Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin.

Telomeres, repetitive DNA sequences at chromosome ends, are shielded against the DNA damage response (DDR) by the shelterin complex. To understand how shelterin protects telomere ends, we investigated the structural organization of telomeric chromatin in human cells using super-resolution microscopy. We found that telomeres form compact globular structures through a complex network of interactions between shelterin subunits and telomeric DNA, but not by DNA methylation, histone deacetylation, or histone trimethylation at telomeres and subtelomeric regions. Mutations that abrogate shelterin assembly or removal of individual subunits from telomeres cause up to a 10-fold increase in telomere volume. Decompacted telomeres accumulate DDR signals and become more accessible to telomere-associated proteins. Recompaction of telomeric chromatin using an orthogonal method displaces DDR signals from telomeres. These results reveal the chromatin remodeling activity of shelterin and demonstrate that shelterin-mediated compaction of telomeric chromatin provides robust protection of chromosome ends against the DDR machinery.

Unraveling the influence of CRISPR/Cas13a reaction components on enhancing trans-cleavage activity for ultrasensitive on-chip RNA detection.

The CRISPR/Cas13 nucleases have been widely documented for nucleic acid detection. Understanding the intricacies of CRISPR/Cas13's reaction components is pivotal for harnessing its full potential for biosensing applications. Herein, we report on the influence of CRISPR/Cas13a reaction components on its trans-cleavage activity and the development of an on-chip total internal reflection fluorescence microscopy (TIRFM)-powered RNA sensing system. We used SARS-CoV-2 synthetic RNA and pseudovirus as a model system. Our results show that optimizing Mg2+ concentration, reporter length, and crRNA combination significantly improves the detection sensitivity. Under optimized conditions, we detected 100 fM unamplified SARS-CoV-2 synthetic RNA using a microtiter plate reader. To further improve sensitivity and provide a new amplification-free RNA sensing toolbox, we developed a TIRFM-based amplification-free RNA sensing system. We were able to detect RNA down to 100 aM. Furthermore, the TIRM-based detection system developed in this study is 1000-fold more sensitive than the off-coverslip assay. The possible clinical applicability of the system was demonstrated by detecting SARS-CoV-2 pseudovirus RNA. Our proposed sensing system has the potential to detect any target RNA with slight modifications to the existing setup, providing a universal RNA detection platform.

The Integrated Bioinformatic Approach Reveals the Prognostic Significance of LRP1 Expression in Ovarian Cancer.

A hyperactive tumour microenvironment (TME) drives unrestricted cancer cell survival, drug resistance, and metastasis in ovarian carcinoma (OC). However, therapeutic targets within the TME for OC remain elusive, and efficient methods to quantify TME activity are still limited. Herein, we employed an integrated bioinformatics approach to determine which immune-related genes (IRGs) modulate the TME and further assess their potential theragnostic (therapeutic + diagnostic) significance in OC progression. Using a robust approach, we developed a predictive risk model to retrospectively examine the clinicopathological parameters of OC patients from The Cancer Genome Atlas (TCGA) database. The validity of the prognostic model was confirmed with data from the International Cancer Genome Consortium (ICGC) cohort. Our approach identified nine IRGs, AKT2, FGF7, FOS, IL27RA, LRP1, OBP2A, PAEP, PDGFRA, and PI3, that form a prognostic model in OC progression, distinguishing patients with significantly better clinical outcomes in the low-risk group. We validated this model as an independent prognostic indicator and demonstrated enhanced prognostic significance when used alongside clinical nomograms for accurate prediction. Elevated LRP1 expression, which indicates poor prognosis in bladder cancer (BLCA), OC, low-grade gliomas (LGG), and glioblastoma (GBM), was also associated with immune infiltration in several other cancers. Significant correlations with immune checkpoint genes (ICGs) highlight the potential importance of LRP1 as a biomarker and therapeutic target. Furthermore, gene set enrichment analysis highlighted LRP1's involvement in metabolism-related pathways, supporting its prognostic and therapeutic relevance also in BLCA, OC, low-grade gliomas (LGG), GBM, kidney cancer, OC, BLCA, kidney renal clear cell carcinoma (KIRC), stomach adenocarcinoma (STAD), and stomach and oesophageal carcinoma (STES). Our study has generated a novel signature of nine IRGs within the TME across cancers, that could serve as potential prognostic predictors and provide a valuable resource to improve the prognosis of OC.

