. (B) Expression of Ag85B by DNA and Ad vectors was also confirmed by Western blot, lane 1 DNA-85B, 2 DNA-85B-FliC, 3 DNA-FliC, 4 Ad-85B, 5 mock. (C) Biological activity of flagellin was tested by bioassay using THP1-Blue-CD14 cells. SEAP levels were read at 620 nm. Data shown are mean of fold-increase in SEAP ± SEM over respective controls (dotted line), which are supernatants of cells transfected with empty DNA vector (for DNA vaccines), or of mock infected cells (for Ad vaccine) (* p
Figure Legend Snippet: DNA and adenovirus vaccine vectors encoding Ag85B and expression of biologically-active flagellin. (A) Supernatants from DNA-transfected or Ad-infected 293A cells were tested for expression of flagellin by Western blot, lane 1 DNA-FliC, lane 2 DNA-85B-FliC, lane 3 DNA-control, lane 4 Ad-FliC, lane 5 mock. (B) Expression of Ag85B by DNA and Ad vectors was also confirmed by Western blot, lane 1 DNA-85B, 2 DNA-85B-FliC, 3 DNA-FliC, 4 Ad-85B, 5 mock. (C) Biological activity of flagellin was tested by bioassay using THP1-Blue-CD14 cells. SEAP levels were read at 620 nm. Data shown are mean of fold-increase in SEAP ± SEM over respective controls (dotted line), which are supernatants of cells transfected with empty DNA vector (for DNA vaccines), or of mock infected cells (for Ad vaccine) (* p

Techniques Used: Expressing, Transfection, Infection, Western Blot, Activity Assay, Plasmid Preparation

Co-expression of flagellin at the priming phase of immunization increased numbers of splenic and mucosal Ag85B-specific CD4+ and CD8+ T cells. Mice were primed twice via the IM route with DNA vaccines encoding either Ag85B or flagellin, or both, and boosted IM with Ad vaccine vectors encoding Ag85B or flagellin, or with a cocktail of both, three weeks later as shown in Table 1 . At week 3 post-boosting, CD4+ T and CD8+ T cell responses in spleen (A C respectively) and lung (B D respectively) were assayed by IFN-γ ELISpot. Data shown are mean counts of SFCs ± SEM, (* p
Figure Legend Snippet: Co-expression of flagellin at the priming phase of immunization increased numbers of splenic and mucosal Ag85B-specific CD4+ and CD8+ T cells. Mice were primed twice via the IM route with DNA vaccines encoding either Ag85B or flagellin, or both, and boosted IM with Ad vaccine vectors encoding Ag85B or flagellin, or with a cocktail of both, three weeks later as shown in Table 1 . At week 3 post-boosting, CD4+ T and CD8+ T cell responses in spleen (A C respectively) and lung (B D respectively) were assayed by IFN-γ ELISpot. Data shown are mean counts of SFCs ± SEM, (* p

Techniques Used: Expressing, Mouse Assay, Enzyme-linked Immunospot

Flagellin enhanced anti-Ag85B antibody responses following either systemic or mucosal prime-boost immunization. Mice were primed twice with DNA vaccine via the IM route and boosted either IM or IN with Ad vaccine three weeks later as shown in Table 1 . Sera were collected and tested by ELISA for anti-Ag85B IgG antibodies at week 3 post systemic (A) or mucosal (B) boosting. Data shown are means of endpoint antibody titers ± SEM per group. (C) Lungs were harvested from IN-boosted mice at week 14 post-boosting and tested for mucosal IgA-secreting B cells by ELISpot. Data shown are mean of SFCs ± SEM per group. (* p
Figure Legend Snippet: Flagellin enhanced anti-Ag85B antibody responses following either systemic or mucosal prime-boost immunization. Mice were primed twice with DNA vaccine via the IM route and boosted either IM or IN with Ad vaccine three weeks later as shown in Table 1 . Sera were collected and tested by ELISA for anti-Ag85B IgG antibodies at week 3 post systemic (A) or mucosal (B) boosting. Data shown are means of endpoint antibody titers ± SEM per group. (C) Lungs were harvested from IN-boosted mice at week 14 post-boosting and tested for mucosal IgA-secreting B cells by ELISpot. Data shown are mean of SFCs ± SEM per group. (* p

Techniques Used: Mouse Assay, Enzyme-linked Immunosorbent Assay, Enzyme-linked Immunospot

30) Product Images from "A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-L-proline"

Article Title: A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-L-proline

Journal: Science (New York, N.Y.)

doi: 10.1126/science.aai8386

An abundant, uncharacterized GRE in the human gut is a trans -4-hydroxy-L-proline dehydratase ( t 4LHypD) ( A ) Per-site abundance of GRE Cluster 15 across six body sites. ( B ) Conserved genomic context of GRE Cluster 15 in Clostridiales. ( C ) Hypothesized pathway for anaerobic Hyp metabolism involving uncharacterized GRE Cluster 15. ( D ) EPR spectrum of the glycine-centered radical of activated t 4LHypD. An average of 0.51 ± 0.01 (mean ± SD) glycyl radical per t 4LHypD monomer was observed with hyperfine coupling A = 1.44 mT. ( E ) LC-MS/MS detection of L-proline produced in vitro from Hyp by t 4LHypD and P5C reductase (time = 1 h). Error bars represent the mean ± SD of three replicates. AE, t 4LHypD activating enzyme.
Figure Legend Snippet: An abundant, uncharacterized GRE in the human gut is a trans -4-hydroxy-L-proline dehydratase ( t 4LHypD) ( A ) Per-site abundance of GRE Cluster 15 across six body sites. ( B ) Conserved genomic context of GRE Cluster 15 in Clostridiales. ( C ) Hypothesized pathway for anaerobic Hyp metabolism involving uncharacterized GRE Cluster 15. ( D ) EPR spectrum of the glycine-centered radical of activated t 4LHypD. An average of 0.51 ± 0.01 (mean ± SD) glycyl radical per t 4LHypD monomer was observed with hyperfine coupling A = 1.44 mT. ( E ) LC-MS/MS detection of L-proline produced in vitro from Hyp by t 4LHypD and P5C reductase (time = 1 h). Error bars represent the mean ± SD of three replicates. AE, t 4LHypD activating enzyme.

Techniques Used: Electron Paramagnetic Resonance, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Produced, In Vitro

31) Product Images from "Optimization of DNA extraction for advancing coral microbiota investigations"

Article Title: Optimization of DNA extraction for advancing coral microbiota investigations

Journal: Microbiome

doi: 10.1186/s40168-017-0229-y

Overview of experimental design. During phase I, DNA extraction treatments were performed on subdivided tissue, with efficiency of SSU gene amplification assessed using gel screening of PCR products. The green check mark and red X indicate that amplicons from the treatment were and were not chosen for sequencing, respectively. During phase II, well-performing PB, VG, PG, and VGl extracts were amplified and sequenced for microbial community analysis. PS PowerSoil, PP PowerPlant Pro, PB PowerBiofilm, VG UC Vortex Garnet, PG UC Powerlyzer Glass, VGl UC Vortex Glass
Figure Legend Snippet: Overview of experimental design. During phase I, DNA extraction treatments were performed on subdivided tissue, with efficiency of SSU gene amplification assessed using gel screening of PCR products. The green check mark and red X indicate that amplicons from the treatment were and were not chosen for sequencing, respectively. During phase II, well-performing PB, VG, PG, and VGl extracts were amplified and sequenced for microbial community analysis. PS PowerSoil, PP PowerPlant Pro, PB PowerBiofilm, VG UC Vortex Garnet, PG UC Powerlyzer Glass, VGl UC Vortex Glass

