Shorter Alkanesulfonate Carbon Chains Destabilize the Active Site Architecture of SsuD for Desulfonation.

Bacteria have evolved to utilize alternative organosulfur sources when sulfur is limiting. The SsuE/SsuD and MsuE/MsuD enzymes expressed when sulfur sources are restricted, are responsible for providing specific bacteria with sulfur in the form of alkanesulfonates. In this study, we evaluated why two structurally and functionally similar FMNH2-dependent monooxygenase enzymes (MsuD and SsuD) are needed for the acquisition of alkanesulfonates in some bacteria. In desulfonation assays, MsuD was able to utilize the entire range of alkanesulfonates (C1-C10). However, SsuD was not able to utilize smaller alkanesulfonate substrates. Interestingly, SsuD had a similar binding affinity for methanesulfonate (MES) (15 ± 1 µM) as MsuD (12 ± 1 µM) even though SsuD was not able to catalyze the desulfonation of the MES substrate. SsuD and MsuD showed decreased proteolytic susceptibility in the presence of FMNH2 with MES and octanesulfonate (OCS). Tighter loop closure was observed for the MsuD/FMNH2 complex with MES and OCS compared to SsuD under comparable conditions. Analysis of the SsuD/FMNH2/MES structure using accelerated molecular dynamics simulations found three different conformations for MES, demonstrating the instability of the bound structure. Even when MES was bound in a similar fashion to OCS within the active site, the smaller alkane chain resulted in a shift of FMNH2 so that it was no longer in a position to catalyze the desulfonation of MES. The active site of SsuD requires a longer alkane chain to maintain the appropriate architecture for desulfonation.

NMCMDA: neural multicategory MiRNA-disease association prediction.

MOTIVATION: There is growing evidence showing that the dysregulations of miRNAs cause diseases through various kinds of the underlying mechanism. Thus, predicting the multiple-category associations between microRNAs (miRNAs) and diseases plays an important role in investigating the roles of miRNAs in diseases. Moreover, in contrast with traditional biological experiments which are time-consuming and expensive, computational approaches for the prediction of multicategory miRNA-disease associations are time-saving and cost-effective that are highly desired for us. RESULTS: We present a novel data-driven end-to-end learning-based method of neural multiple-category miRNA-disease association prediction (NMCMDA) for predicting multiple-category miRNA-disease associations. The NMCMDA has two main components: (i) encoder operates directly on the miRNA-disease heterogeneous network and leverages Graph Neural Network to learn miRNA and disease latent representations, respectively. (ii) Decoder yields miRNA-disease association scores with the learned latent representations as input. Various kinds of encoders and decoders are proposed for NMCMDA. Finally, the NMCMDA with the encoder of Relational Graph Convolutional Network and the neural multirelational decoder (NMR-RGCN) achieves the best prediction performance. We compared the NMCMDA with other baselines on three experimental datasets. The experimental results show that the NMR-RGCN is significantly superior to the state-of-the-art method TDRC in terms of Top-1 precision, Top-1 Recall, and Top-1 F1. Additionally, case studies are provided for two high-risk human diseases (namely, breast cancer and lung cancer) and we also provide the prediction and validation of top-10 miRNA-disease-category associations based on all known data of HMDD v3.2, which further validate the effectiveness and feasibility of the proposed method.

Immune microenvironment: novel perspectives on bone regeneration disorder in osteoradionecrosis of the jaws.

