Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape.

Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.

A platform for rapid exploration of aging and diseases in a naturally short-lived vertebrate.

VIDEO ABSTRACT: Aging is a complex process that affects multiple organs. Modeling aging and age-related diseases in the lab is challenging because classical vertebrate models have relatively long lifespans. Here, we develop the first platform for rapid exploration of age-dependent traits and diseases in vertebrates, using the naturally short-lived African turquoise killifish. We provide an integrative genomic and genome-editing toolkit in this organism using our de-novo-assembled genome and the CRISPR/Cas9 technology. We mutate many genes encompassing the hallmarks of aging, and for a subset, we produce stable lines within 2-3 months. As a proof of principle, we show that fish deficient for the protein subunit of telomerase exhibit the fastest onset of telomere-related pathologies among vertebrates. We further demonstrate the feasibility of creating specific genetic variants. This genome-to-phenotype platform represents a unique resource for studying vertebrate aging and disease in a high-throughput manner and for investigating candidates arising from human genome-wide studies.

The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan.

Lifespan is a remarkably diverse trait ranging from a few days to several hundred years in nature, but the mechanisms underlying the evolution of lifespan differences remain elusive. Here we de novo assemble a reference genome for the naturally short-lived African turquoise killifish, providing a unique resource for comparative and experimental genomics. The identification of genes under positive selection in this fish reveals potential candidates to explain its compressed lifespan. Several aging genes are under positive selection in this short-lived fish and long-lived species, raising the intriguing possibility that the same gene could underlie evolution of both compressed and extended lifespans. Comparative genomics and linkage analysis identify candidate genes associated with lifespan differences between various turquoise killifish strains. Remarkably, these genes are clustered on the sex chromosome, suggesting that short lifespan might have co-evolved with sex determination. Our study provides insights into the evolutionary forces that shape lifespan in nature.

Imaging GPCR Dimerization in Living Cells with Cucurbit[7]uril and Hemicyanine as a "Turn-On" Fluorescence Probe.

Although multiple forms of dimers have been described for GPCR, their dynamics and function are still controversially discussed field. Fluorescence microscopy allows GPCR to be imaged within their native context; however, a key challenge is to site-specifically incorporate reporter moieties that can produce high-quality signals upon formation of GPCR dimers. To this end, we propose a supramolecular sensor approach to detect agonist-induced dimer formation of µ-opioid receptors (µORs) at the surface of intact cells. With the macrocyclic host cucurbit[7]uril and its guest hemicyanine dye tethered to aptamer strands directed against the histidine residues, the sensing module is assembled by host-guest complexation once the histidine-tagged µORs dimerize and bring the discrete supramolecular units into close proximity. With the enhanced sensitivity attributed by the "turn-on" fluorescence emission and high specificity afforded by the intermolecular recognition, in situ visualization of dynamic GPCR dimerization was realized with high precision, thereby validating the supramolecular sensing entity as a sophisticated and versatile strategy to investigate GPCR dimers, which represent an obvious therapeutic target.

Enhancing Zinc Electrode Stability Through Pre-Desolvation and Accelerated Charge Transfer via a Polyimide Interface for Zinc-Ion Batteries.

Aqueous zinc-based energy storage devices possess superior safety, cost-effectiveness, and high energy density; however, dendritic growth and side reactions on the zinc electrode curtail their widespread applications. In this study, these issues are mitigated by introducing a polyimide (PI) nanofabric interfacial layer onto the zinc substrate. Simulations reveal that the PI nanofabric promotes a pre-desolvation process, effectively desolvating hydrated zinc ions from Zn(H2O)6 2+ to Zn(H2O)4 2+ before approaching the zinc surface. The exposed zinc ion in Zn(H2O)4 2+ provides an accelerated charge transfer process and reduces the activation energy for zinc deposition from 40 to 21 kJ mol-1. The PI nanofabric also acts as a protective barrier, reducing side reactions at the electrode. As a result, the PI-Zn symmetric cell exhibits remarkable cycling stability over 1200 h, maintaining a dendrite-free morphology and minimal byproduct formation. Moreover, the cell exhibits high stability and low voltage hysteresis even under high current densities (20 mA cm-2, 10 mAh cm-2) thanks to the 3D porous structure of PI nanofabric. When integrated into full cells, the PI-Zn||AC hybrid zinc-ion capacitor and PI-Zn||MnVOH@SWCNT zinc-ion battery achieve impressive lifespans of 15000 and 600 cycles with outstanding capacitance retention. This approach paves a novel avenue for high-performance zinc metal electrodes.

