Structured Review

Promega m mlv reverse transcriptase
Phenotypes of the lpa2 mutant compared with wild type and complemented lines. (A) Alignment of LPA2 amino acid sequences from different organisms. Predicted chloroplast transit peptides are shown in gray; predicted transmembrane helices are underlined and indicated with pipes. Peptides identified by mass spectrometry are in red letters, twin-arginines in bold letters. Ath, Arabidopsis (AT5G51545); Zma, Zea mays (NP_001145487); Psi, Picea sitchensis (ABK23742); Ppa, Physcomitrella patens (XP_024366975); Cva, Chlorella variabilis (XP_005849843); Ota, Ostreococcus tauri (XP_003084445); Cre, Chlamydomonas reinhardtii (Cre02.g105650). (B) Structure of the Chlamydomonas LPA2 gene, insertion site of the CIB1 cassette in the lpa2 mutant, and construct for complementation. Protein coding regions are shown as black boxes, untranslated regions as bars, and introns and promoter regions as thin lines. Arrows indicate transcriptional start sites. The purple box indicates a 165-bp fragment derived from the 19th intron of gene Cre13.g573450 in <t>reverse</t> orientation that has integrated with the CIB1 cassette. (C) qRT-PCR analysis of LPA2 transcript accumulation in the lpa2 mutant and two complemented lines expressing the LPA2 cDNA without (c10, c11) or with a 3×HA coding region (cHA) relative to the wild type. Values are means from two independent biological replicates normalized against CBLP2 (circles) or TUB1 (diamonds). Error bars indicate SD. (D) Comparison of F v / F <t>m</t> values. Values are averages from three to four independent experiments; error bars indicate SD. Significant differences were assessed via two-tailed, unpaired Student’s t -test with Bonferroni–Holm correction (* P
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1) Product Images from "Complexome profiling on the Chlamydomonas lpa2 mutant reveals insights into PSII biogenesis and new PSII associated proteins"

Article Title: Complexome profiling on the Chlamydomonas lpa2 mutant reveals insights into PSII biogenesis and new PSII associated proteins

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/erab390

Phenotypes of the lpa2 mutant compared with wild type and complemented lines. (A) Alignment of LPA2 amino acid sequences from different organisms. Predicted chloroplast transit peptides are shown in gray; predicted transmembrane helices are underlined and indicated with pipes. Peptides identified by mass spectrometry are in red letters, twin-arginines in bold letters. Ath, Arabidopsis (AT5G51545); Zma, Zea mays (NP_001145487); Psi, Picea sitchensis (ABK23742); Ppa, Physcomitrella patens (XP_024366975); Cva, Chlorella variabilis (XP_005849843); Ota, Ostreococcus tauri (XP_003084445); Cre, Chlamydomonas reinhardtii (Cre02.g105650). (B) Structure of the Chlamydomonas LPA2 gene, insertion site of the CIB1 cassette in the lpa2 mutant, and construct for complementation. Protein coding regions are shown as black boxes, untranslated regions as bars, and introns and promoter regions as thin lines. Arrows indicate transcriptional start sites. The purple box indicates a 165-bp fragment derived from the 19th intron of gene Cre13.g573450 in reverse orientation that has integrated with the CIB1 cassette. (C) qRT-PCR analysis of LPA2 transcript accumulation in the lpa2 mutant and two complemented lines expressing the LPA2 cDNA without (c10, c11) or with a 3×HA coding region (cHA) relative to the wild type. Values are means from two independent biological replicates normalized against CBLP2 (circles) or TUB1 (diamonds). Error bars indicate SD. (D) Comparison of F v / F m values. Values are averages from three to four independent experiments; error bars indicate SD. Significant differences were assessed via two-tailed, unpaired Student’s t -test with Bonferroni–Holm correction (* P
Figure Legend Snippet: Phenotypes of the lpa2 mutant compared with wild type and complemented lines. (A) Alignment of LPA2 amino acid sequences from different organisms. Predicted chloroplast transit peptides are shown in gray; predicted transmembrane helices are underlined and indicated with pipes. Peptides identified by mass spectrometry are in red letters, twin-arginines in bold letters. Ath, Arabidopsis (AT5G51545); Zma, Zea mays (NP_001145487); Psi, Picea sitchensis (ABK23742); Ppa, Physcomitrella patens (XP_024366975); Cva, Chlorella variabilis (XP_005849843); Ota, Ostreococcus tauri (XP_003084445); Cre, Chlamydomonas reinhardtii (Cre02.g105650). (B) Structure of the Chlamydomonas LPA2 gene, insertion site of the CIB1 cassette in the lpa2 mutant, and construct for complementation. Protein coding regions are shown as black boxes, untranslated regions as bars, and introns and promoter regions as thin lines. Arrows indicate transcriptional start sites. The purple box indicates a 165-bp fragment derived from the 19th intron of gene Cre13.g573450 in reverse orientation that has integrated with the CIB1 cassette. (C) qRT-PCR analysis of LPA2 transcript accumulation in the lpa2 mutant and two complemented lines expressing the LPA2 cDNA without (c10, c11) or with a 3×HA coding region (cHA) relative to the wild type. Values are means from two independent biological replicates normalized against CBLP2 (circles) or TUB1 (diamonds). Error bars indicate SD. (D) Comparison of F v / F m values. Values are averages from three to four independent experiments; error bars indicate SD. Significant differences were assessed via two-tailed, unpaired Student’s t -test with Bonferroni–Holm correction (* P

Techniques Used: Mutagenesis, Mass Spectrometry, Construct, Derivative Assay, Quantitative RT-PCR, Expressing, Two Tailed Test

2) Product Images from "Oxygen Regulates Human Pluripotent Stem Cell Metabolic Flux"

