scholarly journals Current Progression: Application of High-Throughput Sequencing Technique in Space Microbiology

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Yanwu Chen ◽  
Bin Wu ◽  
Cheng Zhang ◽  
Zhiqi Fan ◽  
Ying Chen ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Life Support ◽  
Confined Space ◽  
Sustainable Operation ◽  
Detection Technology ◽  
Long Time ◽  
Space Life Support ◽  
Confined Environment ◽  
The Relationship

During a spaceflight, astronauts need to live in a spacecraft on orbit for a long time, and the relationship between humans and microorganisms in the closed environment of space is not the same as on the ground. The dynamic study of microorganisms in confined space shows that with the extension of the isolation time, harmful bacteria gradually accumulate. Monitoring and controlling microbial pollution in a confined environment system are very important for crew health and the sustainable operation of a space life support system. Culture-based assays have been used traditionally to assess the microbial loads in a spacecraft, and uncultured-based techniques are already under way according to the NASA global exploration roadmap. High-throughput sequencing technology has been used generally to study the communities of the environment and human on the ground and shows its broad prospects applied onboard. We here review the recent application of high-throughput sequencing on space microbiology and analyze its feasibility and potential as an on-orbit detection technology.

scholarly journals High-throughput sequencing analysis of the rhizosphere arbuscular mycorrhizal fungi (AMF) community composition associated with Ferula sinkiangensis

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yunfeng Luo ◽  
Zhongke Wang ◽  
Yaling He ◽  
Guifang Li ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Total Phosphorus ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Nitrate Nitrogen ◽  
Soil Depth ◽  
Slope Position ◽  
Soil Physicochemical Properties ◽  
Ferula Sinkiangensis ◽  
The Relationship

Abstract Background Ferula sinkiangensis is an increasingly endangered medicinal plant. Arbuscular mycorrhiza fungi (AMF) are symbiotic microorganisms that live in the soil wherein they enhance nutrient uptake, stress resistance, and pathogen defense in host plants. While such AMF have the potential to contribute to the cultivation of Ferula sinkiangensis, the composition of AMF communities associated with Ferula sinkiangensis and the relationship between these fungi and other pertinent abiotic factors still remains to be clarified. Results Herein, we collected rhizosphere and surrounding soil samples at a range of depths (0–20, 20–40, and 40–60 cm) and a range of slope positions (bottom, middle, top). These samples were then subjected to analyses of soil physicochemical properties and high-throughput sequencing (Illumina MiSeq). We determined that Glomus and Diversispora species were highly enriched in all samples. We further found that AMF diversity and richness varied significantly as a function of slope position, with this variation primarily being tied to differences in relative Glomus and Diversispora abundance. In contrast, no significant relationship was observed between soil depth and overall AMF composition, although some AMF species were found to be sensitive to soil depth. Many factors significantly affected AMF community composition, including organic matter content, total nitrogen, total potassium, ammonium nitrogen, nitrate nitrogen, available potassium, total dissolvable salt levels, pH, soil water content, and slope position. We further determined that Shannon diversity index values in these communities were positively correlated with total phosphorus, nitrate-nitrogen levels, and pH values (P < 0.05), whereas total phosphorus, total dissolvable salt levels, and pH were positively correlated with Chao1 values (P < 0.05). Conclusion In summary, our data revealed that Glomus and Diversispora are key AMF genera found within Ferula sinkiangensis rhizosphere soil. These fungi are closely associated with specific environmental and soil physicochemical properties, and these soil sample properties also differed significantly as a function of slope position (P < 0.05). Together, our results provide new insights regarding the relationship between AMF species and Ferula sinkiangensis, offering a theoretical basis for further studies of their development.

Analysis of microbial changes in the rhizosphere of unplanted and planted Atractylodes lancea via high-throughput sequencing

2020 ◽  
Author(s):  
Yan Xu ◽  
Junfeng Niu ◽  
Lijun Chen ◽  
Xiaoqiang Wu ◽  
Zhongmin Dong ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Continuous Cropping ◽  
Pests And Diseases ◽  
Atractylodes Lancea ◽  
Bacteria And Fungi ◽  
The Relationship

