Journal: bioRxiv

Article Title: Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions

doi: 10.1101/2024.11.20.624553

Figure Lengend Snippet: Haloarchaeal species exhibit differential susceptibility to oxidative stress conditions. Growth is plotted as the log10 optical density at 600 nm (OD600) over time (hours). Each curve represents the generalized additive model (GAM) fit to the raw data from at least 3 biological replicate experiments (seeded from starter cultures inoculated with separate colonies), each with 3 technical replicates (aliquots from the same starter culture). Shaded grey ribbons indicate the standard error. Error is low where ribbons are not visible. Concentrations are written above the corresponding growth curve in each panel. Concentrations surrounded by a box is that condition chosen for testing Δ rosR growth in subsequent experiments. (A) Hfx. volcanii growth under a titration of peroxide (H 2 O 2 ) concentrations. (B) Hfx. mediterranei growth under H 2 O 2 . (C) Hfx. volcanii growth under varying paraquat (PQ) concentrations. (D) Hfx. mediterranei growth under PQ.

Article Snippet: Wild-type strains Halobacterium salinarum NRC-1 ( Hs) , Haloferax volcanii strain DS2 ( Hv) , and Haloferax mediterranei ( Hm) ATCC 33500 were used in this study.

Techniques: Titration

Journal: bioRxiv

Article Title: Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions

doi: 10.1101/2024.11.20.624553

Figure Lengend Snippet: hv RosR activates arlA1 and arlA2 , encoding structural components of the archaellum in Hfx. volcanii . (A) Top, genomic region encoding the archaellum and related motility functions; middle, ChIP-seq data for the region highlighted in teal (read depth y-axis is shown at right); bottom, chromosomal coordinates for genes in the zoomed region, with genes on the forward strand depicted on top of the line and reverse strand below the line. (B) Scatterplot of normalized counts from RNA-seq data, with parental control strain counts on the X-axis and hv Δ rosR counts on the y-axis. Genes passing the significance threshold of p < 0.05 and log2 fold change >= |1| are shown in blue, those significant genes also bound in ChIP-seq data in pink (see legend). (C) ChIP-qPCR validation of ChIP-seq data. Bar height represents the mean enrichment of hv RosR binding each site relative to a control region. Error bars represent the standard deviation from the mean of triplicate samples. hv RosR-HA enrichment is shown in salmon and PyrE2-HA parent strain control in grey. Amplicons tested are shown in orange below the bar graph (“peak 1, peak 2, peak 3”) and are set relative to chromosomal position of the corresponding genes. Asterisks indicate the statistical significance of enrichment for each peak (salmon bars) relative to the parent control (grey bars) by two-sided unpaired Student’s t-test, * p < 1.02 x 10 -3 , ** p < 4.71 x 10 -4 , *** p < 6.31 x 10 -5 . (D) Logo of the consensus binding motif detected computationally from hv RosR ChIP-seq binding site sequences. Motif position in nucleotides is given on the x-axis and bit score of per-base representation in the position weight matrix is given on the y-axis. See also Supplementary Table S4 for detailed RNA-seq, ChIP-seq, and motif data.

Article Snippet: Wild-type strains Halobacterium salinarum NRC-1 ( Hs) , Haloferax volcanii strain DS2 ( Hv) , and Haloferax mediterranei ( Hm) ATCC 33500 were used in this study.

Techniques: ChIP-sequencing, RNA Sequencing, Control, ChIP-qPCR, Biomarker Discovery, Binding Assay, Standard Deviation

Journal: British journal of pharmacology

Article Title: Decreased extrasynaptic δ-GABA A receptors in PNN-associated parvalbumin interneurons correlates with anxiety in APP and tau mouse models of Alzheimer's disease.

doi: 10.1111/bph.16441

Figure Lengend Snippet: FIGURE 9 Treatment with positive allosteric modulator (DS2) of δ-GABAA receptors (δ-GABAARs) reduced anxiety in App mouse models of Alzheimer's disease (AD). (a) Schematic of DS2 drug injection and light–dark chamber test. (b) Dose response curve of DS2 drug in WT and AppNL-

Article Snippet: Therefore, in in vivo dosing experiments, mice were treated with the DS2 drug (Tocris UK), dissolved in DMSO (ThermoFisher Scientific, Cambridge, UK), 1, 2 and 4 mg kg 1, intraperitoneal injection (ip) or vehicle.

