Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae.

Living fossils are evidence of long-term sustained ecological success. However, whether living fossils have little molecular changes remains poorly known, particularly in plants. Here, we have introduced a novel method that integrates phylogenomic, comparative genomic, and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae, a Cretaceous relict angiosperm family endemic to East Asia. We assembled a high-quality chromosome-level nuclear genome, and the chloroplast and mitochondrial genomes of a member of Eupteleaceae (Euptelea pleiosperma). Our results show that Eupteleaceae is most basal in Ranunculales, the earliest-diverging order in eudicots, and shares an ancient whole-genome duplication event with the other Ranunculales. We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms. The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture, ancestral woody habit, and conserved niche requirements. Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.

The Effect of Theaflavins on the Gut Microbiome and Metabolites in Diabetic Mice.

With the development of diabetes, the gut microbiome falls into a state of dysbiosis, further affecting its progression. Theaflavins (TFs), a type of tea polyphenol derivative, show anti-diabetic properties, but their effect on the gut microbiome in diabetic mice is unclear. It is unknown whether the improvement of TFs on hyperglycemia and hyperlipidemia in diabetic mice is related to gut microbiota. Therefore, in this study, different concentrations of TFs were intragastrically administered to mice with diabetes induced by a high-fat-diet to investigate their effects on blood glucose, blood lipid, and the gut microbiome in diabetic mice, and the plausible mechanism underlying improvement in diabetes was explored from the perspective of the gut microbiome. The results showed that the TFs intervention significantly improved the hyperglycemia and hyperlipidemia of diabetic mice and affected the structure of the gut microbiome by promoting the growth of bacteria positively related to diabetes and inhibiting those negatively related to diabetes. The changes in short-chain fatty acids in mice with diabetes and functional prediction analysis suggested that TFs may affect carbohydrate metabolism and lipid metabolism by regulating the gut microbiome. These findings emphasize the ability of TFs to shape the diversity and structure of the gut microbiome in mice with diabetes induced by a high-fat diet combined with streptozotocin and have practical implications for the development of functional foods with TFs.

Antibacterial Effects of Theaflavins against Staphylococcus aureus and Salmonella paratyphi B: Role of Environmental Factors and Food Matrices.

This study aimed to investigate the effects of different environmental factors (temperature, pH, and NaCl) and food matrices (skimmed milk powder, lecithin, and sucrose) on the antibacterial activity of theaflavins (TFs) against Staphylococcus aureus (S. aureus) and Salmonella paratyphi B (S. paratyphi B). TFs showed a larger diameter of inhibition zone (DIZ, 12.58 ± 0.09 mm-16.36 ± 0.12 mm) value against S. aureus than that of S. paratyphi B (12.42 ± 0.43 mm-15.81 ± 0.24 mm) at the same concentration (2-10 mg/mL). When temperatures were 25-121 °C, the DIZ of TFs against both S. aureus and S. paratyphi B was not significantly different. As pH increased from 2 to 10, their DIZ values decreased significantly from 16.78 ± 0.23 mm to 13.43 ± 0.08 mm and 15.63 ± 0.42 mm to 12.18 ± 0.14 mm, respectively. Their DIZ values increased slightly as the NaCl concentration increased from 0.2 mol/L to 0.8 mol/L, while their DIZ values decreased significantly for skimmed milk powder concentrations in the range of 20-120 g/L. Regarding the concentrations of lecithin and sucrose were 2-12 g/L and 10-60 g/L, their DIZ values showed no significant change against S. paratyphi B, but an increased trend for S. aureus. Under the above different environmental factors and food matrices, TFs maintained excellent antibacterial activity against S. aureus and S. paratyphi B, providing a theoretical guidance for applying TFs as novel antibacterial additives in the food industry.

Diversification of ranunculaceous petals in shape supports a generalized model for plant lateral organ morphogenesis and evolution.

Peltate organs, such as the prey-capturing traps of carnivorous plants and nectary-bearing petals of ranunculaceous species, are widespread in nature and have intrigued and perplexed scientists for centuries. Shifts in the expression domains of adaxial/abaxial genes have been shown to control leaf peltation in some carnivorous plants, yet the mechanisms underlying the generation of other peltate organs remain unclear. Here, we show that formation of various peltate ranunculaceous petals was also caused by shifts in the expression domains of adaxial/abaxial genes, followed by differentiated regional growth sculpting the margins and/or other parts of the organs. By inducing parameters to specify the time, position, and degree of the shifts and growth, we further propose a generalized modeling system, through which various unifacial, bifacial, and peltate organs can be simulated. These results demonstrate the existence of a hierarchical morphospace system and pave the way to understand the mechanisms underlying plant organ diversification.