Abstract Background Atractylodes lancea is a traditional Chinese medicine, which typically requires more than 3–4 years of continuous cropping to obtain the underground medicinal components. With continuous cropping years, the quality and yields of A. lancea medicinal materials decrease, while pests and diseases increase. These aspects are intimately correlated with rhizospheric microorganisms. Methods This research paper employed high-throughput sequencing for its detection in soil that was cultivated for three years and never cultivated to clarify the relationship between the microbial diversity of the rhizosphere and continuous A. lancea cropping. Results The rhizosphere microbial community was altered following the continuous cropping of A. lancea. The bacterial diversity and richness were observed to decrease, while the fungal community diversity increased, and richness decreased. The total OUTs of the soil bacteria and fungi of unplanted and planted A. lancea were 59.58% and 37.65%, respectively. At the phylum level, the relative abundance of Proteobacteria, Gemmatimonadetes, Acidobacteria and Chloroflexi decreased, whereas the relative abundance of Mortierellomycota increased. At the genus level, Bradyrhizobium, Striaticonidium, Dactylonectria, Sphingomonas, Burkholderiaceae, Rhodanobacter, Arthrobacter, Scleroderma, Mortierella and Penicillium were significantly different between the two sample groups. Conclusions Our results revealed that following the cultivation of A. lancea, the rhizospheric microbial community was altered. This study preliminarily determined the

scholarly journals High-throughput sequencing analysis of the rhizosphere arbuscular mycorrhizal fungi (AMF) community composition associated with Ferula sinkiangensis

2020 ◽  
Author(s):  
Yunfeng Luo ◽  
Zhongke Wang ◽  
Yaling He ◽  
Guifang Li ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Total Phosphorus ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Nitrate Nitrogen ◽  
Soil Depth ◽  
Slope Position ◽  
Soil Physicochemical Properties ◽  
Ferula Sinkiangensis ◽  
The Relationship

Abstract Background: Ferula sinkiangensis is an increasingly endangered medicinal plant. Arbuscular mycorrhiza fungi (AMF) are symbiotic microorganisms that live in the soil wherein they enhance nutrient uptake, stress resistance, and pathogen defense in host plants. While such AMF have the potential to aid in Ferula sinkiangensis cultivation, the composition of AMF communities associated with Ferula sinkiangensis and the relationship between these fungi and other pertinent abiotic factors remain to be clarified.Results: Herein, we collected samples of rhizosphere and surrounding soil at a range of depths (0-20, 20-40, and 40-60 cm) and a range of slope positions (bottom, middle, top). These samples were then subjected to analyses of soil physicochemical properties and high-throughput sequencing (Illumina MiSeq). We determined that Glomus and Diversispora species were highly enriched in all samples. We further found that AMF diversity and richness varied significantly as a function of slope position, with this variation primarily being tied to differences in relative Glomus and Diversispora abundance. In contrast, no significant relationship was observed between soil depth and overall AMF composition, although some AMF species were found to be sensitive to soil depth. Many factors were found to significantly affect AMF community composition, including organic matter content, total nitrogen, total potassium, ammonium nitrogen, nitrate nitrogen, available potassium, total dissolvable salt levels, pH, soil water content, and slope position. We further found that Shannon diversity index values in these communities were positively correlated with total phosphorus, nitrate-nitrogen levels, and pH values (P<0.05), whereas total phosphorus, total dissolvable salt levels, and pH were positively correlated with Chao1 values (P<0.05).Conclusion: In summary, these findings reveal that Glomus and Diversispora are key AMF genera found within the rhizosphere soil of Ferula sinkiangensis. These fungi are closely associated with specific environmental and soil physicochemical properties. The physical and chemical properties of these soil samples also differed significantly as a function of slope position (P<0.05). Together, our results provide new insights regarding the relationship between AMF species and Ferula sinkiangensis, providing a theoretical basis for further studies of their development.

scholarly journals High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding

2017 ◽  
Vol 114 (21) ◽  
pp. 5461-5466 ◽  
Author(s):  
Evan A. Boyle ◽  
Johan O. L. Andreasson ◽  
Lauren M. Chircus ◽  
Samuel H. Sternberg ◽  
Michelle J. Wu ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Adaptive Immune System ◽  
Dna Interaction ◽  
Biophysical Parameters ◽  
Guide Rna ◽  
Binding Behavior ◽  
Versatile Tool ◽  
Long Time ◽  
Target Binding

The bacterial adaptive immune system CRISPR–Cas9 has been appropriated as a versatile tool for editing genomes, controlling gene expression, and visualizing genetic loci. To analyze Cas9’s ability to bind DNA rapidly and specifically, we generated multiple libraries of potential binding partners for measuring the kinetics of nuclease-dead Cas9 (dCas9) interactions. Using a massively parallel method to quantify protein–DNA interactions on a high-throughput sequencing flow cell, we comprehensively assess the effects of combinatorial mismatches between guide RNA (gRNA) and target nucleotides, both in the seed and in more distal nucleotides, plus disruption of the protospacer adjacent motif (PAM). We report two consequences of PAM-distal mismatches: reversal of dCas9 binding at long time scales, and synergistic changes in association kinetics when other gRNA–target mismatches are present. Together, these observations support a model for Cas9 specificity wherein gRNA–DNA mismatches at PAM-distal bases modulate different biophysical parameters that determine association and dissociation rates. The methods we present decouple aspects of kinetic and thermodynamic properties of the Cas9–DNA interaction and broaden the toolkit for investigating off-target binding behavior.

