Gap-free genome assembly of anadromous Coilia nasus.

The Chinese tapertail anchovy, Coilia nasus, is a socioeconomically important anadromous fish that migrates from near ocean waters to freshwater to spawn every spring. The analysis of genomic architecture and information of C. nasus were hindered by the previously released versions of reference genomes with gaps. Here, we report the assembly of a chromosome-level gap-free genome of C. nasus by incorporating high-coverage and accurate long-read sequence data with multiple assembly strategies. All 24 chromosomes were assembled without gaps, representing the highest completeness and assembly quality. We assembled the genome with a size of 851.67 Mb and used BUSCO to estimate the completeness of the assembly as 92.5%. Using a combination of de novo prediction, protein homology and RNA-seq annotation, 21,900 genes were functionally annotated, representing 99.68% of the total predicted protein-coding genes. The availability of gap-free reference genomes for C. nasus will provide the opportunity for understanding genome structure and function, and will also lay a solid foundation for further management and conservation of this important species.

Guided-deconvolution for correlative light and electron microscopy.

Correlative light and electron microscopy is a powerful tool to study the internal structure of cells. It combines the mutual benefit of correlating light (LM) and electron (EM) microscopy information. The EM images only contain contrast information. Therefore, some of the detailed structures cannot be specified from these images alone, especially when different cell organelle are contacted. However, the classical approach of overlaying LM onto EM images to assign functional to structural information is hampered by the large discrepancy in structural detail visible in the LM images. This paper aims at investigating an optimized approach which we call EM-guided deconvolution. This applies to living cells structures before fixation as well as previously fixed sample. It attempts to automatically assign fluorescence-labeled structures to structural details visible in the EM image to bridge the gaps in both resolution and specificity between the two imaging modes. We tested our approach on simulations, correlative data of multi-color beads and previously published data of biological samples.

A proteomics approach reveals digestive and nutritional responses to food intake in anadromous Coilia nasus.

The estuarine tapertail anchovy, Coilia nasus, is an anadromous fish that undertakes over a 600-km spawning migration along the Yangtze River of China. They generally cease feeding during this process, but we recently documented that a small proportion of them appear to feed. Research on proteomic responses is essential for understanding the phenomenon of C. nasus feeding. In this study, we used an iTRAQ-based proteomics approach to study the changes in protein expression in response to food intake in C. nasus following voluntary fasting. Coilia nasus in the feeding group (CSI) were fed shrimp or small fish, whereas those in the control group (CSN) were starved. We identified 3279 proteins in the gastric tissue/stomach, of which 279 were significantly differentially expressed. In all, 133 differentially expressed proteins (DEPs) were upregulated and 146 proteins were downregulated in CSI compared with those in CSN C. nasus. In addition to gastric acid secretion caused by gastric distention, a functional analysis suggested that a series of DEPs were involved mainly in the regulation of protein digestion (e.g., carboxypeptidase A1 and chymotrypsin A-like), immune response (e.g., lysozyme and alpha 2-macroglobulin), and nutrition metabolism (e.g., glyceraldehyde 3-phosphate dehydrogenase, glycogenin, long-chain acyl-CoA synthetase, and creatine kinase). Real-time PCR confirmed that the mRNA levels of the DEPs were similar those obtained using iTRAQ. These results indicate that the nutrients obtained through food were effectively utilized by C. nasus, thereby providing energy for swimming, gonadal maturation, primary metabolism, and an enhanced immune function to better resist pathogen interference. This research contributes to the elucidation of nutritional regulation mechanisms of C. nasus to better protect the wild population.

Metabolic mechanisms of Coilia nasus in the natural food intake state during migration.

As a prominent member of freshwater and coastal fish faunas, Coilia nasus migrates annually from the sea up the Yangtze River in China to spawn. It is traditionally believed that C. nasus generally do not feed during their spawning migration. However, we recently documented the occurrence of food intake phenomenon in C. nasus following voluntary fasting. The purpose of the current study is to explore the metabolic mechanisms on C. nasus in response to food intake during migration. A total of 23,159 differentially expressed mRNA molecules and 204 metabolites were identified in transcriptome and metabolome analyses. Our results provide insights into the activation of energy consumption and reinforcement of energy storage during migration, and also identify key genes involved in food intake regulation. Our findings will be useful for future research on population recruitment and energy utilization in wild C. nasus.

Approximate equation-of-motion coupled-cluster methods for electron affinities of closed-shell molecules.

