Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins.

The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically important targets in human cells, including membrane proteins and large macromolecular assemblies, hampering mechanistic studies and drug development efforts. Here we describe a method combining CRISPR-Cas gene editing and fluorescence-activated cell sorting to rapidly tag and purify endogenous proteins in HEK cells for structural characterization. We applied this approach to study the human proteasome from HEK cells and rapidly determined cryogenic electron microscopy structures of major proteasomal complexes, including a high-resolution structure of intact human PA28αß-20S. Our structures reveal that PA28 with a subunit stoichiometry of 3α/4ß engages tightly with the 20S proteasome. Addition of a hydrophilic peptide shows that polypeptides entering through PA28 are held in the antechamber of 20S prior to degradation in the proteolytic chamber. This study provides critical insights into an important proteasome complex and demonstrates key methodologies for the tagging of proteins from endogenous sources.

Phase and detuning control of the unidirectional reflection amplification based on the broken spatial symmetry.

In order to achieve the tunable unidirectional reflection amplification in a uniform atomic medium that is of vital importance to design high-quality nonreciprocal photonic devices, we propose a coherent closed three-level Δ-type atomic system by applying a microwave field, and a strong coupling field of linear variation along the x direction to control a probe field. In our scheme, the linearly increased coupling field destroys the spatial symmetry of probe susceptibility and effectively suppresses the reflection of one side; the microwave field constructs closed loop transitions to amplify the probe field and causes phase changes. The numerical simulation indicates that the unidirectional reflection amplification is sensitive to the relative phase ϕ and the coupling detuning Δc. Our results will open a new route toward harnessing optical non-reciprocity, which can provide more convenience and possibilities in the experimental realization.

The causal relationship of female infertility and psychiatric disorders in the European population: a bidirectional two-sample Mendelian randomization study.

BACKGROUND: Infertility affects many couples globally, causing physical, emotional, and financial burdens. While observational studies suggest a link between psychiatric disorders and female infertility, causal relationships remain uncertain. Mendelian randomization analysis, using genome-wide association studies data, minimizes confounding factors and reverse causation, providing valuable insights into causal associations. METHODS: We conducted Mendelian randomization analysis to explore the potential causal relationship between female infertility and psychiatric disorders. Genome-wide association studies summary data for female infertility (112,105 individuals of European ancestry, comprising 11,442 cases and 100,663 controls), depression (807,553 individuals of European ancestry, comprising 246,363 cases and 561,190 controls), anxiety (21,763 individuals of European ancestry, comprising 7,016 cases and 14,745 controls), bipolar disorder (51,710 individuals of European ancestry, comprising 20,352 cases and 31,358 controls), and eating disorders (72,517 individuals of European ancestry, comprising 16,992 cases and 55,525 controls) were utilized. Instrumental variables were selected based on significant single nucleotide polymorphisms associated with each phenotype. We assessed instrumental variable strength, examined confounding factors, and employed inverse variance weighting, weighted median, and MR-Egger approaches for analysis. RESULTS: Our analysis included 85 single nucleotide polymorphisms for female infertility and 62 single nucleotide polymorphisms for psychiatric disorders. Results suggest a potential causal relationship between depression and female infertility, with both inverse variance weighting and weighted median methods showing increased infertility risk in depressed patients. Evidence is weak regarding bipolar disorder not increasing female infertility risk. We found no evidence supporting causal links between anxiety, eating disorders, and female infertility. Similarly, no causal relationship was found between female infertility and psychiatric disorders in the opposite direction. Sensitivity analyses and tests for heterogeneity and polymorphism supported result robustness. CONCLUSIONS: This analysis provides evidence for a potential causal relationship between depression and female infertility. Addressing depression in infertile women may improve fertility outcomes. Further research is needed to explore underlying mechanisms and potential interventions for improving fertility outcomes in women with psychiatric disorders.

Manipulation of single stored-photon with microwave field based on Rydberg polariton.