scholarly journals Targeted DNA Methylation Analysis by High-Throughput Sequencing in Hepatic Carcinoma Tissue and Adjacent Normal Tissues

2020 ◽  
Author(s):  
Guangmou Zhang ◽  
Huigen Feng ◽  
Zhiqing Yuan
Keyword(s):  
Dna Methylation ◽  
Liver Cancer ◽  
Clinical Diagnosis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Methylation Analysis ◽  
Hepatic Carcinoma ◽  
Sequencing Technology ◽  
The Relationship ◽  
Dna Methylation Analysis

Abstract Background: The relationship between epigenetic abnormalities and tumorigenesi has been investigated in the past decade and made major advances, particularly the abnormal expression of small RNAs, DNA methylation, and histone modification in cancer. In many tumor-related studies, the regulatory changes in DNA methylation during cancer development and the development of resistance to anticancer drugs have show that DNA methylation can be used as a biomarker for cancer diagnosis and concomitant diagnosis, but there is a lack of clinically useful biomarkers associated with hepatic carcinoma. Using high-throughput sequencing technology, appropriate testing and validation can be carried out in large samples. The relationship between DNA methylation and tumor development can be explored, contributing to clinical diagnosis and personalized treatment of hepatic carcinoma. Methods: In this study, we implemented and evaluated the effectiveness of high-throughput sequencing for DNA methylation analysis in hepatic carcinoma. For the relationship between DNA methylation and gene expression, Pearson correlation analysis was used to evaluate the correlation. Twenty-five isolated genomic regions were amplified by PCR using bisulfite-transformed liver cancer tissue (Ca) and paracancer tissue (T) as template DNA. PCR final product sequence information was obtained by sequence analysis using Illumina Hiseq/Miseq platform. Results: The average depth of coverage across all amplicons was 30,548 for T and 29,346 for Ca, with a maximum of 3,675 at the ARID1A amplicon and a minimum of 65 at the PTEN amplicon. Methylation spectra were obtained for each genomic locus of the two groups of samples, and the results showed that methylation was significantly different at the X target loci and slightly different at the Y target loci. Cluster analysis showed that all T tissues were clustered in one group (except tissues T2 and T3), while Ca tissues were clustered on the other side. The results showed that DNA methylation at the loci may be closely related to liver cancer, providing references for the research and development of biomarkers in clinical diagnosis. Conclusions: The study demonstrates that high-throughput sequencing technology is a powerful and cost-effective method for methylation analysis of target DNA in cancer tissues.

scholarly journals High-throughput Sequencing Analysis of the Rhizosphere Arbuscular Mycorrhizal Fungi (AMF) Community Composition Associated with Ferula Sinkiangensis

2020 ◽  
Author(s):  
Yunfeng Luo ◽  
Yaling He ◽  
Guifang Li ◽  
Xinhua Lv ◽  
Zhongke Wang ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Community Composition ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Slope Position ◽  
Sequencing Analysis ◽  
Soil Physicochemical Properties ◽  
Ferula Sinkiangensis ◽  
The Relationship

Abstract Background: Ferula sinkiangensis is an important and increasingly endangered medicinal plant. Arbuscular mycorrhiza fungi (AMF) are microbes that live in the soil and can enhance nutrient uptake, stress resistance, and pathogen defens in host plants. The composition of AMF communities associated with Ferula sinkiangensis and the relationship between these fungi and other pertinent abiotic factors, however, remains uncertain. Herein, we collected samples of rhizosphere and surrounding soil at a range of depths (0-20, 20-40, and 40-60 cm) and a range of slop positions (bottom, middle, top). These samples were then subjected to analyses of soil physicochemical properties and high-throughput sequencing (Illumina MiSeq), enabling us to examine AMF community composition and diversity, as well as the relationship between these parameters and other abiotic factors. Results: Through this analysis, we determined that Glomus and Diversispora were enriched in all samples. AMF diversity and richness varied significantly as a function of slope position, with this variation primarily being tied to differences in Glomus and Diversispora abundance. In contrast, no significant relationship between soil depth and overall AMF composition was noted, although some AMF were found to be sensitive to depth. Many factors were found to significantly affect AMF community composition, including organic matter (OM), TN (total nitrogen), TK (total potassium), AN (ammonium nitrogen), NN (nitrate nitrogen), AK (available potassium), TDS (total soluble salt), pH, SM (soil water content), and AE (slope position). We further found that Shannon diversity index values in these communities were positively correlated with TP (total phosphorus), NN, and pH values (p<0.05), while TP, TDS, and pH were positively correlated with Chao1 values (p<0.05). Conclusion: In summary, these findings reveal that Glomus and Diversispora are key AMF genera found within the rhizosphere soil of Ferula sinkiangensis. These fungi are closely associated with specific environmental and soil physicochemical properties. And The physical and chemical properties of soil were significantly different (p<0.05) because of slope position. Together, our results provide a novel understanding of the relationship between AMF species and Ferula sinkiangensis, providing a theoretical basis for further studies of their development.