CRISPR-Cas12-based field-deployable system for rapid detection of synthetic DNA sequence of the monkeypox virus genome.

The global outbreak of the monkeypox virus (MPXV) highlights the need for rapid and cost-effective MPXV detection tools to effectively monitor and control the monkeypox disease. Herein, we demonstrated a portable CRISPR-Cas-based system for naked-eye detection of MPXV. The system harnesses the high selectivity of CRISPR-Cas12 and the isothermal nucleic acid amplification potential of recombinase polymerase amplification. It can detect both the current circulating MPXV clade and the original clades. We reached a limit of detection (LoD) of 22.4 aM (13.5 copies/µl) using a microtiter plate reader, while the visual LoD of the system is 75 aM (45 copies/µl) in a two-step assay, which is further reduced to 25 aM (15 copies/µl) in a one-pot system. We compared our results with quantitative polymerase chain reaction and obtained satisfactory consistency. For clinical application, we demonstrated a sensitive and precise visual detection method with attomolar sensitivity and a sample-to-answer time of 35 min.

Improved photoacoustic images via wavefront shaping modulation based on the scattering structure: retraction.

The referenced article [Opt. Express30, 36489 (2022)10.1364/OE.470330] has been retracted by the authors.

Sparse deconvolution for background noise suppression with total variation regularization in light field microscopy.

In this Letter, we present a method aiming at background noise removal in the 3D reconstruction of light field microscopy (LFM). Sparsity and Hessian regularization are taken as two prior knowledges to process the original light field image before 3D deconvolution. Due to the noise suppression function of total variation (TV) regularization, we add the TV regularization term to the 3D Richardson-Lucy (RL) deconvolution. By comparing the light field reconstruction results of our method with another state-of-the-art method that is also based on RL deconvolution, the proposed method shows improved performance in terms of removing background noise and detail enhancement. This method will be beneficial to the application of LFM in biological high-quality imaging.

Prevalence Patterns and Onset Prediction of High Myopia for Children and Adolescents in Southern China via Real-World Screening Data: Retrospective School-Based Study.

BACKGROUND: Patients with high myopia have an increased lifetime risk of complications. The prevalence patterns of high myopia in children and adolescents in southern China are unclear. Early identification of high-risk individuals is critical for reducing the occurrence and development of high myopia and avoiding the resulting complications. OBJECTIVE: This study aimed to determine the prevalence of high myopia in children and adolescents in southern China via real-world screening data and to predict its onset by studying the risk factors for high myopia based on machine learning. METHODS: This retrospective school-based study was conducted in 13 cities with different gross domestic products in southern China. Through data acquisition and filtering, we analyzed the prevalence of high myopia and its association with age, school stage, gross domestic product, and risk factors. A random forest algorithm was used to predict high myopia among schoolchildren and then assessed in an independent hold-out group. RESULTS: There were 1,285,609 participants (mean age 11.80, SD 3.07, range 6-20 years), of whom 658,516 (51.2%) were male. The overall prevalence of high myopia was 4.48% (2019), 4.88% (2020), and 3.17% (2021), with an increasing trend from the age of 11 to 17 years. The rates of high myopia increased from elementary schools to high schools but decreased at all school stages from 2019 to 2021. The coastal and southern cities had a higher proportion of high myopia, with an overall prevalence between 2.60% and 5.83%. Age, uncorrected distance visual acuity, and spherical equivalents were predictive factors for high myopia onset in schoolchildren. The random forest algorithm achieved a high accuracy of 0.948. The area under the receiver operator characteristic curve (AUC) was 0.975. Both indicated sufficient model efficacy. The performance of the model was validated in an external test with high accuracy (0.971) and a high AUC (0.957). CONCLUSIONS: High myopia had a high incidence in Guangdong Province. Its onset in children and adolescents was well predicted with the random forest algorithm. Efficient use of real-world data can contribute to the prevention and early diagnosis of high myopia.