Osteoradionecrosis of the jaws (ORNJ) is a severe complication that occurs after radiotherapy of head and neck malignancies. Clinically, conservative treatments and surgeries for ORNJ exhibited certain therapeutic effects, whereas the regenerative disorder of the post-radiation jaw remains a pending problem to be solved. In recent years, the recognition of the role of the immune microenvironment has led to a shift from an osteoblasts (OBs) or bone marrow mesenchymal stromal cells (BMSCs)-centered view of bone regeneration to the concept of a complicated microecosystem that supports bone regeneration. Current advances in osteoimmunology have uncovered novel targets within the immune microenvironment to help improve various regeneration therapies, notably therapies potentiating the interaction between BMSCs and immune cells. However, these researches lack a thorough understanding of the immune microenvironment and the interaction network of immune cells in the course of bone regeneration, especially for the post-operative defect of ORNJ. This review summarized the composition of the immune microenvironment during bone regeneration, how the immune microenvironment interacts with the skeletal system, and discussed existing and potential strategies aimed at targeting cellular and molecular immune microenvironment components.

Prognostic model based on telomere-related genes predicts the risk of oral squamous cell carcinoma.

BACKGROUND: This study investigated a potential prognostic model based on telomere-related genes (TRGs) for the clinical prediction of oral squamous cell carcinoma (OSCC). METHODS: Gene expression data and associated clinical phenotypes were obtained from online databases. Differentially expressed (DE)-TRGs were identified between OSCC and normal samples, followed by protein-protein interaction and enrichment analyses. Subsequently, the prognostic genes explored based on the DE-TRGs and survival data were applied in the establishment of the current prognostic model, and an integrated analysis was performed between high- and low-risk groups using a prognostic model. The expression of certain prognostic genes identified in the present study was validated using qPCR analysis and/or western blot in OSCC cell lines and clinical samples. RESULTS: 169 DE-TRGs were identified between the OSCC samples and controls. DE-TRGs are mainly involved in functions such as hypoxia response and pathways such as the cell cycle. Eight TRGs (CCNB1, PDK4, PLOD2, RACGAP1, MET, PLK1, KPNA2, and CCNA2) associated with OSCC survival and prognosis were used to construct a prognostic model. qPCR analysis and western blot showed that most of the eight prognostic genes were consistent with the current bioinformatics results. Analysis of the high- and low-risk groups for OSCC determined by the prognostic model showed that the current prognostic model was reliable. CONCLUSIONS: A novel prognostic model for OSCC was constructed by TRGs. PLOD2 and APLK1 may participate in the progression of OSCC via responses to hypoxia and cell cycle pathways, respectively. TRGs, including KPNA2 and CCNA2, may serve as novel prognostic biomarkers for OSCC.

REHE: Fast variance components estimation for linear mixed models.

Linear mixed models are widely used in ecological and biological applications, especially in genetic studies. Reliable estimation of variance components is crucial for using linear mixed models. However, standard methods, such as the restricted maximum likelihood (REML), are computationally inefficient in large samples and may be unstable with small samples. Other commonly used methods, such as the Haseman-Elston (HE) regression, may yield negative estimates of variances. Utilizing regularized estimation strategies, we propose the restricted Haseman-Elston (REHE) regression and REHE with resampling (reREHE) estimators, along with an inference framework for REHE, as fast and robust alternatives that provide nonnegative estimates with comparable accuracy to REML. The merits of REHE are illustrated using real data and benchmark simulation studies.

The stalk domain of SARS-CoV-2 NSP13 is essential for its helicase activity.

COVID-19, caused by SARS-CoV-2, has been spreading worldwide for more than two years and has led to immense challenges to human health. Despite the great efforts that have been made, our understanding of SARS-CoV-2 is still limited. The viral helicase, NSP13 is an important enzyme involved in SARS-CoV-2 replication and transcription. Here we highlight the important role of the stalk domain in the enzymatic activity of NSP13. Without the stalk domain, NSP13 loses its dsRNA unwinding ability due to the lack of ATPase activity. The stalk domain of NSP13 also provides a rigid connection between the ZBD and helicase domain. We found that the tight connection between the stalk and helicase is necessary for NSP13-mediated dsRNA unwinding. When a short flexible linker was inserted between the stalk and helicase domains, the helicase activity of NSP13 was impaired, although its ATPase activity remained intact. Further study demonstrated that linker insertion between the stalk and helicase domains attenuated the RNA binding ability and affected the thermal stability of NSP13. In summary, our results suggest the crucial role of the stalk domain in NSP13 enzymatic activity and provide mechanistic insight into dsRNA unwinding by SARS-CoV-2 NSP13.

netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis.

