Abundant long, noncoding RNAs (lncRNAs) in mammals can bind to DNA sequences and recruit histone- and DNA-modifying enzymes to binding sites to epigenetically regulate target genes. However, most ...lncRNAs' binding motifs and target sites are unknown. The large numbers of lncRNAs and target sites in the whole genome make it infeasible to examine lncRNA binding to DNA purely experimentally. Here, we report a protocol for lncRNA/DNA-binding analysis that is built upon a database containing the GENCODE-annotated human and mouse lncRNAs, the orthologs of these lncRNAs in 17 mammals, and the genome sequences of the 17 mammals. Cross-species and genome-wide lncRNA/DNA-binding analysis begins with and is driven by database search. The predicted DNA-binding motifs and binding sites answer the general question of which lncRNAs may epigenetically regulate which genes, and can be used to identify potential sites for genome and epigenome editing. To use the protocol, preliminary knowledge of the base-pairing rules that guide the binding of noncoding RNAs to DNA to form triplexes, as well as the skills required to use the UCSC Genome Browser, are needed. A genome-wide prediction takes from 2 to 10 d, and the results are sent to users automatically by e-mail. The platform is updated continuously, making it possible to study more lncRNAs and larger genomic regions in less computational time.
Correlation between objects is prone to occur coincidentally, and exploring correlation or association in most situations does not answer scientific questions rich in causality. Causal discovery ...(also called causal inference) infers causal interactions between objects from observational data. Reported causal discovery methods and single-cell datasets make applying causal discovery to single cells a promising direction. However, evaluating and choosing causal discovery methods and developing and performing proper workflow remain challenges. We report the workflow and platform CausalCell (http://www.gaemons.net/causalcell/causalDiscovery/) for performing single-cell causal discovery. The workflow/platform is developed upon benchmarking four kinds of causal discovery methods and is examined by analyzing multiple single-cell RNA-sequencing (scRNA-seq) datasets. Our results suggest that different situations need different methods and the constraint-based PC algorithm with kernel-based conditional independence tests work best in most situations. Related issues are discussed and tips for best practices are given. Inferred causal interactions in single cells provide valuable clues for investigating molecular interactions and gene regulations, identifying critical diagnostic and therapeutic targets, and designing experimental and clinical interventions.
Zooplankton play a pivotal role in connecting primary producers and high trophic levels, and changes in their temporal and spatial distribution may affect the entire marine ecosystem. The spatial and ...seasonal taxonomic composition patterns of mesozooplankton in Bohai Bay were investigated in relation to a number of water parameters. Bohai Bay is a eutrophic semi-enclosed bay with dynamic physico-chemical conditions influenced by terrestrial inputs and seawater intrusion. The results showed that under the condition of terrigenous input, the diversity of mesozooplankton species near the eutrophic Haihe River Estuary and Jiyun River Estuary was lower than that in the central Bohai Bay, with gelatinous Oikopleura dioica as the dominant species. The mesozooplankton diversity was highest in the bay mouth affected by seawater intrusion, and the dominant oceanic species, mainly copepods Corycaeus affinis, Calanus sinicus, and Oithona similis, entered the inner bay from the bay mouth. Meanwhile, the abundance of mesozooplankton in summer was significantly higher than that in autumn. Compared with historical data, the dominant species in Bohai Bay has evolved from arrow worm Sagitta crassa to copepod Paracalanus parvus, probably due to global warming, indicating the effects of human activities on the succession of mesozooplankton community.
The dilution experiment technique was used in two cruises in July-August (summer) and October-November (autumn) 2020, with a total of 14 stations. The grazing impact of microzooplankton on ...phytoplankton in the interior of Bohai Bay was comprehensively investigated. We compared phytoplankton growth rates (μ
0
) and microzooplankton grazing rates (m) spatially (distance between experimental stations and shore far vs. near) and seasonally (summer vs. autumn). Both m and μ
0
values were significantly higher in summer than in autumn, and the phytoplankton growth rate μ
0
was positively correlated to temperature. Offshore stations showed higher values. There is no significant spatial and seasonal differences in the ratio of microzooplankton grazing rate and phytoplankton growth rate (m/μ
0
) indicating that daily consumption of primary production by microzooplankton was similar in the two seasons. Therefore, our research showed a close coupling between microzooplankton grazing with phytoplankton growth in the Bohai Bay.