Dual light source compensation method for improving the quality of LC-SLM holographic displays.

The inherent "grid" effect of LC-SLM in holographic displays can lead to issues such as the presence of zero-order spots and multi-level diffraction images, resulting in a decrease in the quality of reconstructed images. In this Letter, a dual light source compensation method is proposed to address this problem. By analyzing the influence of the LC-SLM "grid" effect on the diffraction field and the rule of change of light intensity distribution and position of the reconstructed image, the dual light source is introduced on the basis of the rule of change of energy distribution at the symmetric position of the reconstructed image so as to compensate for the quality of the display results. The results show that the method not only avoids the influence of zero-order spot and multi-level diffraction image on the holographic display results but also especially highlights that the uniformity of light energy distribution of the reconstructed image is greatly improved, which provides a reference for LC-SLM to perform a higher-quality holographic display.

Dynamic iterative correction algorithm for designing diffractive optical elements.

When utilizing the Gerchberg-Saxton (GS) algorithm to design diffractive optical elements, correction coefficients are introduced to improve the quality of the design results. The main design idea is to correct the target information dynamically during the iterative calculation process. The effectiveness of the proposed method is demonstrated through the verification of beam shaping and phase-type hologram designs. Compared to the traditional GS algorithm, the results of beam shaping show that the light intensity nonuniformity and the root-mean-square error (RMSE) of the shaped spot are reduced by an order of magnitude. The results of phase-type holograms show that the reconstructed image's peak signal-to-noise ratio (PSNR) is improved by about 12 dB. Finally, the paper also discusses the selection of correction coefficients, providing insights into the selection of optimal design correction coefficients. The simulation and experimental results show that the improved algorithm proposed in this paper is not only simple in design but also highly efficient in obtaining a high-quality phase structure, which is of great help in designing high-quality diffractive optical elements.

Restraint Stress-Induced Neutrophil Inflammation Contributes to Concurrent Gastrointestinal Injury in Mice.

Psychological stress increases risk of gastrointestinal tract diseases. However, the mechanism behind stress-induced gastrointestinal injury is not well understood. The objective of our study is to elucidate the putative mechanism of stress-induced gastrointestinal injury and develop an intervention strategy. To achieve this, we employed the restraint stress mouse model, a well-established method to study the pathophysiological changes associated with psychological stress in mice. By orally administering gut-nonabsorbable Evans blue dye and monitoring its plasma levels, we were able to track the progression of gastrointestinal injury in live mice. Additionally, flow cytometry was utilized to assess the viability, death, and inflammatory status of splenic leukocytes, providing insights into the stress-induced impact on the innate immune system associated with stress-induced gastrointestinal injury. Our findings reveal that neutrophils represent the primary innate immune leukocyte lineage responsible for stress-induced inflammation. Splenic neutrophils exhibited elevated expression levels of the pro-inflammatory cytokine IL-1, cellular reactive oxygen species, mitochondrial burden, and cell death following stress challenge compared to other innate immune cells such as macrophages, monocytes, and dendritic cells. Regulated cell death analysis indicated that NETosis is the predominant stress-induced cell death response among other analyzed regulated cell death pathways. NETosis culminates in the formation and release of neutrophil extracellular traps, which play a crucial role in modulating inflammation by binding to pathogens. Treatment with the NETosis inhibitor GSK484 rescued stress-induced neutrophil extracellular trap release and gastrointestinal injury, highlighting the involvement of neutrophil extracellular traps in stress-induced gastrointestinal inflammation. Our results suggest that neutrophil NETosis could serve as a promising drug target for managing psychological stress-induced gastrointestinal injuries.

Nickel-Carbon Bond Oxygenation with Green Oxidants via High-Valent Nickel Species.