We demonstrate a coherent microwave manipulation of a single optical photon based on a single Rydberg excitation in an atomic ensemble. Due to the strong nonlinearities in a Rydberg blockade region, a single photon can be stored in the formation of Rydberg polariton using electromagnetically induced transparency (EIT). The manipulation of the stored single photon is performed by applying a microwave field that resonantly couples the nS1/2 and nP3/2, while the coherent readout is performed by mapping the excitation into a single photon. We achieve a single photon source with g(2)(0) = 0.29 ± 0.08 at 80S1/2 without applying microwave fields. By implementing the microwave field during the storage time and retrieval process, we show the Rabi oscillation and modulation of stored photons that can be controlled to retrieve early or late. Rapid modulation frequencies up to 50 MHz can be obtained. Our experimental observations can be well explained via numerical simulations based on an improved superatom model accounting for the dipole-dipole interactions in a Rydberg EIT medium. Our work provides a way to manipulate the stored photons by employing the microwave field, which is significant for developing quantum technologies.

Spatial susceptibility modulation and controlled unidirectional reflection amplification via four-wave mixing.

Control of unidirectional light propagation is of paramount importantance to optical signal processing and optical communication. Especially, the amplified optical signal can isolate noise well that may provide more applications. In this work, we propose a dynamically modulated regime to realize unidirectional reflection amplification in a short and dense uniform atomic medium, and all atoms are driven into four-level double-Λ type by two coupling fields with linearly varied intensities along x direction and two weak probe fields. Based on four-wave mixing resonance and the broken spatial symmetry, the complete nonreciprocal reflection (unidirectional reflection) can be amplified with reflectivity more than 2.0, even to 6.0. In addition, the width, height, and position of the unidirectional reflection bands can be tunable. Thus, our regime is feasible and may inspire further applications in all-optical networks that require controllable unidirectional light amplification.

Two-color unidirectional reflections by modulating the spatial susceptibility in a homogeneous atomic medium.

Non-reciprocal reflections of optical signals are unusual yet fascinating to achieve the imminent applications of non-reciprocal photonic devices and circuits. The complete non-reciprocal reflection (unidirectional reflection) was recently found to be achievable in a homogeneous medium, if the real and imaginary parts of the probe susceptibility satisfy the spatial Kramers-Kronig (KK) relation. We propose a coherent four-level tripod model for realizing dynamically tunable two-color non-reciprocal reflections by applying two control fields with linearly modulated intensities. We found that, the unidirectional reflection can be obtained if the non-reciprocal frequency regions are located in the electromagnetically induced transparency (EIT) windows. This mechanism is to break the spatial symmetry by the spatial modulation of susceptibility to induce unidirectional reflections, the real and imaginary parts of the probe susceptibility are no longer required to satisfy the spatial KK relation.

SESLA suppresses the activation of macrophages and dendritic cells after Gram-positive bacterial challenge.

BACKGROUND: Secoeudesma sesquiterpenes lactone A (SESLA) is a sesquiterpene derived from Inula japonica Thunb. and is known to possess many pharmacological properties, e.g. anti-tumor and anti-inflammatory activities. However, the immunomodulatory role of SESLA in gram-positive (G+) bacterial infection is not clear. MATERIALS AND METHODS: To set up a G+ bacterial infection model in vitro, we carried out a bacterial mimic (PGN or Pam3CSK4) or Methicillin-resistant Staphylococcus aureus (MRSA) stimulated experiment using macrophages or dendritic cells (DCs). ELISA and qPCR were performed to measure the expression of inflammatory cytokines. Flow cytometry was used to detect the expression of MHC II and co-stimulatory molecules on the surface of DCs. The network pharmacology was used to identify the molecular mechanism and potential targets of SESLA that are predicted to be involved in the MRSA-elicited inflammation. Western blot and dual luciferase reporter assay were adopted to certify possible molecular mechanism of SESLA. RESULTS: This study demonstrated that SESLA treatment significantly reduced the levels of inflammatory cytokines stimulated by PGN, Pam3CSK4 or even MRSA in vitro, and it also reduced PGN-induced expression of MHC II and co-stimulatory molecules on the surface of DCs. Mechanistically, the inhibition of IκBα phosphorylation and the suppression of T cells activation could account for its anti-inflammatory activity. CONCLUSION: The present study validated the notable anti-inflammatory activity of SESLA and discovered its previously uncharacterized immunoregulatory role and the underlying mechanism in G+ bacterial infections. Overall, SESLA has a potential to be an antibiotic adjuvant for the treatment of G+ bacterial infections.

