Cryo-EM structure of HQNO-bound alternative complex III from the anoxygenic phototrophic bacterium Chloroflexus aurantiacus.

Alternative complex III (ACIII) couples quinol oxidation and electron acceptor reduction with potential transmembrane proton translocation. It is compositionally and structurally different from the cytochrome bc1/b6f complexes but functionally replaces these enzymes in the photosynthetic and/or respiratory electron transport chains (ETCs) of many bacteria. However, the true compositions and architectures of ACIIIs remain unclear, as do their structural and functional relevance in mediating the ETCs. We here determined cryogenic electron microscopy structures of photosynthetic ACIII isolated from Chloroflexus aurantiacus (CaACIIIp), in apo-form and in complexed form bound to a menadiol analog 2-heptyl-4-hydroxyquinoline-N-oxide. Besides 6 canonical subunits (ActABCDEF), the structures revealed conformations of 2 previously unresolved subunits, ActG and I, which contributed to the complex stability. We also elucidated the structural basis of menaquinol oxidation and subsequent electron transfer along the [3Fe-4S]-6 hemes wire to its periplasmic electron acceptors, using electron paramagnetic resonance, spectroelectrochemistry, enzymatic analyses, and molecular dynamics simulations. A unique insertion loop in ActE was shown to function in determining the binding specificity of CaACIIIp for downstream electron acceptors. This study broadens our understanding of the structural diversity and molecular evolution of ACIIIs, enabling further investigation of the (mena)quinol oxidoreductases-evolved coupling mechanism in bacterial energy conservation.

The mutual regulation between DcEBF1/2 and DcEIL3-1 is involved in ethylene induced petal senescence in carnation (Dianthus caryophyllus L.).

Carnation (Dianthus caryophyllus L.) is a respiratory climacteric flower, comprising one of the most important cut flowers that is extremely sensitive to plant hormone ethylene. Ethylene signaling core transcription factor DcEIL3-1 plays a key role in ethylene induced petal senescence in carnation. However, how the dose of DcEIL3-1 is regulated in the carnation petal senescence process is still not clear. Here, we screened out two EBF (EIN3 Binding F-box) genes, DcEBF1 and DcEBF2, which showed quick elevation by ethylene treatment according to the ethylene induced carnation petal senescence transcriptome. Silencing of DcEBF1 and DcEBF2 accelerated, whereas overexpression of DcEBF1 and DcEBF2 delayed, ethylene induced petal senescence in carnation by influencing DcEIL3-1 downstream target genes but not DcEIL3-1 itself. Furthermore, DcEBF1 and DcEBF2 interact with DcEIL3-1 to degrade DcEIL3-1 via an ubiquitination pathway in vitro and in vivo. Finally, DcEIL3-1 binds to the promoter regions of DcEBF1 and DcEBF2 to activate their expression. In conclusion, the present study reveals the mutual regulation between DcEBF1/2 and DcEIL3-1 during ethylene induced petal senescence in carnation, which not only expands our understanding about ethylene signal regulation network in the carnation petal senescence process, but also provides potential targets with respect to breeding a cultivar of long-lived cut carnation.

DNA methylation remodeled amino acids biosynthesis regulates flower senescence in carnation (Dianthus caryophyllus).

Dynamic DNA methylation regulatory networks are involved in many biological processes. However, how DNA methylation patterns change during flower senescence and their relevance with gene expression and related molecular mechanism remain largely unknown. Here, we used whole genome bisulfite sequencing to reveal a significant increase of DNA methylation in the promoter region of genes during natural and ethylene-induced flower senescence in carnation (Dianthus caryophyllus L.), which was correlated with decreased expression of DNA demethylase gene DcROS1. Silencing of DcROS1 accelerated while overexpression of DcROS1 delayed carnation flower senescence. Moreover, among the hypermethylated differentially expressed genes during flower senescence, we identified two amino acid biosynthesis genes, DcCARA and DcDHAD, with increased DNA methylation and reduced expression in DcROS1 silenced petals, and decreased DNA methylation and increased expression in DcROS1 overexpression petals, accompanied by decreased or increased amino acids content. Silencing of DcCARA and DcDHAD accelerates carnation flower senescence. We further showed that adding corresponding amino acids could largely rescue the senescence phenotype of DcROS1, DcCARA and DcDHAD silenced plants. Our study not only demonstrates an essential role of DcROS1-mediated remodeling of DNA methylation in flower senescence but also unravels a novel epigenetic regulatory mechanism underlying DNA methylation and amino acid biosynthesis during flower senescence.

Method for fabricating circular polarization beam splitters based on polarization holography.

