Journal: Nature structural & molecular biology

Article Title: Polλ promotes microhomology-mediated end-joining

doi: 10.1038/s41594-022-00895-4

Figure Lengend Snippet: a, Top, schematic of MMEJ reporter containing 5′-streptavidin-biotin linkages. Middle, internal termini of left and right MMEJ reporter DNA constructs. Bottom, schematic of MMEJ reporter assay. b−f, Bar plots showing relative GFP frequencies following cotransfection of left and right MMEJ reporter DNA constructs, with immunoblots showing abundance of protein shown in c and e−g. b, GFP+ frequencies are shown relative to nontargeting siRNA (siControl = 1) in wildtype HEK293T cells; n = 3; P = 0.01. c, GFP+ frequencies relative to POLλ+/+ 293T cells (POLλ+/+ = 1). n = 3, P = 0.01. d, Same as in b in POLλ−/− 293T cells. n = 3, P = 0.03. e, GFP+ frequencies relative to nontargeting siRNA (siControl = 1). n = 3, P = 0.04. f, GFP+ frequencies relative to nontargeting siRNA (siControl = 1) in XRCC4−/− 293T cells. Data represent means. n = 2, P = 0.04. g, MMEJ GFP reporter assay. Schematic of GFP reporter assay (top). Bar plot of percentage of GFP cells following transient expression of I-SceI and cotransfection of either Polλ siRNA or Control siRNA. n = 2, P = 0.04. h, Bar plots showing percentage of colonies relative to control after siRNA transfection in DLD1 BRCA2−/− or DLD1 Parental cells (top), in MDA-MB-436 BRCA1 mut or MDA-MB-231 cells (bottom). Percentage of colonies are normalized to nontargeting siRNA (siControl = 100). n = 1. Colony images are on the right. In b and c−g, GFP+ frequencies are normalized to transfection efficiency. Data represent means. ‘n’ denotes number of independent experiments with triplicates for each condition, ± s.e.m. *P < 0.05, **P < 0.01, ***P < 0.001. Statistical significance was measured from two-sample t-test and P values are indicated.

Article Snippet: For overexpression of Polλ WT, 1 × 10 4 HEK293T cells were plated and, after 24 h, 200 ng either Polλ WT-Myc-DDK-tagged (Origene catalog no. RC230157) or Empty vector control plasmid was transfected using lipofectamine 2000.

Techniques: Construct, Reporter Assay, Cotransfection, Western Blot, Expressing, Control, Transfection

Journal: Nature structural & molecular biology

Article Title: Polλ promotes microhomology-mediated end-joining

doi: 10.1038/s41594-022-00895-4

Figure Lengend Snippet: a. RT qPCR analysis of Polθ expression. mRNA levels were corrected with internal control for Actin in siRNA-treated cells used in Fig. 3b, ​,dd as well as normalized to non-targeting siRNA (siControl = 1). Data represent mean. n = 1 experiment with triplicate for each condition ±SEM. b. gRNA sequence used to generate POLL−/− HEK293T cells via CRISPR-Cas9 engineering. Schematic representation of three isoforms of human Polλ with protein domains as well as location of gRNA sequence (red) is indicated. The genome sequence flanking the gRNA sequence (red) is shown in gray. POLL −/− clone # T2 was generated by CRISPR-Cas9 engineering and carries 7 bp deletion in both alleles. Sequence of the region harboring the 7 bp deletion is indicated in blue. c. Bar plot showing relative GFP following overexpression of indicated plasmids and co- transfection of left and right MMEJ reporter DNA constructs in HEK293T cells. GFP+ frequencies are normalized to transfection efficiency. Data represent mean. n = 1 experiment with triplicates for each condition, +/− s.e.m. Bottom panel: Immunoblot showing abundance of protein. d. gRNA sequence used to generate LIG4 −/− HEK293T cells (top) and XRCC4 −/− HEK293T cells (bottom) via CRISPR-Cas9 engineering. Schematic representation of human Lig4 (top) and Xrcc4 (bottom) with protein domains as well as location of gRNA sequence is indicated (red). e. Same as in Fig. 3f in XRCC4−/− HCT116 cells. Data represent mean. n = 1 experiment with triplicate for each condition, +/− s.e.m. Bottom panel: Immunoblot showing abundance of protein. f. Western blot of Polλ (top) and Gapdh (bottom) following transfection of either Polλ siRNA or siControl in DLD1 BRCA2+/+ (left) and DLD1 BRCA2 −/− cells (right).

Article Snippet: For overexpression of Polλ WT, 1 × 10 4 HEK293T cells were plated and, after 24 h, 200 ng either Polλ WT-Myc-DDK-tagged (Origene catalog no. RC230157) or Empty vector control plasmid was transfected using lipofectamine 2000.

