Search Results (30)

An acidic shift in the pH profile of Clonostachys rosea zearalenone hydrolase (ZHD), the most effective and well-studied zearalenone-specific lactone hydrolase, is required to extend the range of applications for the enzyme as a decontamination agent in the feed and food production industries. Amino acid substitutions were engineered in the active center of the enzyme to decrease the pKa values of the catalytic residues E126 and H242. The T216K substitution provided a shift in the pH optimum by one unit to the acidic region, accompanied by a notable expansion in the pH profile under acidic conditions. The engineered enzyme demonstrated enhanced activity within the pH range of 3–5 and improved the activity within the pH ranging from 6 to 10. The D31N and D31A substitutions also resulted in a two-unit shift in the pH optimum towards acidic conditions, although this was accompanied by a significant reduction in the enzyme activity. The D31S substitution resulted in a shift in the pH profile towards the alkaline region. The alterations in the enzyme properties observed following the T216K substitution were consistent with the conditions required for the ZHD application as decontamination enzymes at acidic pH values (from 3.0 to 6.0). Full article

Accurate tropospheric delays are of great importance for both Global Navigation Satellite System (GNSS)-based positioning and precipitable water vapor monitoring. The gridded tropospheric delay products, including zenith hydrostatic delays (ZHD) and zenith wet delays (ZWD), are the most ideal method for accessing accurate tropospheric delays. The vertical adjustment method is critical for implementing the gridded tropospheric products. In this work, we consider the different models used for grid products and assess their performance over Yunnan mountains with complex topography. We summarize the main results as follows: (1) The products can provide accurate ZHD with mean biases of −2.6 mm and mean Standard Deviation (STD) of 1.5 mm while the ZWD results from grid products show a performance with biases of −0.4 mm and STD of 1.3 cm over the Yunnan area. (2) The $T_v$-based model shows a better performance than the $T_0$-based model and IGPZWD in rugged areas with large height differences. The grid products can provide hourly ZHD with biases of 3 mm and wet delay with mean biases of within 2 cm and mean STD of below 3 cm in the Yunnan mountains, which exhibit a large height difference of around 1.5 km. (3) The radiosondes results confirm that the $T_v$-based model has an obvious advantage in calculating ZHD height corrections for differences within 2 km while the $T_0$-model suffers from a loss in accuracy in the case of large height differences. If the site is located more than 1 km below the reference height, the IGPZWD model can provide a better ZWD with a mean bias of 1.5 cm and a mean STD of 1.7 cm. With vertical reduction models, the grid products can provide accurate ZHD and ZWD in real time, even if in complex area. Full article

In this paper, I study two intermediate luminosity optical transients (ILOTs), classified as luminous red novae (LRNe), and argue that their modeling with a common envelope evolution (CEE) without jets encounters challenges. LRNe are ILOTs powered by violent binary interaction. Although in the literature it is popular to assume a CEE is the cause of LRNe, I here repeat an old claim that many LRNe are powered by grazing envelope evolution (GEE) events; the GEE might end in a CEE or a detached binary system. I find that the LRN AT 2021biy might have continued to experience mass ejection episodes after its eruption and, therefore, might not have suffered a full CEE during the outburst. This adds to an earlier finding that a jetless model does not account for some of its properties. I find that a suggested jetless CEE model for the LRN AT 2019zhd does not reproduce its photosphere radius evolution. These results that challenge jetless models of two LRNe strengthen a previous claim that jets play major roles in powering ILOTs and shaping their ejecta and that, in many LRNe, the more compact companion launches the jets during a GEE. Full article

ZF-HD transcription factors, which are unique to land plants, are involved in the regulation of abiotic stress response and related signaling pathways, and play a crucial role in plant growth and development. Dendrobium is one of the largest genera of orchids, with a high ornamental and ecological value. However, the specific functions of the ZF-HDs in Dendrobium remain unknown. In this study, we identified a total of 53 ZF-HDs from D. chrysotoxum (17), D. catenatum (23), and D. huoshanense (13), and analyzed their physicochemical properties, phylogenetic relationships, chromosomal locations, protein structures, conserved motifs, and expression patterns. The phylogenetic relationships revealed that 53 ZF-HDs were classified into six subfamilies (ZHDI–V and MIF), and all ZF-HD proteins contained motif 1 and motif 4 conserved domains, while a minority of these proteins had exons. The analysis of cis-elements in the promoters of ZF-HDs from three Dendrobium species showed that growth- and development-related elements were the most prevalent, followed by hormone response and abiotic stress response elements. Through collinearity analysis, 14 DchZF-HDs were found to be collinear with DhuZF-HDs, and 12 DchZF-HDs were found to be collinear with DcaZF-HDs. Furthermore, RT-qPCR analysis revealed that DchZF-HDs play a regulatory role in the development of lateral organs during the flowering process. The results indicated that DchZHD2 plays a role in the unpigmented bud stage, while DchMIF8 and DchZHD16 play significant roles during the pigmented bud and initial bloom stages. Hence, this study provides a crucial basis for further exploring ZF-HDs functions in regulating the floral organs of orchids. Full article

