iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize.

The advent of full-length transcriptome sequencing technologies has accelerated the discovery of novel splicing isoforms. However, existing alternative splicing (AS) tools are either tailored for short-read RNA-Seq data or designed for human and animal studies. The disparities in AS patterns between plants and animals still pose a challenge to the reliable identification and functional exploration of novel isoforms in plants. Here, we developed integrated full-length alternative splicing analysis (iFLAS), a plant-optimized AS toolkit that introduced a semi-supervised machine learning method known as positive-unlabeled (PU) learning to accurately identify novel isoforms. iFLAS also enables the investigation of AS functions from various perspectives, such as differential AS, poly(A) tail length, and allele-specific AS (ASAS) analyses. By applying iFLAS to three full-length transcriptome sequencing datasets, we systematically identified and functionally characterized maize (Zea mays) AS patterns. We found intron retention not only introduces premature termination codons, resulting in lower expression levels of isoforms, but may also regulate the length of 3'UTR and poly(A) tail, thereby affecting the functional differentiation of isoforms. Moreover, we observed distinct ASAS patterns in two genes within heterosis offspring, highlighting their potential value in breeding. These results underscore the broad applicability of iFLAS in plant full-length transcriptome-based AS research.

Spatiotemporal response of water quality in fragmented mangroves to anthropogenic activities and recommendations for restoration.

Mangroves have received substantial attention for their pivotal role as ecological barriers between land and sea, owing to their capacity to effectively capture considerable quantities of terrestrial pollutants. Mangrove fragmentation has been a widespread global trend. There is limited information on the water quality status of these small scattered mangrove patches in coastal sub-developed areas, coupled with a paucity of efficient and intuitive assessment methodologies. To address this gap, the Water Quality Index (WQI) was introduced to evaluate the spatiotemporal characteristics of mangrove water quality. The major sources of pollution and anthropogenic activities that affect mangrove water quality were identified. The results revealed an average WQI value of 44.1 ± 13.3 for mangrove patches, consistently indicating a "low" water quality classification throughout all seasons. Both the size and natural conditions impact the water quality of mangroves. The large artificial patch (WQI: 56.4 ± 7.61) and the natural patch (WQI: 46.6 ± 13.6) exhibited relatively superior water quality, while the WQI value of a size-equivalent artificial patch compared with the natural patch is 38.6 ± 11.8. Aquaculture was the primary human activity that adversely affected the water quality of mangroves, and the potential sources of pollution were rainfall runoff and river discharge. These findings elucidate the unfavorable water quality characteristics and dominant pollution of fragmented mangroves, and validate the applicability of the WQI method for long-term evaluation of the water quality in mangrove patches. This study provides a basis for decision-making in water quality assessment and management of coastal wetlands and marine ecosystems. Scientific guidance to the management for mangrove protection and restoration was offered, such as regulating aquaculture activities, controlling non-point source pollution, implementing mangrove reforestation by using native species in historical mangrove sites.

Source, transport, and fate of perfluoroalkyl acids (PFAAs) in turbid bay environments: Significant roles of suspended sediment and water column stratification.

The coastal area was the major region receiving pollution from land-based sources into the sea. Perfluoroalkyl acids (PFAAs) in famous bays had aroused wide concern, but the importance of underdeveloped or small bays with notable levels of PFAAs were often neglected. Moreover, the roles of suspended sediment (SPS) and water column stratification on PFAA behaviors were unclear. In this study, PFAAs distribution in multiphase-multilayer in four underdeveloped bays (two urban bays and two island bays) were investigated. The urban bays not only had higher PFAA contamination but also posed a greater threat of short-chain PFAAs in water-SPS-sediment system than the island bays. The major source of PFAAs in water and SPS was domestic sewage in urban bays and was rainfall-runoff in island bays. Water column stratification with higher PFAA partition in water-SPS system in the surface layer than in the bottom layer was only found in the urban bays due to the higher human activity intensity. These provided new perspectives for managing emerging contaminants and establishing water quality criteria in the turbid coastal environment. The key role of SPS as a carrier offered possibilities to accurately differentiate the effects of dissolved and particulate PFAAs on bioavailability.

Export and risk from antibiotic remobilization from surrounding water to lake in the extreme 2020 Yangtze River basin flooding.

Global climate change increased the frequency of extreme rainfall events, leading to higher flood risk. In addition to the personal and property losses, another important consequence of a flood disaster was release and exposure risks from emerging contaminants, which was usually overlooked. The remobilization and fate of the antibiotics induced by floods remain unclear. We captured antibiotic concentrations around the Chaohu Lake after an unprecedented flood with a range of 5.0-317 ng/L. Higher concentrations in polder waters than their receiving rivers were attributed to the antibiotic release from soil particles and the sharp increase of water: soil ratio by flood storage. Source apportionment analysis of antibiotics implied that diffuse pollution by manure application and aquaculture activity was the predominant sources. Commonalities of spatial variations of antibiotics in polders were related to the condition of waterlogging and pollution source. The total antibiotic storage for all submerged polders was estimated at 27.9 kg. The concentrations and risks from pumping floodwater detained by polders into the lake were much higher than that from discharging flood directly into the lake. The retention-reaction-remobilization process would pose unexpectedly high risks for the lake. This study provided a new sight for constructing ecological wetland flood storage areas.

High-throughput methods for genome editing: the more the better.

During the last decade, targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) technologies, have permitted efficient targeting of genomes, thereby modifying these genomes to offer tremendous opportunities for deciphering gene function and engineering beneficial traits in many biological systems. As a powerful genome-editing tool, the CRISPR/Cas systems, combined with the development of next-generation sequencing and many other high-throughput techniques, have thus been quickly developed into a high-throughput engineering strategy in animals and plants. Therefore, here, we review recent advances in using high-throughput genome-editing technologies in animals and plants, such as the high-throughput design of targeted guide RNA (gRNA), construction of large-scale pooled gRNA, and high-throughput genome-editing libraries, high-throughput detection of editing events, and high-throughput supervision of genome-editing products. Moreover, we outline perspectives for future applications, ranging from medication using gene therapy to crop improvement using high-throughput genome-editing technologies.