Techniques Used: DNA Extraction, Amplification, Polymerase Chain Reaction, Sequencing

32) Product Images from "A sensitive, specific and reproducible real-time polymerase chain reaction method for detection of Plasmodium vivax andPlasmodium falciparum infection in field-collected anophelines"

Article Title: A sensitive, specific and reproducible real-time polymerase chain reaction method for detection of Plasmodium vivax andPlasmodium falciparum infection in field-collected anophelines

Journal: Memórias do Instituto Oswaldo Cruz

doi: 10.1590/0074-02760150031

: real-time polymerase chain reaction (PCR) amplification plot of a monoplex Plasmodium spp assay. The four quantitative PCR controls are shown: Plasmodium vivax infected Anopheles darlingi (black, solid line), Plasmodium falciparum infected Anopheles stephensi (black, dashed line), uninfected An. darlingi (no template control) (grey, solid line) and water (negative control) (grey, dashed line). ΔRn: baseline corrected normalised fluorescence.
Figure Legend Snippet: : real-time polymerase chain reaction (PCR) amplification plot of a monoplex Plasmodium spp assay. The four quantitative PCR controls are shown: Plasmodium vivax infected Anopheles darlingi (black, solid line), Plasmodium falciparum infected Anopheles stephensi (black, dashed line), uninfected An. darlingi (no template control) (grey, solid line) and water (negative control) (grey, dashed line). ΔRn: baseline corrected normalised fluorescence.

Techniques Used: Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Amplification, Infection, Negative Control, Fluorescence

: real-time polymerase chain reaction (PCR) amplification plot of a triplex Plasmodium spp assay. The two quantitative PCR positive controls are shown: Plasmodium vivax infected Anopheles darlingi (black lines) (solid line: Plasmodium spp positive; dashed line: P. vivax species positive; dashed/dotted line: Plasmodium falciparum negative) and P. falciparum infected Anopheles stephensi (grey lines) (solid line: Plasmodium spp positive; dashed line: P. vivax negative; dashed/dotted line: P . falciparum positive). ΔRn: baseline corrected normalised fluorescence.
Figure Legend Snippet: : real-time polymerase chain reaction (PCR) amplification plot of a triplex Plasmodium spp assay. The two quantitative PCR positive controls are shown: Plasmodium vivax infected Anopheles darlingi (black lines) (solid line: Plasmodium spp positive; dashed line: P. vivax species positive; dashed/dotted line: Plasmodium falciparum negative) and P. falciparum infected Anopheles stephensi (grey lines) (solid line: Plasmodium spp positive; dashed line: P. vivax negative; dashed/dotted line: P . falciparum positive). ΔRn: baseline corrected normalised fluorescence.

Techniques Used: Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Amplification, Infection, Fluorescence

33) Product Images from "Detection of duo-schistosome infection from filtered urine samples from school children in Zambia after MDA"

Article Title: Detection of duo-schistosome infection from filtered urine samples from school children in Zambia after MDA

Journal: PLoS ONE

doi: 10.1371/journal.pone.0189400

Agarose gel image of the repeat fragment amplicons for both S . mansoni and S . haematobium with species-specific primers.
Figure Legend Snippet: Agarose gel image of the repeat fragment amplicons for both S . mansoni and S . haematobium with species-specific primers.

Techniques Used: Agarose Gel Electrophoresis

Detection of dual infection (both S . mansoni and S . haematobium ) by species-specific repeat DNA amplification from single urine sample. The dual infection for both species is categorized into two different age groups (Group A: 7–12 years and Group B: 13–15 years) and for both female and male participants.
Figure Legend Snippet: Detection of dual infection (both S . mansoni and S . haematobium ) by species-specific repeat DNA amplification from single urine sample. The dual infection for both species is categorized into two different age groups (Group A: 7–12 years and Group B: 13–15 years) and for both female and male participants.

Techniques Used: Infection, Amplification

34) Product Images from "Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and wholerrn operon"

Article Title: Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and wholerrn operon

Journal: F1000Research

doi: 10.12688/f1000research.16817.1

Microbiota composition of complex communities: skin samples of healthy dogs. ( A ) Chin samples: upper part of the graphic, bar plot of the composition at the genus level using WIMP (left) and Minimap2 (right); lower part, heat map of the Pseudomonas species within the community (scaled at 100%). ( B ) Dorsal skin samples: upper part of the graphic, bar plot of the composition at the genus level using WIMP (left) and Minimap2 (right); lower part, heat map of the ten most abundant taxa within the community. N/A, taxon was not present in the database.
Figure Legend Snippet: Microbiota composition of complex communities: skin samples of healthy dogs. ( A ) Chin samples: upper part of the graphic, bar plot of the composition at the genus level using WIMP (left) and Minimap2 (right); lower part, heat map of the Pseudomonas species within the community (scaled at 100%). ( B ) Dorsal skin samples: upper part of the graphic, bar plot of the composition at the genus level using WIMP (left) and Minimap2 (right); lower part, heat map of the ten most abundant taxa within the community. N/A, taxon was not present in the database.

Techniques Used:

35) Product Images from "Structure, Activity, and Inhibition of the Carboxyltransferase β-Subunit of Acetyl Coenzyme A Carboxylase (AccD6) from Mycobacterium tuberculosis"

Article Title: Structure, Activity, and Inhibition of the Carboxyltransferase β-Subunit of Acetyl Coenzyme A Carboxylase (AccD6) from Mycobacterium tuberculosis

Journal: Antimicrobial Agents and Chemotherapy

doi: 10.1128/AAC.02574-13

M. tuberculosis AccD6 in vitro assays. (A) Reaction velocity plotted versus malonyl-CoA concentration ( K m = 390 ± 70 μM; V max = 5.5 ± 0.4 μM min −1 ). (B) IC 50 (70.2 ± 1 μM) plot of racemic haloxyfop
Figure Legend Snippet: M. tuberculosis AccD6 in vitro assays. (A) Reaction velocity plotted versus malonyl-CoA concentration ( K m = 390 ± 70 μM; V max = 5.5 ± 0.4 μM min −1 ). (B) IC 50 (70.2 ± 1 μM) plot of racemic haloxyfop

Techniques Used: In Vitro, Concentration Assay

Ribbon diagram of M. tuberculosis AccD6. (A) Ribbon diagram of the two subunit AccD6 holoenzyme, with the haloxyfop ligands depicted as sticks and balls. Subunits are depicted by differences in color, both colored by secondary structure. Subunit 1 is
Figure Legend Snippet: Ribbon diagram of M. tuberculosis AccD6. (A) Ribbon diagram of the two subunit AccD6 holoenzyme, with the haloxyfop ligands depicted as sticks and balls. Subunits are depicted by differences in color, both colored by secondary structure. Subunit 1 is

Techniques Used:

ITC curve of binding of haloxyfop- R to M. tuberculosis AccD6.
Figure Legend Snippet: ITC curve of binding of haloxyfop- R to M. tuberculosis AccD6.

