Journal: Molecules

Article Title: In Vitro Studies of the Activity of Dithiocarbamate Organoruthenium Complexes against Clinically Relevant Fungal Pathogens

doi: 10.3390/molecules19045402

Figure Lengend Snippet: In vitro susceptibility of species of Candida dubliniensis clinical isolates for L1 , C1 , L2 and C2 complexes by microdilution methods—MIC: μg mL −1 (10 −5 mol L −1 ).

Article Snippet: Nevertheless, the first work that describes the investigation of dithiocarbamate ruthenium (III) complexes as antifungal agent [ ] has been developed by our own research group, and in this work the susceptibility of seven different species of Aspergillus ( A. clavatus, A. flavus, A. fumigatus (ATCC 16913 and CI, clinical isolated), A. niger , A. nomius , A. tamarii and A.terreu s) was tested with promising results considering that Aspergillus spp. has also became a recognized pathogen related to IFIs [ , ].

Techniques: In Vitro

Journal: Molecules

Article Title: In Vitro Studies of the Activity of Dithiocarbamate Organoruthenium Complexes against Clinically Relevant Fungal Pathogens

doi: 10.3390/molecules19045402

Figure Lengend Snippet: In vitro susceptibility—MIC: μg mL −1 (10 −5 mol L −1 ) of Candida dubliniensis clinical isolate CD28 for pentakis-dithiocarbamate diruthenium complexes and free ligands by microdilution methods.

Article Snippet: Nevertheless, the first work that describes the investigation of dithiocarbamate ruthenium (III) complexes as antifungal agent [ ] has been developed by our own research group, and in this work the susceptibility of seven different species of Aspergillus ( A. clavatus, A. flavus, A. fumigatus (ATCC 16913 and CI, clinical isolated), A. niger , A. nomius , A. tamarii and A.terreu s) was tested with promising results considering that Aspergillus spp. has also became a recognized pathogen related to IFIs [ , ].

Techniques: In Vitro

Journal: Molecules

Article Title: In Vitro Studies of the Activity of Dithiocarbamate Organoruthenium Complexes against Clinically Relevant Fungal Pathogens

doi: 10.3390/molecules19045402

Figure Lengend Snippet: In vitro susceptibility of clinical isolates of Paracoccidioides brasiliensis for pentakis-dithiocarbamate diruthenium complexes by microdilution methods—MIC: μg mL −1 (10 −5 mol L −1 ).

Article Snippet: Nevertheless, the first work that describes the investigation of dithiocarbamate ruthenium (III) complexes as antifungal agent [ ] has been developed by our own research group, and in this work the susceptibility of seven different species of Aspergillus ( A. clavatus, A. flavus, A. fumigatus (ATCC 16913 and CI, clinical isolated), A. niger , A. nomius , A. tamarii and A.terreu s) was tested with promising results considering that Aspergillus spp. has also became a recognized pathogen related to IFIs [ , ].

Techniques: In Vitro

Journal: Molecules

Article Title: In Vitro Studies of the Activity of Dithiocarbamate Organoruthenium Complexes against Clinically Relevant Fungal Pathogens

doi: 10.3390/molecules19045402

Figure Lengend Snippet: In vitro susceptibility of clinical isolates of Cryptococcus neoformans for pentakis-dithiocarbamate diruthenium complexes by broth microdilution methods—MIC: μg mL −1 (10 −5 mol L −1 ).

Article Snippet: Nevertheless, the first work that describes the investigation of dithiocarbamate ruthenium (III) complexes as antifungal agent [ ] has been developed by our own research group, and in this work the susceptibility of seven different species of Aspergillus ( A. clavatus, A. flavus, A. fumigatus (ATCC 16913 and CI, clinical isolated), A. niger , A. nomius , A. tamarii and A.terreu s) was tested with promising results considering that Aspergillus spp. has also became a recognized pathogen related to IFIs [ , ].

Techniques: In Vitro

Journal: Molecules

Article Title: In Vitro Studies of the Activity of Dithiocarbamate Organoruthenium Complexes against Clinically Relevant Fungal Pathogens

doi: 10.3390/molecules19045402

Figure Lengend Snippet: In vitro susceptibility of clinical isolates of Sporotrix schenckii for pentakis-dithiocarbamate diruthenium ( C1 – C5 ) complexes by microdilution methods—MIC: μg mL −1 (10 −5 mol L −1 ).

Article Snippet: Nevertheless, the first work that describes the investigation of dithiocarbamate ruthenium (III) complexes as antifungal agent [ ] has been developed by our own research group, and in this work the susceptibility of seven different species of Aspergillus ( A. clavatus, A. flavus, A. fumigatus (ATCC 16913 and CI, clinical isolated), A. niger , A. nomius , A. tamarii and A.terreu s) was tested with promising results considering that Aspergillus spp. has also became a recognized pathogen related to IFIs [ , ].