Based on polarization holography, circular polarization beam splitters with separation angles of up to 100° have been fabricated. The left- and right-handed circularly polarized waves can be reconstructed by the two holograms that were designed by the tensor theory of polarization holography, respectively. In the fabrication of circular polarization beam splitters, two holograms were recorded only by the interference method in the same area of the polarization-sensitive material. This method is simple, inexpensive, and easy to adjust the separation angles and element size. The diffraction efficiency and the polarization state of the reconstructed waves were tested under different incident waves, and the experimental results are in good agreement with the theory. This work not only deepens our understanding of polarization holography but also expands the applications of polarization holography.

An LC-MS/MS method for serum cystatin C quantification and its comparison with two commercial immunoassays.

OBJECTIVES: The standardization of cystatin C (CysC) measurement has received increasing attention in recent years due to its importance in estimating glomerular filtration rate (GFR). Mass spectrometry-based assays have the potential to provide an accuracy base for CysC measurement. However, a precise, accurate and sustainable LC-MS/MS method for CysC is still lacking. METHODS: The developed LC-MS/MS method quantified CysC by detecting signature peptide (T3) obtained from tryptic digestion. Stable isotope labeled T3 peptide (SIL-T3) was spiked to control matrix effects and errors caused by liquid handling. The protein denaturation, reduction and alkylation procedures were combined into a single step with incubation time of 1 h, and the digestion lasted for 3.5 h. In the method validation, digestion time-course, imprecision, accuracy, matrix effect, interference, limit of quantification (LOQ), carryover, linearity, and the comparability to two routine immunoassays were evaluated. RESULTS: No significant matrix effect or interference was observed with the CysC measurement. The LOQ was 0.21 mg/L; the within-run and total imprecision were 1.33-2.05 % and 2.18-3.90 % for three serum pools (1.18-5.34 mg/L). The LC-MS/MS method was calibrated by ERM-DA471/IFCC and showed good correlation with two immunoassays traceable to ERM-DA471/IFCC. However, significant bias was observed for immunoassays against the LC-MS/MS method. CONCLUSIONS: The developed LC-MS/MS method is robust and simpler and holds the promise to provide an accuracy base for routine immunoassays, which will promote the standardization of CysC measurement.

Screening and analysis of the targeted compounds in Choerospondias axillaris extract by receptor chromatographic column with immobilized angiotensin II type 1 receptor.

As a result of the lack of modern techniques, the study of Tibetan medicine has been hindered in identifying bioactive compounds. Herein, we established a chromatographic approach using an immobilized angiotensin II type 1 receptor (AT1R) via a one-step method triggered by haloalkane dehalogenase. The bioactive compounds from Choerospondias axillaris (Guangzao) were screened and identified using the immobilized AT1R followed by MS. Frontal analysis (FA) and adsorption energy distribution (AED) were used to evaluate the association constants. Molecular docking was used to investigate the binding configurations, and the surface efficiency index, binding efficiency index, and ligand-lipophilicity efficiency (LLE) were calculated to assess the drug-like properties. The results identified naringenin, pinocembrin, and chrysin as the compounds that specifically bind to AT1R in Guangzao. FA and AED confirmed that there is only one type of binding site between these compounds and AT1R. The association constants were (2.40 ± 0.02) × 104 M-1 for naringenin (5.22 ± 0.26) × 104 M-1 for pinocembrin, and (4.27 ± 0.14) × 104 M-1 for chrysin, respectively. These compounds can bind with AT1R through the orthosteric binding pocket. Naringenin exhibited better LLE than pinocembrin and chrysin. These results confirmed the feasibility of using the immobilized AT1R column for screening and analyzing bioactive compounds in Tibetan medicines.

Attentional Bias in Older Adults with Non-Clinical Depression: An Eye-Tracking Study.

BACKGROUND: Cognitive models of depression assert that attentional biases play an important role in the maintenance of depression. However, few studies have explored attentional bias in depressed older adults, and no consistent conclusions have been reached. METHODS: In the current study, we investigated attentional bias in older adults with non-clinical depression. Older adults aged over 60 with non-clinical depression and without depression were instructed to perform a free viewing task while their eye movements were tracked. RESULTS: The results showed that, compared to older adults without depression, non-clinically depressed older adults had longer total fixation durations and a greater number of fixations on sad stimuli. Moreover, non-depressed older adults exhibited a preference for pleasant images, whereas this effect was not observed in older adults with non-clinical depression. CONCLUSION: This study suggested that non-clinically depressed older adults have attentional bias, which is manifested as increased attention to sad stimuli and decreased attention to pleasant stimuli.The current study has functional and potential functional implications.