Techniques Used: Binding Assay

(A) Electron density of haloxyfop (yellow sticks) and composite OMIT map electron density (blue contoured at 1 σ). (B) Haloxyfop interaction with M. tuberculosis AccD6 binding site 1; (C) haloxyfop interaction with M. tuberculosis AccD6 at binding
Figure Legend Snippet: (A) Electron density of haloxyfop (yellow sticks) and composite OMIT map electron density (blue contoured at 1 σ). (B) Haloxyfop interaction with M. tuberculosis AccD6 binding site 1; (C) haloxyfop interaction with M. tuberculosis AccD6 at binding

Techniques Used: Binding Assay

M. tuberculosis AccD6 active site. (A) Two sets of oxyanion-stabilizing residues are highly conserved among the CT domains of different species, including the NH of Gly137 and Gly138 and the NH of Gly336′ and Ala367′. The structural similarity
Figure Legend Snippet: M. tuberculosis AccD6 active site. (A) Two sets of oxyanion-stabilizing residues are highly conserved among the CT domains of different species, including the NH of Gly137 and Gly138 and the NH of Gly336′ and Ala367′. The structural similarity

Techniques Used:

(A) Haloxyfop- R entry points to binding sites 1 and 2. A surface representation of AccD6 (tan) and the relationship of site 1 (haloxyfop in yellow) with site 2 (haloxyfop in cyan) is shown. Ligands are shown as sticks. (B and C) Comparison of the M. tuberculosis
Figure Legend Snippet: (A) Haloxyfop- R entry points to binding sites 1 and 2. A surface representation of AccD6 (tan) and the relationship of site 1 (haloxyfop in yellow) with site 2 (haloxyfop in cyan) is shown. Ligands are shown as sticks. (B and C) Comparison of the M. tuberculosis

Techniques Used: Binding Assay

(A) Superimposition of M. tuberculosis AccD6 and AccD5. Cα RMSD, 1.6 Å. AccD6 is in blue and AccD5 (PDB code 2A7S ) is in green. (B) Comparison of stacking interactions between M. tuberculosis AccD6 (green) and the yeast CT domain (red).
Figure Legend Snippet: (A) Superimposition of M. tuberculosis AccD6 and AccD5. Cα RMSD, 1.6 Å. AccD6 is in blue and AccD5 (PDB code 2A7S ) is in green. (B) Comparison of stacking interactions between M. tuberculosis AccD6 (green) and the yeast CT domain (red).

Techniques Used:

36) Product Images from "Biochemical evidence for relaxed substrate specificity of Nα-acetyltransferase (Rv3420c/rimI) of Mycobacterium tuberculosis"

Article Title: Biochemical evidence for relaxed substrate specificity of Nα-acetyltransferase (Rv3420c/rimI) of Mycobacterium tuberculosis

Journal: Scientific Reports

doi: 10.1038/srep28892

Relaxed substrate specificity of RimI Mtb . Results of NAT assays with substrate peptides DP8, DP9, DP10 and DP11 analyzed using MALDI-TOF/TOF. ( a ) MS/MS of 910.5 Da precursor ion (S/N = 4201) of unmodified and 952.5 Da precursor ion (S/N = 5894) of modified substrate peptide representing novel substrate specificity of RimI Mtb ( b ) MS/MS of 999.5 Da precursor ion (S/N = 7037) of unmodified and 1041.5 Da precursor ion (S/N = 4256) of modified substrate peptide representing N-terminus of conventional NatE substrate ( c ) MS/MS of 1057.8 Da precursor ion (S/N = 15916) of unmodified and 1099.5 Da precursor ion (S/N = 1011) of modified substrate peptide representing N-terminus of conventional NatB substrate ( d ) MS/MS of 1041.5 Da precursor ion (S/N=17767) of unmodified and 1083.5 Da precursor ion (S/N = 14629) of modified substrate peptide representing N-terminus of conventional NatC substrate.
Figure Legend Snippet: Relaxed substrate specificity of RimI Mtb . Results of NAT assays with substrate peptides DP8, DP9, DP10 and DP11 analyzed using MALDI-TOF/TOF. ( a ) MS/MS of 910.5 Da precursor ion (S/N = 4201) of unmodified and 952.5 Da precursor ion (S/N = 5894) of modified substrate peptide representing novel substrate specificity of RimI Mtb ( b ) MS/MS of 999.5 Da precursor ion (S/N = 7037) of unmodified and 1041.5 Da precursor ion (S/N = 4256) of modified substrate peptide representing N-terminus of conventional NatE substrate ( c ) MS/MS of 1057.8 Da precursor ion (S/N = 15916) of unmodified and 1099.5 Da precursor ion (S/N = 1011) of modified substrate peptide representing N-terminus of conventional NatB substrate ( d ) MS/MS of 1041.5 Da precursor ion (S/N=17767) of unmodified and 1083.5 Da precursor ion (S/N = 14629) of modified substrate peptide representing N-terminus of conventional NatC substrate.

Techniques Used: Mass Spectrometry, Modification, Nucleic Acid Templated Chemistry

Small-Scale Tryptic Peptide Library (STPL) assay. ( a ) Schematic representation of STPL assay ( b ) Sequences of peptides (belonging to tryptic digests of CarD, RpoA and TsaD) Nα-acetylated at neo-terminal amino acid residues by RimI Mtb , in vitro . Nα-acetylated N-terminus of TsaD is highlighted in red.
Figure Legend Snippet: Small-Scale Tryptic Peptide Library (STPL) assay. ( a ) Schematic representation of STPL assay ( b ) Sequences of peptides (belonging to tryptic digests of CarD, RpoA and TsaD) Nα-acetylated at neo-terminal amino acid residues by RimI Mtb , in vitro . Nα-acetylated N-terminus of TsaD is highlighted in red.

Techniques Used: In Vitro

Acetylation of N-termini of neighboring proteins by RimI Mtb . ( a ) MS/MS of 672.4 Da precursor ion (S/N = 1999) of unmodified and 714.4 Da precursor ion (S/N = 557) of modified substrate peptide representing N-terminus of GroES ( b ) MS/MS of 752.3 Da precursor ion (S/N = 11634) of unmodified and 794.4 Da precursor ion (S/N = 1984) of modified substrate peptide representing N-terminus of GroEL1 ( c ) MS/MS of 689.4 Da precursor ion (S/N = 409) of unmodified and 731.3 Da precursor ion (S/N = 138.5) of modified substrate peptide representing N-terminus of TsaB.
Figure Legend Snippet: Acetylation of N-termini of neighboring proteins by RimI Mtb . ( a ) MS/MS of 672.4 Da precursor ion (S/N = 1999) of unmodified and 714.4 Da precursor ion (S/N = 557) of modified substrate peptide representing N-terminus of GroES ( b ) MS/MS of 752.3 Da precursor ion (S/N = 11634) of unmodified and 794.4 Da precursor ion (S/N = 1984) of modified substrate peptide representing N-terminus of GroEL1 ( c ) MS/MS of 689.4 Da precursor ion (S/N = 409) of unmodified and 731.3 Da precursor ion (S/N = 138.5) of modified substrate peptide representing N-terminus of TsaB.

Techniques Used: Mass Spectrometry, Modification

Determination of specific activity of RimI Mtb towards peptide substrates using DTNB assay. The amount of product (CoASH) generated as a result of acetyl transfer was monitored at 412 nm. The concentration of the product was quantified using CoASH calibration curve (inset) and specific activity of RimI Mtb against each substrate plotted in terms of μmoles/mg/min. The results shown here represent mean ± SD of experiments performed in triplicate.
Figure Legend Snippet: Determination of specific activity of RimI Mtb towards peptide substrates using DTNB assay. The amount of product (CoASH) generated as a result of acetyl transfer was monitored at 412 nm. The concentration of the product was quantified using CoASH calibration curve (inset) and specific activity of RimI Mtb against each substrate plotted in terms of μmoles/mg/min. The results shown here represent mean ± SD of experiments performed in triplicate.

