Proteome Fishing for CRISPR/Cas12a-Based Orthogonal Multiplex Aptamer Sensing.

Detection of serum protein biomarkers is extremely challenging owing to the superior complexity of serum. Here, we report a method of proteome fishing from the serum. It uses a magnetic nanoparticle-protein corona and a multiplexed aptamer panel, which we incubated with the nanoparticle-protein corona for biomarker recognition. To transfer protein biomarker detection to aptamer detection, we established a CRISPR/Cas12a-based orthogonal multiplex aptamer sensing (COMPASS) platform by profiling the aptamers of protein corona with clinical nonsmall cell lung cancer (NSCLC) serum samples. Furthermore, we determined the four out of nine (FOON) panel (including HE4, NSE, AFP, and VEGF165) to be the most cost-effective and accurate panel for COMPASS in NSCLC diagnosis. The diagnostic accuracy of NSCLC by the FOON panel with internal and external cohorts was 95.56% (ROC-AUC = 99.40%) and 89.58% (ROC-AUC = 95.41%), respectively. Our developed COMPASS technology circumvents the otherwise challenging multiplexed serum protein amplification problem and avoids aptamer degradation in serum. Therefore, this novel COMPASS could lead to the development of a facile, cost-effective, intelligent, and high-throughput diagnostic platform for large-cohort cancer screening.

Nanoparticle-Protein Corona-Based Tissue Proteomics for the Aging Mouse Proteome Atlas.

Highly abundant proteins present in biological fluids and tissues significantly interfere with low-abundance protein identification by mass spectrometry (MS), limiting proteomic depth and hindering protein biomarker discovery. Herein, to enhance the coverage of tissue proteomics, we developed a nanoparticle-protein corona (NP-PC)-based method for the aging mouse proteome atlas. Based on this method, we investigated the complexity of life process of 5 major organs, including the heart, liver, spleen, lungs, and kidneys, from 4 groups of mice at different ages. Compared with the conventional strategy, NP-PC-based proteomics significantly increased the number of identified protein groups in the heart (from 3007 to 3927; increase of 30.6%), liver (from 2982 to 4610; increase of 54.6%), spleen (from 5047 to 7351; increase of 45.7%), lungs (from 4984 to 6903; increase of 38.5%), and kidneys (from 3550 to 5739; increase of 61.7%), and we identified a total of 10 104 protein groups. The overall data indicated that 3-week-old mice showed more differences compared with the other three age groups. The proteins of amino acid-related metabolism were increased in aged mice compared with those in the 3-week-old mice. Protein-related infections were increased in the spleen of the aged mice. Interestingly, the spliceosome-related pathway significantly changed from youth to elders in the liver, spleen, and lungs, indicating the vital role of the spliceosome during the aging process. Our established aging mouse organ proteome atlas provides comprehensive insights into understanding the aging process, and it may help in prevention and treatment of age-related diseases.

Synthesis of novel 4-substituted isatin Schiff base derivatives as potential autophagy inducers and evaluation of their antitumour activity.

Induction of autophagic death in cancer cells is one of the promising strategies for the development of anti-cancer therapeutics. In the present study, we designed and synthesized a series of isatin Schiff base derivatives containing thioether structures. After discovering the highly active target compound H13 (IC50 = 4.83 µM) based on in vitro antiproliferation, we also found it had a high safety against normal cells HEK293 with CC50 of 69.01 µM, indicating a sufficient therapeutic window. In addition, to provide reference for subsequent studies, a model was successfully constructed by Sybyl software. Preliminary mechanistic studies suggested that H13-induced apoptosis may be closely related to ROS accumulation and mitochondrial dysfunction. Subsequent studies revealed that H13 inhibited cell proliferation by inducing cellular autophagy mainly through blocking signal of the PI3K/AKT/mTOR pathway. Altogether, these results suggested that H13 was potentially valuable as a lead compound.

Primary and Recurrent Intraosseous Adenoid Cystic Carcinoma-Analysis of Two Cases and Literature Review.

