Journal: Mutagenesis

Article Title: Functional analysis of the new barley gene HvKu80 indicates that it plays a key role in double-strand DNA break repair and telomere length regulation.

doi: 10.1093/mutage/gev033

Figure Lengend Snippet: Figure 4. Relative HvKu80 gene expression levels in the parent cultivar ‘Sebastian’ (A), mutant ku80.c (B) and mutant ku80.j (C) after the treatment with bleomycin (100 µg/ml) and in the untreated material were analysed at various time points. ‘C’: seedlings after 36 h of growth at 24°C, ‘0’ in the untreated material denotes 36-h-old seedlings of barley that were treated with sterile water for 2 h at 37°C, ‘0’ in the treated material denotes 36-hold seedlings of barley that were treated with bleomycin for 2 h at 37°C. The value of the relative expression level was normalised to the standard control (HvARF1 gene, accession no. AJ508228.2). The expression level (2−ΔΔCt) in the untreated material was calculated relative to the control roots (C). The expression level (2−ΔΔCt) in the treated material was calculated relative to the untreated material at a particular time point. #Statistically significant difference vs. the control (C) (P < 0.05); *Statistically significant difference compared to the untreated material at the corresponding time point (P < 0.05).

Article Snippet: After this time, the seeds were incubated at 24°C for 36 h. Thirty-six-hour-old barley seedlings were transferred to 100 μg/ ml solution of bleomycin A5 hydrochloride (LKT Laboratories) and incubated at 37°C for 2 h. Upon the mutagenic treatment the seedlings were washed three times in sterile water for 15 min.

Techniques: Gene Expression, Mutagenesis, Sterility, Expressing, Control

Journal: Mutagenesis

Article Title: Functional analysis of the new barley gene HvKu80 indicates that it plays a key role in double-strand DNA break repair and telomere length regulation.

doi: 10.1093/mutage/gev033

Figure Lengend Snippet: Figure 5. The number of DSBs that were induced by bleomycin. Ethidium bromide-stained agarose gel visualising the induction of DSBs by bleomycin treatment in barley genomic DNA (A), concentration-dependent increase in DSB number in roots of the cultivar ‘Sebastian’ (B), the number of DSBs that were induced by 100 µg/ml bleomycin in the roots of the parent cultivar ‘Sebastian’ and the mutants ku80 after the bleomycin treatment (C). The DSB frequency was calculated for whole roots of the analysed genotypes. ‘M’: marker size 1 kb, ‘C’: measurement of DSB number was done on DNA isolated from whole roots after 36 h of growth at 24°C, ‘0’-treated material: measurement of DSB number was done on DNA isolated from whole 36-h-old roots of barley that were treated with bleomycin for 2 h at 37°C, *Statistically significant difference in relation to the parent cultivar ‘Sebastian’ (P < 0.05) at corresponding time points, #Statistically significant difference in relation to 0 µg/ml concentration of bleomycin (P < 0.05).

Article Snippet: After this time, the seeds were incubated at 24°C for 36 h. Thirty-six-hour-old barley seedlings were transferred to 100 μg/ ml solution of bleomycin A5 hydrochloride (LKT Laboratories) and incubated at 37°C for 2 h. Upon the mutagenic treatment the seedlings were washed three times in sterile water for 15 min.

Techniques: Staining, Agarose Gel Electrophoresis, Concentration Assay, Marker, Isolation

Journal: Mutagenesis

Article Title: Functional analysis of the new barley gene HvKu80 indicates that it plays a key role in double-strand DNA break repair and telomere length regulation.

doi: 10.1093/mutage/gev033

Figure Lengend Snippet: Figure 6. Number of MCD nuclei after the treatment of the roots of the cultivar ‘Sebastian’ and the mutants ku80.c and ku80.j with bleomycin. ‘C’: seedlings after 36 h of growth at 24°C, ‘0’-treated material: 36-h-old barley seedlings that were treated with bleomycin for 2 h at 37°C; *Statistically significant difference in relation to the parent cultivar ‘Sebastian’ (P < 0.05) at corresponding time points.

