The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights.

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.

ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation.

Competing endogenous RNAs (ceRNAs) are vital regulators of gene networks in mammals. The involvement of noncoding RNAs (ncRNAs) as ceRNA in genotypic sex determination (GSD) and environmental sex determination (ESD) in fish is unknown. The Chinese tongue sole, which has both GSD and ESD mechanisms, was used to map the dynamic expression pattern of ncRNAs and mRNA in gonads during sex determination and differentiation. Transcript expression patterns shift during the sex differentiation phase, and ceRNA modulation occurs through crosstalk of differentially expressed long ncRNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs), and sex-related genes in fish. Of note was the significant up-regulation of a circRNA from the sex-determining gene dmrt1 (circular RNA dmrt1) and a lncRNA, called AMSDT (which stands for associated with male sex differentiation of tongue sole) in Chinese tongue sole testis. These two ncRNAs both share the same miRNA response elements with gsdf, which has an up-regulated expression when they bind to miRNA cse-miR-196 and concurrent down-regulated female sex-related genes to facilitate testis differentiation. This is the first demonstration in fish that ceRNA crosstalk mediated by ncRNAs modulates sexual development and unveils a novel regulatory mechanism for sex determination and differentiation.

Heat-Set Supramolecular Hydrogelation by Regulating the Hydrophilic-Lipophilic Balance for a Tunable Circularly Polarized Luminescent Switch.

Heat-set supramolecular gels exhibited totally opposite phase behaviors of dissolution upon cooling and gelation on heating. They are commonly discovered by chance and their rational design remains a great challenge. Herein, a rational design strategy is proposed to realize heat-set supramolecular hydrogelation through regulation of the hydrophilic-lipophilic balance of the system. A newly synthesized amphiphile hydrogelator with pyrene embedded in its lipophilic terminal can self-assemble into a hydrogel through a heating and cooling cycle. However, the host-guest complex of the gelator and hydrophilic γ-cyclodextrin (γ-CyD) results in a sol at room temperature. Thus, heat-set hydrogelation is realized from the sol state in a controllable manner. Heat-set gelation mechanism is revealed by exploring critical heat-set supramolecular gelation and the related findings provide a general strategy for developing new functional molecular gels with tunable hydrophilic-lipophilic balance.

Single-cell transcriptome landscape of zebrafish liver reveals hepatocytes and immune cell interactions in understanding nonalcoholic fatty liver disease.

Nonalcoholic fatty liver disease (NAFLD) is becoming the most common chronic liver disease in the world. Immunity is the major contributing factor in NAFLD; however, the interaction of immune cells and hepatocytes in disease progression has not been fully elucidated. As a popular species for studying NAFLD, zebrafish, whose liver is a complex immune system mediated by immune cells and non-immune cells in maintaining immune tolerance and homeostasis. Understanding the cellular composition and immune environment of zebrafish liver is of great significance for its application in NAFLD. Here, we established a liver atlas that consists of 10 cell types using single-cell RNA sequencing (scRNA-seq). By examining the heterogeneity of hepatocytes and analyzing the expression of NAFLD-associated genes in the specific cluster, we provide a potential target cell model to study NAFLD. Additionally, our analysis identified two subtypes of distinct resident macrophages with inflammatory and non-inflammatory functions and characterized the successive stepwise development of T cell subclusters in the liver. Importantly, we uncovered the possible regulation of macrophages and T cells on target cells of fatty liver by analyzing the cellular interaction between hepatocytes and immune cells. Our data provide valuable information for an in-depth study of immune cells targeting hepatocytes to regulate the immune balance in NAFLD.

Polarization-Sensitive Photodetector Based on High Crystallinity Quasi-1D BiSeI Nanowires Synthesized via Chemical Vapor Deposition.

Bismuth chalcohalides (BiSeI and BiSI), a class of superior light absorbers, have recently garnered great attention owing to their promise in constructing next-generation optoelectronic devices. However, to date, the photodetection application of bismuth chalcohalides is still limited due to the challenge in controllable preparation. Herein, the synthesis of large-scale quasi-1D BiSeI nanowires via chemical vapor deposition growth is reported. By precisely tuning the growth temperature and the Se supply, it can effectively control the growth thermodynamics and kinetics of BiSeI crystal, and thus achieve high purity quasi-1D BiSeI nanowires with high crystal quality, uniform diameter, and tunable domain length. Theory and optical characterizations of the quasi-1D BiSeI nanowires reveal an indirect bandgap of 1.57 eV with prominent optical linear dichroism. As a result, the quasi-1D BiSeI nanowire-based photodetector demonstrates a broadband photoresponse (400-800 nm) with high responsivity of 5880 mA W-1 , fast response speed of 0.11 ms and superior air stability. More importantly, the photodetector displays strong polarization sensitivity (anisotropic ratio = 1.77) under the 532 nm light irradiation. This work will provide important guides to the synthesis of other quais-1D metal chalcohalides and shed light on their potential in constructing novel multifunctional optoelectronic devices.

