scholarly journals Analysis of high-throughput sequencing for cecal microbiota diversity and function in hens under different rearing systems

3 Biotech ◽  
2019 ◽  
Vol 9 (12) ◽  
Author(s):  
Shuiqin Shi ◽  
Zhao Qi ◽  
Bintao Gu ◽  
Baoyan Cheng ◽  
Jian Tu ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Cecal Microbiota ◽  
And Function ◽  
Microbiota Diversity

scholarly journals Behavior Individuality: A Focus on Drosophila melanogaster

2021 ◽  
Vol 12 ◽  
Author(s):  
Rubén Mollá-Albaladejo ◽  
Juan A. Sánchez-Alcañiz
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Great Effort ◽  
Behavioral Differences ◽  
Adult Behavior ◽  
Large Numbers ◽  
Environmental Variations ◽  
And Function

Among individuals, behavioral differences result from the well-known interplay of nature and nurture. Minute differences in the genetic code can lead to differential gene expression and function, dramatically affecting developmental processes and adult behavior. Environmental factors, epigenetic modifications, and gene expression and function are responsible for generating stochastic behaviors. In the last decade, the advent of high-throughput sequencing has facilitated studying the genetic basis of behavior and individuality. We can now study the genomes of multiple individuals and infer which genetic variations might be responsible for the observed behavior. In addition, the development of high-throughput behavioral paradigms, where multiple isogenic animals can be analyzed in various environmental conditions, has again facilitated the study of the influence of genetic and environmental variations in animal personality. Mainly, Drosophila melanogaster has been the focus of a great effort to understand how inter-individual behavioral differences emerge. The possibility of using large numbers of animals, isogenic populations, and the possibility of modifying neuronal function has made it an ideal model to search for the origins of individuality. In the present review, we will focus on the recent findings that try to shed light on the emergence of individuality with a particular interest in D. melanogaster.

scholarly journals Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology

2020 ◽  
Vol 21 (22) ◽  
pp. 8774
Author(s):  
Natalia Komarova ◽  
Daria Barkova ◽  
Alexander Kuznetsov
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Combinatorial Libraries ◽  
Structure And Function ◽  
Huge Number ◽  
Systematic Evolution ◽  
And Function ◽  
Exponential Enrichment

Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.

scholarly journals Diagnostic high-throughput sequencing of 2,390 patients with bleeding, thrombotic and platelet disorders

2018 ◽  
Author(s):  
Kate Downes ◽  
Karyn Megy ◽  
Daniel Duarte ◽  
Minka Vries ◽  
Johanna Gebhart ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Clinical Phenotype ◽  
Careful Consideration ◽  
Clinical Diagnostics ◽  
Genomic Variation ◽  
Panel Test ◽  
Platelet Disorders ◽  
Normal Hemostasis ◽  
And Function

A targeted high-throughput sequencing (HTS) panel test for clinical diagnostics requires careful consideration of the inclusion of appropriate diagnostic-grade genes, the ability to detect multiple types of genomic variation with high levels of analytic sensitivity and reproducibility, and variant interpretation by a multi-disciplinary team (MDT) in the context of the clinical phenotype. We have sequenced 2,390 index patients using the ThromboGenomics HTS panel test of diagnostic-grade genes known to harbour variants associated with rare bleeding, thrombotic or platelet disorders (BPD). The diagnostic rate was determined by the clinical phenotype, with an overall rate of 50.4% for all thrombotic, coagulation, platelet count and function disorder patients and a rate of 6.2% for patients with unexplained bleeding disorders characterized by normal hemostasis test results. The MDT classified 756 unique variants, including copy number and intronic variants, as Pathogenic, Likely Pathogenic or Variants of Uncertain Significance. Almost half (49.7%) of these variants are novel and 41 unique variants were identified in 7 genes recently found to be implicated in BPD. Inspection of canonical hemostasis pathways identified 29 patients with evidence of oligogenic inheritance. A molecular diagnosis has been reported for 897 index patients providing evidence that introducing a HTS genetic test for BPD patients is meeting an important unmet clinical need.

scholarly journals High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers

2021 ◽  
Vol 22 (17) ◽  
pp. 9202
Author(s):  
Alissa Drees ◽  
Markus Fischer
Keyword(s):  
High Throughput ◽  
High Performance ◽  
High Throughput Sequencing ◽  
Selection Process ◽  
Next Generation ◽  
Binding Assays ◽  
Ligand Interaction ◽  
Modified Dna ◽  
Sequencing Platforms ◽  
And Function

Aptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. ‘High-throughput sequencing fluorescent ligand interaction profiling’ (HiTS–FLIP) significantly increases the selection efficiency and is consequently a very powerful and versatile technology for the selection of high-performance aptamers. It is the first experiment to allow the direct and quantitative measurement of the affinity and specificity of millions of aptamers simultaneously by harnessing the potential of optical next-generation sequencing platforms to perform fluorescence-based binding assays on the clusters displayed on the flow cells and determining their sequence and position in regular high-throughput sequencing. Many variants of the experiment have been developed that allow automation and in situ conversion of DNA clusters into base-modified DNA, RNA, peptides, and even proteins. In addition, the information from mutational assays, performed with HiTS–FLIP, provides deep insights into the relationship between the sequence, structure, and function of aptamers. This enables a detailed understanding of the sequence-specific rules that determine affinity, and thus, supports the evolution of aptamers. Current variants of the HiTS–FLIP experiment and its application in the field of aptamer selection, characterisation, and optimisation are presented in this review.

scholarly journals Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

Minerals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 596 ◽  
Author(s):  
Shuang Zhou ◽  
Min Gan ◽  
Jianyu Zhu ◽  
Xinxing Liu ◽  
Guanzhou Qiu
Keyword(s):  
Community Structure ◽  
Next Generation Sequencing ◽  
Microbial Ecology ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Structure And Function ◽  
Next Generation ◽  
Sequencing Technologies ◽  
And Function ◽  
Generation Sequencing

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

scholarly journals Auxiliary rapid identification of pathogenic and antagonistic microorganisms associated with Coptis chinensis root rot by high-throughput sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hailang Liao ◽  
Ling Huang ◽  
Na Li ◽  
Wenjia Ke ◽  
Yiqing Xiang ◽  
...  
Keyword(s):  
High Throughput ◽  
Root Rot ◽  
High Throughput Sequencing ◽  
Microbial Community Composition ◽  
Rapid Identification ◽  
Suppression Effect ◽  
Medical Quality ◽  
Antagonistic Microorganisms ◽  
Animal Pathogens ◽  
And Function

AbstractRoot rot reduces the yield and medical quality of C. chinensis (Cc). Previous studies of Coptis root rot focused on the identification of pathogens and the rhizosphere microbial community composition. The present study aimed to identify potential pathogenic and antagonistic microorganisms associated with root rot based on a high-throughput sequencing technique to prevent this disease. Healthy and diseased Cc in the endosphere and rhizosphere from the same field were collected to investigate the differences in microbiome composition and function. The results showed that the composition and function of microbes were different. The numbers of animal pathogens, soil saprotrophs, plant saprotrophs, and wood saprotrophs in the endosphere of diseased Cc were higher than those in the healthy endosphere and were dominated by Phaeosphaeriaceae, Cladorrhinum, Fusarium, Exophiala, and Melanommataceae. Fusarium, Volutella, Cladorrhinum, Cylindrocarpon, and Exophiala were significantly enriched in the endosphere of the diseased plants. Co-occurrence network analysis showed that Bacillus was negatively correlated with Fusarium, Volutella, and Cylindrocarpon, indicating that Bacillus may be antagonistic microorganisms. To verify the sequencing results, F. solani and F. avenaceum were isolated and verified as pathogens, and 14 Bacillus strains were isolated, which displayed an apparent suppression effect against the two pathogens on PDA medium and detached roots. The strategy of high-throughput sequencing has the potential for the comprehensive identification of pathogenic and antagonistic microorganisms for plant disease. These results provide research ideas and microbial resources for future studies on mitigating or preventing root rot damage to Cc.

scholarly journals High-Throughput Sequencing Analysis of the Composition and Diversity of the Bacterial Community in Cinnamomum camphora Soil

2021 ◽  
Vol 10 (1) ◽  
pp. 72
Author(s):  
Deqiang Chen ◽  
Weihong Sun ◽  
Shuang Xiang ◽  
Shuangquan Zou
Keyword(s):  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bulk Soil ◽  
Slope Position ◽  
Available Phosphorus ◽  
Sequencing Analysis ◽  
Sample Type ◽  
Cinnamomum Camphora ◽  
And Function

Soil bacterial communities and root-associated microbiomes play important roles in the nutrient absorption and healthy growth of host plants. Cinnamomum camphora is an important timber and special economic forest tree species in Fujian Province. In this study, the high-throughput sequencing technique was used to analyze the composition, diversity, and function of the bacterial communities present in the soil from different samples and slope positions of C. camphora. The results of this analysis demonstrated that the related bacterial communities in C. camphora soil were mainly clustered based on sample type. Bacterial alpha diversity in the rhizosphere and bulk soil of C. camphora growing downhill was higher than that of C. camphora growing uphill. At the phylum level, Bacteroidetes, Proteobacteria, Chloroflexi, and Gemmatimonadetes were positively correlated with pH, available phosphorus, total phosphorus, available potassium, and total potassium, while Acidobacteria and Verrucomicrobia were negatively correlated with alkaline-hydrolyzable nitrogen. These results show that there were remarkable differences in the composition, diversity, and function of related bacterial communities between different sample types of C. camphora soil. The slope position had a marked effect on the bacterial communities in the rhizosphere and bulk soil, while the root endosphere remained unaffected.

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