Improved photoacoustic images via wavefront shaping modulation based on the scattering structure.

Multispectral optoacoustic tomography (MSOT) has become the dominant technical solution for photoacoustic imaging (PAI). However, the laser source of fiber output in the current MSOT method is typically a TEM00 Gaussian beam, which is prone to artifacts and incomplete due to the uneven distribution of the irradiated light intensity. Here, we propose a novel method to improve the quality of photoacoustic image reconstruction by modulating the wavefront shaping of the incident laser beam based on the designed scattering structure. In the experiment, we add the designed scattering structure to the current hemispherical photoacoustic transducer array device. Through experiments and simulations, we investigate and compare the effects of different scattering structures on laser intensity modulation. The results show that an ED1-C20 diffusion structure with a scattering angle of 20 degrees has the most effective modulation of the beam intensity distribution. And we choose gold nanoparticles of 50-100 nanometers (nm) diameters and index finger capillary vessels respectively as the medium of PAI. We obtain the highest ratio of PAI area increases of gold nanoparticles and index finger to devices compare without scattering structure is 29.69% and 634.94%, respectively. Experimental results demonstrate that our method is significantly higher quality than traditional methods, which has great potential for theoretical application in medical PAI.

Characterization of anisotropy of the porous anodic alumina by the Mueller matrix imaging method.

Porous anodic alumina (PAA) is a photonic crystal with a hexagonal porous structure. To learn more about the effects brought by pores on the anisotropy of the PAA, we use the orientation sensitive Mueller matrix imaging (MMI) method to study it. We fabricated the PAA samples with uniform pores and two different pore diameters. By the MMI experiments with these samples, we found that the birefringence is the major anisotropy of the PAA and that there are many small areas with different orientations that formed spontaneously in the process of production on the surface of the PAA. By the MMI experiments at different orientations of the sample with two different pore diameters, we found that the pores affect the birefringence of the sample and the effect increases with the increased inclination of the sample. To further analyze the PAA, we present a symmetrical rotation measurement method according to the Mueller matrix of the retarder. With this method, we can calculate the average refractive index (RI) of birefringence and the orientation of the optical axis of uniaxial crystal. The results also show the effect of the pores on the anisotropy of PAA.

Structured mRNA induces the ribosome into a hyper-rotated state.

During protein synthesis, mRNA and tRNA are moved through the ribosome by the process of translocation. The small diameter of the mRNA entrance tunnel only permits unstructured mRNA to pass through. However, there are structured elements within mRNA that present a barrier for translocation that must be unwound. The ribosome has been shown to unwind RNA in the absence of additional factors, but the mechanism remains unclear. Here, we show using single molecule Förster resonance energy transfer and small angle X-ray scattering experiments a new global conformational state of the ribosome. In the presence of the frameshift inducing dnaX hairpin, the ribosomal subunits are driven into a hyper-rotated state and the L1 stalk is predominantly in an open conformation. This previously unobserved conformational state provides structural insight into the helicase activity of the ribosome and may have important implications for understanding the mechanism of reading frame maintenance.

DNA Virus Detection System Based on RPA-CRISPR/Cas12a-SPM and Deep Learning.

We report a fast, easy-to-implement, highly sensitive, sequence-specific, and point-of-care (POC) DNA virus detection system, which combines recombinase polymerase amplification (RPA) and CRISPR/Cas12a system for trace detection of DNA viruses. Target DNA is amplified and recognized by RPA and CRISPR/Cas12a separately, which triggers the collateral cleavage activity of Cas12a that cleaves a fluorophore-quencher labeled DNA reporter and generalizes fluorescence. For POC detection, portable smartphone microscopy is built to take fluorescent images. Besides, deep learning models for binary classification of positive or negative samples, achieving high accuracy, are deployed within the system. Frog virus 3 (FV3, genera Ranavirus, family Iridoviridae) was tested as an example for this DNA virus POC detection system, and the limits of detection (LoD) can achieve 10 aM within 40 min. Without skilled operators and bulky instruments, the portable and miniature RPA-CRISPR/Cas12a-SPM with artificial intelligence (AI) assisted classification shows great potential for POC DNA virus detection and can help prevent the spread of such viruses.

