Investigation of steric hindrance effect on the interactions between four alkaloids and HSA by isothermal titration calorimetry and molecular docking.

The binding of four alkaloids with human serum albumin (HSA) was investigated by isothermal titration calorimetry (ITC), spectroscopy and molecular docking techniques. The findings demonstrated that theophylline or caffeine can bind to HAS, respectively. The number of binding sites and binding constants are obtained. The binding mode is a static quenching process. The effects of steric hindrance, temperature, salt concentration and buffer solution on the binding indicated that theophylline and HSA have higher binding affinity than caffeine. The fluorescence and ITC results showed that the interaction between HSA and theophylline or caffeine is an entropy-driven spontaneous exothermic process. The hydrophobic force was the primary driving factor. The experimental results were consistent with the molecular docking data. Based on the molecular structures of the four alkaloids, steric hindrance might be a major factor in the binding between HSA and these four alkaloids. This study elucidates the mechanism of interactions between four alkaloids and HSA.

Pyroptosis of Vascular Smooth Muscle Cells as a Potential New Target for Preventing Vascular Diseases.

Vascular remodeling is the adaptive response of the vessel wall to physiological and pathophysiological changes, closely linked to vascular diseases. Vascular smooth muscle cells (VSMCs) play a crucial role in this process. Pyroptosis, a form of programmed cell death characterized by excessive release of inflammatory factors, can cause phenotypic transformation of VSMCs, leading to their proliferation, migration, and calcification-all of which accelerate vascular remodeling. Inhibition of VSMC pyroptosis can delay this process. This review summarizes the impact of pyroptosis on VSMCs and the pathogenic role of VSMC pyroptosis in vascular remodeling. We also discuss inhibitors of key proteins in pyroptosis pathways and their effects on VSMC pyroptosis. These findings enhance our understanding of the pathogenesis of vascular remodeling and provide a foundation for the development of novel medications that target the control of VSMC pyroptosis as a potential treatment strategy for vascular diseases.

Positive role of plateau pika (Ochotona coronae) on environmental quality at low and moderate density on the Tibetan plateau: Evidence from a meta-analysis.

The roles of plateau pika (Ochotona coronae) in the Tibetan Plateau are often controversial, because it is often regarded as a destructive pest or an ecosystem engineer. Here a meta-analysis using 72 paired observations was conducted to examine whether the impacts of plateau pika on environmental quality (i.e., plant and soil properties) depend on population density in the Tibetan Plateau. Pika population density was used as a proxy for disturbance intensity. The pika disturbance intensity was divided into five groups based on the number of burrows, including low disturbance intensity (LD) (9-30 burrows per ha), medium disturbance intensity (MD) (31-100 burrows per ha), high disturbance intensity (HD) (101-170 burrows per ha), extreme disturbance intensity (ED) (171-240 burrows per ha) and uncontrolled (or excessive) disturbance intensity (UD) (>241 burrows per ha). Given that sample sizes in some of the groups are small (especially for the HD), we further pooled the disturbance groups including the LD-MD and HD-UD. Overall, relative to control (i.e., no disturbing), there was a great increase (80.3%) in aboveground biomass under the LD-MD, whereas a decrease of 41.1% occurred under the HD-UD. At the same time, plant coverage, species richness, height, and belowground biomass greatly decreased only in the HD-UD. Furthermore, the effect size of plant coverage, species richness, and aboveground biomass also declined with pika burrow density significantly. With regard to soil properties, there was a significant increase in soil organic carbon, ammonium nitrogen, and soil organic carbon stock under the LD-MD, whereas a decrease under the HD-UD. In addition, soil total nitrogen, total potassium, and nitrate nitrogen increased at the LD-MD and HD-UD. Nevertheless, the effect size of these soil properties (with >20 observations) was not related to pika burrow density. In summary, there is an implication that the low and moderate disturbance of pikas is beneficial to maintain and promote ecosystem functioning in the Tibetan grasslands. In the future pikas' eradication policy should be reconsidered in alpine grassland management.

Investigation of the Performance of Hastelloy X as Potential Bipolar Plate Materials in Proton Exchange Membrane Fuel Cells.