Described herein is the synthesis of the NiII complex (tBuMe2tacn)NiII(cycloneophyl) (tBuMe2tacn = 1-tert-butyl-4,7-dimethyl-1,4,7-triazacyclononane, cycloneophyl = -CH2CMe2-o-C6H4-) and its reactivity with dioxygen and peroxides. The new tBuMe2tacn ligand is designed to enhance the oxidatively induced bond-forming reactivity of high-valent Ni intermediates. Tunable chemoselectivity for Csp2-O vs Csp2-Csp3 bond formation was achieved by selecting the appropriate solvent and reaction conditions. Importantly, the use of cumene hydroperoxide and meta-chloroperbenzoic acid suggests a heterolytic O-O bond cleavage upon reaction with (tBuMe2tacn)NiII(cycloneophyl). Mechanistic studies using isotopically labeled H2O2 support the generation of a high-valent Ni-oxygen species via an inner-sphere mechanism and subsequent reductive elimination to form the Csp2-O bond. Kinetic studies of the exceptionally fast Csp2-O bond-forming reaction reveal a first-order dependence on both (tBuMe2tacn)NiII(cycloneophyl) and H2O2, and thus an overall second-order reaction. Eyring analysis further suggests that the oxidation of the NiII complex by H2O2 is the rate-determining step, which can be modulated by the presence of coordinating solvents. Moreover, computational studies fully support the conclusions drawn from experimental results. Overall, this study reveals for the first time the ability to control the oxidatively induced C-C vs C-O bond formation reactions at a Ni center. Importantly, the described system merges the known organometallic reactivity of Ni with the biomimetic oxidative transformations resembling oxygenases and peroxidases, and involving high-valent metal-oxygen intermediates, which is a novel approach that should lead to unprecedented oxidative catalytic transformations.

Magnetic Liposomes Infused with GPCR-Expressing Cell Membrane for Targeted Extraction Using Minimum Organic Solvent: An Investigative Study of Trace THC in Sewage.

Trace analysis of lipophilic substances in complex environmental, food, or biological matrices has proven to be a challenge, on account of their high susceptibility to adsorption by particulate matter and liquid-solid interfaces. For this purpose, liquid-liquid extraction (LLE) is often employed as the separation method, which uses water-immiscible organic solvents. As an alternative, magnetic solid-phase extraction (MSPE) allows for adsorption, separation, and recovery of analytes from large volumes of aqueous samples with minimum usage of organic solvents. However, the poor selectivity hampers its performance in various scenarios, especially in sewage samples where complicated and unpredictable interference exists, resulting in block of the active adsorption sites of the sorbent. To this end, we propose receptor-affinity MSPE employing magnetic liposomes decorated with cell membranes expressing G-protein-coupled receptor as the sorbents. Application of the novel sorbent CM@Lip@Fe infused with CB1 cannabinoid receptors was demonstrated for the targeted extraction and enrichment of tetrahydrocannabinol from sewage matrix. Thanks to the high affinity and molecular selectivity of the ligand-receptor interactions, a limit of quantitation of 5.17 ng/L was achieved coupled with HPLC-MS/MS in unfiltered raw sewage, featuring minimum usage of organic solvents, fivefold enhanced sensitivity, low sorbent dosage (75 mg/L of sewage), and high efficiency as major advantages over conventional LLE. This work establishes a framework for efficient separation of specific molecules from complex media, thus promising to extend and refine standard LLE as the clean-up procedure for trace analysis.

Research on improving holographic display quality based on phase compensation of reproduced image light energy distribution.

Liquid crystal spatial light modulator (LC-SLM) holographic display is affected by its structure, which products multi-level diffracted image with zero-order spot, resulting in low light energy utilization and poor uniformity of the reproduced image. This paper presents a method to improve the uniformity of light energy distribution in the reproduced image by using phase compensation, and the uniformity of the image can be effectively improved by using digital blazed grating to deviate the image and performing phase compensation according to the light energy distribution. Analyzing the uniformity of light energy distribution, the phase distribution is compensated, and experiments verify the phase compensation. The experimental results show that the uniformity and light energy utilization of the reproduced image after compensation has been improved. The results show that the proposed phase compensation method can be applied to both Fresnel holography and Fourier holography; both can effectively improve the uniformity and efficiency of light energy. Therefore, this method has a specific application value to enhance the quality of holographic reproduction and light field modulation based on LC-SLM.

