scholarly journals Bioaugmentation of Atrazine-Contaminated Soil With Paenarthrobacter sp. Strain AT-5 and Its Effect on the Soil Microbiome

2021 ◽  
Vol 12 ◽  
Author(s):  
Weibin Jia ◽  
Ning Li ◽  
Tunan Yang ◽  
Weixian Dai ◽  
Jiandong Jiang ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Contaminated Soil ◽  
Agricultural Soils ◽  
Potential Method ◽  
Soil Microbiome ◽  
Pcr Analysis ◽  
Triazine Herbicide ◽  
Qrt Pcr ◽  
The World ◽  
Atrazine Degradation

Atrazine, a triazine herbicide, is widely used around the world. The residue of atrazine due to its application in the fore-rotating crop maize has caused phytotoxicity to the following crop sweet potato in China. Bioaugmentation of atrazine-contaminated soil with atrazine-degrading strains is considered as the most potential method to remove atrazine from soil. Nevertheless, the feasibility of bioaugmentation and its effect on soil microbiome still need investigation. In this study, Paenarthrobacter sp. AT-5, an atrazine-degrading strain, was inoculated into agricultural soils contaminated with atrazine to investigate the bioaugmentation process and the reassembly of the soil microbiome. It was found that 95.9% of 5 mg kg−1 atrazine was removed from the soils when inoculated with strain AT-5 with 7 days, and the phytotoxicity of sweet potato caused by atrazine was significantly alleviated. qRT-PCR analysis revealed that the inoculated strain AT-5 survived well in the soils and maintained a relatively high abundance. The inoculation of strain AT-5 significantly affected the community structure of the soil microbiome, and the abundances of bacteria associated with atrazine degradation were improved.

scholarly journals ITRAQ-based quantitative proteomic analysis of Fusarium moniliforme (Fusarium verticillioides) in response to Phloridzin inducers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Rong Zhang ◽  
Weitao Jiang ◽  
Xin Liu ◽  
Yanan Duan ◽  
Li Xiang ◽  
...  
Keyword(s):  
Fusarium Moniliforme ◽  
Abiotic Factors ◽  
Fusarium Verticillioides ◽  
Protein Profile ◽  
Sugar Metabolism ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Differentially Expressed Proteins ◽  
Apple Replant Disease ◽  
Qrt Pcr

Abstract Background Apple replant disease (ARD) has been reported from all major fruit-growing regions of the world, and is often caused by biotic factors (pathogen fungi) and abiotic factors (phenolic compounds). In order to clarify the proteomic differences of Fusarium moniliforme under the action of phloridzin, and to explore the potential mechanism of F. moniliforme as the pathogen of ARD, the role of Fusarium spp. in ARD was further clarified. Methods In this paper, the quantitative proteomics method iTRAQ analysis technology was used to analyze the proteomic differences of F. moniliforme before and after phloridzin treatment. The differentially expressed protein was validated by qRT-PCR analysis. Results A total of 4535 proteins were detected, and 293 proteins were found with more than 1.2 times (P< 0.05) differences. In-depth data analysis revealed that 59 proteins were found with more than 1.5 times (P< 0.05) differences, and most proteins were consistent with the result of qRT-PCR. Differentially expressed proteins were influenced a variety of cellular processes, particularly metabolic processes. Among these metabolic pathways, a total of 8 significantly enriched KEGG pathways were identified with at least 2 affiliated proteins with different abundance in conidia and mycelium. Functional pathway analysis indicated that up-regulated proteins were mainly distributed in amino sugar, nucleotide sugar metabolism, glycolysis/ gluconeogenesis and phagosome pathways. Conclusions This study is the first to perform quantitative proteomic investigation by iTRAQ labeling and LC-MS/MS to identify differentially expressed proteins in F. moniliforme under phloridzin conditions. The results confirmed that F. moniliforme presented a unique protein profile that indicated the adaptive mechanisms of this species to phloridzin environments. The results deepened our understanding of the proteome in F. moniliforme in response to phloridzin inducers and provide a basis for further exploration for improving the efficiency of the fungi as biocontrol agents to control ARD.

scholarly journals Lactobacillus reuteri BM53-1 Produces a Compound That Inhibits Sticky Glucan Synthesis by Streptococcus mutans

