PeposX-Exhaust: A lightweight and efficient tool for identification of short peptides

Short peptides have become the focus of recent research due to their variable bioactivities, good digestibility and wide existences in food-derived protein hydrolysates. However, due to the high complexity of the samples, identifying short peptides still remains a challenge. In this work, a tool, named PeposX-Exhaust, was developed for short peptide identification. Through validation with known peptides, PeposX-Exhaust identified all the submitted spectra and the accuracy rate reached 75.36%, and the adjusted accuracy rate further reached 98.55% when with top 5 candidates considered. Compared with other tools, the accuracy rate by PeposX-Exhaust was at least 70% higher than two database-search tools and 15% higher than the other two de novo-sequencing tools, respectively. For further application, the numbers of short peptides identified from soybean, walnut, collagen and bonito protein hydrolysates reached 1145, 628, 746 and 681, respectively. This fully demonstrated the superiority of the tool in short peptide identification.

Prioritizing resource allocation to reduce adverse effects of pesticide risk for endangered species

The use of pesticides promotes food security because of the multiple benefits it brings to agriculture, such as reduction in crop losses. However, the use of pesticides can be potentially harmful to non-target species. In the U.S., the Environmental Protection Agency regulates the use of pesticides to manage the risks associated with these agents and to protect species under the Endangered Species Act. As part of these regulations, pesticides must be registered and then reviewed every 15 years to ensure the use conditions are updated with the best available data. The registration and review process can invoke corrective measures to ensure protection of endangered species. However, the registration review process is highly resource and time consuming. There is currently a backlog of unreviewed pesticides, leaving a large quantity of pesticides without updated use conditions to protect species. Identifying ways to streamline this process is urgently needed. We develop a sequencing approach to address the risk assessment bottleneck in the pesticide registration and review process and identify species that would benefit most from detailed assessments. We then demonstrate the magnitude of potential efficiencies using this sequencing process for 61 terrestrial listed species in the state of California. Our results show a consistent ranking of listed species according to their relative benefits from assessment, with 90 % of the species being robustly classified across scenarios in the sensitivity analysis. We found that prioritizing the assessment of a small group of species could potentially result in high conservation benefits, and identify species in need of more detailed data for a robust sequencing. We examine how a sequencing approach can guide decisions about what species might benefit most from different levels of assessment. Our results demonstrate the conservation benefits of employing a sequencing approach to prioritize the allocation of limited resources for endangered species.

CLIP-Seq to identify targets and interactions of RNA binding proteins and RNA modifying enzymes

The study of RNA chemical modifications is currently one of the most rapid-growing fields. Many types of RNA modifications in diverse RNA species have been shown to play versatile roles in a wide array of cellular processes. These modifications are installed and erased by writer and eraser enzymes, respectively. Additionally, RNA chemical modifications have downstream biological effects through either influencing changes in the chemistry or structure of RNA molecules or through recognition of the modification; these functions are primarily executed by the modification reader proteins. Reader proteins may bind to the modification site and cause a downstream signal cascade. One of the essential tools for studying erasers, writers, and readers is cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq). This method can detect the sites on endogenous RNAs bound by RNA-binding proteins or RNA modifying enzymes. Essentially, this strategy allows for snapshots of the epitranscriptome and molecular events occurring within the cell. In this article, we go through in detail the various steps involved in CLIP-seq.

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage

The objective of this study was to analyze the changes in the microbiota of milk products during fermentation and storage. Two kinds of Yoghurt, one Kefir, and one Acidophilus milk were observed during the fermentation process and storage using 16S rDNA amplicon sequencing. Cow's, goat's, raw and pasteurized milk were also examined. The most represented organisms in all manufactured products were shown to be those of the phylum Firmicutes. In some products, Proteobacteria, Bacteroidetes and Actinobacteria were also present in high amounts.