Techniques: Injection

Journal: NPJ Vaccines

Article Title: DS2 designer pre-fusion F vaccine induces strong and protective antibody response against RSV infection

doi: 10.1038/s41541-024-01059-9

Figure Lengend Snippet: A The pre-fusion and post-fusion conformational states of the RSV F glycoprotein are depicted, with colored antigenic sites (Ø, V, IV, III, II, and I) recognized by distinct groups of monoclonal antibodies (mAbs). B Specific mutations introduced to maintain the prefusion conformation in the three designer pre-F glycoproteins DS2, DS-Cav1, and SC-TM. C A schematic diagram illustrates the recombinant AdC68 vector expressing the three designer pre-F glycoproteins of RSV. Each glycoprotein was presented with signal peptide (SP), transmembrane (TM), and cytoplasmic tail (CT) from RSV A2 strain. The coding sequences of each designer pre-F were inserted into the E1 region of the AdC68 vector, controlled of the cytomegalovirus (CMV) promoter, and terminated by a bovine growth hormone (BGH) polyadenylation signal sequence. D A comparison of the expression and epitope display of various designer pre-F on the surface of infected HEK 293T cells. Following infection with recombinant AdC68, HEK 293T cells were analyzed by flow cytometry using a panel of mAbs targeting various epitopes in the pre- and post-F glycoproteins of RSV. The names and sites specificity of each mAb in the F glycoprotein of RSV are indicated. Motavizumab and Palivizumab, two clinically evaluated antibody drugs, recognize the identical epitope within site II. The X-axis indicates the PE fluorescence intensity while Y-axis denotes the number (counts) of the events. The percentage in each of the flow cytometry graph represents the percentage of PE-positive cells.

Article Snippet: Codon-optimized genes encoding the wild-type (WT) fusion glycoprotein (F) of RSV A2 strain (GenBank accession no: ACO83301.1), along with structure-based designer DS2, DS-Cav1, and SC-TM prefusion F glycoproteins – , were synthesized by GenScript Biotech Corporation, China.

Techniques: Recombinant, Plasmid Preparation, Expressing, Sequencing, Comparison, Infection, Flow Cytometry, Fluorescence

Journal: NPJ Vaccines

Article Title: DS2 designer pre-fusion F vaccine induces strong and protective antibody response against RSV infection

doi: 10.1038/s41541-024-01059-9

Figure Lengend Snippet: A Timeline and grouping for vaccination and monitoring of antibody response among five groups of vaccinated mice. Fifty 6-week-old BALB/c mice, ten in each group, were immunized with indicated dose and route of designer vaccines or controls at week 0 and again at week 3. Blood samples were collected every two weeks to monitor the binding and neutralizing titers to RSV pre-F and live RSV, respectively. B , C Comparison of serum neutralizing activity to live RSV and binding activity to each of the designer pre-F and WT F recombinant glycoproteins among the five groups of vaccinated mice (n = 10). Bar graphs depict the week 10 neutralizing titers (ID 50 ) and binding activities (ED 50 ) to recombinant DS2, DS-Cav1, SC-TM, and WT. Each dot represents one animal and color-coded according to the vaccinated group as shown in Fig. . Dotted lines represent assay limit of detection. D Experimental design for evaluating the protective activity of AdC68-DS2 in mice. Ten weeks after immunization with either AdC68-DS2 or AdC68 empty vector, mice were intranasally challenged with 3 × 10 5 PFU of live RSV Long strain. E , F All animals were carefully monitored for body weight changes, for viral loads in the lungs by qPCR and plaque assays, and for pathological analysis of lung tissue by H&E staining (n = 5). The scale bar is 200 μm for 5× and 50 μm for 20×. VL vascular lumen, BL bronchiolar lumen. All data are presented as median ±interquartile range. The Mann–Whitney U test is used for comparisons between two independent groups and Kruskal–Wallis H test for comparisons among multiple independent groups, as the data sets are not uniformly normally distributed. The results shown are representatives of two independent experiments. The p -values are marked in the graphs.

Article Snippet: Codon-optimized genes encoding the wild-type (WT) fusion glycoprotein (F) of RSV A2 strain (GenBank accession no: ACO83301.1), along with structure-based designer DS2, DS-Cav1, and SC-TM prefusion F glycoproteins – , were synthesized by GenScript Biotech Corporation, China.

