Journal: bioRxiv

Article Title: A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies

doi: 10.1101/2020.10.29.361287

Figure Lengend Snippet: ( a ) The workflow takes linear DNA library as input. ( b ) Ribosome display links genotype (RNAs transcribed from DNA input library that are stop codon free, and stall ribosome at the end of the transcript) and phenotype (folded VHH protein tethered to ribosomes due to the lack of stop codon in the RNA). ( c ) Selection cycle that enriches DNA encoding for VHHs that binds immobilized targets. ( d ) High throughput sequencing of full-length VHHs. ( e ) Sequences are grouped into clusters based on similarity of their CDRs, each cluster is distinct and represent a unique binding family. ( f ) The system outputs one representative sequence from each cluster to be synthesized and characterized for specific downstream applications. ( g ) Workflow for generating VHH library. VHH CDR randomization was introduced by PCR using a hairpin oligo (blocks DNA end from ligation) and an oligo with random 5’ sequence, followed by orientation-controlled ligation. Three successive PCR plus ligation cycles randomizes all three CDRs. ( h ) The final DNA library sequence structure. ( i ) One round of ribosome display and anti-Myc selection was performed after randomization of CDR1 and CDR2. The pie chart shows percentage of indicated sequence categories before and after anti-Myc selection. ( j ) Length distribution of DNA region encoding CDR1 of the VHH library before and after anti-Myc selection. Arrows indicate all correct-frame lengths showing increased percentage after anti-Myc selection.

Article Snippet: DNA encoding VHHs were obtained by gene synthesis (IDT) and cloned into pET vector in frame with a C-terminal 6XHis tag by Gibson assembly (NEBuilder® HiFi DNA Assembly Master Mix, New England Biolabs).

Techniques: Selection, Next-Generation Sequencing, Binding Assay, Sequencing, Synthesized, Ligation

Journal: bioRxiv

Article Title: A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies

doi: 10.1101/2020.10.29.361287

Figure Lengend Snippet: ( a ) Position-wise amino acid profile of natural VHHs (298 VHHs, PDB) and ( b ) synthetic VHHs. Amino acids were color coded according to labels to the right, B indicates an empty position. Bar height is the relative percentage of each amino acids. The two most common amino acids were shown as patterned bars while others were shown as solid bars. ( c ) Plot of diversity index (as 1 – Gini index) for each amino acid position of natural VHHs and ( d ) synthetic VHHs.

Article Snippet: DNA encoding VHHs were obtained by gene synthesis (IDT) and cloned into pET vector in frame with a C-terminal 6XHis tag by Gibson assembly (NEBuilder® HiFi DNA Assembly Master Mix, New England Biolabs).

Techniques:

Journal: bioRxiv

Article Title: A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies

doi: 10.1101/2020.10.29.361287

Figure Lengend Snippet: ( a ) Amino acid sequences encoded by frames that serve as templates for VHH library generation were aligned to the corresponding segments of the human IGHV3-23 (hIGHV3-23) or IGHJ4 (hIGHJ4). Positions in hIGHV3-23/hIGHJ4 that are identical to the corresponding position in at least one VHH frames are highlighted in orange. Positions in VHH frames that are identical to the corresponding position in hIGHV3-23/hIGHJ4 are highlighted in orange. hIGHV3-23 positions not identical to any VHH frames are numbered according to its position within the segment. Asterisks indicate VHH hallmark residues thought to be required for VHH’s independence of light chain. ( b ) Percent homology of VHH frames to the closest human gene. ( c ) List of VHH residues at positions numbered in (a) and representative human IGHV genes that encode the same VHH residue at the corresponding position. None: no human IGHV genes has the VHH residue at the corresponding position.

Article Snippet: DNA encoding VHHs were obtained by gene synthesis (IDT) and cloned into pET vector in frame with a C-terminal 6XHis tag by Gibson assembly (NEBuilder® HiFi DNA Assembly Master Mix, New England Biolabs).

