dna colonic hiv rna  (Qiagen)

 
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    Name:
    QIAamp Viral RNA Mini Kit
    Description:
    For isolation of viral RNA from cell free body fluids Kit contents Qiagen QIAamp Viral RNA Mini Kit 50 preps 140L Sample 50L Elution Volume Liquid Media Sample Viral RNA Purification Silica Technology Spin Column Format Manual Processing 90 Yield 20 to 40 min Time Run Ideal for PCR qPCR Real time PCR For Isolation of Viral RNA from Cell free Body Fluids Includes 50 QIAamp Mini Spin Columns Carrier RNA 2mL Collection Tubes RNase free Buffers Benefits Rapid isolation of high quality ready to use RNA No organic extraction or alcohol precipitation Consistent high yields Complete removal of contaminants and inhibitors
    Catalog Number:
    52904
    Price:
    257
    Category:
    QIAamp Viral RNA Mini Kit
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    Structured Review

    Qiagen dna colonic hiv rna
    QIAamp Viral RNA Mini Kit
    For isolation of viral RNA from cell free body fluids Kit contents Qiagen QIAamp Viral RNA Mini Kit 50 preps 140L Sample 50L Elution Volume Liquid Media Sample Viral RNA Purification Silica Technology Spin Column Format Manual Processing 90 Yield 20 to 40 min Time Run Ideal for PCR qPCR Real time PCR For Isolation of Viral RNA from Cell free Body Fluids Includes 50 QIAamp Mini Spin Columns Carrier RNA 2mL Collection Tubes RNase free Buffers Benefits Rapid isolation of high quality ready to use RNA No organic extraction or alcohol precipitation Consistent high yields Complete removal of contaminants and inhibitors
    https://www.bioz.com/result/dna colonic hiv rna/product/Qiagen
    Average 90 stars, based on 6755 article reviews
    Price from $9.99 to $1999.99
    dna colonic hiv rna - by Bioz Stars, 2020-09
    90/100 stars

    Images

    1) Product Images from "Initiation of antiretroviral therapy before detection of colonic infiltration by HIV reduces viral reservoirs, inflammation and immune activation"

    Article Title: Initiation of antiretroviral therapy before detection of colonic infiltration by HIV reduces viral reservoirs, inflammation and immune activation

    Journal: Journal of the International AIDS Society

    doi: 10.7448/IAS.19.1.21163

    HIV RNA in the peripheral blood and cerebrospinal fluid during acute HIV infection. HIV RNA measurements during acute HIV infection are compared between participants with detectable colonic HIV RNA and undetectable colonic HIV RNA. Statistically significant pairwise comparisons ( p
    Figure Legend Snippet: HIV RNA in the peripheral blood and cerebrospinal fluid during acute HIV infection. HIV RNA measurements during acute HIV infection are compared between participants with detectable colonic HIV RNA and undetectable colonic HIV RNA. Statistically significant pairwise comparisons ( p

    Techniques Used: Infection

    Total HIV DNA in the peripheral blood and colon before and after ART. Total HIV DNA measurements in the (a) peripheral blood and (b) colon are compared before and after 24 weeks of ART. Statistically significant pairwise comparisons ( p
    Figure Legend Snippet: Total HIV DNA in the peripheral blood and colon before and after ART. Total HIV DNA measurements in the (a) peripheral blood and (b) colon are compared before and after 24 weeks of ART. Statistically significant pairwise comparisons ( p

    Techniques Used:

    2) Product Images from "Lack of Bax Prevents Influenza A Virus-Induced Apoptosis and Causes Diminished Viral Replication ▿"

    Article Title: Lack of Bax Prevents Influenza A Virus-Induced Apoptosis and Causes Diminished Viral Replication ▿

    Journal: Journal of Virology

    doi: 10.1128/JVI.02672-08

    Influenza A virus replication is dependent upon opposite virus-induced effects on Bax and Bak activity that are unlikely to be interferon related. (A) Influenza A virus replication was analyzed by plaque assay. Virus replication is severely attenuated in Bax KO cells, resulting in a 2-log decrease in PFU/ml compared to the WT. Bak KO cells allow a maximum replication similar to that of the WT, while Bax/Bak DKO cells show a slight elevation of infectious titers during infection. These results indicate that Bax is proviral during infection, while Bak is dispensable for replication. (B) Bax was transiently expressed in all cell types by Lipofectamine 2000 transfection of a C2-Bax-GFP construct prior to infection, and supernatant samples were collected for plaque assay at 48 hpi. Baseline virus replication in each cell type was evaluated using empty C2-GFP plasmid transfection. Bax reconstitution in Bax KO cells resulted in a fivefold increase in infectious titers compared to the control ( P = 0.0007). A minimal effect on the virus titer was seen after Bax overexpression by transient transfection in WT cells compared to empty plasmid controls. (C) Influenza A virus replication was assessed by reverse transcription-PCR. Serial dilutions of stock virus at known concentrations were also analyzed to generate a standard curve to which experimental samples were compared, thus calculating the approximate number of influenza A virus particles/ml in each sample. By 24 hpi, Bax KO, Bak KO, and Bax/Bak DKO cells all showed significantly higher levels of influenza A virus RNA released into the cell culture supernatant than did WT cells. (D) Interferon activity was assessed by infecting mock- and influenza A virus-infected cells with interferon-sensitive, GFP-linked NDV and quantifying the mean GFP expression levels of 10,000 events per condition by FACS analysis. Each assay was run in triplicate, and data are expressed as the ratio of the numbers of influenza A virus-infected to mock-infected cells per cell type. After influenza A virus infection, Bak KO cells exhibited a slight decrease in ratio compared to the WT, representing a 30% increase in interferon activity ( P = 0.002). Bax KO and Bax/Bak DKO cells both showed similar fluorescence changes compared to the WT after infection. Due the high degree of similarity between cell types, these results suggest that the interferon response in infected cells is modulated by viral replication in the presence of Bak and is only slightly modified by Bax activity during influenza A virus infection. As an elevated interferon response typically leads to a reduced virus replication capacity, these results also suggest that it is unlikely that the observed trends in infectious virus titer are due to virus-induced interferon signaling.
    Figure Legend Snippet: Influenza A virus replication is dependent upon opposite virus-induced effects on Bax and Bak activity that are unlikely to be interferon related. (A) Influenza A virus replication was analyzed by plaque assay. Virus replication is severely attenuated in Bax KO cells, resulting in a 2-log decrease in PFU/ml compared to the WT. Bak KO cells allow a maximum replication similar to that of the WT, while Bax/Bak DKO cells show a slight elevation of infectious titers during infection. These results indicate that Bax is proviral during infection, while Bak is dispensable for replication. (B) Bax was transiently expressed in all cell types by Lipofectamine 2000 transfection of a C2-Bax-GFP construct prior to infection, and supernatant samples were collected for plaque assay at 48 hpi. Baseline virus replication in each cell type was evaluated using empty C2-GFP plasmid transfection. Bax reconstitution in Bax KO cells resulted in a fivefold increase in infectious titers compared to the control ( P = 0.0007). A minimal effect on the virus titer was seen after Bax overexpression by transient transfection in WT cells compared to empty plasmid controls. (C) Influenza A virus replication was assessed by reverse transcription-PCR. Serial dilutions of stock virus at known concentrations were also analyzed to generate a standard curve to which experimental samples were compared, thus calculating the approximate number of influenza A virus particles/ml in each sample. By 24 hpi, Bax KO, Bak KO, and Bax/Bak DKO cells all showed significantly higher levels of influenza A virus RNA released into the cell culture supernatant than did WT cells. (D) Interferon activity was assessed by infecting mock- and influenza A virus-infected cells with interferon-sensitive, GFP-linked NDV and quantifying the mean GFP expression levels of 10,000 events per condition by FACS analysis. Each assay was run in triplicate, and data are expressed as the ratio of the numbers of influenza A virus-infected to mock-infected cells per cell type. After influenza A virus infection, Bak KO cells exhibited a slight decrease in ratio compared to the WT, representing a 30% increase in interferon activity ( P = 0.002). Bax KO and Bax/Bak DKO cells both showed similar fluorescence changes compared to the WT after infection. Due the high degree of similarity between cell types, these results suggest that the interferon response in infected cells is modulated by viral replication in the presence of Bak and is only slightly modified by Bax activity during influenza A virus infection. As an elevated interferon response typically leads to a reduced virus replication capacity, these results also suggest that it is unlikely that the observed trends in infectious virus titer are due to virus-induced interferon signaling.

    Techniques Used: Activity Assay, Plaque Assay, Infection, Transfection, Construct, Plasmid Preparation, Over Expression, Polymerase Chain Reaction, Cell Culture, Expressing, FACS, Fluorescence, Modification

    3) Product Images from "Nucleic acid assay system for tier II labs and moderately complex clinics to detect HIV in low-resource settings"

    Article Title: Nucleic acid assay system for tier II labs and moderately complex clinics to detect HIV in low-resource settings

    Journal: The Journal of infectious diseases

    doi: 10.1086/650388

    Integrated assays using plasma spiked with Armored RNA HIV. Armored RNA HIV was spiked into human plasma at concentrations ranging from 10,000 copies/mL to 1,000 copies/mL amd extracted with a QIAamp® Viral RNA Mini Kit according to the manufacturer’s
    Figure Legend Snippet: Integrated assays using plasma spiked with Armored RNA HIV. Armored RNA HIV was spiked into human plasma at concentrations ranging from 10,000 copies/mL to 1,000 copies/mL amd extracted with a QIAamp® Viral RNA Mini Kit according to the manufacturer’s

    Techniques Used:

    4) Product Images from "Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR"

    Article Title: Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.41.11.5273-5276.2003

    Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .
    Figure Legend Snippet: Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .

    Techniques Used: Amplification, Serial Dilution, Nested PCR, Negative Control

    Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).
    Figure Legend Snippet: Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).

    Techniques Used: Amplification, Serial Dilution, Plasmid Preparation, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Software, Hybridization, Fluorescence

    5) Product Images from "High level of HIV-1 drug resistance mutations in patients with unsuppressed viral loads in rural northern South Africa"

    Article Title: High level of HIV-1 drug resistance mutations in patients with unsuppressed viral loads in rural northern South Africa

    Journal: AIDS Research and Therapy

    doi: 10.1186/s12981-017-0161-z

    Comparing the DRM in RNA (plasma) and DNA (peripheral blood mononuclear cells). a NRTI. b NNRTI
    Figure Legend Snippet: Comparing the DRM in RNA (plasma) and DNA (peripheral blood mononuclear cells). a NRTI. b NNRTI

    Techniques Used:

    6) Product Images from "Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses"

    Article Title: Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses

    Journal: Nature microbiology

    doi: 10.1038/nmicrobiol.2017.101

    NS1 unique regions are important for modulating host responses Human monocyte-derived dendritic cells (MDDCs) were transduced with either only empty lentiviral vectors (empty) or lentivirus vectors that express either EBOV-VP35, hRSV-NS1, hRSV-NS1-(1-118), hRSV-NS1-L132A/L133A. RNA was isolated from transduced MDDCs that were either mock-infected or infected with SeV. RNA was extracted at the indicated hours post-infection; and a, IFN-β, b, TNF-α, c, ISG54, and d, ISG56 mRNA levels were quantified RT-qPCR, normalizing their levels to that of β-actin mRNA. The graph indicates the fold-change relative to the mock-infected samples. For a–d, symbols are: ○, empty vector; ▲, hRSV NS1 1-118; ▼, hRSV NS1 L132A/L133A; ■, hRSV NS1 WT; and ●, EBOV VP35. hRSV NS1 inhibits upregulation of DC maturation markers. Transduced MDDCs were infected with SeV for 20h, harvested and stained for expression of CD40, CD80, CD83 and CD86. Fold change in mean fluorescence intensity (MFI) for the indicated proteins in transduced MDDCs where fold increase indicates comparisons of SeV-infected to uninfected MDDCs. Error bars indicate standard deviations from three independent experiments (*p
    Figure Legend Snippet: NS1 unique regions are important for modulating host responses Human monocyte-derived dendritic cells (MDDCs) were transduced with either only empty lentiviral vectors (empty) or lentivirus vectors that express either EBOV-VP35, hRSV-NS1, hRSV-NS1-(1-118), hRSV-NS1-L132A/L133A. RNA was isolated from transduced MDDCs that were either mock-infected or infected with SeV. RNA was extracted at the indicated hours post-infection; and a, IFN-β, b, TNF-α, c, ISG54, and d, ISG56 mRNA levels were quantified RT-qPCR, normalizing their levels to that of β-actin mRNA. The graph indicates the fold-change relative to the mock-infected samples. For a–d, symbols are: ○, empty vector; ▲, hRSV NS1 1-118; ▼, hRSV NS1 L132A/L133A; ■, hRSV NS1 WT; and ●, EBOV VP35. hRSV NS1 inhibits upregulation of DC maturation markers. Transduced MDDCs were infected with SeV for 20h, harvested and stained for expression of CD40, CD80, CD83 and CD86. Fold change in mean fluorescence intensity (MFI) for the indicated proteins in transduced MDDCs where fold increase indicates comparisons of SeV-infected to uninfected MDDCs. Error bars indicate standard deviations from three independent experiments (*p