Article Snippet: After this time, the seeds were incubated at 24°C for 36 h. Thirty-six-hour-old barley seedlings were transferred to 100 μg/ ml solution of bleomycin A5 hydrochloride (LKT Laboratories) and incubated at 37°C for 2 h. Upon the mutagenic treatment the seedlings were washed three times in sterile water for 15 min.

Techniques:

Journal: Mutagenesis

Article Title: Functional analysis of the new barley gene HvKu80 indicates that it plays a key role in double-strand DNA break repair and telomere length regulation.

doi: 10.1093/mutage/gev033

Figure Lengend Snippet: Figure 7. Reduced growth of seedlings from the cultivar ‘Sebastian’ and the mutants ku80.c and ku80.j after treatment with bleomycin (100 µg/ml). Representative image of seedlings from the cultivar ‘Sebastian’ and the mutants ku80.c and ku80.j after treatment with bleomycin (A). Reduction of roots and shoots length of cultivar ‘Sebastian’ and the mutants ku80.c and ku80.j after bleomycin treatment (B). Control; ‘C’: seedlings after 60 h of growth at 24°C; scale = 3 cm, *Statistically significant difference in relation to root or shoot in control conditions (P < 0.05).

Article Snippet: After this time, the seeds were incubated at 24°C for 36 h. Thirty-six-hour-old barley seedlings were transferred to 100 μg/ ml solution of bleomycin A5 hydrochloride (LKT Laboratories) and incubated at 37°C for 2 h. Upon the mutagenic treatment the seedlings were washed three times in sterile water for 15 min.

Techniques: Control

Journal: Data in Brief

Article Title: Data on plasma tumour and metabolism related proteins’ potential in differentiation of HFpEF-PH from PAH and in prognosis of left heart failure patients with pulmonary hypertension

doi: 10.1016/j.dib.2021.107747

Figure Lengend Snippet: Plasma levels of metabolism and tumour related proteins in controls and patients.

Article Snippet: NT-proBNP and 69 tumour and metabolism related proteins were analysed: 5′-nucleotidase (5′-NT), protein AMBP or alpha-1-microglobulin/bikunin precursor (AMBP), aminopeptidase N (AP-N), bleomycin hydrolase (BLM-H), brother of cell adhesion molecule-related/down-regulated by oncogenes (CDO) or (BOC), carbonic anhydrase 9 (CA9), cathepsin Z, cyclin-dependant kinase inhibitor 1A (CDKN1A) or p21, carcinoembryonic antigen-related cell adhesion molecule (CEACAM) 1 and 5, contactin-1, cornulin, carboxypeptidase (CP) A1, B1 and E, cystatin B, decorin, endothelial cell-specific molecule 1 or endocan, epithelial cell adhesion molecule (EpCAM), fatty acid-binding protein 4 (FABP4), fibroblast growth factor (FGF-) 21 and 23, folate receptor gamma (FR-gamma), furin, gastrotropin, glyoxalase I or lactoylglutathione lyase, insulin-like growth factor 1 receptor (IGF1R), insulin-like growth factor-binding protein (IGFBP) 2, 3 and 7, kallikrein 6, 8, 11, 13 and 14, low-density lipoprotein receptor (LDL-R), leptin, lectin-like oxidized LDL receptor 1 (LOX-1), lipoprotein lipase (LPL), Ly6/PLAUR domain-containing protein 3 (LYPD3) or C4.4A, mesothelin, methionine aminopeptidase 2 (MetAP2), melanoma-derived growth regulatory protein (MIA), midkine, mucin-16 or CA125, nectin-4 or PVRL4, pappalysin-1, proprotein convertase subtilisin/kexin type 9 (PCSK9), podocalyxin, paraoxonase-3 (PON-3), prostasin, protein S100A4 (S100A4), protein S100A11 (S100A11), retinoic acid receptor responder protein 2 (RARRES2), resistin, secretory carrier-associated membrane protein 3 (SCAMP3), secretoglobin family 3A member 2 (SCGB3A2), serpin A12, tyrosine-protein phosphatase non-receptor type substrate 1 (SHPS-1), sortillin, soluble receptor for advanced glycation end products (sRAGE; all soluble forms of RAGE), T-cell leukaemia/lymphoma protein 1A (TCL1A), trefoil factor 3 (TFF3), protein-glutamine gamma-glutamyltransferase 2 (TGM2), transferrin receptor protein 1 (TR), WAP four-disulfide core domain protein 2 (WFDC2), vimentin, V-set and immunoglobulin domain-containing protein 2 (VSIG2) and Xaa-Pro aminopeptidase 2 (XPNPEP2).

