A TeZla micromixer for interrogating the early and broad folding landscape of G-quadruplex via multistage velocity descending.

Biomacromolecular folding kinetics involves fast folding events and broad timescales. Current techniques face limitations in either the required time resolution or the observation window. In this study, we developed the TeZla micromixer, integrating Tesla and Zigzag microstructures with a multistage velocity descending strategy. TeZla achieves a significant short mixing dead time (40 µs) and a wide time window covering four orders of magnitude (up to 300 ms). Using this unique micromixer, we explored the folding landscape of c-Myc G4 and its noncanonical-G4 derivatives with different loop lengths or G-vacancy sites. Our findings revealed that c-Myc can bypass folding intermediates and directly adopt a G4 structure in the cation-deficient buffer. Moreover, we found that the loop length and specific G-vacancy site could affect the folding pathway and significantly slow down the folding rates. These results were also cross-validated with real-time NMR and circular dichroism. In conclusion, TeZla represents a versatile tool for studying biomolecular folding kinetics, and our findings may ultimately contribute to the design of drugs targeting G4 structures.

Predicting functional consequences of SNPs on mRNA translation via machine learning.

The functional impact of single nucleotide polymorphisms (SNPs) on translation has yet to be considered when prioritizing disease-causing SNPs from genome-wide association studies (GWAS). Here we apply machine learning models to genome-wide ribosome profiling data to predict SNP function by forecasting ribosome collisions during mRNA translation. SNPs causing remarkable ribosome occupancy changes are named RibOc-SNPs (Ribosome-Occupancy-SNPs). We found that disease-related SNPs tend to cause notable changes in ribosome occupancy, suggesting translational regulation as an essential pathogenesis step. Nucleotide conversions, such as 'G → T', 'T → G' and 'C → A', are enriched in RibOc-SNPs, with the most significant impact on ribosome occupancy, while 'A → G' (or 'A→ I' RNA editing) and 'G → A' are less deterministic. Among amino acid conversions, 'Glu → stop (codon)' shows the most significant enrichment in RibOc-SNPs. Interestingly, there is selection pressure on stop codons with a lower collision likelihood. RibOc-SNPs are enriched at the 5'-coding sequence regions, implying hot spots of translation initiation regulation. Strikingly, ∼22.1% of the RibOc-SNPs lead to opposite changes in ribosome occupancy on alternative transcript isoforms, suggesting that SNPs can amplify the differences between splicing isoforms by oppositely regulating their translation efficiency.

Neuropsychiatric symptoms associated multimodal brain networks in Alzheimer's disease.

Concomitant neuropsychiatric symptoms (NPS) are associated with accelerated Alzheimer's disease (AD) progression. Identifying multimodal brain imaging patterns associated with NPS may help understand pathophysiology correlates AD. Based on the AD continuum, a supervised learning strategy was used to guide four-way multimodal neuroimaging fusion (Amyloid, Tau, gray matter volume, brain function) by using NPS total score as the reference. Loadings of the identified multimodal patterns were compared across the AD continuum. Then, regression analyses were performed to investigate its predictability of longitudinal cognition performance. Furthermore, the fusion analysis was repeated in the four NPS subsyndromes. Here, an NPS-associated pathological-structural-functional covaried pattern was observed in the frontal-subcortical limbic circuit, occipital, and sensor-motor region. Loading of this multimodal pattern showed a progressive increase with the development of AD. The pattern significantly correlates with multiple cognitive domains and could also predict longitudinal cognitive decline. Notably, repeated fusion analysis using subsyndromes as references identified similar patterns with some unique variations associated with different syndromes. Conclusively, NPS was associated with a multimodal imaging pattern involving complex neuropathologies, which could effectively predict longitudinal cognitive decline. These results highlight the possible neural substrate of NPS in AD, which may provide guidance for clinical management.

Transition-Metal-Free Electrochemical Selenylative Cyclization of Alkynyl Phosphonates.

Unprecedented regioselective electrochemical tandem selenation/cyclization of alkynyl phosphonates with diselenide is described here. These obtained selenoether products can be chemo-selectively converted into halogen-functionalized cyclic enol phosphonates under our electrochemical conditions. These protocols provide straightforward access to valuable cyclic enol phosphonate or phosphaisocoumarins under the electrochemical and transition-metal-free conditions. The robustness of these transformations was illustrated by their compatibility with various complex natural products and bioactive molecules. The selenoether and halogen functional groups allow the further diversification of the phosphorus heterocycles thus obtained.