Adenoid cystic carcinoma (ACC) is a rare malignant tumor that mostly occurs in minor glands, especially in the palate. Intraosseous adenoid cystic carcinoma (IACC) is rarer. There is no clear conclusion on the clinical, radiologic and pathological characteristics of IACC because of few reported IACC cases, leading to insufficient understanding of IACC. We reviewed 52 previous reports of primary IACC (PIACC) and analyzed the clinical features of those patients involved, attempting to provide a better understanding of PIACC. Moreover, we present a case of primary PIACC and a case of recurrent IACC (RIACC). The two patients showed similarities in clinical and pathological results, along with slight differences in radiological and immunohistochemical results. The patient of case 1 seemed to display a worse prognosis, which can only be proved after long term follow-up.

Periostin-targeted SDSSD peptide decorated calcium phosphate nanocomposites incorporation with simvastatin for osteoporosis treatment.

The limited options of anabolic drugs restrict their application potential in osteoporosis treatment, despite their theoretical superiority in therapeutic efficacy over antiresorptive drugs. As a prevailing strategy, nano-delivery systems could offer a wider choice of anabolic drugs. In this study, calcium phosphate nanocomposites incorporated with simvastatin (Sim) with periostin-targeting ability were designed and prepared for osteoporosis treatment. Carboxymethyl dextran (CMD) as an anionic and hydrophilic dextran derivative was used to stabilize CaP. In addition, periosteum-targeted peptide (SDSSD) was further grafted on CMD to achieve the bone targeting function. In a one-step coordination assembly strategy, hydrophobic anabolic agent Sim and SDSSD-CMD graft (SDSSD-CMD) were incorporated into the CaP nanoparticles forming SDSSD@CaP/Sim nanocomposites. The resulting SDSSD@CaP/Sim possesses uniform size, great short-term stability and excellent biocompatibility. Moreover, SDSSD@CaP/Sim exhibited a reduced release rate of Sim and showed slow-release behaviour. As anticipated, the nanocomposites exhibited bone bonding capacity in both cellular and animal studies. Besides, SDSSD@CaP/Sim achieved obviously enhanced osteoporosis treatment effect compared to direct injection of Simin vivo. Therefore, our findings highlight the potential of SDSSD-incorporated and CaP-based nanocomposites as a viable strategy to enhance the therapeutic efficacy of anabolic drugs for osteoporosis treatment.

Combination of engineering the substrate and Ca2+ binding domains of heparinase I to improve the catalytic activity.

Heparinase I (EC 4.2.2.7), is an enzyme that cleaves heparin, showing great potential for eco-friendly production of low molecular weight heparin (LMWH). However, owing to its poor catalytic activity and thermal stability, the industrial application of heparinase I has been severely hindered. To improve the catalytic activity, we proposed to engineer both the substrate and Ca2+ binding domains of heparinase I. Several heparinases I from different organisms were selected for multiple sequence alignment and molecular docking to screen the key residues in the binding domain. Nine single-point mutations were selected to enhance the catalytic activity of heparinase I. Among them, T250D was the most highly active one, whereas mutations around Ca2+ binding domain yielded two active mutants. Mutant D152S/R244K/T250D with significantly increased catalytic activity was obtained by combined mutation. The catalytic efficiency of the mutant was 118,875.8 min-1·µM-1, which was improved 5.26 times. Molecular modeling revealed that the improved activity and stability of the mutants were probably attributed to the formation of new hydrogen bonds. The highly active mutant had great potential applications in industry and the strategy could be used to improve the performance of other enzymes.

HighlightsImproved catalytic activity of heparinase I by engineering the binding domains of substrate and Ca²⁺.The mutant D152S/R244K/T250D showed the highest catalytic performance.The increased hydrogen bonds attribute to the increased activity.

Giant Mandibular Ameloblastoma with Rare Hypercalcemia: A Case Report and Literature Review.