Nontargeted screening based on EI-MS spectra using statistical methods: An investigative study of synthetic indole/indazole cannabinoids.

RATIONALE: Mass spectrometry has evolved into a highly powerful tool for qualitative and quantitative chemical analyses. However, the identification of trace amounts of previously unknown structures in complex chemical matrix environments remains challenging. The rapid emergence of new synthetic cannabinoid substances is a typical example of this. Existing laboratory techniques are mostly based on methods used for lists of known illegal compounds. This situation poses a challenge to traditional data analysis and the risk of missing the compounds. Therefore, we propose to develop and validate a statistical model to classify newly emerging synthetic cannabinoid substances into a structural class or subclass. METHODS: We obtained 70 electrospray ionization spectra of indole/indazole synthetic cannabinoids from both the actual standard analysis and the SWGDRUG mass spectral library (version 3.10). Each sample consisted of 330 m/z variables and corresponding relative intensities. We first cleared the variables with a variance below 0.1. Principal component analysis (PCA) was performed on the variance-filtered data, and the two principal components were retained to generate new data for hierarchical clustering. After hierarchical clustering, we used the receiver operating characteristic method in this cluster. RESULTS: Seventy synthetic indole/indazole cannabinoids were classified into four clusters. The side chain of cluster 1 is mainly fluorobenzyl, cluster 2 is pentyl, cluster 3 includes compounds from several structures, and cluster 4 is mainly fluoropentyl. The most relevant characteristic ions are m/z 109, m/z 252, and m/z 253 for cluster 1; m/z 144 and m/z 214 for cluster 2; and m/z 232 and m/z 233 for cluster 4. CONCLUSIONS: This study provides a more objective and less time-consuming solution for characterizing synthetic cannabinoids. And this work validates the ability of PCA to extract characteristic fragment ions.

Cucurbituril-protected dual-readout gold nanoclusters for sensitive fentanyl detection.

A large number of cases showed that fentanyl (FEN) has become the main cause of death from illegal drug overdose owing to its potent effect on respiratory depression, which has emerged as a grave threat to public health and safety. However, traditional analytical methods require cost-prohibitive equipment, complex pretreatment procedures, and technically trained experts, thus highlighting the urgent need to develop a cost-effective, straightforward, and highly sensitive method to detect FEN. This work demonstrated a dual-readout sensor FGGC-AuNCs@Q7 for FEN detection, which is based on the molecular recognition and self-assembly between the macrocycle cucurbit[7]uril (Q7) and FEN, accompanying spontaneous visual Tyndall effect and fluorescence optical responses of the gold nanoclusters within seconds. A detection limit of 1 ng mL-1 and a linear range of 9 to 148 000 ng mL-1 were achieved for fluorescence detection on FEN, with favorable selectivity in the presence of other illicit drugs or common interferents. The proposed method has been proved by its satisfactory application for the analysis of human urine.

Effect of nanoclay supported nanosilver on the growth inhibition of aquatic pathogens and immunomodulatory effect in Penaeusvannamei.