Microbial community structure and interactions between Aspergillus oryzae and bacteria in traditional solid-state fermentation of Jiangqu.

Microbial interactions play an important role in the formation, stabilization and functional performance of natural microbial communities. However, little is known about how the microbes present interactions to build a stable natural microbial community. Here, we developed Jiangqu, the solid-state fermented starters of thick broad-bean sauce formed naturally in factory, as model microbial communities by characterizing its diversity of microbial communities and batch stability. The dominant microbial strains and their fungi-bacteria interactions during solid-state fermentation of Jiangqu were characterized. In all batches of Jiangqu, Aspergillus oryzae, Bacillus, Staphylococcus and Weissella dominated in the communities and such a community structure could almost reduplicate between batches. Direct adsorption and competition were identified as the main interactions between A. oryzae and dominant bacteria during solid-state fermentation, which were quite different from liquid co-cultivation of A. oryzae and dominant bacteria. These results will help us better understand the intrinsic mechanism in the formation and stabilization of microbial communities from traditional solid-state qu-making and fermentation.

Large-area Free-standing Metalloporphyrin-based Covalent Organic Framework Films by Liquid-air Interfacial Polymerization for Oxygen Electrocatalysis.

Synthesizing large-area free-standing covalent organic framework (COF) films is of vital importance for their applications but is still a big challenge. Herein, we reported the synthesis of large metalloporphyrin-based COF films and their applications for oxygen electrocatalysis. The reaction of meso-benzohydrazide-substituted metal porphyrins with tris-aldehyde linkers afforded free-standing COF films at the liquid-air interface. These films can be scaled up to 3000 cm2 area and display great mechanical stability and structural integrity. Importantly, the Co-porphyrin-based films are efficient for electrocatalytic O2 reduction and evolution reactions. A flexible, all-solid-state Zn-air battery was assembled using the films and showed high performance with a charge-discharge voltage gap of 0.88 V at 1 mA cm-2 and high stability under bent conditions (0° to 180°). This work thus presents a strategy to synthesize functionalized COF films with high quality for uses in flexible electronics.

Supramolecular Adhesives with Extended Tolerance to Extreme Conditions via Water-Modulated Noncovalent Interactions.

Development of supramolecular adhesives with strong tolerance to extreme conditions has emerged as an important research area. In this study, by balancing supramolecular interactions such as hydrogen bonding interactions, electrostatic interactions, π-π stacking interactions, and cation-π interactions, we designed and prepared a series of two-component supramolecular adhesives derived from small organic molecules. Highly efficient interfacial adhesion with maximum adhesion strength of ≈10.0 MPa was realized on various surfaces in air, organic solvents, or liquid nitrogen. Owing to balanced supramolecular interactions, water participation prolonged and increased the tolerance of the adhesives in extreme environments. We demonstrate that the combination of imidazole-based ionic liquids and phenols can be applied for various interfacial adhesions, thereby aiding the development of next-generation adhesives capable of adapting to various extreme conditions in a controlled manner.

The genetic editing of GS3 via CRISPR/Cas9 accelerates the breeding of three-line hybrid rice with superior yield and grain quality.

Grain size is one of the major traits that determine rice grain yield and quality. The GS3 gene is the first major quantitative trait locus (QTL) that was identified in regulating rice grain length and weight. It was reported that the gs3 allele with a mutation in the organ size regulation (OSR) domain of the GS3 protein produced longer grains. In this study, we used the CRISPR/Cas9 gene editing technology to introduce an edited gs3 allele into our indica maintainer line, Mei1B, to enhance its grain yield and quality. Through molecular analysis and sequencing, a homologous edited-gs3 mutant line without any transgene was obtained in the T1 generation and was named Mei2B. A superior male sterile line Mei2A was generated by backcrossing the cytoplasmic male sterile (CMS) line Mei1A with Mei2B. Mei2B had a higher grain quality and yield compared to its wild-type Mei1B. Its grain length increased by 7.9%, its length/width ratio increased from 3.89 to 4.19, TGW increased by 6.7%, and grain yield per plant increased by 14.9%. In addition, genetic improvement of other quality traits including brown rice length (6.83 mm), brown rice grain length/width ratio (3.61), matched the appearance standards set for traditional Simiao (silk seedling) type cultivars. Two restorer lines were outcrossed to both Mei1A and Mei2A to produce hybrid rice. Compared to two hybrids of Mei1A, the hybrids of Mei2A had longer grains, higher length/width ratio, TGW, and yield per plant. In addition, the hybrids of Mei2A showed a better grain appearance including better translucency, a lower chalky rice rate, and degree of chalkiness than the hybrids of Mei1A. These results demonstrated that the introduction of an elite gs3 allele into Mei1A via CRISPR/Cas9 gene editing technology led to significant genetic improvement of the rice grain. The resultant CMS line Mei2A(gs3) displayed much higher grain quality and yield than the original Mei1A. Therefore, our study demonstrated that the targeted genetic improvement via gene editing technology can enhance rice breeding, especially the breeding of three-line hybrid rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01290-z.

ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress.

Low temperature is one of the important environmental factors that affect rice growth and yield. To better understand the japonica rice responses to cold stress, isobaric tags for a relative and absolute quantification (iTRAQ) labeling-based quantitative proteomics approach was used to detected changes in protein levels. Two-week-old seedlings of the cold tolerant rice variety Kongyu131 were treated at 8°C for 24, 48 and 72 h, then the total proteins were extracted from tissues and used for quantitative proteomics analysis. A total of 5082 proteins were detected for quantitative analysis, of which 289 proteins were significantly regulated, consisting of 169 uniquely up-regulated proteins and 125 uniquely down-regulated proteins in cold stress groups relative to the control group. Functional analysis revealed that most of the regulated proteins are involved in photosynthesis, metabolic pathway, biosynthesis of secondary metabolites and carbon metabolism. Western blot analysis showed that protein regulation was consistent with the iTRAQ data. The corresponding genes of 25 regulated proteins were used for quantitative real time PCR analysis, and the results showed that the mRNA level was not always parallel to the corresponding protein level. The importance of our study is that it provides new insights into cold stress responses in rice with respect to proteomics and provides candidate genes for cold-tolerance rice breeding.

High-Performance Sensing of Formic Acid Vapor Enabled by a Newly Developed Nanofilm-Based Fluorescent Sensor.

Although it is widely used in industry and food products, formic acid can be dangerous owing to its corrosive properties. Accurate determination of formic acid would not only benefit its qualified uses but also be an effective way to avoid corrosion or injury from inhalation, swallowing, or touching. Herein, we present a nanofilm-based fluorescent sensor for formic acid vapor detection with a wide response range, fast response speed, and high sensitivity and selectivity. The nanofilm was synthesized at a humid air/dimethyl sulfoxide (DMSO) interface through dynamic covalent condensation between two typically designed building blocks, de-tert-butyl calix[4]arene-tetrahydrazide (CATH) and 4,4',4″,4‴-(ethene-1,1,2,2-tetrayl)tetra-benzaldehyde (ETBA). The as-prepared nanofilm is uniform, flexible, fluorescent, and photochemically stable. The thickness and fluorescence intensity of the nanofilm can be facilely adjusted by varying the concentration of the building blocks and the sensing performance of the nanofilm can be optimized accordingly. Based on the nanofilm, a fluorescent sensor with a wide response range (4.4 ppt-4400 ppm) for real-time and online detection of formic acid vapor was built. With the sensor, a trace amount (0.01%) of formic acid in petroleum ether (60-90 °C) can be detected within 3 s. Besides, fluorescence quenching of the nanofilm by formic acid vapor can be visualized. It is believed that the sensor based on the nanofilm would find real-life applications in corrosion and injury prevention from formic acid.

Tuning Rheological Behaviors of Supramolecular Aqueous Gels via Charge Transfer Interactions.

Rheological properties are critical for determining real applications of supramolecular gels in various fields. Correspondingly, the modulation of gel rheology will be very important for meeting real requirements. In this aspect, a few strategies were applied to tune the rheological behaviors of supramolecular gels, but some specific interactions like charge transfer (CT) interactions were less explored at the molecular level. Herein, we report a pyrene-containing derivative of diphenylalanine as a donor gelator and naphthalenediimide or 3,5-dinitrobenzene as matching acceptor molecules. It was found that the viscoelastic properties and strength of the original gel could be tuned through addition of different acceptor molecules to the original gel with changing the ratios of the selected acceptor molecules. As a result, storage modulus was continuously adjusted over a wide range from 190,000 to 50,000 Pa by CT interactions. Furthermore, the mechanism of the CT-induced change in rheological properties was understood and clarified through relevant techniques (e.g., UV-Vis, fluorescence, and FT-IR spectroscopy and TEM). The findings in this work would provide a novel strategy to modulate the rheological properties of supramolecular gels for adaption to broader fields of real applications.