Ameloblastoma is the most common benign odontogenic tumor with local invasion and high recurrence, which generally occurs in the jaw bones. Hypercalcemia is a common paraneoplastic syndrome that is commonly observed in patients with malignancies but rarely encountered in patients with benign tumors. Thus far, not many cases of ameloblastoma with hypercalcemia have been reported, and the pathogenic mechanism has not been studied in depth. This paper presents a case report of a 26-year-old male diagnosed with giant ameloblastoma of the mandible, accompanied by rare hypercalcemia. Additionally, a review of the relevant literature is conducted. This patient initially underwent marsupialization, yet this treatment was not effective, which indicated that the selection of the appropriate operation is of prime importance for improving the prognosis of patients with ameloblastoma. The tumor not only failed to shrink but gradually increased in size, accompanied by multiple complications including hypercalcemia, renal dysfunction, anemia, and cachexia. Due to the contradiction between the necessity of tumor resection and the patient's poor systemic condition, we implemented a multi-disciplinary team (MDT) meeting to better evaluate this patient's condition and design an individualized treatment strategy. The patient subsequently received a variety of interventions to improve the general conditions until he could tolerate surgery, and finally underwent the successful resection of giant ameloblastoma and reconstruction with vascularized fibular flap. No tumor recurrence or distance metastasis was observed during 5 years of follow-up. Additionally, the absence of hypercalcemia recurrence was also noted.

Visualizing Single-Nucleotide Variations in a Nuclear Genome Using Colocalization of Dual-Engineered CRISPR Probes.

Direct visualization of single-nucleotide variation (SNV) in single cells is of great importance for understanding the spatial organization of genomes and their relationship with cell phenotypes. Herein, we developed a new strategy for visualizing SNVs in a nuclear genome using colocalization of dual-engineered CRISPR probes (CoDEC). By engineering the structure of sgRNA, we incorporated a hairpin in the spacer domain for improving SNV recognition specificity and a loop in the nonfunctional domain for localized signal amplification. Using guide probe-based colocalization strategy, we can successfully distinguish on-target true positive signals from the off-target false positives with high accuracy. Comparing with a proximity ligation-based assay (CasPLA), the probe colocalization strategy extended applicable target gene sites (the distance between two designed probes can be extended to around 200nt) and improved detection efficiency. This newly developed method provides a facile way for studying in situ information on SNVs in individual cells for basic research and clinical applications with single-molecule and single-nucleotide resolutions.

Exposure to a real traffic environment impairs brain cognition in aged mice.

Traffic-related air pollution (TRAP) has been a common public health problem, which is associated with central nervous system dysfunction according to large-scale epidemiological studies. Current studies are mostly limited to artificial laboratory exposure environments and specific genetic mechanisms remain unclear. Therefore, we chose a real-world transportation environment to expose aged mice, transporting them from the laboratory to a 1-m-high dry platform inside the campus and tunnel, and the mice were exposed daily from 7 a.m. to 7 p.m. for 2, 4 and 12 weeks respectively. Compared with the control group (in campus), the memory function of mice in the experimental group (in tunnel) was significantly impaired in the Morris water maze test. TRAP exposure increased the number of activated microglia in the hippocampal DG, CA1, CA3 regions and dorsolateral prefrontal cortex (dPFC). And neuroinflammation and oxidative stress levels were up-regulated in both hippocampus and dPFC of aged mice. By screening the risk genes of Alzheimer's disease, we found the mRNA and protein levels of ABCA7 were down-regulated and those of PYK2 were up-regulated. The DNA methylation ratios increased in four CpG sites of abca7 promoter region and decreased in one CpG site of pyk2 promoter region, which were consistent with the altered expression of ABCA7 and PYK2. In conclusion, exposure to the real traffic environment impaired memory function and enhanced neuroinflammation and oxidative stress responses, which could be relevant to the altered expression and DNA methylation levels of ABCA7 and PYK2. Our work provides a new and promising understanding of the pathological mechanisms of cognitive impairment caused by traffic-related air pollution.

Low-stray-light gratings fabricated with scanning exposure method based on Lloyd's mirror for a high-contrast near-eye display in augmented reality.

The stray light of gratings lowers the image contrast of augmented reality display devices based on lightguide gratings. We propose to reduce the stray light of gratings fabricated with the scanning exposure method in a Lloyd's mirror interferometer setup. The photoresist-coated substrate is moved in the longitudinal direction parallel to the exposure interference fringes during exposure to average out the laser speckle-induced noise. A phase locking module is designed to compensate for the unwanted lateral displacement caused by the straightness error and vibration of the translation stage. The stability and accuracy of phase locking in the Lloyd's mirror interferometer are analyzed with control system theory. Low-stray-light lightguide gratings were fabricated successfully. The stray light level was decreased by more than 50%, and the imaging contrast was increased from 65% to 85%.