Hybrid of nanosilver and nanoscale silicate platelet (AgNSP) is a safe, non-toxic nanomaterial which has been applied in medical use due to its strong antibacterial activity. The application of AgNSP in aquaculture was first proposed in the present study by evaluating the in vitro antibacterial activities against four aquatic pathogens, in vitro effects toward shrimp haemocytes as well as the immune responses and disease resistance in Penaeus vannamei fed with AgNSP for 7 days. For evaluating the antibacterial activities of AgNSP in culture medium, the minimum bactericidal concentration (MBC) values against Aeromonas hydrophila, Edwardsiella tarda, Vibrio alginolyticus and Vibrio parahaemolyticus were 100, 15, 625 and 625 mg/L, respectively. Moreover, the inhibition of pathogen growth over a period of 48 h could be achieved by the appropriate treatment of AgNSP in culturing water. In freshwater containing bacterial size of 103 and 106 CFU/mL, the effective doses of AgNSP against A. hydrophila were 12.5 and 450 mg/L, respectively while the effective doses against E. tarda were 0.2 and 50 mg/L, respectively. In seawater with same bacterial size, the effective doses against V. alginolyticus were 150 and 2000 mg/L, respectively while the effective doses against V. parahaemolyticus were 40 and 1500 mg/L, respectively. For the in vitro immune tests, the superoxide anion production and phenoloxidase activity in haemocytes were elevated after in vitro incubation with 0.5-10 mg/L of AgNSP. In the assessment of dietary supplemental effects of AgNSP (2 g/kg), no negative effect on the survival was found at the end of 7 day feeding trail. In addition, the gene expression of superoxide dismutase, lysozyme and glutathione peroxidase were up-regulated in haemocytes taken from shrimps received AgNSP. The following challenge test against Vibrio alginolyticus showed that the survival of shrimp fed with AgNSP was higher than that of shrimp fed with control diet (p = 0.083). Dietary AgNSP improved the Vibrio resistance of shrimp by increasing 22.7% of survival rate. Therefore, AgNSP could potentially be used as a feed additive in shrimp culture.

Catalase associated with antagonistic changes of abscisic acid and gibberellin response, biosynthesis and catabolism is involved in eugenol-inhibited seed germination in rice.

KEY MESSAGE: The inhibitory effect of eugenol on rice germination is mediated by a two-step modulatory process: Eugenol first regulates the antagonism of GA and ABA, followed by activation of catalase activity. The natural monoterpene eugenol has been reported to inhibit preharvest sprouting in rice. However, the inhibitory mechanism remains obscure. In this study, simultaneous monitoring of GA and ABA responses by the in vivo GA and ABA-responsive dual-luciferase reporter system showed that eugenol strongly inhibited the GA response after 6 h of imbibition, whereas eugenol significantly enhanced the ABA response after 12 h of imbibition. Gene expression analysis revealed that eugenol significantly induced the ABA biosynthetic genes OsNCED2, OsNCED3, and OsNCED5, but notably suppressed the ABA catabolic genes OsABA8ox1 and OsABA8ox2. Conversely, eugenol inhibited the GA biosynthetic genes OsGA3ox2 and OsGA20ox4 but significantly induced the GA catabolic genes OsGA2ox1 and OsGA2ox3 during imbibition. OsABI4, the key signaling regulator of ABA and GA antagonism, was notably induced before 12 h and suppressed after 24 h by eugenol. Moreover, eugenol markedly reduced the accumulation of H2O2 in seeds after 36 h of imbibition. Further analysis showed that eugenol strongly induced catalase activity, protein accumulation, and the expression of three catalase genes. Most importantly, mitigation of eugenol-inhibited seed germination was found in the catc mutant. These findings indicate that catalase associated with antagonistic changes of ABA and GA is involved in the sequential regulation of eugenol-inhibited seed germination in rice.

Fish models for investigating nutritional regulation of embryonic development.

In recent decades, biologist have focused on the spatiotemporal regulation and function of genes to understand embryogenesis. It is clear that maternal diet impacts fetal development but how nutrients, like lipids and vitamins, modify developmental programs is not completely understood. Fish are useful research organisms for such investigations. Most species of fish produce eggs that develop outside the mother, dependent on a finite amount of yolk to form and grow. The developing embryo is a closed system that can be readily biochemically analyzed, easily visualized, and manipulated to understand the role of nutrients in tissue specification, organogenesis, and growth. Natural variation in yolk composition observed across fish species may be related to unique developmental strategies. In this review, we discuss the reasons that teleost fishes are powerful models to understand nutritional control of development and highlight three species that are particularly valuable for future investigations: the zebrafish, Danio rerio, the African Killifish, Nothobranchius furzeri, and the Mexican tetra, Astyanax mexicanus. This review is a part of a special issue on nutritional, hormonal, and metabolic drivers of development.

Urine DNA biomarkers for hepatocellular carcinoma screening.