Article Title: Oxygen Regulates Human Pluripotent Stem Cell Metabolic Flux

Journal: Stem Cells International

doi: 10.1155/2019/8195614

Global acetylation is increased, and methylation is decreased at 5% oxygen. (a) H3K9ac, H3K27ac, and K3K27me3 fold change of MEL2 hPSC at 5% relative to 20% oxygen. Scale is 50 μ m. (b) Workflow for RNA-seq analysis using https://usegalaxy.org/ , DAVID, and NetworkAnalayst. (c) Venn diagrams showing the overlap of genes upregulated in two hPSC lines at 5% oxygen and 20% oxygen and total DEG count. (d) Functional clusters with enrichment scores greater than 2 derived from Biological Process and Molecular Function GO terms. (e) Volcano plot of MEL2 hPSC transcriptional response to 5% and 20% oxygen. Red genes indicate a fold change value greater than 2 and an adjusted p value (Benjamini FDR) less than 0.05. All assays performed in biological triplicate. Error bars represent the SEM. ∗∗∗∗ p
Figure Legend Snippet: Global acetylation is increased, and methylation is decreased at 5% oxygen. (a) H3K9ac, H3K27ac, and K3K27me3 fold change of MEL2 hPSC at 5% relative to 20% oxygen. Scale is 50 μ m. (b) Workflow for RNA-seq analysis using https://usegalaxy.org/ , DAVID, and NetworkAnalayst. (c) Venn diagrams showing the overlap of genes upregulated in two hPSC lines at 5% oxygen and 20% oxygen and total DEG count. (d) Functional clusters with enrichment scores greater than 2 derived from Biological Process and Molecular Function GO terms. (e) Volcano plot of MEL2 hPSC transcriptional response to 5% and 20% oxygen. Red genes indicate a fold change value greater than 2 and an adjusted p value (Benjamini FDR) less than 0.05. All assays performed in biological triplicate. Error bars represent the SEM. ∗∗∗∗ p

Techniques Used: Methylation, RNA Sequencing Assay, Functional Assay, Derivative Assay

3) Product Images from "Genome-Wide Identification, Classification and Expression Analysis of m6A Gene Family in Solanum lycopersicum"

Article Title: Genome-Wide Identification, Classification and Expression Analysis of m6A Gene Family in Solanum lycopersicum

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms23094522

Chromosomal location and collinearity analysis of the m 6 A genes in tomato. ( A ) Locations of the m 6 A genes in tomato chromosomes. The scale at the left side of the figure is shown in Mb. The number of each chromosome is indicated at the top of the corresponding chromosome. ( B ) Synteny analysis of the m 6 A genes in tomato. The gray lines represent the collinearity result of the tomato genome, and the red lines represent the segmental duplication events. ( C ) Synteny analysis of the m 6 A genes between tomato and Arabidopsis . The gray lines represent the collinearity result between tomato and Arabidopsis genomes, and the red lines represent homologous gene pairs.
Figure Legend Snippet: Chromosomal location and collinearity analysis of the m 6 A genes in tomato. ( A ) Locations of the m 6 A genes in tomato chromosomes. The scale at the left side of the figure is shown in Mb. The number of each chromosome is indicated at the top of the corresponding chromosome. ( B ) Synteny analysis of the m 6 A genes in tomato. The gray lines represent the collinearity result of the tomato genome, and the red lines represent the segmental duplication events. ( C ) Synteny analysis of the m 6 A genes between tomato and Arabidopsis . The gray lines represent the collinearity result between tomato and Arabidopsis genomes, and the red lines represent homologous gene pairs.

Techniques Used:

The amount of m 6 A and m 6 Am in tomato leaves by LC-MS/MS analysis. The changes in ( A ) m 6 A and ( B ) m 6 Am contents under cold and heat treatment. The 30-day-old tomato seedlings were treated under cold and heat conditions for 48 h. * Refer to significant differences with p
Figure Legend Snippet: The amount of m 6 A and m 6 Am in tomato leaves by LC-MS/MS analysis. The changes in ( A ) m 6 A and ( B ) m 6 Am contents under cold and heat treatment. The 30-day-old tomato seedlings were treated under cold and heat conditions for 48 h. * Refer to significant differences with p

Techniques Used: Liquid Chromatography with Mass Spectroscopy

Expression profiles of tomato m 6 A genes in different abiotic stress by qPCR analysis. The 30-day-old tomato seedlings were treated under cold and heat conditions for 12, 24, and 48 h. Tomato seedlings were treated under drought and salt condition for 1, 7, and 14 d. Tomato seedlings without treatment was considered the control. Each value represents the mean ± SE of three replicates.
Figure Legend Snippet: Expression profiles of tomato m 6 A genes in different abiotic stress by qPCR analysis. The 30-day-old tomato seedlings were treated under cold and heat conditions for 12, 24, and 48 h. Tomato seedlings were treated under drought and salt condition for 1, 7, and 14 d. Tomato seedlings without treatment was considered the control. Each value represents the mean ± SE of three replicates.

Techniques Used: Expressing, Real-time Polymerase Chain Reaction

Heat map representation of the tomato m 6 A genes in various tissues. ( A ) Expression levels of tomato m 6 A genes in Heinz 1706 tomato based on transcriptome expression data. Each column represents a different tissue at different developmental stages of tomato. The bar on the right indicates normalized expression data from high to low (red to green). ( B ) STEM analysis. The expression data of each gene in root was normalized as 0. ( C , D ) Expression of SlYTHDF1 and SlYTHDF3A in different tissues of Ailsa Craig tomato. RT, root; ST, stem; YL, young leaf; ML, mature leaf; SL, senescent leaf; SE, sepal; FL, flower; IMG, immature green; MG, mature green; B, breaker stage; B+4, 4 days after breaker stage; B+7, 7 days after breaker stage. Data are the mean ± SE of three independent experiments.
Figure Legend Snippet: Heat map representation of the tomato m 6 A genes in various tissues. ( A ) Expression levels of tomato m 6 A genes in Heinz 1706 tomato based on transcriptome expression data. Each column represents a different tissue at different developmental stages of tomato. The bar on the right indicates normalized expression data from high to low (red to green). ( B ) STEM analysis. The expression data of each gene in root was normalized as 0. ( C , D ) Expression of SlYTHDF1 and SlYTHDF3A in different tissues of Ailsa Craig tomato. RT, root; ST, stem; YL, young leaf; ML, mature leaf; SL, senescent leaf; SE, sepal; FL, flower; IMG, immature green; MG, mature green; B, breaker stage; B+4, 4 days after breaker stage; B+7, 7 days after breaker stage. Data are the mean ± SE of three independent experiments.