An insertion of transposon in DcNAP inverted its function in the ethylene pathway to delay petal senescence in carnation (Dianthus caryophyllus L.).

Petal senescence is the final stage of flower development. Transcriptional regulation plays key roles in this process. However, whether and how post-transcriptional regulation involved is still largely unknown. Here, we identified an ethylene-induced NAC family transcription factor DcNAP in carnation (Dianthus caryophyllus L.). One allele, DcNAP-dTdic1, has an insertion of a dTdic1 transposon in its second exon. The dTdic1 transposon disrupts the structure of DcNAP and causes alternative splicing, which transcribes multiple domain-deleted variants (DcNAP2 and others). Conversely, the wild type allele DcNAP transcribes DcNAP1 encoding an intact NAC domain. Silencing DcNAP1 delays and overexpressing DcNAP1 accelerates petal senescence in carnation, while silencing and overexpressing DcNAP2 have the opposite effects, respectively. Further, DcNAP2 could interact with DcNAP1 and interfere the binding and activation activity of DcNAP1 to the promoters of its downstream target ethylene biosynthesis genes DcACS1 and DcACO1. Lastly, ethylene signalling core transcriptional factor DcEIL3-1 can activate the expression of DcNAP1 and DcNAP2 in the same way by binding their promoters. In summary, we discovered a novel mechanism by which DcNAP regulates carnation petal senescence at the post-transcriptional level. It may also provide a useful strategy to manipulate the NAC domains of NAC transcription factors for crop genetic improvement.

Generation of vector beams based on diffraction characteristics of a linear polarization hologram in coaxial recording.

Polarization holography is an effective tool for realizing light field manipulation and can be utilized to generate vector beams. Based on the diffraction characteristics of a linear polarization hologram in coaxial recording, an approach for generating arbitrary vector beams is proposed. Unlike the previous methods for generating vector beams, in this work, it is independent of faithful reconstruction effect and the arbitrary linear polarization waves can be used as reading waves. The desired generalized vector beam polarization patterns can be adjusted by changing the polarized direction angle of the reading wave. Therefore, it is more flexible than the previously reported methods in generating vector beams. The experimental results are consistent with the theoretical prediction.

Post-ovulatory aging affects mitochondria, spindle and protein metabolism in mouse oocytes.

In brief: Post-ovulatory aging (POA) results in a decline in oocyte quality and embryonic developmental capacity although the underlying mechanisms remain elusive. This study provides comprehensive mRNA expression profiles of fresh and aging oocytes in mice for the first time. Abstract: POA impairs the quality of mammalian oocytes with harmful effects on the developmental potential of the embryo. This is a major problem for humans since it is associated with low rate of natural fertility, with high rate of spontaneous abortion and low efficiency of in vitro fertilization. However, the molecular mechanisms underlying this process remain unclear and new methods are demanded to control POA. In this study, we performed single-cell RNA-sequencing (scRNA-seq) analysis on fresh and aging MII mouse oocytes and compared their global RNA transcription patterns. Nine hundred and twenty-one differentially expressed genes (DEGs) were identified. Five hundred and sixty-nine genes were downregulated, while 356 were upregulated in the group of aging oocytes. Gene ontology (GO) enrichment analysis demonstrated that a series of DEGs were significantly enriched involving mitochondrial functions, spindle functions and protein metabolism. The results of qPCR and a series of functional tests further confirmed that the disorder of mitochondrial functions, spindle functions and impairment of protein metabolism were actually involved in the progression of POA. In this study, panoramic mRNA expression profiles of fresh and aging oocytes were depicted and fully validated. Our data will provide a useful resource for further research on the regulation of gene expression of POA and suggest potential strategies to delay and reverse POA.

Polarization splitters with designable separation angles based on polarization holography of tensor theory.

We propose a simple and inexpensive method for the fabrication of polarization splitters with designable separation angles and a controllable active area, based on polarization holography of tensor theory. First, we design two polarization holograms that reconstruct waves with only p- or s-polarization components, respectively. Then, after we recorded these two holograms on the same position of the recording material using the interference approach, as a result, a polarization splitter could readily be prepared. The separation angles of fabricated polarization splitters can be easily adjusted by changing the interference angle, and the active area can also be easily modified by changing the sizes of the interference beams and recording material during the recording process. The experimental results verify the reliability and accuracy of this method. We believe that this work may broaden the application field of polarization holography.

Developmental toxicity of 2-bromoacetamide on peri- and early post-implantation mouse embryos in vitro.