Development of machine learning model to predict pulmonary function with low-dose CT-derived parameter response mapping in a community-based chest screening cohort.

PURPOSE: To construct and evaluate the performance of a machine learning-based low dose computed tomography (LDCT)-derived parametric response mapping (PRM) model for predicting pulmonary function test (PFT) results. MATERIALS AND METHODS: A total of 615 subjects from a community-based screening population (40-74 years old) with PFT parameters, including the ratio of the first second forced expiratory volume to forced vital capacity (FEV1/FVC), the percentage of forced expiratory volume in the one second predicted (FEV1%), and registered inspiration-to-expiration chest CT scanning were enrolled retrospectively. Subjects were classified into a normal, high risk, and COPD group based on PFT. Data of 72 PRM-derived quantitative parameters were collected, including volume and volume percentage of emphysema, functional-small airways disease, and normal lung tissue. A machine-learning with random forest regression model and a multilayer perceptron (MLP) model were constructed and tested on PFT prediction, which was followed by evaluation of classification performance based on the PFT predictions. RESULTS: The machine-learning model based on PRM parameters showed better performance for predicting PFT than MLP, with a coefficient of determination (R2 ) of 0.749 and 0.792 for FEV1/FVC and FEV1%, respectively. The Mean Squared Errors (MSE) for FEV1/FVC and FEV1% are 0.0030 and 0.0097 for the random forest model, respectively. The Root Mean Squared Errors (RMSE) for FEV1/FVC and FEV1% are 0.055 and 0.098, respectively. The sensitivity, specificity, and accuracy for differentiating between the normal group and high-risk group were 34/40 (85%), 65/72 (90%), and 99/112 (88%), respectively. For differentiating between the non-COPD group and COPD group, the sensitivity, specificity, and accuracy were 8/9 (89%), 112/112 (100%), 120/121 (99%), respectively. CONCLUSIONS: The machine learning-based random forest model predicts PFT results in a community screening population based on PRM, and it identifies high risk COPD from normal populations with high sensitivity and reliably predicts of high-risk COPD.

The Role of mTORC1 Pathway and Autophagy in Resistance to Platinum-Based Chemotherapeutics.

Cisplatin (cis-diamminedichloroplatinum I) is a platinum-based drug, the mainstay of anticancer treatment for numerous solid tumors. Since its approval by the FDA in 1978, the drug has continued to be used for the treatment of half of epithelial cancers. However, resistance to cisplatin represents a major obstacle during anticancer therapy. Here, we review recent findings on how the mTORC1 pathway and autophagy can influence cisplatin sensitivity and resistance and how these data can be applicable for the development of new therapeutic strategies.

A Semisynthetic Bioluminescence Sensor for Ratiometric Imaging of Metal Ions In Vivo Using DNAzymes Conjugated to An Engineered Nano-Luciferase.

DNA-based probes have gained significant attention as versatile tools for biochemical analysis, benefiting from their programmability and biocompatibility. However, most existing DNA-based probes rely on fluorescence as the signal output, which can be problematic due to issues like autofluorescence and scattering when applied in complex biological materials such as living cells or tissues. Herein, we report the development of bioluminescent nucleic acid (bioLUNA) sensors that offer laser excitation-independent and ratiometric imaging of the target in vivo. The system is based on computational modelling and mutagenesis investigations of a genetic fusion between circular permutated Nano-luciferase (NLuc) and HaloTag, enabling the conjugation of the protein with a DNAzyme. In the presence of Zn2+ , the DNAzyme sensor releases the fluorophore-labelled strand, leading to a reduction in bioluminescent resonance energy transfer (BRET) between the luciferase and fluorophore. Consequently, this process induces ratiometric changes in the bioluminescent signal. We demonstrated that this bioLUNA sensor enabled imaging of both exogenous Zn2+ in vivo and endogenous Zn2+ efflux in normal epithelial prostate and prostate tumors. This work expands the DNAzyme sensors to using bioluminescence and thus has enriched the toolbox of nucleic acid sensors for a broad range of biomedical applications.

