Deep learning enhancing guide RNA design for CRISPR/Cas12a-based diagnostics.

Rapid and accurate diagnostic tests are fundamental for improving patient outcomes and combating infectious diseases. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas12a-based detection system has emerged as a promising solution for on-site nucleic acid testing. Nonetheless, the effective design of CRISPR RNA (crRNA) for Cas12a-based detection remains challenging and time-consuming. In this study, we propose an enhanced crRNA design system with deep learning for Cas12a-mediated diagnostics, referred to as EasyDesign. This system employs an optimized convolutional neural network (CNN) prediction model, trained on a comprehensive data set comprising 11,496 experimentally validated Cas12a-based detection cases, encompassing a wide spectrum of prevalent pathogens, achieving Spearman's ρ = 0.812. We further assessed the model performance in crRNA design for four pathogens not included in the training data: Monkeypox Virus, Enterovirus 71, Coxsackievirus A16, and Listeria monocytogenes. The results demonstrated superior prediction performance compared to the traditional experiment screening. Furthermore, we have developed an interactive web server (https://crispr.zhejianglab.com/) that integrates EasyDesign with recombinase polymerase amplification (RPA) primer design, enhancing user accessibility. Through this web-based platform, we successfully designed optimal Cas12a crRNAs for six human papillomavirus (HPV) subtypes. Remarkably, all the top five predicted crRNAs for each HPV subtype exhibited robust fluorescent signals in CRISPR assays, thereby suggesting that the platform could effectively facilitate clinical sample testing. In conclusion, EasyDesign offers a rapid and reliable solution for crRNA design in Cas12a-based detection, which could serve as a valuable tool for clinical diagnostics and research applications.

Comparison of the therapeutic effects of three minimally invasive approaches for laparoscopic cholecystectomy combined with common bile duct exploration-- a 5-year retrospective analysis.

OBJECTIVE: The aim of this retrospective study was to explore the indications for three minimally invasive approaches-T-tube external drainage, double J-tube internal drainage, and primary closure-in laparoscopic cholecystectomy combined with common bile duct exploration. METHODS: Three hundred eighty-nine patients with common bile duct stones who were treated at the Second People's Hospital of Hefei between February 2018 and January 2023 were retrospectively included. Patients were divided into three groups based on the surgical approach used: the T-tube drainage group, the double J-tube internal drainage group, and the primary closure group. General data, including sex, age, and BMI, were compared among the three groups preoperatively. Surgical time, length of hospital stay, pain scores, and other aspects were compared among the three groups. Differences in liver function, inflammatory factors, and postoperative complications were also compared among the three groups. RESULTS: There were no significant differences among the three groups in terms of sex, age, BMI, or other general data preoperatively (P > 0.05). There were significant differences between the primary closure group and the T-tube drainage group in terms of surgical time and pain scores (P < 0.05). The primary closure group and double J-tube drainage group differed from the T-tube drainage group in terms of length of hospital stay, hospitalization expenses, and time to passage of gas (P <0.05). Among the three groups, there were no statistically significant differences in inflammatory factors or liver function, TBIL, AST, ALP, ALT, GGT, CRP, or IL-6, before surgery or on the third day after surgery (P > 0.05). However, on the third day after surgery, liver function in all three groups was significantly lower than that before surgery (P<0.05). In all three groups, the levels of CRP and IL-6 were significantly lower than their preoperative levels. The primary closure group had significantly lower CRP and IL-6 levels than did the T-tube drainage group (P < 0.05). The primary closure group differed from the T-tube drainage group in terms of the incidences of bile leakage and electrolyte imbalance (P < 0.05). The double J-tube drainage group differed from the T-tube drainage group in terms of the tube dislodgement rate (P < 0.05). CONCLUSION: Although primary closure of the bile ducts has clear advantages in terms of length of hospital stay and hospitalization expenses, it is associated with a higher incidence of postoperative complications, particularly bile leakage. T-tube drainage and double J-tube internal drainage also have their own advantages. The specific surgical approach should be selected based on the preoperative assessment, indications, and other factors to reduce the occurrence of postoperative complications.

A Cas12a-based fluorescent microfluidic system for rapid on-site human papillomavirus diagnostics.

Persistent infection with human papillomavirus (HPV) is the leading cause of cervical cancer, and early diagnosis is crucial for clinical management. However, the easy and rapid on-site diagnostic for HPV genotyping remains challenging. Here, we develop a Cas12a-based fluorescent microfluidic detection system for diagnosing six HPV subtypes (HPV6, HPV11, HPV16, HPV18, HPV31, and HPV33). A panel of crRNAs and recombinase polymerase amplification (RPA) primers targeting the HPV L1 gene was screened for sensitive and specific detection. Furthermore, a one-pot RPA reaction was developed to amplify the six HPV subtypes without cross-reactivity. For on-site detection, we integrated the RPA-Cas12a detection into a microfluidic device, enabling the detection of processed clinical samples within 35 minutes. The assay was validated using 112 clinical swab samples and obtained consistent results with the qPCR assay, with a concordance rate of 99.1%. Overall, our diagnostic method offers a rapid, sensitive, and easy-to-use on-site assay for detecting HPV genotypes and holds promise for improving cervical cancer screening and prevention. KEY POINTS: • The Cas12a-based fluorescent microfluidic detection system for the diagnosis of six HPV subtypes. • A one-pot RPA reaction for amplifying the six HPV subtypes without cross-reactivity. • The RPA-Cas12a-microfluidic system provides results within 35 minutes for on-site detection.