Techniques Used: Expressing

4) Product Images from "Inhibition of Ras1-MAPK pathways for hypha formation by novel drug candidates in Candida albicans"

Article Title: Inhibition of Ras1-MAPK pathways for hypha formation by novel drug candidates in Candida albicans

Journal: bioRxiv

doi: 10.1101/2021.07.06.451239

The effects of small molecules B and C on the expression of HSG, Ume6, and Nrg1 genes. (A) Total RNA of yeast cells (Y), the small molecules treated hyphae-induced cells (HB, HC), or hyphae-induced cells (H) were isolated using the TRIzol reagent method. Total RNA was measured using Nanodrop Spectrophotometer and was reverse transcribed into cDNAs using oligo-d(T) and M-MLV reverse transcriptase. Real-time PCR was performed with the specific primers listed in Table 2 . (B) Immunoblotting was performed by preparing protein samples for 0–4 h, and Real-time PCR (C) was performed as previously described using the Nrg1-myc strain. (D) Immunoblotting was performed by preparing protein samples for 0– 4 h, and Real-time PCR (E) was performed as described above using the Ume6-myc strain. Western blotting was performed with an anti-myc antibody to detect Nrg1-myc and Ume6-myc. In the western blotting, β-actin was used as a loading control by detecting with the anti-β-actin antibody. Each experiment was conducted in triplicate. The data represent the mean and standard deviation of three independent experiments. *; P
Figure Legend Snippet: The effects of small molecules B and C on the expression of HSG, Ume6, and Nrg1 genes. (A) Total RNA of yeast cells (Y), the small molecules treated hyphae-induced cells (HB, HC), or hyphae-induced cells (H) were isolated using the TRIzol reagent method. Total RNA was measured using Nanodrop Spectrophotometer and was reverse transcribed into cDNAs using oligo-d(T) and M-MLV reverse transcriptase. Real-time PCR was performed with the specific primers listed in Table 2 . (B) Immunoblotting was performed by preparing protein samples for 0–4 h, and Real-time PCR (C) was performed as previously described using the Nrg1-myc strain. (D) Immunoblotting was performed by preparing protein samples for 0– 4 h, and Real-time PCR (E) was performed as described above using the Ume6-myc strain. Western blotting was performed with an anti-myc antibody to detect Nrg1-myc and Ume6-myc. In the western blotting, β-actin was used as a loading control by detecting with the anti-β-actin antibody. Each experiment was conducted in triplicate. The data represent the mean and standard deviation of three independent experiments. *; P

Techniques Used: Expressing, Isolation, Spectrophotometry, Real-time Polymerase Chain Reaction, Western Blot, Standard Deviation

5) Product Images from "Pharmacological Perturbation of Mechanical Contractility Enables Robust Transdifferentiation of Human Fibroblasts into Neurons, Pharmacological Perturbation of Mechanical Contractility Enables Robust Transdifferentiation of Human Fibroblasts into Neurons"

Article Title: Pharmacological Perturbation of Mechanical Contractility Enables Robust Transdifferentiation of Human Fibroblasts into Neurons, Pharmacological Perturbation of Mechanical Contractility Enables Robust Transdifferentiation of Human Fibroblasts into Neurons

Journal: Advanced Science

doi: 10.1002/advs.202104682

Enhancing lineage specialization promotes neuronal maturation. A) Schematic of the strategy to convert human foreskin fibroblasts (HFFs) into neurons using (−)‐blebbistatin (Ble) and ISX‐9 (top panel). Cd‐iNs displayed complex neuronal morphologies and expressed TUJ1, MAP2, NEUN, and NF200 at day 30 (bottom). Scale bar, 50 µm. B) Quantitation of TUJ1, MAP2, NEUN, and NF200‐positive cells relative to Hoechst‐stained cells at day 30. n = 10 randomly selected fields from three repeated experiments. C) Neuron‐like HFF cells expressed SYT1 and PSD95 after Ble and ISX‐9 treatment for 22 days. Scale bar, 50 µm. D) Current‐clamp recordings of Cd‐iNs showed a representative train of action potentials. E) The portion of multi‐spike peaks in (D) ( n = 15). F) Representative traces showing Na + and K + currents recorded from Cd‐iNs (left panel). Tetrodotoxin (10 µ m ) treatment inhibited voltage‐dependent sodium currents (right panel). G) Quantitative evaluation of inward current and outward current in (F). n = 11 for inward current, n = 10 for outward current. H) Gene ontology analysis of genes upregulated in Cd‐iNs (D30/D45). The font size represents p‐ values. I) Principal component analysis of single‐cell transcriptomes from day 0 (D0), 3 and 6 h, D1, D2, D7, D14, D30, and D45 Cd‐iNs and human primary neurons (Neurons 1–6). J) Violin plot showing RNA‐seq‐derived distribution of the neuronal marker NEFH during transdifferentiation across the indicated time points. Data represent means ± SEM. *** p
Figure Legend Snippet: Enhancing lineage specialization promotes neuronal maturation. A) Schematic of the strategy to convert human foreskin fibroblasts (HFFs) into neurons using (−)‐blebbistatin (Ble) and ISX‐9 (top panel). Cd‐iNs displayed complex neuronal morphologies and expressed TUJ1, MAP2, NEUN, and NF200 at day 30 (bottom). Scale bar, 50 µm. B) Quantitation of TUJ1, MAP2, NEUN, and NF200‐positive cells relative to Hoechst‐stained cells at day 30. n = 10 randomly selected fields from three repeated experiments. C) Neuron‐like HFF cells expressed SYT1 and PSD95 after Ble and ISX‐9 treatment for 22 days. Scale bar, 50 µm. D) Current‐clamp recordings of Cd‐iNs showed a representative train of action potentials. E) The portion of multi‐spike peaks in (D) ( n = 15). F) Representative traces showing Na + and K + currents recorded from Cd‐iNs (left panel). Tetrodotoxin (10 µ m ) treatment inhibited voltage‐dependent sodium currents (right panel). G) Quantitative evaluation of inward current and outward current in (F). n = 11 for inward current, n = 10 for outward current. H) Gene ontology analysis of genes upregulated in Cd‐iNs (D30/D45). The font size represents p‐ values. I) Principal component analysis of single‐cell transcriptomes from day 0 (D0), 3 and 6 h, D1, D2, D7, D14, D30, and D45 Cd‐iNs and human primary neurons (Neurons 1–6). J) Violin plot showing RNA‐seq‐derived distribution of the neuronal marker NEFH during transdifferentiation across the indicated time points. Data represent means ± SEM. *** p