Mitochondrial UCP1: Potential thermogenic mechanistic switch for the treatment of obesity and neurodegenerative diseases using natural and epigenetic drug candidates.

BACKGROUND: Brown fat is known to provide non-shivering thermogenesis through mitochondrial uncoupling mediated by uncoupling protein 1 (UCP1). Non-shivering is not dependent on UCP2, UCP4, and BMCP1/UCP5 genes, which are distinct from UCP1 in a way that they are not constitutive uncouplers. Although they are susceptible to free fatty acid and free radical activation, their functioning has a significant impact on the performance of neurons. METHODOLOGY: Using subject-specific keywords (Adipose tissue; Adipocytes; Mitochondria; Obesity; Thermogenesis; UCP's in Neurodegeneration; Alzheimer's disease; Parkinson's disease), research articles and reviews were retrieved from Web of Science, ScienceDirect, Google Scholar, and PubMed. This article includespublications published between 2018 and 2023. The drugs that upregulate UCP1 are included in the study while the drugs that do not impact UCP1 are were not included. RESULTS: Neuronal UCPs have a direct impact on synaptic plasticity, neurodegenerative processes, and neurotransmission, by modulating calcium flux, mitochondrial biogenesis, local temperature, and free radical generation. Numerous significant advances in the study of neuronal UCPs and neuroprotection are still to be made. Identification of the tissue-dependent effects of UCPs is essential first. Pharmacologically targeting neuronal UCPs is a key strategy for preventing both neurodegenerative diseases and physiological aging. Given that UCP2 has activities that are tissue-specific, it will be essential to develop treatments without harmful side effects. The triggering of UCPs by CoQ, an essential cofactor, produces nigral mitochondrial uncoupling, reduces MPTP-induced toxicity, and may even decrease the course of Parkinson's disease, according to early indications. CONCLUSION: Herein, we explore the potential of UCP1 as a therapeutic target for treating obesity, neurodegenerative diseases as well as a potential activator of both synthetic and natural drugs. A deeper knowledge of synaptic signaling and neurodegeneration may pave the way to new discoveries regarding the functioning and controlling of these genes.

Towards carbon neutrality: Sustainable recycling and upcycling strategies and mechanisms for polyethylene terephthalate via biotic/abiotic pathways.

Polyethylene terephthalate (PET), one of the most ubiquitous engineering plastics, presents both environmental challenges and opportunities for carbon neutrality and a circular economy. This review comprehensively addressed the latest developments in biotic and abiotic approaches for PET recycling/upcycling. Biotically, microbial depolymerization of PET, along with the biosynthesis of reclaimed monomers [terephthalic acid (TPA), ethylene glycol (EG)] to value-added products, presents an alternative for managing PET waste and enables CO2 reduction. Abiotically, thermal treatments (i.e., hydrolysis, glycolysis, methanolysis, etc.) and photo/electrocatalysis, enabled by catalysis advances, can depolymerize or convert PET/PET monomers in a more flexible, simple, fast, and controllable manner. Tandem abiotic/biotic catalysis offers great potential for PET upcycling to generate commodity chemicals and alternative materials, ideally at lower energy inputs, greenhouse gas emissions, and costs, compared to virgin polymer fabrication. Remarkably, over 25 types of upgraded PET products (e.g., adipic acid, muconic acid, catechol, vanillin, and glycolic acid, etc.) have been identified, underscoring the potential of PET upcycling in diverse applications. Efforts can be made to develop chemo-catalytic depolymerization of PET, improve microbial depolymerization of PET (e.g., hydrolysis efficiency, enzymatic activity, thermal and pH level stability, etc.), as well as identify new microorganisms or hydrolases capable of degrading PET through computational and machine learning algorithms. Consequently, this review provides a roadmap for advancing PET recycling and upcycling technologies, which hold the potential to shape the future of PET waste management and contribute to the preservation of our ecosystems.

