Classification and identification of bacteria in the soil treated by AcMNPV using high-throughput sequencing technique

2015 ◽  
Vol 20 (5) ◽  
pp. 931-936 ◽  
Author(s):  
Yuejun Fu ◽  
Xing Li ◽  
Shuhua Zheng ◽  
Jun Du ◽  
Aihua Liang
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Technique ◽  
Identification Of Bacteria

scholarly journals Targeted high-throughput sequencing technique for the molecular diagnosis of primary immunodeficiency disorders

Medicine ◽  
2018 ◽  
Vol 97 (40) ◽  
pp. e12695 ◽  
Author(s):  
Zuo Hua Chi ◽  
Wei Wei ◽  
Ding Fang Bu ◽  
Huan Huan Li ◽  
Fei Ding ◽  
...  
Keyword(s):  
Primary Immunodeficiency ◽  
Molecular Diagnosis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Primary Immunodeficiency Disorders ◽  
Sequencing Technique

scholarly journals Removal of H2S by vermicompost biofilter and analysis on bacterial community

2020 ◽  
Vol 18 (1) ◽  
pp. 720-731
Author(s):  
Weiping Tian ◽  
Xuemin Chen ◽  
Peng Zhou ◽  
Xiaoyong Fu ◽  
Honghua Zhao
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Flow Rate ◽  
Gas Flow ◽  
High Throughput Sequencing ◽  
Community Characteristics ◽  
Microbial Inoculation ◽  
Sequencing Technique ◽  
Good Potential ◽  
Maximum Elimination Capacity

AbstractThe vermicompost collected from dewatered domestic sludge as packing material in biofilter was investigated for hydrogen sulfide (H2S) removal. No nutrients or microbial inoculation was added throughout the experiment. The corresponding bacterial community characteristics in the vermicompost biofilter of different spatial levels were evaluated by Miseq high-throughput sequencing technique. The results showed that the vermicompost biofilter performed well during operation. The H2S removal efficiency reached nearly 100% under condition of the inlet concentration <350 mg m−3 and 0.25−0.35 m3 h−1 gas flow rate. The maximum elimination capacity of 20.2 g m−3 h−1 was observed at a flow rate of 0.35 m3 h−1. Furthermore, the amounts of biodegraded products and pH varied accordingly. In addition, the results from high-throughput sequencing revealed pronouncedly spatial variation of the vermicompost, and the Rhodanobacter, Halothiobacillus, Mizugakiibacter as well as Thiobacillus, which can play an important role in removing H2S, were predominant in the final vermicompost. These results imply that the vermicompost with diverse microbial communities has a good potential for eliminating H2S.

scholarly journals Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap

2015 ◽  
Author(s):  
Hao Wang ◽  
Joel McManus ◽  
Carl Kingsford
Keyword(s):  
Alternative Splicing ◽  
Open Source ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Repetitive Sequences ◽  
Transcript Abundance ◽  
Accurate Estimate ◽  
Ribosome Profiling ◽  
Occupancy Estimation ◽  
Sequencing Technique

Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30 bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. We present a technique and software that addresses this problem by assigning reads to potential origins proportional to estimated transcript abundance. This yields a more accurate estimate of ribosome profiles compared with a naïve mapping. Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomap.

scholarly journals Application of high throughput sequencing in veterinary science

2022 ◽  
Vol 78 (02) ◽  
pp. 6622-2022
Author(s):  
ALEKSANDRA GIZA ◽  
EWELINA IWAN ◽  
DARIUSZ WASYL
Keyword(s):  
High Throughput ◽  
Environmental Samples ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Veterinary Science ◽  
Expression Of Genes ◽  
Outbreak Investigations ◽  
Genomic Studies ◽  
Identification Of Bacteria ◽  
The One