Programmed Death of Injured Pseudomonas aeruginosa on Mechano-Bactericidal Surfaces.

Mechano-bactericidal surfaces deliver lethal effects to contacting bacteria. Until now, cell death has been attributed to the mechanical stress imparted to the bacterial cell envelope by the surface nanostructures; however, the process of bacterial death encountering nanostructured surfaces has not been fully illuminated. Here, we perform an in-depth investigation of the mechano-bactericidal action of black silicon (bSi) surfaces toward Gram-negative bacteria Pseudomonas aeruginosa. We discover that the mechanical injury is not sufficient to kill the bacteria immediately due to the survival of the inner plasma membrane. Instead, such sublethal mechanical injury leads to apoptosis-like death (ALD) in affected bacteria. In addition, when the mechanical stress is removed, the self-accumulated reactive oxygen species (ROS) incur poststress ALD in damaged cells in a nonstressed environment, revealing that the mechano-bactericidal actions have sustained physiological effects on the bacterium. This work creates a new facet and can introduce many new regulation tools to this field.

Discovery of Novel Mono-Carbonyl Curcumin Derivatives as Potential Anti-Hepatoma Agents.

Curcumin possesses a wide spectrum of liver cancer inhibition effects, yet it has chemical instability and poor metabolic properties as a drug candidate. To alleviate these problems, a series of new mono-carbonyl curcumin derivatives G1-G7 were designed, synthesized, and evaluated by in vitro and in vivo studies. Compound G2 was found to be the most potent derivative (IC50 = 15.39 µM) compared to curcumin (IC50 = 40.56 µM) by anti-proliferation assay. Subsequently, molecular docking, wound healing, transwell, JC-1 staining, and Western blotting experiments were performed, and it was found that compound G2 could suppress cell migration and induce cell apoptosis by inhibiting the phosphorylation of AKT and affecting the expression of apoptosis-related proteins. Moreover, the HepG2 cell xenograft model and H&E staining results confirmed that compound G2 was more effective than curcumin in inhibiting tumor growth. Hence, G2 is a promising leading compound with the potential to be developed as a chemotherapy agent for hepatocellular carcinoma.

The association of enlarged perivascular space with microglia-related inflammation and Alzheimer's pathology in cognitively normal elderly.

BACKGROUND: Glymphatic dysfunction may contribute to the accumulation of Alzheimer's disease (AD) pathologies. Conversely, AD pathologic change might also cause neuroinflammation and aggravate glymphatic dysfunction, forming a loop that accelerates AD progression. In vivo validations are needed to confirm their relationships. METHODS: In this study, we included 144 cognitively normal participants with AD pathological biomarker data (baseline CSF Aß1-42, T-Tau, P-Tau181; plasma P-Tau181 at baseline and at least one follow-up) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Each subject had completed structural MRI scans. Among them, 117 subjects have available neuroinflammatory biomarker (soluble triggering receptor expressed on myeloid cells 2 (sTREM2), and 123 subjects have completed two times [18F]-florbetapir PET. The enlarged PVS (EPVS) visual rating scores in basal ganglia (BG) and centrum semiovale (CS) were assessed on T1-weighted images to reflect glymphatic dysfunction. Intracranial volume and white matter hyperintensities (WMH) volume were also calculated for further analysis. We performed stepwise linear regression models and mediation analyses to estimate the association between EPVS severity, sTREM2, and AD biomarkers. RESULTS: CS-EPVS degree was associated with CSF sTREM2, annual change of plasma P-tau181 and total WMH volume, whereas BG-EPVS severity was associated with age, gender and intracranial volume. The sTREM2 mediated the association between CSF P-tau181 and CS-EPVS. CONCLUSION: Impaired glymphatic dysfunction could contribute to the accumulation of pathological tau protein. The association between tauopathy and glymphatic dysfunction was mediated by the microglia inflammatory process. These findings may provide evidence for novel treatment strategies of anti-neuroinflammation therapy in the early stage.

Redox-neutral rhodium(III)-catalyzed divergent synthesis of tetrasubstituted 1,3-enynes and alkynylated benzofurans.

With the assistance of the acetamido directing group (DG), a rhodium-catalyzed C-H alkenylation/DG migration cascade for the synthesis of tetrasubstituted 1,3-enynes from N-phenoxyacetamides and 1,3-diynes has been achieved in this work. Alternatively, a rhodium-catalyzed [3 + 2] annulation for the synthesis of alkynylated benzofurans from the same set of substrates has also been achieved by simply changing the reaction conditions. This work highlights the tunable divergent synthesis of valuable compounds triggered by C-H activation.