Cu/Au nanoclusters with peroxidase-like activity for chemiluminescence detection of α-amylase.

Herein, a novel chemiluminescence method was developed for efficient and sensitive detection of α-amylase activity. α-Amylase is closely related to our life, and α-amylase concentration is a marker for the diagnosis of acute pancreatitis. In this paper, Cu/Au nanoclusters with peroxidase-like activity were prepared using starch as a stabilizer. Cu/Au nanoclusters can catalyze H2O2 to generate reactive oxygen species and increase the CL signal. The addition of α-amylase makes the starch decompose and causes the nanoclusters to aggregate. The aggregation of the nanoclusters caused them to increase in size and decrease in the peroxidase-like activity, resulting in a decrease in the CL signal. α-Amylase was detected by the CL method of signal changes caused by dispersion-aggregation in the range of 0.05-8 U mL-1 with a low detection limit of 0.006 U mL-1. The chemiluminescence scheme based on the luminol-H2O2-Cu/Au NC system is of great significance for the sensitive and selective determination of α-amylase in real samples, and the detection time is short. This work provides new ideas for the detection of α-amylase based on the chemiluminescence method and the signal lasts for a long time, which can realize timely detection.

Mechanisms underlying the formation of complex color patterns on Nigella orientalis (Ranunculaceae) petals.

Complex color patterns on petals are widespread in flowering plants, yet the mechanisms underlying their formation remain largely unclear. Here, by conducting detailed morphological, anatomical, biochemical, optical, transcriptomic, and functional studies, we investigated the cellular bases, chromogenic substances, reflectance spectra, developmental processes, and underlying mechanisms of complex color pattern formation on Nigella orientalis petals. We found that the complexity of the N. orientalis petals in color pattern is reflected at multiple levels, with the amount and arrangement of different pigmented cells being the key. We also found that biosynthesis of the chromogenic substances of different colors is sequential, so that one color/pattern is superimposed on another. Expression and functional studies further revealed that a pair of R2R3-MYB genes function cooperatively to specify the formation of the eyebrow-like horizontal stripe and the Mohawk haircut-like splatters. Specifically, while NiorMYB113-1 functions to draw a large splatter region, NiorMYB113-2 functions to suppress the production of anthocyanins from the region where a gap will form, thereby forming the highly specialized pattern. Our results provide a detailed portrait for the spatiotemporal dynamics of the coloration of N. orientalis petals and help better understand the mechanisms underlying complex color pattern formation in plants.

Delphinieae flowers originated from the rewiring of interactions between duplicated and diversified floral organ identity and symmetry genes.

Species of the tribe Delphinieae (Ranunculaceae) have long been the focus of morphological, ecological, and evolutionary studies due to their highly specialized, nearly zygomorphic (bilaterally symmetrical) spiral flowers with nested petal and sepal spurs and reduced petals. The mechanisms underlying the development and evolution of Delphinieae flowers, however, remain unclear. Here, by conducting extensive phylogenetic, comparative transcriptomic, expression, and functional studies, we clarified the evolutionary histories, expression patterns, and functions of floral organ identity and symmetry genes in Delphinieae. We found that duplication and/or diversification of APETALA3-3 (AP3-3), AGAMOUS-LIKE6 (AGL6), CYCLOIDEA (CYC), and DIVARICATA (DIV) lineage genes was tightly associated with the origination of Delphinieae flowers. Specifically, an AGL6-lineage member (such as the Delphinium ajacis AGL6-1a) represses sepal spur formation and petal development in the lateral and ventral parts of the flower while determining petal identity redundantly with AGL6-1b. By contrast, two CYC2-like genes, CYC2b and CYC2a, define the dorsal and lateral-ventral identities of the flower, respectively, and form complex regulatory links with AP3-3, AGL6-1a, and DIV1. Therefore, duplication and diversification of floral symmetry genes, as well as co-option of the duplicated copies into the preexisting floral regulatory network, have been key for the origin of Delphinieae flowers.