2021 ◽  
Vol 9 (7) ◽  
pp. 1390
Author(s):  
Masafumi Noda ◽  
Naho Sugihara ◽  
Yoshimi Sugimoto ◽  
Ikue Hayashi ◽  
Sachiko Sugimoto ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Lactic Acid ◽  
Dental Caries ◽  
Lactobacillus Reuteri ◽  
Early Stage ◽  
Pcr Analysis ◽  
Cariogenic Bacteria ◽  
Qrt Pcr ◽  
Actinidia Polygama ◽  
Glucan Synthesis

Cariogenic bacteria, such as Streptococcus (S.) mutans and S. sobrinus, produce insoluble and sticky glucans as a biofilm material. The present study demonstrates that a lactic acid bacterium (LAB) named BM53-1 produces a substance that inhibits the sticky glucan synthesis. The BM53-1 strain was isolated from a flower of Actinidia polygama and identified as Lactobacillus reuteri. The substance that inhibits sticky glucan synthesis does not exhibit antibacterial activity against S. mutans. The cariogenic S. mutans produces glucans under the control of three glucosyltransferase (GTF) enzymes, named GtfB, GtfC, and GtfD. Although GtfB and GtfC produce insoluble glucans, GtfD forms soluble glucans. Through quantitative reverse-transcriptional (qRT)-PCR analysis, it was revealed that the BM53-1-derived glucan-production inhibitor (GI) enhances the transcriptions of gtfB and gtfC genes 2- to 7-fold at the early stage of cultivation. However, that of gtfD was not enhanced in the presence of the GI, indicating that the glucan stickiness produced by S. mutans was significantly weaker in the presence of the GI. Our result demonstrates that Lb. reuteri BM53-1 is useful to prevent dental caries.

scholarly journals Identification of miRNAs and Their Response to Cold Stress in Astragalus Membranaceus

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 182 ◽  
Author(s):  
Merhaba Abla ◽  
Huigai Sun ◽  
Zhuyun Li ◽  
Chunxiang Wei ◽  
Fei Gao ◽  
...  
Keyword(s):  
Cold Stress ◽  
Redox Homeostasis ◽  
Astragalus Membranaceus ◽  
Pcr Analysis ◽  
Small Rna Sequencing ◽  
Factors Affecting ◽  
Gene Regulation Network ◽  
Qrt Pcr ◽  
Yield And Quality ◽  
Regulation Network

Astragalus membranaceus is an important medicinal plant widely cultivated in East Asia. MicroRNAs (miRNAs) are endogenous regulatory molecules that play essential roles in plant growth, development, and the response to environmental stresses. Cold is one of the key environmental factors affecting the yield and quality of A. membranaceus, and miRNAs may mediate the gene regulation network under cold stress in A. membranaceus. To identify miRNAs and reveal their functions in cold stress response in A. membranaceus, small RNA sequencing was conducted followed by bioinformatics analysis, and quantitative real time PCR (qRT-PCR) analysis was performed to profile the expression of miRNAs under cold stress. A total of 168 conserved miRNAs belonging to 34 families and 14 putative non-conserved miRNAs were identified. Many miRNA targets were predicted and these targets were involved in diversified regulatory and metabolic pathways. By using qRT-PCR, 27 miRNAs were found to be responsive to cold stress, including 4 cold stress-induced and 17 cold-repressed conserved miRNAs, and 6 cold-induced non-conserved miRNAs. These cold-responsive miRNAs probably mediate the response to cold stress by regulating development, hormone signaling, defense, redox homeostasis, and secondary metabolism in A. membranaceus. These cold-corresponsive miRNAs may be used as the candidate genes in further molecular breeding for improving cold tolerance of A. membranaceus.

scholarly journals Small Non-Coding RNAome of Ageing Chondrocytes

2020 ◽  
Vol 21 (16) ◽  
pp. 5675
Author(s):  
Panagiotis Balaskas ◽  
Jonathan A. Green ◽  
Tariq M. Haqqi ◽  
Philip Dyer ◽  
Yalda A. Kharaz ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Differential Expression Analysis ◽  
Cartilage Tissue ◽  
Pcr Analysis ◽  
Small Rna Sequencing ◽  
High Grade ◽  
Human Cartilage ◽  
Fragment Analysis ◽  
Qrt Pcr ◽  
Age Related