We investigate performance of the equation-of-motion coupled-cluster method at the single and doubles level (EOM-CCSD) and a series of approximate methods based on EOM-CCSD on electron affinities (EA) of closed-shell cations and neutral molecules with positive and negative EAs in this work. Our results confirm that P-EOM-MBPT2 can provide reasonable EAs when molecules with significant multireference character are not considered and its mean absolute error on EAs of these molecules is around or less than 0.2 eV. Its accuracy is comparable to that of the more expensive EOM-CCSD(2) method. Results of EOM-CCSD(2), P-EOM-MBPT2, and CIS(D∞) indicate that the [[H, ac +], T2] term in the 1h2p-1h block is more important on EAs than the term neglected in the 1h2p-1h2p block in P-EOM-MBPT2. We proposed an economical method where EAs from CIS(D∞) are corrected by treating this [[H, ac +], T2] term in the 1h2p-1h block perturbatively [corr-CIS(D∞)]. EAs with corr-CIS(D∞) agree very well with those of P-EOM-MBPT2 with a difference of less than 0.02 eV. Computational scaling of this method is N4 for the iterative part and N5 for some non-iterative steps. Its storage requirement is only of OV3. Corr-CIS(D∞) is an economical and reliable method on EAs, and it can be applied to EAs of large molecules.

Progressive aggregation-induced emission strategy for imaging of aluminum ions in cellular microenvironment.

A progressive aggregation-induced emission (AIE) strategy is established based on two diverse stimulus-responsive patterns of copper nanoclusters (CuNCs) for imaging of aluminum ions (Al3+) in cellular microenvironment. The non-emissive CuNCs were facilely synthesized with l-glutathione (GSH) as both stabilizing agent and reducing agent, and demonstrated the excellent AIE characteristics in the ethanol/water mixture. Moreover, the dispersed CuNCs can be aggregated to give the AIE behavior in aqueous solutions by reducing the pH value, and could be further aggregated with 94-fold reinforce by introducing Al3+ ascribe to the strong coordination ability between Al3+ and the functional groups of GSH, demonstrating the progressive AIE process. Under endocytosis, the progressive AIE strategy can be employed to distinguish the Al3+ in the locations of lysosome against other organelles due to the acidic microenvironment of lysosome. The progressive AIE advantages of CuNCs provide a new concept for signal transduction, and have the promising applications in decoding the functions of intracellular biomolecules.

Digestive enzyme activity of the Japanese grenadier anchovy Coilia nasus during spawning migration: influence of the migration distance and the water temperature.

In this study, we investigated the activity levels of two major digestive enzymes (pepsin and lipase) in the commercially important Japanese grenadier anchovy Coilia nasus during its upstream migration to analyse the digestive physiological responses to starvation and to analyse the influence of the water temperature on enzyme activity. Water temperature had a significant effect on pepsin activity, while long-term starvation resulted in a significant decrease in pepsin activity. As starvation continued, however, a slight increase in pepsin activity between the Wuhu (440 river km) and Anqing (620 river km) regions may indicate that C. nasus had refeeding behaviour due to its large expenditure of energy reserves. In contrast, lipase activity was not significantly affected by the water temperature but the effect of fasting increased as much as 13% of lipase activity from the Chongming region (20 river km) to Anqing region, suggesting that the stored lipids of grenadier anchovy were mobilised to meet energy requirements of upstream migration activity and gonad development. Lipid mobilisation activated lipoprotein lipase (LPL; proteins with lipase activity) to hydrolyse triacylglycerides (TAG), which is the first step of lipid assimilation and obtained energy from fatty acids under fasting conditions. Therefore, the increased lipase activity is attributed mainly to the lipase that is involved in endogenous lipid hydrolysis. Grenadier anchovy appears to adapt to long-term starvation during migration and the increased lipase activity may indicate a crucial effect on lipid metabolism. This study demonstrated that distinct alterations occur in pepsin and lipase activities during the spawning migration of grenadier anchovy due to exogenous nutrition and endogenous metabolism. Furthermore, it provides a basis for further research on the digestive physiology and energy metabolism in this species.

Application and Selection of Remediation Technology for OCPs-Contaminated Sites by Decision-Making Methods.

The production and use of organochlorine pesticides (OCPs) for agricultural and industrial applications result in high levels of their residues, posing a significant risk to environmental and human health. At present, there are many techniques for OCP-contaminated soil remediation. However, the remediation of contaminated sites may suffer from a series of problems, such as a long recovery cycle, high costs, and secondary pollution, all of which could affect land redevelopment and reuse. Therefore, the selection of an appropriate technology is crucial for contaminated sites. In order to improve and support decision-making for the selection of remediation techniques, we provide a decision-making strategy for the screening of remediation techniques of OCP-contaminated sites. The screening procedure is proposed based on combining the analytic hierarchy process (AHP) and the technique for order preference by similarity to ideal solution (TOPSIS). The screening indexes include economic indicator, environmental indicator, and technical indicator. The assessment results show that co-processing in cement kiln obtained the highest overall score and was thus considered to be the most sustainable option. This suggested remediation technology was similar to the practical remediation project, indicating that the screening method could be applied for the selection of remediation technologies for sites contaminated with persistent organic pollutants.

Single-Sided Competitive Axial Coordination of G-Quadruplex/Hemin as Molecular Switch for Imaging Intracellular Nitric Oxide.