The phase, mechanical properties, corrosion resistance, hydrophobicity, and interfacial contact resistance of Hastelloy X were investigated to evaluate its performance in proton exchange membrane fuel cells (PEMFCs). For comparison, the corresponding performance of 304 stainless steel (304SS) was also tested. Hastelloy X exhibited a single-phase face-centered cubic structure with a yield strength of 445.5 MPa and a hardness of 262.7 HV. Both Hastelloy X and 304SS exhibited poor hydrophobicity because the water contact angles were all below 80°. In a simulated PEMFC working environment (0.5 M H2SO4 + 2 ppm HF, 80 °C, H2), Hastelloy X exhibited better corrosion resistance than 304SS. At 140 N·cm-2, the interfacial contact resistance of Hastelloy X can reach as low as 7.4 mΩ·cm2. Considering its overall performance, Hastelloy X has better potential application than 304SS as bipolar plate material in PEMFCs.

A novel PSMA targeted dual-function near-infrared fluorescence and PET probe for the image-guided surgery and detection of prostate cancer.

PURPOSE: Prostate-specific membrane antigen (PSMA) is a promising diagnostic biomarker for prostate cancer (PCa). NYM016, a novel small-molecule PSMA-targeted fluorescence probe for the surgical navigation of PCa, was designed in this work. Furthermore, the potential of the PET agent [68Ga]Ga-NYM016 for the radionuclide imaging of PCa was evaluated. METHODS: NYM016 was designed with the near-infrared fluorescent group Cyanine 7 (Cy7) and the chelating group NOTA. The radioactive probe [68Ga]Ga-NYM016 was designed and synthesized on the basis of NYM016. The abovementioned probes were assessed in PSMA-positive xenograft-bearing models and patients diagnosed with PCa. RESULTS: NYM016 obviously aggregated in the tumor site of the mouse model, and its fluorescence intensity was stable within 24 h. NYM016 was well-tolerated, and no adverse events were found in the clinical study. Moreover, it was also observed in the excised lesions from the patient with PCa, and its fluorescence aggregated at the same site where PSMA was highly expressed. In addition, the PSMA xenograft demonstrated intense [68Ga]Ga-NYM016 uptake at 2.5 min after injection. At 3 h after injection, [68Ga]Ga-NYM016 uptake by the PSMA xenograft gradually increased to 6.40 ± 0.19%ID/g, which was higher that by the blocked and negative groups (2.28 ± 0.07%ID/g, P < 0.05; 2.28 ± 0.22%ID/g, P < 0.05). In the clinical study, [68Ga]Ga-NYM016 was well-tolerated and no adverse events were observed. Substantial accumulation was observed in primary and metastatic lesions in a patient with recurrence with the maximum standardized uptake value of 18.93. Meanwhile, negative [68Ga]Ga-NYM016 uptake was observed at the prostate site of a patient with prostatitis. CONCLUSION: The novel fluorescence probe NYM016 and the radioactive tracer [68Ga]Ga-NYM016 are promising candidates for the surgical navigation and radionuclide imaging of PCa, respectively. TRIAL REGISTRATION: The clinical evaluation of this study was registered at Clinicaltrial.gov (NCT05623878) on 21 Dec, 2022.

TMT quantitative proteomics reveals key proteins relevant to microRNA-1-mediated regulation in osteoarthritis.