Techniques Used: Activity Assay, DTNB Assay, Generated, Concentration Assay

Structural alignment of RimI Mtb model (docked with peptide DP9-MARYFRR) with crystal structures of Naa50p (NatE) and TvArd1. Cyan: RimI Mtb model (developed using ITSSAR), Yellow: Substrate peptide DP9 (docked using Flexpepdock), Magenta: TvArd1 (4pV6) and Green: Naa50p (3TFY). ( a ) Key catalytic residues conserved between three structures and as listed in Supplementary Figure S5D , aligned at identical positions. Residues Y138 and Y139 (from Naa50p) and Y140 and Y141 (from TvArd1) (not shown in cartoon) and Y139 and Y140 of RimI Mtb (shown in cartoon), aligned perfectly. E25 of RimI Mtb is identified as distinctively placed in comparison with corresponding residues V29 of Naa50p and E34 of TvArd1. Hydrogen-bond between N-terminal Met of docked peptide and Y140 of RimI Mtb is represented by dotted line ( b ) Residues involved in hydrophobic contact between RimI Mtb and N-terminal Met of docked substrate peptide, defining substrate binding pocket of the enzyme ( c ) Surface cartoon of binding pocket of Naa50p/NatE ( d ) Surface cartoon of binding pocket of TvArd1 ( e ) Surface cartoon of binding pocket of RimI Mtb .
Figure Legend Snippet: Structural alignment of RimI Mtb model (docked with peptide DP9-MARYFRR) with crystal structures of Naa50p (NatE) and TvArd1. Cyan: RimI Mtb model (developed using ITSSAR), Yellow: Substrate peptide DP9 (docked using Flexpepdock), Magenta: TvArd1 (4pV6) and Green: Naa50p (3TFY). ( a ) Key catalytic residues conserved between three structures and as listed in Supplementary Figure S5D , aligned at identical positions. Residues Y138 and Y139 (from Naa50p) and Y140 and Y141 (from TvArd1) (not shown in cartoon) and Y139 and Y140 of RimI Mtb (shown in cartoon), aligned perfectly. E25 of RimI Mtb is identified as distinctively placed in comparison with corresponding residues V29 of Naa50p and E34 of TvArd1. Hydrogen-bond between N-terminal Met of docked peptide and Y140 of RimI Mtb is represented by dotted line ( b ) Residues involved in hydrophobic contact between RimI Mtb and N-terminal Met of docked substrate peptide, defining substrate binding pocket of the enzyme ( c ) Surface cartoon of binding pocket of Naa50p/NatE ( d ) Surface cartoon of binding pocket of TvArd1 ( e ) Surface cartoon of binding pocket of RimI Mtb .

Techniques Used: Binding Assay

Purification of RimI Mtb and identification of Nα-acetyltransferase activity of RimI Mtb . ( a ) Gel filtration of RimI Mtb using superdex 75 10/300GL. Ni-NTA purified RimI Mtb (as shown in protein gel) eluted as monomer (calibration curve given in inset) ( b ) Confirmation of intact mass (19.1 kDa) of purified RimI Mtb monomer using LC-ESI-MS ( c ) MS analysis of control assay (without enzyme) using DPC peptide (ARYFRR) as substrate ( d ) MS/MS analysis of precursor ion (868.5 Da) of DPC peptide in control assay ( e ) MS analysis of enzyme assay confirming acetylation of DPC peptide by RimI Mtb . Modified peptide was observed (910.5) with an increase of 42.0105 Da as compared to unmodified peptide (868.5 Da) concomitant to the addition of acetyl group ( f ) MS/MS analysis of modified (910.5 Da) precursor ion of the substrate (DPC) peptide. An increase of 42.0105 Da was observed in all the b-ions (in black) while the y-ions (in grey) remained the same as that of unmodified substrate, confirming the site of acetylation as the N-terminal amino acid i.e. Ala.
Figure Legend Snippet: Purification of RimI Mtb and identification of Nα-acetyltransferase activity of RimI Mtb . ( a ) Gel filtration of RimI Mtb using superdex 75 10/300GL. Ni-NTA purified RimI Mtb (as shown in protein gel) eluted as monomer (calibration curve given in inset) ( b ) Confirmation of intact mass (19.1 kDa) of purified RimI Mtb monomer using LC-ESI-MS ( c ) MS analysis of control assay (without enzyme) using DPC peptide (ARYFRR) as substrate ( d ) MS/MS analysis of precursor ion (868.5 Da) of DPC peptide in control assay ( e ) MS analysis of enzyme assay confirming acetylation of DPC peptide by RimI Mtb . Modified peptide was observed (910.5) with an increase of 42.0105 Da as compared to unmodified peptide (868.5 Da) concomitant to the addition of acetyl group ( f ) MS/MS analysis of modified (910.5 Da) precursor ion of the substrate (DPC) peptide. An increase of 42.0105 Da was observed in all the b-ions (in black) while the y-ions (in grey) remained the same as that of unmodified substrate, confirming the site of acetylation as the N-terminal amino acid i.e. Ala.

Techniques Used: Purification, Activity Assay, Filtration, Mass Spectrometry, Control Assay, Enzymatic Assay, Modification

In vivo protein-protein interactions between RimI Mtb and neighboring proteins. ( a ) Schematic representation of genetic context of rimI in Mtb ( b ) Mycobacterial Protein Fragment Complementation (MPFC) assay elucidating in vivo protein-protein interactions between 1) RimI Mtb and GroES 2) RimI Mtb and TsaD and 3) TsaD and TsaE, where corresponding co-transformants got selected on Trimethoprim supplemented at a concentration of 50 μg/ml.
Figure Legend Snippet: In vivo protein-protein interactions between RimI Mtb and neighboring proteins. ( a ) Schematic representation of genetic context of rimI in Mtb ( b ) Mycobacterial Protein Fragment Complementation (MPFC) assay elucidating in vivo protein-protein interactions between 1) RimI Mtb and GroES 2) RimI Mtb and TsaD and 3) TsaD and TsaE, where corresponding co-transformants got selected on Trimethoprim supplemented at a concentration of 50 μg/ml.

Techniques Used: In Vivo, Concentration Assay

37) Product Images from "The Rapid-Heat LAMPellet Method: A Potential Diagnostic Method for Human Urogenital Schistosomiasis"

Article Title: The Rapid-Heat LAMPellet Method: A Potential Diagnostic Method for Human Urogenital Schistosomiasis

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0003963

PCR verification, detection limit and specificity using outer primers F3 and B3. (A) PCR verification of expected 199 bp target length amplicon. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sh, S . haematobium DNA (1 ng); lane N, negative control (no DNA template). (B) Detection limit of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sh: S . haematobium DNA (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions of S . haematobium DNA; lane N, negative control (no DNA template). (C) Specificity of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh, Sm, Sj, Sb, Fh, Dd, Hd, Cd, Ll, Bp, As, Sv, Ts, Tt, Eg, Gi, Eh, Cp, Po, Pv, Pm, S . haematobium , S . mansoni , S . japonicum , S . bovis , Fasciola hepatica , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Strongyloides venezuelensis , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Giardia intestinalis , Entamoeba histolytica , Cryptosporidium parvum , Plasmodium ovale , P . vivax and P . malariae DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template).
Figure Legend Snippet: PCR verification, detection limit and specificity using outer primers F3 and B3. (A) PCR verification of expected 199 bp target length amplicon. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sh, S . haematobium DNA (1 ng); lane N, negative control (no DNA template). (B) Detection limit of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lane Sh: S . haematobium DNA (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions of S . haematobium DNA; lane N, negative control (no DNA template). (C) Specificity of PCR. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh, Sm, Sj, Sb, Fh, Dd, Hd, Cd, Ll, Bp, As, Sv, Ts, Tt, Eg, Gi, Eh, Cp, Po, Pv, Pm, S . haematobium , S . mansoni , S . japonicum , S . bovis , Fasciola hepatica , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Strongyloides venezuelensis , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Giardia intestinalis , Entamoeba histolytica , Cryptosporidium parvum , Plasmodium ovale , P . vivax and P . malariae DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template).