Ageing is a leading risk factor predisposing cartilage to osteoarthritis. However, little research has been conducted on the effect of ageing on the expression of small non-coding RNAs (sncRNAs). RNA from young and old chondrocytes from macroscopically normal equine metacarpophalangeal joints was extracted and subjected to small RNA sequencing (RNA-seq). Differential expression analysis was performed in R using package DESeq2. For transfer RNA (tRNA) fragment analysis, tRNA reads were aligned to horse tRNA sequences using Bowtie2 version 2.2.5. Selected microRNA (miRNAs or miRs) and small nucleolar RNA (snoRNA) findings were validated using real-time quantitative Polymerase Chain Reaction (qRT-PCR) in an extended cohort of equine chondrocytes. tRNA fragments were further investigated in low- and high-grade OA human cartilage tissue. In total, 83 sncRNAs were differentially expressed between young and old equine chondrocytes, including miRNAs, snoRNAs, small nuclear RNAs (snRNAs), and tRNAs. qRT-PCR analysis confirmed findings. tRNA fragment analysis revealed that tRNA halves (tiRNAs), tiRNA-5035-GluCTC and tiRNA-5031-GluCTC-1 were reduced in both high grade OA human cartilage and old equine chondrocytes. For the first time, we have measured the effect of ageing on the expression of sncRNAs in equine chondrocytes. Changes were detected in a number of different sncRNA species. This study supports a role for sncRNAs in ageing cartilage and their potential involvement in age-related cartilage diseases.

scholarly journals MiR-107 inhibits proliferation of lung cancer cells through regulating TP53 regulated inhibitor of apoptosis 1 (TRIAP1)

2017 ◽  
Vol 12 (1) ◽  
pp. 200-205 ◽  
Author(s):  
Bing Wang ◽  
Zhanjie Zuo ◽  
Fang Lv ◽  
Liang Zhao ◽  
Minjun Du ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cell Proliferation ◽  
Western Blot ◽  
Cancer Cells ◽  
A549 Cells ◽  
Lung Cancer Cells ◽  
Pcr Analysis ◽  
Aberrant Expression ◽  
Small Interference Rna ◽  
Qrt Pcr

AbstractAimsAccumulating evidence indicates that aberrant expression of miR-107 plays a crucial role in cancers. This study aims to display the function of miR-107 and its novel target genes in the progression of lung cancer.Methods and MaterialMiR-107 or miR-107 inhibitor was transfected into lung cancer cells A549. The levels of miR-107 and TP53 regulated inhibition of apoptosis 1 (TRIAP1) were examined by quantitative real-time Polymerase Chain Reaction (qRT-PCR) analysis and Western Blot. Functionally, MTT and colony formation assays were carried out to test the effect of miR-107 inhibitor and/or small interference RNA (siRNA) targeting TRIAP1 mRNA on proliferation of lung cancer cells. Levels of miR-107 or TRIAP1 were detected in clinical lung cancer samples by using qRT-PCR analysis.ResultsQRT-PCR analysis revealed that miR-107 inhibitor or miR-107 was successfully transfected into A549 cells. Western Blot indicated that miR-107 decreased the expression of TRIAP1 protein in the cells. In contrast, miR-107 inhibitor augmented the levels of TRIAP1 protein. Functionally, miR-107 inhibitor remarkably suppressed A549 cell proliferation, whereas, TRIAP1 siRNAs could abrogate the miR-107 inhibitor-induced proliferation of cells. Then, we validated that TRIAP1 was increased in clinical lung cancer samples. MiR-107 expression was negatively related to TRIAP1 expression in clinical lung cancer samples.ConclusionsMiR-107 suppresses cell proliferation by targeting TRIAP1 in lung cancer. Our finding allows new insights into the mechanisms of lung cancer that is mediated by miR-107.

scholarly journals Choice of a Stable Set of Reference Genes for qRT-PCR Analysis in Amblyomma maculatum (Acari: Ixodidae)

2012 ◽  
Vol 49 (6) ◽  
pp. 1339-1346 ◽  
Author(s):  
Rebecca Browning ◽  
Steven Adamson ◽  
Shahid Karim
Keyword(s):  
Reference Genes ◽  
Stable Set ◽  
Pcr Analysis ◽  
Amblyomma Maculatum ◽  
Qrt Pcr

scholarly journals Circular RNA Expression Profiling Identifies Prostate Cancer- Specific circRNAs in Prostate Cancer