Covalent organic framework linked with amination luminol derivative as enhanced ECL luminophore for ultrasensitive analysis of cytochrome c.

Cytochrome c (cyt c) plays a critical role in mitochondrial respiratory chain, whose absence is detrimental to electron transport and reduce adenosine triphosphate. For ultrasensitive detection of cyt c, sheet-like covalent organic frameworks (COFs) were prepared by orderly accumulation of 1,3,5-benzenetricarboxaldehyde (BTA) and p-phenylenediamine (PDA), and further grafted with N-(4-aminobutyl)-N-ethylisoluminol (ABEI) - an electrochemiluminescence (ECL) emitter. Specifically, the morphology and structure of the COFs-ABEI were mainly characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD) analysis, and X-ray photoelectron spectroscopy (XPS). In parallel, the optical properties of the emitter were certified by UV-vis absorbance spectroscopy, Fourier infrared spectroscopy (FTIR), fluorescence (FL), and ECL measurements, showing 2.25-time enhanced ECL efficiency over pure ABEI, coupled by illustrating the interfacial electron transport mechanism. On the above foundation, a label-free "signal off" ECL biosensor was constructed by virtue of the specific immune recognition between the aptamer of the target cyt c with its capture DNA (cDNA) anchored on the biosensing platform, exhibiting a wider linear range of 1.00 fg mL-1-0.10 ng mL-1 (R2 = 0.998) and a lower limit of detection (LOD) down to 0.73 fg mL-1. This work offers some constructive guidelines for sensitive bioassays of disease-related biomarkers in the clinical field.

Advanced Glycation End Products, Bone Health, and Diabetes Mellitus.

Advanced glycation end products (AGEs), the compounds resulting from the non-enzymatic glycosylation between reducing sugars and proteins, are derived from food or produced de novo. Over time, more and more endogenous and exogenous AGEs accumulate in various organs such as the liver, kidneys, muscle, and bone, threatening human health. Among these organs, bone is most widely reported. AGEs accumulating in bone reduce bone strength by participating in bone structure formation and breaking bone homeostasis by binding their receptors to alter the proliferation, differentiation, and apoptosis of cells involved in bone remodeling. In this review, we summarize the research about the effects of AGEs on bone health and highlight their associations with bone health in diabetes patients to provide some clues toward the discovery of new treatment and prevention strategies for bone-related diseases caused by AGEs.

Petal development and elaboration.

Petals can be simple or elaborate, depending on whether they have complex basic structures and/or highly specialized epidermal modifications. It has been proposed that the independent origin and diversification of elaborate petals have promoted plant-animal interactions and, therefore, the evolutionary radiation of corresponding plant groups. Recent advances in floral development and evolution have greatly improved our understanding of the processes, patterns, and mechanisms underlying petal elaboration. In this review, we compare the developmental processes of simple and elaborate petals, concluding that elaborate petals can be achieved through four main paths of modifications (i.e. marginal elaboration, ventral elaboration, dorsal elaboration, and surface elaboration). Although different types of elaborate petals were formed through different types of modifications, they are all results of changes in the expression patterns of genes involved in organ polarity establishment and/or the proliferation, expansion, and differentiation of cells. The deployment of existing genetic materials to perform a new function was also shown to be a key to making elaborate petals during evolution.

The Protective Effect of Theaflavins on the Kidney of Mice with Type II Diabetes Mellitus.

Diabetic nephropathy, primarily caused by advanced glycation end products (AGEs), is a serious complication resulting from type 2 diabetes mellitus (T2DM). Reportedly, theaflavins (TFs) can improve diabetic nephropathy; however, the underlying molecular mechanism is not fully clear. In this study, T2DM mice were treated with different concentrations of TFs by gavage for 10 weeks to investigate the effect of TFs on diabetic nephropathy and their potential molecular mechanism of action. Biochemical and pathological analysis showed that the TFs effectively improved blood glucose, insulin resistance, kidney function, and other symptoms in diabetic mice. The mechanism studies indicated that TFs inhibited the formation of AGEs, thereby inhibiting the activation of the MAPK/NF-κB signaling pathway. Therefore, our study suggested that TFs improved diabetic nephropathy by inhibiting the formation of AGEs.

Colorimetric determination of cysteine based on Au@Pt nanoparticles as oxidase mimetics with enhanced selectivity.