Existing software tools for topology-based pathway enrichment analysis are either computationally inefficient, have undesirable statistical power, or require expert knowledge to leverage the methods' capabilities. To address these limitations, we have overhauled NetGSA, an existing topology-based method, to provide a computationally-efficient user-friendly tool that offers interactive visualization. Pathway enrichment analysis for thousands of genes can be performed in minutes on a personal computer without sacrificing statistical power. The new software also removes the need for expert knowledge by directly curating gene-gene interaction information from multiple external databases. Lastly, by utilizing the capabilities of Cytoscape, the new software also offers interactive and intuitive network visualization.

Elucidating the interaction of rhizosphere bacteria and environmental factors in influencing active ingredient content of Lycium barbarum fruit in China.

AIMS: This study aimed to compare the differences in the bacterial community structure of Lycium barbarum rhizosphere and elucidate the contribution of rhizosphere bacteria to the active ingredients of L. barbarum fruit. METHODS AND RESULTS: This study investigated the soil and meteorological characteristics of L. barbarum rhizosphere during three growth stages across three production regions of China. High-throughput sequencing showed significant differences in the bacterial community diversity of L. barbarum rhizosphere across the three production regions, and norank_o_Gaiellales, norank_f_Anaerolineaceae and norank_f_AKYG1722 were the highest in Ningxia. In addition, regression and path analysis revealed that pH, norank_o_Gaiellales and norank_f_AKYG1722 significantly promoted the accumulation of total sugar and flavonoids in L. barbarum fruit directly or indirectly. Soil organic matter (SOM), norank_f_Anaerolineaceae and humidity significantly promoted the accumulation of betaine. The average temperature during the growth stages, norank_f_AKYG1722, and norank_o_Gaiellales promoted the accumulation of polysaccharides. CONCLUSIONS: The interaction between rhizosphere bacteria and environmental factors promoted the accumulation of active ingredients in L. barbarum fruits. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results provided insights to improve the quality of L. barbarum fruit.

Inter-Defect Septal Puncture Technique For Single Device Closure of Wide-Spaced Multi-Hole Atrial Septal Defect.

Closure of a wide-spaced multi-hole secundum atrial septal defect (MHASD) using a single occluder is difficult to accomplish. Multiple occluder implantation has risks such as incomplete endothelialisation, device embolisation, and residual shunt. Blade or balloon septotomy enables single device occlusion; however, the aforementioned may cause a short circumferential rim with subsequent device instability. This paper describes an inter-defect septal puncture technique for single device closure of different layouts of wide-spaced MHASDs via per-atrial or percutaneous approach under exclusive transoesophageal echocardiographic guidance. This technique combined with anti-tenting puncture equally befits a small caval atrial septal defect and MHASD with a floppy aneurysmal septum.

Influence of Electronic Modulation of Phenanthroline-Derived Ligands on Separation of Lanthanides and Actinides.

The solvent extraction, complexing ability, and basicity of tetradentate N-donor 2,9-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzotriazin-3-yl)-1,10-phenanthroline (CyMe4-BT- Phen) and its derivatives functionalized by Br, hydroxyphenyl, nitryl were discussed and compared. It was demonstrated that four BTPhen ligands are able to selectively extract Am(lll) over Eu(lll). It was notable that the distribution ratio of 5-nitryl-CyMe4-BTPhen for Eu(lll) was suppressed under 0.02, which was much lower compared to DEu(lll) = 1 by CyMe4-BTPhen. The analysis of the effect of the substituent on the affinity to lanthanides was conducted by UV/vis and fluorescence spectroscopic titration. The stability constants of various ligands with Eu(lll) were obtained by fitting titration curve. Additionally, the basicity of various ligands was determined to be 3.1 ± 0.1, 2.3 ± 0.2, 0.9 ± 0.2, 0.5 ± 0.1 by NMR in the media of CD3OD with the addition of DClO4. The basicity of ligands follows the order of L1 > L2 > L3 > L4, indicating the tendency of protonation decreases with the electron-withdrawing ability increase.