2018 ◽  
Vol 50 (5) ◽  
pp. 1903-1915 ◽  
Author(s):  
Qianlin Xia ◽  
Tao Ding ◽  
Guihong Zhang ◽  
Zehuan Li ◽  
Ling Zeng ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Polymerase Chain Reaction Analysis ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
High Morbidity ◽  
Qrt Pcr ◽  
Diagnosis And Prognosis ◽  
Novel Biomarkers ◽  
Rna Expression Profiling

Background/Aims: Prostate cancer (PCa) is one of the main cancers that damage males’ health severely with high morbidity and mortality, but there is still no ideal molecular marker for the diagnosis and prognosis of prostate cancer. Methods: To determine whether the differentially expressed circRNAs in prostate cancer can serve as novel biomarkers for prostate cancer diagnosis, we screened differentially expressed circRNAs using SBC-ceRNA array in 4 pairs of prostate tumor and paracancerous tissues. A circRNA-miRNA-mRNA regulatory network for the differential circRNAs and their host genes was constructed by Cytoscape3.5.1 software. Quantitative real-time polymerase chain reaction analysis (qRT-PCR) was performed to confirm the microarray data. Results: We found 1021 differentially expressed circRNAs in PCa tumor using SBC-ceRNA array and confirmed the expression of circ_0057558, circ_0062019 and SLC19A1 in PCa cell lines and tumor tissues through qRT-PCR analysis. We demonstrated that combination of PSA level and two differentially expressed circRNAs showed significantly increased AUC, sensitivity and specificity (0.938, 84.5% and 90.9%, respectively) than PSA alone (AUC of serum PSA was 0.854). Moreover, circ_0057558 was correlated positively with total cholesterol. The functional network of circRNA-miRNA-mRNA analysis showed that circ_0057558 and circ_0034467 regulated miR-6884, and circ_0062019 and circ_0060325 regulated miR-5008. Conclusion: Our results demonstrated that differentially expressed circRNAs (circ_0062019 and circ_0057558) and host gene SLC19A1 of circ_0062019 could be used as potential novel biomarkers for prostate cancer.

scholarly journals 1724. Plasmid-free CRISPR-Cas9 System for Genetic Engineering of Rhizopus delemar

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S632-S632
Author(s):  
Yiyou Gu ◽  
Clara Baldin ◽  
Teklegiorgis Gebremariam ◽  
Abdullah Alqarihi ◽  
Zeinab Mamouei ◽  
...  
Keyword(s):  
Genetic Manipulation ◽  
Etiologic Agent ◽  
Pcr Analysis ◽  
Free System ◽  
Rhizopus Delemar ◽  
Additional Tool ◽  
Qrt Pcr ◽  
Enzyme Screening ◽  
Serious Infection ◽  
Short Palindromic Repeat

Abstract Background Mucormycosis is a serious infection caused by fungi of the order Mucorales. Rhizopus delemar is the most common etiologic agent of mucormycosis. Pathogenesis studies of mucormycosis have been hampered by poor genetic trackability of the organism, owing to rare chromosomal integration events and multinucleated nature of the cells. The clustered regularly interspaced short palindromic repeat (CRISPR)-associated nuclease 9 (Cas9) system has been widely used in genetic manipulation through efficient homologous and non-homologous break points in a variety of organisms including R. delemar. However, plasmid-free CRISPR/Cas9 system has not been previously described in the fungus. Here, we introduce a rapid plasmid-free system for inducing orotidine 5’-phosphate decarboxylase (pyrF) gene mutation in R. delemar. Methods Protoplasts of R. delemar 99–880 strain were transformed with 20 nucleotide gRNA targeting the N-terminus of pyrF gene and the Cas9 enzyme. Screening for pyrF auxotrophy was carried out by plating transformed protoplasts on potato dextrose agar (PDA) plates containing 1 mg/mL 5-fluoroorotic acid (5-FOA) and 100 µg/mL uracil. Putative mutant strains were selected for uracil auxotrophy by plating simultaneously on media with or without uracil. pyrF disruption was verified by using PCR and qRT–PCR. Results Approximately100 transformants were generated through plating on 5-FOA plates. Only three transformants did not grow on minimal medium lacking uracil, indicating that they were true pyrF null mutants. PCR analysis showed that these three transformants have undergone nucleotide deletion events within the pyrF gene. The lack of pyrF gene expression was further verified by using qRT–PCR relative to wild-type R. delemar 99–880. Conclusion Similar to the plasmid-based genome manipulation strategy, the plasmid-free CRISPR/Cas9 system can induce gene editing in R. delemar. This rapid and simple approach adds an additional tool in our conquest to understand pathogenesis of mucormycosis. Disclosures All authors: No reported disclosures.

