Journal: Microbes and Environments

Article Title: Nitrogen-fixing Ability and Nitrogen Fixation-related Genes of Thermophilic Fermentative Bacteria in the Genus Caldicellulosiruptor

doi: 10.1264/jsme2.ME21018

Figure Lengend Snippet: Nitrogen fixation gene clusters for strain YA01 and its closest relatives, Caldicellulosiruptor hydrothermalis 108 and Caldicellulosiruptor kronotskyensis 2002. The arrow indicates the transcriptional direction.

Article Snippet: Caldicellulosiruptor hydrothermalis 108, Caldicellulosiruptor bescii DSM 6725, and Caldicellulosiruptor kronotskyensis 2002 were obtained from DSMZ (Germany) ( Miroshnichenko et al. , 2008 ; Yang et al. , 2010 ).

Techniques:

Journal: Microbes and Environments

Article Title: Nitrogen-fixing Ability and Nitrogen Fixation-related Genes of Thermophilic Fermentative Bacteria in the Genus Caldicellulosiruptor

doi: 10.1264/jsme2.ME21018

Figure Lengend Snippet: Growth of strain YA01 (A) and its closest species, Caldicellulosiruptor hydrothermalis 108 (B), Caldicellulosiruptor kronotskyensis 2002 (C), Caldicellulosiruptor bescii DSM 6275 (D) with (open symbols) or without (closed symbols) ammonium under a N 2 or Ar atmosphere. Error bars indicate the standard deviation of three replicates.

Article Snippet: Caldicellulosiruptor hydrothermalis 108, Caldicellulosiruptor bescii DSM 6725, and Caldicellulosiruptor kronotskyensis 2002 were obtained from DSMZ (Germany) ( Miroshnichenko et al. , 2008 ; Yang et al. , 2010 ).

Techniques: Standard Deviation

Journal: Microbes and Environments

Article Title: Nitrogen-fixing Ability and Nitrogen Fixation-related Genes of Thermophilic Fermentative Bacteria in the Genus Caldicellulosiruptor

doi: 10.1264/jsme2.ME21018

Figure Lengend Snippet: Acetylene-reducing activities of strain YA01 and its closest relatives, Caldicellulosiruptor hydrothermalis 108 and Caldicellulosiruptor kronotskyensis 2002 in the absence and presence of ammonium at 70°C.

Article Snippet: Caldicellulosiruptor hydrothermalis 108, Caldicellulosiruptor bescii DSM 6725, and Caldicellulosiruptor kronotskyensis 2002 were obtained from DSMZ (Germany) ( Miroshnichenko et al. , 2008 ; Yang et al. , 2010 ).

Techniques: Activity Assay

Journal: Redox Biology

Article Title: SARS-CoV-2 mitochondriopathy in COVID-19 pneumonia exacerbates hypoxemia

doi: 10.1016/j.redox.2022.102508

Figure Lengend Snippet: SARS-CoV-2 infection of Calu-3 human AEC causes mitochondrial fission. A) Calu-3 cells were infected with SARS-CoV-2 for 72 h and then loaded with TMRM, revealing mitochondrial structure (red), and DAPI, identifying the nucleus (blue). Infection causes mitochondrial fission, evident as mitochondrial fragmentation. Scale bar = 10 μm. B–C) Mitochondrial fission was quantified by machine learning, which uses an algorithm to automatically categorize and colour code mitochondria as punctate, intermediate, or filamentous, as described . Quantitative analysis shows that SARS-CoV-2 significantly increases the percentage area of punctate mitochondria and reduces the number of filamentous mitochondria. (**** P < 0.0001; n = 21 cells/group). D-E) Confocal imaging shows increased expression of activated and total Drp1 48 -h post SARS-CoV-2 infection. Tomm 20 is used to image the mitochondria (red) with p-Drp1 S616 and Drp1 imaged in green. Scale bar = 2–15 μm. Representative images (i), 400% zoom (ii) and mean data (iii) are shown. (*** P < 0.001 n = 5/group). The mean data in panel iii derive from analysis of the low power images (Di and Ei). Note the increase in p-Drp1 S616 primarily occurs in the mitochondria, seen as increased yellow (from red/green colocalization in low power images, Di) and seen directly on high power STED images (Dii), with most green p-Drp1 S616 localizing to the mitochondrial outer membrane, F–I) Immunoblot confirms that SARS-CoV-2 infection increases the expression of activated Drp1, increases the expression of the apoptosis mediator AIF and activates caspase 7. (F) Marked increase in SASR-CoV-2 N protein expression only in infected cells confirms infection. The Calu-3 cells were harvested for immunoblot analyses after 48 h of infection with SARs-C0V-2. Representative image of the immunoblots and the densitometry of the expressions of (G) p-Drp1 ser616 , (H) AIF and (I) cleaved caspase 7. (* P < 0.05; ** P < 0.01; n = 3–5 technical replicates/group).