A H2O2-free colorimetric protocol based on urchin-like Au@Pt nanoparticles (Au@Pt NPs) has been developed for the sensitive and selective determination of cysteine (Cys). We verified the intrinsic oxidase-like activity of the Au@Pt NPs. They can act as artificial mimic oxidases to catalyse the oxidization of 3,3',5,5'-tetramethylbenzidine (TMB) with the assistance of dissolved oxygen, avoiding the use of H2O2 in the colorimetric determination of Cys. In addition, the discrimination of Cys from the other two biothiol analogues, homocysteine and glutathione, can be easily realized through a simple ageing process. HNO3 is added to this colorimetric system to terminate the reaction by oxidizing ox-TMB (oxidized form of TMB) to diphenoquinone (DPQ), thus generating a characteristic absorption peak of DPQ at 450 nm. By recording the absorbance at 450 nm, interference from the aggregated Au@Pt NPs (absorption peak at 670 nm) when 650 nm (the characteristic absorption peak of ox-TMB) is used as the absorption wavelength can be eliminated. We investigated this H2O2-free colorimetric protocol and obtained high sensitivity, with a detection limit of 1.5 nM and relatively high selectivity. The analytical performance for real samples was further explored. The Au@Pt NP-based H2O2-free colorimetric protocol is of great significance for the sensitive and selective determination of Cys in practical samples in different scenarios.

Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome.

Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.

Characterization of a transcription factor SlNAC7 gene from Suaeda liaotungensis and its role in stress tolerance.

NAC (NAM, ATAF1/2, CUC2) transcription factors play important roles in plant growth, development, and responses to abiotic stress. In this study, we cloned an NAC2 subfamily transcription factor gene (SlNAC7) from the halophyte Suaeda liaotungensis K., and conducted a series of studies to determine the characteristics and functions of this gene. The SlNAC7 coding region contains 1719 base pairs that encode a 573 amino acid long protein. SlNAC7 is expressed in the roots, stems, and leaves of S. liaotungensis, with the highest expression in the leaves. We found that SlNAC7 expression can be induced by drought, salt, cold, and abscisic acid. Transient expression in onion epidermal cells revealed that SlNAC7 is located in both the nucleus and cytoplasm. A transcriptional activation experiment in yeast showed that the transcriptional activation domain of SlNAC7 is located at the C terminus. When SlNAC7 was transformed into Arabidopsis under the control of a CaMV 35S promoter its overexpression was found to enhance the ability of transgenic plants to resist drought, salt, and cold stress. Moreover, these plants showed multiple changes in growth characteristics and physiological and biochemical indices in response to different stresses, as well as the upregulation of numerous stress-related genes. We have thus characterized a new halophyte-derived NAC transcription factor, SlNAC7, which can regulate plant growth and physiological and biochemical changes under adverse conditions by regulating the expression of stress-related genes, thereby enhancing plant stress resistance. SlNAC7 is a promising candidate for breeding new varieties of stress-tolerant crops.

A Fast Dual-responsive OFF-ON Fluorescent Probe for Cysteine and Glutathione without Interference from Homocysteine.

Abnormal levels of biothiols, such as cysteine (Cys), homocystine (Hcy), and glutathione (GSH), are generally known to result in various diseases. A fast dual-responsive OFF-ON fluorescent probe HBO-AC was synthesized and developed. Non-fluorescent HBO-AC can sense Cys by regaining fluorescence at 444 nm within 10 min and a response to GSH by restoring fluorescence at 349 nm within 20 min. There is no mutual interference with Δλ ca. 100 nm. A novel method was developed by utilizing a low reaction rate between HBO-AC and Hcy to eliminate common interference from Hcy. A successful determination of Cys and GSH in fetal bovine serum (FBS) indicated that the probe had potential application for clinical diagnosis. Moreover, it was confirmed that HBO-AC can resist interference from protein to some extent, since FBS was not pretreated before use.

A colorimetric sensor for detecting thiourea based on inhibiting peroxidase-like activity of gold-platinum nanoparticles.