Techniques:

Journal: Data in Brief

Article Title: Data on plasma tumour and metabolism related proteins’ potential in differentiation of HFpEF-PH from PAH and in prognosis of left heart failure patients with pulmonary hypertension

doi: 10.1016/j.dib.2021.107747

Figure Lengend Snippet: Proteins’ classification and p-values of Kruskal Wallis and Mann Whitney's tests in comparing metabolism and tumour related proteins in controls and disease groups.

Article Snippet: NT-proBNP and 69 tumour and metabolism related proteins were analysed: 5′-nucleotidase (5′-NT), protein AMBP or alpha-1-microglobulin/bikunin precursor (AMBP), aminopeptidase N (AP-N), bleomycin hydrolase (BLM-H), brother of cell adhesion molecule-related/down-regulated by oncogenes (CDO) or (BOC), carbonic anhydrase 9 (CA9), cathepsin Z, cyclin-dependant kinase inhibitor 1A (CDKN1A) or p21, carcinoembryonic antigen-related cell adhesion molecule (CEACAM) 1 and 5, contactin-1, cornulin, carboxypeptidase (CP) A1, B1 and E, cystatin B, decorin, endothelial cell-specific molecule 1 or endocan, epithelial cell adhesion molecule (EpCAM), fatty acid-binding protein 4 (FABP4), fibroblast growth factor (FGF-) 21 and 23, folate receptor gamma (FR-gamma), furin, gastrotropin, glyoxalase I or lactoylglutathione lyase, insulin-like growth factor 1 receptor (IGF1R), insulin-like growth factor-binding protein (IGFBP) 2, 3 and 7, kallikrein 6, 8, 11, 13 and 14, low-density lipoprotein receptor (LDL-R), leptin, lectin-like oxidized LDL receptor 1 (LOX-1), lipoprotein lipase (LPL), Ly6/PLAUR domain-containing protein 3 (LYPD3) or C4.4A, mesothelin, methionine aminopeptidase 2 (MetAP2), melanoma-derived growth regulatory protein (MIA), midkine, mucin-16 or CA125, nectin-4 or PVRL4, pappalysin-1, proprotein convertase subtilisin/kexin type 9 (PCSK9), podocalyxin, paraoxonase-3 (PON-3), prostasin, protein S100A4 (S100A4), protein S100A11 (S100A11), retinoic acid receptor responder protein 2 (RARRES2), resistin, secretory carrier-associated membrane protein 3 (SCAMP3), secretoglobin family 3A member 2 (SCGB3A2), serpin A12, tyrosine-protein phosphatase non-receptor type substrate 1 (SHPS-1), sortillin, soluble receptor for advanced glycation end products (sRAGE; all soluble forms of RAGE), T-cell leukaemia/lymphoma protein 1A (TCL1A), trefoil factor 3 (TFF3), protein-glutamine gamma-glutamyltransferase 2 (TGM2), transferrin receptor protein 1 (TR), WAP four-disulfide core domain protein 2 (WFDC2), vimentin, V-set and immunoglobulin domain-containing protein 2 (VSIG2) and Xaa-Pro aminopeptidase 2 (XPNPEP2).