Techniques: Quantitative RT-PCR, Expressing, Control, Sequencing, CRISPR, Generated, Over Expression, Cotransfection, Construct, Transfection, Western Blot

Journal:

Article Title: Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

doi:

Figure Lengend Snippet: Restriction patterns from AseI digests of M. avium isolates resolved by PFGE. Lanes: 1 and 6, bacteriophage lambda DNA concatemers (sizes [in kilobases] are indicated on the left); 2, isolate 100A8; 3 and 4, pattern P7 (isolates 100A28 and 100A32, respectively); 5, isolate 100A25; 7 to 11, five sequential isolates from one patient, respectively (pattern P1); 12 to 15, four isolates from two patients, respectively (pattern P2).

Article Snippet: Lanes 6 and 18, bacteriophage lambda DNA- Bst EII digest; lane 12, pBR322 DNA- Msp I digest (New England Biolabs); lanes 1 to 5, five sequential isolates from one patient, respectively (PCR profile A, PFGE pattern P1); lanes 7, 8, and 9, three sequential isolates from one patient, respectively (PCR profile A, PFGE pattern P2) (no amplification product was detected in lane 8 in that experiment); lane 10, isolate 100A31 from another patient (PCR profile A, PFGE pattern P2); lanes 11 and 13, two sequential isolates from one patient, respectively; lane 14, isolate 100A7 from a different patient (PCR profile E, PFGE pattern P6 or a unique pattern); lanes 15, 16, and 17, isolates 100A13, 100A26, and 100A30, respectively.

Techniques: Lambda DNA Preparation

Journal:

Article Title: Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

doi:

Figure Lengend Snippet: PCR typing of clinical M. avium isolates. Lanes: 1 to 5, 7 to 11, and 13 to 17, patterns of isolates obtained from 15 unrelated patients; lanes 6 and 18, bacteriophage lambda DNA-BstEII digest molecular weight marker; and lane 12, pBR322 DNA-MspI digest (New England Biolabs).

Article Snippet: Lanes 6 and 18, bacteriophage lambda DNA- Bst EII digest; lane 12, pBR322 DNA- Msp I digest (New England Biolabs); lanes 1 to 5, five sequential isolates from one patient, respectively (PCR profile A, PFGE pattern P1); lanes 7, 8, and 9, three sequential isolates from one patient, respectively (PCR profile A, PFGE pattern P2) (no amplification product was detected in lane 8 in that experiment); lane 10, isolate 100A31 from another patient (PCR profile A, PFGE pattern P2); lanes 11 and 13, two sequential isolates from one patient, respectively; lane 14, isolate 100A7 from a different patient (PCR profile E, PFGE pattern P6 or a unique pattern); lanes 15, 16, and 17, isolates 100A13, 100A26, and 100A30, respectively.

Techniques: Lambda DNA Preparation, Molecular Weight, Marker

Journal:

Article Title: Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

doi:

Figure Lengend Snippet: Electrophoretic PCR patterns for M. avium isolates. Lanes 6 and 18, bacteriophage lambda DNA-BstEII digest; lane 12, pBR322 DNA-MspI digest (New England Biolabs); lanes 1 to 5, five sequential isolates from one patient, respectively (PCR profile A, PFGE pattern P1); lanes 7, 8, and 9, three sequential isolates from one patient, respectively (PCR profile A, PFGE pattern P2) (no amplification product was detected in lane 8 in that experiment); lane 10, isolate 100A31 from another patient (PCR profile A, PFGE pattern P2); lanes 11 and 13, two sequential isolates from one patient, respectively; lane 14, isolate 100A7 from a different patient (PCR profile E, PFGE pattern P6 or a unique pattern); lanes 15, 16, and 17, isolates 100A13, 100A26, and 100A30, respectively.

Article Snippet: Lanes 6 and 18, bacteriophage lambda DNA- Bst EII digest; lane 12, pBR322 DNA- Msp I digest (New England Biolabs); lanes 1 to 5, five sequential isolates from one patient, respectively (PCR profile A, PFGE pattern P1); lanes 7, 8, and 9, three sequential isolates from one patient, respectively (PCR profile A, PFGE pattern P2) (no amplification product was detected in lane 8 in that experiment); lane 10, isolate 100A31 from another patient (PCR profile A, PFGE pattern P2); lanes 11 and 13, two sequential isolates from one patient, respectively; lane 14, isolate 100A7 from a different patient (PCR profile E, PFGE pattern P6 or a unique pattern); lanes 15, 16, and 17, isolates 100A13, 100A26, and 100A30, respectively.

Techniques: Lambda DNA Preparation, Amplification