The Mediating Effect of the Choline-to-Betaine Ratio on the Association Between PEMT rs7946 and Digestive System Cancer: A Nested Case-Control Study in a Chinese Population.

Background: The enzyme phosphatidylethanolamine N-methyltransferase (PEMT) is responsible for synthesizing phosphatidylcholine by methylating phosphatidylethanolamine. We hypothesized that a polymorphism of the PEMT gene, rs7946, is involved in carcinogenesis. Objectives: We aimed to investigate the relationship between PEMT rs7946 and digestive system cancer and examine possible effect modifiers and mediators. Methods: We conducted a nested, case-control study within the China H-type Hypertension Registry Study, including 751 cases and 1:1 matched controls. To assess the association of PEMT rs7946 and digestive system cancer, we estimated odds ratios with 95% confidence intervals (CIs) using conditional logistic regression. We used the bootstrap test to examine the potential mediating effects of related metabolites. Results: Our results revealed that wild-type homozygous CC genotype carriers of PEMT rs7946 had a significantly increased risk [odds ratio (OR): 1.31; 95% CI: 1.04, 1.66; P = 0.023] compared with the TT/CT combined genotypes. The effect was found to be more pronounced in individuals with a lower choline-to-betaine ratio (<0.412, P-interaction = 0.021). Furthermore, the mediation analysis indicated that the choline-to-betaine ratio played a significant role in mediating 13.55% of the association between PEMT rs7946 and digestive system cancer (P = 0.018). Conclusions: Our study suggested that PEMT rs7946 may affect risk of digestive system cancer through direct and indirect pathways, and the choline-to-betaine ratio may partially mediate the indirect effect.This trial was registered at Chinese Clinical Trial Registry as ChiCTR1800017274.

Unleashing the potential of tungsten disulfide: Current trends in biosensing and nanomedicine applications.

The discovery of graphene ignites a great deal of interest in the research and advancement of two-dimensional (2D) layered materials. Within it, semiconducting transition metal dichalcogenides (TMDCs) are highly regarded due to their exceptional electrical and optoelectronic properties. Tungsten disulfide (WS2) is a TMDC with intriguing properties, such as biocompatibility, tunable bandgap, and outstanding photoelectric characteristics. These features make it a potential candidate for chemical sensing, biosensing, and tumor therapy. Despite the numerous reviews on the synthesis and application of TMDCs in the biomedical field, no comprehensive study still summarizes and unifies the research trends of WS2 from synthesis to biomedical applications. Therefore, this review aims to present a complete and thorough analysis of the current research trends in WS2 across several biomedical domains, including biosensing and nanomedicine, covering antibacterial applications, tissue engineering, drug delivery, and anticancer treatments. Finally, this review also discusses the potential opportunities and obstacles associated with WS2 to deliver a new outlook for advancing its progress in biomedical research.

COVID-19: Post infection implications in different age groups, mechanism, diagnosis, effective prevention, treatment, and recommendations.