scholarly journals N2-neutrophils Promote Invasion and Metastasis of Ovarian Cancer by Upregulating MAPK Signaling

2020 ◽  
Author(s):  
caixia li ◽  
Chuandi Men ◽  
Weihong Yang ◽  
Qi Liu ◽  
Shupeng Liu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Molecular Biology ◽  
Signaling Pathway ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Invasion And Metastasis ◽  
Relationship Of ◽  
The Relationship

Abstract Background: Metastasis is an important factor of high mortality in ovarian cancer. Neutrophils are involved in multiple pathologic mechanisms of cancer,including invasion and metastasis. However, the relationship of neutrophils and invasion and metastasis in ovarian cancer is unclear,as well as the exact mechanism.Methods:To verify the relationship of neutrophils and invasion and metastasis in ovarian cancer,we tested the expression of CD11b in 24 groups of benign and malignant ovarian tumor tissues.And then,we tested the expression of CD11b,CXCL8,and CXCR1 in 16 cases of ovarian cancer,including primary lesions, metastatic lesions and adjacent carcinoma tissues.We successfully build tumor associated neutrophils research model (N1 and N2) and prove that N2-neutrophils can promote the invasion and metastasis of ovarian cancer. Next,we screened the significantly changed MAPK signaling pathway by high-throughput sequencing. And then confirmed this conclusion by molecular biology experiments. Results:The expression of CD11b was significantly higher in malignant tumor than benign tumor tissues tested by western blot and Immunohistochemistry.The expression of CD11b,CXCL8 and CXCR1 is highest in ovarian cancermetastases ,followed by the primary lessions, and then the adjacent carcinoma tissues tested by PCR and WB methods.We proved that N2-neutrophils can promote the invasion and metastasis of ovarian cancer by transwell assay.Forthermore,we detected the related indicators of metastasis including MMP-2,MMP-9,E-Cadherin,N-cadherin and Vimentin by PCR and WB methods.Next,we screened the significantly changed MAPK signaling pathway by High-throughput sequencing through comparing ovarian cancer cells before and after co-cultured with N2-neutrophils. At last,we found the key gene P38 of MAPK signaling pathway by molecular biology experiments. Conclusions: N2-neutrophils promote the invasion and metastasis of ovarian cancer by Upregulating MAPK signaling pathway, find a key gene P38.

scholarly journals Analysis of the relationship between caecal flora difference and production performance of two rabbit species by high-throughput sequencing

2021 ◽  
Author(s):  
Zhiqiang Guo ◽  
Bin Wang ◽  
Jingzhi Lu ◽  
Congyan Li ◽  
Liangde Kuang ◽  
...  
Keyword(s):  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Average Daily Gain ◽  
Intestinal Flora ◽  
Nutritional Composition ◽  
Production Performance ◽  
Light Cycle ◽  
The Difference ◽  
The Relationship

The purpose of this experiment is to study the relationship between the difference in production performance between Sichuan White (SC) rabbits and New Zealand (NZL) rabbits and the diversity of caecal flora. Twelve pregnant SC rabbits and 12 NZL female rabbits were selected for this experiment. After delivery, the young rabbits were divided into two groups according to breeds, each group had 30 replicates, and each replicate had one rabbit. During the experiments, these rabbits were kept in the same room, and the temperature in the room was controlled at 12–25 °C, with a 16-hour light cycle every 24 hours. The nutritional composition of the feed and other environmental conditions were consistent. On the 59<sup>th</sup> day of the experiment, the caecum contents of the two groups of young rabbits were collected. The results showed that the survival rate of the SC rabbit group was higher than that of the NZL rabbit group, and the diarrhoea rate and average daily gain were lower than those of the NZL rabbit group (P &lt; 0.05). The results of high-throughput sequencing of the 16S gene showed that compared with the NZL rabbit group, the relative abundance of Bacteroides increased, and the abundance of harmful flora Verrucomicrobia and Proteobacteria decreased (P &lt; 0.05). Functional analysis of the microflora showed that the relative abundance of carbohydrate metabolism genes in the SC rabbit group was higher than in the NZL rabbit group. In conclusion, compared with the NZL rabbits, the SC rabbits have a more optimized intestinal flora structure and lower abundance of harmful bacteria. Moreover, the intestinal health level of SC rabbits is improved, and the tolerance to roughage of SC rabbits is increased.