Osteoarthritis (OA) is the second-commonest arthritis, but pathogenic and regulatory mechanisms underlying OA remain incompletely understood. Here, we aimed to identify the mechanisms associated with microRNA-1 (miR-1) treatment of OA in rodent OA models using a proteomic approach. First, N = 18 Sprague Dawley (SD) rats underwent sham surgery (n = 6) or ACL transection (n = 12), followed at an interval of one week by randomization of the ACL transection group to intra-articular administration of either 50 µL placebo (control group) or miR-1 agomir, a mimic of endogenous miR-1 (experimental group). After allowing for eight weeks of remodeling, articular cartilage tissue was harvested and immunohistochemically stained for the presence of MMP-13. Second, N = 30 Col2a1-cre-ERT2 /GFPf1/fl -RFP-miR-1 transgenic mice were randomized to intra-articular administration of either placebo (control group, N = 15) or tamoxifen, an inducer of miR-1 expression (experimental group, N = 15), before undergoing surgical disruption of the medial meniscus (DMM) after an interval of five days. After allowing for eight weeks of remodeling, articular cartilage tissue was harvested and underwent differential proteomic analysis. Specifically, tandem mass tagging (TMT) quantitative proteomic analysis was employed to identify inter-group differentially-expressed proteins (DEP), and selected DEPs were validated using real-time quantitative polymerase chain reaction (RT-qPCR) technology. Immunohistochemically-detected MMP-13 expression was significantly lower in the experimental rat group, and proteomic analyses of mouse tissue homogenate demonstrated that of 3526 identified proteins, 345 were differentially expressed (relative up- and down-regulation) in the experimental group. Proteins Fn1, P4ha1, P4ha2, Acan, F2, Col3a1, Fga, Rps29, Rpl34, and Fgg were the *top ten most-connected proteins, implying that miR-1 may regulate an expression network involving these proteins. Of these ten proteins, three were selected for further validation by RT-qPCR: the transcript of Fn1, known to be associated with OA, exhibited relative upregulation in the experimental group, whereas the transcripts of P4ha1 and Acan exhibited relative downregulation. These proteins may thus represent key miR-1 targets during OA-regulatory mechanisms, and may provide additional insights regarding therapeutic mechanisms of miR-1 in context of OA.

Tuning transcription factor DegU for developing extracellular protease overproducer in Bacillus pumilus.

BACKGROUND: Global transcription machinery engineering (gTME) is an effective approach employed in strain engineering to rewire gene expression and reshape cellular metabolic fluxes at the transcriptional level. RESULTS: In this study, we utilized gTME to engineer the positive transcription factor, DegU, in the regulation network of major alkaline protease, AprE, in Bacillus pumilus. To validate its functionality when incorporated into the chromosome, we performed several experiments. First, three negative transcription factors, SinR, Hpr, and AbrB, were deleted to promote AprE synthesis. Second, several hyper-active DegU mutants, designated as DegU(hy), were selected using the fluorescence colorimetric method with the host of the Bacillus subtilis ΔdegSU mutant. Third, we integrated a screened degU(L113F) sequence into the chromosome of the Δhpr mutant of B. pumilus SCU11 to replace the original degU gene using a CRISPR/Cas9 system. Finally, based on transcriptomic and molecular dynamic analysis, we interpreted the possible mechanism of high-yielding and found that the strain produced alkaline proteases 2.7 times higher than that of the control strain (B. pumilus SCU11) in LB medium. CONCLUSION: Our findings serve as a proof-of-concept that tuning the global regulator is feasible and crucial for improving the production performance of B. pumilus. Additionally, our study established a paradigm for gene function research in strains that are difficult to handle.

Anchoring grassland sustainability with a nature-based small burrowing mammal control strategy.

Over the last 40 years, a burrowing mammal eradication policy has been prevalent on the Qinghai-Tibetan Plateau (QTP). This policy is based on similar burrowing mammal eradication programs in other areas and is justified on the assumptions that burrowing mammals compete with livestock for forage and contribute to grassland degradation. However, there is no clear theoretical or experimental evidence supporting these assumptions. This paper synthesizes the ecological functioning of small burrowing mammals in natural grasslands and discusses the irrationality and consequences of burrowing mammal eradication for sustainable livestock grazing and grassland degradation. Past burrowing mammal eradication efforts have failed because increased food availability for the remaining rodents and reduced predator populations led to rapid population rebounds. Herbivores differ in diet, and there is clear evidence that burrowing mammals, especially plateau zokors Myospalax baileyi, have a different diet than livestock. In QTP meadows, burrowing mammal eradication induces a shift towards plant communities with fewer species preferred by livestock and more species preferred by burrowing mammals. Thus, eradicating burrowing mammals has the opposite effect, a reduction in livestock preferred vegetation. We suggest that the policy of poisoning burrowing mammals needs to be reconsidered and revoked as soon as possible. We argue that incorporating density-dependent factors such as predation and food availability are essential for maintaining a low burrowing mammal density. For degraded grasslands, we suggest that the optimal sustainable approach is to decrease the intensity of livestock grazing. Lower grazing induces changes in vegetation structure and plant species composition that increases predation on burrowing mammals and decreases the abundance of plants preferred by burrowing mammals. Such a nature-based grassland management system maintains the density of burrowing mammals at a low stable density while minimizing human management and interventions.