Techniques: In Vitro

Journal: iScience

Article Title: SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data

doi: 10.1016/j.isci.2022.103777

Figure Lengend Snippet: scRNA-seq gene body coverage skewness and skewness distribution Three scRNA-seq datasets. (A) Distribution of mapped reads (tags) across genes. Each panel shows the gene body coverage percentile per dataset. The x axis represents the gene body from 5′ end to 3′ end scaled from 0 to 100, and the y axis denotes gene coverage (0–1). lThe plot of the dataset (ArrayExpress: E-MTAB-2600 ) generated by SMARTer protocol (full-length sequence) contains cells with low coverage in the middle of the gene region and cells with high coverage in the 3′ -end of the gene region. Although the dataset (NCBI GEO: GSE29087 ) generated by STRT (5′ -end sequence) contains cells with high coverage both in the middle and the 3′ -end region of the gene. The third dataset from 10x Genomics generated by single-cell 3′ -end protocol contains cells with high coverage in the 5′ -end region of the gene and cells with low coverage in the middle of the gene. (B) Mean of the gene body coverage for different scRNA-seq methods. Error bars represents the standard error of the mean (SEM). (C) Skewness and bias in gene body coverage for cells highlighted with a red dashed box.

Article Snippet: We generated our own 10x Genomic Chromium dataset from MCF10A cells (ATCC).

Techniques: Generated, Sequencing

Journal: iScience

Article Title: SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data

doi: 10.1016/j.isci.2022.103777

Figure Lengend Snippet: Overview of SkewC workflow The figure illustrates the SkewC workflow and implementation to discriminate skewed cells with skewed gene coverage distribution. The circle numbers callout points to the main inputs, processing, and outputs of SkewC. SkewC inputs are the gene model in. bed format and the aligned reads in BAM format per each cell. For scRNA-seq dataset generated by 10x Genomics libraries, the input to SkewC is the postsorted BAM file together with the cell barcode text file. SkewC bash command to supply the inputs (0_split10XbyBarcode.sh) the batch split the postsorted BAM file into individual BAM files. Compute gene body coverage for each cell. SkewC batch script 1_geneBodyCoverage.sh used to compute gene body coverage and produce a text file.r which contains vector of normalized values. The normalized values are stored as a matrix (coverage matrix with bin size = 100), the coverage matrix should be processed by computing the mean of the coverage matrix and reduce the bin size to be 10. The mean coverage matrix used as in put for the batch script 2_SkewC.sh, which use the trimming clustering function in R (tclust) to cluster the coverage matrix, the script designed to auto approximate the optimal trimming level alpha ( α ) and select the clustering result with optimal alpha ( α ). Other option is to apply the trim clustering with user-defined trimming level alpha ( α ). The output provided in different formats, two text files each with the list of the typical and skewed cells. The other format was R data frame object SkewCAnnotation.rds. The list of annotated single-cells can be added to the R Bioconductor SingleCellExperiment Class or Seurat R package object to be used in QC for filtering skewed cells from analysis.

Article Snippet: We generated our own 10x Genomic Chromium dataset from MCF10A cells (ATCC).

Techniques: Generated, Plasmid Preparation

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Antibody-opsonized bacteria evoke an inflammatory dendritic cell phenotype and polyfunctional Th cells by cross-talk between TLRs and FcRs.

doi: 10.4049/jimmunol.1303126

Figure Lengend Snippet: FIGURE 2. Both FcgRII and MyD88-dependent TLRs are essential for cross-talk. (A) FcgRI, FcgRIIa, FcgRIIb, and FcgRIII expression on iDCs (shaded graphs). Open graphs represent isotype control. iDCs were stimulated for 16 h with FITC-labeled E. coli, IgG, or IgG-opsonized FITC-labeled E. coli in the presence or absence of pan FcgRII (AT10)-blocking Ab (B and C) or anti-FcgRIIb (2B6) Ab (D), after which supernatants were analyzed for production of the indicated cytokines. (E and F) iDCs were stimulated for 24 h with the TLR ligands Pam3CSK4 (Pam; 5 mg/ml), LPS (100 ng/ml), flagellin (Flag; 5 mg/ml), PGN-SA (10 mg/ml), Poly-I:C (40 mg/ml), or R848 (2.5 mg/ml) in the presence or absence of IgG-B (to activate FcgRs) or BSA-B (as control beads). IL-1b (Ε) or IL-23 (F) was determined in the supernatants of iDCs after the indicated stimulation. (G) TNF-a production was determined after stimulation with R848 (2.5 mg/ml) in the presence or absence of IgG-B or BSA-B. Data are mean 6 SD (n = 3). *p , 0.05, **p , 0.01,***p , 0.001.

Article Snippet: FcgR surface expression was determined with anti-CD64, anti-CD32, and anti-CD16 (all from BD Biosciences) or 2B6 Ab (anti-FcgRIIb, own hybridoma production ATCC PTA-4591) for 1 h at 4 ̊C.