Techniques Used: Polymerase Chain Reaction, Amplification, Molecular Weight, Marker, Negative Control

Examination of aliquots of whole urine from S . haematobium -positive patients´ urine samples by LAMP. Figure shows the LAMP results (up, by color change; down, by agarose electrophoresis) when using aliquots of 100 μL of whole urine to obtain DNA as template by using (A) the i-genomic Urine DNA Extraction Mini Kit (Intron Biotechnology, UK); (B) the heating NaOH-SDS method and (C) the rapid heating method. Lanes M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 1–18: S . haematobium -positive samples; lanes N: negative controls (no DNA template).
Figure Legend Snippet: Examination of aliquots of whole urine from S . haematobium -positive patients´ urine samples by LAMP. Figure shows the LAMP results (up, by color change; down, by agarose electrophoresis) when using aliquots of 100 μL of whole urine to obtain DNA as template by using (A) the i-genomic Urine DNA Extraction Mini Kit (Intron Biotechnology, UK); (B) the heating NaOH-SDS method and (C) the rapid heating method. Lanes M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 1–18: S . haematobium -positive samples; lanes N: negative controls (no DNA template).

Techniques Used: Electrophoresis, DNA Extraction, Molecular Weight, Marker

Sensitivity of the LAMP assay in simulated human urine samples artificially contaminated with DNA from S . haematobium . (A) Sensitivity assessment of LAMP when performing the DNA extraction with the i-genomic Urine DNA Extraction Mini Kit (Intron Biotechnology, UK) from serial dilutions of S . haematobium genomic DNA. (B) Sensitivity assessment of LAMP when performing the DNA extraction with a simple heating method from serial dilutions of S . haematobium genomic DNA. Lanes M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 10 −1 –10 −11 : 10-fold serially dilutions; lanes N: negative controls (no DNA template).
Figure Legend Snippet: Sensitivity of the LAMP assay in simulated human urine samples artificially contaminated with DNA from S . haematobium . (A) Sensitivity assessment of LAMP when performing the DNA extraction with the i-genomic Urine DNA Extraction Mini Kit (Intron Biotechnology, UK) from serial dilutions of S . haematobium genomic DNA. (B) Sensitivity assessment of LAMP when performing the DNA extraction with a simple heating method from serial dilutions of S . haematobium genomic DNA. Lanes M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 10 −1 –10 −11 : 10-fold serially dilutions; lanes N: negative controls (no DNA template).

Techniques Used: Lamp Assay, DNA Extraction, Molecular Weight, Marker

Examination of aliquots of supernatants from S . haematobium -positive patients´ urine samples by LAMP. Figure shows the LAMP results (up, by color change; down, by agarose electrophoresis) when using aliquots of 100 μL of supernatants to obtain DNA as template by using (A) the i-genomic Urine DNA Extraction Mini Kit (Intron Biotechnology, UK); (B) the heating NaOH-SDS method and (C) the rapid heating method. Lanes M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 1–18: S . haematobium -positive samples; lanes N: negative controls (no DNA template).
Figure Legend Snippet: Examination of aliquots of supernatants from S . haematobium -positive patients´ urine samples by LAMP. Figure shows the LAMP results (up, by color change; down, by agarose electrophoresis) when using aliquots of 100 μL of supernatants to obtain DNA as template by using (A) the i-genomic Urine DNA Extraction Mini Kit (Intron Biotechnology, UK); (B) the heating NaOH-SDS method and (C) the rapid heating method. Lanes M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 1–18: S . haematobium -positive samples; lanes N: negative controls (no DNA template).

Techniques Used: Electrophoresis, DNA Extraction, Molecular Weight, Marker

Setting up LAMP assay. (A) LAMP amplification results obtained at different incubation times (30, 50 and 60 min) tested in a heating block by the addition of SYBR Green I (up) or by visualization on agarose gel (down). Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes 30, 50, 60, amplification results of S . haematobium DNA (1 ng) for 30, 50 and 60 minutes of incubation time, respectively. (B) Specificity of the LAMP assay for S . haematobium . A ladder of multiple bands of different sizes could be only observed in S . haematobium DNA sample. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh, Sm, Sj, Sb, Fh, Dd, Hd, Cd, Ll, Bp, As, Sv, Ts, Tt, Eg, Gi, Eh, Cp, Po, Pv and Pm, S . haematobium , S . mansoni , S . japonicum , S . bovis , Fasciola hepatica , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Strongyloides venezuelensis , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Giardia intestinalis , Entamoeba histolytica , Cryptosporidium parvum , Plasmodium ovale , P . vivax and P . malariae DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template). (C) Sensitivity assessment performed with LAMP at 63°C for 50 min using serial dilutions of S . haematobium genomic DNA. Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions; lane N: negative controls (no DNA template).
Figure Legend Snippet: Setting up LAMP assay. (A) LAMP amplification results obtained at different incubation times (30, 50 and 60 min) tested in a heating block by the addition of SYBR Green I (up) or by visualization on agarose gel (down). Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes 30, 50, 60, amplification results of S . haematobium DNA (1 ng) for 30, 50 and 60 minutes of incubation time, respectively. (B) Specificity of the LAMP assay for S . haematobium . A ladder of multiple bands of different sizes could be only observed in S . haematobium DNA sample. Lane M, 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh, Sm, Sj, Sb, Fh, Dd, Hd, Cd, Ll, Bp, As, Sv, Ts, Tt, Eg, Gi, Eh, Cp, Po, Pv and Pm, S . haematobium , S . mansoni , S . japonicum , S . bovis , Fasciola hepatica , Dicrocoelium dendriticum , Hymenolepis diminuta , Calicophoron daubneyi , Loa loa , Brugia pahangi , Anisakis simplex , Strongyloides venezuelensis , Trichinella spiralis , Taenia taeniformis , Echinococcus granulosus , Giardia intestinalis , Entamoeba histolytica , Cryptosporidium parvum , Plasmodium ovale , P . vivax and P . malariae DNA samples (1 ng/each), respectively; lane N, negative control (no DNA template). (C) Sensitivity assessment performed with LAMP at 63°C for 50 min using serial dilutions of S . haematobium genomic DNA. Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 10 −1 –10 −9 : 10-fold serially dilutions; lane N: negative controls (no DNA template).

Techniques Used: Lamp Assay, Amplification, Incubation, Blocking Assay, SYBR Green Assay, Agarose Gel Electrophoresis, Molecular Weight, Marker, Negative Control

Examination of aliquots of urinary sediment (pellets) from S . haematobium -positive patients´ urine samples by LAMP. Figure shows the LAMP results (up, by color change; down, by agarose electrophoresis) when using aliquots of 100 μL of pellets to obtain DNA as template by using (A) the i-genomic Urine DNA Extraction Mini Kit (Intron Biotechnology, UK); (B) the heating NaOH-SDS method and (C) the rapid heating method-the rapid-heat LAMPellet method-. Lanes M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 1–18: S . haematobium -positive samples; lanes N: negative controls (no DNA template).
Figure Legend Snippet: Examination of aliquots of urinary sediment (pellets) from S . haematobium -positive patients´ urine samples by LAMP. Figure shows the LAMP results (up, by color change; down, by agarose electrophoresis) when using aliquots of 100 μL of pellets to obtain DNA as template by using (A) the i-genomic Urine DNA Extraction Mini Kit (Intron Biotechnology, UK); (B) the heating NaOH-SDS method and (C) the rapid heating method-the rapid-heat LAMPellet method-. Lanes M: 50 bp DNA ladder (Molecular weight marker XIII, Roche); lanes Sh: genomic DNA from S . haematobium (1 ng); lanes 1–18: S . haematobium -positive samples; lanes N: negative controls (no DNA template).