Article Snippet: The following antibodies were used: Cell Signaling Technologies (Beverly MA, USA) - Bid 2002S, AIF (1D39D2), SMAC/Diablo (D5S3R), and Caspase 1 (2225S), phospho-DRP serine 616 (3455S); Proteintech, Tucson, AZ, USA), cyclin dependent kinase 4, CDK4 (110026-1-AP).

Techniques: Infection, Imaging, Expressing, Western Blot

Journal: Redox Biology

Article Title: SARS-CoV-2 mitochondriopathy in COVID-19 pneumonia exacerbates hypoxemia

doi: 10.1016/j.redox.2022.102508

Figure Lengend Snippet: HCoV-OC43 infection increases expression of apoptosis mediators and reduces oxidative metabolism in BEAS-2B cells and causes mitochondrial fission in HPAEC Assessment of the effects of HCoV-OC43 infection of BEAS-2B cells and HPAEC occurred at 72 h post infection. A) HCoV-OC43 infection increases expression of apoptosis and mitochondrial fission mediators in BEAS-2B cells. Representative immunoblots and densitometry i) confirming infection with HCoV-OC43 (inset showing viral N-protein only in infected cells). Infection of human AEC upregulates ii) mediators of mitochondrial fission (total and activated Drp1, p-Drp1 S616 ). iii) downregulates CDK4, a cyclin dependent kinase responsible for cell cycle progression. iv-vii) upregulates apoptosis mediators (Smac/Diablo, Caspase 1, Bid, and AIF). * P < 0.05; ** P < 0.01; *** P < 0.001; n = 3/group. viii) Using STED microscopy at 50 nm resolution, coronavirus HCov-OC43 (green; nucleoprotein-targeted antibody) colocalizes with AIF (yellow) on the mitochondrial outer membrane (red) in AEC; AIF expression is also increased in infected cells (bottom) versus mock cells in these images (top), as in the immunoblot (vii). Scale bar = 1–5 μm B) HCoV-OC43 infection inhibits oxidative metabolism and increases mitochondrial fission in BEAS-2B cells i-iv) Infection of human AEC with HCoV-OC43, inhibits basal and FCCP-stimulated maximal respiration and ATP-linked OCR, as measured by micropolarimetry. * P < 0.05; n = 5/group. v) Infection with HCoV-OC43 reduces ATP concentration in BEAS-2B cells. * P < 0.05; n = 9/group. vi) Infection with HCoV-OC43 inhibits ETC Complex I activity in BEAS-2B cells. *** P < 0.001; n = 5/group. vii-viii) TEM shows that mitochondria in infected cells are more swollen with increased intercristal space. **** P < 0.0001; n = 39 mitochondria/group. ix) TEM shows HCoV-OC43 virus in an intracellular vesicle. C) HCoV-OC43 fragments mitochondria in HPAEC. Infection of HPAEC with HCoV-OC43 causes mitochondrial fission (more punctate mitochondria in infected cells on right vs control cells on left). The mitochondrial network is red (loaded with the potentiometric dye tetra methylrhodamine, TMRM). We used machine learning to allow a computer algorithm to classify mitochondria as punctate, intermediate, or filamentous, as described . Infection increases the percentage area of intermediate and punctate mitochondria, consistent with induction of mitochondrial fission. ** P < 0.01, **** P < 0.0001; n = 20 cells/group.

