Journal: Scientific Reports

Article Title: Bacterial DNA promotes Tau aggregation

doi: 10.1038/s41598-020-59364-x

Figure Lengend Snippet: Effect of DNA extracted from diverse sources on tau aggregation. To study the effect of DNA on tau aggregation, monomeric tau (22 µM) under the conditions described in Fig. , was incubated with preparations containing 100 ng of DNA extracted from different bacterial species including Pseudomonas aeruginosa (PA), Tetzosporium hominis (TH), Tetzerella alzheimeri (TA), Escherichia coli ATCC 25922 (EC25), Escherichia coli ATCC 472217 (EC47), Porphyromonas gingivalis (PG), Borrelia burgdorferi (BB). We also incubated tau with same amount of DNA extracted from Candida albicans (CA) and human samples. In all experiments the signal at time zero, corresponding to buffer + DNA + heparin + ThT + monomeric tau was substracted from the values. ( A ) tau aggregation was monitored over time by ThT fluorescence. Data corresponds to the average ± standard error of experiments done in triplicate (except for control without seeds that was performed in quintuplicate). ( B ) The lag phase, estimated as the time in which ThT fluorescence was higher than the threshold of 40 arbitrary units, was calculated for each experiment. The points represent the values obtained in each of the replicates. Data was analyzed by one-way ANOVA, followed by Tukey multiple comparison post-test. *P < 0.01; **P < 0.001.

Article Snippet: Lane 1, XL 1 kb Plus DNA Marker; Lane 2 DNA P. aeruginosa ; Lane 3 DNA T. hominis ; Lane 4 DNA T. alzheimeri ; Lane 5 DNA C. albicans ; Lane 6 DNA E. coli ATCC 472217; Lane 7 DNA E. coli ATCC 25922; Lane 8 Human DNA; Lane 9 DNA B. burgdorferi ; Lane 10 DNA P. gingivalis .

Techniques: Incubation, Fluorescence, Control, Comparison

Journal: Scientific Reports

Article Title: Bacterial DNA promotes Tau aggregation

doi: 10.1038/s41598-020-59364-x

Figure Lengend Snippet: Influence of different concentration of E. coli ATCC 25922 DNA on tau aggregation. To study whether the promoting effect of E. coli DNA can be observed at different concentrations of DNA, we incubated monomeric tau under the conditions described above (Figs. and ) with 1000, 100 and 10 ng of DNA extracted from E. coli ATCC 25922. ( A ) tau aggregation was monitored overtime by ThT fluorescence. Data corresponds to the average ± standard error of experiments done in triplicate. ( B ) The lag phase, estimated as the time in which ThT fluorescence was higher than the threshold of 40 arbitrary units, was calculated for each experiment. The points represent the values obtained in each of the replicates. Data was analyzed by one-way ANOVA, followed by Tukey multiple comparison post-test. *P < 0.01; **P < 0.001.

Article Snippet: Lane 1, XL 1 kb Plus DNA Marker; Lane 2 DNA P. aeruginosa ; Lane 3 DNA T. hominis ; Lane 4 DNA T. alzheimeri ; Lane 5 DNA C. albicans ; Lane 6 DNA E. coli ATCC 472217; Lane 7 DNA E. coli ATCC 25922; Lane 8 Human DNA; Lane 9 DNA B. burgdorferi ; Lane 10 DNA P. gingivalis .

Techniques: Concentration Assay, Incubation, Fluorescence, Comparison

Journal: Scientific Reports

Article Title: Bacterial DNA promotes Tau aggregation

doi: 10.1038/s41598-020-59364-x

Figure Lengend Snippet: Agarose gel electrophoresis images of DNA. Lane 1, XL 1 kb Plus DNA Marker; Lane 2 DNA P. aeruginosa ; Lane 3 DNA T. hominis ; Lane 4 DNA T. alzheimeri ; Lane 5 DNA C. albicans ; Lane 6 DNA E. coli ATCC 472217; Lane 7 DNA E. coli ATCC 25922; Lane 8 Human DNA; Lane 9 DNA B. burgdorferi ; Lane 10 DNA P. gingivalis .

Article Snippet: Lane 1, XL 1 kb Plus DNA Marker; Lane 2 DNA P. aeruginosa ; Lane 3 DNA T. hominis ; Lane 4 DNA T. alzheimeri ; Lane 5 DNA C. albicans ; Lane 6 DNA E. coli ATCC 472217; Lane 7 DNA E. coli ATCC 25922; Lane 8 Human DNA; Lane 9 DNA B. burgdorferi ; Lane 10 DNA P. gingivalis .

Techniques: Agarose Gel Electrophoresis, Marker

Journal:

Article Title: Direct Cloning from Enrichment Cultures, a Reliable Strategy for Isolation of Complete Operons and Genes from Microbial Consortia

doi: 10.1128/AEM.67.1.89-99.2001

Figure Lengend Snippet: (A) E. coli biotin biosynthesis pathway; (B) genetic organization of the E. coli biotin biosynthesis operon.

Article Snippet: To assess the biotin biosynthesis capabilities of the three environmentally derived cosmid libraries, cosmid DNA from the recombinant E. coli clones was extracted and used to transduce the E. coli biotin-auxotrophic strain ATCC 33767 (Fig. ).