Aptamers dimerization inspired biomimetic clamp assay towards impedimetric SARS-CoV-2 antigen detection.

Antigen-detecting rapid diagnostic testing (Ag-RDT) has contributed to containing the spread of SARS-CoV-2 variants of concern (VOCs). In this study, we proposed a biomimetic clamp assay for impedimetric SARS-CoV-2 nucleocapsid protein (Np) detection. The DNA biomimetic clamp (DNA-BC) is formed by a pair of Np aptamers connected via a T20 spacer. The 5'- terminal of the DNA-BC is phosphate-modified and then anchored on the surface of the screen-printed gold electrode, which has been pre-coated with Au@UiO-66-NH2. The integrated DNA-material sensing biochip is fabricated through the strong Zr-O-P bonds to form a clamp-type impedimetric aptasensor. It is demonstrated that the aptasensor could achieve Np detection in one step within 11 min and shows pronounced sensitivity with a detection limit of 0.31 pg mL-1. Above all, the aptasensor displays great specificity and stability under physiological conditions as well as various water environments. It is a potentially promising strategy to exploit reliable Ag-RDT products to confront the ongoing epidemic.

Low dose of liraglutide combined with metformin leads to a significant weight loss in Chinese Han women with polycystic ovary syndrome: a retrospective study.

BACKGROUND: Polycystic ovary syndrome (PCOS) is the most common endocrine disorder with complex pathophysiological mechanism. It is reported that even a modest weight loss of 5-10% substantially may improve the reproductive and metabolic profile. This study aims to assess the efficacy of the low dose of liraglutide (0.6 mg QD) combined with metformin (0.85 mg BID) in weight loss in Chinese Han women with PCOS. METHODS: We included clinical data of 102 obese/overweight (≥18 years, body mass index ≥28 kg/m2 or ≥24 kg/m2) women who were diagnosed with PCOS from October 2016 to March 2018 in Wuhan Union Hospital initially. They were treated with dinae-35, low dose of liraglutide (0.6 mg QD) and metformin (0.85 mg BID) for 12 weeks. The demographic and clinical data were retrieved retrospectively, and weight loss was the main outcome measure. Student's paired t-test and Wilcoxon rank sum test were used to compare the differences before and after therapy, p < 0.05 was considered statistically significant. RESULTS: Participants(n = 102)had lost a mean of 7.20 ± 3.42 kg of body weight (95%CI: 6.55-7.86, p < 0.001), and the mean reduction of BMI was 2.87 ± 1.36 kg/m2 (95%CI: 0.02-0.27, p < 0.001). A total of 88.24% of participants lost more than 5% of their body weight. CONCLUSION: The combination of low dose of liraglutide and metformin was associated with significant reduction of body weight in Chinese Han women with PCOS. Additionally, a larger randomized double-blind multicenter controlled clinical trial is needed to confirm that. TRIAL REGISTRATION: The study was registered on http://www.chictr.org.cn as ChiCTR1900024384.

Fatigue behavior of zirconia with microgrooved surfaces produced using femtosecond laser.