Ammonia-Oxidizing Archaea (AOA) Play with Ammonia-Oxidizing Bacteria (AOB) in Nitrogen Removal from Wastewater.

An increase in the number of publications in recent years indicates that besides ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal from wastewater, gaining wide attention in the wastewater engineering field. This paper reviews the current knowledge on AOA and AOB involved in wastewater treatment systems and summarises the environmental factors affecting AOA and AOB. Current findings reveal that AOA have stronger environmental adaptability compared with AOB under extreme environmental conditions (such as low temperature and low oxygen level). However, there is still little information on the cooperation and competition relationship between AOA and AOB, and other microbes related to nitrogen removal, which needs further exploration. Furthermore, future studies are proposed to develop novel nitrogen removal processes dominated by AOA by parameter optimization.

Mode detection of misaligned orbital angular momentum beams based on convolutional neural network.

The utilization of beam-carrying orbital angular momentum (OAM) for free-space optical (FSO) communication can increase channel capacity. However, the misalignment of the beam is an effect that must be mitigated in FSO communication systems. Due to the robustness of deep learning technology in pattern recognition, a neural network structure is proposed and improved to mitigate the effect of misalignment error. First, compared with the simple convolutional neural network proposed, data augmentation is adopted in the training. Then, a view-pooling layer is added after the convolutional layer. This layer can longitudinally compress feature maps from multiple receiving angles. In order to verify the performance of the proposed method, related experiments are reported in this paper. It can be seen from the results that when the tilt angle is less than 35°, the accuracy of OAM mode detection is above 99%, 93%, and 88%, respectively, corresponding to the condition of weak (Cn2=1×10-15 m-2/3), medium (Cn2=1×10-14 m-2/3) and strong (Cn2=1×10-13 m-2/3) turbulence.

Correction: Li et al. Fabrication of Poly Dopamine@poly (Lactic Acid-Co-Glycolic Acid) Nanohybrids for Cancer Therapy via a Triple Collaboration Strategy. Nanomaterials 2023, 13, 1447.

The authors regret that, in the published article [...].

Heparinase III with High Activity and Stability: Heterologous Expression, Biochemical Characterization, and Application in Depolymerization of Heparin.

A novel heparinase III from Pedobacter schmidteae (PsHep-III) with high activity and good stability was successfully cloned, expressed, and characterized. PsHep-III displayed the highest specific activity ever reported of 192.8 U mg-1 using heparin as the substrate. It was stable at 25 °C with a half-life of 323 h in an aqueous solution. PsHep-III was employed for the depolymerization of heparin, and the enzymatic hydrolyzed products were analyzed with gel permeation chromatography and high-performance liquid chromatography. PsHep-III can break glycosidic bonds in heparin like →4]GlcNAc/GlcNAc6S/GlcNS/GlcNS6S/GlcN/GlcN6S(1 → 4)ΔUA/ΔUA2S[1 → and efficiently digest heparin into seven disaccharides including N-acetylated, N-sulfated, and N-unsubstituted modification, with molecular masses of 503, 605, 563, 563, 665, 360, and 563 Da, respectively. These results indicated that PsHep-III with broad substrate specificity could be combined with heparinase I to overcome the low selectivity at the N-acetylated modification binding sites of heparinase I. This work will contribute to the application of PsHep-III for characterizing heparin and producing low-molecular-weight heparin effectively.

Study on synergistic mechanism of molybdenum disulfide/sodium carboxymethyl cellulose composite nanofiber mats for photothermal/photodynamic antibacterial treatment.