    Techniques Used: Derivative Assay, Transduction, Isolation, Infection, Quantitative RT-PCR, Plasmid Preparation, Staining, Expressing, Fluorescence

    7) Product Images from "DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP"

    Article Title: DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP

    Journal: bioRxiv

    doi: 10.1101/2020.03.20.001008

    SARS-CoV-2 RNA can be detected from COVID-19 patient nasopharyngeal swabs by RT-qPCR without an RNA extraction step ( a ) Nasopharyngeal (NP) swab diluents from two confirmed COVID-19 patients were pooled, and using the 2019-nCoV_N3 primer/probe set, the mixture was either i) subjected to RNA extraction using the Qiagen QIAamp Viral RNA Mini kit followed by subsequent testing by RT-qPCR (using the equivalent of 11.3 ul swab diluent) or ii) directly added to the RT-qPCR reaction, with or without a preheating step (five minutes at 70°C, “NP sample + heat”). As a control, the indicated quantities of the CDC 2019-nCoV Positive Control SARS-CoV-2 synthetic RNA was spiked into M6 transport media, purified using the QIAamp Viral RNA Mini kit, and screened by RT-qPCR. NP swab samples from seven additional donors were screened by direct RT-qPCR for SARS-CoV-2 RNA using ( b ) the 2019-nCoV_N1 primer/probe set, ( c ) the 2019-nCoV_N2 primer/probe set, or ( d ) for human RNase P RNA using the RP primer probe set. NP swab samples from donors 1 – 4 were previously shown to contain SARS-CoV-2 RNA by standard clinical RT-qPCR, while donors 5 – 7 were negative. For each primer/probe set, 7 µL ( a ) or 3 µL ( b, c, d ) of NP swab diluent was tested in the RT-qPCR reaction per donor. For the N1 and N2 primer probe sets, the fully synthetic SARS-CoV-2 RNA Control 2 from Twist Bioscience was loaded at serial 10-fold dilutions (A, 3×10 6 copies; B, 3×10 5 copies; C, 3×10 4 copies; D, 3×10 3 copies; E, 3×10 2 copies; F, 3×10 1 copies) as indicated in panels b and c . No template control (NTC) wells were included for each primer/probe set and each was negative. For panels b and c , the correlation coefficients (R 2 ) of the standard curves were 0.999 and 0.995, respectively. The dashed line at cycle 40 in each graph indicates the limit of detection.
    Figure Legend Snippet: SARS-CoV-2 RNA can be detected from COVID-19 patient nasopharyngeal swabs by RT-qPCR without an RNA extraction step ( a ) Nasopharyngeal (NP) swab diluents from two confirmed COVID-19 patients were pooled, and using the 2019-nCoV_N3 primer/probe set, the mixture was either i) subjected to RNA extraction using the Qiagen QIAamp Viral RNA Mini kit followed by subsequent testing by RT-qPCR (using the equivalent of 11.3 ul swab diluent) or ii) directly added to the RT-qPCR reaction, with or without a preheating step (five minutes at 70°C, “NP sample + heat”). As a control, the indicated quantities of the CDC 2019-nCoV Positive Control SARS-CoV-2 synthetic RNA was spiked into M6 transport media, purified using the QIAamp Viral RNA Mini kit, and screened by RT-qPCR. NP swab samples from seven additional donors were screened by direct RT-qPCR for SARS-CoV-2 RNA using ( b ) the 2019-nCoV_N1 primer/probe set, ( c ) the 2019-nCoV_N2 primer/probe set, or ( d ) for human RNase P RNA using the RP primer probe set. NP swab samples from donors 1 – 4 were previously shown to contain SARS-CoV-2 RNA by standard clinical RT-qPCR, while donors 5 – 7 were negative. For each primer/probe set, 7 µL ( a ) or 3 µL ( b, c, d ) of NP swab diluent was tested in the RT-qPCR reaction per donor. For the N1 and N2 primer probe sets, the fully synthetic SARS-CoV-2 RNA Control 2 from Twist Bioscience was loaded at serial 10-fold dilutions (A, 3×10 6 copies; B, 3×10 5 copies; C, 3×10 4 copies; D, 3×10 3 copies; E, 3×10 2 copies; F, 3×10 1 copies) as indicated in panels b and c . No template control (NTC) wells were included for each primer/probe set and each was negative. For panels b and c , the correlation coefficients (R 2 ) of the standard curves were 0.999 and 0.995, respectively. The dashed line at cycle 40 in each graph indicates the limit of detection.

    Techniques Used: Quantitative RT-PCR, RNA Extraction, Positive Control, Purification

    8) Product Images from "Antiviral Hammerhead Ribozymes Are Effective for Developing Transgenic Suppression of Chikungunya Virus in Aedes aegypti Mosquitoes"

    Article Title: Antiviral Hammerhead Ribozymes Are Effective for Developing Transgenic Suppression of Chikungunya Virus in Aedes aegypti Mosquitoes

    Journal: Viruses

    doi: 10.3390/v8060163

    Generalized structure of a minimal hammerhead ribozyme (hRz) and organization of the chikungunya virus (CHIKV) viral genome showing hRz target sites. ( A ) hRzs consist of helix I and III which mediate complementary base-pairing with the target, and helix II which acts as the catalytic core mediating cleavage of the target RNA; ( B ) Schematic of the CHIKV genome. nsP1–nsP4 = polyprotein encoded by the genomic RNA. Capsid, E3, E2, 6K and E1 = polyprotein encoded by the sub-genomic RNA. 9–15 = target sites for hRz#9-#15.
    Figure Legend Snippet: Generalized structure of a minimal hammerhead ribozyme (hRz) and organization of the chikungunya virus (CHIKV) viral genome showing hRz target sites. ( A ) hRzs consist of helix I and III which mediate complementary base-pairing with the target, and helix II which acts as the catalytic core mediating cleavage of the target RNA; ( B ) Schematic of the CHIKV genome. nsP1–nsP4 = polyprotein encoded by the genomic RNA. Capsid, E3, E2, 6K and E1 = polyprotein encoded by the sub-genomic RNA. 9–15 = target sites for hRz#9-#15.

    Techniques Used:

    9) Product Images from "Lack of Bax Prevents Influenza A Virus-Induced Apoptosis and Causes Diminished Viral Replication ▿"

    Article Title: Lack of Bax Prevents Influenza A Virus-Induced Apoptosis and Causes Diminished Viral Replication ▿

    Journal: Journal of Virology

    doi: 10.1128/JVI.02672-08

    Influenza A virus replication is dependent upon opposite virus-induced effects on Bax and Bak activity that are unlikely to be interferon related. (A) Influenza A virus replication was analyzed by plaque assay. Virus replication is severely attenuated in Bax KO cells, resulting in a 2-log decrease in PFU/ml compared to the WT. Bak KO cells allow a maximum replication similar to that of the WT, while Bax/Bak DKO cells show a slight elevation of infectious titers during infection. These results indicate that Bax is proviral during infection, while Bak is dispensable for replication. (B) Bax was transiently expressed in all cell types by Lipofectamine 2000 transfection of a C2-Bax-GFP construct prior to infection, and supernatant samples were collected for plaque assay at 48 hpi. Baseline virus replication in each cell type was evaluated using empty C2-GFP plasmid transfection. Bax reconstitution in Bax KO cells resulted in a fivefold increase in infectious titers compared to the control ( P = 0.0007). A minimal effect on the virus titer was seen after Bax overexpression by transient transfection in WT cells compared to empty plasmid controls. (C) Influenza A virus replication was assessed by reverse transcription-PCR. Serial dilutions of stock virus at known concentrations were also analyzed to generate a standard curve to which experimental samples were compared, thus calculating the approximate number of influenza A virus particles/ml in each sample. By 24 hpi, Bax KO, Bak KO, and Bax/Bak DKO cells all showed significantly higher levels of influenza A virus RNA released into the cell culture supernatant than did WT cells. (D) Interferon activity was assessed by infecting mock- and influenza A virus-infected cells with interferon-sensitive, GFP-linked NDV and quantifying the mean GFP expression levels of 10,000 events per condition by FACS analysis. Each assay was run in triplicate, and data are expressed as the ratio of the numbers of influenza A virus-infected to mock-infected cells per cell type. After influenza A virus infection, Bak KO cells exhibited a slight decrease in ratio compared to the WT, representing a 30% increase in interferon activity ( P = 0.002). Bax KO and Bax/Bak DKO cells both showed similar fluorescence changes compared to the WT after infection. Due the high degree of similarity between cell types, these results suggest that the interferon response in infected cells is modulated by viral replication in the presence of Bak and is only slightly modified by Bax activity during influenza A virus infection. As an elevated interferon response typically leads to a reduced virus replication capacity, these results also suggest that it is unlikely that the observed trends in infectious virus titer are due to virus-induced interferon signaling.
    Figure Legend Snippet: Influenza A virus replication is dependent upon opposite virus-induced effects on Bax and Bak activity that are unlikely to be interferon related. (A) Influenza A virus replication was analyzed by plaque assay. Virus replication is severely attenuated in Bax KO cells, resulting in a 2-log decrease in PFU/ml compared to the WT. Bak KO cells allow a maximum replication similar to that of the WT, while Bax/Bak DKO cells show a slight elevation of infectious titers during infection. These results indicate that Bax is proviral during infection, while Bak is dispensable for replication. (B) Bax was transiently expressed in all cell types by Lipofectamine 2000 transfection of a C2-Bax-GFP construct prior to infection, and supernatant samples were collected for plaque assay at 48 hpi. Baseline virus replication in each cell type was evaluated using empty C2-GFP plasmid transfection. Bax reconstitution in Bax KO cells resulted in a fivefold increase in infectious titers compared to the control ( P = 0.0007). A minimal effect on the virus titer was seen after Bax overexpression by transient transfection in WT cells compared to empty plasmid controls. (C) Influenza A virus replication was assessed by reverse transcription-PCR. Serial dilutions of stock virus at known concentrations were also analyzed to generate a standard curve to which experimental samples were compared, thus calculating the approximate number of influenza A virus particles/ml in each sample. By 24 hpi, Bax KO, Bak KO, and Bax/Bak DKO cells all showed significantly higher levels of influenza A virus RNA released into the cell culture supernatant than did WT cells. (D) Interferon activity was assessed by infecting mock- and influenza A virus-infected cells with interferon-sensitive, GFP-linked NDV and quantifying the mean GFP expression levels of 10,000 events per condition by FACS analysis. Each assay was run in triplicate, and data are expressed as the ratio of the numbers of influenza A virus-infected to mock-infected cells per cell type. After influenza A virus infection, Bak KO cells exhibited a slight decrease in ratio compared to the WT, representing a 30% increase in interferon activity ( P = 0.002). Bax KO and Bax/Bak DKO cells both showed similar fluorescence changes compared to the WT after infection. Due the high degree of similarity between cell types, these results suggest that the interferon response in infected cells is modulated by viral replication in the presence of Bak and is only slightly modified by Bax activity during influenza A virus infection. As an elevated interferon response typically leads to a reduced virus replication capacity, these results also suggest that it is unlikely that the observed trends in infectious virus titer are due to virus-induced interferon signaling.