Article Snippet: The following antibodies were used: Cell Signaling Technologies (Beverly MA, USA) - Bid 2002S, AIF (1D39D2), SMAC/Diablo (D5S3R), and Caspase 1 (2225S), phospho-DRP serine 616 (3455S); Proteintech, Tucson, AZ, USA), cyclin dependent kinase 4, CDK4 (110026-1-AP).

Techniques: Infection, Expressing, Western Blot, Microscopy, Concentration Assay, Activity Assay

Journal: Oncology Letters

Article Title: Identification of a novel FOXO3‑associated prognostic model in hepatocellular carcinoma

doi: 10.3892/ol.2025.14976

Figure Lengend Snippet: Identification of the 5-gene signature. (A) Forest plot of univariate Cox regression analysis in The Cancer Genome Atlas dataset. Cox results for the top five and bottom five genes. (B) Least absolute shrinkage and selection operator regression analysis. (C) λ curves show the least absolute shrinkage and the best λ was selected based on the minimum criteria. (D) The protein-protein interaction network between FOXO3 and 294 genes. FOXO3, DDX55, RAB10, RAB7A, TAF1B and TAF3 are highlighted by red dots and the remaining genes are represented by green dots. The color of the edges was determined by the combined score obtained from STRING. FOXO3, Forkhead box O3; DDX55, DEAD-box helicase 55; RAB10, RAB10, member RAS oncogene family; RAB7A, RAB7A, member RAS oncogene family; TAF1B, TATA-box binding protein associated factor, RNA polymerase I subunit B; TAF3, TATA-box binding protein associated factor 3; SLC4A1AP, solute carrier family 4 member 1 adaptor protein; ZNF765, zinc finger protein 765; MORC3, MORC family CW-type zinc finger 3; WWC2, WW and C2 domain containing 2; UBE3A, ubiquitin protein ligase E3A; SECISBP2L, SECIS binding protein 2 like; FAN1, FANCD2 And FANCI associated nuclease 1.

Article Snippet: The following antibodies were used: β-actin (1:1,000; cat. no. ET1702-52; HUABIO), DDX55 (1:1,000; cat. no. ER63225; HUABIO), RAB10 (1:1,000; cat. no. 11808-1-AP; Proteintech Group, Inc.), RAB7A (1:1,500; cat. no. 55469-1-AP; Proteintech Group, Inc.), TAF1B (1:500; cat. no. 12818-1-AP; Proteintech Group, Inc.), FOXO3 (1:1,000; cat. no. A9270; ABclonal Biotech Co., Ltd.) and TAF3 (1:500; cat. no. 18901-1-AP; Proteintech Group, Inc.), HRP conjugated goat anti-rabbit IgG polyclonal antibody (1:30000, HA1001, HUABIO), HRP conjugated goat anti-mouse IgG polyclonal antibody (1:30,000, HA1006, HUABIO).

Techniques: Selection, Binding Assay, Ubiquitin Proteomics

Journal: Oncology Letters

Article Title: Identification of a novel FOXO3‑associated prognostic model in hepatocellular carcinoma

doi: 10.3892/ol.2025.14976

Figure Lengend Snippet: Construction and validation of a 5-gene prognostic model. (A) The distribution of RS, survival status and expression of the 5-gene signature between the high- and low-risk groups in TCGA dataset. (B) Overall survival of patients with HCC in the high- and low- RS groups in TCGA dataset. (C) Time-dependent ROC curve of RS in TCGA dataset. (D) The distribution of RS, survival status and expression of the 5-gene signature between the high- and low-risk groups in the ICGC dataset. (E) Overall survival of patients with HCC in the high- and low-RS groups in the ICGC dataset. (F) Time-dependent ROC curve of RS in the ICGC dataset. RS, risk score; TCGA, The Cancer Genome Atlas; ICGC, International Cancer Genome Consortium; ROC, receiver operating characteristic; DDX55, DEAD-box helicase 55; RAB10, RAB10, member RAS oncogene family; RAB7A, RAB7A, member RAS oncogene family; TAF1B, TATA-box binding protein associated factor, RNA polymerase I subunit B; TAF3, TATA-box binding protein associated factor 3; AUC, area under the curve.