3D Printed Embedded Metamaterials.

The manufacturing of 3D and conformal metamaterials remains a major challenge. The projection micro-stereolithography 3D printing technology combined with the liquid metal filling method is employed here to fabricate the metamaterials, which are characterized with embedded features that can effectively protect the metal resonance layer from external influence, and integrated molding of macro-micro structures and function-structure. To demonstrate the robustness and flexibility of the proposed method, three types of metamaterials are fabricated: 3D orthogonal split-ring resonator metamaterial, bionic compound eye conformal metamaterial, and a five-layer broadband conformal metamaterial in the form of hemispherical moth-eye, which are costly, tedious, and time consuming in conventional fabrication methods. And the layout of the filling channel is optimized and the polydimethylsiloxane coating post-treatment process is applied to smooth the surface roughness caused by the staircase effect of 3D printing to improve the transmission performance of metamaterial devices. The transmission properties are measured using terahertz time-domain spectroscopy system and the experimental results show that the method proposed in this paper makes metamaterial manufacture no longer limited to complex structures, which effectively expands the application range of metamaterials.

Characterization of YAG:Ce phosphor dosimeter by the co-precipitation method for radiotherapy.

Yttrium aluminum garnet (YAG) doped with Ce was synthesized via the co-precipitation method with NH4HCO3 as the precipitant. The spectroscopic properties and the effects of the Ce doping concentration and sintering atmosphere on the crystal phase were investigated. The dosimeter of YAG:Ce phosphor material was prepared to study the radioluminescence (RL) characteristics of a clinical linear accelerator. A satisfying linear relationship between the radiation dose and RL signal was obtained, which provided a reference for the YAG:Ce phosphor material used in radiotherapy and real-time remote radiation detection.

Substrate-Dependent Mobile Loop Conformational Changes in Alkanesulfonate Monooxygenase from Accelerated Molecular Dynamics.

Substrate-induced conformational changes present in alkanesulfonate monooxygenase (SsuD) are crucial to catalysis and lead to distinct interactions between a dynamic loop region and the active site. Accelerated molecular dynamics (aMD) simulations have been carried out to examine this potential correlation by studying wild-type SsuD and variant enzymes bound with different combinations of reduced flavin (FMNH2), C4a-peroxyflavin intermediate (FMNOO-), and octanesulfonate (OCS). Three distinct mobile loop conformations were identified: "open", "closed", and "semiclosed". The substrate-free SsuD system possessed a wide opening capable of providing full access for substrates to enter the active site. Upon binding FMNH2, SsuD adopts a closed conformation that would prevent unproductive oxidation reactions in the absence of OCS. Two salt bridges, Asp111-Arg263 and Glu205-Arg271, were identified as particularly important in maintaining the closed conformation. Experimental substitution of Arg271 to Ala did not alter the catalytic activity, but the variant in the presence of reduced flavin was more susceptible to proteolytic digestion compared to wild-type. With both FMNH2 and OCS bound in SsuD, a second conformation was formed dependent upon a favorable π-π interaction between His124 and Phe261. Accordingly, there was no observed activity with the F261W SsuD variant in steady-state kinetic assays. This semiclosed conformation may be more appropriate for accepting O2 into the binding pocket and/or may properly orient the active site for the ensuing oxygenolytic cleavage. Finally, simulations of SsuD simultaneously bound with FMNOO- and OCS found an open mobile loop region that suggests alternative flavin intermediates may participate in the reaction mechanism.