In this study, gold-platinum nanoparticles (Au@PtNPs) with peroxidase-like activity were synthesized. In the absence of thiourea (TU), the Au@PtNPs can catalyze the decomposition of hydrogen peroxide, and oxidize 3,3',5,5'-tetramethylbenzidine dihydrochloride (TMB, colorless) into oxidized 3,3',5,5'-tetramethylbenzidine dihydrochloride (oxTMB, blue). The peroxidase-like activity of the Au@PtNPs is inhibited in the presence of TU, and TMB cannot be oxidized to oxTMB effectively, and no blue color could be observed. Based on this finding, a novel colorimetric sensor for detecting TU is proposed. The absorbance response curve showed a good linearity for the concentration of TU in the range of 10 nmol L-1 to 10 µmol L-1 with a correlation coefficient of R2 = 0.999, and the limit of detection is 9.57 nmol L-1. The colorimetric sensor possesses excellent selectivity, anti-interference ability, and application value in actual samples.

Parallel evolution of apetalous lineages within the buttercup family (Ranunculaceae): outward expansion of AGAMOUS1, rather than disruption of APETALA3-3.

Complete loss of petals, or becoming apetalous, has occurred independently in many flowering plant lineages. However, the mechanisms underlying the parallel evolution of naturally occurring apetalous lineages remain largely unclear. Here, by sampling representatives of all nine apetalous genera/tribes of the family Ranunculaceae and conducting detailed morphological, expression, molecular evolutionary and functional studies, we investigate the mechanisms underlying parallel petal losses. We found that while non-expression/downregulation of the petal identity gene APETALA3-3 (AP3-3) is tightly associated with complete petal losses, disruptions of the AP3-3 orthologs were unlikely to be the real causes for the parallel evolution of apetalous lineages. We also found that, compared with their close petalous relatives, naturally occurring apetalous taxa usually bear slightly larger numbers of stamens, whereas the number of sepals remains largely unchanged, suggestive of petal-to-stamen rather than petal-to-sepal transformations. In addition, in the recently originated apetalous genus Enemion, the petal-to-stamen transformations have likely been caused by the mutations that led to the elevation and outward expansion of the expression of the C-function gene, AGAMOUS1 (AG1). Our results not only provide a general picture of parallel petal losses within the Ranunculaceae but also help understand the mechanisms underlying the independent originations of other apetalous lineages.

Identification of the Key Regulatory Genes Involved in Elaborate Petal Development and Specialized Character Formation in Nigella damascena (Ranunculaceae).

Petals can be simple or elaborate, depending on whether they have lobes, teeth, fringes, or appendages along their margins, or possess spurs, scales, or other types of modifications on their adaxial/abaxial side, or both. Elaborate petals have been recorded in 23 orders of angiosperms and are generally believed to have played key roles in the adaptive evolution of corresponding lineages. The mechanisms underlying the formation of elaborate petals, however, are largely unclear. Here, by performing extensive transcriptomic and functional studies on Nigella damascena (Ranunculaceae), we explore the mechanisms underlying elaborate petal development and specialized character formation. In addition to the identification of genes and programs that are specifically/preferentially expressed in petals, we found genes and programs that are required for elaborate rather than simple petal development. By correlating the changes in gene expression with those in petal development, we identified 30 genes that are responsible for the marginal/ventral elaboration of petals and the initiation of several highly specialized morphological characters (e.g., pseudonectaries, long hairs, and short trichomes). Expression and functional analyses further confirmed that a class I homeodomain-leucine zipper family transcription factor gene, Nigella damascena LATE MERISTEM IDENTITY1 (NidaLMI1), plays important roles in the development of short trichomes and bifurcation of the lower lip. Our results not only provide the first portrait of elaborate petal development but also pave the way to understanding the mechanisms underlying lateral organ diversification in plants.

A turn-on fluorescent probe based on quinoline and coumarin for rapid, selective and sensitive detection of hypochlorite in water samples.

A fluorescent probe L-Cu2+ based on quinoline, coumarin and Cu2+ has been synthesized and characterized for hypochlorite determination. After copper ion was added to the solution of ligand L, the fluorescence quenching at 490 nm might result from a ligand-metal charge transfer (LMCT) process and its strong coordination ability for Cu2+ . In the presence of hypochlorite, the structure of ligand L was destroyed to form 7-(diethylamino)-coumarin-3-carboxylic acid, and the fluorescence was restored at 460 nm. In this case, L-Cu2+ complex could be used as a fluorescent probe to detect hypochlorite, with the advantages of rapid, selective, wide linear range and low detection limit.