Analysis of resonance Raman data on the blue copper site in pseudoazurin: excited state π and σ charge transfer distortions and their relation to ground state reorganization energy

The short Cu^(2+)-S(Met) bond in pseudoazurin (PAz) results in the presence of two relatively intense S_p(π) and S_p(σ) charge transfer (CT) transitions. This has enabled resonance Raman (rR) data to be obtained for each excited state. The rR data show very different intensity distribution patterns for the vibrations in the 300-500 cm^(-1) region. Time-dependent density functional theory (TDDFT) calculations have been used to determine that the change in intensity distribution between the S_p(π) and S_p(σ) excited states reflects the differential enhancement of S(Cys) backbone modes with Cu-S(Cys)-C_β out-of-plane (oop) and in-plane (ip) bend character in their respective potential energy distributions (PEDs). The rR excited state distortions have been related to ground state reorganization energies (λ s) and predict that, in addition to M-L stretches, the Cu-S(Cys)-C_β oop bend needs to be considered. DFT calculations predict a large distortion in the Cu-S(Cys)-C_β oop bending coordinate upon reduction of a blue copper (BC) site; however, this distortion is not present in the X-ray crystal structures of reduced BC sites. The lack of Cu-S(Cys)-C_β oop distortion upon reduction corresponds to a previously unconsidered constraint on the thiolate ligand orientation in the reduced state of BC proteins and can be considered as a contribution to the entatic/rack nature of BC sites

Investigating Graph Structure Information for Entity Alignment with Dangling Cases

Entity alignment (EA) aims to discover the equivalent entities in different knowledge graphs (KGs), which play an important role in knowledge engineering. Recently, EA with dangling entities has been proposed as a more realistic setting, which assumes that not all entities have corresponding equivalent entities. In this paper, we focus on this setting. Some work has explored this problem by leveraging translation API, pre-trained word embeddings, and other off-the-shelf tools. However, these approaches over-rely on the side information (e.g., entity names), and fail to work when the side information is absent. On the contrary, they still insufficiently exploit the most fundamental graph structure information in KG. To improve the exploitation of the structural information, we propose a novel entity alignment framework called Weakly-Optimal Graph Contrastive Learning (WOGCL), which is refined on three dimensions : (i) Model. We propose a novel Gated Graph Attention Network to capture local and global graph structure similarity. (ii) Training. Two learning objectives: contrastive learning and optimal transport learning are designed to obtain distinguishable entity representations via the optimal transport plan. (iii) Inference. In the inference phase, a PageRank-based method is proposed to calculate higher-order structural similarity. Extensive experiments on two dangling benchmarks demonstrate that our WOGCL outperforms the current state-of-the-art methods with pure structural information in both traditional (relaxed) and dangling (consolidated) settings. The code will be public soon

Nitric oxide-induced lipophagic defects contribute to testosterone deficiency in rats with spinal cord injury

IntroductionMales with acute spinal cord injury (SCI) frequently exhibit testosterone deficiency and reproductive dysfunction. While such incidence rates are high in chronic patients, the underlying mechanisms remain elusive.Methods and resultsHerein, we generated a rat SCI model, which recapitulated complications in human males, including low testosterone levels and spermatogenic disorders. Proteomics analyses showed that the differentially expressed proteins were mostly enriched in lipid metabolism and steroid metabolism and biosynthesis. In SCI rats, we observed that testicular nitric oxide (NO) levels were elevated and lipid droplet-autophagosome co-localization in testicular interstitial cells was decreased. We hypothesized that NO impaired lipophagy in Leydig cells (LCs) to disrupt testosterone biosynthesis and spermatogenesis. As postulated, exogenous NO donor (S-nitroso-N-acetylpenicillamine (SNAP)) treatment markedly raised NO levels and disturbed lipophagy via the AMPK/mTOR/ULK1 pathway, and ultimately impaired testosterone production in mouse LCs. However, such alterations were not fully observed when cells were treated with an endogenous NO donor (L-arginine), suggesting that mouse LCs were devoid of an endogenous NO-production system. Alternatively, activated (M1) macrophages were predominant NO sources, as inducible NO synthase inhibition attenuated lipophagic defects and testosterone insufficiency in LCs in a macrophage-LC co-culture system. In scavenging NO (2-4-carboxyphenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (CPTIO)) we effectively restored lipophagy and testosterone levels both in vitro and in vivo, and importantly, spermatogenesis in vivo. Autophagy activation by LYN-1604 also promoted lipid degradation and testosterone synthesis.DiscussionIn summary, we showed that NO-disrupted-lipophagy caused testosterone deficiency following SCI, and NO clearance or autophagy activation could be effective in preventing reproductive dysfunction in males with SCI