Femtosecond laser is a promising surface treatment tool for zirconia implant. In this study, the fatigue behavior of zirconia specimens with microgrooved surfaces formed by femtosecond laser is reported. One hundred sixty CAD/CAM zirconia bars (20 mm × 4 mm × 1.4 mm) were evenly divided into four groups with different surface: as sintered; sandblasted with 110 µm Al2O3; femtosecond laser produced microgrooves having 50 µm width, 30 µm depth, and 100 µm pitch; microgrooves having 30 µm width, 20 µm depth, and 60 µm pitch. The femtosecond laser formed micro/nanostructured microgrooves with precise size on zirconia surfaces. XRD analysis indicated that microgrooved surface showed no obvious tetragonal-to-monoclinic phase transformation. The fatigue strength of sandblasted specimens (728 MPa) was significantly higher than that of as sintered specimens (570 MPa). However, the fatigue strength of specimens with microgrooved surface decreased to about 360-380 MPa. The results suggest femtosecond laser is an effective technique to regulate the surface microtopography of zirconia, while further investigations are needed to improve its fatigue behavior.

Rice OsMRG702 and Its Partner OsMRGBP Control Flowering Time through H4 Acetylation.

MORF-RELATED GENE702 (OsMRG702) regulates flowering time genes in rice, but how it controls transcription is not well known. Here, we found that OsMRGBP can directly interact with OsMRG702. Both Osmrg702 and Osmrgbp mutants show the delayed flowering phenotype with the reduction in the transcription of multiple key flowering time genes, including Ehd1 and RFT1. Chromatin immunoprecipitation study showed that both OsMRG702 and OsMRGBP bind to the Ehd1 and RFT1 loci and the absence of either OsMRG702 or OsMRGBP leads to a decrease of H4K5 acetylation at these loci, indicating OsMRG702 and OsMRGBP cooperatively together to promote the H4K5 acetylation. In addition, whilst Ghd7 are upregulated in both Osmrg702 and Osmrgbp mutants, only OsMRG702 binds to the loci, together with the global increased and Ghd7 locus-specific increased H4K5ac levels in Osmrg702 mutants, suggesting an additional negative effect of OsMRG702 on H4K5 acetylation. In summary, OsMRG702 controls flowering gene regulation by altering H4 acetylation in rice; it works either together with OsMRGBP to enhance transcription by promoting H4 acetylation or with other unknown mechanisms to dampen transcription by preventing H4 acetylation.

Mesoporous Polymeric Ionic Liquid via Confined Polymerization for Laccase Immobilization towards Efficient Degradation of Phenolic Pollutants.

Laccase immobilization is a promising method that can be used for the recyclable treatment of refractory phenolic pollutants (e.g., chlorophenols) under mild conditions, but the method is still hindered by the trade-off limits of supports in terms of their high specific surface area and rich functional groups. Herein, confined polymerization was applied to create abundant amino-functionalized polymeric ionic liquids (PILs) featuring a highly specific surface area and mesoporous structure for chemically immobilizing laccase. Benefiting from this strategy, the specific surface area of the as-synthesized PILs was significantly increased by 60-fold, from 5 to 302 m2/g. Further, a maximum activity recovery of 82% towards laccase was recorded. The tolerance and circulation of the immobilized laccase under harsh operating conditions were significantly improved, and the immobilized laccase retained more than 84% of its initial activity after 15 days. After 10 cycles, the immobilized laccase was still able to maintain 80% of its activity. Compared with the free laccase, the immobilized laccase exhibited enhanced stability in the biodegradation of 2,4-dichlorophenol (2,4-DCP), recording around 80% (seven cycles) efficiency. It is proposed that the synergistic effect between PILs and laccase plays an important role in the enhancement of stability and activity in phenolic pollutant degradation. This work provides a strategy for the development of synthetic methods for PILs and the improvement of immobilized laccase stability.

Aggregation of Electrochemically Active Conjugated Organic Molecules and Its Impact on Aqueous Organic Redox Flow Batteries.

Molecule aggregation in solution is acknowledged to be universal and can regulate the molecule's physiochemical properties, which however has been rarely investigated in electrochemistry. Herein, an electrochemical method is developed to quantitatively study the aggregation behavior of the target molecule methyl viologen dichloride. It is found that the oxidation state dicationic ions stay discrete, while the singly-reduced state monoradicals yield a concentration-dependent aggregation behavior. As a result, the molecule's energy level and its redox potential can be effectively regulated. This work does not only provide a method to investigate the molecular aggregation, but also demonstrates the feasibility to tune redox flow battery's performance by regulating the aggregation behavior.