Techniques Used: Electrophoresis, DNA Extraction, Molecular Weight, Marker

Lamp primer set targeting the selected sequence (GenBank Accession No. AJ223838) for ribosomal intergenic spacer S . haematobium DNA region amplification. (A) The location of the LAMP primers within the selected sequence is shown. Arrows indicate the direction of extension. (B). Sequence of LAMP primers: F3, forward outer primer; B3, reverse outer primer; FIP, forward inner primer (comprising F1c and F2 sequences); BIP, reverse inner primer (comprising B1c and B2 sequences); LF (loop forward primer); LB (loop backward primer).
Figure Legend Snippet: Lamp primer set targeting the selected sequence (GenBank Accession No. AJ223838) for ribosomal intergenic spacer S . haematobium DNA region amplification. (A) The location of the LAMP primers within the selected sequence is shown. Arrows indicate the direction of extension. (B). Sequence of LAMP primers: F3, forward outer primer; B3, reverse outer primer; FIP, forward inner primer (comprising F1c and F2 sequences); BIP, reverse inner primer (comprising B1c and B2 sequences); LF (loop forward primer); LB (loop backward primer).

Techniques Used: Sequencing, Amplification

38) Product Images from "Expression and characterization of the first snail-derived UDP-N-acetyl-?-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase"

Article Title: Expression and characterization of the first snail-derived UDP-N-acetyl-?-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase

Journal: Glycoconjugate Journal

doi: 10.1007/s10719-013-9486-6

Branch (group Ib according to [ 3 ]) of the phylogenetic tree of ppGalNAcTs. The phylogenetic tree is based on the neighbor-joining method based on amino acid sequences using ClustalW software. The branch length represents evolutionary distance between the members of the family ppGalNAcT enzymes. The following Genbank accession numbers were used: Gallus gallus T16 (XP_001231965.1), Xenopus tropicalis T16 (NP_001039091.1), Homo sapiens T16 (AJ505951), Danio rerio T16 (XP_001339749.3), Danio rerio T14 (NP_001038460.1), Xenopus tropicalis T14 (NP_001072369), Gallus gallus T14 (XM_419370.2), Homo sapiens T14 (Y09324), Drosophila melanogaster T2 (NP_608773.2), Danio rerio T2 (NP_001121823.1), Xenopus tropicalis T2 (XP_002931524.1), Gallus gallus T2 (XP_419581.2), Homo sapiens T2 (X85019), Biomphalaria glabrata (KC182513), Crassostrea gigas T2 (EKC38600), Caenorhabditis elegans GLY4 (NP_507850.2), Toxoplasma gondii T1 (XP_002365147.1), Toxoplasma gondii T3 (XP_002369811.1), Toxoplasma gondii T2 (XP_002365091.1)
Figure Legend Snippet: Branch (group Ib according to [ 3 ]) of the phylogenetic tree of ppGalNAcTs. The phylogenetic tree is based on the neighbor-joining method based on amino acid sequences using ClustalW software. The branch length represents evolutionary distance between the members of the family ppGalNAcT enzymes. The following Genbank accession numbers were used: Gallus gallus T16 (XP_001231965.1), Xenopus tropicalis T16 (NP_001039091.1), Homo sapiens T16 (AJ505951), Danio rerio T16 (XP_001339749.3), Danio rerio T14 (NP_001038460.1), Xenopus tropicalis T14 (NP_001072369), Gallus gallus T14 (XM_419370.2), Homo sapiens T14 (Y09324), Drosophila melanogaster T2 (NP_608773.2), Danio rerio T2 (NP_001121823.1), Xenopus tropicalis T2 (XP_002931524.1), Gallus gallus T2 (XP_419581.2), Homo sapiens T2 (X85019), Biomphalaria glabrata (KC182513), Crassostrea gigas T2 (EKC38600), Caenorhabditis elegans GLY4 (NP_507850.2), Toxoplasma gondii T1 (XP_002365147.1), Toxoplasma gondii T3 (XP_002369811.1), Toxoplasma gondii T2 (XP_002365091.1)

Techniques Used: Software

39) Product Images from "The DNA-binding network of Mycobacterium tuberculosis"

Article Title: The DNA-binding network of Mycobacterium tuberculosis

Journal: Nature Communications

doi: 10.1038/ncomms6829

A global view of DNA binding. ( a ) TF-binding sites identified by ChIP-seq plotted with Circos 59 . Sense (blue) and antisense (orange) CDS and operon boundaries illustrated with black edges. The 4.4-Mb H37Rv chromosome is divided into nonoverlapping 50-bp windows, and green spikes represent the total number of TF-binding events within each window. ( b ) Histogram of number of TF-binding events per 50-bp window. ( c ) Number of ChIP-binding events (out-degree) for each of the 156 DNA-binding proteins with at least one binding site.
Figure Legend Snippet: A global view of DNA binding. ( a ) TF-binding sites identified by ChIP-seq plotted with Circos 59 . Sense (blue) and antisense (orange) CDS and operon boundaries illustrated with black edges. The 4.4-Mb H37Rv chromosome is divided into nonoverlapping 50-bp windows, and green spikes represent the total number of TF-binding events within each window. ( b ) Histogram of number of TF-binding events per 50-bp window. ( c ) Number of ChIP-binding events (out-degree) for each of the 156 DNA-binding proteins with at least one binding site.

Techniques Used: Binding Assay, Chromatin Immunoprecipitation, DNA Binding Assay

40) Product Images from "The NIH-NIAID Filariasis Research Reagent Resource Center"

Article Title: The NIH-NIAID Filariasis Research Reagent Resource Center

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0001261

The geographic locations of recipient laboratories for FR3 molecular reagents. Country flags obtained from http://www.public-domain-image.com and http://www.clker.com .
Figure Legend Snippet: The geographic locations of recipient laboratories for FR3 molecular reagents. Country flags obtained from http://www.public-domain-image.com and http://www.clker.com .

Techniques Used:

The geographic locations of recipient laboratories for FR3 parasite reagents. Country flags obtained from http://www.public-domain-image.com and http://www.clker.com .
Figure Legend Snippet: The geographic locations of recipient laboratories for FR3 parasite reagents. Country flags obtained from http://www.public-domain-image.com and http://www.clker.com .

Techniques Used:

Related Articles

Amplification:

Article Title: High rates of parasite recrudescence following intermittent preventive treatment with sulphadoxine-pyrimethamine during pregnancy in Benin
Article Snippet: .. Samples underwent 40 cycles of amplification using the ViiA™ 7 Real-Time PCR system (Applied Biosystem) and were quantified using a DNA standard range made from a suspension of in vitro cultured 3D7 P. falciparum line (obtained through the MR4 as part of the BEI Resources Repository, NIAID, NIH: Plasmodium falciparum 3D7 GL, MRA-1001, deposited by Megan Dowler, Walter Reed Army Institute of Research). .. Nested PCR amplification of pfdhfr and pfdhps genes and detection of SNPs Parasite DNA was amplified with outer and nested specific primers targeting the pfdhfr and pfdhps genes, as described [ , ].