Techniques Used: Quantitation Assay, Staining, RNA Sequencing Assay, Derivative Assay, Marker

6) Product Images from "A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing"

Article Title: A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkt1256

VP5 facilitates RT initiation via a CPV panhandle. ( A ) Schematic illustrations of the predicted panhandle structure formed by 36 bases from the 5′-end and 30 bases from the 3′-end of HaCPV-5 RNA segment 8 (upper panel) and the primer complementary to the 3′-end of the panhandle (lower panel). ( B ) The RT reactions were conducted using the RNA panhandle structure and the DNA primer in the presence of M-MLV reverse transcriptase for 30 min at 25°C in the absence (lanes 1 and 4) or presence of MBP-VP5 (lane 2) or MBP alone (lane 3). For lane 1, the panhandle and primer were prehybridized via a thermal annealing treatment at 68°C before the reaction. ( C ) The RT reactions were conducted using the indicated amounts of RNA panhandles in the presence of indicated amounts of MBP-VP5 for 30 min at 25°C. The samples were analyzed on 6% urea PAGE, followed by northern blotting.
Figure Legend Snippet: VP5 facilitates RT initiation via a CPV panhandle. ( A ) Schematic illustrations of the predicted panhandle structure formed by 36 bases from the 5′-end and 30 bases from the 3′-end of HaCPV-5 RNA segment 8 (upper panel) and the primer complementary to the 3′-end of the panhandle (lower panel). ( B ) The RT reactions were conducted using the RNA panhandle structure and the DNA primer in the presence of M-MLV reverse transcriptase for 30 min at 25°C in the absence (lanes 1 and 4) or presence of MBP-VP5 (lane 2) or MBP alone (lane 3). For lane 1, the panhandle and primer were prehybridized via a thermal annealing treatment at 68°C before the reaction. ( C ) The RT reactions were conducted using the indicated amounts of RNA panhandles in the presence of indicated amounts of MBP-VP5 for 30 min at 25°C. The samples were analyzed on 6% urea PAGE, followed by northern blotting.

Techniques Used: Polyacrylamide Gel Electrophoresis, Northern Blot

7) Product Images from "Rapid detection of wheat yellow mosaic virus by reverse transcription loop-mediated isothermal amplification"

Article Title: Rapid detection of wheat yellow mosaic virus by reverse transcription loop-mediated isothermal amplification

Journal: Virology Journal

doi: 10.1186/1743-422X-8-550

Agarose gel analysis of different RT-LAMP reactions . I-IV were four sets of primers; AMV was AMV-mediated RT-LAMP; M-MLV was M-MLV-mediated RT-LAMP. M: 100-bp DNA ladder marker; 1 and 2: healthy controls; 3 and 4: virus-infected samples
Figure Legend Snippet: Agarose gel analysis of different RT-LAMP reactions . I-IV were four sets of primers; AMV was AMV-mediated RT-LAMP; M-MLV was M-MLV-mediated RT-LAMP. M: 100-bp DNA ladder marker; 1 and 2: healthy controls; 3 and 4: virus-infected samples

Techniques Used: Agarose Gel Electrophoresis, Marker, Infection

8) Product Images from "Rapid detection of wheat yellow mosaic virus by reverse transcription loop-mediated isothermal amplification"

Article Title: Rapid detection of wheat yellow mosaic virus by reverse transcription loop-mediated isothermal amplification

Journal: Virology Journal

doi: 10.1186/1743-422X-8-550

Agarose gel analysis of different RT-LAMP reactions . I-IV were four sets of primers; AMV was AMV-mediated RT-LAMP; M-MLV was M-MLV-mediated RT-LAMP. M: 100-bp DNA ladder marker; 1 and 2: healthy controls; 3 and 4: virus-infected samples
Figure Legend Snippet: Agarose gel analysis of different RT-LAMP reactions . I-IV were four sets of primers; AMV was AMV-mediated RT-LAMP; M-MLV was M-MLV-mediated RT-LAMP. M: 100-bp DNA ladder marker; 1 and 2: healthy controls; 3 and 4: virus-infected samples

Techniques Used: Agarose Gel Electrophoresis, Marker, Infection

9) Product Images from "Complexome profiling on the lpa2 mutant reveals insights into PSII biogenesis and new PSII associated proteins"

Article Title: Complexome profiling on the lpa2 mutant reveals insights into PSII biogenesis and new PSII associated proteins