Construction of indazolo[3,2-a]isoquinolines via [3 + 2] cycloaddition of benzynes.

A [3 + 2] annulation protocol for the construction of N-substituted indazolo[3,2-a]isoquinolines starting from benzynes and C,N-cyclic azomethine imines was developed. A diverse range of highly functionalized products indazolo[3,2-a]isoquinolines featuring an indazole scaffold can be easily accessed via a one-step reaction under mild conditions, and they show good anti-proliferative activity on cancer cells.

A P-Loop NTPase Regulates Quiescent Center Cell Division and Distal Stem Cell Identity through the Regulation of ROS Homeostasis in Arabidopsis Root.

Reactive oxygen species (ROS) are recognized as important regulators of cell division and differentiation. The Arabidopsis thaliana P-loop NTPase encoded by APP1 affects root stem cell niche identity through its control of local ROS homeostasis. The disruption of APP1 is accompanied by a reduction in ROS level, a rise in the rate of cell division in the quiescent center (QC) and the promotion of root distal stem cell (DSC) differentiation. Both the higher level of ROS induced in the app1 mutant by exposure to methyl viologen (MV), and treatment with hydrogen peroxide (H2O2) rescued the mutant phenotype, implying that both the increased rate of cell division in the QC and the enhancement in root DSC differentiation can be attributed to a low level of ROS. APP1 is expressed in the root apical meristem cell mitochondria, and its product is associated with ATP hydrolase activity. The key transcription factors, which are defining root distal stem niche, such as SCARECROW (SCR) and SHORT ROOT (SHR) are both significantly down-regulated at both the transcriptional and protein level in the app1 mutant, indicating that SHR and SCR are important downstream targets of APP1-regulated ROS signaling to control the identity of root QC and DSCs.

PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root.

In plants, the generation of new cell types and tissues depends on coordinated and oriented formative cell divisions. The plasma membrane-localized receptor kinase ARABIDOPSIS CRINKLY 4 (ACR4) is part of a mechanism controlling formative cell divisions in the Arabidopsis root. Despite its important role in plant development, very little is known about the molecular mechanism with which ACR4 is affiliated and its network of interactions. Here, we used various complementary proteomic approaches to identify ACR4-interacting protein candidates that are likely regulators of formative cell divisions and that could pave the way to unraveling the molecular basis behind ACR4-mediated signaling. We identified PROTEIN PHOSPHATASE 2A-3 (PP2A-3), a catalytic subunit of PP2A holoenzymes, as a previously unidentified regulator of formative cell divisions and as one of the first described substrates of ACR4. Our in vitro data argue for the existence of a tight posttranslational regulation in the associated biochemical network through reciprocal regulation between ACR4 and PP2A-3 at the phosphorylation level.

Arabidopsis research requires a critical re-evaluation of genetic tools.

HIGHLIGHT: An increasing number of reports question conclusions based on loss-of-function lines that have unexpected genetic backgrounds. In this opinion paper, we urge researchers to meticulously (re)investigate phenotypes retrieved from various genetic backgrounds and be critical regarding some previously drawn conclusions. As an example, we provide new evidence that acr4-2 mutant phenotypes with respect to columella stem cells are due to the lack of ACR4 and not - at least not as a major contributor - to a mutation in QRT1. In addition, we take the opportunity to alert the scientific community about the qrt1-2 background of a large number of Syngenta Arabidopsis Insertion Library (SAIL) T-DNA lines, a feature that is not commonly recognized by Arabidopsis researchers. This qrt1-2 background might have an important impact on the interpretation of the results obtained using these research tools, now and in the past. In conclusion, as a community, we should continuously assess and - if necessary - correct our conclusions based on the large number of (genetic) tools our work is built on. In addition, the positive or negative results of this self-criticism should be made available to the scientific community.

The roles of apo(a) size, phenotype, and dominance pattern in PCSK9-inhibition-induced reduction in Lp(a) with alirocumab.