Article Snippet: The following antibodies were used: β-actin (1:1,000; cat. no. ET1702-52; HUABIO), DDX55 (1:1,000; cat. no. ER63225; HUABIO), RAB10 (1:1,000; cat. no. 11808-1-AP; Proteintech Group, Inc.), RAB7A (1:1,500; cat. no. 55469-1-AP; Proteintech Group, Inc.), TAF1B (1:500; cat. no. 12818-1-AP; Proteintech Group, Inc.), FOXO3 (1:1,000; cat. no. A9270; ABclonal Biotech Co., Ltd.) and TAF3 (1:500; cat. no. 18901-1-AP; Proteintech Group, Inc.), HRP conjugated goat anti-rabbit IgG polyclonal antibody (1:30000, HA1001, HUABIO), HRP conjugated goat anti-mouse IgG polyclonal antibody (1:30,000, HA1006, HUABIO).

Techniques: Biomarker Discovery, Expressing, Binding Assay

Journal: Oncology Letters

Article Title: Identification of a novel FOXO3‑associated prognostic model in hepatocellular carcinoma

doi: 10.3892/ol.2025.14976

Figure Lengend Snippet: Identification of five biomarkers in HCC. (A) mRNA expression of DDX55, RAB10, RAB7A, TAF1B and TAF3 in HCC and normal tissues from TCGA. Overall survival curves in patients with HCC with high or low expression of (B) DDX55, (C) RAB10, (D) RAB7A, (E) TAF1B and (F) TAF3 from TCGA dataset. The best cut-off value for each gene was obtained using the X-tile software. (G) mRNA expression of DDX55, RAB10, RAB7A, TAF1B and TAF3 in HCC and paired paracancerous tissues from 10 patients with HCC, assessed using reverse transcription-quantitative PCR. (H) Immunohistochemical images of DDX55, RAB10 and RAB7A in HCC and normal tissues obtained from the HPA. (I) Protein expression of DDX55, RAB10, RAB7A, TAF1B and TAF3 in HCC and paired paracancerous tissues from 10 patients with HCC, evaluated using western blot analysis. The figure on the right is a relative semi-quantitative histogram of protein expression. The gray values were obtained by ImageJ and analyzed using GraphPad Prism. (J) Cell Counting Kit-8 curves after knockdown of RAB10, RAB7A and TAF3 in Huh7 cells by siRNA. *P<0.05; **P<0.01; ***P<0.001; ****P<0.0001. T, tumor; NT, not-tumor; HCC, hepatocellular carcinoma; TCGA, The Cancer Genome Atlas; DDX55, DEAD-box helicase 55; RAB10, RAB10, member RAS oncogene family; RAB7A, RAB7A, member RAS oncogene family; TAF1B, TATA-box binding protein associated factor, RNA polymerase I subunit B; TAF3, TATA-box binding protein associated factor 3; HPA, The Human Protein Atlas; NC, negative control.

Article Snippet: The following antibodies were used: β-actin (1:1,000; cat. no. ET1702-52; HUABIO), DDX55 (1:1,000; cat. no. ER63225; HUABIO), RAB10 (1:1,000; cat. no. 11808-1-AP; Proteintech Group, Inc.), RAB7A (1:1,500; cat. no. 55469-1-AP; Proteintech Group, Inc.), TAF1B (1:500; cat. no. 12818-1-AP; Proteintech Group, Inc.), FOXO3 (1:1,000; cat. no. A9270; ABclonal Biotech Co., Ltd.) and TAF3 (1:500; cat. no. 18901-1-AP; Proteintech Group, Inc.), HRP conjugated goat anti-rabbit IgG polyclonal antibody (1:30000, HA1001, HUABIO), HRP conjugated goat anti-mouse IgG polyclonal antibody (1:30,000, HA1006, HUABIO).