Journal: bioRxiv

doi: 10.1101/2021.01.04.425283

Growth and chlorophyll fluorescence phenotypes of the lpa2 mutant compared to wild type and complemented lines. A, Alignment of LPA2 amino acid sequences from different organisms. Predicted chloroplast transit peptides are shown in grey, predicted transmembrane helices are underlined and indicated with pipes. Peptides identified by mass spectrometry are given in red letters, twin-arginines in bold letters. Ath – Arabidopsis thaliana (AT5G51545), Zma – Zea mays (NP_001145487), Psi – Picea sitchensis (ABK23742), Ppa – Physcomitrella patens (XP_024366975), Cva – Chlorella variabilis (XP_005849843), Ota – Ostreococcus tauri (XP_003084445), Cre – Chlamydomonas reinhardtii (Cre02.g105650). B, Structure of the Chlamydomonas LPA2 gene, insertion site of the CIB1 cassette in the lpa2 mutant, and construct for complementation. Protein coding regions are drawn as black boxes, untranslated regions as bars, and introns and promoter regions as thin lines. Arrows indicate transcriptional start sites. The purple box indicates a 165-bp fragment derived from the 19th intron of gene Cre13.g573450 in reverse orientation that has integrated together with the CIB1 cassette. C, qRT-PCR analysis of LPA2 transcript accumulation. Values are means from two independent biological replicates and indicate LPA2 transcript levels in the lpa2 mutant and two complemented lines expressing the LPA2 cDNA without (c10, c11) or with a 3xHA coding region (cHA) relative to the wild type. Error bars indicate SD. D, Comparison of PSII maximum quantum efficiency (Fv/Fm). Shown are averages from 3-6 independent experiments, error bars indicate SD. Significant differences were assessed via T-test, (*** p
Figure Legend Snippet: Growth and chlorophyll fluorescence phenotypes of the lpa2 mutant compared to wild type and complemented lines. A, Alignment of LPA2 amino acid sequences from different organisms. Predicted chloroplast transit peptides are shown in grey, predicted transmembrane helices are underlined and indicated with pipes. Peptides identified by mass spectrometry are given in red letters, twin-arginines in bold letters. Ath – Arabidopsis thaliana (AT5G51545), Zma – Zea mays (NP_001145487), Psi – Picea sitchensis (ABK23742), Ppa – Physcomitrella patens (XP_024366975), Cva – Chlorella variabilis (XP_005849843), Ota – Ostreococcus tauri (XP_003084445), Cre – Chlamydomonas reinhardtii (Cre02.g105650). B, Structure of the Chlamydomonas LPA2 gene, insertion site of the CIB1 cassette in the lpa2 mutant, and construct for complementation. Protein coding regions are drawn as black boxes, untranslated regions as bars, and introns and promoter regions as thin lines. Arrows indicate transcriptional start sites. The purple box indicates a 165-bp fragment derived from the 19th intron of gene Cre13.g573450 in reverse orientation that has integrated together with the CIB1 cassette. C, qRT-PCR analysis of LPA2 transcript accumulation. Values are means from two independent biological replicates and indicate LPA2 transcript levels in the lpa2 mutant and two complemented lines expressing the LPA2 cDNA without (c10, c11) or with a 3xHA coding region (cHA) relative to the wild type. Error bars indicate SD. D, Comparison of PSII maximum quantum efficiency (Fv/Fm). Shown are averages from 3-6 independent experiments, error bars indicate SD. Significant differences were assessed via T-test, (*** p

Techniques Used: Fluorescence, Mutagenesis, Mass Spectrometry, Construct, Derivative Assay, Quantitative RT-PCR, Expressing

10) Product Images from "Participation of 5-lipoxygenase and LTB4 in liver regeneration after partial hepatectomy"

Article Title: Participation of 5-lipoxygenase and LTB4 in liver regeneration after partial hepatectomy

Journal: Scientific Reports

doi: 10.1038/s41598-019-54652-7

Effect of oral administration of zileuton in liver proliferation in PH-rats. ( a ) Liver weight to body weight (LW/BW) ratio 24 and 48 h post-PH. ( b ) Representative images of Proliferating Cell Nuclear Antigen (PCNA) immunohistochemistry from rat liver tissue 24 h post-PH obtained by optical microscopy (200X). ( c ) Proliferation Index (PI) determined by PCNA staining 24 h post-PH. PI was calculated as the number of cells in G 1 , S, G 2 and M phases of the cell cycle per 100 hepatocytes. ( d ) Number of PCNA-positive cells in each phase of the cell cycle per 100 hepatocytes 24 h post-PH. ( e ) Quantification of mitotic figures by analysis of H E images 24 h post-PH. Analysis of cyclin D1 24 h post-PH by ( f ) immunoblotting studies in liver nuclear extracts and ( g ) immunohistochemistry (100X). Selected lanes were cropped from different parts of the same gel and they are shown after cropping, aligning and separating them by white space. Full-length blots are available in Supplementary Information. ( h ) Proliferation Index determination by PCNA immunohistochemistry in 48 h post-PH rat liver tissue. ( i ) PCNA-positive cells in each phase of the cell cycle per 100 hepatocytes 48 h post-PH. Sh: sham animals, PH: partial-hepatectomized animals treated with vehicle, PHZi10: PH-animals treated with zileuton 10 mg/Kg body weight, PHZi40: PH-animals treated with zileuton 40 mg/Kg body weight. Bars represent mean ± SEM ( n ≥ 4 per experimental group). *p
Figure Legend Snippet: Effect of oral administration of zileuton in liver proliferation in PH-rats. ( a ) Liver weight to body weight (LW/BW) ratio 24 and 48 h post-PH. ( b ) Representative images of Proliferating Cell Nuclear Antigen (PCNA) immunohistochemistry from rat liver tissue 24 h post-PH obtained by optical microscopy (200X). ( c ) Proliferation Index (PI) determined by PCNA staining 24 h post-PH. PI was calculated as the number of cells in G 1 , S, G 2 and M phases of the cell cycle per 100 hepatocytes. ( d ) Number of PCNA-positive cells in each phase of the cell cycle per 100 hepatocytes 24 h post-PH. ( e ) Quantification of mitotic figures by analysis of H E images 24 h post-PH. Analysis of cyclin D1 24 h post-PH by ( f ) immunoblotting studies in liver nuclear extracts and ( g ) immunohistochemistry (100X). Selected lanes were cropped from different parts of the same gel and they are shown after cropping, aligning and separating them by white space. Full-length blots are available in Supplementary Information. ( h ) Proliferation Index determination by PCNA immunohistochemistry in 48 h post-PH rat liver tissue. ( i ) PCNA-positive cells in each phase of the cell cycle per 100 hepatocytes 48 h post-PH. Sh: sham animals, PH: partial-hepatectomized animals treated with vehicle, PHZi10: PH-animals treated with zileuton 10 mg/Kg body weight, PHZi40: PH-animals treated with zileuton 40 mg/Kg body weight. Bars represent mean ± SEM ( n ≥ 4 per experimental group). *p