Innovative antibacterial therapies using nanomaterials, such as photothermal (PTT) and photodynamic (PDT) treatments, have been developed for treating wound infections. However, creating secure wound dressings with these therapies faces challenges. The primary focus of this study is to prepare an antibacterial nanofiber dressing that effectively incorporates stable loads of functional nanoparticles and demonstrates an efficient synergistic effect between PTT and PDT. Herein, a composite nanofiber mat was fabricated, integrating spherical molybdenum disulfide (MoS2) nanoparticles. MoS2 was deposited onto polylactic acid (PLA) nanofiber mats using vacuum filtration, which was further stabilized by sodium carboxymethyl cellulose (CMC) adhesion and glutaraldehyde (GA) cross-linking. The composite nanofibers demonstrated synergistic antibacterial effects under NIR light irradiation, and the underlying mechanism was explored. They induce bacterial membrane permeability, protein leakage, and intracellular reactive oxygen species (ROS) elevation, ultimately leading to >95 % antibacterial activity against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli), which is higher than that of single thermotherapy (almost no antibacterial activity) or ROS therapy (about 80 %). In addition, the composite nanofiber mats exhibited promotion effects on infected wound healing in vivo. This study demonstrates the great prospects of composite nanofiber dressings in clinical treatment of bacterial-infected wounds.

OXPHOS-targeted nanoparticles for boosting photodynamic therapy against hypoxia tumor.

Hypoxia as an inherent feature in tumors is firmly associated with unsatisfactory clinical outcomes of photodynamic therapy (PDT) since the lack of oxygen leads to ineffective reactive oxygen species (ROS) productivity for tumor eradication. In this study, an oxidative phosphorylation (OXPHOS) targeting nanoplatform was fabricated to alleviate hypoxia and enhance the performance of PDT by encapsulating IR780 and OXPHOS inhibitor atovaquone (ATO) in triphenylphosphine (TPP) modified poly(ethylene glycol) methyl ether-block-poly(L-lactide-co-glycolide) (mPEG-PLGA) nanocarriers (TNPs/IA). ATO by interrupting the electron transfer in OXPHOS could suppress mitochondrial respiration of tumor cells, economising on oxygen for the generation of ROS. Benefiting from the mitochondrial targeting function of TPP, ATO was directly delivered to its site of action to obtain highlighted effect at a lower dosage. Furthermore, positioning the photosensitizer IR780 to mitochondria, a more vulnerable organelle to ROS, was a promising method to attenuate the spatiotemporal limitation of ROS caused by its short half-life and narrow diffusion radius. As a result, TNPs/IA exhibited accurate subcellular localization, lead to the collapse of ATP production by damaging mitochondrion and elicited significant antitumor efficacy via oxygen-augmented PDT in the HeLa subcutaneous xenograft model. Overall, TNPs/IA was a potential strategy in photodynamic eradication of tumors.

Serum Protein Fishing for Machine Learning-Boosted Diagnostic Classification of Small Nodules of Lung.

Diagnosis of benign and malignant small nodules of the lung remains an unmet clinical problem which is leading to serious false positive diagnosis and overtreatment. Here, we developed a serum protein fishing-based spectral library (ProteoFish) for data independent acquisition analysis and a machine learning-boosted protein panel for diagnosis of early Non-Small Cell Lung Cancer (NSCLC) and classification of benign and malignant small nodules. We established an extensive NSCLC protein bank consisting of 297 clinical subjects. After testing 5 feature extraction algorithms and six machine learning models, the Lasso algorithm for a 15-key protein panel selection and Random Forest was chosen for diagnostic classification. Our random forest classifier achieved 91.38% accuracy in benign and malignant small nodule diagnosis, which is superior to the existing clinical assays. By integrating with machine learning, the 15-key protein panel may provide insights to multiplexed protein biomarker fishing from serum for facile cancer screening and tackling the current clinical challenge in prospective diagnostic classification of small nodules of the lung.

[Mechanism on differential gene expression and heterosis formation].