scholarly journals High-throughput sequencing analysis of the rhizosphere arbuscular mycorrhizal fungi (AMF) community composition associated with Ferula sinkiangensis

2020 ◽  
Author(s):  
Yunfeng Luo ◽  
Zhongke Wang ◽  
Yaling He ◽  
Guifang Li ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Total Phosphorus ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Nitrate Nitrogen ◽  
Soil Depth ◽  
Slope Position ◽  
Soil Physicochemical Properties ◽  
Ferula Sinkiangensis ◽  
The Relationship

Abstract Background: Ferula sinkiangensis is an increasingly endangered medicinal plant. Arbuscular mycorrhiza fungi (AMF) are symbiotic microorganisms that live in the soil wherein they enhance nutrient uptake, stress resistance, and pathogen defense in host plants. While such AMF have the potential to contribute to the cultivation of Ferula sinkiangensis, the composition of AMF communities associated with Ferula sinkiangensis and the relationship between these fungi and other pertinent abiotic factors still remains to be clarified.Results: Herein, we collected rhizosphere and surrounding soil samples at a range of depths (0-20, 20-40, and 40-60 cm) and a range of slope positions (bottom, middle, top). These samples were then subjected to analyses of soil physicochemical properties and high-throughput sequencing (Illumina MiSeq). We determined that Glomus and Diversispora species were highly enriched in all samples. We further found that AMF diversity and richness varied significantly as a function of slope position, with this variation primarily being tied to differences in relative Glomus and Diversispora abundance. In contrast, no significant relationship was observed between soil depth and overall AMF composition, although some AMF species were found to be sensitive to soil depth. Many factors significantly affected AMF community composition, including organic matter content, total nitrogen, total potassium, ammonium nitrogen, nitrate nitrogen, available potassium, total dissolvable salt levels, pH, soil water content, and slope position. We further determined that Shannon diversity index values in these communities were positively correlated with total phosphorus, nitrate-nitrogen levels, and pH values (P<0.05), whereas total phosphorus, total dissolvable salt levels, and pH were positively correlated with Chao1 values (P<0.05). Conclusion: In summary, our data revealed that Glomus and Diversispora are key AMF genera found within Ferula sinkiangensis rhizosphere soil. These fungi are closely associated with specific environmental and soil physicochemical properties, and these soil sample properties also differed significantly as a function of slope position (P<0.05). Together, our results provide new insights regarding the relationship between AMF species and Ferula sinkiangensis, offering a theoretical basis for further studies of their development.

scholarly journals Up－Regulated miR-224-5p Can Target the Expression of Neuritin in Hearing Loss

2021 ◽  
Author(s):  
Yin Song ◽  
Xue Zhang ◽  
Jiawei Sun ◽  
Lina Li ◽  
Xiaofei Zhang ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Western Blot ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Differentially Expressed ◽  
Qrt Pcr ◽  
Kanamycin Sulfate ◽  
Differentially Expressed Mirnas ◽  
Mouse Hearing ◽  
The Relationship

Abstract Objective: This study screened the differentially expressed miRNAs in the mouse cochlea during hearing loss and explored the relationship between miR-224-5p and Neuritin.Methods: The combination of kanamycin sulfate and furosemide was used to establish a mouse hearing loss model. High-throughput sequencing was used to screen the differentially expressed miRNAs during hearing loss. qRT-PCR was used to identify the expression of differential miRNAs in hearing loss. Western Blot was used to detect the expression of Neuritin protein. Luciferase was used to identify the binding site of miRNA and Neuritin.Results: The expression of miR-224-5p in the mouse cochlea increased during hearing loss (p<0.05). MiR-224-5p mimics can reduce Neuritin protein expression in 293T cells (p<0.05). MiR-224-5p can specifically bind to Neuritin (p<0.05).Conclusion: The expression of miR-224-5p increases in hearing loss and targets the expression of Neuritin

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