Time-Lagged Flux in the Transition Path Ensemble: Flux Maximization and Relation to Transition Path Theory.

The transition path ensemble is of special interest in reaction coordinate identification as it consists of reactive trajectories that start from the reactant state and end in the product one. As a theoretical framework for describing the transition path ensemble, the transition path theory has been introduced more than 10 years ago, and so far, its applications have only been illustrated in several low-dimensional systems. Given the transition path ensemble, expressions for calculating flux, current (a vector field), and principal curves are derived here in the space of collective variables from the transition path theory, and they are applicable to time series obtained from molecular dynamics simulations of high-dimensional systems, i.e., the position coordinates as a function of time in the transition path ensemble. The connection of the transition path theory is made to a density-weighted average flux, a quantity proposed in a previous work to appraise the relevance of a coordinate to the reaction coordinate [Li, W. J. Chem. Phys. 2022, 156, 054117]. Most importantly, as an extension of the existing quantities, time-lagged quantities such as flux and current are also proposed. The main insights and objects provided by these time-lagged quantities are illustrated in the application to the alanine peptide in vacuum.

Potential Energy Weighted Reactive Flux and Total Rate of Change of Potential Energy: Theory and Illustrative Applications.

Reactive flux can be largely nonzero in a nonequilibrium ensemble of trajectories and provide insightful information for reactive transitions from the reactant state to the product state. Based on the reactive flux, a theoretical framework is proposed here for two quantities, the potential energy weighted reactive flux and the total rate of change of potential energy, which are useful for the identification of the mechanism from a nonequilibrium ensemble. From such quantities, two multidimensional free-energy analogues can be derived in the subspace of collective variables and they are equivalent in the regions where the reactive flux is divergence-free. These free-energy analogues are assumed to be closely related to the free energy in the subspace of collective variables, and they are reduced in the one-dimensional case to be the ensemble average of the potential energy weighted with reactive flux intensity, which was proposed recently [Li, W. J. Phys. Chem. A 2022, DOI: 10.1021/acs.jpca.2c04130] and could be decomposed into energy components at the per-coordinate level. In the subspace of collective variables, the decomposition of the multidimensional free-energy analogues at the per-coordinate level is theoretically possible and is numerically difficult to be calculated. Interestingly, the total rate of change of potential energy is able to identify the location of the transition state ensemble or the stochastic separatrix, in addition to the locations of the reactant and product states. The total rate of change of potential energy can be decomposed at the per-coordinate level, and its components can quantify the contribution of a coordinate to the reactive transition in the subspace of collective variables. We then illustrated the main insights and objects that can be provided by the approach in the applications to a two-dimensional system with various diffusion anisotropies and the alanine peptide in vacuum in various nonequilibrium ensembles of short trajectories, from which the results were found to be consistent.

Energy Decomposition along Reaction Coordinate: Theory and Applications to Nonequilibrium Ensembles of Trajectories.

A theoretical framework is proposed for an energy decomposition scheme along the reaction coordinate, in which the ensemble average of the potential energy weighted with reactive flux intensity is decomposed into energy components at the per-coordinate level. The decomposed energy quantity is demonstrated to be closely related to the free energy along the reaction coordinate, and its connection to the emergent potential energy is provided. In the application to alanine dipeptide under vacuum, illustrative calculations were performed in three nonequilibrium ensembles of trajectories: (1) transition path ensemble sampled with transition path sampling; (2) ensemble of short trajectories initiated from configurations around the transition-state region; and (3) ensemble of short trajectories shooting from configurations in several transition paths. The energy components on each coordinate were found to be consistent among the three ensembles of trajectories, indicating a broad applicability of the approach in biomolecular studies. In addition, the free energies along an optimized reaction coordinate obtained with these nonequilibrium ensembles were largely overlapped with a reference free energy calculated from a long equilibrium trajectory.

Optimizing reaction coordinate by flux maximization in the transition path ensemble.