Many long noncoding RNAs (lncRNAs) can bind to DNA sequences proximal and distal to abundant genes, thereby regulating gene expression by recruiting epigenomic modification enzymes to binding sites. ...Because a lncRNA's target genes scattering in a genome have correlated functions, epigenetic analyses should often be genome-wide on both genome and transcriptome levels. Multiple tools have been developed for predicting lncRNA/DNA binding, but fast and accurate genome-wide prediction remains a challenge. Here we report Fasim-LongTarget (a revised version of LongTarget), compare its performance with TDF and LongTarget using the experimental data of the lncRNA MEG3, NEAT1, and MALAT1, and describe a case of genome-wide prediction. Fasim-LongTarget is as accurate as LongTarget and more accurate than TDF and is 200 times faster than LongTarget, making accurate genome-wide prediction feasible. The code is available on the Github website (https://github.com/LongTarget/Fasim-LongTarget), and the online service is available on the LongTarget website (https://lncRNA.smu.edu.cn).
The Haihe River system is a major conduit of land-based pollution into the Bohai Sea in North China, This study presented the first-ever observation of hypoxia in the Haihe River estuary, providing ...valuable insights into the complex interplay between physical and biochemical factors influencing hypoxia in estuarine systems. The research found seasonal variations in DO distribution in the estuaries of the Haihe and Yongdingxin Rivers. Hypoxia emerged in summer at the bottom of the Haihe River estuary and dissipated in autumn, with the minimum DO concentration of 1.85 mg/L recorded at the bottom of the HH-2 station. Within the hypoxic zone, the average DO concentration was 4.02 mg/L, and the average of DO saturation was less than 0.4. This study also identified the primary drivers of summer hypoxia as a combination of physical and biochemical factors, with water stratification due to hydrodynamic factors limiting exchange and reoxygenation between different water layers. In addition, the decomposition of organic matter in the bottom consumed a significant amount of dissolved oxygen.The significantly higher DO concentration and saturation in autumn compared to summer suggested the possible existence of seasonal hypoxia in the Haihe estuary. This study of hypoxia in the Haihe River estuary contribute to a better understanding of the factors that influence seasonal hypoxia. The findings have important implications for the management and remediation of hypoxia in the Haihe estuary and other estuarine systems.
Introduction
Polluted bays are one of the critical areas for the production and emissions of marine nitrous oxide (N2O), which has a strong effect on global warming and plays a critical role in ...stratospheric ozone depletion.
Methods
In 2020, the distributions of N2O concentrations and emissions in the water column of Bohai Bay (BHB) were surveyed during two cruises.
Results and discussion
The average N2O concentrations were higher in summer compared to autumn, with the oversaturation of N2O in both seasons. A declining gradient of N2O was found from the Hai River and Yellow River estuarine areas to the offshore sea, particularly in summer, implying riverine input was an important source of N2O. The vertical distribution of N2O was uniform in each season owing to the vertical mixing of water columns in the offshore sea, with N2O hotspots at the bottom of the two estuaries in summer and at the surface of the Hai River estuary in autumn. Moreover, the dominant sources of dissolved N2O were analyzed. N2O in the water column was predominately produced by nitrification and coupled nitrification-denitrification on suspended particulate matter. The mixing of water masses, particularly polluted water masses from coastal input, provides high N2O to the entire area of BHB, particularly in summer. Notably, nutrient and organic matter input from the coast could also indirectly drive N2O production by stimulating microbe activities of nitrification and denitrification under the water currents. In addition, statistical analysis revealed that ammonium, dissolved oxygen, and temperature were the dominant controlling factors of N2O in BHB. The annual flux of N2O in BHB was evaluated to be 6.5 Gg, accounting for 0.15% of the global oceanic N2O emission with 0.0044% of the global ocean area. Hence, as a typical polluted bay, BHB acted as a strong N2O source to the atmosphere on a per-unit-area basis.