Techniques:

Journal:

Article Title: Direct Cloning from Enrichment Cultures, a Reliable Strategy for Isolation of Complete Operons and Genes from Microbial Consortia

doi: 10.1128/AEM.67.1.89-99.2001

Figure Lengend Snippet: Strains and constructs used

Article Snippet: To assess the biotin biosynthesis capabilities of the three environmentally derived cosmid libraries, cosmid DNA from the recombinant E. coli clones was extracted and used to transduce the E. coli biotin-auxotrophic strain ATCC 33767 (Fig. ).

Techniques: Construct, Cloning, Plasmid Preparation

Journal:

Article Title: Direct Cloning from Enrichment Cultures, a Reliable Strategy for Isolation of Complete Operons and Genes from Microbial Consortia

doi: 10.1128/AEM.67.1.89-99.2001

Figure Lengend Snippet: Identified genes, GenBank accession numbers, and observed similarities

Article Snippet: To assess the biotin biosynthesis capabilities of the three environmentally derived cosmid libraries, cosmid DNA from the recombinant E. coli clones was extracted and used to transduce the E. coli biotin-auxotrophic strain ATCC 33767 (Fig. ).

Techniques:

Journal:

Article Title: Direct Cloning from Enrichment Cultures, a Reliable Strategy for Isolation of Complete Operons and Genes from Microbial Consortia

doi: 10.1128/AEM.67.1.89-99.2001

Figure Lengend Snippet: Dot blot hybridization of DNA extracted from environmental samples and enrichment cultures. (A) Nylon membrane with DNA directly isolated from the HE sample and DNA from a corresponding HE enrichment culture, which was grown in the presence of avidin; 780 ng of DNA was spotted per dot, and hybridizations were done with the E. coli biotin biosynthesis genes as a DNA probe. (B) Nylon membrane loaded with DNA which was isolated from two different enrichment cultures inoculated with soil from an agricultural site (AS); one of the cultures was grown in the presence of added avidin, while no avidin was added to the other culture. DNA was extracted after 48 h of growth, and 930 ng of DNA was spotted per dot onto the nylon membranes. Hybridizations were performed overnight under high-stringency conditions at 68°C employing the bio genes on pCosAS1 as a DNA probe.

Article Snippet: To assess the biotin biosynthesis capabilities of the three environmentally derived cosmid libraries, cosmid DNA from the recombinant E. coli clones was extracted and used to transduce the E. coli biotin-auxotrophic strain ATCC 33767 (Fig. ).

Techniques: Dot Blot, Hybridization, Environmental Sampling, Membrane, Isolation, Avidin-Biotin Assay

Journal:

Article Title: Direct Cloning from Enrichment Cultures, a Reliable Strategy for Isolation of Complete Operons and Genes from Microbial Consortia

doi: 10.1128/AEM.67.1.89-99.2001

Figure Lengend Snippet: Growth characteristics and biotin production of E. coli strain ATCC 33767 carrying cosmids containing bio operons derived from three different enrichment cultures a

Article Snippet: To assess the biotin biosynthesis capabilities of the three environmentally derived cosmid libraries, cosmid DNA from the recombinant E. coli clones was extracted and used to transduce the E. coli biotin-auxotrophic strain ATCC 33767 (Fig. ).

Techniques: Derivative Assay, Control

Journal:

Article Title: Direct Cloning from Enrichment Cultures, a Reliable Strategy for Isolation of Complete Operons and Genes from Microbial Consortia

doi: 10.1128/AEM.67.1.89-99.2001

Figure Lengend Snippet: Restriction maps of the central parts of the different biotin cosmids isolated in this work; arrows indicate locations and directions of transcription of the identified ORFs on the different cosmids. (A) pCosHE1 restriction map of the bio cosmid derived from horse excrement showing highest homologies to genes of E. herbicola; (B) pCosHE2 bio cosmid isolated from an enrichment culture derived from the same source as in panel A but highly similar to E. coli; (C) pCosAS1 restriction map of a bio cosmid isolated from an agricultural soil; (D) pCosFS1 restriction map of a bio cosmid isolated from a forest soil enrichment culture. The bio genes identified in panels C and D show highest similarities to E. herbicola and S. marcescens, respectively. Observed similarities for selected ORFS are listed in Table ​Table4,4, together with the assigned GenBank accession numbers. For genes of pCosHE1 and of pCosFS1, only partial sequences were obtained during the shotgun sequencing approach. DNA restriction enzymes: N, NcoI, B, BamHI; E, EcoRI; Sm, SmaI; P, PstI; K, KpnI; H, HindIII; Sc, SacI.

Article Snippet: To assess the biotin biosynthesis capabilities of the three environmentally derived cosmid libraries, cosmid DNA from the recombinant E. coli clones was extracted and used to transduce the E. coli biotin-auxotrophic strain ATCC 33767 (Fig. ).

Techniques: Isolation, Derivative Assay, Shotgun Sequencing

Journal: International Journal of Biochemistry and Molecular Biology

Article Title: Comparison of the functions of glutathionylspermidine synthetase/amidase from E. coli and its predicted homologues YgiC and YjfC

doi:

Figure Lengend Snippet: Analysis of thiol content in E. coli cells. Analysis of the thiol content of wild type and gsp, yjfC, and ygiC gene knockout E. coli strains grown in LB media to stationary phase under anaerobic conditions was performed using HPLC. Labeled peaks represent DTNB derivatives of G-Sp and GSH. Peak immediately followed GSH (14 min) corresponds to DTNB derivative of γ-glutamylcysteine. Peaks at 18 min and 21 min are 2-nitro-5-thiobenzoate and the excess of DTNB correspondently.

Article Snippet: Materials E. coli K-12 genomic DNA was from ATCC (Manassas).

Techniques: Gene Knockout, Labeling