In Vitro:

Article Title: High rates of parasite recrudescence following intermittent preventive treatment with sulphadoxine-pyrimethamine during pregnancy in Benin
Article Snippet: .. Samples underwent 40 cycles of amplification using the ViiA™ 7 Real-Time PCR system (Applied Biosystem) and were quantified using a DNA standard range made from a suspension of in vitro cultured 3D7 P. falciparum line (obtained through the MR4 as part of the BEI Resources Repository, NIAID, NIH: Plasmodium falciparum 3D7 GL, MRA-1001, deposited by Megan Dowler, Walter Reed Army Institute of Research). .. Nested PCR amplification of pfdhfr and pfdhps genes and detection of SNPs Parasite DNA was amplified with outer and nested specific primers targeting the pfdhfr and pfdhps genes, as described [ , ].

Isolation:

Article Title: The potential for flower nectar to allow mosquito to mosquito transmission of Francisella tularensis
Article Snippet: .. To confirm that PCR specifically identified F . tularensis , cell extracts of isolated bacteria were subjected to Western blotting using an anti-IglC monoclonal antibody (BEI resources) as a probe. ..

Cell Culture:

Article Title: High rates of parasite recrudescence following intermittent preventive treatment with sulphadoxine-pyrimethamine during pregnancy in Benin
Article Snippet: .. Samples underwent 40 cycles of amplification using the ViiA™ 7 Real-Time PCR system (Applied Biosystem) and were quantified using a DNA standard range made from a suspension of in vitro cultured 3D7 P. falciparum line (obtained through the MR4 as part of the BEI Resources Repository, NIAID, NIH: Plasmodium falciparum 3D7 GL, MRA-1001, deposited by Megan Dowler, Walter Reed Army Institute of Research). .. Nested PCR amplification of pfdhfr and pfdhps genes and detection of SNPs Parasite DNA was amplified with outer and nested specific primers targeting the pfdhfr and pfdhps genes, as described [ , ].

Real-time Polymerase Chain Reaction:

Article Title: High rates of parasite recrudescence following intermittent preventive treatment with sulphadoxine-pyrimethamine during pregnancy in Benin
Article Snippet: .. Samples underwent 40 cycles of amplification using the ViiA™ 7 Real-Time PCR system (Applied Biosystem) and were quantified using a DNA standard range made from a suspension of in vitro cultured 3D7 P. falciparum line (obtained through the MR4 as part of the BEI Resources Repository, NIAID, NIH: Plasmodium falciparum 3D7 GL, MRA-1001, deposited by Megan Dowler, Walter Reed Army Institute of Research). .. Nested PCR amplification of pfdhfr and pfdhps genes and detection of SNPs Parasite DNA was amplified with outer and nested specific primers targeting the pfdhfr and pfdhps genes, as described [ , ].

Polymerase Chain Reaction:

Article Title: The potential for flower nectar to allow mosquito to mosquito transmission of Francisella tularensis
Article Snippet: .. To confirm that PCR specifically identified F . tularensis , cell extracts of isolated bacteria were subjected to Western blotting using an anti-IglC monoclonal antibody (BEI resources) as a probe. ..

Article Title: Associations between gut microbial colonization in early life and respiratory outcomes in cystic fibrosis
Article Snippet: .. Positive PCR controls composed of a mock community DNA preparation originally developed for the Human Microbiome Project (BEI Resources) were also included. .. Our quality control procedures required exact matches to the barcode and to the proximal primer and eliminated any sequence that contained an ambiguous base call at any position.

Selection:

Article Title: Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound
Article Snippet: .. The pbgst knockout plasmids (pbgst-ko 1A and pbgst-ko 1B ) have the pL0001 plasmid backbone (MRA-770, BEI Resources), which contains the Toxoplasma gondii dihydrofolate reductase/thymidylate synthase (tgdhfr/ts ) selection marker cassette. .. For plasmid design, the pbgst DNA sequence (gene identifier in PlasmoDB as PB301263.00.0) was retrieved from PlasmoDB as an incomplete sequence.

Knock-Out:

Article Title: Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound
Article Snippet: .. The pbgst knockout plasmids (pbgst-ko 1A and pbgst-ko 1B ) have the pL0001 plasmid backbone (MRA-770, BEI Resources), which contains the Toxoplasma gondii dihydrofolate reductase/thymidylate synthase (tgdhfr/ts ) selection marker cassette. .. For plasmid design, the pbgst DNA sequence (gene identifier in PlasmoDB as PB301263.00.0) was retrieved from PlasmoDB as an incomplete sequence.

Marker:

Article Title: Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound
Article Snippet: .. The pbgst knockout plasmids (pbgst-ko 1A and pbgst-ko 1B ) have the pL0001 plasmid backbone (MRA-770, BEI Resources), which contains the Toxoplasma gondii dihydrofolate reductase/thymidylate synthase (tgdhfr/ts ) selection marker cassette. .. For plasmid design, the pbgst DNA sequence (gene identifier in PlasmoDB as PB301263.00.0) was retrieved from PlasmoDB as an incomplete sequence.

Western Blot:

Article Title: The potential for flower nectar to allow mosquito to mosquito transmission of Francisella tularensis
Article Snippet: .. To confirm that PCR specifically identified F . tularensis , cell extracts of isolated bacteria were subjected to Western blotting using an anti-IglC monoclonal antibody (BEI resources) as a probe. ..

Plasmid Preparation:

Article Title: Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound
Article Snippet: .. The pbgst knockout plasmids (pbgst-ko 1A and pbgst-ko 1B ) have the pL0001 plasmid backbone (MRA-770, BEI Resources), which contains the Toxoplasma gondii dihydrofolate reductase/thymidylate synthase (tgdhfr/ts ) selection marker cassette. .. For plasmid design, the pbgst DNA sequence (gene identifier in PlasmoDB as PB301263.00.0) was retrieved from PlasmoDB as an incomplete sequence.

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  • 93
    BEI Resources genomic dna
    Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic <t>DNA,</t> amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine <t>microbiome</t> composition.
    Genomic Dna, supplied by BEI Resources, used in various techniques. Bioz Stars score: 93/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    BEI Resources influenza virus genomic dna
    Hierarchical clustering of mixed samples demonstrates the resolution capabilities of the UBDA array . This dendogram and heat map illustrates a unique bio-signature pattern obtained from Lactobacillus <t>plantarum</t> , mixed sample (synthetic mixture in a 4:1 ratio of L. plantarum and Streptococcus mitis ), S. mitis , mixed sample (a synthetic mixture of L. plantarum and S. mitis genomic <t>DNA</t> in a ratio of 4:1 with a spike-in of pBluescript plasmid at 50 ng) and pBluescript plasmid. Normalized data from the 9-mer data set were filtered for intensity signals greater than the 20 th percentile. Only intensity signals with a fold change of 5 or greater were included. These 36,059 elements were subjected to hierarchical clustering with Euclidean distance being used as a similarity measure. The signal intensity values were represented on a log 2 scale and range from 8.4 to 13.4.
    Influenza Virus Genomic Dna, supplied by BEI Resources, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    BEI Resources dna standard range
    Prevalence rates of recurrent infections. Plasmodium parasites were counted against 200 leukocytes with a 100 × objective lens under oil immersion. Each qPCR reaction mixture contained 5 μL <t>DNA</t> template in a final volume of 20 μL, 10 μL of Master Mix (Applied Biosystem), both the genus-specific and P. falciparum specific primers and probes detection system (Plasmo/Pf) as described [ 24 ]. Panel A : Prevalence rates of recurrent infections assessed by microscopy (BS) and <t>PCR.</t> Data are shown as pooled (covering the two months following treatment) or split into first and second month (days 7–30 or 31–60). Panel B : Prevalence rates of recurrent infections assessed by PCR according to the IPTp dose received. Data are shown as pooled (covering the two months following treatment) or split into first and second month (days seven-30 or 31–60).
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    90
    BEI Resources s mansoni dna
    A sequence of images illustrating the plasma separation process. (A) A 200 μL of blood sample spiked with S. <t>mansoni</t> <t>DNA</t> was loaded into the superhydrophobic plasma separator. (B) When the top cover was closed, the blood was sandwiched between
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    Image Search Results


    Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic DNA, amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine microbiome composition.