    Techniques Used: Activity Assay, Plaque Assay, Infection, Transfection, Construct, Plasmid Preparation, Over Expression, Polymerase Chain Reaction, Cell Culture, Expressing, FACS, Fluorescence, Modification

    10) Product Images from "Tracking echovirus eleven outbreaks in Guangdong, China: a metatranscriptomic, phylogenetic, and epidemiological study"

    Article Title: Tracking echovirus eleven outbreaks in Guangdong, China: a metatranscriptomic, phylogenetic, and epidemiological study

    Journal: Virus Evolution

    doi: 10.1093/ve/veaa029

    Metatranscriptomics analysis on different samples types from the three fatal cases. (A) The workflow for metatranscriptomics NGS sequencing and sequencing data analysis. Anal (B) and oral swabs (C) were sampled from Cases 1 and 3 in autopsy diagnosis. The transcriptomes abundance of different microbe families in Cases 1 and 3 was investigated by CCMetagen. The relative coverage and depth at each position of E11 genome is shown by aligning sequencing data from Cases 1 and 3 to the E11 reference genome (KY981558); (D) Serial blood samples were collected from the fatal Case 5 at different time points (marked with black dots). The dynamic change of transcriptomes abundance of different microbe families was shown in left panel. The relative coverage and depth mapping to E11 genome were shown from Day 8. Micrococci and Picornavirus which were commonly identified in all types of samples with a relative high abundance were marked with asterisk.
    Figure Legend Snippet: Metatranscriptomics analysis on different samples types from the three fatal cases. (A) The workflow for metatranscriptomics NGS sequencing and sequencing data analysis. Anal (B) and oral swabs (C) were sampled from Cases 1 and 3 in autopsy diagnosis. The transcriptomes abundance of different microbe families in Cases 1 and 3 was investigated by CCMetagen. The relative coverage and depth at each position of E11 genome is shown by aligning sequencing data from Cases 1 and 3 to the E11 reference genome (KY981558); (D) Serial blood samples were collected from the fatal Case 5 at different time points (marked with black dots). The dynamic change of transcriptomes abundance of different microbe families was shown in left panel. The relative coverage and depth mapping to E11 genome were shown from Day 8. Micrococci and Picornavirus which were commonly identified in all types of samples with a relative high abundance were marked with asterisk.

    Techniques Used: Next-Generation Sequencing, Sequencing

    11) Product Images from "Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding"

    Article Title: Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding

    Journal: bioRxiv

    doi: 10.1101/2020.05.28.122648

    SARS-CoV2 genome coverage plots for different amplicon sets. We performed amplicon sequencing of the SARS-CoV-2 genome with amplicons ranging from 400 bp (top) to 2000 bp in size (bottom). Amplicon sets are shown as grey bars, with the amplicons in ‘Pool 1’ numbered (see Methods). Read coverage is scaled so that mean coverage is 1000X for all amplicon sets. For each set of amplicons we sequenced a low C q sample (20.3) and a high C q sample (31.2). Each amplicon set is shown in pairs. The upper plot is the C q 20.3 sample; the lower plot is the C q 31.2 sample. The 1200 bp and 2000 bp amplicon sets exhibit relatively even coverage across the entire SARS-CoV-2 genome. However, note that for the high C q 2000 bp amplicon set, all amplicons in ‘Pool 1’ are approximately 1.5-fold higher levels than those in ‘Pool 2’. In contrast to the 1200 bp and 2000 bp amplicon sets, several dropout regions are apparent in the 400 bp and 1500 bp amplicon sets. In all cases, the variation in genome coverage is higher for the sample with higher C q .
    Figure Legend Snippet: SARS-CoV2 genome coverage plots for different amplicon sets. We performed amplicon sequencing of the SARS-CoV-2 genome with amplicons ranging from 400 bp (top) to 2000 bp in size (bottom). Amplicon sets are shown as grey bars, with the amplicons in ‘Pool 1’ numbered (see Methods). Read coverage is scaled so that mean coverage is 1000X for all amplicon sets. For each set of amplicons we sequenced a low C q sample (20.3) and a high C q sample (31.2). Each amplicon set is shown in pairs. The upper plot is the C q 20.3 sample; the lower plot is the C q 31.2 sample. The 1200 bp and 2000 bp amplicon sets exhibit relatively even coverage across the entire SARS-CoV-2 genome. However, note that for the high C q 2000 bp amplicon set, all amplicons in ‘Pool 1’ are approximately 1.5-fold higher levels than those in ‘Pool 2’. In contrast to the 1200 bp and 2000 bp amplicon sets, several dropout regions are apparent in the 400 bp and 1500 bp amplicon sets. In all cases, the variation in genome coverage is higher for the sample with higher C q .

    Techniques Used: Amplification, Sequencing

    12) Product Images from "Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing ▿"

    Article Title: Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing ▿

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.02255-08

    Bland-Altman analysis of HIV-1 viral loads in patient samples ( n = 47) of plasma versus DPS after RNA extraction with a QIAamp viral RNA mini kit (Qiagen) (A), the Abbott sample preparation system (B), and a Nuclisens manual extraction kit (bioMérieux)
    Figure Legend Snippet: Bland-Altman analysis of HIV-1 viral loads in patient samples ( n = 47) of plasma versus DPS after RNA extraction with a QIAamp viral RNA mini kit (Qiagen) (A), the Abbott sample preparation system (B), and a Nuclisens manual extraction kit (bioMérieux)

    Techniques Used: RNA Extraction, Sample Prep

    HIV-1 viral loads in patient samples ( n = 47) of plasma and DPS after RNA extractions with a QIAamp viral RNA mini kit (Qiagen), the Abbott sample preparation system, or a Nuclisens manual extraction kit (bioMérieux). (A) Comparison of
    Figure Legend Snippet: HIV-1 viral loads in patient samples ( n = 47) of plasma and DPS after RNA extractions with a QIAamp viral RNA mini kit (Qiagen), the Abbott sample preparation system, or a Nuclisens manual extraction kit (bioMérieux). (A) Comparison of

    Techniques Used: Sample Prep

    13) Product Images from "Paper-Based RNA Extraction, in Situ Isothermal Amplification, and Lateral Flow Detection for Low-Cost, Rapid Diagnosis of Influenza A (H1N1) from Clinical Specimens"

    Article Title: Paper-Based RNA Extraction, in Situ Isothermal Amplification, and Lateral Flow Detection for Low-Cost, Rapid Diagnosis of Influenza A (H1N1) from Clinical Specimens

    Journal: Analytical chemistry

    doi: 10.1021/acs.analchem.5b01594

    Clinical nasopharyngeal specimens. (a) Paper extractions and QIAamp kit extractions of clinical specimens A–L. (b) RT-LAMP assay performed in solution with Qiagen-extracted purified RNA from clinical specimens A–L, and gel electrophoresis of products. (c) Lateral flow detection of amplified products; test line intensities plotted as a percentage of control line intensities. (d) Paper extraction of clinical specimens A–L followed by in situ RT-LAMP and lateral flow detection. + = positive control (10 9 cp/mL RNA standard); − = negative control (no RNA).
    Figure Legend Snippet: Clinical nasopharyngeal specimens. (a) Paper extractions and QIAamp kit extractions of clinical specimens A–L. (b) RT-LAMP assay performed in solution with Qiagen-extracted purified RNA from clinical specimens A–L, and gel electrophoresis of products. (c) Lateral flow detection of amplified products; test line intensities plotted as a percentage of control line intensities. (d) Paper extraction of clinical specimens A–L followed by in situ RT-LAMP and lateral flow detection. + = positive control (10 9 cp/mL RNA standard); − = negative control (no RNA).

    Techniques Used: RT Lamp Assay, Purification, Nucleic Acid Electrophoresis, Flow Cytometry, Amplification, In Situ, Positive Control, Negative Control

    14) Product Images from "Efficacy of Human Monoclonal Antibody Monotherapy Against Bundibugyo Virus Infection in Nonhuman Primates"

    Article Title: Efficacy of Human Monoclonal Antibody Monotherapy Against Bundibugyo Virus Infection in Nonhuman Primates

    Journal: The Journal of Infectious Diseases

    doi: 10.1093/infdis/jiy295

    Therapeutic potency of monoclonal antibody (mAb) BDBV289-N to prevent death and reduce viremia. Nonhuman primates (NHPs) received 825 plaque-forming units (PFU) of Bundibugyo virus (BDBV) intramuscularly and a dose of mAb (35 mg/kg) intravenously 8 and 11 days after inoculation (data are for 6 treated animals and 1 untreated control this study and for 9 untreated historical controls). A , Kaplan-Meier survival plot. Arrows indicate the day of mAb dosing. Untreated groups represent 1 animal from this study, and 9 historical controls represent animals (cumulative 60% survival) inoculated by the same route with the same stock of virus. The proportion surviving at day 28 after infection was compared using a 2-sided exact unconditional test of homogeneity. A P value of ≤ .05 was considered significant. B , A comparison of blood viral RNA load was determined at 11 days after virus inoculation for treated or control animals, as described in panel A . The group of 6 untreated animals included 1 NHP from this study and 5 historical controls that also were assessed for viremia on day 11 after infection. Virus titers were compared using the Mann–Whitney U test. The median titer for each group is shown. C , Kinetics of the blood viral RNA load, as determined by real-time quantitative polymerase chain reaction, for 6 treated or 6 of 10 control animals, comprising 1 NHP assessed at the same time point and 9 historical controls. The dotted line indicates the limit of detection (LOD), which was 3.7 log 10 genome equivalents (GEq) per milliliter. Each measurement represented the mean value of technical duplicates. Numbers indicate individual NHPs from the respective group. Abbreviations: C, untreated, this study (gray); HC, untreated, historical control (gray curves); M, treated, this study (orange curves).
    Figure Legend Snippet: Therapeutic potency of monoclonal antibody (mAb) BDBV289-N to prevent death and reduce viremia. Nonhuman primates (NHPs) received 825 plaque-forming units (PFU) of Bundibugyo virus (BDBV) intramuscularly and a dose of mAb (35 mg/kg) intravenously 8 and 11 days after inoculation (data are for 6 treated animals and 1 untreated control this study and for 9 untreated historical controls). A , Kaplan-Meier survival plot. Arrows indicate the day of mAb dosing. Untreated groups represent 1 animal from this study, and 9 historical controls represent animals (cumulative 60% survival) inoculated by the same route with the same stock of virus. The proportion surviving at day 28 after infection was compared using a 2-sided exact unconditional test of homogeneity. A P value of ≤ .05 was considered significant. B , A comparison of blood viral RNA load was determined at 11 days after virus inoculation for treated or control animals, as described in panel A . The group of 6 untreated animals included 1 NHP from this study and 5 historical controls that also were assessed for viremia on day 11 after infection. Virus titers were compared using the Mann–Whitney U test. The median titer for each group is shown. C , Kinetics of the blood viral RNA load, as determined by real-time quantitative polymerase chain reaction, for 6 treated or 6 of 10 control animals, comprising 1 NHP assessed at the same time point and 9 historical controls. The dotted line indicates the limit of detection (LOD), which was 3.7 log 10 genome equivalents (GEq) per milliliter. Each measurement represented the mean value of technical duplicates. Numbers indicate individual NHPs from the respective group. Abbreviations: C, untreated, this study (gray); HC, untreated, historical control (gray curves); M, treated, this study (orange curves).

    Techniques Used: Infection, MANN-WHITNEY, Real-time Polymerase Chain Reaction

    15) Product Images from "Multiple Layers of Chimerism in a Single-Stranded DNA Virus Discovered by Deep Sequencing"

    Article Title: Multiple Layers of Chimerism in a Single-Stranded DNA Virus Discovered by Deep Sequencing

    Journal: Genome Biology and Evolution

    doi: 10.1093/gbe/evv034

    Confirmation of contaminated columns as origin of CHIV14 DNA by qPCR. ( A ) Verification of CHIV14 genome assembled from the Illumina deep-sequencing data by overlapping PCR and inverted PCR. Five sets of overlapping primer pairs and one set of inverted primer pair were designed and used to amplify overlapping DNA fragments. (Left) Schematic diagram of the positions of primer pairs for the overlapping PCR and inverted PCR. (Right) Amplification overlapping viral DNA fragments. The numbers above indicate the primer pair used for the PCR as illustrated on the left. The numbers on the left indicate the molecular weight in base pairs. ( B ) Scatterplot showing copy number of CHIV14 per microliter of DNA extraction. DNA from patients ( n = 13), healthy controls ( n = 13), and water ( n = 31) was extracted using QIAamp mini spin columns (QIAamp Viral RNA Mini kit; Qiagen). In parallel, seven DNA extractions for each specimen type (patients, healthy individuals, and water) were performed using the UCP columns. Each dot represents one specimen. Bars show the average copy numbers of the viral genome.
    Figure Legend Snippet: Confirmation of contaminated columns as origin of CHIV14 DNA by qPCR. ( A ) Verification of CHIV14 genome assembled from the Illumina deep-sequencing data by overlapping PCR and inverted PCR. Five sets of overlapping primer pairs and one set of inverted primer pair were designed and used to amplify overlapping DNA fragments. (Left) Schematic diagram of the positions of primer pairs for the overlapping PCR and inverted PCR. (Right) Amplification overlapping viral DNA fragments. The numbers above indicate the primer pair used for the PCR as illustrated on the left. The numbers on the left indicate the molecular weight in base pairs. ( B ) Scatterplot showing copy number of CHIV14 per microliter of DNA extraction. DNA from patients ( n = 13), healthy controls ( n = 13), and water ( n = 31) was extracted using QIAamp mini spin columns (QIAamp Viral RNA Mini kit; Qiagen). In parallel, seven DNA extractions for each specimen type (patients, healthy individuals, and water) were performed using the UCP columns. Each dot represents one specimen. Bars show the average copy numbers of the viral genome.