Techniques:

Journal: Journal of pharmacological and toxicological methods

Article Title: A novel murine model of pulmonary fibrosis: the role of platelets in chronic changes induced by bleomycin.

doi: 10.1016/j.vascn.2021.107057

Figure Lengend Snippet: Fig. 1. Representative images of Ashcroft scoring. Images captured using a x20 objective lens. The images show a healthy lung section with an Ashcroft score of 0 (A) and sections with Ashcroft scores of 2 (B), 3 (C) and 4 (D). Average scores of 2–4 are what are most commonly observed in bleomycin treated animals.

Article Snippet: Mice were administered 6 intranasal doses of either saline or 0.25 mg/kg bleomycin A5 hydrochloride (Carbosynth Europe, Batch AB463321601) prepared in saline on Days 0, 1, 2, 5, 6 and 7.

Techniques:

Journal: Journal of pharmacological and toxicological methods

Article Title: A novel murine model of pulmonary fibrosis: the role of platelets in chronic changes induced by bleomycin.

doi: 10.1016/j.vascn.2021.107057

Figure Lengend Snippet: Fig. 3. Lung function and histological changes confirm successful induction of IPF. A decline in lung function is seen in the bleomycin-dosed animals that is consistent with what would be expected in IPF. The decline in FVC (A) shows a decrease in the ability of the lung to draw in and expel air. This is likely due to the increase stiffness of the scarred lung tissue as demonstrated by the increase in elastance (B). The induction of IPF in the animals was confirmed histo pathologically by observing a significant increase in Ashcroft score (C). An increase in the number of platelets recovered in the BAL was observed (D), this was correlated by an increase in the number of platelets observed in the lung tissue of bleomycin treated animals (E). n = 7–11 per group. Data is means± SEM. ** p < 0.01, *** p < 0.001 compared to saline treated group.

Article Snippet: Mice were administered 6 intranasal doses of either saline or 0.25 mg/kg bleomycin A5 hydrochloride (Carbosynth Europe, Batch AB463321601) prepared in saline on Days 0, 1, 2, 5, 6 and 7.

Techniques: Saline

Journal: Journal of pharmacological and toxicological methods

Article Title: A novel murine model of pulmonary fibrosis: the role of platelets in chronic changes induced by bleomycin.

doi: 10.1016/j.vascn.2021.107057

Figure Lengend Snippet: Fig. 2. Determination of standardized threshold for quantitative anal ysis of lung tissue sections in ImageJ. Threshold is chosen based on the criteria of minimal noise signal being presented as well as least platelets being lost in the resulting grey and grayscale image when comparing to the RGB images and DAB component images. (A) and (D) Representa tive CD41 immunostaining of lung tissue sections (x40 magnification) of sham and bleomycin-induced IPF mice respectively, taken under light microscopy. Platelets are immuno-stained in brown while lung tissues are counterstained in blue. (B) and (E) Representative DAB component images obtained from (A) and (D) respectively after processing with a colour deconvolution plugin. (C) and (F) Resulting representative grey and grayscale images produced after (B) and (E) underwent thresh olding of 130. Black dots represents platelets that will be counted in the subsequent quantitative analysis of number and size of platelets after a suitable size filter is chosen.

Article Snippet: Mice were administered 6 intranasal doses of either saline or 0.25 mg/kg bleomycin A5 hydrochloride (Carbosynth Europe, Batch AB463321601) prepared in saline on Days 0, 1, 2, 5, 6 and 7.