Acute toxic effects of diclofenac exposure on freshwater crayfish (Procambarus clarkii): Insights from hepatopancreatic pathology, molecular regulation and intestinal microbiota.

In this study, we exposed adult male crayfish (Procambarus clarkii) to different concentrations of diclofenac (DCF) for 96 h. In the meantime, we investigated the alternations of hepatopancreatic pathology, molecular regulation and intestinal microbiota of P. clarkii exposed to DCF. The results demonstrated DCF led to histological changes including epithelium vacuolization and tubule lumen dilatation in the hepatopancreas. Transcriptome sequencing analysis showed that 642 and 586 genes were differentially expressed in the hepatopancreas of P. clarkii exposed to 1 and 10 mg/L DCF, respectively. DCF could affect the functions of antioxidation, immunity and metabolism of hepatopancreas by inducing the abnormal expressions of immune- and redox-related genes. GO enrichment results demonstrated that 10 mg/L DCF exposure could modulate the processes of molting, amino sugar metabolism, protein hydrolysis and intracellular protein translocation of P. clarkii. Additionally, the abundances of bacterial families including Shewanellaceae, Bacteroidaceae, Vibrionaceae, Erysipelotrichaceae, Aeromonadaceae, Moraxellaceae, etc. in the intestine were significantly changed after DCF exposure, and the disruption of intestinal flora might further cause abnormal intestinal metabolism in P. clarkii. This study provides novel mechanistic insights into the toxic effects of anti-inflammatory drugs on aquatic crustaceans.

Progressive Memory Circuit Impairments along with Alzheimer's Disease Neuropathology Spread: Evidence from in vivo Neuroimaging.

During the progression of Alzheimer's disease (AD), neuropathology may propagate transneuronally, cause disruption in memory circuit, and lead to memory impairment. However, there is a lack of in vivo evidence regarding this process. Thus, we aim to simulate and observe the progression of neuropathology in AD continuum. We included cognitively normal (CN), mild cognitive impairments (MCI), and AD subjects, and further classified them using the A/T/N scheme (Group 0: CN, A - T-; Group 1: CN, A + T-; Group 2: CN, A + T+; Group 3: MCI, A + T+; Group 4: AD, A + T+). We investigated alterations of three core memory circuit structures: hippocampus (HP) subfields volume, cingulum-angular bundles (CAB) fiber integrity, and precuneus cortex volume. HP subfields volume showed the trend of initially increased and then decreased (starting from Group 2), while precuneus volume decreased in Groups 3 and 4. The CAB integrity degenerated in Groups 3 and 4 and aggravated with higher disease stages. Further, memory circuit impairments were correlated with neuropathology biomarkers and memory performance. Conclusively, our results demonstrated a pattern of memory circuit impairments along with AD progression: starting from the HP, then propagating to the downstream projection fiber tract and cortex. These findings support the tau propagation theory to some extent.

First total synthesis of a new phenylpropanoid glycoside: natural cytotoxic compound from Cirsium japonicum.

Phenylpropanoid glycoside compound 1, the natural anti-tumor compound isolated from the erial parts of Cirsium japonicum, was first totally synthesized using easily available materials in short, convenient route with overall yield of 13.9%.

The first total synthesis of anemarchalconyn and anemarcoumarin A.

Anemarchalconyn (1) and anemarcoumarin A (2), the natural bioactive compounds isolated from the rhizomes of Anemarrhena asphodeloides Bunge (Liliaceae), were first totally synthesized using easily available materials in short, convenient routes with overall yields of 32 and 48%.

Dune-slope activity due to frost and wind throughout the north polar erg, Mars.

Repeat, high-resolution imaging of dunes within the Martian north polar erg have shown that these dune slopes are very active, with alcoves forming along the dune brink each Mars year. In some areas, a few hundred cubic metres of downslope sand movement have been observed, sometimes moving the dune brink 'backwards'. Based on morphological and activity-timing similarities of these north polar features to southern dune gullies, identifying the processes forming these features is likely to have relevance for understanding the general evolution/modification of dune gullies. To determine alcove-formation model constraints, we have surveyed seven dune fields, each over 1-4 Mars winters. Consistent with earlier reports, we found that alcove-formation activity occurs during the autumn-winter seasons, before or while the stable seasonal frost layer is deposited. We propose a new model in which alcove formation occurs during the autumn, and springtime sublimation activity then enhances the feature. Summertime winds blow sand into the new alcoves, erasing small alcoves over a few Mars years. Based on the observed rate of alcove erasure, we estimated the effective aeolian sand transport flux. From this, we proposed that alcove formation may account for 2-20% of the total sand movement within these dune fields.