    Journal: Scientific Reports

    Article Title: The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization

    doi: 10.1038/s41598-017-11427-2

    Figure Lengend Snippet: Experimental Workflow. Approximately 1 mL of saliva was collected from study participants using a commercially available kit from OMNIgene. Bacteria within the saliva samples were then vigorously lysed using both enzymatic and mechanical techniques. After purifying genomic DNA, amplicons from the 16S rRNA gene were generated, sequenced on an Illumina MiSeq, and analyzed using the DADA2 computational pipeline to determine microbiome composition.

    Article Snippet: To do so, we compared the performance of two commonly utilized regions, V1V2 and V4V5, using a mock community composed of bacterial genomic DNA, developed for the Human Microbiome Project (HMP) and available through BEI Resources (HM-783D).

    Techniques: Generated

    Hierarchical clustering of mixed samples demonstrates the resolution capabilities of the UBDA array . This dendogram and heat map illustrates a unique bio-signature pattern obtained from Lactobacillus plantarum , mixed sample (synthetic mixture in a 4:1 ratio of L. plantarum and Streptococcus mitis ), S. mitis , mixed sample (a synthetic mixture of L. plantarum and S. mitis genomic DNA in a ratio of 4:1 with a spike-in of pBluescript plasmid at 50 ng) and pBluescript plasmid. Normalized data from the 9-mer data set were filtered for intensity signals greater than the 20 th percentile. Only intensity signals with a fold change of 5 or greater were included. These 36,059 elements were subjected to hierarchical clustering with Euclidean distance being used as a similarity measure. The signal intensity values were represented on a log 2 scale and range from 8.4 to 13.4.

    Journal: BMC Microbiology

    Article Title: A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms

    doi: 10.1186/1471-2180-11-132

    Figure Lengend Snippet: Hierarchical clustering of mixed samples demonstrates the resolution capabilities of the UBDA array . This dendogram and heat map illustrates a unique bio-signature pattern obtained from Lactobacillus plantarum , mixed sample (synthetic mixture in a 4:1 ratio of L. plantarum and Streptococcus mitis ), S. mitis , mixed sample (a synthetic mixture of L. plantarum and S. mitis genomic DNA in a ratio of 4:1 with a spike-in of pBluescript plasmid at 50 ng) and pBluescript plasmid. Normalized data from the 9-mer data set were filtered for intensity signals greater than the 20 th percentile. Only intensity signals with a fold change of 5 or greater were included. These 36,059 elements were subjected to hierarchical clustering with Euclidean distance being used as a similarity measure. The signal intensity values were represented on a log 2 scale and range from 8.4 to 13.4.

    Article Snippet: Brucella species, Cryptosporidium parvum, Lactobacillus plantarum , Streptococcus mitis , Escherichia coli and Influenza virus genomic DNA was obtained from BEI resources and ATCC (Manasses, VA).

    Techniques: Plasmid Preparation

    Prevalence rates of recurrent infections. Plasmodium parasites were counted against 200 leukocytes with a 100 × objective lens under oil immersion. Each qPCR reaction mixture contained 5 μL DNA template in a final volume of 20 μL, 10 μL of Master Mix (Applied Biosystem), both the genus-specific and P. falciparum specific primers and probes detection system (Plasmo/Pf) as described [ 24 ]. Panel A : Prevalence rates of recurrent infections assessed by microscopy (BS) and PCR. Data are shown as pooled (covering the two months following treatment) or split into first and second month (days 7–30 or 31–60). Panel B : Prevalence rates of recurrent infections assessed by PCR according to the IPTp dose received. Data are shown as pooled (covering the two months following treatment) or split into first and second month (days seven-30 or 31–60).

    Journal: Malaria Journal

    Article Title: High rates of parasite recrudescence following intermittent preventive treatment with sulphadoxine-pyrimethamine during pregnancy in Benin

    doi: 10.1186/1475-2875-12-195

    Figure Lengend Snippet: Prevalence rates of recurrent infections. Plasmodium parasites were counted against 200 leukocytes with a 100 × objective lens under oil immersion. Each qPCR reaction mixture contained 5 μL DNA template in a final volume of 20 μL, 10 μL of Master Mix (Applied Biosystem), both the genus-specific and P. falciparum specific primers and probes detection system (Plasmo/Pf) as described [ 24 ]. Panel A : Prevalence rates of recurrent infections assessed by microscopy (BS) and PCR. Data are shown as pooled (covering the two months following treatment) or split into first and second month (days 7–30 or 31–60). Panel B : Prevalence rates of recurrent infections assessed by PCR according to the IPTp dose received. Data are shown as pooled (covering the two months following treatment) or split into first and second month (days seven-30 or 31–60).

    Article Snippet: Samples underwent 40 cycles of amplification using the ViiA™ 7 Real-Time PCR system (Applied Biosystem) and were quantified using a DNA standard range made from a suspension of in vitro cultured 3D7 P. falciparum line (obtained through the MR4 as part of the BEI Resources Repository, NIAID, NIH: Plasmodium falciparum 3D7 GL, MRA-1001, deposited by Megan Dowler, Walter Reed Army Institute of Research).

    Techniques: Real-time Polymerase Chain Reaction, Microscopy, Polymerase Chain Reaction

    A sequence of images illustrating the plasma separation process. (A) A 200 μL of blood sample spiked with S. mansoni DNA was loaded into the superhydrophobic plasma separator. (B) When the top cover was closed, the blood was sandwiched between

    Journal: Lab on a chip

    Article Title: A High-Efficiency Superhydrophobic Plasma Separator

    doi: 10.1039/c5lc01235j

    Figure Lengend Snippet: A sequence of images illustrating the plasma separation process. (A) A 200 μL of blood sample spiked with S. mansoni DNA was loaded into the superhydrophobic plasma separator. (B) When the top cover was closed, the blood was sandwiched between

    Article Snippet: 200 μL of the whole blood spiked with S. mansoni DNA (obtained from the Schistosomiasis Resource Center, for distribution by BEI Resources, NIAID, NIH) was loaded into the blood well ( ).

    Techniques: Sequencing

    (A) Recovery efficiency of S. mansoni genomic DNA on our plasma separator at various concentrations. (B) Endpoint, fluorescence images of intercalating dye in three amplification chambers, target DNA amount in each chamber is 10 fg, 1 fg and 0 fg (negative

    Journal: Lab on a chip

    Article Title: A High-Efficiency Superhydrophobic Plasma Separator

    doi: 10.1039/c5lc01235j

    Figure Lengend Snippet: (A) Recovery efficiency of S. mansoni genomic DNA on our plasma separator at various concentrations. (B) Endpoint, fluorescence images of intercalating dye in three amplification chambers, target DNA amount in each chamber is 10 fg, 1 fg and 0 fg (negative

    Article Snippet: 200 μL of the whole blood spiked with S. mansoni DNA (obtained from the Schistosomiasis Resource Center, for distribution by BEI Resources, NIAID, NIH) was loaded into the blood well ( ).

    Techniques: Fluorescence, Amplification