Techniques: Residue

Journal: bioRxiv

Article Title: A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies

doi: 10.1101/2020.10.29.361287

Figure Lengend Snippet: ( a ) Immobilization strategy for the target proteins: 3xFlag-tagged EGFP or RBD. ( b ) Pair-wise CDR match score (based on BLOSUM62 matrix) were calculated for 2000 randomly selected sequences from input library and output libraries after 3 rounds of selection. High match score populations appeared in the output libraries. Combining CDR1 and 2 match scores further separated high and low score population and a match score of 35 (black dashed line) was chosen as cut-off for downstream clustering analysis. ( c ) Percentage of indicated sequence categories in the input library and output libraries (EGFP, RBD). ( d ) Number of unique and shared clusters identified in EGFP and RBD output libraries. ( e ) Number of sequences for each size of RBD unique clusters. ( f ) ELISA assay revealed 3 strong binders (“s”) to RBD, 7 weak binders (“w”) and ( g ) 4 non-binders (“n”) among the 14 VHHs chosen for characterization. ( h ) SARS-CoV-2 S pseudotyped lentivirus neutralization assay showed 6 VHHs inhibiting infection >30% at 1μM on HEK293T expressing ACE2 and TMPRSS2. Data shown are two technical replicates, bars indicate the average of data, circles indicate values of each replicate.

Article Snippet: DNA encoding VHHs were obtained by gene synthesis (IDT) and cloned into pET vector in frame with a C-terminal 6XHis tag by Gibson assembly (NEBuilder® HiFi DNA Assembly Master Mix, New England Biolabs).

Techniques: Selection, Sequencing, Enzyme-linked Immunosorbent Assay, Neutralization, Infection, Expressing

Journal: bioRxiv

Article Title: A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies

doi: 10.1101/2020.10.29.361287

Figure Lengend Snippet: ( a ) Amino acid profile of representative VHH sequence for each unique cluster identified from RBD and EGFP output libraries (“output binders”, 932 sequences). Plotted as described in . ( b ) Plot of diversity index (as 1 – Gini index) for each amino acid position of output binder VHHs.

Article Snippet: DNA encoding VHHs were obtained by gene synthesis (IDT) and cloned into pET vector in frame with a C-terminal 6XHis tag by Gibson assembly (NEBuilder® HiFi DNA Assembly Master Mix, New England Biolabs).

Techniques: Sequencing

Journal: bioRxiv

Article Title: A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies

doi: 10.1101/2020.10.29.361287

Figure Lengend Snippet: ( a ) r 2 values for the amino acid percentages in the indicated sequence group pairs at each CDR position. 298 natural VHHs (natural) and 298 randomly sampled sequences from input library (input) and output binders (output) were analyzed. Three random sampling trials were performed to generate three r 2 for each position. ( b ) Scatter plots of the percentage of each amino acid in the input library and the output binders and ( c ) that in the natural VHHs and the output binders at representative CDR positions. Circles are the mean and error bars are the standard deviation of data. ( d ) Root mean square error (RMSE, relative to Y = X line) values for the indicated sequence group pairs at each CDR position. Using the same randomly sampled sequences as (a). ( e ) Plot showing the similarity distances between the three sequence groups, with each connecting line length between two sequence groups indicating their RMSE. Vertical dashed lines indicate the middle point of the distance between output and natural sequence groups

Article Snippet: DNA encoding VHHs were obtained by gene synthesis (IDT) and cloned into pET vector in frame with a C-terminal 6XHis tag by Gibson assembly (NEBuilder® HiFi DNA Assembly Master Mix, New England Biolabs).

Techniques: Sequencing, Sampling, Standard Deviation

Journal: bioRxiv

Article Title: A cell-free antibody engineering platform rapidly generates SARS-CoV-2 neutralizing antibodies

doi: 10.1101/2020.10.29.361287

Figure Lengend Snippet: ( a ) Affinity maturation workflow. ( b ) Two representative sections of position-wise post-minus pre-affinity maturation amino acid percent point change profile. White values indicate the original amino acid, yellow values indicate the beneficial mutation. Empty positions indicate amino acids not detected in either the pre-or post-selection libraries. ( c ) ELISA assay of VHH variants. ( d ) SARS-CoV-2 S pseudotyped lentivirus neutralization assay of VHHs on HEK293T expressing ACE2 and TMPRSS2. For (c) and (d), data shown are two technical replicates, bars indicate the average of data, circles indicate values of each replicate. ( e ) Scatter plot of ELISA assay absorbance versus pseudotyped lentivirus neutralization as percent infection inhibited. VHH concentration for both assays were 50 nM. Values are average of two technical replicates. Numbers on linear fitting lines were r 2 value for data within each family. ( f ) Dose-response curve for neutralization of pseudotyped lentiviral infection by VHHs. Markers are average of three technical replicates, error bars are standard deviation. ( g ) IC50 calculated from data in (f), presented as mean ± standard deviation.

Article Snippet: DNA encoding VHHs were obtained by gene synthesis (IDT) and cloned into pET vector in frame with a C-terminal 6XHis tag by Gibson assembly (NEBuilder® HiFi DNA Assembly Master Mix, New England Biolabs).

Techniques: Mutagenesis, Selection, Enzyme-linked Immunosorbent Assay, Neutralization, Expressing, Infection, Concentration Assay, Standard Deviation

Journal: International journal of oncology

Article Title: Although c‑MYC contributes to tamoxifen resistance, it improves cisplatin sensitivity in ER‑positive breast cancer.

doi: 10.3892/ijo.2020.4987

Figure Lengend Snippet: Figure 2. Characteristics of TAM‑resistant cells. (A) Distribution of cells in different phases of the cell cycle in TAM‑sensitive and TAM‑resistant cells detected by flow cytometry. (B) Bar charts representing the percentage of cells in the G0/G1, G2/M or S phase. (C) Western blot analysis and (D) densitometric analysis of cyclin D1 and p21 expression in TAM‑sensitive and TAM‑resistant cells. (E) Representative images of successfully invaded MCF‑7 and MCF‑7R cells and (F) quantitative analysis of invasion measured using a Transwell invasion assay at different times. Magnification, x200. (G) Western blot analysis and (H) densitometric analysis of E‑cadherin and vimentin expression in TAM‑sensitive and TAM‑resistant cells. Data are presented as the means ± standard deviation of mean of three repeats. *P<0.05, **P<0.01, ***P<0.001 vs. respective parental cells. TAM, tamoxifen.

Article Snippet: Non‐specific binding sites were blocked by incubating the membranes with 5% non-fat milk, after which the membranes were incubated overnight at 4 ̊C with the primary antibodies: ERα (1:1,000); HER2 (1:1,000); AKT (1:1,000); p‐AKT (1:1,000); c‐MYC (1:1,000); cyclin D1 (1:1,000); vimentin (1:1,000); E‐cadherin (1:1,000); p21 (1:500); β‐catenin (1:500); GAPDH (1:1,000) Membranes were subsequently incubated with a horseradish peroxidase-conjugated anti-rabbit/mouse immunoglobulin G secondary antibody (1:1,000; cat. no. BA1075 and BA1051; Wuhan Boster Biological Technology, Ltd.).

Techniques: Flow Cytometry, Western Blot, Expressing, Transwell Invasion Assay, Standard Deviation

Journal: bioRxiv

Article Title: Dual-acting gene therapy targeting HIF1A and HIF2A by RNA interference mitigates retinal degeneration in two mouse models of AMD

doi: 10.1101/2024.11.29.626080

Figure Lengend Snippet: (A) Graphical representation of tissue changes leading to hypoxia and degenerative processes during aging and AMD. (B) Gene expression analysis of 661W cells stably expressing shCtrl, shHif1 or shHif2 after normoxic or hypoxic (24 h, 0.2% O 2 ) exposure. Values were normalized to beta Actin ( Actb ) and expressed relatively to normoxic 661W-shCtrl (set to 1). Shown are individual values (n=3) and means ± SD. Significance was tested using a one-way ANOVA with Tukey’s multiple comparison test. *: statistically significant; p-values of all comparisons are given in Table S1. (C) Western blot analysis for HIF1A, HIF2A and ACTB in 661W cells stably expressing shCtrl, shHif1 or shHif2 after normoxic and hypoxic exposure. (D) Schematic representation of the DNA constructs packaged into AAV vectors. AAV-shHif: the construct consists of the GRK1 promotor driving photoreceptor-specific expression of shHif1a embedded in the miR-E scaffold in the 3’UTR of GFP, followed by the VMD2 promotor controlling RPE-specific expression of shHif2a embedded in the miR-E scaffold in the 3’UTR of mCherry. AAV-shCtrl: a scrambled non-targeting control shRNA sequence replaced shHif1a and shHif2a. AAV-shHif1: the GRK1 promotor drives photoreceptor-specific expression of shHif1a embedded in the miR-E scaffold in the 3’UTR of GFP. AAV-shHif2: the VMD2 promotor controls RPE-specific expression of shHif2a embedded in the miR-E scaffold in the 3’UTR of mCherry. Sequences of shRNAs are provided in Fig. S1 and supplemental data SD1. CC: choriocapillaris, BM: Bruch’s membrane, RPE: retinal pigment epithelium, PS: photoreceptor segments, ONL: outer nuclear layer.

Article Snippet: shRNAmiR DNA fragments containing shHif1a , shHif2a or shCtrl sequences were designed using the miR-E backbone following the recommendation by Fellmann ( ) (Fig. S1A-C) and produced by Bio-Synthesis (Bio-Synthesis Inc. TX, USA).

Techniques: Expressing, Stable Transfection, Comparison, Western Blot, Construct, Control, shRNA, Sequencing, Membrane

Journal: The Journal of Experimental Biology

Article Title: Deletion of a specific exon in the voltage-gated calcium channel gene cacophony disrupts locomotion in Drosophila larvae

doi: 10.1242/jeb.191106

Figure Lengend Snippet: Generation of cacophony exon 7 deletion lines. (A) Predicted alternatively spliced cacophony transcripts from FlyBase, showing the position of exon 7 and that a single predicted isoform, cac-RM, lacks exon 7. (B) Schematic diagram showing the process of using CRISPR/Cas9 to delete exon 7 of cacophony. Cas9 was targeted to cut the genomic DNA on either side of exon 7, resulting in two double-stranded breaks, which were repaired via homologous recombination with a donor template containing DsRed, which was then incorporated into the genome. Splicing between exon 6 and 8 excludes the DsRed cassette, yielding cacexon7Δ mRNA. (C) Schematic diagram of the predicted cacophony protein, showing the location of exon 7 near the C-terminus. (D) Location of the primers in exon 6 and 8 used for RT-PCR to confirm the deletion of exon 7. (E) Representative DNA gel of the RT-PCR products from adult heads, showing a major 300 bp band that includes exon 7 and a minor 100 bp band lacking exon 7 from control animals. By contrast, RT-PCR from the cacexon7Δ line only yielded the 100 bp band. (F) Sequencing chromatogram resulting from the sequencing of the 100 bp band from the cacexon7Δ line showed that exon 6 splices directly to exon 8, excluding exon 7.

Article Snippet: To generate cacophony sequence without exon 7, DNA was synthesized (Biomatik, Wilmington, DE, USA) at a length of 1515 bp using sequence from FlyBase as a reference with exon 7 removed.

Techniques: CRISPR, Homologous Recombination, Reverse Transcription Polymerase Chain Reaction, Control, Sequencing

Journal: Materials Today Bio

Article Title: Design considerations for advancing data storage with synthetic DNA for long-term archiving

doi: 10.1016/j.mtbio.2022.100306

Figure Lengend Snippet: Summary of notable related work for synthetic DNA-based data storage. The table is presented in descending order based on the size of stored data. The encoding alphabet includes binary or alphanumeric encoding. The storage refers to the mechanism used for storing the DNA, either in an organism, buffer solution, or silica beads. Sequencing technologies include Illumina's technology based on the sequencing by synthesis (SBS) principle, and ONT's nanopore technology. The Error Correction refers to related work with codes that are able to detect and correct errors. The information density refers to the average number of binary information (bits) encoded in a nucleotide (nt). This binary information totals the data payload and the additional sequences for index, error correction, and primers. The synthetic DNA is stored in ∗ silica beads and ∗∗ an organism ( in vivo ).

Article Snippet: Although initial efforts result in high error rates, it is today becoming a commercially attractive solution with error rates of 0.7% (DNA Script Syntax Enzymatic DNA Synthesis technology).

Techniques: Sequencing, In Vivo

Journal: Materials Today Bio

Article Title: Design considerations for advancing data storage with synthetic DNA for long-term archiving

doi: 10.1016/j.mtbio.2022.100306

Figure Lengend Snippet: Overview Process of a synthetic DNA-based storage system. Digital files are converted into binary data. The binary data is encoded into DNA sequences, additional DNA sequences including index, error correction, and primer for DNA amplification are also appended to the oligos. Oligos are synthesized chemically or enzymatically. Synthetic DNA from chemical or enzymatic synthesis processes is usually single-stranded. It is often stored in the single-stranded step, or the complementary strand is enzymatically synthesized, generating double-stranded DNA before storage. The selective extraction or amplification of the suitable oligos from the pool is enabled by PCR. The obtained oligos are sequences using a DNA sequencer. Then the obtained oligo sequences are decoded to obtain the original binary data.

Article Snippet: Although initial efforts result in high error rates, it is today becoming a commercially attractive solution with error rates of 0.7% (DNA Script Syntax Enzymatic DNA Synthesis technology).

Techniques: Amplification, Synthesized