Interferon Regulatory Factor 5 Regulates the Phagocytosis of Microglia and Alleviate Alzheimer's Pathology.

Microglia play a critical role in the pathophysiology of Alzheimer's disease. They are involved in Aß-induced neuroinflammatory responses, regulating the production of inflammatory mediators. Interferon regulatory factor 5 (IRF5) plays a central role in inflammatory diseases in the periphery, the role of which in central nervous system remains elusive. This study aimed to investigate the role of IRF5 in Aß-induced neuroinflammation and the progression of Aß pathology. We found that Aß1-42 oligomers significantly increased the level of IRF5 in BV2 microglia. The levels of proinflammatory cytokines TNF-α, IL-1ß, and IL-6 were significantly upregulated with Aß treatment. IRF5 knockdown with siRNA in microglia significantly reduced the expression of these proinflammatory factors induced by Aß and promoted Aß phagocytosis. Besides, LC3 upregulation and p62 downregulation were observed in IRF5 knockdown microglia. This was also validated in APP/PS1 mice with IRF5 knockdown, leading to reduced Aß levels in the brain. We conclude that IRF5 mediates Aß-induced microglial inflammatory responses. IRF5 knockdown attenuated Aß-induced inflammatory responses and promoted the phagocytosis and autophagy of Aß by microglia.

Leveraging Cas13a's trans-cleavage on RNA G-quadruplexes for amplification-free RNA detection.

In this study, we investigated Cas13a's efficacy in trans-cleaving RNA G-quadruplexes (rG4s) as an alternative to ssRNA reporters in CRISPR-Cas13a diagnostics. Our findings demonstrate enhanced efficiency due to the structural arrangement of rG4s. Implementing a simplified CRISPR-Cas13a system based on rG4, we identified SARS-CoV-2 infections in 25 patient samples within 1 hour without target pre-amplification.

Multiple Energy Transfer Channels in Rare Earth Doped Multi-Exciton Emissive Perovskites.

Revealing the energy transfer (ET) process from excitons to rare earth ions in halide perovskites has great guiding value for designing optoelectronic materials. Here, the multiple ET channels in multi-exciton emissive Sb3+ /Nd3+ co-doped Cs2 ZrCl6 are explored to comprehend the ET processes. Förster-Dexter ET theory reveals that the sensitizer concentration rather than the overlap integral of the spectra plays the leading function in the comparison of the ET efficiency among multiple ET channels from the host self-trapped excitons (STEs) and dopant triplet STEs to Nd3+ ions. Besides, Sb3+ /Nd3+ co-doped Cs2 ZrCl6 enables varied color delivery and has great potential as anti-counterfeiting material. Under X-ray irradiation, Sb3+ /Nd3+ co-doped Cs2 ZrCl6 presents a high light yield of ≈13300 photons MeV-1 and promising X-ray imaging ability. This work provides new insight for investigating the ET efficiency among multiple ET processes and presents great potentiality of multi-exciton emissive perovskites in the fields of anti-counterfeiting and X-ray imaging.

Cerebrospinal fluid amyloid-ß and cerebral microbleed are associated with distinct neuropsychiatric sub-syndromes in cognitively impaired patients.

BACKGROUND: Neuropsychiatric symptoms (NPS) are prevalent in cognitively impaired individuals including Alzheimer's disease (AD) dementia and mild cognitive impairment (MCI). Whereas several studies have reported the associations between NPS with AD pathologic biomarkers and cerebral small vessel disease (SVD), but it remains unknown whether AD pathology and SVD contribute to different sub-syndromes independently or aggravate same symptoms synergistically. METHOD: We included 445 cognitively impaired individuals (including 316 MCI and 129 AD) with neuropsychiatric, cerebrospinal fluid (CSF) biomarkers (Aß42, p-tau, and t-tau) and multi-model MRI data. Psychiatric symptoms were accessed by using the Neuropsychiatric Inventory (NPI). Visual assessment of SVD (white matter hyperintensity, microbleed, perivascular space, lacune) on MRI images was performed by experienced radiologist. Linear regression analyses were conducted to test the association between neuropsychiatric symptoms with AD pathology and CSVD burden after adjustment for age, sex, education, apolipoprotein E (APOE) ε4 carrier status, and clinical diagnosis. RESULTS: The NPI total scores were related to microbleed (estimate 2.424; 95% CI [0.749, 4.099]; P =0.005). Considering the sub-syndromes, the hyperactivity was associated with microbleed (estimate 0.925; 95% CI [0.115, 1.735]; P =0.025), whereas the affective symptoms were correlated to CSF level of Aß42 (estimate -0.006; 95% CI [-0.011, -0.002]; P =0.005). Furthermore, we found the apathy sub-syndrome was associated with CSF t-tau/Aß42 (estimate 0.636; 95% CI [0.078, 1.194]; P =0.041) and microbleed (estimate 0.693; 95% CI [0.046, 1.340]; P =0.036). In addition, we found a significant interactive effect between CSF t-tau/Aß42 and microbleed (estimate 0.993; 95% CI [0.360, 1.626]; P =0.019) on severity of apathy sub-syndrome. CONCLUSION: Our study showed that CSF Aß42 was associated with affective symptoms, but microbleed was correlated with hyperactivity and apathy, suggesting the effect of AD pathology and SVD on different neuropsychiatric sub-syndromes.