Despite the rediscovery of heterosis about a century ago and the suggestion of various genetic models to explain this phenomenon, little consensus has yet been reached about the genetic basis of heterosis. Following the genome organization variation and gene effects, an understanding of gene differential expression in hybrids and its parents provides a new opportunity to speculate on mechanisms that might lead to heterosis. Investigation on allele-specific gene expression in hybrid and gene differential expression between hybrids and its parents might contribute to improve our understanding of the molecular basis of heterosis and eventually guide breeding practices. In this review, we discussed the recent researches on allelic-specific expression in hybrid which was frequently observed in recent studies and analyzed its regulatory mechanism. All possible modes of gene action, including additivity, high- and low-parent dominance, underdominance, and over-dominance, were observed when investigating gene differential expression between hybrids and its parents. Data from transcriptomic studies screened several heterosis-associated genes and highlighted the importance of certain key biochemical pathways that may prove to be quintessential for the manifestation of heterosis. So far, no uniform global expression pat-terns were observed in these gene expression studies. Most heterosis-associated gene expression analyses have not revealed a predominant functional category to which differentially expressed genes belong. However, these gene expression profiling studies represent a first step towards the definition of the complex gene expression networks that might be relevant in the context of heterosis. New technique on gene expression profile and advancements in bioinformatics will facilitate our understanding of the genetic basis of heterosis at the gene-expression level.

Effects of different doses of lithium on the central nervous system in the rat valproic acid model of autism.

Epidemiological studies have shown that low doses of lithium in the environment can have beneficial effects on mental health. Autism spectrum disorder, a neurodevelopmental disorder in which patients exhibit abnormal behaviors, pharmacological interventions usually relied on a range of psychotropic medications. However, such medications often produce severe side effects or are ineffective in symptoms. Finding alternative ways to improve abnormal behaviors in individuals with autism are warranted, in which case lithium may be a relatively safe and effective medication. Lithium salt therapy is used to treat a variety of neuropsychiatric disorders and has neuroprotective effects. In this study, we investigated the effects of different doses of lithium on neurobehavioural disorders using the rat model of autism established by valproic acid (VPA) injection. Lithium was observed to have an ameliorative effect on the social cognitive, social memory and anxiety levels in the rat model of autism. Immunofluorescence staining showed that subchronic LiCl administration (1.0 mmol/kg) significantly reduced the number of Iba-1 positive cells in the CA1 region of the hippocampus in VPA group and brought it close to the levels of control group. Significantly lower levels of the pro-inflammatory marker IL-6 were observed in the hippocampus and serum after lithium treatment. In addition, the lithium treatment increased the levels of H3K9 acetylation in the hippocampus of VPA-exposed rats. The results showed a defensive effect of environment-related lithium exposure doses on neurobehavioural deficits in the rat valproic acid model of autism, suggesting that it may be a potential drug for the treatment of autism.

Fabrication of Poly Dopamine@poly (Lactic Acid-Co-Glycolic Acid) Nanohybrids for Cancer Therapy via a Triple Collaboration Strategy.

Breast cancer is a common malignant tumor among women and has a higher risk of early recurrence, distant metastasis, and poor prognosis. Systemic chemotherapy is still the most widely used treatment for patients with breast cancer. However, unavoidable side effects and acquired resistance severely limit the efficacy of treatment. The multi-drug combination strategy has been identified as an effective tumor therapy pattern. In this investigation, we demonstrated a triple collaboration strategy of incorporating the chemotherapeutic drug doxorubicin (DOX) and anti-angiogenesis agent combretastatin A4 (CA4) into poly(lactic-co-glycolic acid) (PLGA)-based co-delivery nanohybrids (PLGA/DC NPs) via an improved double emulsion technology, and then a polydopamine (PDA) was modified on the PLGA/DC NPs' surface through the self-assembly method for photothermal therapy. In the drug-loaded PDA co-delivery nanohybrids (PDA@PLGA/DC NPs), DOX and CA4 synergistically induced tumor cell apoptosis by interfering with DNA replication and inhibiting tumor angiogenesis, respectively. The controlled release of DOX and CA4-loaded PDA@PLGA NPs in the tumor region was pH dependent and triggered by the hyperthermia generated via laser irradiation. Both in vitro and in vivo studies demonstrated that PDA@PLGA/DC NPs enhanced cytotoxicity under laser irradiation, and combined therapeutic effects were obtained when DOX, CA4, and PDA were integrated into a single nanoplatform. Taken together, the present study demonstrates a nanoplatform for combined DOX, CA4, and photothermal therapy, providing a potentially promising strategy for the synergistic treatment of breast cancer.