    Techniques Used: Real-time Polymerase Chain Reaction, Sequencing, Polymerase Chain Reaction, Amplification, Molecular Weight, DNA Extraction

    16) Product Images from "Multiple Layers of Chimerism in a Single-Stranded DNA Virus Discovered by Deep Sequencing"

    Article Title: Multiple Layers of Chimerism in a Single-Stranded DNA Virus Discovered by Deep Sequencing

    Journal: Genome Biology and Evolution

    doi: 10.1093/gbe/evv034

    Confirmation of contaminated columns as origin of CHIV14 DNA by qPCR. ( A ) Verification of CHIV14 genome assembled from the Illumina deep-sequencing data by overlapping PCR and inverted PCR. Five sets of overlapping primer pairs and one set of inverted primer pair were designed and used to amplify overlapping DNA fragments. (Left) Schematic diagram of the positions of primer pairs for the overlapping PCR and inverted PCR. (Right) Amplification overlapping viral DNA fragments. The numbers above indicate the primer pair used for the PCR as illustrated on the left. The numbers on the left indicate the molecular weight in base pairs. ( B ) Scatterplot showing copy number of CHIV14 per microliter of DNA extraction. DNA from patients ( n = 13), healthy controls ( n = 13), and water ( n = 31) was extracted using QIAamp mini spin columns (QIAamp Viral RNA Mini kit; Qiagen). In parallel, seven DNA extractions for each specimen type (patients, healthy individuals, and water) were performed using the UCP columns. Each dot represents one specimen. Bars show the average copy numbers of the viral genome.
    Figure Legend Snippet: Confirmation of contaminated columns as origin of CHIV14 DNA by qPCR. ( A ) Verification of CHIV14 genome assembled from the Illumina deep-sequencing data by overlapping PCR and inverted PCR. Five sets of overlapping primer pairs and one set of inverted primer pair were designed and used to amplify overlapping DNA fragments. (Left) Schematic diagram of the positions of primer pairs for the overlapping PCR and inverted PCR. (Right) Amplification overlapping viral DNA fragments. The numbers above indicate the primer pair used for the PCR as illustrated on the left. The numbers on the left indicate the molecular weight in base pairs. ( B ) Scatterplot showing copy number of CHIV14 per microliter of DNA extraction. DNA from patients ( n = 13), healthy controls ( n = 13), and water ( n = 31) was extracted using QIAamp mini spin columns (QIAamp Viral RNA Mini kit; Qiagen). In parallel, seven DNA extractions for each specimen type (patients, healthy individuals, and water) were performed using the UCP columns. Each dot represents one specimen. Bars show the average copy numbers of the viral genome.

    Techniques Used: Real-time Polymerase Chain Reaction, Sequencing, Polymerase Chain Reaction, Amplification, Molecular Weight, DNA Extraction

    17) Product Images from "Detection of Zika virus in mouse mammary gland and breast milk"

    Article Title: Detection of Zika virus in mouse mammary gland and breast milk

    Journal: PLoS Neglected Tropical Diseases

    doi: 10.1371/journal.pntd.0007080

    Transmission of ZIKV RNA in mouse breast milk. Postpartum AG129 dams were retro-orbitally inoculated with 1 x 10 2 FFU of ZIKV FSS13025 or 10% FBS-PBS as Mock within 24 hours of parturition. Pups were sacrificed on d1, d3, d5 and d7 after birth. (A and B) Levels of ZIKV RNA in the head and the rest of the body were measured by qRT-PCR (n = 6 mice, each day). (C and D) ZIKV RNA levels in stomach milk clots (SMC) and stomach tissues were quantified via qRT-PCR (n = 3 mice, each day). (E and F) Presence of infectious ZIKV in SMC and stomach was assessed using FFA (n = 3 mice, each day). Data represent two independent experiments.
    Figure Legend Snippet: Transmission of ZIKV RNA in mouse breast milk. Postpartum AG129 dams were retro-orbitally inoculated with 1 x 10 2 FFU of ZIKV FSS13025 or 10% FBS-PBS as Mock within 24 hours of parturition. Pups were sacrificed on d1, d3, d5 and d7 after birth. (A and B) Levels of ZIKV RNA in the head and the rest of the body were measured by qRT-PCR (n = 6 mice, each day). (C and D) ZIKV RNA levels in stomach milk clots (SMC) and stomach tissues were quantified via qRT-PCR (n = 3 mice, each day). (E and F) Presence of infectious ZIKV in SMC and stomach was assessed using FFA (n = 3 mice, each day). Data represent two independent experiments.

    Techniques Used: Transmission Assay, Quantitative RT-PCR, Mouse Assay

    18) Product Images from "Non-Catalytic Site HIV-1 Integrase Inhibitors Disrupt Core Maturation and Induce a Reverse Transcription Block in Target Cells"

    Article Title: Non-Catalytic Site HIV-1 Integrase Inhibitors Disrupt Core Maturation and Induce a Reverse Transcription Block in Target Cells

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0074163

    NCINIs do not inhibit Gag-Pol processing, ERT, or target cell entry. ( A ) Western blot analysis of purified HIV-1 particles produced in the presence of different inhibitors at 1 µM concentration. Gag/Gag-Pol processing was assessed using anti-CA ( upper ), anti-IN ( middle ), and anti-RT antibodies ( lower ). ( B ) Equal p24 amounts of virus shown in A were analyzed for virion-associated endogenous reverse transcriptase activity. Values were averaged from duplicate measurements. ( C ) Percentage of cells positive for beta-lactamase activity following infection with Blam-Vpr complemented HIV-1 produced in the presence of DMSO or 1 µM tested compounds. Values are normalized to DMSO-treated control and represent a mean of two independent experiments performed in duplicate.
    Figure Legend Snippet: NCINIs do not inhibit Gag-Pol processing, ERT, or target cell entry. ( A ) Western blot analysis of purified HIV-1 particles produced in the presence of different inhibitors at 1 µM concentration. Gag/Gag-Pol processing was assessed using anti-CA ( upper ), anti-IN ( middle ), and anti-RT antibodies ( lower ). ( B ) Equal p24 amounts of virus shown in A were analyzed for virion-associated endogenous reverse transcriptase activity. Values were averaged from duplicate measurements. ( C ) Percentage of cells positive for beta-lactamase activity following infection with Blam-Vpr complemented HIV-1 produced in the presence of DMSO or 1 µM tested compounds. Values are normalized to DMSO-treated control and represent a mean of two independent experiments performed in duplicate.

    Techniques Used: Western Blot, Purification, Produced, Concentration Assay, Activity Assay, Infection

    19) Product Images from "APOBEC3G and APOBEC3F Act in Concert To Extinguish HIV-1 Replication"

    Article Title: APOBEC3G and APOBEC3F Act in Concert To Extinguish HIV-1 Replication

    Journal: Journal of Virology

    doi: 10.1128/JVI.03275-15

    Absolute restriction of HIV in vivo requires both APOBEC3G and APOBEC3F. (A) (Top) The plasma of BLT humanized mice infected with JRCSFvifH42/43D (blue lines) was monitored longitudinally for the presence of HIV RNA. Wild-type JRCSF RNA is presented in aggregate ( n = 7) (black diamonds). (Bottom) Nested PCR to detect HIV DNA was performed on genomic-DNA extracts from each tissue listed from the infected humanized mice. +, tissues positive for HIV DNA; −, tissues where HIV DNA was not detected. (B) (Top) Viral RNA was present in the plasma of 4/4 mice infected with JRCSFvifW79S (red lines) at levels comparable to those of wild-type JRCSF ( n = 7) (black diamonds). (Bottom) Nested PCR to detect HIV DNA was performed on genomic DNA extracted from each tissue listed from the infected BLT humanized mice. +, tissues positive for HIV DNA; −, tissues where HIV DNA was not detected. (C) (Top) Plasma viral RNA was not observed in 4/4 mice infected with JRCSFvifH42/43DW79S (green lines) for up to 8 weeks postexposure, in contrast to infection with wild-type JRCSF (black diamonds). (Bottom) Viral DNA was not detected in any tissue of JRCSFvifH42/43DW79S-inoculated BLT humanized mice (−). (D) Sequencing of viral DNA amplified from the tissues of mice infected with JRCSFvifH42/43D (G3 and G4) revealed heavy G-to-A mutation at GG sites (blue bar). Few G-to-A mutations were present at GA sites in viral DNA from mice infected with JRCSFvifH42/43D or JRCSFvifW79S, and no mutations were observed in WT1 JRCSF DNA. The data are presented as means ± SEM.
    Figure Legend Snippet: Absolute restriction of HIV in vivo requires both APOBEC3G and APOBEC3F. (A) (Top) The plasma of BLT humanized mice infected with JRCSFvifH42/43D (blue lines) was monitored longitudinally for the presence of HIV RNA. Wild-type JRCSF RNA is presented in aggregate ( n = 7) (black diamonds). (Bottom) Nested PCR to detect HIV DNA was performed on genomic-DNA extracts from each tissue listed from the infected humanized mice. +, tissues positive for HIV DNA; −, tissues where HIV DNA was not detected. (B) (Top) Viral RNA was present in the plasma of 4/4 mice infected with JRCSFvifW79S (red lines) at levels comparable to those of wild-type JRCSF ( n = 7) (black diamonds). (Bottom) Nested PCR to detect HIV DNA was performed on genomic DNA extracted from each tissue listed from the infected BLT humanized mice. +, tissues positive for HIV DNA; −, tissues where HIV DNA was not detected. (C) (Top) Plasma viral RNA was not observed in 4/4 mice infected with JRCSFvifH42/43DW79S (green lines) for up to 8 weeks postexposure, in contrast to infection with wild-type JRCSF (black diamonds). (Bottom) Viral DNA was not detected in any tissue of JRCSFvifH42/43DW79S-inoculated BLT humanized mice (−). (D) Sequencing of viral DNA amplified from the tissues of mice infected with JRCSFvifH42/43D (G3 and G4) revealed heavy G-to-A mutation at GG sites (blue bar). Few G-to-A mutations were present at GA sites in viral DNA from mice infected with JRCSFvifH42/43D or JRCSFvifW79S, and no mutations were observed in WT1 JRCSF DNA. The data are presented as means ± SEM.