BACKGROUND: Hepatocellular carcinoma (HCC) occurs in a well-defined high-risk patient population, but better screening tests are needed to improve sensitivity and efficacy. Therefore, we investigated the use of urine circulating tumour DNA (ctDNA) as a screening test. METHODS: Candidate markers in urine were selected from HCC and controls. We then enrolled 609 patients from five medical centres to test the selected urine panel. A two-stage model was developed to combine AFP and urine panel as a screening test. RESULTS: Mutated TP53, and methylated RASSF1a, and GSTP1 were selected as the urine panel markers. Serum AFP outperformed the urine panel among all cases of HCC, but the urine panel identified 49% of HCC cases with low AFP < 20 ng/ml. Using the two-stage model, the combined AFP and urine panel identified 148 of the 186 HCC cases (79.6% sensitivity at 90% specificity), which was 30% more than the cases detected with serum AFP alone. It also increased early-stage HCC detection from 62% to 92% (BCLC stage 0), and 40% to 77% (BCLC stage A). CONCLUSION: Urine ctDNA has promising diagnostic utility in patients in HCC, especially in those with low AFP and can be used as a potential non-invasive HCC screening test.

Teaching PCR for Simultaneous Sensing of Gene Transcription and Downstream Metabolites by Cucurbit[8]uril-Mediated Intervention of Polymerase Activity.

The target of typical PCR analysis is restricted to nucleic acids. To this end, we report here a novel strategy to simultaneously detect genetic and metabolic markers using commercial PCR kits with cucurbit[8]urils (CB[8]) implemented to manipulate the activity of Taq DNA polymerase. CB[8] binds with the nonionic surfactants and displaces them from the polymerase surface, resulting in decreased enzyme activity. Meanwhile, the inhibited enzyme can be reversibly activated when spermine, the downstream metabolite of ornithine decarboxylase (ODC), is present in the sample, which competitively binds to CB[8] and recovers polymerase activity. CB[8] was implemented in conventional PCR kits not only to reduce false-positive results but also to extend the detection range of PCR technology. With this novel method to detect ODC in cell lysates containing both the nucleotides and intracellular metabolites, positive results were only observed in highly active HEK 293T cells, whereas silent cells treated with ODC inhibitor showed negative readouts, therefore providing a simple but elegant dual-modality PCR method for precision diagnosis.

Label-free tumor cell screening based on IDO1-mediated tryptophan metabolism at single cell level.

Indoleamine 2,3-dioxygenase 1 (IDO1) plays a critical role in inflammatory and immunometabolism programming through catalyzing the oxidation of tryptophan (Trp) into downstream N-formylkynurenine. IDO1 is typically up-regulated in malignant tumors, making it a potential biomarker for cancer diagnosis. Here we show an effective strategy for tumor cell detection by integrating IDO1 activity assay with single cell-encapsulated droplets on a microfluidic platform for high-throughput bioanalysis. Mixed cells, as well as other cofactors, are encapsulated in individual droplets, which act as dynamic microreactors for IDO1-catalyzed oxidation of Trp. After pico-injection of a biosensing ensemble consisting of the macrocycle cucurbit [8]uril (Q8) and a fluorescent guest, rapid and robust screening of tumor cells by fluorescence signal is achieved in a few minutes reporting to Trp depletion, expanding the scope of conventional antibody-based detection of protein biomarkers. The results represent the first example of quantifying IDO1 enzymatic activity at the single cell level with a high-throughput performance, therefore promising warning signs and early diagnosis of tumor cells.

Critical issues concerning the assessment sets in agreement assessment.

Since Bland and Altman's pioneering work, the assessment set has been an important constituent of agreement assessment. This article explores critical issues concerning the assessment set. First, we point out the fundamental differences between assessment approaches based on point estimation and those based on hypothesis testing related to the assessment set, and further present how the related disciplines choose between the two. Second, we argue that an assessment set with minimum volume should be preferred, as in the comparison of confidence intervals. Finally, we discuss assessment sets for the assessment of multiple methods, and propose two methods for the construction of assessment sets. Numerical examples further establish the applicability of these approaches.