Zinc finger-homeodomain transcription factors (ZF-HDs) are pivotal in regulating plant growth, development, and diverse stress responses. In this study, we found 8 ZF-HD genes in barley genome. Theses eight HvZF-HD genes were located on five chromosomes, and classified into ZHD and MIF subfamily. The collinearity, gene structure, conserved motif, and cis-elements of HvZF-HD genes were also analyzed. Real-time PCR results suggested that the expression of HvZF-HD4, HvZF-HD6, HvZF-HD7 and HvZF-HD8 were up-regulated after hormones (ABA, GA3 and MeJA) or PEG treatments, especially HvZF-HD6 was significantly induced. These results provide useful information of ZF-HD genes to future study aimed at barley breeding. Full article

Cucumber (Cucumis sativus L.) is a globally prevalent and extensively cultivated vegetable whose yield is significantly influenced by various abiotic stresses, including drought, heat, and salinity. Transcription factors, such as zinc finger-homeodomain proteins (ZHDs), a plant-specific subgroup of Homeobox, play a crucial regulatory role in stress resistance. In this study, we identified 13 CsZHDs distributed across all six cucumber chromosomes except chromosome 7. Phylogenetic analysis classified these genes into five clades (ZHDI-IV and MIF) with different gene structures but similar conserved motifs. Collinearity analysis revealed that members of clades ZHD III, IV, and MIF experienced amplification through segmental duplication events. Additionally, a closer evolutionary relationship was observed between the ZHDs in Cucumis sativus (C. sativus) and Arabidopsis thaliana (A. thaliana) compared to Oryza sativa (O. sativa). Quantitative real-time PCR (qRT-PCR) analysis demonstrated the general expression of CsZHD genes across all tissues, with notable expression in leaf and flower buds. Moreover, most of the CsZHDs, particularly CsZHD9-11, exhibited varying responses to drought, heat, and salt stresses. Virus-induced gene silencing (VIGS) experiments highlighted the potential functions of CsZHD9 and CsZHD10, suggesting their positive regulation of stomatal movement and responsiveness to drought stress. In summary, these findings provide a valuable resource for future analysis of potential mechanisms underlying CsZHD genes in response to stresses. Full article

Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F₂ population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species. Full article

Zinc finger-homeodomain (ZF-HD) proteins play essential roles in plant growth, development and stress responses. However, knowledge of the expression and evolutionary history of ZF-HD genes in moso bamboo remains limited. In this study, a total of 24 ZF-HD genes were found unevenly distributed on 12 chromosomes in moso bamboo (Phyllostachys edulis). Phylogenetic analysis indicated that PeZF-HDs were divided into two subfamilies: ZHD and MIF. The ZHD subfamily genes were further classified into seven groups according to their orthologous relationships among the rice and Arabidopsis ZF-HD gene family. The gene structures and conserved motifs of PeZF-HDs were analyzed. Whole-genome duplication (WGD) or segmental duplication promoted the evolution and expansion of the moso bamboo ZF-HD gene family. Ka/Ks ratios suggested that the twenty-four duplication pairs had undergone purifying selection. Promoter analysis showed that most PeZF-HDs contained cis-elements associated with stress responses and hormones. Expression analysis demonstrated that many PeZF-HDs were responsive to abiotic stress treatment. Overall, this work investigated PeZF-HD genes in moso bamboo using bioinformatic approaches. The evolutionary research on gene structure, motif distribution and cis-regulatory elements indicated that PeZF-HDs play distinct roles in biological processes, which provides a theoretical basis for exploring the physiological functions of ZF-HDs and selecting candidate stress-related genes in moso bamboo. Full article