    Techniques Used: In Vivo, Mouse Assay, Infection, Nested PCR, Sequencing, Amplification, Mutagenesis

    20) Product Images from "NEDD4 family ubiquitin ligases associate with LCMV Z’s PPXY domain and are required for virus budding, but not via direct ubiquitination of Z"

    Article Title: NEDD4 family ubiquitin ligases associate with LCMV Z’s PPXY domain and are required for virus budding, but not via direct ubiquitination of Z

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1008100

    Loss of ubiquitination sites in LCMV Z has little impact on virus particle release. (A-B) Reverse genetics was used to generate recombinant (r)LCMV containing mutations at the two ubiquitination sites (K10 and K77) as well as a virus with a lysine-free (NoK) or a late domain-free (PPPY > AAAA) Z protein. The growth kinetics of these viruses were then measured by infecting A549 cells with these viruses and measuring the infectious titers by plaque assay (A) and DI particle titers by plaque interfering assay (B) at 1, 16, 24, 40, 48 and 72 hours after infection. (C) Summary of a two-way ANOVA with Holm-Sidak’s test for multiple comparisons used to compare the log-transformed mean titer values from the growth curve in (A-B). (D-E) Viral RNA was isolated from clarified cell culture media from the 72 hours post-infection time point in (A-B) and the quantities of genomic S-segment (D) or L-segment (E) vRNA were determined by quantitative real time RT-PCR. (F) The release of virus-like particles (VLPs) from HEK293T cells transfected with plasmids expressing SBP-tagged LCMV Z protein with the indicated mutations was measured. The graphs in (A-B and D-F) represent the mean values ± SEM of three independent experiments with two technical replicates each. A one-way ANOVA with Holm-Sidak’s test for multiple comparisons was used to compare the mean values to the WT control in (D-F). *p
    Figure Legend Snippet: Loss of ubiquitination sites in LCMV Z has little impact on virus particle release. (A-B) Reverse genetics was used to generate recombinant (r)LCMV containing mutations at the two ubiquitination sites (K10 and K77) as well as a virus with a lysine-free (NoK) or a late domain-free (PPPY > AAAA) Z protein. The growth kinetics of these viruses were then measured by infecting A549 cells with these viruses and measuring the infectious titers by plaque assay (A) and DI particle titers by plaque interfering assay (B) at 1, 16, 24, 40, 48 and 72 hours after infection. (C) Summary of a two-way ANOVA with Holm-Sidak’s test for multiple comparisons used to compare the log-transformed mean titer values from the growth curve in (A-B). (D-E) Viral RNA was isolated from clarified cell culture media from the 72 hours post-infection time point in (A-B) and the quantities of genomic S-segment (D) or L-segment (E) vRNA were determined by quantitative real time RT-PCR. (F) The release of virus-like particles (VLPs) from HEK293T cells transfected with plasmids expressing SBP-tagged LCMV Z protein with the indicated mutations was measured. The graphs in (A-B and D-F) represent the mean values ± SEM of three independent experiments with two technical replicates each. A one-way ANOVA with Holm-Sidak’s test for multiple comparisons was used to compare the mean values to the WT control in (D-F). *p

    Techniques Used: Recombinant, Plaque Assay, Infection, Transformation Assay, Isolation, Cell Culture, Quantitative RT-PCR, Transfection, Expressing

    21) Product Images from "Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany"

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany

    Journal: Viruses

    doi: 10.3390/v11100965

    ( A ) Map of Germany highlighting the location of sampling (insert upper left). Serum samples were collected from 392 Thoroughbreds in North Rhine-Westphalia and Lower Saxony. Grey circles highlight the sample location and circle size is scaled to relative the number of examined horses (see legend lower right). ( B ) Serum samples were analysed for the presence of anti-equine parvovirus-hepatitis (anti-EqPV-H) VP1 AB and EqPV-H DNA performing luciferase immunoprecipitation system (LIPS) and qPCR, respectively. Individual horses were assigned to three different groups: Seronegative and EqPV-H DNA negative (DNA − /AB − ; 65.3%), seropositive and EqPV-H DNA negative (DNA − /AB + ; 27.55%), and seropositive and EqPV-H DNA positive (DNA + /AB + ; 7.14%).
    Figure Legend Snippet: ( A ) Map of Germany highlighting the location of sampling (insert upper left). Serum samples were collected from 392 Thoroughbreds in North Rhine-Westphalia and Lower Saxony. Grey circles highlight the sample location and circle size is scaled to relative the number of examined horses (see legend lower right). ( B ) Serum samples were analysed for the presence of anti-equine parvovirus-hepatitis (anti-EqPV-H) VP1 AB and EqPV-H DNA performing luciferase immunoprecipitation system (LIPS) and qPCR, respectively. Individual horses were assigned to three different groups: Seronegative and EqPV-H DNA negative (DNA − /AB − ; 65.3%), seropositive and EqPV-H DNA negative (DNA − /AB + ; 27.55%), and seropositive and EqPV-H DNA positive (DNA + /AB + ; 7.14%).

    Techniques Used: Sampling, Luciferase, Immunoprecipitation, Real-time Polymerase Chain Reaction

    Heatmaps displaying the occurrence of anti-EqPV-H VP1 AB and EqPV-H DNA with regard to potential risk factors. The three groups based on the EqPV-H infection status were further classified based on ( A ) age, ( B ) breeding history, ( C ) stock size of the stud farm, and ( D ) foreign country. The colouring indicates the number of horses (in %) classified in the specific category. Each row adds up to 100%.
    Figure Legend Snippet: Heatmaps displaying the occurrence of anti-EqPV-H VP1 AB and EqPV-H DNA with regard to potential risk factors. The three groups based on the EqPV-H infection status were further classified based on ( A ) age, ( B ) breeding history, ( C ) stock size of the stud farm, and ( D ) foreign country. The colouring indicates the number of horses (in %) classified in the specific category. Each row adds up to 100%.

    Techniques Used: Infection

    ( A ) Viral loads of EqPV-H (DNA copies/mL) were determined via qPCR ( n = 392). Horses with viral load of > 175 copies/mL were considered EqPV-H DNA positive. ( B ) EqPV-H VP1 antibodies were detected using a LIPS assay and the relative increase of RLU compared to an EqPV-H-negative control sample was calculated ( n = 392). ( C ) Comparison of relative EqPV-H VP1 antibody levels between different groups: (Median values; DNA − /AB − , n = 256; DNA − /AB + , n = 108; DNA + /AB + , n = 28). Statistical significance was determined using a one-way ANOVA with Dunnett’s post-hoc test. (**** p
    Figure Legend Snippet: ( A ) Viral loads of EqPV-H (DNA copies/mL) were determined via qPCR ( n = 392). Horses with viral load of > 175 copies/mL were considered EqPV-H DNA positive. ( B ) EqPV-H VP1 antibodies were detected using a LIPS assay and the relative increase of RLU compared to an EqPV-H-negative control sample was calculated ( n = 392). ( C ) Comparison of relative EqPV-H VP1 antibody levels between different groups: (Median values; DNA − /AB − , n = 256; DNA − /AB + , n = 108; DNA + /AB + , n = 28). Statistical significance was determined using a one-way ANOVA with Dunnett’s post-hoc test. (**** p

    Techniques Used: Real-time Polymerase Chain Reaction, Lips Assay, Negative Control

    22) Product Images from "Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR"

    Article Title: Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.41.11.5273-5276.2003

    Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .
    Figure Legend Snippet: Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .

    Techniques Used: Amplification, Serial Dilution, Nested PCR, Negative Control

    Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).
    Figure Legend Snippet: Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).

    Techniques Used: Amplification, Serial Dilution, Plasmid Preparation, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Software, Hybridization, Fluorescence

    23) Product Images from "Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing ▿"

    Article Title: Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing ▿

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.02255-08

    Bland-Altman analysis of HIV-1 viral loads in patient samples ( n = 47) of plasma versus DPS after RNA extraction with a QIAamp viral RNA mini kit (Qiagen) (A), the Abbott sample preparation system (B), and a Nuclisens manual extraction kit (bioMérieux)
    Figure Legend Snippet: Bland-Altman analysis of HIV-1 viral loads in patient samples ( n = 47) of plasma versus DPS after RNA extraction with a QIAamp viral RNA mini kit (Qiagen) (A), the Abbott sample preparation system (B), and a Nuclisens manual extraction kit (bioMérieux)

    Techniques Used: RNA Extraction, Sample Prep

    HIV-1 viral loads in patient samples ( n = 47) of plasma and DPS after RNA extractions with a QIAamp viral RNA mini kit (Qiagen), the Abbott sample preparation system, or a Nuclisens manual extraction kit (bioMérieux). (A) Comparison of
    Figure Legend Snippet: HIV-1 viral loads in patient samples ( n = 47) of plasma and DPS after RNA extractions with a QIAamp viral RNA mini kit (Qiagen), the Abbott sample preparation system, or a Nuclisens manual extraction kit (bioMérieux). (A) Comparison of

    Techniques Used: Sample Prep

    24) Product Images from "Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing ▿"

    Article Title: Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing ▿

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.02255-08

    Bland-Altman analysis of HIV-1 viral loads in patient samples ( n = 47) of plasma versus DPS after RNA extraction with a QIAamp viral RNA mini kit (Qiagen) (A), the Abbott sample preparation system (B), and a Nuclisens manual extraction kit (bioMérieux)
    Figure Legend Snippet: Bland-Altman analysis of HIV-1 viral loads in patient samples ( n = 47) of plasma versus DPS after RNA extraction with a QIAamp viral RNA mini kit (Qiagen) (A), the Abbott sample preparation system (B), and a Nuclisens manual extraction kit (bioMérieux)

    Techniques Used: RNA Extraction, Sample Prep

    HIV-1 viral loads in patient samples ( n = 47) of plasma and DPS after RNA extractions with a QIAamp viral RNA mini kit (Qiagen), the Abbott sample preparation system, or a Nuclisens manual extraction kit (bioMérieux). (A) Comparison of
    Figure Legend Snippet: HIV-1 viral loads in patient samples ( n = 47) of plasma and DPS after RNA extractions with a QIAamp viral RNA mini kit (Qiagen), the Abbott sample preparation system, or a Nuclisens manual extraction kit (bioMérieux). (A) Comparison of

    Techniques Used: Sample Prep

    25) Product Images from "Efficient recovery and enrichment of infectious rotavirus using separation with antibody-integrated graphite-encapsulated magnetic nanobeads produced by argon/ammonia gas plasma technology"

    Article Title: Efficient recovery and enrichment of infectious rotavirus using separation with antibody-integrated graphite-encapsulated magnetic nanobeads produced by argon/ammonia gas plasma technology

    Journal: International Journal of Nanomedicine

    doi: 10.2147/IJN.S191784

    Quantitative analysis of the viral gene of rotavirus adsorbed onto the antibody-integrated MNBs. Notes: Rotavirus-infected cell lysate (10 µL) was diluted with PBS (500 µL) and then incubated with antibody-integrated magnetic beads. After incubation, the following fractions were obtained: 1) diluted rotavirus sample before incubation with the beads (BF), 2) bead fraction after incubation with anti-rotavirus antibody-integrated MNBs (RV-BD), 3) bead fraction after incubation with anti-dengue virus antibody-integrated MNBs (DV-BD), 4) supernatant fraction after incubation with the anti-rotavirus antibody-integrated MNBs (RV-SP), 5) supernatant fraction after incubation with the anti-dengue virus antibody-integrated MNBs (DV-SP), and 6) total sample containing the same quantity of rotavirus as in 10 µL of rotavirus-infected cell lysate (total fraction, TL). Viral genomic RNA was subsequently extracted from the above fractions using a QIAamp Viral RNA mini kit and subjected to RT-reaction. The resultant cDNA was analyzed by real-time PCR using primers for the rotavirus VP7 gene as described in Materials and methods. The value of the TL sample was taken as 100%. Abbreviations: MNBs, magnetic nanobeads; RT, reverse transcription.
    Figure Legend Snippet: Quantitative analysis of the viral gene of rotavirus adsorbed onto the antibody-integrated MNBs. Notes: Rotavirus-infected cell lysate (10 µL) was diluted with PBS (500 µL) and then incubated with antibody-integrated magnetic beads. After incubation, the following fractions were obtained: 1) diluted rotavirus sample before incubation with the beads (BF), 2) bead fraction after incubation with anti-rotavirus antibody-integrated MNBs (RV-BD), 3) bead fraction after incubation with anti-dengue virus antibody-integrated MNBs (DV-BD), 4) supernatant fraction after incubation with the anti-rotavirus antibody-integrated MNBs (RV-SP), 5) supernatant fraction after incubation with the anti-dengue virus antibody-integrated MNBs (DV-SP), and 6) total sample containing the same quantity of rotavirus as in 10 µL of rotavirus-infected cell lysate (total fraction, TL). Viral genomic RNA was subsequently extracted from the above fractions using a QIAamp Viral RNA mini kit and subjected to RT-reaction. The resultant cDNA was analyzed by real-time PCR using primers for the rotavirus VP7 gene as described in Materials and methods. The value of the TL sample was taken as 100%. Abbreviations: MNBs, magnetic nanobeads; RT, reverse transcription.