A sensitive fluorescence biosensor based on metal ion-mediated DNAzyme activity for amplified detection of acetylcholinesterase.

In this paper, we developed an amplified fluorescence biosensor for acetylcholinesterase (AChE) activity detection by taking advantage of the mercury ion-mediated Mgzyme (Mg2+-dependent DNAzyme) activity. The catalytic activity of Mgzyme can be inhibited by the formation of T-Hg2+-T base pairs between the Mgzyme and mercury ions. Therefore, the Mgzyme-Hg2+ complex has no activity on a molecular beacon (MB) substrate, which afforded a very weak fluorescence background for this biosensor. After the addition of acetylcholinesterase (AChE), the substrate acetylthiocholine could be hydrolyzed to thiocholine, which has a stronger binding power with mercury ions than T-Hg2+-T base pairs. Therefore, the Mgzyme activity was recovered. The activated Mgzyme could hybridize with the MB substrate and undergo many cleavage cycles, resulting in a significant increase of fluorescence intensity. This biosensor displayed high sensitivity with the detection limit as low as 0.01 mU mL-1. Moreover, this design did not require complex composition and sequence design; thus it is simple and convenient. This biosensor was also applied for the determination of AChE in human blood and showed satisfactory results.

Century-Long Homogenization of Algal Communities Is Accelerated by Nutrient Enrichment and Climate Warming in Lakes and Reservoirs of the North Temperate Zone.

Anthropogenic pressures can threaten lake and reservoir ecosystems, leading to harmful algal blooms that have become globally widespread. However, patterns of phytoplankton diversity change and community assembly over long-term scales remain unknown. Here, we explore biodiversity patterns in eukaryotic algal (EA) and cyanobacterial (CYA) communities over a century by sequencing DNA preserved in the sediment cores of seven lakes and reservoirs in the North Temperate Zone. Comparisons within lakes revealed temporal algal community homogenization in mesotrophic lakes, eutrophic lakes, and reservoirs over the last century but no systematic losses of α-diversity. Temporal homogenization of EA and CYA communities continued into the modern day probably due to time-lags related to historical legacies, even if lakes go through a eutrophication phase followed by a reoligotrophication phase. Further, algal community assembly in lakes and reservoirs was mediated by both deterministic and stochastic processes, while homogeneous selection played a relatively important role in recent decades due to intensified anthropogenic activities and climate warming. Overall, these results expand our understanding of global change effects on algal community diversity and succession in lakes and reservoirs that exhibit different successional trajectories while also providing a baseline framework to assess their potential responses to future environmental change.

Climate and Nutrient-Driven Regime Shifts of Cyanobacterial Communities in Low-Latitude Plateau Lakes.

Cyanobacterial blooms that form in response to climate warming and nutrient enrichment in freshwater lakes have become a global environmental challenge. Historical legacy effects and the mechanisms underlying cyanobacterial community succession are not well understood, especially for plateau lakes that are important global freshwater resources. This study investigated the temporal dynamics of cyanobacterial communities over centuries in response to nutrient enrichment and climate warming in low-latitude plateau lakes using high-throughput DNA sequencing of sedimentary DNA combined with traditional paleolimnological analyses. Our results confirmed that nutrients and climate warming drive shifts in cyanobacterial communities over time. Cyanobacterial community turnover was pronounced with regime shifts toward new ecological states, occurring after exceeding a tipping point of aquatic total phosphorus (TP). The inferred species interactions, niche differentiation, and identity of keystone taxa significantly changed after crossing the aquatic TP ecological threshold, as demonstrated by network analysis of cyanobacterial taxa. Further, the contribution of aquatic TP to cyanobacterial community dynamics was greater than that of air temperature when lakes were in an oligotrophic state. In contrast, as the aquatic TP threshold was exceeded, the contribution to community dynamics by air temperature increased and potentially surpassed that of aquatic TP. Overall, these results provide new evidence for how past nutrient levels in lacustrine ecosystems influence contemporary cyanobacterial community responses to global warming in low-latitude plateau lakes.