An elevated level of lipoprotein (a) [Lp(a)] is a risk factor for CVD. Alirocumab, a monoclonal antibody to proprotein convertase subtilisin/kexin type 9, is reported to reduce Lp(a) levels. The relationship of Lp(a) reduction with apo(a) size polymorphism, phenotype, and dominance pattern and LDL cholesterol (LDL-C) reduction was evaluated in a pooled analysis of 155 hypercholesterolemic patients (75 with heterozygous familial hypercholesterolemia) from two clinical trials. Alirocumab significantly reduced total Lp(a) (pooled median: -21%, P = 0.0001) and allele-specific apo(a), an Lp(a) level carried by the smaller (median: -18%, P = 0.002) or the larger (median: -37%, P = 0.0005) apo(a) isoform, at week 8 versus baseline. The percent reduction in Lp(a) level with alirocumab was similar across apo(a) phenotypes (single vs. double bands) and carriers and noncarriers of a small size apo(a) (≤22 kringles). The percent reduction in LDL-C correlated significantly with the percent reduction in Lp(a) level (r = 0.407, P < 0.0001) and allele-specific apo(a) level associated with the smaller (r = 0.390, P < 0.0001) or larger (r = 0.270, P = 0.0183) apo(a) sizes. In conclusion, alirocumab-induced Lp(a) reduction was independent of apo(a) phenotypes and the presence or absence of a small size apo(a).

Protein Subcellular Localization with Gaussian Kernel Discriminant Analysis and Its Kernel Parameter Selection.

Kernel discriminant analysis (KDA) is a dimension reduction and classification algorithm based on nonlinear kernel trick, which can be novelly used to treat high-dimensional and complex biological data before undergoing classification processes such as protein subcellular localization. Kernel parameters make a great impact on the performance of the KDA model. Specifically, for KDA with the popular Gaussian kernel, to select the scale parameter is still a challenging problem. Thus, this paper introduces the KDA method and proposes a new method for Gaussian kernel parameter selection depending on the fact that the differences between reconstruction errors of edge normal samples and those of interior normal samples should be maximized for certain suitable kernel parameters. Experiments with various standard data sets of protein subcellular localization show that the overall accuracy of protein classification prediction with KDA is much higher than that without KDA. Meanwhile, the kernel parameter of KDA has a great impact on the efficiency, and the proposed method can produce an optimum parameter, which makes the new algorithm not only perform as effectively as the traditional ones, but also reduce the computational time and thus improve efficiency.

[Tongjingling improves sperm DNA integrity and reduces oxidative stress in the testis of experimental varicocele rats].

OBJECTIVE: To explore the protective effect of Tongjingling (TJL) against sperm DNA damage and oxidative stress in the rat model of experimental varicocele (EVC). METHODS: We randomly divided 75 Wistar male rats into five groups of equal number: sham operation, EVC model, high-dose TJL, mid-dose TJL, and low-dose TJL. The EVC model was established in the rats by partial ligation of the left renal vein, followed by 8 weeks of medication from the 4th week after modeling. Then we observed the general status of the rats, detected the sperm DNA fragmentation index (DFI) in the epididymis by sperm chromatin structure assay (SCSA), and measured the content of hydroperoxide (H2O2) and the activities of catalase (CAT) and superoxide dismutase (SOD) in the testis by colorimetry. RESULTS: Compared with the sham operation group, the EVC models showed significantly increased sperm DFI in the epididymis (P <0.01) and elevated level of H2O2 and activities of CAT and SOD in the testis (P <0.01). In comparison with the EVC models, the rats of the TJL groups exhibited remarkably reduced sperm DFI and H2O2 content, but increased activities of SOD and CAT. CONCLUSIONS: TJL can improve sperm DNA integrity by increasing the activities of SOD and CAT and reducing the H2O2 level and hence oxidative stress in the testis tissue.