Zearalenone (ZEN) is one of the most prevalent estrogenic mycotoxins, is produced mainly by the Fusarium family of fungi, and poses a risk to the health of animals. Zearalenone hydrolase (ZHD) is an important enzyme capable of degrading ZEN into a non-toxic compound. Although previous research has investigated the catalytic mechanism of ZHD, information on its dynamic interaction with ZEN remains unknown. This study aimed to develop a pipeline for identifying the allosteric pathway of ZHD. Using an identity analysis, we identified hub genes whose sequences can generalize a set of sequences in a protein family. We then utilized a neural relational inference (NRI) model to identify the allosteric pathway of the protein throughout the entire molecular dynamics simulation. The production run lasted 1 microsecond, and we analyzed residues 139–222 for the allosteric pathway using the NRI model. We found that the cap domain of the protein opened up during catalysis, resembling a hemostatic tape. We used umbrella sampling to simulate the dynamic docking phase of the ligand–protein complex and found that the protein took on a square sandwich shape. Our energy analysis, using both molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area (MMPBSA) and Potential Mean Force (PMF) analysis, showed discrepancies, with scores of −8.45 kcal/mol and −1.95 kcal/mol, respectively. MMPBSA, however, obtained a similar score to that of a previous report. Full article

Lipid-lowering is one of the most effective methods of prevention and treatment for cardiovascular diseases. However, most clinical lipid-lowering drugs have adverse effects and cannot achieve the desired efficacy in some complex hyperlipidemia patients, so it is of great significance to develop safe and effective novel lipid-lowering drugs. In the course of our project aimed at discovering the chemical novelty and bioactive natural products of marine-derived actinomycetes, we found that the organic crude extracts (OCEs) of Nocardiopsis sp. ZHD001 exhibited strong in vivo efficacies in reducing weight gain, lowering LDL-C, TC, and TG levels, and improving HDL-C levels in high-fat-diet-fed mice models. Chemical investigations of the active OCEs led to identifying two new sphydrofuran-derived compounds (1–2) and one known 2-methyl-4-(1-glycerol)-furan (3). Their structures were elucidated by the analysis of HRESIMS, 1D and 2D NMR spectroscopic data, and ECD calculations. Among these compounds, compound 1 represents a novel rearranged sphydrofuran-derived derivative. Bioactivity evaluations of these pure compounds showed that all the compounds exhibited significant lipid-lowering activity with lower cytotoxicity in vitro compared to simvastatin. Our results demonstrate that sphydrofuran-derived derivatives might be promising candidates for lipid-lowering drugs. Full article

The prior zenith hydrostatic delay (ZHD) is an essential parameter for the Global Navigation Satellite System (GNSS) and very long baseline interferometry (VLBI) high-precision data processing. Meanwhile, the precise ZHD facilitates the separation of the high-precision zenith wet delay (ZWD) to derive precipitable water vapor (PWV). This paper analyzes the temporal variations in the residuals between GPT3 ZHD and reference ZHD from radiosonde (RS) sites, and a calibrated GPT3 (CGPT3) model is proposed for the site-specific ZHD estimation in the Chinese mainland and its surrounding areas based on the annual, semi-annual, and diurnal variations in residuals. Based on the validation using modeling RS data, the mean absolute error (MAE) and root mean square (RMS) of the CGPT3 model are 7.3 and 9.6 mm, respectively. The validation with RS ZHD not involved in the modeling suggests that the MAE and RMS of the CGPT3 model are 7.9 and 10.2 mm, respectively. These results show improvements of 16.8%/16.8% and 14.3%/13.6%, respectively, compared with the MAE and RMS of the GPT3 model and the newly proposed model (GTrop). In addition, the CGPT3 model has excellent spatial and temporal stability in the study area. Full article

Zinc finger-homeodomain proteins are amongst the most prominent transcription factors (TFs) involved in biological processes, such as growth, development, and morphogenesis, and assist plants in alleviating the adverse effects of abiotic and biotic stresses. In the present study, genome-wide identification and expression analyses of the maize ZHD gene family were conducted. A total of 21 ZHD genes with different physicochemical properties were found distributed on nine chromosomes in maize. Through sequence alignment and phylogenetic analysis, we divided ZHD proteins into eight groups that have variations in gene structure, motif distribution, and a conserved ZF domain. Synteny analysis indicated duplication in four pairs of genes and the presence of orthologues of maize in monocots. Ka/Ks ratios suggested that strong pure selection occurred during evolution. Expression profiling revealed that the genes are evenly expressed in different tissues. Most of the genes were found to make a contribution to abiotic stress response, plant growth, and development. Overall, the evolutionary research on exons and introns, motif distributions, and cis-acting regions suggests that these genes play distinct roles in biological processes which may provide a basis for further study of these genes’ functions in other crops. Full article

