Journal: bioRxiv

Article Title: Towards molecular-based functional classification of fetal bovine serum

doi: 10.64898/2026.03.16.712020

Figure Lengend Snippet: (A) Hierarchical clustering dendrograms of FBS conditions based on differential gene expression profiles in MRC-5 (left), Jurkat (middle), and THP-1 (right) cells. Clustering was performed using the number of differentially expressed genes (DEGs; |log2FC| > 0.6, adjusted p-value < 0.05) as a distance metric. Horizontal red lines indicate the clustering threshold of 100 DEGs, defining distinct FBS clusters. MRC-5 and THP-1 cells show 4 distinct clusters, while Jurkat cells display 5 clusters, revealing cell type-specific responses to FBS alternatives. (B) Module size distributions from WGCNA for MRC-5 (left), Jurkat (middle), and THP-1 (right) cells. Bar colors represent distinct co-expression modules identified using signed networks with Pearson correlation (soft-thresholding power selected to achieve scale-free topology R ≥ 0.8; minimum module size = 30 genes; merge cut height = 0.25). MRC-5 cells: 7 modules (turquoise: 4,728 genes; blue: 3,580; brown: 2,417; grey: 936; yellow: 634; green: 447; red: 234). Jurkat cells: 7 modules (turquoise: 4,234; blue: 3,635; grey: 2,289; brown: 1,464; yellow: 660; green: 240; red: 204). THP-1 cells: 5 modules (turquoise: 4,201; blue: 4,16; grey: 2,478; brown: 2,184; yellow: 434). (C) Module-trait relationship heatmaps showing Pearson correlations between module eigengenes and FBS cluster assignments for MRC-5 (left), Jurkat (middle), and THP-1 (right) cells. Each cell displays the correlation coefficient (color scale: blue = -0.5, white = 0, red = 0.5) and corresponding p-value. Significant correlations (p < 0.05, calculated using corPvalueStudent) indicate modules with expression patterns specifically associated with FBS clusters. Notable associations include: MRC-5 turquoise module with Cluster 1 (r = - 0.45, p = 3.22×10 ); Jurkat red module with Cluster 2 (r = 0.76, p = 1.38×10 ); THP-1 yellow module with Cluster 1 (r = 0.65, p = 2.54×10 8).

Article Snippet: The adherent human lung fibroblast cell line MRC-5 (CCL-171), the suspension human monocytic cell line THP-1 (TIB-202), and the human acute T-cell leukemic cell line Jurkat Clone E6-1 (TIB-152) were purchased from American Type Culture Collection (ATCC, USA).

Techniques: Gene Expression, Expressing

Journal: Frontiers in Microbiology

Article Title: Transcription factors Asg1p and Hal9p regulate pH homeostasis in Candida glabrata

doi: 10.3389/fmicb.2015.00843

Figure Lengend Snippet: Strains and plasmids used in this study .

Article Snippet: C. glabrata ATCC 55/ GFP , C. glabrata ATCC 55 (pY13- GFP ) , This study.

Techniques: Mutagenesis

Journal: Frontiers in Microbiology

Article Title: Transcription factors Asg1p and Hal9p regulate pH homeostasis in Candida glabrata

doi: 10.3389/fmicb.2015.00843

Figure Lengend Snippet: Growth assays in different YNB media. (A) Deletion of CgASG1 has no effect on the utilization of non-fermentative carbon sources in C. glabrata . (B) CgAsg1p plays a role under acid-stress conditions. (C) CgHAL9 serves an important role in cell growth under hypersaline conditions in C. glabrata . (D) CgHal9p plays a role under acid-stress conditions. Logarithmic-phase cells of each C. glabrata strain were adjusted to 2 × 10 7 cells/mL, and then 4 μL of serial tenfold dilutions were spotted onto the corresponding YNB media, as indicated. Pictures were taken after 4 days of growth at 30°C.

Article Snippet: C. glabrata ATCC 55/ GFP , C. glabrata ATCC 55 (pY13- GFP ) , This study.

Techniques:

Journal: Frontiers in Microbiology

Article Title: Transcription factors Asg1p and Hal9p regulate pH homeostasis in Candida glabrata

doi: 10.3389/fmicb.2015.00843

Figure Lengend Snippet: Intracellular pH of wild-type, mutant and complemented strains of C. glabrata as below ^a .

Article Snippet: C. glabrata ATCC 55/ GFP , C. glabrata ATCC 55 (pY13- GFP ) , This study.