    Techniques Used: Infection, Incubation, Magnetic Beads, Real-time Polymerase Chain Reaction

    Detection of viral RNA of rotavirus adsorbed onto antibody-integrated MNBs. Notes: Rotavirus-infected cell lysate (10 µL) was diluted with PBS (500 µL) and then incubated with antibody-integrated magnetic beads. After incubation, the following fractions were obtained: 1) diluted rotavirus sample before incubation with the beads (BF), 2) bead fraction after incubation with anti-rotavirus antibody-integrated MNBs (RV-BD), 3) bead fraction after incubation with anti-dengue virus antibody-integrated MNBs (DV-BD), 4) supernatant fraction after incubation with the anti-rotavirus antibody-integrated MNBs (RV-SP), 5) supernatant fraction after incubation with the anti-dengue virus antibody-integrated MNBs (DV-SP), and 6) total sample containing the same quantity of rotavirus as in 10 µL of rotavirus-infected cell lysate (total fraction, TL). Viral genomic RNA was subsequently extracted from the above fractions using a QIAamp Viral RNA mini kit and subjected to a RT-reaction. Rotavirus viral protein 7 (VP7) gene (552 bp) in the cDNA was amplified by PCR as described in Materials and methods. PCR products were analyzed by agarose gel electrophoresis (1.2% gel). The identity of the amplified products was confirmed by DNA sequencing. The left-hand lane is size marker (M), which includes DNA of 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 1,200, and 1,500 bp. The position of the 552 bp band for VP7 is indicated by an arrow. The NC comprised a water sample (no rotavirus) that was subjected to RT-PCR. Abbreviations: MNBs, magnetic nanobeads; NC, negative control; RT, reverse transcription.
    Figure Legend Snippet: Detection of viral RNA of rotavirus adsorbed onto antibody-integrated MNBs. Notes: Rotavirus-infected cell lysate (10 µL) was diluted with PBS (500 µL) and then incubated with antibody-integrated magnetic beads. After incubation, the following fractions were obtained: 1) diluted rotavirus sample before incubation with the beads (BF), 2) bead fraction after incubation with anti-rotavirus antibody-integrated MNBs (RV-BD), 3) bead fraction after incubation with anti-dengue virus antibody-integrated MNBs (DV-BD), 4) supernatant fraction after incubation with the anti-rotavirus antibody-integrated MNBs (RV-SP), 5) supernatant fraction after incubation with the anti-dengue virus antibody-integrated MNBs (DV-SP), and 6) total sample containing the same quantity of rotavirus as in 10 µL of rotavirus-infected cell lysate (total fraction, TL). Viral genomic RNA was subsequently extracted from the above fractions using a QIAamp Viral RNA mini kit and subjected to a RT-reaction. Rotavirus viral protein 7 (VP7) gene (552 bp) in the cDNA was amplified by PCR as described in Materials and methods. PCR products were analyzed by agarose gel electrophoresis (1.2% gel). The identity of the amplified products was confirmed by DNA sequencing. The left-hand lane is size marker (M), which includes DNA of 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 1,200, and 1,500 bp. The position of the 552 bp band for VP7 is indicated by an arrow. The NC comprised a water sample (no rotavirus) that was subjected to RT-PCR. Abbreviations: MNBs, magnetic nanobeads; NC, negative control; RT, reverse transcription.

    Techniques Used: Infection, Incubation, Magnetic Beads, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, DNA Sequencing, Marker, Reverse Transcription Polymerase Chain Reaction, Negative Control

    26) Product Images from "Discordant congenital Zika syndrome twins show differential in vitro viral susceptibility of neural progenitor cells"

    Article Title: Discordant congenital Zika syndrome twins show differential in vitro viral susceptibility of neural progenitor cells

    Journal: Nature Communications

    doi: 10.1038/s41467-017-02790-9

    NPC gene expression analyses by RNA-Seq in cultured cells prior to ZIKV infection (see also Supplementary Fig. 3 ). a Heatmap representation and clusterization of top 20 most significant DEGs ( p
    Figure Legend Snippet: NPC gene expression analyses by RNA-Seq in cultured cells prior to ZIKV infection (see also Supplementary Fig. 3 ). a Heatmap representation and clusterization of top 20 most significant DEGs ( p

    Techniques Used: Expressing, RNA Sequencing Assay, Cell Culture, Infection

    27) Product Images from "A Portable, Pressure Driven, Room Temperature Nucleic Acid Extraction and Storage System for Point of Care Molecular Diagnostics"

    Article Title: A Portable, Pressure Driven, Room Temperature Nucleic Acid Extraction and Storage System for Point of Care Molecular Diagnostics

    Journal: Analytical methods : advancing methods and applications

    doi: 10.1039/C3AY40162F

    Recovery results from SNAP and QIAmp Viral Kit over four orders of magnitude. A . Absolute recovery of RNA from the SNAP device (n=6). A clear distinction is observed between each order of magnitude, enabling an accurate viral load determination directly
    Figure Legend Snippet: Recovery results from SNAP and QIAmp Viral Kit over four orders of magnitude. A . Absolute recovery of RNA from the SNAP device (n=6). A clear distinction is observed between each order of magnitude, enabling an accurate viral load determination directly

    Techniques Used:

    28) Product Images from "Lack of Bax Prevents Influenza A Virus-Induced Apoptosis and Causes Diminished Viral Replication ▿"

    Article Title: Lack of Bax Prevents Influenza A Virus-Induced Apoptosis and Causes Diminished Viral Replication ▿

    Journal: Journal of Virology

    doi: 10.1128/JVI.02672-08

    Influenza A virus replication is dependent upon opposite virus-induced effects on Bax and Bak activity that are unlikely to be interferon related. (A) Influenza A virus replication was analyzed by plaque assay. Virus replication is severely attenuated in Bax KO cells, resulting in a 2-log decrease in PFU/ml compared to the WT. Bak KO cells allow a maximum replication similar to that of the WT, while Bax/Bak DKO cells show a slight elevation of infectious titers during infection. These results indicate that Bax is proviral during infection, while Bak is dispensable for replication. (B) Bax was transiently expressed in all cell types by Lipofectamine 2000 transfection of a C2-Bax-GFP construct prior to infection, and supernatant samples were collected for plaque assay at 48 hpi. Baseline virus replication in each cell type was evaluated using empty C2-GFP plasmid transfection. Bax reconstitution in Bax KO cells resulted in a fivefold increase in infectious titers compared to the control ( P = 0.0007). A minimal effect on the virus titer was seen after Bax overexpression by transient transfection in WT cells compared to empty plasmid controls. (C) Influenza A virus replication was assessed by reverse transcription-PCR. Serial dilutions of stock virus at known concentrations were also analyzed to generate a standard curve to which experimental samples were compared, thus calculating the approximate number of influenza A virus particles/ml in each sample. By 24 hpi, Bax KO, Bak KO, and Bax/Bak DKO cells all showed significantly higher levels of influenza A virus RNA released into the cell culture supernatant than did WT cells. (D) Interferon activity was assessed by infecting mock- and influenza A virus-infected cells with interferon-sensitive, GFP-linked NDV and quantifying the mean GFP expression levels of 10,000 events per condition by FACS analysis. Each assay was run in triplicate, and data are expressed as the ratio of the numbers of influenza A virus-infected to mock-infected cells per cell type. After influenza A virus infection, Bak KO cells exhibited a slight decrease in ratio compared to the WT, representing a 30% increase in interferon activity ( P = 0.002). Bax KO and Bax/Bak DKO cells both showed similar fluorescence changes compared to the WT after infection. Due the high degree of similarity between cell types, these results suggest that the interferon response in infected cells is modulated by viral replication in the presence of Bak and is only slightly modified by Bax activity during influenza A virus infection. As an elevated interferon response typically leads to a reduced virus replication capacity, these results also suggest that it is unlikely that the observed trends in infectious virus titer are due to virus-induced interferon signaling.
    Figure Legend Snippet: Influenza A virus replication is dependent upon opposite virus-induced effects on Bax and Bak activity that are unlikely to be interferon related. (A) Influenza A virus replication was analyzed by plaque assay. Virus replication is severely attenuated in Bax KO cells, resulting in a 2-log decrease in PFU/ml compared to the WT. Bak KO cells allow a maximum replication similar to that of the WT, while Bax/Bak DKO cells show a slight elevation of infectious titers during infection. These results indicate that Bax is proviral during infection, while Bak is dispensable for replication. (B) Bax was transiently expressed in all cell types by Lipofectamine 2000 transfection of a C2-Bax-GFP construct prior to infection, and supernatant samples were collected for plaque assay at 48 hpi. Baseline virus replication in each cell type was evaluated using empty C2-GFP plasmid transfection. Bax reconstitution in Bax KO cells resulted in a fivefold increase in infectious titers compared to the control ( P = 0.0007). A minimal effect on the virus titer was seen after Bax overexpression by transient transfection in WT cells compared to empty plasmid controls. (C) Influenza A virus replication was assessed by reverse transcription-PCR. Serial dilutions of stock virus at known concentrations were also analyzed to generate a standard curve to which experimental samples were compared, thus calculating the approximate number of influenza A virus particles/ml in each sample. By 24 hpi, Bax KO, Bak KO, and Bax/Bak DKO cells all showed significantly higher levels of influenza A virus RNA released into the cell culture supernatant than did WT cells. (D) Interferon activity was assessed by infecting mock- and influenza A virus-infected cells with interferon-sensitive, GFP-linked NDV and quantifying the mean GFP expression levels of 10,000 events per condition by FACS analysis. Each assay was run in triplicate, and data are expressed as the ratio of the numbers of influenza A virus-infected to mock-infected cells per cell type. After influenza A virus infection, Bak KO cells exhibited a slight decrease in ratio compared to the WT, representing a 30% increase in interferon activity ( P = 0.002). Bax KO and Bax/Bak DKO cells both showed similar fluorescence changes compared to the WT after infection. Due the high degree of similarity between cell types, these results suggest that the interferon response in infected cells is modulated by viral replication in the presence of Bak and is only slightly modified by Bax activity during influenza A virus infection. As an elevated interferon response typically leads to a reduced virus replication capacity, these results also suggest that it is unlikely that the observed trends in infectious virus titer are due to virus-induced interferon signaling.

    Techniques Used: Activity Assay, Plaque Assay, Infection, Transfection, Construct, Plasmid Preparation, Over Expression, Polymerase Chain Reaction, Cell Culture, Expressing, FACS, Fluorescence, Modification

    29) Product Images from "Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery"

    Article Title: Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery

    Journal: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America

    doi: 10.1093/cid/cix518

    High viral load and identical genomes within a single patient with Ebola virus disease. A , Viral load in semen and serum. We measured viral load from extracted RNA using primers in Supplementary Table 2 (Trombley et al, 2010). Samples were quantified against a standard curve (assay limit of detection [LOD]: 1 copy/µL) to determine copies per microliter of extracted RNA. Based on the different extraction methods, we converted these values into copies per milliliter of indicated fluid (blue: serum, n = 6 replicates per sample; orange: semen, n = 3). Asterisk indicates below-assay LOD. B , Quantification of Ebola virus (EBOV) antisense (vRNA) and sense (c/mRNA) RNA in semen samples using strand-specific quantitative reverse-transcription polymerase chain reaction (RT-qPCR). We designed RT primers for a 2-step RT-qPCR to detect antisense or sense viral RNA separately. Day 180 semen sample was not tested. C , Quantification of EBOV vRNA and c/mRNA in semen samples using single-molecule tagged amplicon sequencing. We uniquely tagged and amplified RNA molecules with random barcodes in a strand-specific manner. We deduplicated reads and counted unique numbers of barcodes. Molecules at day 180 likely represent background amplification. See Supplementary Figure 1 C for quantification in peripheral blood leukocyte (PBL) samples. D , Deep sequencing metrics. We performed RNA-seq either without (unbiased) or with hybrid selection using EBOV-specific baits to reduce host RNA background. Lower viral genome coverage is observed in PBL and semen samples due to abundant cellular RNA. E , Phylogeny of the SL4 clade. We combined 1489 publicly available genomes (Diehl et al 2016) with this patient’s viral genome and generated a phylogenetic tree with 1000 bootstrap replicates. The patient sample falls within a SL4 subclade (maroon; 100% bootstrap support) of samples collected near Freetown, Sierra Leone, from late January 2015 through March 2015, representing a likely transmission network. See Supplementary Figure 2 for full tree.
    Figure Legend Snippet: High viral load and identical genomes within a single patient with Ebola virus disease. A , Viral load in semen and serum. We measured viral load from extracted RNA using primers in Supplementary Table 2 (Trombley et al, 2010). Samples were quantified against a standard curve (assay limit of detection [LOD]: 1 copy/µL) to determine copies per microliter of extracted RNA. Based on the different extraction methods, we converted these values into copies per milliliter of indicated fluid (blue: serum, n = 6 replicates per sample; orange: semen, n = 3). Asterisk indicates below-assay LOD. B , Quantification of Ebola virus (EBOV) antisense (vRNA) and sense (c/mRNA) RNA in semen samples using strand-specific quantitative reverse-transcription polymerase chain reaction (RT-qPCR). We designed RT primers for a 2-step RT-qPCR to detect antisense or sense viral RNA separately. Day 180 semen sample was not tested. C , Quantification of EBOV vRNA and c/mRNA in semen samples using single-molecule tagged amplicon sequencing. We uniquely tagged and amplified RNA molecules with random barcodes in a strand-specific manner. We deduplicated reads and counted unique numbers of barcodes. Molecules at day 180 likely represent background amplification. See Supplementary Figure 1 C for quantification in peripheral blood leukocyte (PBL) samples. D , Deep sequencing metrics. We performed RNA-seq either without (unbiased) or with hybrid selection using EBOV-specific baits to reduce host RNA background. Lower viral genome coverage is observed in PBL and semen samples due to abundant cellular RNA. E , Phylogeny of the SL4 clade. We combined 1489 publicly available genomes (Diehl et al 2016) with this patient’s viral genome and generated a phylogenetic tree with 1000 bootstrap replicates. The patient sample falls within a SL4 subclade (maroon; 100% bootstrap support) of samples collected near Freetown, Sierra Leone, from late January 2015 through March 2015, representing a likely transmission network. See Supplementary Figure 2 for full tree.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Amplification, Sequencing, RNA Sequencing Assay, Selection, Generated, Transmission Assay