Techniques: Immunostaining, Light Microscopy, Staining, Produced

Journal: Journal of pharmacological and toxicological methods

Article Title: A novel murine model of pulmonary fibrosis: the role of platelets in chronic changes induced by bleomycin.

doi: 10.1016/j.vascn.2021.107057

Figure Lengend Snippet: Fig. 5. Effect of platelet depletion on development of fibrotic endpoints. The success of the platelet depletion was confirmed by measuring circulating platelet levels in n = 3 animals from the saline treated platelet normal and platelet depleted animals (A). An improved survival rate was observed in platelet depleted animals compared to platelet normal animals treated with bleomycin (B). There was also an improved recovery in initial weight loss observed in platelet depleted animals compared to platelet normal animals treated with bleomycin (C). An increase in platelet numbers recovered in the BAL was observed in both the platelet normal and platelet depleted bleomycin treated animals compared to the saline treated controls. There was no difference in the number of platelets in the BAL of the platelet- normal and platelet-depleted bleomycin treated animals (D). An improvement in lung function was observed in platelet-depleted bleomycin treated animals as seen by an increase in FVC (E) and a decrease in elastance (F) compared to the platelet normal bleomycin treated animals. A significant improvement in Ashcroft score was also recorded in platelet-depleted bleomycin treated animals compared to platelet-normal bleomycin treated animals (G). A reduction in TGF-β concentration in the BAL of platelet-depleted animals compared to platelet-normal bleomycin treated animals was also observed (H).). n = 7–11 per group. Data are represented as mean ± SEM. * p < 0.05 ** p < 0.01, *** p < 0.001 compared to saline treated group. ## p < 0.01 compared to the platelet normal group. For the TGF-β analysis where 66% or greater of the group had values that were below the level of quantification (BLQ) the whole group is reported as BLQ. Where less than 66% of the group are outside the limits of quantification 0.5× the lowest level of quantification (LLOQ) has been used for the purposes of deriving a group mean. The LLOQ for this assay was 31.3 pg/mL.

Article Snippet: Mice were administered 6 intranasal doses of either saline or 0.25 mg/kg bleomycin A5 hydrochloride (Carbosynth Europe, Batch AB463321601) prepared in saline on Days 0, 1, 2, 5, 6 and 7.

Techniques: Saline, Concentration Assay

Journal: Nature Plants

Article Title: Suppression of plastid-to-nucleus gene transfer by DNA double-strand break repair

doi: 10.1038/s41477-025-02005-w

Figure Lengend Snippet: a , The main pathways of DSBR in eukaryotes. LIG4 and POLQ are the main factors acting in NHEJ and TMEJ, respectively. b , Physical map of the engineered region in the plastid genome of Nt-RB98 plants containing an EGT reporter between the trnfM and trnG genes. nptII is a kanamycin resistance marker under the control of the strong nuclear CaMV (cauliflower mosaic virus) 35S promoter. Cells can become kanamycin resistant only upon translocation of this cassette to the nucleus. The aadA gene is under the control of the strong plastid promoter P rrn and confers constitutive resistance to spectinomycin. c , Plants after 45 days of growth in sterile culture followed by 24 days of growth in soil. The images are representative of three independent cultivation experiments. Scale bar, 20 cm. d , Seedlings germinated in medium containing bleomycin (a DSB-generating drug) at 17 days after sowing. At 0.5 mg l −1 , bleomycin sensitivity is evidenced by pointed cotyledons and the lack of true leaves in the lig4 mutants, whereas in polq mutants, the emerging true leaves (white arrows) are narrow and stunted compared with the Nt-RB98 control (black arrows). At 2.5 mg l −1 bleomycin, lig4 mutants fail to grow, and polq mutants display pointed cotyledons. The images are representative of two independent experiments. Scale bar, 1 cm.

Article Snippet: Surface-sterilized seeds from mutant lines and control tobacco plants were sown directly on medium containing 0, 0.5 or 2.5 mg l −1 bleomycin A5 hydrochloride (1,477.02 g mol −1 ; BLEOCIN Merck KGaA; Cat. No. 203408).

Techniques: Marker, Control, Virus, Translocation Assay, Sterility