Oral administration of MnCl2 attenuated hyperlipidemia-related cardiac remodeling in ApoE-/- mice.

Manganese chloride (MnCl2) has been shown to inhibit the Yes-associated protein (YAP) in high-fat diet-fed ApoE-/- mice. Although YAP has been implicated in atherogenesis, there are limited data on the effects of MnCl2 on cardiac remodeling. In this study, we discovered, by electrocardiography, that hyperlipidemia led to spontaneous supraventricular arrhythmia (SVA) in ApoE-/- (KO) mice, with 3 of 9 KO + MnCl2 mice (33%) exhibiting lower incidence of spontaneous SVA than KO mice (6 of 10 mice, 60%). Echocardiography revealed that reduced systolic function in KO mice was reversed by MnCl2 treatment. Oil Red O staining of the aortas and biochemical analysis of lipid levels showed that MnCl2 inhibited plaque formation in a lipid metabolism-independent manner. MnCl2 inhibited inflammatory cell infiltration and reduced fibrosis, as evidenced by hematoxylin and eosin, immunohistochemical and Masson's trichrome staining, respectively. Our findings demonstrate that spontaneous SVA and reduced systolic function were blocked by MnCl2. Our findings show that MnCl2 was useful in delaying cardiac remodeling and reducing susceptibility to spontaneous SVA in a mouse model of hyperlipidemia.

Electrophysiological Response to Acehytisine Was Modulated by Aldosterone in Rats with Aorto-Venocaval Shunts.

Aldosterone induces cardiac electrical and structural remodeling, which leads to the development of heart failure and/or atrial fibrillation (AF). However, it remains unknown whether aldosterone-induced remodeling may modulate the efficacy of anti-AF drugs. In this study, we aimed to jeopardize the structural and functional remodeling by aldosterone in rats with aorto-venocaval shunts (AVS rats) and evaluate the effect of acehytisine in this model. An AVS operation was performed on rats (n = 6, male) and it was accompanied by the intraperitoneal infusion of aldosterone (AVS + Ald) at 2.0 µg/h for 28 d. The cardiopathy was characterized by echocardiography, electrophysiologic and hemodynamic testing, and morphometric examination in comparison with sham-operated rats (n = 3), sham + Ald (n = 6), and AVS (n = 5). Aldosterone accelerated the progression from asymptomatic heart failure to overt heart failure and induced sustained AF resistant to electrical fibrillation in one out of six rats. In addition, it prolonged PR, QT interval and Wenckebach cycle length. Acehytisine failed to suppress AF in the AVS + Ald rats. In conclusion, aldosterone jeopardized electrical remodeling and blunted the electrophysiological response to acehytisine on AF.

Source emissions and climate change impacts on the multimedia transport and fate of persistent organic pollutants, Chaohu watershed, eastern China.

Emission intensity and climate change control the transport flux and fate of persistent organic pollutants (POPs) in multiple environmental compartments. This study applied a multimedia model (BETR model) to explore alternations in the spatio-temporal trends of concentrations and transport flux of benzopyrene (BaP), phenanthrene (Phe), perfluorooctane sulfonates (PFOS) and polychlorinated biphenyls (PCBs) in the Chaohu watershed, located in the lower reaches of the Yangtze River, China in response to changes in source emissions and climate. The potential historic and future risks of these pollutants also were assessed. The results suggest that current trends in concentrations and transport were similar to that of their emissions between 2005 and 2018. During the next 100 years, temporal trends and spatial patterns were not predicted to change significantly, which is consistent with climate change. Based on sensitivity and correlation analyses, climate change had significant effects on multi-media concentrations and transport fluxes of BaP, Phe, PFOS and PCBs, and rainfall intensity was the predominant controlling factor. Risk quotients (RQs) of BaP and Phe-in soil increased from 0.42 to 0.95 and 0.06 to 0.35, respectively, from 2005 to 2090, indicating potential risks. The RQs of the other examined contaminants exhibited little potential risk in soil, water, or sediment. Based on spatial patterns, it was inferred that the ecosystem around Lake Chaohu is the most at risk. The study provides insights needed for local pollution control of POPs in the Chaohu watershed. In addition, the developed approach can be applied to other watersheds world-wide.