Techniques: Mutagenesis

Journal: Frontiers in Microbiology

Article Title: Transcription factors Asg1p and Hal9p regulate pH homeostasis in Candida glabrata

doi: 10.3389/fmicb.2015.00843

Figure Lengend Snippet: Quantitative reverse-transcribed PCR (qRT-PCR) validation of transcriptional profiles in an acidic environment . Logarithmic-phase C. glabrata cells were incubated in YNB or YNB-pH 2.0 media for 2 h. qRT-PCR analyses of the indicated genes was performed as described in the Materials and Methods Section. The means and standard deviations for three independent experiments are shown. C. glabrata strains: wild-type, Cgasg1 Δ and Cghal9 Δ strains. ( * P < 0.05 compared to the corresponding wild-type control, as determined by t -test).

Article Snippet: C. glabrata ATCC 55/ GFP , C. glabrata ATCC 55 (pY13- GFP ) , This study.

Techniques: Reverse Transcription, Quantitative RT-PCR, Biomarker Discovery, Incubation, Control

Journal: International Journal of Nanomedicine

Article Title: Preparation, characterization, and transfection efficiency of low molecular weight polyethylenimine-based nanoparticles for delivery of the plasmid encoding CD200 gene

doi: 10.2147/ijn.s140734

Figure Lengend Snippet: Figure 6 Cellular toxicity and transfection efficiency. Notes: Viability and gene transfer ability of unmodified and modified PEI derivatives complexed with pDNA encoding CD200 gene at polymer:plasmid (weight:weight) ratios of 0.25, 4, and 8 determined in triplicate in SH-SY5Y cell cultures in 96-well plates. (A) Cell survival was assayed by the MTT method, and expressed as the percentages of cell viability. (B) CD200 expression level measured by flow cytometry. *P,0.05, PEI derivative compared to unmodified parent polymer at the same C/P ratio. (n=3; error bars represent mean ± standard deviation). Abbreviations: C/P, carrier to plasmid ratio; pDNA, plasmid DNA; PEI, polyethylenimine; PEI-SUC, PEI-succinate conjugate; PEI-SUC-PEI, PEI-succinate-PEI conjugate.

Article Snippet: Human CD200 plasmid (pCMV-XL5-hCD200) was obtained from OriGene (Rockville, MD, USA).

Techniques: Transfection, Modification, Polymer, Plasmid Preparation, Expressing, Flow Cytometry, Standard Deviation

Journal: International Journal of Nanomedicine

Article Title: Preparation, characterization, and transfection efficiency of low molecular weight polyethylenimine-based nanoparticles for delivery of the plasmid encoding CD200 gene

doi: 10.2147/ijn.s140734

Figure Lengend Snippet: Figure 7 In vivo imaging of MS induced mice using fluorescently labeled plasmid encoding CD200 at C/P ratio 8. Notes: Mice were injected with the final volume of 100 μL of the polyplex formulation. (A) The control mice received 100 μL of HBG buffer. (B–I) Mice were injected with the polyplexes and imaging was performed at the time points of 0, 15, 30, 60, 120, 180 min and 24 h post injection. Magnification ×10. Abbreviations: C/P, carrier to plasmid ratio; MS, multiple sclerosis; HBG, HEPES buffered glucose.

Article Snippet: Human CD200 plasmid (pCMV-XL5-hCD200) was obtained from OriGene (Rockville, MD, USA).

Techniques: In Vivo Imaging, Labeling, Plasmid Preparation, Injection, Formulation, Control, Imaging

Journal: Neoplasia (New York, N.Y.)

Article Title: A Truncated form of CD200 (CD200S) Expressed on Glioma Cells Prolonged Survival in a Rat Glioma Model by Induction of a Dendritic Cell-Like Phenotype in Tumor-Associated Macrophages.

doi: 10.1016/j.neo.2016.02.006

Figure Lengend Snippet: Figure 3. Characterization of established cell lines expressing CD200L and CD200S. (A–C) Immunocytochemical confirmation of CD200 expression with antibodies recognizing N- (OX2) or C-termini of CD200. The C6 cell line transfected with an empty vector (A, C6-e) did not display positive immunostaining against either antibody. (B) The C6-L cell line was positive for both antibodies. (C) The C6-S line was only reactive to the C-terminal antibody. (D) qPCR confirmed the specific expression of CD200L or CD200S. A primer set amplifying cDNA derived from both CD200L- and CD200S-mRNA was called common ‘Com’ (see Supplementary Table 1). The other primer set ‘L’ amplified cDNA only derived from CD200L-mRNA. C6-e cells expressed none of the cDNA, C6-L cells expressed both, and C6-S cells expressed cDNA amplified only by the Com primer set. (E) Growth curves of each cell line. Data from four independent cultures are expressed as means ± SD except for the data of Empty at 5 days, which is expressed as mean −SD.

