Journal: Nature Communications

Article Title: Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory

doi: 10.1038/s41467-018-05868-0

Figure Lengend Snippet: Overexpression of Per1 in the dorsal hippocampus ameliorates age-related impairments in object location memory. a Schematic of lentivirus construct used to overexpress v5-tagged Per1 (pLVX-v5Per1) compared to the empty vector control (pLVX-EV). b Per1 mRNA was significantly increased 24 and 48 h after transfection of pLVX-v5Per1 in HT22 cells compared to cells transfected with EV (Two-way ANOVA: Group x Timepoint interaction ( F (1,8) = 52.8, p < 0.001), Sidak’s post hoc tests, *** p < 0.001, n = 3, 3, 3, 3). c 18-m.o. mice given hippocampal infusions of pLVX-v5Per1 showed significantly better memory for OLM than mice given pLVX-EV control virus (Two-way ANOVA: virus x session interaction, ( F (1,29) = 7.15, p < 0.05), Sidak’s post hoc tests, ** p < 0.01, *** p < 0.001, n = 16, 15, all males). d Total exploration was similar for both groups at test ( t (29) = 0.57, p = 0.57). e Schematic of CRISPR/dCas9 Synergistic Activation Mediator (SAM) system used to drive Per1 transcription. Top: Individual components of SAM. Bottom: Components assembled at the Per1 promoter, driving Per1 transcription. f Per1 mRNA was significantly increased 48 h after transfection of CRISPR-SAM components in HT22 cells compared to cells transfected with the control sgRNA (Two-way ANOVA: Group x Timepoint interaction ( F (1,8) = 14.77, p < 0.01), Sidak’s post hoc tests, ** p < 0.001, n = 3,3,3,3). g 18-m.o. mice given hippocampal infusions of the CRISPR-SAM system with sgRNA targeting Per1 showed significantly better memory for OLM compared to EV control mice with control sgRNA (Two-way ANOVA: Virus x Session interaction ( F (1,30) = 5.83, p < 0.05), Sidak’s post hoc tests, *** p < 0.001, n = 17, 15, all males). h Total exploration was similar for both groups at test ( t (30) = 0.41, p = 0.68). Data are presented as mean ± SEM

Article Snippet: Similarly, to verify that the CRISPR-SAM system can effectively drive Per1 transcription, HT22 cells were transfected with dCas9-VP64 (lenti MS2-P65_HSF1_Blast was a gift from Feng Zhang Addgene plasmid #61425), MS2-P65-HSF1 (lenti dCAS-VP64_Blast was a gift from Feng Zhang, Addgene plasmid #61426), and either Per1 sgRNA (Per1 sgRNA) or the non-targeting control sgRNA (ctrl sgRNA) (lenti sgRNA (MS2)_zeo backbone was a gift from Feng Zhang, Addgene plasmid #61427) using Lipofectamine LTX (Invitrogen).

Techniques: Over Expression, Construct, Plasmid Preparation, Control, Transfection, Virus, CRISPR, Activation Assay

Journal: Cancer Research Communications

Article Title: Netrin-1 and UNC5B Cooperate with Integrins to Mediate YAP-Driven Cytostasis

doi: 10.1158/2767-9764.CRC-24-0101

Figure Lengend Snippet: A CRISPR screen identifies UNC5B as a YAP effector. A, Z -scores comparing YAP-expressing (day 25) to Empty (day 25) cells for each sgRNA in the CRISPR screen. Select genes are indicated. n = 4. B, TEAD1 knockout rescues YAP-induced cytostasis in Y79 cells (left). Western blot showing TEAD1 knockout efficiency and expression of ectopic YAP (right). *, P < 0.05 compared with sgControl cells, n = 3. C, UNC5B knockout rescues YAP-induced cytostasis in Y79 cells (left). Western blot showing UNC5B knockout efficiency and expression of ectopic YAP (right). ***, P < 0.001 compared with sgControl cells, n = 4. D, RT-qPCR for YAP target genes ( AJUBA, AMOTL2, CYR61 and AHNAK ) or a control gene ( RER1 ) in control or UNC5B knockout Y79 cells ± ectopic YAP expression. n = 3.

Article Snippet: Briefly, a pooled CRISPR sgRNA library was constructed by cloning sgRNA sequences (4/gene plus 50 nontargeting controls) into the LentiCRISPR v2 lentiviral backbone (Addgene plasmid #52961; RRID:Addgene_52961).