Techniques: Expressing, Control, Labeling, Blocking Assay

Journal:

Article Title: Survival and Epiphytic Fitness of a Nonpathogenic Mutant of Xanthomonas campestris pv. Glycines

doi:

Figure Lengend Snippet: Bacterial strains and plasmids used a

Article Snippet: Bacterial strains and plasmids used in this work and their relevant characteristics are described in Table . table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Strain or plasmid Relevant characteristics Reference(s) or source Bacterial strains E. coli DH5α F − lacZ ΔM15 recA hsdR17 gyrA thi 20 HB101 Res − Mod − recA13 Sm r 20 S17-1λ pir Pro − Res − Mod + recA , integrated plasmid RP4-Tc::Mu-Km::Tn 7 , lysogenized with λ pir phage 21 P. fluorescens 5064 Wild type 4 X. campestris pv. glycines YR32 Wild type, Rif r 18 , 30 8ra Wild type 7 M715 Rif r Km r This study YR32(Ice+) YR32 containing pJL1703; Rif r Km r inaZ This study X. campestris pv. campestris 33913 Wild type ATCC R. sphaeroides 2.4.1 Wild type 24 Plasmids pJL1703 Km r , inaZ with its own promoter 15 pYR103 pUTmini-Tn 5 Km r -Tp r 19 pRK2013 ColE1 replicon, Tra + of RK2, Km r 5 Open in a separate window a Abbreviations: Rif, rifampin; Km, kanamycin; Sm, streptomycin; Tp, trimethoprim; ATCC, American Type Culture Collection.

Techniques: Plasmid Preparation

Journal: bioRxiv

Article Title: Basic and translational science of cyst wall proteins of the eye pathogen Acanthamoeba

doi: 10.1101/2024.02.02.578540

Figure Lengend Snippet: (A) Western blots show pre-bleeds from rabbits (negative control) fail to bind to proteins of trophozoites or cysts, while rAbs fail to bind to trophozoite proteins (a second negative control) but bind well to cyst proteins of Neff strain. As discussed in detail in the Results, rAbs to the BHF of Jonah-1 binds to the expected 55-kDa band and to two lower mol wt bands. Anti-Luke-2 rAbs bind to a heavy and broad 50-kDa band, which is greater than the expected size of 27-kDa. Anti-Leo rAbs bind to a 13-kDa band, which is slightly smaller than the expected size of 17-kDA. Anti-laccase rAbs bind to a 75-kDa band, which is slightly bigger than the expected size of 64-kDa, as well as to a less abundant 55-kDa band. (B) High power confocal microscopy shows rAbs to Jonah-1 bind in a patchy distribution to the surface of Neff strain of Ac and other Acanthamoeba species, which are shown in . (C) Anti-Luke-2 rAbs bind strongly to ostioles and weakly to endocyst layer of some but not all Neff strain Ac. An asterisk is attached to “ostioles” because anti-Luke-2 rAbs can also bind to ectocyst layer, as shown in . (D) Anti-Leo-A rAbs also bind strongly to ostioles with a variable binding to the endocyst layer of some but not all of Neff strain Ac. Again, an asterisk indicates that anti-Leo-A rAbs can also bind to the ectocyst layer, as shown in . (E) Anti-laccase-1 rAbs bind in a homogenous manner to cysts of Neff strain, as well as to cyst of other Acanthamoeba species, which are shown in . (F to I) . Low power confocal micrographs shows rAbs to Jonah-1, Luke-2, Leo-A and laccase-1 detect well CFW-labeled cysts of the Neff strain. (J) A plot shows the percentage of CFW-labeled cysts detected by four rAbs in two independent experiments (average plus SEM), in which 100+ cysts were counted in random low power fields. Rabbit antibodies to Luke-2, Leo-A, and Laccase-1 each detect >95% of cysts 10 of 11 Acanthamoeba isolates tested, while rAbs to Jonah-1 are slightly less efficient in detecting three isolates of Acanthamoeba . The exception is A. mauritaniensis , which was poorly detected with all four rAbs, suggesting a problem with cyst formation under the conditions used here. Single scale bar for B to E is 5 µm.

Article Snippet: Jonah-1 (ACA1_164810), which has a long, unstructured Thr-rich domain in addition to a single BHF, is expressed early during encystation and localizes to the ectocyst layer when tagged with GFP and expressed under its own promoter in transformed Ac of the Neff strain (ATCC 30010) ( , and ) (Supporting Information S1 and S2) [ , – ].

Techniques: Western Blot, Negative Control, Confocal Microscopy, Binding Assay, Labeling

Journal: Molecular Therapy. Methods & Clinical Development

Article Title: Preclinical Proof-of-Concept, Analytical Development, and Commercial Scale Production of Lentiviral Vector in Adherent Cells

doi: 10.1016/j.omtm.2019.08.006

Figure Lengend Snippet: Comparison of Flow Cytometry Titers Based on GFP Transgene Expression Using Two Different Sources for HeLa Cells

Article Snippet: An example of how the cell line used affects was shown here with the samples titered using both our own ATCC-derived HeLa cell line and another, originally also ATCC-derived HeLa cell line from a collaborating laboratory.

Techniques: Comparison, Flow Cytometry, Expressing