SARS-CoV-2 is a highly contagious pathogen that predominantly caused the COVID-19 pandemic. The persistent effects of COVID-19 are defined as an inflammatory or host response to the virus that begins four weeks after initial infection and persists for an undetermined length of time. Chronic effects are more harmful than acute ones thus, this review explored the long-term effects of the virus on various human organs, including the pulmonary, cardiovascular, and neurological, reproductive, gastrointestinal, musculoskeletal, endocrine, and lymphoid systems and found that SARS-CoV-2 adversely affects these organs of older adults. Regarding diagnosis, the RT-PCR is a gold standard method of diagnosing COVID-19; however, it requires specialized equipment and personnel for performing assays and a long time for results production. Therefore, to overcome these limitations, artificial intelligence employed in imaging and microfluidics technologies is the most promising in diagnosing COVID-19. Pharmacological and non-pharmacological strategies are the most effective treatment for reducing the persistent impacts of COVID-19 by providing immunity to post-COVID-19 patients by reducing cytokine release syndrome, improving the T cell response, and increasing the circulation of activated natural killer and CD8 T cells in blood and tissues, which ultimately reduces fever, nausea, fatigue, and muscle weakness and pain. Vaccines such as inactivated viral, live attenuated viral, protein subunit, viral vectored, mRNA, DNA, or nanoparticle vaccines significantly reduce the adverse long-term virus effects in post-COVID-19 patients; however, no vaccine was reported to provide lifetime protection against COVID-19; consequently, protective measures such as physical separation, mask use, and hand cleansing are promising strategies. This review provides a comprehensive knowledge of the persistent effects of COVID-19 on people of varying ages, as well as diagnosis, treatment, vaccination, and future preventative measures against the spread of SARS-CoV-2.

Distinct correlation network of clinical characteristics in suicide attempters having adolescent major depressive disorder with non-suicidal self-injury.

Suicidal behavior and non-suicidal self-injury (NSSI) are common in adolescent patients with major depressive disorder (MDD). Thus, delineating the unique characteristics of suicide attempters having adolescent MDD with NSSI is important for suicide prediction in the clinical setting. Here, we performed psychological and biochemical assessments of 130 youths having MDD with NSSI. Participants were divided into two groups according to the presence/absence of suicide attempts (SAs). Our results demonstrated that the age of suicide attempters is lower than that of non-attempters in participants having adolescent MDD with NSSI; suicide attempters had higher Barratt Impulsiveness Scale (BIS-11) impulsivity scores and lower serum CRP and cortisol levels than those having MDD with NSSI alone, suggesting levels of cortisol and CRP were inversely correlated with SAs in patients with adolescent MDD with NSSI. Furthermore, multivariate regression analysis revealed that NSSI frequency in the last month and CRP levels were suicidal ideation predictors in adolescent MDD with NSSI, which may indicate that the increased frequency of NSSI behavior is a potential risk factor for suicide. Additionally, we explored the correlation between psychological and blood biochemical indicators to distinguish suicide attempters among participants having adolescent MDD with NSSI and identified a unique correlation network that could serve as a marker for suicide attempters. Our research data further suggested a complex correlation between the psychological and behavioral indicators of impulsivity and anger. Therefore, our study findings may provide clues to identify good clinical warning signs for SA in patients with adolescent MDD with NSSI.

Characterization of the weak calcium binding of trimeric globular adiponectin.

Adiponectin is secreted from adipose tissue and functions as a protein hormone in regulating glucose metabolism and fatty acid catabolism. Adiponectin plays an important role as a novel risk factor and potential diagnostic and prognostic biomarker in cancer. Crystal structures of globular adiponectin have been resolved with three calcium-binding sites on the top of its central tunnel. However, the calcium-binding property of adiponectin remains elusive. Mouse globular adiponectin was cloned into pET11a and expressed in Escherichia coli. The folding of adiponectin was indicated by the spread of resonances in HSQC spectrum. Luminescence resonance energy transfer was used to obtain the binding constant (K(d)) of Tb(3+) and the inhibitor constant (K(i)) of Ca(2+) for globular adiponectin. The obtained calcium-binding affinity to adiponectin is relatively low (~2 mM), which indicates that the high concentration of adiponectin in circulating system may function as calcium storage bank and buffer the free calcium concentration.

AutoUnmix: an autoencoder-based spectral unmixing method for multi-color fluorescence microscopy imaging.

Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models, and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A transfer learning framework is further devised to allow our AutoUnmix to adapt to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve the highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. For experiments where spectral profiles and morphology are akin to simulated data, our method realizes the quantitative performance demonstrated above. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool for studying the interaction process of different organelles labeled by multiple fluorophores.

Micro- and nanosystems for the detection of hemorrhagic fever viruses.

Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.