Alteration of functional connectivity network in population of objectively-defined subtle cognitive decline.

The objectively-defined subtle cognitive decline individuals had higher progression rates of cognitive decline and pathological deposition than healthy elderly, indicating a higher risk of progressing to Alzheimer's disease. However, little is known about the brain functional alterations during this stage. Thus, we aimed to investigate the functional network patterns in objectively-defined subtle cognitive decline cohort. Forty-two cognitive normal, 29 objectively-defined subtle cognitive decline and 55 mild cognitive impairment subjects were included based on neuropsychological measures from the Alzheimer's disease Neuroimaging Initiative dataset. Thirty cognitive normal, 22 objectively-defined subtle cognitive declines and 48 mild cognitive impairment had longitudinal MRI data. The degree centrality and eigenvector centrality for each participant were calculated by using resting-state functional MRI. For cross-sectional data, analysis of covariance was performed to detect between-group differences in degree centrality and eigenvector centrality after controlling age, sex and education. For longitudinal data, repeated measurement analysis of covariance was used for comparing the alterations during follow-up period among three groups. In order to classify the clinical significance, we correlated degree centrality and eigenvector centrality values to Alzheimer's disease biomarkers and cognitive function. The results of analysis of covariance showed significant between-group differences in eigenvector centrality and degree centrality in left superior temporal gyrus and left precuneus, respectively. Across groups, the eigenvector centrality value of left superior temporal gyrus was positively related to recognition scores in auditory verbal learning test, whereas the degree centrality value of left precuneus was positively associated with mini-mental state examination total score. For longitudinal data, the results of repeated measurement analysis of covariance indicated objectively-defined subtle cognitive decline group had the highest declined rate of both eigenvector centrality and degree centrality values than other groups. Our study showed an increased brain functional connectivity in objectively-defined subtle cognitive decline individuals at both local and global level, which were associated with Alzheimer's disease pathology and neuropsychological assessment. Moreover, we also observed a faster declined rate of functional network matrix in objectively-defined subtle cognitive decline individuals during the follow-ups.

Computationally efficient adaptive decompression for whole slide image processing.

Whole slide image (WSI) analysis is increasingly being adopted as an important tool in modern pathology. Recent deep learning-based methods have achieved state-of-the-art performance on WSI analysis tasks such as WSI classification, segmentation, and retrieval. However, WSI analysis requires a significant amount of computation resources and computation time due to the large dimensions of WSIs. Most of the existing analysis approaches require the complete decompression of the whole image exhaustively, which limits the practical usage of these methods, especially for deep learning-based workflows. In this paper, we present compression domain processing-based computation efficient analysis workflows for WSIs classification that can be applied to state-of-the-art WSI classification models. The approaches leverage the pyramidal magnification structure of WSI files and compression domain features that are available from the raw code stream. The methods assign different decompression depths to the patches of WSIs based on the features directly retained from compressed patches or partially decompressed patches. Patches from the low-magnification level are screened by attention-based clustering, resulting in different decompression depths assigned to the high-magnification level patches at different locations. A finer-grained selection based on compression domain features from the file code stream is applied to select further a subset of the high-magnification patches that undergo a full decompression. The resulting patches are fed to the downstream attention network for final classification. Computation efficiency is achieved by reducing unnecessary access to the high zoom level and expensive full decompression. With the number of decompressed patches reduced, the time and memory costs of downstream training and inference procedures are also significantly reduced. Our approach achieves a 7.2× overall speedup, and the memory cost is reduced by 1.1 orders of magnitudes, while the resulting model accuracy is comparable to the original workflow.