Genome-wide identification and expression analysis of 3-ketoacyl-CoA synthase gene family in rice (Oryza sativa L.) under cadmium stress

3-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme for the synthesis of very long-chain fatty acids (VLCFAs) in plants, which determines the carbon chain length of VLCFAs. However, a comprehensive study of KCSs in Oryza sativa has not been reported yet. In this study, we identified 22 OsKCS genes in rice, which are unevenly distributed on nine chromosomes. The OsKCS gene family is divided into six subclasses. Many cis-acting elements related to plant growth, light, hormone, and stress response were enriched in the promoters of OsKCS genes. Gene duplication played a crucial role in the expansion of the OsKCS gene family and underwent a strong purifying selection. Quantitative Real-time polymerase chain reaction (qRT-PCR) results revealed that most KCS genes are constitutively expressed. We also revealed that KCS genes responded differently to exogenous cadmium stress in japonica and indica background, and the KCS genes with higher expression in leaves and seeds may have functions under cadmium stress. This study provides a basis for further understanding the functions of KCS genes and the biosynthesis of VLCFA in rice

Effects of Hepatitis B Virus S Protein Exposure on Sperm Membrane Integrity and Functions

Background: Hepatitis B is a public health problem worldwide. Viral infection can affect a man’s fertility, but only scant information about the influence of hepatitis B virus (HBV) infection on sperm quality is available. The purpose of this study was to investigate the effect of hepatitis B virus S protein (HBs) on human sperm membrane integrity and functions. Methods/Principal Findings: Reactive oxygen species (ROS), lipid peroxidation (LP), total antioxidant capacity (TAC) and phosphatidylserine (PS) externalization were determined. The terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assays and flow cytometric analyses were performed. (1) After 3 h incubation with 25 mg/ml of HBs, the average rates of ROS positive cells, annexin V–positive/propidium iodide (PI)-negative cells, Caspases-3,-8,-9 positive cells and TUNEL-positive cells were significantly increased in the test groups as compared to those in the control groups, while TAC level was decreased when compared with the control. The level of malondialdehyde (MDA) in the sperm cells exposed to 50 mg/ml of HBs for 3 h was significantly higher than that in the control (P,0.05–0.01). (2) HBs increased the MDA levels and the numbers of ROS positive cells, annexin V–positive/PI-negative cells, caspases-3,-8,-9 positive cells and TUNEL-positive cells in a dose-dependent manner. (3) HBs monoclonal antibody (MAb) and N-Acetylcysteine (NAC) reduced the number of ROS-positive sperm cells. (4) HBs decreased the TAC levels in sperm cells in a dose-dependent manner. Conclusion: HBs exposure could lead to ROS generation, lipid peroxidation, TAC reduction, PS externalization, activation o

Global Mixup: Eliminating Ambiguity with Clustering

Data augmentation with Mixup has been proven an effective method to regularize the current deep neural networks. Mixup generates virtual samples and corresponding labels simultaneously by linear interpolation. However, the one-stage generation paradigm and the use of linear interpolation have two defects: (1) The label of the generated sample is simply combined from the labels of the original sample pairs without reasonable judgment, resulting in ambiguous labels. (2) Linear combination significantly restricts the sampling space for generating samples. To address these issues, we propose a novel and effective augmentation method, Global Mixup, based on global clustering relationships. Specifically, we transform the previous one-stage augmentation process into two-stage by decoupling the process of generating virtual samples from the labeling. And for the labels of the generated samples, relabeling is performed based on clustering by calculating the global relationships of the generated samples. Furthermore, we are no longer restricted to linear relationships, which allows us to generate more reliable virtual samples in a larger sampling space. Extensive experiments for CNN, LSTM, and BERT on five tasks show that Global Mixup outperforms previous baselines. Further experiments also demonstrate the advantage of Global Mixup in low-resource scenarios