In-phase and anti-phase entanglement dynamics of Rydberg atomic pairs.

We study the correlated evolutions of two far-spaced Rydberg atomic pairs with different resonant frequencies, interacting via van der Waals (vdW) potentials and driven by a common laser field. They are found to exhibit in-phase (anti-phase) beating dynamics characterized by identical (complementary) intra-pair entanglements under a specific condition in regard of inter-pair vdW potentials and driving field detunings. This occurs when each atomic pair just oscillates between its ground state and symmetric entangled state because its doubly excited state and asymmetric entangled state are forbidden due to rigid dipole blockade and perfect destructive interference, respectively. More importantly, optimal inter-pair overall entanglement can be attained at each beating node corresponding to semi-optimal intra-pair entanglements, and inevitable dissipation processes just result in a slow decay of intra-pair and inter-pair entanglements yet without destroying in-phase and anti-phase beating dynamics.

Acehytisine suppresses atrial fibrillation in rats with dilated atria caused by chronic volume overload.

Atrial dilation is an independent risk factor for the development of atrial fibrillation (AF) and modulates the efficacy of anti-AF drugs, leading to the unsatisfactory control of AF. Pre-clinical studies showed anti-AF effects of acehytisine, a multi-ion channel inhibitor, in atria without structural and/or electrophysiological abnormalities, but information is limited regarding its anti-AF efficacy in dilated atria. We evaluated anti-AF effects of acehytisine at 4 and 10 mg/kg intravenously infused over 10 min using 8-week-old Wistar rats (n = 5; male) with atrial dilation caused by aorto-venocaval shunt (AVS). Echocardiography showed that atria were enlarged by +26.9% after one month of operation in AVS rats compared with sham-operated rats (n = 4; male). Electrophysiological examinations indicated burst pacing-induced AF reached 206 s. Acehytisine at doses of 4 and 10 mg/kg decreased the duration of burst pacing-induced AF with prolongation of Wenckebach cycle length and P wave duration in a dose-dependent manner. Importantly, the drug effectively terminated the persistent AF that was resistant to multiple programmed electrical stimulations in one rat. Therefore, these results provide in vivo evidence that acehytisine may be beneficial for preventing and terminating persistent AF in dilated atria.

Electropharmacological profile of an atrial-selective sodium channel blocker acehytisine assessed in the isoflurane-anesthetized guinea-pig model.

Experimental evidence regarding the risk of proarrhythmic potential of acehytisine is limited. We assessed its electropharmacological effect together with proarrhythmic potential at intravenous doses of 4 and 10 mg/kg (n = 6) using isoflurane-anesthetized guinea pigs in comparison with that of bepridil at 1 and 3 mg/kg, intravenously (n = 6). Acehytisine at therapeutic dose (4 mg/kg) decreased the heart rate, prolonged P wave duration, QRS width, QT interval, QTc, MAP90(sinus), MAP90(CL300) and MAP90(CL250). At supratherapeutic dose (10 mg/kg), it prolonged the PR interval besides enhancing the changes induced by the therapeutic dose. Quantitative assessment showed that peak changes in P wave duration by acehytisine at 10 mg/kg were 1.7 times longer than bepridil, and in MAP90(sinus), MAP90(CL300) and MAP90(CL250) by acehytisine were 1.9, 1.5 and 1.5 times shorter than bepridil, respectively. Importantly, qualitative assessment indicated that bepridil increased beat-to-beat variability and J-Tpeakc in a dose-related manner, confirming a higher proarrhythmic risk, whereas such dose-related responses were not observed in acehytisine, suggesting a lower proarrhythmic risk. These results suggest that acehytisine exhibits favorable pharmacological characters, i.e. potent atrial inhibition and lower proarrhythmic toxicity compared with bepridil, being a promising candidate for the treatment of paroxysmal supraventricular tachycardia.