Early response to heat stress in Chinese tongue sole (Cynoglossus semilaevis): performance of different sexes, candidate genes and networks.

BACKGROUND: Temperature is known to affect living organisms and alter the expression of responsive genes, which affects a series of life processes, such as development, reproduction and metabolism. Several genes and gene families have been involved in high temperature responses, such as heat shock protein (hsp) family, Jumonji family and genes related to cortisol synthesis. Gonad is a vital organ related to the existence of a species. However, the comprehensive understanding of gonadal responses to environmental temperature is limited. RESULTS: To explore the effects of environmental temperature on genes and gene networks in gonads, we performed acute heat treatment (48 h) on Chinese tongue sole (Cynoglossus semilaevis). Gonadal transcriptome analysis was conducted on females, pseudomales and males exposed to high (28 °C) and normal (22 °C) temperatures. A total of 1226.24 million clean reads were obtained from 18 libraries. Principal component analysis (PCA) and differentially expressed gene (DEG) analysis revealed different performance of sex responses to heat stress. There were 4565, 790 and 1117 specific genes altered their expression level in females, pseudomales and males, respectively. Of these, genes related to hsp gene family, cortisol synthesis and metabolism and epigenetic regulation were involved in early heat response. Furthermore, a total of 1048 DEGs were shared among females, pesudomales and males, which may represent the inherent difference between high and normal temperatures. Genes, such as eef1akmt3, eef1akmt4, pnmt and hsp family members, were found. CONCLUSIONS: Our results depicted for the first time the gonadal gene expression under acute high temperature treatment in Chinese tongue sole. The findings may provide a clue for understanding the responses of genes and networks to environmental temperature.

Self-Assembled Perylene Bisimide-Cored Trigonal Prism as an Electron-Deficient Host for C60 and C70 Driven by "Like Dissolves Like".

Poor processability of fullerenes is a major remaining drawback for them to be studied monomolecularly and to find real-life applications. One of the strategies to tackle this problem is to encapsulate them within a host, which is however quite often, accompanied by significant alteration of their physical/chemical properties as encountered in chemical modification. To minimize the effect, an electron-deficient entities-based, dissolvable, and fluorescence active supramolecular host was designed and constructed via coordination-driven self-assembly of o-tetrapyridyl perylene bisimide (PBI) with cis-(PEt3)2Pt(OTf)2. The trigonal prism 1 possesses a trigonal-prismatic inner cavity with 14.7 Šas the diameter of its inscribed circle. Host-guest chemistry investigations revealed that both C60 and C70 could be quantitatively encapsulated by the host in a 1:1 ratio. Further studies demonstrated that the produced host-guest complex 1⊃C70 is significantly more stable than 1⊃C60, allowing complete transformation of the latter to the former and separation of C70 from its mixture with C60. The fullerenes in the inclusion state could rotate freely within the cavity. Electrochemistry and spectroscopy studies disclosed that the encapsulation of the guests shows little effect upon the reduction of the host and its fluorescence properties. Thus, "like dissolves like" is believed to be the main driving force for the formation of the host-guest complexes. Moreover, the host and host-guest complexes can be fabricated into monomolecular membranes using the conventional Langmuir-Blodgett technique. We propose that these unique host-guest complexes could be used as model ensembles for further studies of the physical/chemical properties of fullerenes in both single molecular and 2D membrane states. In addition, their reversible four-electron reduction property may allow them to find applications in photo/electrocatalysis, organic electronics, etc.

Dynamic covalent bond-based hydrogels with superior compressive strength, exceptional slice-resistance and self-healing properties.

A novel dynamic-covalent bond-based single network hydrogel was developed, of which the failure compressive stress and strain as well as the failure tensile stress and strain could exceed 27.3 MPa and 98.4% as well as 0.23 MPa and 282.3%, respectively. In addition, the gel shows remarkable slice-resistance and self-healing properties.

Calix[4]arene-Based Dynamic Covalent Gels: Marriage of Robustness, Responsiveness, and Self-Healing.

Herein, the report on a new class of self-healing and pH/temperature responsive mixed solvent (ethanol and water) gels shows unusual mechanical properties to resist slicing, sustain high compression, and withstand stretching as evidenced by the cutting breaking stress, the fracture compressive stress, and the stretching ratio of one of the gels as obtained can reach or exceed 26.4 MPa, 9.2 MPa, and ≈5 times, respectively. The gels are designed by introducing dynamic covalent bond, acylhydrazone, which is believed to combine the merits of conventional chemical bonds and those of supramolecular interactions. Specifically, a hydrazide-modified calix[4]arene derivative and linear benzaldehyde-terminated poly(ethylene glycol)s are synthesized and used as reactive components to build gel networks. Interestingly, acid-degradable hydrogel can be obtained via natural drying of the mixed solvent gel first and then swelling in pure water.