    30) Product Images from "Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing ▿"

    Article Title: Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing ▿

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.02255-08

    Bland-Altman analysis of HIV-1 viral loads in patient samples ( n = 47) of plasma versus DPS after RNA extraction with a QIAamp viral RNA mini kit (Qiagen) (A), the Abbott sample preparation system (B), and a Nuclisens manual extraction kit (bioMérieux)
    Figure Legend Snippet: Bland-Altman analysis of HIV-1 viral loads in patient samples ( n = 47) of plasma versus DPS after RNA extraction with a QIAamp viral RNA mini kit (Qiagen) (A), the Abbott sample preparation system (B), and a Nuclisens manual extraction kit (bioMérieux)

    Techniques Used: RNA Extraction, Sample Prep

    HIV-1 viral loads in patient samples ( n = 47) of plasma and DPS after RNA extractions with a QIAamp viral RNA mini kit (Qiagen), the Abbott sample preparation system, or a Nuclisens manual extraction kit (bioMérieux). (A) Comparison of
    Figure Legend Snippet: HIV-1 viral loads in patient samples ( n = 47) of plasma and DPS after RNA extractions with a QIAamp viral RNA mini kit (Qiagen), the Abbott sample preparation system, or a Nuclisens manual extraction kit (bioMérieux). (A) Comparison of

    Techniques Used: Sample Prep

    31) Product Images from "Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR"

    Article Title: Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.41.11.5273-5276.2003

    Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .
    Figure Legend Snippet: Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .

    Techniques Used: Amplification, Serial Dilution, Nested PCR, Negative Control

    Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).
    Figure Legend Snippet: Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).

    Techniques Used: Amplification, Serial Dilution, Plasmid Preparation, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Software, Hybridization, Fluorescence

    32) Product Images from "Enhanced pathogenicity of low-pathogenic H9N2 avian influenza virus after vaccination with infectious bronchitis live attenuated vaccine"

    Article Title: Enhanced pathogenicity of low-pathogenic H9N2 avian influenza virus after vaccination with infectious bronchitis live attenuated vaccine

    Journal: Veterinary World

    doi: 10.14202/vetworld.2018.977-985

    Column chart showing RNA copies of H9 using rRT-polymerase chain reaction in chicken groups and different time conditions. (a) Experiment 1, (b) Experiment 2.
    Figure Legend Snippet: Column chart showing RNA copies of H9 using rRT-polymerase chain reaction in chicken groups and different time conditions. (a) Experiment 1, (b) Experiment 2.

    Techniques Used: Polymerase Chain Reaction

    33) Product Images from "Development of a Laboratory-safe and Low-cost Detection Protocol for SARS-CoV-2 of the Coronavirus Disease 2019 (COVID-19)"

    Article Title: Development of a Laboratory-safe and Low-cost Detection Protocol for SARS-CoV-2 of the Coronavirus Disease 2019 (COVID-19)

    Journal: Experimental Neurobiology

    doi: 10.5607/en20009

    Experimental scheme for human tissue sampling and total RNA extraction. (A) Each volunteer collects his/her tissue sample through pharyngeal swab, following the detailed procedures in Fig. 1 . (B) The collected human sample on polyester swab was dissolved in DMEM and transferred to a Trizol containing tube. (C) Following the Trizol-based total RNA extraction, the RNA was further processed.
    Figure Legend Snippet: Experimental scheme for human tissue sampling and total RNA extraction. (A) Each volunteer collects his/her tissue sample through pharyngeal swab, following the detailed procedures in Fig. 1 . (B) The collected human sample on polyester swab was dissolved in DMEM and transferred to a Trizol containing tube. (C) Following the Trizol-based total RNA extraction, the RNA was further processed.

    Techniques Used: Sampling, RNA Extraction

    Determination of detection efficiency and limit of rtPCR system using Lentivirus. (A) A standard calibration curve of Ct vs. genomic copy number was generated based on rtPCR results from LTR targeting primer set and known genomic copy number of LTR. (B) rtPCR results for RNA extraction by QIAmp kit or Trizol-based method. The known number of Lentivirus was tested with the two extraction methods and compared. (C) The average Ct values are compared between QIAmp and Trizol methods.
    Figure Legend Snippet: Determination of detection efficiency and limit of rtPCR system using Lentivirus. (A) A standard calibration curve of Ct vs. genomic copy number was generated based on rtPCR results from LTR targeting primer set and known genomic copy number of LTR. (B) rtPCR results for RNA extraction by QIAmp kit or Trizol-based method. The known number of Lentivirus was tested with the two extraction methods and compared. (C) The average Ct values are compared between QIAmp and Trizol methods.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Generated, RNA Extraction

    34) Product Images from "Prime-boost vaccination strategy against avian influenza and Newcastle disease viruses reduces shedding of the challenge viruses"

    Article Title: Prime-boost vaccination strategy against avian influenza and Newcastle disease viruses reduces shedding of the challenge viruses

    Journal: VirusDisease

    doi: 10.1007/s13337-018-0463-3

    qRT-PCR analysis of interferon-γ (IFN-γ) mRNA expression in chickens’ peripheral blood mononuclear cells (PBMCs) at 1 and 2 weeks post vaccination. Different letters within the same week are significantly different at p value (≤ 0.05)
    Figure Legend Snippet: qRT-PCR analysis of interferon-γ (IFN-γ) mRNA expression in chickens’ peripheral blood mononuclear cells (PBMCs) at 1 and 2 weeks post vaccination. Different letters within the same week are significantly different at p value (≤ 0.05)

    Techniques Used: Quantitative RT-PCR, Expressing

    35) Product Images from "Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR"

    Article Title: Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.41.11.5273-5276.2003

    Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .
    Figure Legend Snippet: Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .

    Techniques Used: Amplification, Serial Dilution, Nested PCR, Negative Control

    Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).
    Figure Legend Snippet: Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).

    Techniques Used: Amplification, Serial Dilution, Plasmid Preparation, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Software, Hybridization, Fluorescence

    36) Product Images from "Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR"

    Article Title: Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.41.11.5273-5276.2003

    Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .
    Figure Legend Snippet: Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .

    Techniques Used: Amplification, Serial Dilution, Nested PCR, Negative Control

    Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).
    Figure Legend Snippet: Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).

    Techniques Used: Amplification, Serial Dilution, Plasmid Preparation, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Software, Hybridization, Fluorescence

    37) Product Images from "Nucleic acid assay system for tier II labs and moderately complex clinics to detect HIV in low-resource settings"

    Article Title: Nucleic acid assay system for tier II labs and moderately complex clinics to detect HIV in low-resource settings

    Journal: The Journal of infectious diseases

    doi: 10.1086/650388

    Integrated assays using plasma spiked with Armored RNA HIV. Armored RNA HIV was spiked into human plasma at concentrations ranging from 10,000 copies/mL to 1,000 copies/mL amd extracted with a QIAamp® Viral RNA Mini Kit according to the manufacturer’s
    Figure Legend Snippet: Integrated assays using plasma spiked with Armored RNA HIV. Armored RNA HIV was spiked into human plasma at concentrations ranging from 10,000 copies/mL to 1,000 copies/mL amd extracted with a QIAamp® Viral RNA Mini Kit according to the manufacturer’s

    Techniques Used:

    38) Product Images from "Capturing and concentrating adenovirus using magnetic anionic nanobeads"

    Article Title: Capturing and concentrating adenovirus using magnetic anionic nanobeads

    Journal: International Journal of Nanomedicine

    doi: 10.2147/IJN.S104926

    Detection of the DNA genome of adenovirus adsorbed onto anionic polymer-coated magnetic beads. Notes: Adenovirus AxCAwt2 (20 μL) in 500 μL PBS were mixed with poly(MVE-MA)-coated magnetic beads. After incubation, the following fractions were obtained: BD, supernatant after incubation with the beads (SP), sample before incubation with the beads (BF), and samples containing the same quantity of adenovirus as in the BD (total fraction, TL). Viral genomic DNA was subsequently extracted from the various fractions using a QIAamp Viral RNA mini kit. These experiments confirmed that adenoviral DNA could be extracted from the beads and subjected to the PCR. DNA corresponding to the adenovirus hexon gene (1597-bp) was amplified by PCR. The identity of the amplified products was confirmed by DNA sequencing. The left-hand lane is size marker (M), which includes DNA of 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 1,200, and 1,500 bp. The positions of the 100 bp, 500 bp, and 1,500 bp bands are indicated by arrows. Abbreviations: BD, bead fraction; PBS, phosphate-buffered solution; poly(MVE-MA), poly(methyl vinyl ether-maleic anhydrate); PCR, polymerase chain reaction.
    Figure Legend Snippet: Detection of the DNA genome of adenovirus adsorbed onto anionic polymer-coated magnetic beads. Notes: Adenovirus AxCAwt2 (20 μL) in 500 μL PBS were mixed with poly(MVE-MA)-coated magnetic beads. After incubation, the following fractions were obtained: BD, supernatant after incubation with the beads (SP), sample before incubation with the beads (BF), and samples containing the same quantity of adenovirus as in the BD (total fraction, TL). Viral genomic DNA was subsequently extracted from the various fractions using a QIAamp Viral RNA mini kit. These experiments confirmed that adenoviral DNA could be extracted from the beads and subjected to the PCR. DNA corresponding to the adenovirus hexon gene (1597-bp) was amplified by PCR. The identity of the amplified products was confirmed by DNA sequencing. The left-hand lane is size marker (M), which includes DNA of 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 1,200, and 1,500 bp. The positions of the 100 bp, 500 bp, and 1,500 bp bands are indicated by arrows. Abbreviations: BD, bead fraction; PBS, phosphate-buffered solution; poly(MVE-MA), poly(methyl vinyl ether-maleic anhydrate); PCR, polymerase chain reaction.

    Techniques Used: Magnetic Beads, Incubation, Polymerase Chain Reaction, Amplification, DNA Sequencing, Marker

    39) Product Images from "West Nile Virus Temperature Sensitivity and Avian Virulence Are Modulated by NS1-2B Polymorphisms"

    Article Title: West Nile Virus Temperature Sensitivity and Avian Virulence Are Modulated by NS1-2B Polymorphisms

    Journal: PLoS Neglected Tropical Diseases

    doi: 10.1371/journal.pntd.0004938

    Growth and temperature sensitivity of WNV NY99/KN3829 chimeras in AMCR PBMCs. (A) Growth of chimeric viruses in PBMCs at 37°C. (B) Growth of selected chimeric viruses in PBMCs at 42°C. N = 3 replicates per virus. (C) Variability among replicates in PBMC culture at 37°C. Individual replicates of PBMC cultures of KN-str/KN-NS3-4B and NY-str/KN-NS1-4B are shown. No supernatant was available for one replicate of NY-str/KN-NS1-4B at 6 dpi due to fungal contamination. Filled squares represent KN-str/KN-NS3-4B, and open diamonds represent NY-str/KN-NS1-4B. Viral RNA was extracted from 5 dpi (NY-str/KN-NS1-4B) or 6 dpi (KN-str/KN-NS3-4B) supernatants of cultures shown in black, and the NS3-249 region was sequenced. Cultures shown in grey were not sequenced.
    Figure Legend Snippet: Growth and temperature sensitivity of WNV NY99/KN3829 chimeras in AMCR PBMCs. (A) Growth of chimeric viruses in PBMCs at 37°C. (B) Growth of selected chimeric viruses in PBMCs at 42°C. N = 3 replicates per virus. (C) Variability among replicates in PBMC culture at 37°C. Individual replicates of PBMC cultures of KN-str/KN-NS3-4B and NY-str/KN-NS1-4B are shown. No supernatant was available for one replicate of NY-str/KN-NS1-4B at 6 dpi due to fungal contamination. Filled squares represent KN-str/KN-NS3-4B, and open diamonds represent NY-str/KN-NS1-4B. Viral RNA was extracted from 5 dpi (NY-str/KN-NS1-4B) or 6 dpi (KN-str/KN-NS3-4B) supernatants of cultures shown in black, and the NS3-249 region was sequenced. Cultures shown in grey were not sequenced.