Compared to the zenith hydrostatic delay (ZHD) obtained from the Saastamonien model based on in-situ measured meteorological (IMM) data and radiosonde-derived weighted mean temperature ($T_m$), the ZHD and $T_m$ deviations of the GPT3 model have shown obvious periodic trends. This article analyzed the seasonal variations of GPT3-ZHD and GPT3-$T_m$ during the 2016–2020 period in the Yangtze River Delta region, and the new improved ZHD and $T_m$ models were established by the multi-order Fourier function. The precision of the improved-ZHD model was verified using IMM-ZHD products from 7 GNSS stations during the 2016–2020 period. Furthermore, the precisions of improved $T_m$ and precipitable water vapor (PWV) were verified by radiosonde-derived $T_m$ and PWV in the 2016–2019 period. Compared with the IMM-ZHD and GNSS-PWV products, the mean Bias and RMS of GPT3-ZHD are −0.5 mm and 2.1 mm, while those of GPT3-PWV are 2.7 mm and 11.1 mm. Compared to the radiosonde-derived $T_m$, the mean Bias and RMS of GPT3-$T_m$ are −0.8 K and 3.2 K. The mean Bias and RMS of the improved-ZHD model from 2019 to 2020 are −0.1 mm and 0.5 mm, respectively, decreasing by 0.4 mm and 1.6 mm compared to the GPT3-ZHD, while those of the improved-$T_m$ are −0.6 K and 2.7 K, respectively, decreasing by 0.2 K and 0.5 K compared to GPT3-$T_m$. The mean Bias and RMS of PWV calculated by GNSS-ZTD, improved-ZHD, and improved-$T_m$ are 0.5 mm and 0.6 mm, respectively, compared to the GNSS-PWV, decreasing by 2.2 mm and 10.5 mm compared to the GPT3-PWV. It indicates that the improved ZHD and $T_m$ models can be used to obtain the high-precision PWV. It can be applied effectively in the retrieval of high-precision PWV in real-time in the Yangtze River Delta region. Full article

Zearalenone is a common mycotoxin contaminant in cereals that causes severe economic losses and serious risks to health of human and animals. Many strategies have been devised to degrade ZEN and keep food safe. The hydrolase ZHD101 from Clonostachys rosea, which catalyzes the hydrolytic degradation of ZEN, has been studied widely. In the current research, three new enzymes that have the capacity to detoxify ZEN were identified, namely CLA, EXO, and TRI, showing 61%, 63%, and 97% amino acids identities with ZHD101, respectively. Three coding genes was expressed as heterologous in Escherichia coli BL21. Through biochemical analysis, the purified recombinant CLA, EXO, TRI, and ZHD101 exhibited high activities of degrading ZEN with the specific activity of 114.8 U/mg, 459.0 U/mg, 239.8 U/mg, and 242.8 U/mg. The optimal temperatures of CLA, EXO, TRI, and ZHD101 were 40 °C, 40 °C, 40 °C, and 45 °C, and their optimum pH were 7.0, 9.0, 9.5, and 9.0, respectively. Our study demonstrated that the novel enzymes CLA, EXO, and TRI possessed high ability to degrade ZEN from the model solutions and could be the promising candidates for ZEN detoxification in practical application. Full article

This study investigates the sensitivity of the GNSSseg segmentation method to change in: GNSS data processing method, length of time series (17 to 25 years), auxiliary data used in the integrated water vapor (IWV) conversion, and reference time series used in the segmentation (ERA-Interim versus ERA5). Two GNSS data sets (IGS repro1 and CODE REPRO2015), representative of the first and second IGS reprocessing, were compared. Significant differences were found in the number and positions of detected change-points due to different a priori ZHD models, antenna/radome calibrations, and mapping functions. The more recent models used in the CODE solution have reduced noise and allow the segmentation to detect smaller offsets. Similarly, the more recent reanalysis ERA5 has reduced representativeness errors, improved quality compared to ERA-Interim, and achieves higher sensitivity of the segmentation. Only 45–50% of the detected change-points are similar between the two GNSS data sets or between the two reanalyses, compared to 70–80% when the length of the time series or the auxiliary data are changed. About 35% of the change-points are validated with respect to metadata. The uncertainty in the homogenized trends is estimated to be around 0.01–0.02 kg m${}^{-2}$ year${}^{-1}$. Full article