Techniques Used: Immunohistochemistry, Microscopy, Staining

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    Promega m mlv reverse transcriptase
    Phenotypes of the lpa2 mutant compared with wild type and complemented lines. (A) Alignment of LPA2 amino acid sequences from different organisms. Predicted chloroplast transit peptides are shown in gray; predicted transmembrane helices are underlined and indicated with pipes. Peptides identified by mass spectrometry are in red letters, twin-arginines in bold letters. Ath, Arabidopsis (AT5G51545); Zma, Zea mays (NP_001145487); Psi, Picea sitchensis (ABK23742); Ppa, Physcomitrella patens (XP_024366975); Cva, Chlorella variabilis (XP_005849843); Ota, Ostreococcus tauri (XP_003084445); Cre, Chlamydomonas reinhardtii (Cre02.g105650). (B) Structure of the Chlamydomonas LPA2 gene, insertion site of the CIB1 cassette in the lpa2 mutant, and construct for complementation. Protein coding regions are shown as black boxes, untranslated regions as bars, and introns and promoter regions as thin lines. Arrows indicate transcriptional start sites. The purple box indicates a 165-bp fragment derived from the 19th intron of gene Cre13.g573450 in <t>reverse</t> orientation that has integrated with the CIB1 cassette. (C) qRT-PCR analysis of LPA2 transcript accumulation in the lpa2 mutant and two complemented lines expressing the LPA2 cDNA without (c10, c11) or with a 3×HA coding region (cHA) relative to the wild type. Values are means from two independent biological replicates normalized against CBLP2 (circles) or TUB1 (diamonds). Error bars indicate SD. (D) Comparison of F v / F <t>m</t> values. Values are averages from three to four independent experiments; error bars indicate SD. Significant differences were assessed via two-tailed, unpaired Student’s t -test with Bonferroni–Holm correction (* P
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    Phenotypes of the lpa2 mutant compared with wild type and complemented lines. (A) Alignment of LPA2 amino acid sequences from different organisms. Predicted chloroplast transit peptides are shown in gray; predicted transmembrane helices are underlined and indicated with pipes. Peptides identified by mass spectrometry are in red letters, twin-arginines in bold letters. Ath, Arabidopsis (AT5G51545); Zma, Zea mays (NP_001145487); Psi, Picea sitchensis (ABK23742); Ppa, Physcomitrella patens (XP_024366975); Cva, Chlorella variabilis (XP_005849843); Ota, Ostreococcus tauri (XP_003084445); Cre, Chlamydomonas reinhardtii (Cre02.g105650). (B) Structure of the Chlamydomonas LPA2 gene, insertion site of the CIB1 cassette in the lpa2 mutant, and construct for complementation. Protein coding regions are shown as black boxes, untranslated regions as bars, and introns and promoter regions as thin lines. Arrows indicate transcriptional start sites. The purple box indicates a 165-bp fragment derived from the 19th intron of gene Cre13.g573450 in reverse orientation that has integrated with the CIB1 cassette. (C) qRT-PCR analysis of LPA2 transcript accumulation in the lpa2 mutant and two complemented lines expressing the LPA2 cDNA without (c10, c11) or with a 3×HA coding region (cHA) relative to the wild type. Values are means from two independent biological replicates normalized against CBLP2 (circles) or TUB1 (diamonds). Error bars indicate SD. (D) Comparison of F v / F m values. Values are averages from three to four independent experiments; error bars indicate SD. Significant differences were assessed via two-tailed, unpaired Student’s t -test with Bonferroni–Holm correction (* P

    Journal: Journal of Experimental Botany

    Article Title: Complexome profiling on the Chlamydomonas lpa2 mutant reveals insights into PSII biogenesis and new PSII associated proteins

    doi: 10.1093/jxb/erab390

    Figure Lengend Snippet: Phenotypes of the lpa2 mutant compared with wild type and complemented lines. (A) Alignment of LPA2 amino acid sequences from different organisms. Predicted chloroplast transit peptides are shown in gray; predicted transmembrane helices are underlined and indicated with pipes. Peptides identified by mass spectrometry are in red letters, twin-arginines in bold letters. Ath, Arabidopsis (AT5G51545); Zma, Zea mays (NP_001145487); Psi, Picea sitchensis (ABK23742); Ppa, Physcomitrella patens (XP_024366975); Cva, Chlorella variabilis (XP_005849843); Ota, Ostreococcus tauri (XP_003084445); Cre, Chlamydomonas reinhardtii (Cre02.g105650). (B) Structure of the Chlamydomonas LPA2 gene, insertion site of the CIB1 cassette in the lpa2 mutant, and construct for complementation. Protein coding regions are shown as black boxes, untranslated regions as bars, and introns and promoter regions as thin lines. Arrows indicate transcriptional start sites. The purple box indicates a 165-bp fragment derived from the 19th intron of gene Cre13.g573450 in reverse orientation that has integrated with the CIB1 cassette. (C) qRT-PCR analysis of LPA2 transcript accumulation in the lpa2 mutant and two complemented lines expressing the LPA2 cDNA without (c10, c11) or with a 3×HA coding region (cHA) relative to the wild type. Values are means from two independent biological replicates normalized against CBLP2 (circles) or TUB1 (diamonds). Error bars indicate SD. (D) Comparison of F v / F m values. Values are averages from three to four independent experiments; error bars indicate SD. Significant differences were assessed via two-tailed, unpaired Student’s t -test with Bonferroni–Holm correction (* P

    Article Snippet: DNA contamination was removed with RNase-free Turbo DNase (Ambion) and complementary DNA (cDNA) synthesis was performed using the M-MLV reverse transcriptase (Promega), deoxynucleotide triphosphates, and oligo-d(T)18 primers.