The transition path ensemble is a collection of reactive trajectories, all of which largely keep going forward along the transition channel from the reactant state to the product one, and is believed to possess the information necessary for the identification of reaction coordinates. Previously, the full coordinates (both position and momentum) of the snapshots in the transition path ensemble were utilized to obtain the reaction coordinate [W. Li and A. Ma, J. Chem. Phys. 144, 114103 (2016) and W. Li, J. Chem. Phys. 148, 084105 (2018)]. Here, with the conformational (or position) coordinates alone, it is suggested that a meaningful one-dimensional representation of the reaction coordinate can be obtained by maximizing the flux (the net number of transitions through the dividing surface) of a given coordinate in the transition path ensemble. In the application to alanine dipeptide in vacuum, dihedral angles ϕ and θ were identified to be the two best reaction coordinates, which was consistent with the results in the existing studies. A linear combination of these two coordinates gave a better reaction coordinate, which is highly correlated with the committor. Most importantly, the method obtained a linear combination of pairwise distances between heavy atoms, which was highly correlated with the committor as well. The standard deviation of the committor at the transition region defined by the optimized reaction coordinate is as small as 0.08. In addition, the effects of practical factors, such as the choice of transition path sub-ensembles and saving interval between frames in transition paths, on reaction coordinate optimization were also considered.

Role of UCHL1 in axonal injury and functional recovery after cerebral ischemia.

Ubiquitin C-terminal hydrolase L1 (UCHL1) is a unique brain-specific deubiquitinating enzyme. Mutations in and aberrant function of UCHL1 have been linked to many neurological disorders. UCHL1 activity protects neurons from hypoxic injury, and binding of stroke-induced reactive lipid species to the cysteine 152 (C152) of UCHL1 unfolds the protein and disrupts its function. To investigate the role of UCHL1 and its adduction by reactive lipids in inhibiting repair and recovery of function following ischemic injury, a knock-in (KI) mouse expressing the UCHL1 C152A mutation was generated. Neurons derived from KI mice had less cell death and neurite injury after hypoxia. UCHL1 C152A KI and WT mice underwent middle cerebral artery occlusion (MCAO) or sham surgery. White matter injury was significantly decreased in KI compared with WT mice 7 d after MCAO. Histological analysis revealed decreased tissue loss at 21 d after injury in KI mice. There was also significantly improved sensorimotor recovery in postischemic KI mice. K63- and K48-linked polyubiquitinated proteins were increased in penumbra of WT mouse brains but not in KI mouse brains at 24 h post MCAO. The UCHL1 C152A mutation preserved excitatory synaptic drive to pyramidal neurons and their excitability in the periinfarct zone; axonal conduction velocity recovered by 21 d post MCAO in KI mice in corpus callosum. These results demonstrate that UCHL1 activity is an important determinant of function after ischemia and further demonstrate that the C152 site of UCHL1 plays a significant role in functional recovery after stroke.

Roles of Physicochemical and Structural Properties of RNA-Binding Proteins in Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning.

Trans-acting splicing factors play a pivotal role in modulating alternative splicing by specifically binding to cis-elements in pre-mRNAs. There are approximately 1500 RNA-binding proteins (RBPs) in the human genome, but the activities of these RBPs in alternative splicing are unknown. Since determining RBP activities through experimental methods is expensive and time consuming, the development of an efficient computational method for predicting the activities of RBPs in alternative splicing from their sequences is of great practical importance. Recently, a machine learning model for predicting the activities of splicing factors was built based on features of single and dual amino acid compositions. Here, we explored the role of physicochemical and structural properties in predicting their activities in alternative splicing using machine learning approaches and found that the prediction performance is significantly improved by including these properties. By combining the minimum redundancy-maximum relevance (mRMR) method and forward feature searching strategy, a promising feature subset with 24 features was obtained to predict the activities of RBPs. The feature subset consists of 16 dual amino acid compositions, 5 physicochemical features, and 3 structural features. The physicochemical and structural properties were as important as the sequence composition features for an accurate prediction of the activities of splicing factors. The hydrophobicity and distribution of coil are suggested to be the key physicochemical and structural features, respectively.