Dynamic Chemistry-Based Sensing: A Molecular System for Detection of Saccharide, Formaldehyde, and the Silver Ion.

Development of artificial complex molecular systems is of great importance in understanding complexity in natural processes and for achieving new functionalities. One of the strategies is to create them via optimized utilization of noncovalent interactions and dynamic covalent bonds. We report here on a new complex molecular system, which was constructed by integrating the multiple interactions containing a dynamic covalent interaction between 1,2-diol and boronic acid, a coordination interaction between the silver ion and pyridyl, and an easy accessible reaction between secondary amine and formaldehyde. By employing the three dynamic interactions, a pyrene (Py) labeled fluorophore, PPB, was designed and synthesized. The compound reacts with fructose (F), a monosaccharide, in aqueous phase and produces a fluorescent adduct, PPB-F, which can be further used as a sensing platform for formaldehyde (FA) and the silver ion. The respective dynamic interactions are accompanied with color changes due to the reversible switching between Py-monomer emission and excimer emission. The respective experimental detection limits (DLs) for the three analytes are much lower than 0.2 mM, 0.1 mM, and 2.5 µM, respectively. The presence of relevant compounds or ions shows little effect upon the sensing. No doubt, the results as presented show that the integration of supramolecular interactions including dynamic covalent bonds can be employed as a general strategy to develop new functional molecular systems or materials.

Rapid identification of a new gene influencing low amylose content in rice landraces (Oryza sativa L.) using genome-wide association study with specific-locus amplified fragment sequencing.

Starch is the major component of milled rice, and amylose content (AC) affects eating quality. In this study, a genome-wide association study (GWAS) with specific-locus amplified fragment sequencing (SLAF-seq) data was performed for AC on a core collection of 419 rice landraces. Using the compressed mixed linear method based on the Q+K model, we identified a new gene, LAC6 (Chr6: 5.65-6.04 Mb), associated with AC in the low amylose content panel. The LAC6 candidate gene was detected by qRT-PCR in rice panicles. Results indicate that LOC_Os06g11130 was up-regulated, and LOC_Os06g11340 was significantly down-regulated, making it most likely a key candidate gene of LAC6. In conclusion, the findings provide a certain theoretiacal basis of molecular biology for genetic improvement of AC in rice and rice quality variety breeding.

Dynamic covalent bonding-triggered supramolecular gelation derived from tetrahydroxy-bisurea derivatives.

A new class of bisurea derivatives bearing tetrahydroxy groups have been proven to be non-gelators in water and various organic solvents even under long-term sonication or efficient heating treatment. We found that it is possible to trigger physical gelation behaviour by constructing dynamic covalent bonding. The results show that formation of dynamic covalent bonding between the borate anion and ethanediol substituent in these bisurea derivatives brings about rapid physical gelation at ambient temperature in a mixture of DMSO and water. During dynamic covalent bonding-triggered gelation, the stepgrowth polymerization from the B-O bonds would increase the size of the molecules and reduce the entropy of mixing as well as facilitate ion-dipole interactions in the linear polymeric gelators. They would drive a self-assembly transition and boost the construction of gel networks in coordination with α-tape urea-urea hydrogen bonding. The gelation mechanism was explored by 1H NMR, FTIR and rheology techniques. Moreover, the resulting gels are transparent and thixotropic, and could be turned into the sol state under CO2 or water-stimulus. Furthermore, they are stable in the presence of HAuCl4 and alkali. Therefore, they would afford another new medium for the growth of Au nanocrystals via in situ reduction and a new sensing medium for detecting Hg2+ ions.

Specially Treated Aramid Fiber Stabilized Gel-Emulsions: Preparation of Porous Polymeric Monoliths and Highly Efficient Removing of Airborne HCHO.

Porous polymeric monoliths with densities as low as ≈0.060 g cm-3 are prepared in a gel-emulsion template way, of which the stabilizer employed is a newly discovered acidified aramid fiber that is so efficient that 0.05% (w/v, accounts for continuous phase) is enough to gel the system. The porous monoliths as obtained can be dried at ambient conditions, avoiding energy-consuming processes. Importantly, the monoliths show selective adsorption to HCHO, and the corresponding adsorption capacity (M6) is ≈2700 mg g-1 , the best result that is reported until now. More importantly, the monoliths can be reused after drying.