Axial coordination is a crucial biological process to regulate biomolecules' functions in natural enzymes. However, it is a great challenge to determine the single or dual axial interaction between the metal center of enzymes and the ligand. In this work, a controllable axial coordination system was developed based on G-quadruplex/hemin complex by designing a series of fluorescent derivatives. The mechanism on axial coordination of G-quadruplex/hemin with coumarin-imidazole ligands was proposed to be single-sided, and led to fluorescence quenching of ligands. Upon addition of nitric oxide, the fluorescence of ligands was recovered through competitive axial coordination, providing a "signal on" strategy for signal transduction. More significantly, the fluorescent imaging of intracellular nitric oxide was achieved after conjugating with gold nanoparticles. Also, the proposed protocol provided a smart strategy to monitor the relationship between nitric oxide and p53 protein activity in living cells.

In situ simultaneous profiling of phosphorylation and ubiquitination by single excitation-duplexed luminescence resonance energy transfer.

A dual luminescence resonance energy transfer system is developed based on aptamer-functionalized upconversion nanoparticles as the energy donor and a synthetic dye derivative as the acceptor, which can be applied in the simultaneous profiling and relative quantification of phosphorylation and ubiquitination on a specific protein, even at low levels of protein expression.

Target-triggered cascade assembly of a catalytic network as an artificial enzyme for highly efficient sensing.

Determining the catalytic activity of artificial enzymes is an ongoing challenge. In this work, we design a porphyrin-based enzymatic network through the target-triggered cascade assembly of catalytic nanoparticles. The nanoparticles are synthesized via the covalent binding of hemin to amino-coated gold nanoparticles and then the axial coordination of the Fe center with a dual-functional imidazole or pyridine derivative. The network, which is specifically formed by coordination polymerization triggered by Hg2+ as the target, shows high catalytic activity due to the triple amplification of enzymatic activity during the cascade assembly. The catalytic dynamics are comparable to those of natural horseradish peroxidase. The catalytic characteristics can be ultrasensitively regulated by the target, leading to a selective methodology for the analysis of sub-attomolar Hg2+. It has also been used for "signal-on" imaging of reactive oxygen species in living cells. This work provides a new avenue for the design of enzyme mimics, and a powerful biocatalyst with signal switching for the development of biosensing protocols.

Persistent luminescence nanoprobe for biosensing and lifetime imaging of cell apoptosis via time-resolved fluorescence resonance energy transfer.

Time-resolved fluorescence technique can reduce the short-lived background luminescence and auto-fluorescence interference from cells and tissues by exerting the delay time between pulsed excitation light and signal acquisition. Here, we prepared persistent luminescence nanoparticles (PLNPs) to design a universal time-resolved fluorescence resonance energy transfer (TR-FRET) platform for biosensing, lifetime imaging of cell apoptosis and in situ lifetime quantification of intracellular caspase-3. Three kinds of PLNPs-based nanoprobes are assembled by covalently binding dye-labeled peptides or DNA to carboxyl-functionalized PLNPs for the efficient detection of caspase-3, microRNA and protein. The peptides-functionalized nanoprobe is also employed for fluorescence lifetime imaging to monitor cell apoptosis, which shows a dependence of cellular fluorescence lifetime on caspase-3 activity and thus leads to an in situ quantification method. This work provides a proof-of-concept for PLNPs-based TR-FRET analysis and demonstrates its potential in exploring dynamical information of life process.

A porphyrin photosensitized metal-organic framework for cancer cell apoptosis and caspase responsive theranostics.

A photosensitized and caspase-responsive multifunctional nanoprobe was designed by assembling a porphyrin, a folate targeting-motif and a dye-labelled peptide in a metal-organic framework (MOF) cage, which significantly increases the singlet oxygen quantum yield of porphyrin by 6.2 times, and achieves high efficient cancer therapy and in situ therapeutic monitoring with caspase-3 activation. The integration of theranostic functions in a single nanocarrier holds great promise in precision cancer diagnosis and treatment.

In situ activation and monitoring of the evolution of the intracellular caspase family.

The evolution of the intracellular caspase family is crucial in cell apoptosis. To evaluate this process, a universal platform of in situ activation and monitoring of the evolution of intracellular caspase is designed. Using well-known gold nanostructure as a model of both nanocarrier and matter inducing the cell apoptosis for photothermal therapy, a nanoprobe is prepared by assembly of two kinds of dye-labelled peptides specific to upstream caspase-9 and downstream caspase-3 as the signal switch, and folic acid as a targeting moiety. The energy transfer from dyes to the gold nanocarrier at two surface plasmon resonance absorption wavelengths leads to their fluorescence quenching. Upon endocytosis of the nanoprobe to perform the therapy against cancer cells, the peptides are successively cleaved by intracellular caspase activation with the evolution from upstream to downstream, which lights up the fluorescence of the dyes sequentially, and can be used to quantify both caspase-9 and caspase-3 activities in cancer cells and to monitor their evolution in living mice. The recovered fluorescence could also be used to assess therapeutic efficiency. This work provides a novel powerful tool for studying the evolution of the intracellular caspase family and elucidating the biological roles of caspases in cancer cell apoptosis.