scholarly journals Jasmonate and Melatonin Act Synergistically to Potentiate Cold Tolerance in Tomato Plants

2022 ◽  
Vol 12 ◽  
Author(s):  
Fei Ding ◽  
Liming Ren ◽  
Fang Xie ◽  
Meiling Wang ◽  
Shuoxin Zhang
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Feedback Loop ◽  
Pcr Analysis ◽  
Tomato Plants ◽  
Qrt Pcr ◽  
Cold Condition ◽  
Tomato Cultivars ◽  
Cold Responses ◽  
Ja Signaling

Both jasmonic acid (JA) and melatonin (MT) have been demonstrated to play positive roles in cold tolerance, however, whether and how they crosstalk in the cold responses in plants remain elusive. Here, we report that JA and MT act synergistically in the cold tolerance in tomato plants (Solanum lycopersicum). It was found that JA and MT were both substantially accumulated in response to cold stress and foliar applications of methyl jasmonate (MeJA) and MT promoted cold tolerance as evidenced by increased Fv/Fm, decreased relative electrolyte leakage (EL) and declined H2O2 accumulation in tomato plants. Inhibition of MT biosynthesis attenuated MeJA-induced cold tolerance, while inhibition of JA biosynthesis reduced MT accumulation in tomato plants under cold conditions. Furthermore, qRT-PCR analysis showed that the expressions of two MT biosynthetic genes, SlSNAT and SlAMST, were strongly induced by MeJA, whereas suppression of SlMYC2, a master JA signaling regulator, abated the expressions of SlSNAT and SlAMST under cold stress. Additionally, suppression of SlMYC2 reduced MT accumulation, decreased Fv/Fm and increased EL in cold-stressed tomato plants. Interestingly, exogenous MT promoted JA accumulation, while inhibition of MT biosynthesis significantly reduced JA accumulation in tomato plants under the cold condition. Taken together, these results suggest that JA and MT act cooperatively in cold tolerance and form a positive feedback loop, amplifying the cold responses of tomato plants. Our findings might be translated into the development of cold-resistant tomato cultivars by genetically manipulating JA and MT pathways.

scholarly journals Investigation of olfactory receptor family 51 subfamily j member 1 (OR51J1) gene susceptibility as a potential breast cancer-associated biomarker

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246752
Author(s):  
Maryam Asadi ◽  
Nahid Ahmadi ◽  
Simin Ahmadvand ◽  
Ali Akbar Jafari ◽  
Akbar Safaei ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Statistical Analysis ◽  
Protein Expression ◽  
Olfactory Receptor ◽  
Mrna Level ◽  
Expression Level ◽  
Pcr Analysis ◽  
Normal Tissues ◽  
Qrt Pcr ◽  
Human Protein Atlas

Among cancer treatment methods, targeted therapy using cancer-associated biomarkers has minimum side effects. Recently olfactory receptor (OR) family attracts the researcher’s attention as a favorable biomarker of cancer. Here, a statistical approach using complete data from the human protein atlas database was used to evaluate the potential of OR51J1 gene as a cancer-associated biomarker. To confirm the findings of statistical analysis, the OR51J1 mRNA and protein expression levels in breast tumor and normal tissue were measured using quantitative Real Time PCR (qRT-PCR) and immunohistochemistry (IHC) techniques. The association with clinicopathological factors was analyzed. Statistical analysis revealed that OR51J1 has a high expression level in more than 20 types of cancer tissues without any expression in 44 normal tissues. In 15 cancer types, including breast cancer, expression score was more than 90%. The qRT-PCR analysis in breast cancer showed OR51J1 have significantly higher expression level in tumors than normal tissues (2.91 fold). The IHC results showed OR51J1 expression on other cellular subtypes than tumor and normal cells, including myoepithelium, fibroblast, and lymphocytes. OR51J1 protein expression in invasive cells, as well as its overall score, showed a significant correlation with ER and PR expression and breast cancer (BC) subtypes. Results revealed the potential of OR51J1 as a cancer-associated biomarker for the diagnosis of breast cancer at the mRNA level.

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