2-bromoacetamide (BAcAm), a new class of disinfection by-products (DBPs), is widely detected in drinking water across the world. Reports of the high cytogenetic toxicity of BAcAm have aroused public attention concerning its toxic effects on early embryonic development. In this study, we optimized an in vitro culture (IVC) system for peri- and early post-implantation mouse embryos and used this system to determine the developmental toxicity of BAcAm. We found that exposure to BAcAm caused a reduction in egg cylinder formation rate and abnormal lineage differentiation in a dose-dependent manner. Transcriptomic analysis further revealed that BAcAm exposure at early developmental stages altered the abundance of transcripts related to a variety of biological processes including gene expression, metabolism, cell proliferation, cell death and embryonic development, thus indicating its toxic effects on embryonic development. Thus, we developed a robust tool for studying the toxicology of chemicals at the early stages of embryonic development and demonstrated the developmental toxicity of BAcAm in the early embryonic development of mammals.

Simultaneously characterized Stokes parameters of a lightwave utilizing the tensor polarization holography theory.

Polarization is a natural property of a lightwave and makes a significant contribution to various scientific and technological applications, due to the different states of polarization (SoP) of a lightwave that may manifest distinct behaviors. Hence, it is important to determine the SoP of the lightwave. Generally, the SoP of a lightwave can be recognized by the Stokes parameters. In this paper, we proposed a novel method to simultaneously characterize the Stokes parameters of a lightwave, by employing the tensor polarization holography theory. This is done through merely a piece of polarization-sensitive material. Compared with the traditional method, this method requires only one measurement to obtain all the Stokes parameters, without using additional polarizing elements. The experimental result shows excellent agreement with the theoretical one, which confirmed the reliability and accuracy of the proposed method. We believe that this work may broaden the application field of polarization holography.

Functional substitution of zona pellucida with modified sodium hyaluronate gel in human embryos.

PURPOSE: Zona pellucida-free (ZP-free) embryos often fail to achieve good developmental outcomes and are routinely discarded in assisted reproductive laboratories. Existing attempts to rescue ZP-free embryos are not widely used due to operational complexity and high technical requirements. To handle cases with missing ZP, we applied modified sodium hyaluronate gel (MSHG) to embryo culture to determine if it can function as a substitute for human zona pellucida. METHODS: The developmental process and the blastocyst formation rate of embryos were analyzed in both mouse and human. The first clinical application of MSHG was reported, and the pregnancy outcome was continuously followed up. RESULTS: Human and mouse ZP-free embryos cultured with MSHG showed a blastocyst formation rate similar to ZP-intact embryos. MSHG improves blastocysts formation rate by maintaining blastomere spatial arrangement at early stages. Compared to ZP-free embryos, the proportion of tetrahedrally arranged blastomeres at the 4-cell stage increased significantly in embryos cultured with MSHG in humans. A ZP-free blastocyst cultured in MSHG with the highest score was successfully implanted after day 5 transplantation and developed normally. CONCLUSION: These data demonstrate that MSHG can substitute the function of zona pellucida and rescue human ZP-free embryos during assisted reproductive technology.

Diffraction characteristics of a linear polarization hologram in coaxial recording.

Diffraction characteristics of polarization holograms have important research significance and application prospects. In this paper, the Tensor theory was used to investigate the diffraction characteristics of a linear polarization hologram in a coaxial recording. The results show that, when the signal and reference waves are coaxial aligned, the sum of the polarized direction angles of two waves in the reconstruction process is equal to the sum of these in the recording process under the condition that, the gratings of recorded intensity response and the polarization response are in balance. The study on the diffraction characteristics of linear polarization holograms based on the Tensor theory in the coaxial recording may help us with a deeper insight into the polarization holography theory. Again, our results helped in the use of a proper design for the polarizer to change the polarization direction of the incident linear polarization waves.

Covalent Inhibitor-Based One-Step Method for Endothelin Receptor A Immobilization: from Ligand Recognition to Lead Identification.

Protein immobilization is particularly significant in proteomics, interactomics, and in vitro drug screening. It is an essential primary step for numerous biological techniques that rely on immobilized proteins with controlled orientation, high conformational stability, and high activity (CHH). These have challenged the current immobilization strategy and demanded increasing efforts for an efficient method to meet the CHH immobilization in a single step. Herein, we proposed a covalent inhibitor-based, one-step method for G protein-coupled receptor (GPCR) immobilization inspired by the covalent reaction between an epidermal growth factor receptor (EGFR)-tag and its inhibitor ibrutinib. We immobilized endothelin receptor A (ETA) containing a fusion EGFR tag onto an ibrutinib-coated macroporous silica gel. The immobilized ETA proved to have demonstrable ligand-binding activity and specificity, thus resulting in a chromatographic technology allowing receptor-ligand interaction analysis and lead identification. Such immobilization method is attractable, owing to the properties of mild reacting conditions, fast rate, high yield, and good stability of the conjugated protein. It will be applicable to biochips, biosensors, and biocatalysts.