Techniques: Vaccines, Binding Assay, Comparison, Activity Assay, Recombinant, Plasmid Preparation, Staining, MANN-WHITNEY

Journal: NPJ Vaccines

Article Title: DS2 designer pre-fusion F vaccine induces strong and protective antibody response against RSV infection

doi: 10.1038/s41541-024-01059-9

Figure Lengend Snippet: A Overall experimental procedure for isolating and characterizing DS2-specific mAbs from bone marrow antibody-secreting cells (ASCs). The image was created with BioRender.com, with permission. B Representative bone marrow ASCs secreting DS2-specific antibodies were captured by the surrounding DS2-coated polystyrene particles, detected using a secondary anti-mouse IgG antibody conjugated with Alexa Fluor™ 488, and visualized under a fluorescence microscope. C Phylogenetic analysis of the heavy and light chains of 29 DS2-specific mAbs, and their relative genetic relatedness to control mAbs (D25, CR9501, 101F, MPE8, Motavizumab, and 4D7) targeting six major antigenic sites (Ø, V, IV, III, II and I) in the F glycoprotein of RSV. Nirsevimab, a commercially available antibody drug derived from D25, specifically recognizes the site Ø antigenic site. The epitope specificity for each of the 29 DS2-specific mAbs, defined by the competitive SPR with the six control mAbs, is indicated along with their binding (ED 50 ) and neutralizing (ID 50 ) abilities. The results shown are representatives of two independent experiments. The branch length is drawn to scale to assess genetic relatedness among the mAbs.

Article Snippet: Codon-optimized genes encoding the wild-type (WT) fusion glycoprotein (F) of RSV A2 strain (GenBank accession no: ACO83301.1), along with structure-based designer DS2, DS-Cav1, and SC-TM prefusion F glycoproteins – , were synthesized by GenScript Biotech Corporation, China.

Techniques: Fluorescence, Microscopy, Control, Derivative Assay, Binding Assay

Journal: NPJ Vaccines

Article Title: DS2 designer pre-fusion F vaccine induces strong and protective antibody response against RSV infection

doi: 10.1038/s41541-024-01059-9

Figure Lengend Snippet: Phenotypic and genotypic characterization of the DS2-specific neutralizing mAbs

Article Snippet: Codon-optimized genes encoding the wild-type (WT) fusion glycoprotein (F) of RSV A2 strain (GenBank accession no: ACO83301.1), along with structure-based designer DS2, DS-Cav1, and SC-TM prefusion F glycoproteins – , were synthesized by GenScript Biotech Corporation, China.

Techniques: Sequencing, Control

Journal: NPJ Vaccines

Article Title: DS2 designer pre-fusion F vaccine induces strong and protective antibody response against RSV infection

doi: 10.1038/s41541-024-01059-9

Figure Lengend Snippet: A Lateral and top view of mAb60 Fab in complex with DS2 pre-fusion F trimer. The heavy chain of mAb60 Fab is shown in red, and the light chain in magenta. The DS2 pre-fusion F trimer is depicted in dark gray as a molecular surface, with one of the protomers depicted in green as a ribbon diagram. B Modeling analysis of mAb60 Fab binding to both pre- and post-fusion F monomers. mAb60 binds to the antigenic site II, similar to Motavizumab, but distinct from antibodies to antigenic site Ø, which are only present in the pre-fusion F and are bound by D25 (in teal) and Nirsevimab (in coral). C The epitope and the paratope residues involved in mAb60 Fab binding to the DS2 pre-fusion F. Epitope residues are shown in green and depicted as a molecular surface, while paratope residues are highlighted with yellow circles and represented as ribbon diagrams. The epitope of Motavizumab is outlined by a dark orange dashed line. D Interactions between mAb60 Fab and DS2 pre-fusion F at the binding interface. Hydrogen bonds are shown as pure-blue dotted lines, and salt bridges as light-yellow lines. E Superimpose of mAb60 Fab onto the post-fusion F (PDB: 5J3D).

Article Snippet: Codon-optimized genes encoding the wild-type (WT) fusion glycoprotein (F) of RSV A2 strain (GenBank accession no: ACO83301.1), along with structure-based designer DS2, DS-Cav1, and SC-TM prefusion F glycoproteins – , were synthesized by GenScript Biotech Corporation, China.

Techniques: Binding Assay