High throughput sequencing (HTS) creates an opportunity for comprehensive genomic studies. It can be applied in veterinary science, bacteriology and virology, diagnostics of animal diseases, food safety, examinations of the composition of environmental samples, and even in veterinary vaccinology. Thus HTS a wide-ranging method that can be applied in different areas of the One Health approach. In particular, the whole genome sequencing (WGS) of bacteria is routinely used in food hygiene and outbreak investigations for phylogenetic analysis of pathogenic bacteria isolated from various sources across timeline, molecular characterisation of bacteria, plasmids, antibiotic resistance and identification of virulence factors. Metagenomics can be used to characterize the composition of microbiota in environmental samples. It makes it possible to obtain a taxonomic identification of bacteria, fungi or plants present in a metasample. It can also be used for the monitoring and epidemiological tracing of viruses, such as SARS-CoV-2. The transcriptomic approach makes it possible to study the expression of genes associated with various infections and diseases. HTS is a highly versatile method, but the selection of the proper application is crucial to obtain expected outcomes. The paper presents some HTS approaches and examples of research in veterinary science.

scholarly journals Heterologous expression of a novel β-1, 4-glucosidase originated from Aspergillus fresenii and its enzymatic characters

2019 ◽  
Author(s):  
Yongzhi Yang ◽  
Jian Wang ◽  
Henan Guo ◽  
Yunhe Cao
Keyword(s):  
Amino Acid ◽  
Enzymatic Activity ◽  
Heterologous Expression ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Enzymatic Reaction ◽  
Sequencing Analysis ◽  
The Novel ◽  
Amino Acid Residues ◽  
Sequencing Technique

Abstract Background: β-1, 4-glucosidases play important roles in the degradation of lignocellulosic biomass. It helps generate glucose from cellobiose and oligosaccharides, which could enhance the productivity in biorefinery and bioconversion process for energy and chemicals. Discovering novel β-1, 4-glucosidases can provide broader possibilities and understanding. The purpose of this study was to find a new β-1, 4-glucosidase in Aspergillus fresenii by an efficient method based on the high throughput sequencing technique. Results: With the high throughput sequencing technique, a novel β-1, 4-glucosidase, named bgl T2, was cloned from Aspergillus fresenii , which was 2586 bp encoding 862 amino acid residues based on the sequencing analysis. Its amino acid sequence shared 91%, 80%, 80%, and 78% identity with the β-glucosidases of Aspergillus steynii IBT 23096 (XP_024702113.1), Aspergillus oryzae (5FJJ_A), Aspergillus aculeatus (P48825.1), and Aspergillus fumigatus A1163 (B0XPE1.1), respectively. The β-glucosidase bgl T2 gene was optimized according to the codon bias of Komagataella phaffii (≡ Pichia pastoris (nom. illeg.)) and synthetized. The optimized bgl T2 gene was inserted into plasmid pPICZαA, and transformed into K.phaffii X33 for its heterologous expression and enzymatic characters determination. The heterologous expressed β-glucosidase bgl T2 presented the highest activity at 55 °C and pH 5.5. When bgl T2 treated in citric acid- disodium hydrogen phosphate buffer (from pH 2.5 to pH 8.0) for one hour, the enzymatic activity was stable for pH 3.0 to pH 8.0 treatment, while the enzymatic activity dropped down to 22% with the pH 2.5 treatment. The thermostability half-life of bgl T2 was 9 min 36 s, 4 min 22 s, 117 s, and 68 s under 50 °C, 55 °C, 60 °C, 65 °C incubation, respectively. The Michaelis constant ( K m ) of bgl T2 was 0.0007 mol/L. The maximum rate of bgl T2 theoretical enzymatic reaction ( V max ) was 9×10 -8 mol/L/s. In a 5 L fermentation vessel, the recombinant K.phaffii X33 could yield a β-1, 4-glucosidase activity of 4.45 U/mL after 96 h methanol inducement. Conclusions: As the important enzyme to release glucose in the hydrolysis processes of cellulose, the novel bgl T2 provide a possibility to apply in bioenergy engineering, food processing, feed industry, and nutritional study, etc. This study also developed a path to obtain new enzymes depending on high throughput sequencing technique.

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