Article Snippet: RNA splicing generates CD200S with a shorter C–C′ loop or CDR2, all of which are responsible for the binding to a cells to generate C6-L or C6-S cell lines. fragments of CD200L or CD200S were amplified by PCR using CD200 cDNA purchased from Origene (Rockville, MD) with the following cloning primers containing BamHI and NotI respectively (see Figure 1): CD200L; forward 5′-GGA TCC ATG GGC AGT CCG GTA TTC AG-3′ and reverse 5′-ATG CGG CCG CTT ATT TCA TTC TTT GCA TCC CCT G-3′, CD200S; forward 5′-ACG GAT CCA TGA TCA CTT ACA GCA AAG CC-3′ and the same reverse primer as for CD200L.

Techniques: Expressing, Transfection, Plasmid Preparation, Immunostaining, Derivative Assay, Amplification

Journal: Neoplasia (New York, N.Y.)

Article Title: A Truncated form of CD200 (CD200S) Expressed on Glioma Cells Prolonged Survival in a Rat Glioma Model by Induction of a Dendritic Cell-Like Phenotype in Tumor-Associated Macrophages.

doi: 10.1016/j.neo.2016.02.006

Figure Lengend Snippet: Figure 7. Expression levels in tumors and isolated TAMs of mRNA encoding molecules related to CD200, DCs, lymphocytes and T cells, as revealed by qPCR. Data are shown in an alphabetical order. (A) cDNA was prepared from tumor masses dissected out 21 days after transplantation. CD200-mRNA amplified with ‘CD200 com’ primers was highly expressed by C6-L and C6-S tumors, whereas the CD200L-mRNA level was high only in the C6-L-tumors. The C6-S-tumors expressed DC markers, MHC class II α, CD11c, and CD80 at significantly higher levels than other tumors. Expression of mRNA encoding lymphocyte markers CD8α and β, CTL-related apoptosis-inducing molecules, granzyme, and perforin was significantly higher in the C6-S tumors. Despite not showing statistical significance, CD4 and IFNγ-mRNA were also highly expressed in the C6-S tumors. CLEC9A, which is expressed by myeloid DCs and responsible for cross-presentation, and chemokines (CCL12, CXCL10 and CXCL16), which are invovlved in recruitment of monocytes and lymphocytes, are also highly expressed in the C6-S tumor. (B) Shortly after isolation from the tumor mass, TAMs were subjected to qPCR analysis. TAMs from the C6-S-tumors expressed MHC class II α-, and CD11c-mRNA was expressed at significantly higher levels than in TAMs from other tumors. CD86-mRNA expression in TAMs from the C6-S tumors was also high. Data from 3 tumors of each cell lines are expressed as means ± SEM. *P b .05, **P b .01, ***P b .001 versus CD200S; #P b .05, ##P b .01 versus CD200L.

Article Snippet: RNA splicing generates CD200S with a shorter C–C′ loop or CDR2, all of which are responsible for the binding to a cells to generate C6-L or C6-S cell lines. fragments of CD200L or CD200S were amplified by PCR using CD200 cDNA purchased from Origene (Rockville, MD) with the following cloning primers containing BamHI and NotI respectively (see Figure 1): CD200L; forward 5′-GGA TCC ATG GGC AGT CCG GTA TTC AG-3′ and reverse 5′-ATG CGG CCG CTT ATT TCA TTC TTT GCA TCC CCT G-3′, CD200S; forward 5′-ACG GAT CCA TGA TCA CTT ACA GCA AAG CC-3′ and the same reverse primer as for CD200L.

Techniques: Expressing, Isolation, Transplantation Assay, Amplification

Journal: Stroke

Article Title: Neuronal CD200 Signaling Is Protective in the Acute Phase of Ischemic Stroke.

doi: 10.1161/STROKEAHA.120.032374

Figure Lengend Snippet: Figure 1. Effects of neuronal CD200 signaling on stroke outcomes and neuronal apoptosis at 3 days after stroke. (A) Representative images of brain slices stained with cresyl violet (CV) and quantification of brain infarct volumes, NDS, and corner test scores in TMX vs. VEH mice. (B) TUNEL labelled cell apoptosis in peri-infarct area of TMX and VEH treated mice and the quantification of percent of TUNEL positive cells in ipsilateral hemispheres Each dot represents the average of % apoptotic cells from eight 20× fields/animal in the peri-infarct area. N=3 for sham and 6–7 for stroke per group; *P < 0.05.