Comprising one of the major carbon pools on Earth, marine dissolved organic matter (DOM) plays an essential role in global carbon dynamics. The objective of this study was to better characterize DOM ...in the eastern Indian Ocean. To better understand the underlying mechanisms, seawater samples were collected in October and November of 2020 from sampling stations in three subregions: the mouth of the Bay of Bengal, Southern Sri Lanka, and Western Sumatra. We calculated and evaluated different hydrological parameters and organic carbon concentrations. In addition, we used excitation emission matrix (EEM) spectroscopy combined with parallel factor analysis (PARAFAC) to analyze the natural water samples directly. Parameters associated with chromophoric DOM did not behave conservatively in the study areas as a result of biogeochemical processes. We further evaluated the sources and processing of DOM in the eastern Indian Ocean by determining four fluorescence indices (the fluorescence index, the biological index, the humification index, and the freshness index β
/
α). Based on EEM-PARAFAC, we identified six components (five fluorophores) using the peak picking technique. Commonly occurring fluorophores were present within the sample set: peak A (humic-like), peak B (protein-like), peak C (humic-like), and peak T (tryptophan-like). The fluorescence intensity levels of the protein-like components (peaks B and T) were highest in the surface ocean and decreased with depth. In contrast, the ratio of the two humic-like components (peaks A and C) remained in a relatively narrow range in the bathypelagic layer compared to the surface layer, which indicates a relatively constant composition of humic-like fluorophores in the deep layer.
Marine dissolved organic matter (DOM) plays an important role in aquatic ecosystems and is an essential reservoir of organic carbon in the marine carbon cycle. In this study, seawater DOM samples ...from 33 stations were collected in spring 2022 (April to May, 20 stations) and autumn 2020 (October to November, 13 stations) to better characterize and compare DOM variability within 200 m water layer in the eastern Indian Ocean (EIO). Hydrological parameters, nutrients and spectroscopic indices were calculated and evaluated for two cruises. In addition, excitation emission matrix spectroscopy combined with parallel factor analysis (EEM-PARAFAC) was used to directly analyse seawater DOM samples. The sources and processes of DOM in the EIO were assessed by fluorescence index (FI), freshness index (β/α), Biological index (BIX), and humification index (HIX). Three fluorescent components were identified in DOM samples from two cruises, including: C1 (tryptophan- and tyrosine-like), C2 (marine and/or terrestrial humic-like), and C3 (terrestrial humic-like). The components of C1 accounted for 39.45 % ± 8.79 %, C2 for 33.05 % ± 6.42 %, and C3 for 27.20 % ± 4.47 % within 200 m water layer. The intensity of the DOM fluorescence seems to varied due to seasonal differences. In particular, the source of the DOM fraction varied at <100 m layer, which may also be related to the structure of the microbial community. Further, there is a strong correlation between the depth of seawater and hydrographic parameters, fluorescence indices and fluorescence components. Nutrients (nitrate, dissolved inorganic phosphate, and dissolved silicate) and humic-like fractions are more likely to accumulate in the deeper layers of the ocean. Thus, these results provide some data support for the variability of DOM fractions on a vertical scale in the EIO.
•Protein-like and humic-like components were found in DOM samples from the EIO.•The protein-like component is predominant in the <200 m water layer.•Nutrients and humic-like components are more likely to accumulate in the deeper layers of the ocean.•No significant effect of seasonal differences on the proportion of DOM components in the oligotrophic EIO.
This study investigated the structure and function of macrobenthic community in Bohai Bay upon improvement of water quality due to pollution abatement. A total of 166 species were collected in the ...summer and autumn sampling, with an increase in sensitive species recorded as compared to data from previous studies. While historical variations in species richness indicated signs of improvement in community structure, results of functional diversity indices revealed that the macrobenthic community in Bohai Bay was still in an early stage of recovery. From BIO-ENV analysis, habitat instability may hinder how community responded to water quality improvement. Results of the benthic habitat quality assessment also indicated that the ecological status in most areas of Bohai Bay was classified as good, while a few estuarine regions were categorized in a poor status.
•Signs of recovery in species richness were detected.•Sensitive species have shown signs of dominance.•Seasonal and spatial variation in species and functional diversity was observed.•Most sampling sites in Bohai Bay could be classified as good ecological status.
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