Comprehensive evaluation and type selection of energy storage based on analytic hierarchy process

Owing to its high controllability and time transfer characteristics， energy storage technology is worth being applied in new-type power systems. The rational judgment of energy storage in various scenarios and the selection with a clear aim are of practical significance. First， 10 types of technical and economic indicators of energy storage are proposed for various demand scenarios of power systems， and a comprehensive evaluation index system of energy storage is constructed. Then， comprehensive evaluation and calculation on the above indexes is carried out by using analytic hierarchy process （AHP）， during which the relative importance of the judgment matrix is valuated by Delphi method， and the consistency check and correction are carried out to solve the combination weight of the scheme layer in relation to the target layer； then， a comprehensive evaluation and calculation of various types of energy storage is performed to obtain an optimal energy storage selection scheme. Finally， a regional power grid is simulated， and the ranking results of various types of energy storage under multiple scenarios are derived to verify the effectiveness of the proposed method

Analysis of resonance Raman data on the blue copper site in pseudoazurin: excited state π and σ charge transfer distortions and their relation to ground state reorganization energy

The short Cu^(2+)-S(Met) bond in pseudoazurin (PAz) results in the presence of two relatively intense S_p(π) and S_p(σ) charge transfer (CT) transitions. This has enabled resonance Raman (rR) data to be obtained for each excited state. The rR data show very different intensity distribution patterns for the vibrations in the 300-500 cm^(-1) region. Time-dependent density functional theory (TDDFT) calculations have been used to determine that the change in intensity distribution between the S_p(π) and S_p(σ) excited states reflects the differential enhancement of S(Cys) backbone modes with Cu-S(Cys)-C_β out-of-plane (oop) and in-plane (ip) bend character in their respective potential energy distributions (PEDs). The rR excited state distortions have been related to ground state reorganization energies (λ s) and predict that, in addition to M-L stretches, the Cu-S(Cys)-C_β oop bend needs to be considered. DFT calculations predict a large distortion in the Cu-S(Cys)-C_β oop bending coordinate upon reduction of a blue copper (BC) site; however, this distortion is not present in the X-ray crystal structures of reduced BC sites. The lack of Cu-S(Cys)-C_β oop distortion upon reduction corresponds to a previously unconsidered constraint on the thiolate ligand orientation in the reduced state of BC proteins and can be considered as a contribution to the entatic/rack nature of BC sites

A variable temperature spectroscopic study on Paracoccus pantotrophus pseudoazurin: protein constraints on the blue Cu site

The blue or Type 1 (T1) copper site of Paracoccuspantotrophus pseudoazurin exhibits significant absorption intensity in both the 450 and 600 nm regions. These are sigma and π S_(Cys) to Cu^(2+) charge transfer (CT) transitions. The temperature dependent absorption, EPR, and resonance Raman (rR) vibrations enhanced by these bands indicate that a single species is present at all temperatures. This contrasts the temperature dependent behavior of the T1 center in nitrite reductase [S. Ghosh, X. Xie, A. Dey, Y. Sun, C. Scholes, E. Solomon, Proc. Natl. Acad. Sci. 106 (2009) 4969-4974] which has a thioether ligand that is unconstrained by the protein. The lack of temperature dependence in the T1 site in pseudoazurin indicates the presence of a protein constraint similar to the blue Cu site in plastocyanin where the thioether ligand is constrained at 2.8 A. However, plastocyanin exhibits only π CT. This spectral difference between pseudoazurin and plastocyanin reflects a coupled distortion of the site where the axial thioether in pseudoazurin is also constrained, but at a shorter Cu-S_(Met) bond length. This leads to an increase in the Cu^(2+)-S_(Cys) bond length, and the site undergoes a partial tetragonal distortion in pseudoazurin. Thus, its ground state wavefunction has both sigma and pi character in the Cu^(2+)-S(Cys) bond