Improved pore structure characterization and classification of strong diagenesis sandstones by data-mining analytics in Tazhong area, Tarim Basin.

The Silurian system in Tazhong area is characterized by extensive, low-abundance lithological reservoirs with strong diagenesis, resulting in significant heterogeneity. The complex pore structure in this area significantly impacts fluid control, making accurate characterization and classification of pore structures crucial for understanding reservoir properties and their influence on oil and gas distribution. Based on 314 Mercury Injection Capillary Pressure (MICP) samples in combination with core slices and thin casting slices observation, a pipeline of characterization and classification scheme by data-mining analytics of strong diagenesis sandstone pore structure types in the study zone is established, and the characteristics of different pore structures are clarified. According to the pore structure parameter abstracted by MICP data compression and variable analysis based on hierarchical clustering and principal component analysis (PCA) analysis, the variables are reasonably evaluated and screened, and the screened variables can be divided into three groups: mean pore throat radius-maximum pore throat radius-median pore throat radius-pore throat diameter mean variable group, microscopic mean coefficient variable group, and median pressure displacement pressure-relative sorting coefficient variable group. The combination of classification schemes analysed by decision tree model and linear discriminant analysis (LDA) model was determined. In the two-dimensional projection diagram of LDA model, a relatively obvious distribution of low displacement pressure, middle displacement pressure and high displacement pressure was obtained, and three distribution lines were nearly parallel. Based on the relevant information, 6 combined classification schemes suitable for final pore structure modelling were determined verified by microscopic observation. The correct characterization and classification of pore structure can be applied to the prediction of pore type, which can be used to improve the prediction of oil and gas distribution and oil and gas recovery in the future.

Aerobic Exercise Protects against Cardiotoxin-Induced Skeletal Muscle Injury in a DDAH1-Dependent Manner.

Dimethylarginine dimethylaminohydrolase 1 (DDAH1) is a critical enzyme that regulates nitric oxide (NO) signaling through the degradation of asymmetric dimethylarginine (ADMA). Previous studies have revealed a link between the beneficial effects of aerobic exercise and the upregulation of DDAH1 in bones and hearts. We previously reported that skeletal muscle DDAH1 plays a protective role in cardiotoxin (CTX)-induced skeletal muscle injury and regeneration. To determine the effects of aerobic exercise on CTX-induced skeletal muscle injury and the role of DDAH1 in this process, wild-type (WT) mice and skeletal muscle-specific Ddah1-knockout (Ddah1MKO) mice were subjected to swimming training for 8 weeks and then injected with CTX. In WT mice, swimming training for 8 weeks significantly promoted skeletal muscle regeneration and attenuated inflammation, oxidative stress, and apoptosis in the gastrocnemius (GA) muscle after CTX injection. These phenomena were associated with increases in the protein expression of PAX7, myogenin, MEF2A, eNOS, SOD2, and peroxiredoxin 5 and decreases in iNOS expression in GA muscles. Swimming training also decreased serum ADMA levels and increased serum nitrate/nitrite (NOx) levels and skeletal muscle DDAH1 expression. Interestingly, swimming training in Ddah1MKO mice had no obvious effect on CTX-induced skeletal muscle injury or regeneration and did not repress the CTX-induced inflammatory response, superoxide generation, or apoptosis. In summary, our data suggest that DDAH1 is important for the protective effect of aerobic exercise on skeletal muscle injury and regeneration.

Metagenomic and metabolite analysis reveals microbial community and metabolite dynamics in fermented Indigo naturalis.

The soaking and fermentation of the stems and leaves is an important intermediate step in the processing of Indigo Naturalis. However, the relationship between microbiota and Indigo Naturalis yields is still poorly understood. This study aimed to compare microbial communities and metabolite profiles at various stages of soaking fermentation, followed by validation of the results using HPLC. A total of 731 compounds were identified through metabolite analysis, with the levels of indigo and indirubin peaking after 36 h of fermentation. Metagenomes revealed Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were identified as the most abundant microbial phyla in soaking fermentation. Correlation analysis indicated that the yields of indigo and indirubin may be affected by Lactococcus, Clostridium, and Enterobacter through the regulation of related synthetic enzymes. The findings offered novel perspectives on the relationship of microorganisms and Indigo Naturalis yields.