Article Snippet: Determination of CD200 and cytokine Levels The levels of CD200 in mouse brain, plasma and in the supernatants of primary neuronal culture were measured by a sandwich ELISA kit according to manufacture instruction ((# EK1185, Mouse CD200 PicoKine ELISA Kit, Boster Biological, Pleasanton, CA, USA.).

Techniques: Staining, TUNEL Assay

Journal: Stroke

Article Title: Neuronal CD200 Signaling Is Protective in the Acute Phase of Ischemic Stroke.

doi: 10.1161/STROKEAHA.120.032374

Figure Lengend Snippet: Figure 4. Plasma cytokine levels after ischemic injury. Pro-inflammatory (TNFα, IL-1β and IL-6) and anti-inflammatory (IL-10 and IL-4) cytokine levels (pg/mL) were measured in the plasma of VEH and TMX treated sham/stroke mice at 3d (A) and 7d (B). N=5–6 sham and 6–7 stroke animals per group; *P < 0.05. (C) CD200 levels in naïve brains (left), in the plasma (middle) of TMX and VEH treated mice, and in neuronal culture medium after OGD (right). N=5–6 sham and 6–8 stroke animals per group; *P < 0.05. For neuronal culture medium, N=4 independent OGD experiments; *P < 0.05.

Article Snippet: Determination of CD200 and cytokine Levels The levels of CD200 in mouse brain, plasma and in the supernatants of primary neuronal culture were measured by a sandwich ELISA kit according to manufacture instruction ((# EK1185, Mouse CD200 PicoKine ELISA Kit, Boster Biological, Pleasanton, CA, USA.).

Techniques: Clinical Proteomics

Journal: Stroke

Article Title: Neuronal CD200 Signaling Is Protective in the Acute Phase of Ischemic Stroke.

doi: 10.1161/STROKEAHA.120.032374

Figure Lengend Snippet: Figure 5. Stroke outcomes and flow cytometry in CD200 Fc treated mice. (A) Representative images of brain slices stained with cresyl violet (CV) and quantification of brain infarct volumes, NDS, and corner test scores in CD200Fc vs. IgG treated mice. N=3 for sham and 6–7 for stroke per group; *P < 0.05. (B) Microglial expression of cell membrane markers CD68/CD206 measured as mean fluorescence intensity (MFI). (C) Microglial expression of intracellular markers IL-1β/TNFα. For (B) and (C), n=4/sham group and n=6/stroke group; *P < 0.05.

Article Snippet: Determination of CD200 and cytokine Levels The levels of CD200 in mouse brain, plasma and in the supernatants of primary neuronal culture were measured by a sandwich ELISA kit according to manufacture instruction ((# EK1185, Mouse CD200 PicoKine ELISA Kit, Boster Biological, Pleasanton, CA, USA.).

Techniques: Flow Cytometry, Staining, Expressing, Membrane, Fluorescence

Journal: Stroke

Article Title: Neuronal CD200 Signaling Is Protective in the Acute Phase of Ischemic Stroke.

doi: 10.1161/STROKEAHA.120.032374

Figure Lengend Snippet: Figure 6. Interaction of neuronal CD200 with lymphocytic CD200R1. (A) The purity of CD45+CD3+

Article Snippet: Determination of CD200 and cytokine Levels The levels of CD200 in mouse brain, plasma and in the supernatants of primary neuronal culture were measured by a sandwich ELISA kit according to manufacture instruction ((# EK1185, Mouse CD200 PicoKine ELISA Kit, Boster Biological, Pleasanton, CA, USA.).

Techniques:

Journal: Cell

Article Title: A Public BCR Present in a Unique Dual-Receptor-Expressing Lymphocyte from Type 1 Diabetes Patients Encodes a Potent T Cell Autoantigen

doi: 10.1016/j.cell.2019.05.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: IRR-MRC-5 iRRADIATED Fibroblast , American Type Cell Culture (ATCC) , Cat#ATCC 55-X.

Techniques: Purification, Virus, Cell Culture, Recombinant, Gel Extraction, Plasmid Preparation, cDNA Synthesis, Protein Quantitation, Irradiation, Cloning, Amplification, Nested PCR, Expressing, Software