Techniques: Expressing, Software, Reverse Transcription, Real-time Polymerase Chain Reaction, Immunohistochemical staining, Western Blot, Cell Counting, Knockdown, Binding Assay, Negative Control

Journal: Cancer Science

Article Title: Hypoxia‐inducible hexokinase‐2 enhances anti‐apoptotic function via activating autophagy in multiple myeloma

doi: 10.1111/cas.14614

Figure Lengend Snippet: Cooperative effect of HK2 knockdown and proteasome inhibitor in vivo. A, qRT‐PCR analysis of HK2 for KMS‐11 stably transduced with shHK2 #A, #B, #C, #D, and control scrambled shRNA (Scr). B, Western blot analysis of HK2 for KMS‐11 stably transduced with shHK2 #A, #B, #C, #D, and control scrambled shRNA (Scr). C, qRT‐PCR analysis of HK1 , HK2 , HK3 , and HK4 for KMS‐11 stably transduced with shHK2 #D or control scrambled shRNA (Scr). D, Illustration of the protocol of the in vivo transplantation and treatment; 1 × 10 6 of shHK2 #D or control shRNA stably transduced KMS‐11 were inoculated into NOG mice. Mice were treated with bortezomib (1.0 mg/kg) or phosphate‐buffered saline intraperitoneally. Scr‐vehicle; n = 8, Scr‐BTZ; n = 10, shHK2‐vehicle; n = 8, and shHK2‐BTZ; n = 10. BTZ, bortezomib. E, Tumor growth curves of each groups are shown. x ‐axis, days after transplantation (days); y ‐axis, tumor volume (mm 3 , major × minor 2 /2). Right panel: rates of tumor volume reduction by bortezomib (BTZ) administration for the Scr group and shHK2 group. F, Photograph of tumors from each group are shown. G, Tumor weights of each groups are shown. Asterisks indicate statistical significance: *.01 ≤ P < .05; *** P < .001; NS, not significant.

Article Snippet: Bortezomib (021‐18901) was purchased from FUJIFILM Wako Pure Chemical.

Techniques: Knockdown, In Vivo, Quantitative RT-PCR, Stable Transfection, Transduction, Control, shRNA, Western Blot, Transplantation Assay, Saline

Journal: Cancer Science

Article Title: Hypoxia‐inducible hexokinase‐2 enhances anti‐apoptotic function via activating autophagy in multiple myeloma

doi: 10.1111/cas.14614

Figure Lengend Snippet: Complementary effect of bortezomib and 3‐BrPA under chronic hypoxia in vitro. A, Apoptosis assay of KMS‐11, MM.1S, and normal peripheral blood mononuclear cells (PBMC). Cells were cultured in normoxia or hypoxia (1% O 2 ) for 48 h, and then 3‐bromopyruvate (3‐BrPA; 0, 20, 50, or 100 µmol/L) was added in the medium during 24 h. After the treatment, apoptosis assay was conducted. Left panel: x ‐axis: Annexin V; y ‐axis: 7‐AAD. B, Apoptosis assay of indicated cell lines and a refractory MM sample. Cells were cultured in normoxia or hypoxia (1% O 2 ) for 24 h, and then bortezomib (for cell lines: 10 nmol/L, for patient sample: 50 nmol/L) and/or 3‐BrPA (20 µmol/L) were added in the medium during 24 h. After the treatment, apoptosis assay was conducted. Upper left panel: x ‐axis: Annexin V; y ‐axis: 7‐AAD. Asterisks indicate statistical significance: *.01 ≤ P < .05; **.001 ≤ P < .01; *** P < .001; NS, not significant

Article Snippet: Bortezomib (021‐18901) was purchased from FUJIFILM Wako Pure Chemical.

Techniques: In Vitro, Apoptosis Assay, Cell Culture