    Techniques: Mutagenesis, Mass Spectrometry, Construct, Derivative Assay, Quantitative RT-PCR, Expressing, Two Tailed Test

    Global acetylation is increased, and methylation is decreased at 5% oxygen. (a) H3K9ac, H3K27ac, and K3K27me3 fold change of MEL2 hPSC at 5% relative to 20% oxygen. Scale is 50 μ m. (b) Workflow for RNA-seq analysis using https://usegalaxy.org/ , DAVID, and NetworkAnalayst. (c) Venn diagrams showing the overlap of genes upregulated in two hPSC lines at 5% oxygen and 20% oxygen and total DEG count. (d) Functional clusters with enrichment scores greater than 2 derived from Biological Process and Molecular Function GO terms. (e) Volcano plot of MEL2 hPSC transcriptional response to 5% and 20% oxygen. Red genes indicate a fold change value greater than 2 and an adjusted p value (Benjamini FDR) less than 0.05. All assays performed in biological triplicate. Error bars represent the SEM. ∗∗∗∗ p

    Journal: Stem Cells International

    Article Title: Oxygen Regulates Human Pluripotent Stem Cell Metabolic Flux

    doi: 10.1155/2019/8195614

    Figure Lengend Snippet: Global acetylation is increased, and methylation is decreased at 5% oxygen. (a) H3K9ac, H3K27ac, and K3K27me3 fold change of MEL2 hPSC at 5% relative to 20% oxygen. Scale is 50 μ m. (b) Workflow for RNA-seq analysis using https://usegalaxy.org/ , DAVID, and NetworkAnalayst. (c) Venn diagrams showing the overlap of genes upregulated in two hPSC lines at 5% oxygen and 20% oxygen and total DEG count. (d) Functional clusters with enrichment scores greater than 2 derived from Biological Process and Molecular Function GO terms. (e) Volcano plot of MEL2 hPSC transcriptional response to 5% and 20% oxygen. Red genes indicate a fold change value greater than 2 and an adjusted p value (Benjamini FDR) less than 0.05. All assays performed in biological triplicate. Error bars represent the SEM. ∗∗∗∗ p

    Article Snippet: RNA was isolated using a chloroform-induced triphasic solution before DNase treatment using DNase-I (Ambion). cDNA was synthesized from 1 μ g of RNA using M-MLV Reverse Transcriptase (Promega).

    Techniques: Methylation, RNA Sequencing Assay, Functional Assay, Derivative Assay

    Chromosomal location and collinearity analysis of the m 6 A genes in tomato. ( A ) Locations of the m 6 A genes in tomato chromosomes. The scale at the left side of the figure is shown in Mb. The number of each chromosome is indicated at the top of the corresponding chromosome. ( B ) Synteny analysis of the m 6 A genes in tomato. The gray lines represent the collinearity result of the tomato genome, and the red lines represent the segmental duplication events. ( C ) Synteny analysis of the m 6 A genes between tomato and Arabidopsis . The gray lines represent the collinearity result between tomato and Arabidopsis genomes, and the red lines represent homologous gene pairs.

    Journal: International Journal of Molecular Sciences

    Article Title: Genome-Wide Identification, Classification and Expression Analysis of m6A Gene Family in Solanum lycopersicum

    doi: 10.3390/ijms23094522

    Figure Lengend Snippet: Chromosomal location and collinearity analysis of the m 6 A genes in tomato. ( A ) Locations of the m 6 A genes in tomato chromosomes. The scale at the left side of the figure is shown in Mb. The number of each chromosome is indicated at the top of the corresponding chromosome. ( B ) Synteny analysis of the m 6 A genes in tomato. The gray lines represent the collinearity result of the tomato genome, and the red lines represent the segmental duplication events. ( C ) Synteny analysis of the m 6 A genes between tomato and Arabidopsis . The gray lines represent the collinearity result between tomato and Arabidopsis genomes, and the red lines represent homologous gene pairs.

    Article Snippet: The first-strand cDNA synthesis was performed using 1 μg of total RNAs by M-MLV reverse transcriptase (Promega, Madison, WI, USA).

    Techniques:

    The amount of m 6 A and m 6 Am in tomato leaves by LC-MS/MS analysis. The changes in ( A ) m 6 A and ( B ) m 6 Am contents under cold and heat treatment. The 30-day-old tomato seedlings were treated under cold and heat conditions for 48 h. * Refer to significant differences with p

    Journal: International Journal of Molecular Sciences

    Article Title: Genome-Wide Identification, Classification and Expression Analysis of m6A Gene Family in Solanum lycopersicum

    doi: 10.3390/ijms23094522

    Figure Lengend Snippet: The amount of m 6 A and m 6 Am in tomato leaves by LC-MS/MS analysis. The changes in ( A ) m 6 A and ( B ) m 6 Am contents under cold and heat treatment. The 30-day-old tomato seedlings were treated under cold and heat conditions for 48 h. * Refer to significant differences with p

    Article Snippet: The first-strand cDNA synthesis was performed using 1 μg of total RNAs by M-MLV reverse transcriptase (Promega, Madison, WI, USA).