    Techniques Used:

    40) Product Images from "Paper-Based RNA Extraction, in Situ Isothermal Amplification, and Lateral Flow Detection for Low-Cost, Rapid Diagnosis of Influenza A (H1N1) from Clinical Specimens"

    Article Title: Paper-Based RNA Extraction, in Situ Isothermal Amplification, and Lateral Flow Detection for Low-Cost, Rapid Diagnosis of Influenza A (H1N1) from Clinical Specimens

    Journal: Analytical chemistry

    doi: 10.1021/acs.analchem.5b01594

    Clinical nasopharyngeal specimens. (a) Paper extractions and QIAamp kit extractions of clinical specimens A–L. (b) RT-LAMP assay performed in solution with Qiagen-extracted purified RNA from clinical specimens A–L, and gel electrophoresis of products. (c) Lateral flow detection of amplified products; test line intensities plotted as a percentage of control line intensities. (d) Paper extraction of clinical specimens A–L followed by in situ RT-LAMP and lateral flow detection. + = positive control (10 9 cp/mL RNA standard); − = negative control (no RNA).
    Figure Legend Snippet: Clinical nasopharyngeal specimens. (a) Paper extractions and QIAamp kit extractions of clinical specimens A–L. (b) RT-LAMP assay performed in solution with Qiagen-extracted purified RNA from clinical specimens A–L, and gel electrophoresis of products. (c) Lateral flow detection of amplified products; test line intensities plotted as a percentage of control line intensities. (d) Paper extraction of clinical specimens A–L followed by in situ RT-LAMP and lateral flow detection. + = positive control (10 9 cp/mL RNA standard); − = negative control (no RNA).

    Techniques Used: RT Lamp Assay, Purification, Nucleic Acid Electrophoresis, Flow Cytometry, Amplification, In Situ, Positive Control, Negative Control

    Related Articles

    Real-time Polymerase Chain Reaction:

    Article Title: Multiple Layers of Chimerism in a Single-Stranded DNA Virus Discovered by Deep Sequencing
    Article Snippet: .. Evaluating Spin Columns for the Presence of CHIV14 by Quantitative Real-Time PCR Nucleic acids were extracted from human serum samples or mock-extracted with water using a variety of spin columns , including QIAamp Viral RNA Mini Kit (Qiagen, kit catalog number 52906, lot number 436166748, and spin column lot number 139298432) and QIAamp ultraclean production (UCP) mini spin columns (Qiagen, reagents: catalog number 50112, lot number 142355460; spin columns: lot number 145033759). ..

    Article Title: Efficacy of Human Monoclonal Antibody Monotherapy Against Bundibugyo Virus Infection in Nonhuman Primates
    Article Snippet: .. For real-time qPCR analysis, RNA was isolated from whole blood using the Viral RNA Mini-Kit (Qiagen) using 100 µL of blood into 600 µL of buffer AVL. .. Primers/probe targeting the VP35 intergenic region of BDBV were used for real-time qPCR with the probe sequence of 6 carboxyfluorescein–5′-CGCAACCTCCACAGTCGCCT-3′–6 carboxytetramethylrhodamine (Fisher Scientific).

    Article Title: Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses
    Article Snippet: .. RNA was isolated from medium using Qiagen Viral RNA Mini Kit and hRSV titer was determined by qPCR and expressed as fold change compared to 2 hour time point. .. Quantitative qPCR was conducted by using TaqMan Fast Virus 1-Step Master Mixture (Applied Biosystem) according to the manufacturer’s instructions.

    Isolation:

    Article Title: Efficacy of Human Monoclonal Antibody Monotherapy Against Bundibugyo Virus Infection in Nonhuman Primates
    Article Snippet: .. For real-time qPCR analysis, RNA was isolated from whole blood using the Viral RNA Mini-Kit (Qiagen) using 100 µL of blood into 600 µL of buffer AVL. .. Primers/probe targeting the VP35 intergenic region of BDBV were used for real-time qPCR with the probe sequence of 6 carboxyfluorescein–5′-CGCAACCTCCACAGTCGCCT-3′–6 carboxytetramethylrhodamine (Fisher Scientific).

    Article Title: Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses
    Article Snippet: .. RNA was isolated from medium using Qiagen Viral RNA Mini Kit and hRSV titer was determined by qPCR and expressed as fold change compared to 2 hour time point. .. Quantitative qPCR was conducted by using TaqMan Fast Virus 1-Step Master Mixture (Applied Biosystem) according to the manufacturer’s instructions.

    Centrifugation:

    Article Title: Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma or Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing ▿
    Article Snippet: .. The QIAamp viral RNA minikit (Qiagen, Courtaboeuf, France) combines a silica gel-based membrane with the speed of microspin centrifugation. .. The Abbott sample preparation system (Abbott Molecular, Rungis, France) is an iron particle-based method used for the Abbott RealTime HIV-1 commercial assay for viral load determination.

    other:

    Article Title: Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR
    Article Snippet: Identical results were obtained after extraction of the identical specimens with the QIAamp Viral RNA Mini kit.

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    Qiagen qiaamp viral rna mini kit
    Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic <t>DNA/RNA</t> kit and the <t>QIAamp</t> DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .
    Qiaamp Viral Rna Mini Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 1400 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .

    Journal: Journal of Clinical Microbiology

    Article Title: Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR

    doi: 10.1128/JCM.41.11.5273-5276.2003

    Figure Lengend Snippet: Amplification of a serial dilution of the EUROHEP standard with HBV-specific primers in a nested PCR following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. (A) Chemagen extracts. (B) QIAGEN extracts. Lane M shows a 100-bp ladder, and lane C shows results for the negative control. Lanes 1 through 10 show results for different viral loads expressed in numbers of copies per ml: 1, 4 × 10 5 ; 2, 4 × 10 4 ; 3, 4 × 10 3 ; 4, 4 × 10 2 ; 5, 2 × 10 2 ; 6, 1 × 10 2 ; 7, 8 × 10 1 ; 8, 4 × 10 1 ; 9, 2 × 10 1 ; 10, 1 × 10 1 .

    Article Snippet: Identical results were obtained after extraction of the identical specimens with the QIAamp Viral RNA Mini kit.

    Techniques: Amplification, Serial Dilution, Nested PCR, Negative Control

    Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).

    Journal: Journal of Clinical Microbiology

    Article Title: Efficient Extraction of Viral DNA and Viral RNA by the Chemagic Viral DNA/RNA Kit Allows Sensitive Detection of Cytomegalovirus, Hepatitis B Virus, and Hepatitis G Virus by PCR

    doi: 10.1128/JCM.41.11.5273-5276.2003

    Figure Lengend Snippet: Amplification of a serial dilution of the standard plasmid pCR-gpB by real-time PCR with CMV-specific primers (amplicon, 254 bp) on the LightCycler instrument (software, version 3.5; analysis method, fit points with manual noise band adjustment, hybridization probe format) following extraction with the Chemagic DNA/RNA kit and the QIAamp DNA Blood Mini kit. pCR-gpB concentrations (from left to right) were 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , and 2 × 10 2 copies per ml of serum. Continuous line, Chemagen extracts; broken line, QIAGEN extracts. Cycle number, cycle number of the amplification reaction; F2/F1, quotient of fluorescence channel F2 (hybridization probe) and fluorescence channel F1 (fluorescein).

    Article Snippet: Identical results were obtained after extraction of the identical specimens with the QIAamp Viral RNA Mini kit.

    Techniques: Amplification, Serial Dilution, Plasmid Preparation, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Software, Hybridization, Fluorescence

    NS1 unique regions are important for modulating host responses Human monocyte-derived dendritic cells (MDDCs) were transduced with either only empty lentiviral vectors (empty) or lentivirus vectors that express either EBOV-VP35, hRSV-NS1, hRSV-NS1-(1-118), hRSV-NS1-L132A/L133A. RNA was isolated from transduced MDDCs that were either mock-infected or infected with SeV. RNA was extracted at the indicated hours post-infection; and a, IFN-β, b, TNF-α, c, ISG54, and d, ISG56 mRNA levels were quantified RT-qPCR, normalizing their levels to that of β-actin mRNA. The graph indicates the fold-change relative to the mock-infected samples. For a–d, symbols are: ○, empty vector; ▲, hRSV NS1 1-118; ▼, hRSV NS1 L132A/L133A; ■, hRSV NS1 WT; and ●, EBOV VP35. hRSV NS1 inhibits upregulation of DC maturation markers. Transduced MDDCs were infected with SeV for 20h, harvested and stained for expression of CD40, CD80, CD83 and CD86. Fold change in mean fluorescence intensity (MFI) for the indicated proteins in transduced MDDCs where fold increase indicates comparisons of SeV-infected to uninfected MDDCs. Error bars indicate standard deviations from three independent experiments (*p

    Journal: Nature microbiology

    Article Title: Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses

    doi: 10.1038/nmicrobiol.2017.101

    Figure Lengend Snippet: NS1 unique regions are important for modulating host responses Human monocyte-derived dendritic cells (MDDCs) were transduced with either only empty lentiviral vectors (empty) or lentivirus vectors that express either EBOV-VP35, hRSV-NS1, hRSV-NS1-(1-118), hRSV-NS1-L132A/L133A. RNA was isolated from transduced MDDCs that were either mock-infected or infected with SeV. RNA was extracted at the indicated hours post-infection; and a, IFN-β, b, TNF-α, c, ISG54, and d, ISG56 mRNA levels were quantified RT-qPCR, normalizing their levels to that of β-actin mRNA. The graph indicates the fold-change relative to the mock-infected samples. For a–d, symbols are: ○, empty vector; ▲, hRSV NS1 1-118; ▼, hRSV NS1 L132A/L133A; ■, hRSV NS1 WT; and ●, EBOV VP35. hRSV NS1 inhibits upregulation of DC maturation markers. Transduced MDDCs were infected with SeV for 20h, harvested and stained for expression of CD40, CD80, CD83 and CD86. Fold change in mean fluorescence intensity (MFI) for the indicated proteins in transduced MDDCs where fold increase indicates comparisons of SeV-infected to uninfected MDDCs. Error bars indicate standard deviations from three independent experiments (*p

    Article Snippet: RNA was isolated from medium using Qiagen Viral RNA Mini Kit and hRSV titer was determined by qPCR and expressed as fold change compared to 2 hour time point.

    Techniques: Derivative Assay, Transduction, Isolation, Infection, Quantitative RT-PCR, Plasmid Preparation, Staining, Expressing, Fluorescence

    Integrated assays using plasma spiked with Armored RNA HIV. Armored RNA HIV was spiked into human plasma at concentrations ranging from 10,000 copies/mL to 1,000 copies/mL amd extracted with a QIAamp® Viral RNA Mini Kit according to the manufacturer’s

    Journal: The Journal of infectious diseases

    Article Title: Nucleic acid assay system for tier II labs and moderately complex clinics to detect HIV in low-resource settings

    doi: 10.1086/650388

    Figure Lengend Snippet: Integrated assays using plasma spiked with Armored RNA HIV. Armored RNA HIV was spiked into human plasma at concentrations ranging from 10,000 copies/mL to 1,000 copies/mL amd extracted with a QIAamp® Viral RNA Mini Kit according to the manufacturer’s

    Article Snippet: Note: according to the QIAamp® Viral RNA Mini Kit Handbook, this Kit can also be performed using the QIAvac® 24 Plus (Qiagen, Valencia, CA) if a centrifuge is not available.

    Techniques:

    Comparing the DRM in RNA (plasma) and DNA (peripheral blood mononuclear cells). a NRTI. b NNRTI

    Journal: AIDS Research and Therapy

    Article Title: High level of HIV-1 drug resistance mutations in patients with unsuppressed viral loads in rural northern South Africa

    doi: 10.1186/s12981-017-0161-z

    Figure Lengend Snippet: Comparing the DRM in RNA (plasma) and DNA (peripheral blood mononuclear cells). a NRTI. b NNRTI

    Article Snippet: DNA and RNA extractions Plasma RNA and proviral DNA from total cells were extracted using Qiagen Viral RNA Mini Kit and Qiagen blood DNA Midi Kit (Qiagen, Valencia, CA, USA), respectively, according to the manufacturers’ protocols.

    Techniques: