Journal: BMC Biotechnology

Article Title: Flip-Flop HSV-BAC: bacterial artificial chromosome based system for rapid generation of recombinant herpes simplex virus vectors using two independent site-specific recombinases

doi: 10.1186/1472-6750-6-40

Figure Lengend Snippet: Genomic structure of M24-BAC virus and pM24-BAC plasmid DNA . HindIII restriction analysis of M24-BAC virus DNA (left panel) and pM24-BAC plasmid DNA (right panel) is shown. Closed arrowhead: 9.4 kb HindIII fragment of d120 (containing ICP6 region), Open arrowheads: 15 kb and 2.2 kb HindIII fragments generated by insertion of the BAC sequences. A band present in M24-BAC digest just above the closed triangle is the submolar terminal restriction fragment (9.8 kb) derived from the short terminal repeat. This band is overlapped by the 9.4 kb restriction fragment of d120 and absent from pM24-BAC. The restriction pattern of pM24-BAC indicates that this clone contains both the U L and U S sequences of HSV genome in the forward orientation. Other bands present in the M24-BAC digest but not in pM24-BAC are submolar terminal fragments or L-S junction fragments derived from other isomeric forms of virus genome.

Article Snippet: To generate a stuffer sequence, the 4.0-kb AgeI-digest fragment of bacteriophage lambda DNA (nucleotide position 6562 – 10550) was obtained by digesting a HindIII digest of lambda DNA (New England Biolab, Beverly, MA).

Techniques: Plasmid Preparation, Generated, Derivative Assay

Journal: BMC Biotechnology

Article Title: Flip-Flop HSV-BAC: bacterial artificial chromosome based system for rapid generation of recombinant herpes simplex virus vectors using two independent site-specific recombinases

doi: 10.1186/1472-6750-6-40

Figure Lengend Snippet: Analysis of genomic DNA from recombinant viruses generated using the Flip-Flop HSV-BAC system . DNA from two independent isolates was purified, digested with HindIII and electrophoresed on an agarose gel. The DNAs of parental viruses bM24-BAC and d120 illustrate the common fragments, while the asterisks denote fragments containing inserts derived from the shuttle vector. [see ].

Article Snippet: To generate a stuffer sequence, the 4.0-kb AgeI-digest fragment of bacteriophage lambda DNA (nucleotide position 6562 – 10550) was obtained by digesting a HindIII digest of lambda DNA (New England Biolab, Beverly, MA).

Techniques: Recombinant, Generated, Purification, Agarose Gel Electrophoresis, Derivative Assay, Plasmid Preparation

Journal: Tissue antigens

Article Title: Direct binding to antigen-coated beads refines the specificity and cross-reactivity of four monoclonal antibodies that recognize polymorphic epitopes of HLA class I molecules

doi: 10.1111/tan.12095

Figure Lengend Snippet: (A) HLA class I allotypes represented by the One Lambda Labscreen and Gen-Probe LifeCodes beadsets. (B) Binding of the monomorphic HLA class I antibody W6/32 to beads from One Lambda LabScreen (grey bars) and Gen-Probe LifeCodes (orange bars). The allotypes shown are those common to both beadsets.

Article Snippet: The specific reference as listed in the current publication is noted to the right. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 2 caption a7 (A) HLA class I allotypes represented by the One Lambda Labscreen and Gen-Probe LifeCodes beadsets. (B) Binding of the monomorphic HLA class I antibody W6/32 to beads from One Lambda LabScreen (grey bars) and Gen-Probe LifeCodes (orange bars).

Techniques: Binding Assay

Journal: Tissue antigens

Article Title: Direct binding to antigen-coated beads refines the specificity and cross-reactivity of four monoclonal antibodies that recognize polymorphic epitopes of HLA class I molecules

doi: 10.1111/tan.12095

Figure Lengend Snippet: (A) Binding of MA2.1 (1μg/ml) to beads coated with HLA class I allotypes from the One Lambda LabScreen (left panel) and Gen-Probe LifeCodes (right panel) beadsets. (B) Alignment of HLA class I allotypes showing selected residues in the α1 and α2 domains. Residues from allotypes that form the epitope recognized by MA2.1 are shaded in grey. (C) Space-filling model of the binding surface of HLA-A*02 (grey) with associated peptide (cyan). Residues highlighted in yellow fall within the footprint recognized by MA2.1. Residues 62–65 are critical for formation of the epitope recognized by MA2.1 and are highlighted in red.

Article Snippet: The specific reference as listed in the current publication is noted to the right. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 2 caption a7 (A) HLA class I allotypes represented by the One Lambda Labscreen and Gen-Probe LifeCodes beadsets. (B) Binding of the monomorphic HLA class I antibody W6/32 to beads from One Lambda LabScreen (grey bars) and Gen-Probe LifeCodes (orange bars).

Techniques: Binding Assay

Journal: Tissue antigens

Article Title: Direct binding to antigen-coated beads refines the specificity and cross-reactivity of four monoclonal antibodies that recognize polymorphic epitopes of HLA class I molecules

doi: 10.1111/tan.12095

Figure Lengend Snippet: (A) Binding of PA2.1 (1μg/ml) and BB7.2 (1μg/ml) to beads coated with HLA class I allotypes from the One Lambda LabScreen (left panel) and Gen-Probe LifeCodes (right panel) beadsets. (B) Binding of PA2.1 (50μg/ml) and BB7.2 (50μg/ml) to beads coated with HLA class I allotypes from the One Lambda LabScreen (left panel) and Gen-Probe LifeCodes (right panel) beadsets. (C) Alignment of HLA class I allotypes showing selected residues in the α2 domain. Residues from allotypes that form the epitope recognized by PA2.1 and BB7.2 are shaded in grey. (D) Space-filling model of HLA-A*02 (grey) with associated peptide (cyan). Residues highlighted in yellow fall within the footprint recognized by PA2.1 and BB7.2. Tryptophan at position 107 is considered critical for formation of the epitope recognized by PA2.1 and BB7.2 and is highlighted in red.

Article Snippet: The specific reference as listed in the current publication is noted to the right. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 2 caption a7 (A) HLA class I allotypes represented by the One Lambda Labscreen and Gen-Probe LifeCodes beadsets. (B) Binding of the monomorphic HLA class I antibody W6/32 to beads from One Lambda LabScreen (grey bars) and Gen-Probe LifeCodes (orange bars).

Techniques: Binding Assay

Journal: Tissue antigens

Article Title: Direct binding to antigen-coated beads refines the specificity and cross-reactivity of four monoclonal antibodies that recognize polymorphic epitopes of HLA class I molecules

doi: 10.1111/tan.12095

Figure Lengend Snippet: (A) Binding of BB7.1 (1μg/ml) to beads coated with HLA class I allotypes from the One Lambda LabScreen (left panel) and Gen-Probe LifeCodes (right panel) beadsets. (B) Alignment of HLA class I allotypes showing selected residues in the α1 and α2 domains. Residues from allotypes that form the epitope recognized by BB7.1 are shaded in grey. (C) Space-filling model of the binding surface of HLA-B*07 (grey) with associated peptide (cyan). Residues highlighted in yellow fall within the footprint recognized by BB7.1. Residues 63–71 in the a1 domain and position 131 in the α2 domain are critical for formation of the epitope recognized by BB7.1 and are highlighted in red.

Article Snippet: The specific reference as listed in the current publication is noted to the right. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 2 caption a7 (A) HLA class I allotypes represented by the One Lambda Labscreen and Gen-Probe LifeCodes beadsets. (B) Binding of the monomorphic HLA class I antibody W6/32 to beads from One Lambda LabScreen (grey bars) and Gen-Probe LifeCodes (orange bars).

Techniques: Binding Assay

Journal:

Article Title: CD8 + minor histocompatibility antigen-specific cytotoxic T lymphocyte clones eliminate human acute myeloid leukemia stem cells

doi:

Figure Lengend Snippet: CD8+ minor H antigen-specific CTL clones inhibit AML engraftment in NOD/SCID mice by direct recognition of SL-ICs. Cohorts of mice were transplanted with a mixture of AML cells from patient 10138 (HLA A1+, A3+, B8+, B14+) and patient 11720 (HLA A3+, B7+, B8+) that had been cultured in either medium alone (○; n = 5), with clone MRR-24 (□; n = 3), or with clone ATT-7 (▵; n = 5). Bone marrow was obtained 10 weeks later and examined by flow cytometry using an HLA A1-specific mAb to detect 10138 AML cells (Upper) and an HLA B7-specific mAb to detect 11720 AML cells (Lower). The mean levels of engraftment in each treatment group are indicated by the horizontal bars. P values refer to the comparison between the engraftment in the indicated treatment group and that in control mice, as computed by the Mann–Whitney u test.

Article Snippet: Nucleated cells were counted and prepared for flow cytometry by incubation at 4°C for 20 min in PBS and 5% FCS with one or more of the following antibodies: peridinin chlorophyll protein-conjugated anti-human CD45 and phycoerythrin (PE)-conjugated anti-human CD33 (both from Becton Dickinson Immunocytometry Systems), FITC-conjugated anti-human CD8 (Coulter), biotinylated anti-HLA A1, biotinylated anti-HLA A3 (both from One Lambda, Canoga Park, CA), or PE-conjugated anti-HLA B7 (Chemicon).

Techniques: Clone Assay, Cell Culture, Flow Cytometry, MANN-WHITNEY

Journal: eLife

Article Title: A Brownian ratchet model for DNA loop extrusion by the cohesin complex

doi: 10.7554/eLife.67530

Figure Lengend Snippet:

Article Snippet: Chemical compound, drug , SNAP-Surface Alexa Fluor 647 , New England BioLabs , Cat# S9136S , .

Techniques: Purification, Construct, Recombinant, Lambda DNA Preparation, Staining, Software

Journal: eLife

Article Title: Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers

doi: 10.7554/eLife.87868

Figure Lengend Snippet: In SCA-seq, we used methyltransferases (EcoGII or M.CviPI) to label the accessible chromatin and the restriction enzyme to digest the genome and prepare for the ligation step. Methyltransferase EcoGII transferred the methyl group to the 6′-carbon of adenosine (m6A modification). Due to the high density of adenosines in the genome (~25%), the abundant artificial m6A modification may impair restriction enzyme activity. We used EcoGII to treat the HEK293T genomic DNA (m6A + ), whereas control DNA was left untreated (m6a − ). We tested HindIII, DpnI ( a ), PstI and NdeI ( b ) on the methylated and unmethylated genomic DNAs, and all these restriction enzymes were inhibited by the abundant m6A modifications. DpnI is an m6A-dependent restriction enzyme that digests only genomic loci with the m6A modification. NA indicates the genomic DNA control. In a similar way, we tested the activities of HindIII ( c ) for lambda DNA; DpnII, and NIaIII ( d ) for HEK293T genomic DNA on the GpC methylated DNA preparations that were treated by methyltransferase M.CviPI. DpnII and NIaIII were not significantly inhibited by GpC methylation. ( e ) The HEK293T genomic DNA was digested by DpnII (Digestion) and then ligated by T4 DNA ligase (Ligation). Figure 1—figure supplement 1—source data 1. Original gel images in .

Article Snippet: DpnII digests were heat inactivated at 65°C for 20 min with 700 rpm rotation, average digests to 70 μl per tube, add 14 μl T4 DNA Ligase buffer (NEB M0202L), 14 μl T4 DNA Ligase (NEB M0202L), 1 mM ATP and nuclease-free water to achieve a final volume of 140 μl.

Techniques: Ligation, Modification, Activity Assay, Control, Methylation, Lambda DNA Preparation