    Techniques: Liquid Chromatography with Mass Spectroscopy

    Expression profiles of tomato m 6 A genes in different abiotic stress by qPCR analysis. The 30-day-old tomato seedlings were treated under cold and heat conditions for 12, 24, and 48 h. Tomato seedlings were treated under drought and salt condition for 1, 7, and 14 d. Tomato seedlings without treatment was considered the control. Each value represents the mean ± SE of three replicates.

    Journal: International Journal of Molecular Sciences

    Article Title: Genome-Wide Identification, Classification and Expression Analysis of m6A Gene Family in Solanum lycopersicum

    doi: 10.3390/ijms23094522

    Figure Lengend Snippet: Expression profiles of tomato m 6 A genes in different abiotic stress by qPCR analysis. The 30-day-old tomato seedlings were treated under cold and heat conditions for 12, 24, and 48 h. Tomato seedlings were treated under drought and salt condition for 1, 7, and 14 d. Tomato seedlings without treatment was considered the control. Each value represents the mean ± SE of three replicates.

    Article Snippet: The first-strand cDNA synthesis was performed using 1 μg of total RNAs by M-MLV reverse transcriptase (Promega, Madison, WI, USA).

    Techniques: Expressing, Real-time Polymerase Chain Reaction

    Heat map representation of the tomato m 6 A genes in various tissues. ( A ) Expression levels of tomato m 6 A genes in Heinz 1706 tomato based on transcriptome expression data. Each column represents a different tissue at different developmental stages of tomato. The bar on the right indicates normalized expression data from high to low (red to green). ( B ) STEM analysis. The expression data of each gene in root was normalized as 0. ( C , D ) Expression of SlYTHDF1 and SlYTHDF3A in different tissues of Ailsa Craig tomato. RT, root; ST, stem; YL, young leaf; ML, mature leaf; SL, senescent leaf; SE, sepal; FL, flower; IMG, immature green; MG, mature green; B, breaker stage; B+4, 4 days after breaker stage; B+7, 7 days after breaker stage. Data are the mean ± SE of three independent experiments.

    Journal: International Journal of Molecular Sciences

    Article Title: Genome-Wide Identification, Classification and Expression Analysis of m6A Gene Family in Solanum lycopersicum

    doi: 10.3390/ijms23094522

    Figure Lengend Snippet: Heat map representation of the tomato m 6 A genes in various tissues. ( A ) Expression levels of tomato m 6 A genes in Heinz 1706 tomato based on transcriptome expression data. Each column represents a different tissue at different developmental stages of tomato. The bar on the right indicates normalized expression data from high to low (red to green). ( B ) STEM analysis. The expression data of each gene in root was normalized as 0. ( C , D ) Expression of SlYTHDF1 and SlYTHDF3A in different tissues of Ailsa Craig tomato. RT, root; ST, stem; YL, young leaf; ML, mature leaf; SL, senescent leaf; SE, sepal; FL, flower; IMG, immature green; MG, mature green; B, breaker stage; B+4, 4 days after breaker stage; B+7, 7 days after breaker stage. Data are the mean ± SE of three independent experiments.

    Article Snippet: The first-strand cDNA synthesis was performed using 1 μg of total RNAs by M-MLV reverse transcriptase (Promega, Madison, WI, USA).

    Techniques: Expressing

    The effects of small molecules B and C on the expression of HSG, Ume6, and Nrg1 genes. (A) Total RNA of yeast cells (Y), the small molecules treated hyphae-induced cells (HB, HC), or hyphae-induced cells (H) were isolated using the TRIzol reagent method. Total RNA was measured using Nanodrop Spectrophotometer and was reverse transcribed into cDNAs using oligo-d(T) and M-MLV reverse transcriptase. Real-time PCR was performed with the specific primers listed in Table 2 . (B) Immunoblotting was performed by preparing protein samples for 0–4 h, and Real-time PCR (C) was performed as previously described using the Nrg1-myc strain. (D) Immunoblotting was performed by preparing protein samples for 0– 4 h, and Real-time PCR (E) was performed as described above using the Ume6-myc strain. Western blotting was performed with an anti-myc antibody to detect Nrg1-myc and Ume6-myc. In the western blotting, β-actin was used as a loading control by detecting with the anti-β-actin antibody. Each experiment was conducted in triplicate. The data represent the mean and standard deviation of three independent experiments. *; P

    Journal: bioRxiv

    Article Title: Inhibition of Ras1-MAPK pathways for hypha formation by novel drug candidates in Candida albicans

    doi: 10.1101/2021.07.06.451239

    Figure Lengend Snippet: The effects of small molecules B and C on the expression of HSG, Ume6, and Nrg1 genes. (A) Total RNA of yeast cells (Y), the small molecules treated hyphae-induced cells (HB, HC), or hyphae-induced cells (H) were isolated using the TRIzol reagent method. Total RNA was measured using Nanodrop Spectrophotometer and was reverse transcribed into cDNAs using oligo-d(T) and M-MLV reverse transcriptase. Real-time PCR was performed with the specific primers listed in Table 2 . (B) Immunoblotting was performed by preparing protein samples for 0–4 h, and Real-time PCR (C) was performed as previously described using the Nrg1-myc strain. (D) Immunoblotting was performed by preparing protein samples for 0– 4 h, and Real-time PCR (E) was performed as described above using the Ume6-myc strain. Western blotting was performed with an anti-myc antibody to detect Nrg1-myc and Ume6-myc. In the western blotting, β-actin was used as a loading control by detecting with the anti-β-actin antibody. Each experiment was conducted in triplicate. The data represent the mean and standard deviation of three independent experiments. *; P

    Article Snippet: In brief, total RNA was measured using a Nanodrop 1000 Spectrophotometer (Thermo Scientific, Rockford, IL, USA) and was reverse transcribed into cDNAs using oligo-d(T) and M-MLV reverse transcriptase (Promega).

    Techniques: Expressing, Isolation, Spectrophotometry, Real-time Polymerase Chain Reaction, Western Blot, Standard Deviation