Techniques: CRISPR, Expressing, Knock-Out, Western Blot, Quantitative RT-PCR, Control

Journal: Lab on a chip

Article Title: LabDisk with complete reagent prestorage for sample-to-answer nucleic acid based detection of respiratory pathogens verified with influenza A H3N2 virus.

doi: 10.1039/c5lc00871a

Figure Lengend Snippet: Fig. 3 Fluorescence signal for parallel RT-PCR reactions acquired after the annealing step in each reaction cavity. Except reaction cavity 4 (parainfluenza panel) and reaction cavity 8 (atypical bacteria panel) each reaction cavity contained primers and fluorescence probe also detecting RNA bacteriophage MS2 as internal control. Missing primer and fluorescence probes for internal control led to the negative signal in these two reaction cavities.

Article Snippet: As initial sample material we used the RNA bacteriophage MS2 (DSM-13767, type: Levivirus, species: Enterobacteria phage MS2, DSMZ GmbH, Germany) acting as internal control of the used respiratory panels and was diluted with SM buffer, pH 7.5 (Alfa Aesar GmbH & Co KG, Germany) and applied with the concentration of 75 pfu ml−1.

Techniques: Fluorescence, Reverse Transcription Polymerase Chain Reaction, Bacteria, Control

Journal:

Article Title: Combined Immunomagnetic Separation-Molecular Beacon-Reverse Transcription-PCR Assay for Detection of Hepatitis A Virus from Environmental Samples

doi: 10.1128/AEM.70.7.4371-4374.2004

Figure Lengend Snippet: Pathogens tested to determine the specificity of the assay

Article Snippet: The ability of the assay to detect HAV strains other than HM-175 was confirmed by the observation of a positive response with a clinical isolate (GA76) obtained from the Centers for Disease Control and Prevention. table ft1 table-wrap mode="anchored" t5 TABLE 2. caption a7 Agent Strain Detection Source a HAV HM175 + ATCC HAV GA76 + CDC Coxsackievirus B1 (ATCC VR-28) Conn-5 − ATCC Coxsackievirus B3 (ATCC VR-30) Nancy − ATCC Coxsackievirus B6 (ATCC VR-155) Schmitt − ATCC Echovirus 11 (ATCC VR-41) Gregory − ATCC Echovirus 17 (ATCC VR-1058) CHHE-29 − ATCC Echovirus 19 (ATCC VR-1060) Bruke − ATCC Human paraechovirus type 1 Valencia − CSD Adenovirus type 2 Sewage isolate − CSD Adenovirus type 15 Sewage isolate − CSD Poliovirus 1 LscAb − ATCC Rotavirus Wa − ATCC MS2 (ATCC 15597-B1) − ATCC φX174 (ATCC 13706-B1) − ATCC Open in a separate window a CDC, Hepatitis Branch, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Ga. CSD, County Sanitation Districts of Los Angeles County, Whittier, Calif. Pathogens tested to determine the specificity of the assay

Techniques:

Journal: Current Opinion in Environmental Science & Health

Article Title: Sewage surveillance for SARS-CoV-2: Molecular detection, quantification, and normalization factors

doi: 10.1016/j.coesh.2022.100363

Figure Lengend Snippet: Recent studies on SARS-CoV-2 sampling, sample pre-treatment, RNA gene detection, and sequencing for COVID-19 surveillance via non-clinical approach.

Article Snippet: Wastewater treatment plants (9) , Central Ohio, US , 14,000–49,000 , 24-h composite samples-twice a week , July 2020–January 2021 , Adsorption-precipitation by a positively charged filter followed by flocculation and centrifugal ultrafiltration , Spiking surrogates: male-specific coliphage MS2 (ATCC cat. No. 15597-B1), bovine coronavirus (BCoV strain ML-6 mebus), and human coronavirus OC43 (ATCC cat. No. VR-1558) , dd-PCR, N-gene and E-gene , Firefly ( Coleoptera ) Luciferase control RNA , + (Next generation sequencing) , Ai et al., 2021 [ ] .

Techniques: Sampling, Sequencing, Virus, Filtration, Concentration Assay, Control, Inhibition, RNA Extraction, Adsorption, Flocculation, Luciferase, Next-Generation Sequencing, Modification, Construct, Positive Control, Centrifugation, Cell Culture, Membrane