Journal: Microorganisms

Article Title: In Silico Analysis of a GH3 β-Glucosidase from Microcystis aeruginosa CACIAM 03

doi: 10.3390/microorganisms11040998

Figure Lengend Snippet: Physicochemical parameters of β-glucosidases from Microcystis sp. using Expasy’s Protparam tool.

Article Snippet: ProtParam tool [ ] (SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland) predicted the physicochemical parameters.

Techniques:

Journal: Leukemia

Article Title: Preclinical evaluation of eltrombopag in a PDX model of myelodysplastic syndromes

doi: 10.1038/s41375-021-01327-w

Figure Lengend Snippet: A Schematic experimental setup. CD34+ cells and mesenchymal stromal cells (MSCs) derived from bone marrow aspirations (BMAs) of MDS patients were injected into Busulfan-conditioned NSG mice by bilateral intrafemoral transplantation (IF TX). Long-term engraftment was determined 12 weeks post transplant. Mice with positive human engraftment subsequently received oral treatment of eltrombopag (EPAG) or vehicle control (CTRL) for 18–24 weeks until endpoint. Starting with treatment, peripheral blood (PB) and BM were sampled every 2 and 6 weeks, respectively. B Representative flow cytometry plot showing percentage of human CD45+ (hCD45+) and mouse CD45+ (mCD45+) cells in the BM of patient-derived xenografts (PDXs). Human engraftment was defined as percentage of hCD45+ of total CD45+ cells. C Comparison of engraftment rates between patients’ PDX at starting (orange) and endpoint (green). On the x -axis, patient IDs are shown. D Representative flow cytometry plots showing gating scheme for platelets (PLTs) and beads (left), and percentage of hCD41+ and mCD41+ PLTs in PB of PDX (right). The absolute number of human PLTs per microliter PB was calculated in relation to the number of beads recorded. E Exemplary clustering of variant allele frequencies (VAFs) of mutations and copy number variations into different subclones using the bioinformatic tool SciClone. FSC-A, forward scatter area; SSC-A, side scatter area.

Article Snippet: E Exemplary clustering of variant allele frequencies (VAFs) of mutations and copy number variations into different subclones using the bioinformatic tool SciClone.

Techniques: Derivative Assay, Injection, Transplantation Assay, Control, Flow Cytometry, Comparison, Variant Assay

Journal: Leukemia

Article Title: Preclinical evaluation of eltrombopag in a PDX model of myelodysplastic syndromes

doi: 10.1038/s41375-021-01327-w

Figure Lengend Snippet: Of n = 3 xenografts, n = 2 were treated with eltrombopag (EPAG1 + 2, red) and n = 1 received vehicle control (CTRL, blue). CTRL mouse had to be killed 6 weeks into treatment phase due to excessive weight loss (see Supplementary Fig. ). A Percentage of human engraftment in the bone marrow (BM) of xenografts throughout 18 weeks of treatment. Engraftment was assessed every 6 weeks. B Course of human platelets (PLTs) in the peripheral blood of xenografts during treatment phase. PLTs were analyzed every 2 weeks. C BM smears of CTRL (left) and EPAG1 (right) at endpoint stained with May–Grünwald–Giemsa stain (magnification ×20). D Mutational variant allele frequencies (VAFs) of primary mononuclear cell (MNC) sample of patient P01. Each bar represents one individual clone. Non-synonymous mutations are displayed with their superscripted respective amino acid change. E – G VAFs of patient-specific mutations in the course of treatment detected in the BM of EPAG1, EPAG2, and CTRL, respectively. Mutations were separated into different subclones using the bioinformatic tool SciClone. MDS-associated molecular lesions are highlighted. Thicker lines represent the mean value of the respective clone. H Reconstruction of differential clonal evolution in the xenografts of P01 for both treatment groups. I Mean deltaVAF of EPAG1, EPAG2, and CTRL determined from all identified somatic mutations for any two consecutive WES time points. Data were analyzed using one-way ANOVA and are represented as mean ± SD. ns, not significant.

Article Snippet: E Exemplary clustering of variant allele frequencies (VAFs) of mutations and copy number variations into different subclones using the bioinformatic tool SciClone.

Techniques: Control, Staining, Giemsa Stain, Variant Assay

Journal: Leukemia

Article Title: Preclinical evaluation of eltrombopag in a PDX model of myelodysplastic syndromes

doi: 10.1038/s41375-021-01327-w

Figure Lengend Snippet: Bone marrow clonality of patients and exemplary xenografts during 18–24 weeks of experiment reconstructed by clustering of variant allele frequencies (VAFs) using the bioinformatic tool SciClone. Mutations within the same clone are equally colored. Thicker lines represent the mean clonal VAF. Non-synonymous mutations are displayed with superscripted amino acid change. Dotted black line describes the course of human engraftment. See also Supplementary Fig. for additional data. A , B VAFs of patient P07’s CD34+ cells in the course of 10 months and human CD45+ (hCD45+) cells from EPAG2. C – E VAFs of patient P04’s mononuclear cells (MNCs) and hCD45+ cells from CTRL1 and EPAG3. Dose was escalated after 12 weeks from 50 to 150 mg/kg. EPAG3 had to be eliminated after 20 weeks due to excessive weight loss. F Total mean deltaVAF of P04’s n = 3 CTRL and n = 3 EPAG xenografts. G – I VAFs of patient P05’s MNCs and hCD45+ cells from CTRL1 and EPAG3. Dose was escalated after 12 weeks from 50 to 150 mg/kg. J Total mean deltaVAF of P05’s n = 2 CTRL and n = 3 EPAG xenografts. Data in F and J were analyzed using unpaired, two-tailed t -test and is represented as mean ± SD. ns, not significant; EPAG, eltrombopag; BMA, bone marrow aspiration.

Article Snippet: E Exemplary clustering of variant allele frequencies (VAFs) of mutations and copy number variations into different subclones using the bioinformatic tool SciClone.

Techniques: Variant Assay, Two Tailed Test

Journal: iScience

Article Title: Diversity and evolution of tyrosinase enzymes involved in the adhesive systems of mussels and tubeworms

doi: 10.1016/j.isci.2024.111443

Figure Lengend Snippet:

Article Snippet: ExPASY Translate online tool , SIB (Swiss Institute of Bioinformatics) , https://web.expasy.org/translate/.

Techniques: Recombinant, Labeling, Sample Prep, DC Protein Assay, Reverse Transcription, Sequencing, In Situ Hybridization, Software

Journal: International Journal of Molecular Sciences

Article Title: In-Silico Characterization of Glycosyl Hydrolase Family 1 β-Glucosidase from Trichoderma asperellum UPM1

doi: 10.3390/ijms21114035

Figure Lengend Snippet: Comparison of hydrophobic scores and positions of selected Trichoderma spp. β-glucosidases using ExPASY ProtScale tool.

Article Snippet: Hydrophobicity scores, positions, and hydropathy plots on Kyte and Doolittle scale for all sequences were predicted by ProtScale tool (SIB Swiss Institute of Bioinformatics, Geneva, Switzerland) [ ].

Techniques: Comparison