scholarly journals Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas

2017 ◽  
Vol 11 (S7) ◽  
Author(s):  
Kai-Yao Huang ◽  
Tzu-Hao Chang ◽  
Jhih-Hua Jhong ◽  
Yu-Hsiang Chi ◽  
Wen-Chi Li ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
High Throughput ◽  
Transcriptome Data ◽  
Natural Antimicrobial

scholarly journals High-Throughput Identification of Putative Antimicrobial Peptides from Multi-Omics Data of the Lined Seahorse (Hippocampus erectus)

Marine Drugs ◽  
2019 ◽  
Vol 18 (1) ◽  
pp. 30 ◽  
Author(s):  
Xiyang Chen ◽  
Yunhai Yi ◽  
Xinxin You ◽  
Jie Liu ◽  
Qiong Shi
Keyword(s):  
Antimicrobial Peptides ◽  
High Throughput ◽  
Large Scale ◽  
Food Additives ◽  
The Body ◽  
Transcriptome Data ◽  
Proteomics Data ◽  
Fish Food ◽  
Short Supply ◽  
Hippocampus Erectus

Lined seahorse (Hippocampus erectus), the most widely cultivated seahorse in China, has been in short supply because of its important medicinal value; meanwhile, unnatural deaths caused by various diseases (especially enteritis) have limited their practical large-scale aquaculture. Antimicrobial peptides (AMPs), as the best alternative to antibiotics, have been extensively applied in agricultural practices. In this study, we identified 290 putative AMP sequences from our previously published genome and transcriptome data of the lined seahorse. Among them, 267 are novel, and 118 were validated by our proteome data generated in the present study. It seems that there is a tissue preference in the distribution of AMP/AMP precursor transcripts, such as lectins in the male pouch. In addition, their transcription levels usually varied during development. Interestingly, the representative lectins kept extremely high levels at the pre-pregnancy stage while at relatively lower levels at other stages. Especially Lectin25, with the highest transcription levels and significant developmental changes, has been reported to be involved in seahorse and human pregnancy. The comparison of transcriptome data between one-day and three-month juveniles indicated that Hemoglobin2 (Hemo2) was significantly upregulated in the body, haslet, and brain. Our proteome data of female and male individuals revealed three putative AMP precursors with sexual specificity, including two male-biased cyclin-dependent kinases (CDK-like16 and CDK-like23) and one female-biased bovine pancreatic trypsin inhibitor 2 (BPTI2). In conclusion, our present high-throughput identification of putative AMP sequences from multi-omics (including genomics, transcriptomics, and proteomics) data provides an overview of AMPs in the popular lined seahorse, which lays a solid foundation for further development of AMP-based fish food additives and human drugs.

The role of natural antimicrobial peptides during infection and chronic inflammation

2017 ◽  
Vol 111 (1) ◽  
pp. 5-26 ◽  
Author(s):  
Xiaojing Xia ◽  
Likun Cheng ◽  
Shouping Zhang ◽  
Lei Wang ◽  
Jianhe Hu
Keyword(s):  
Antimicrobial Peptides ◽  
Chronic Inflammation ◽  
Natural Antimicrobial

scholarly journals Natural antimicrobial peptides againstMycobacterium tuberculosis

2015 ◽  
Vol 70 (5) ◽  
pp. 1285-1289 ◽  
Author(s):  
Maria Abedinzadeh ◽  
Mahdieh Gaeini ◽  
Soroush Sardari
Keyword(s):  
Antimicrobial Peptides ◽  
Natural Antimicrobial

scholarly journals Natural Antimicrobial Peptides from Eukaryotic Organisms

10.5772/33293 ◽  
2012 ◽  
Author(s):  
Renaud Conde ◽  
Martha Arguello ◽  
Javier Izquierdo ◽  
Raul Noguez ◽  
Miguel Moreno ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Natural Antimicrobial ◽  
Eukaryotic Organisms

scholarly journals Peptide Antibiotics Developed by Mimicking Natural Antimicrobial Peptides

2017 ◽  
Vol 06 (04) ◽  
Author(s):  
Nihan Unubol ◽  
Suleyman Selim Cinaroglu ◽  
Merve Acikel Elmas ◽  
Sumeyye Akcelik ◽  
Arzu Tugba Ozal Ildeniz ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Peptide Antibiotics ◽  
Natural Antimicrobial

scholarly journals A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Michal Kucharski ◽  
Jaishree Tripathi ◽  
Sourav Nayak ◽  
Lei Zhu ◽  
Grennady Wirjanata ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Rna Extraction ◽  
Transcriptome Data ◽  
High Quality ◽  
Diverse Range ◽  
Human Haemoglobin ◽  
Infected Blood ◽  
Blood Samples ◽  
Total Rna

Abstract Background Sequencing technology advancements opened new opportunities to use transcriptomics for studying malaria pathology and epidemiology. Even though in recent years the study of whole parasite transcriptome proved to be essential in understanding parasite biology there is no compiled up-to-date reference protocol for the efficient generation of transcriptome data from growing number of samples. Here, a comprehensive methodology on how to preserve, extract, amplify, and sequence full-length mRNA transcripts from Plasmodium-infected blood samples is presented that can be fully streamlined for high-throughput studies. Results The utility of various commercially available RNA-preserving reagents in a range of storage conditions was evaluated. Similarly, several RNA extraction protocols were compared and the one most suitable method for the extraction of high-quality total RNA from low-parasitaemia and low-volume blood samples was established. Furthermore, the criteria needed to evaluate the quality and integrity of Plasmodium RNA in the presence of human RNA was updated. Optimization of SMART-seq2 amplification method to better suit AT-rich Plasmodium falciparum RNA samples allowed us to generate high-quality transcriptomes from as little as 10 ng of total RNA and a lower parasitaemia limit of 0.05%. Finally, a modified method for depletion of unwanted human haemoglobin transcripts using in vitro CRISPR-Cas9 treatment was designed, thus improving parasite transcriptome coverage in low parasitaemia samples. To prove the functionality of the pipeline for both laboratory and field strains, the highest  2-hour resolution RNA-seq transcriptome for P. falciparum 3D7 intraerythrocytic life cycle available to  date was generated, and the entire protocol was applied to create the largest transcriptome data from Southeast Asian field isolates. Conclusions Overall, the presented methodology is an inclusive pipeline for generation of good quality transcriptomic data from a diverse range of Plasmodium-infected blood samples with varying parasitaemia and RNA inputs. The flexibility of this pipeline to be adapted to robotic handling will facilitate both small and large-scale future transcriptomic studies in the field of malaria.

scholarly journals High Throughput Identification of Antimicrobial Peptides from Fish Gastrointestinal Microbiota

Toxins ◽  
2017 ◽  
Vol 9 (9) ◽  
pp. 266 ◽  
Author(s):  
Bo Dong ◽  
Yunhai Yi ◽  
Lifeng Liang ◽  
Qiong Shi
Keyword(s):  
Antimicrobial Peptides ◽  
High Throughput ◽  
Gastrointestinal Microbiota
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