A highly sensitively "off-on-off" fluorescence probe for detection of aluminum ion and water as well as application in Chinese Baijiu.

Developing highly sensitive fluorescent probe for Al3+ and H2O detection is highly desirable, due to aluminum toxicity poses a significant threat to public health. On the other hand, the determination of water content holds immense significance in a wide range of fields such as food processing, pharmaceutical manufacturing. In this paper, a novel acylhydrazone-based fluorescent probe P was successfully synthesized and characterized for the sequential detection of Al3+ and water in alcohols. The probe P exhibited a remarkable "turn-on" response towards Al3+ by emitting yellow fluorescence at 567 nm, with high selectivity and large Stokes shift (147 nm). Meanwhile, the in situ formed P-Al3+ complex demonstrated significant solvatofluorochromic characteristic, which could be utilized as a second probe for detecting water via fluorescence quenching with low detection limit in alcohols (0.008%, methanol; 0.013%, ethanol; 0.013%, isopropanol; 0.037%, n-butanol; vol.%) and acetonitrile (0.072%, vol.%). Moreover, the P-Al3+ complex was able to detect the alcoholic strength of Chinese Baijiu without the interference of other alcohols, providing an excellent recovery rate (100.0-107.0%). Different Chinese Baijius, with various alcoholic strength, could be distinguished by simple test strips. Furthermore, the P-Al3+ complex could also analyze the water content in organic solvents .

Cinnamaldehyde-modified chitosan hybrid nanoparticles for DOX delivering to produce synergistic anti-tumor effects.

Cancer cells are under oxidative stress associated with the increased generation of reactive oxygen species (ROS). Therefore, increasing the oxidative stress of tumor cells by delivering ROS generators is an effective strategy to induce apoptosis of cancer cells. Herein, we reported a hybrid nanoparticle based on lactobionic acid (LA) modified chitosan and cinnamaldehyde (CA) modified chitosan, which possesses both active tumor-targeting ability and ROS regulation ability, in order to have a synergistic effect with the anti-tumor drug doxorubicin (DOX). LA can improve the tumor-targeting ability and cellular accumulation of these nanoparticles, and CA can induce apoptotic cell death through ROS generation, mitochondrial permeability transition and caspase activation. The particle size and distribution as well as drug release profiles of these nanoparticles were observed. In vitro and in vivo antitumor studies demonstrated that the hybrid nanoparticles show a significant synergistic antitumor effect. Thus, we anticipate that the hybrid nanoparticles have promising potential as an anticancer drug carrier.

Protective Effects of Lactobacillus plantarum Lac16 on Clostridium perfringens Infection-Associated Injury in IPEC-J2 Cells.

Clostridium perfringens (C. perfringens) causes intestinal injury through overgrowth and the secretion of multiple toxins, leading to diarrhea and necrotic enteritis in animals, including pigs, chickens, and sheep. This study aimed to investigate the protective effects of Lactobacillus plantarum (L. plantarum) Lac16 on C. perfringens infection-associated injury in intestinal porcine epithelial cell line (IPEC-J2). The results showed that L. plantarum Lac16 significantly inhibited the growth of C. perfringens, which was accompanied by a decrease in pH levels. In addition, L. plantarum Lac16 significantly elevated the mRNA expression levels of host defense peptides (HDPs) in IPEC-J2 cells, decreased the adhesion of C. perfringens to IPEC-J2 cells, and attenuated C. perfringens-induced cellular cytotoxicity and intestinal barrier damage. Furthermore, L. plantarum Lac16 significantly suppressed C. perfringens-induced gene expressions of proinflammatory cytokines and pattern recognition receptors (PRRs) in IPEC-J2 cells. Moreover, L. plantarum Lac16 preincubation effectively inhibited the phosphorylation of p65 caused by C. perfringens infection. Collectively, probiotic L. plantarum Lac16 exerts protective effects against C. perfringens infection-associated injury in IPEC-J2 cells.

Effects of Bacillus amyloliquefaciens Instead of Antibiotics on Growth Performance, Intestinal Health, and Intestinal Microbiota of Broilers.

The aim of this study was to evaluate the dietary effects of Bacillus amyloliquefaciens SC06 (SC06) instead of antibiotics on the growth performance, intestinal health, and intestinal microbiota of broilers. A total of 360 30-day-old Lingnan yellow broilers were randomly allocated into two groups with six replicates per group (30 birds per replicate). The broilers were fed either a non-supplemented diet or a diet supplemented with 108 colony-forming units lyophilized SC06 per kilogram feed for 30 days. Results showed that SC06 supplementation had no effect on the growth performance compared with that of the control group. SC06 treatment significantly (P <0.05) increased the total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD) activity in the liver, and the activities of trypsin, α-amylase (AMS), and Na+K+-ATPase in the ileum, whereas it decreased (P < 0.05) lipase, gamma glutamyl transpeptidase (γ-GT), and maltase activities in the ileum. Meanwhile, SC06 treatment also improved the immune function indicated by the significantly (P < 0.05) increased anti-inflammatory cytokine [interleukin (IL)-10] level and the decreased (P < 0.05) pro-inflammatory cytokine [IL-6 and tumor necrosis factor (TNF)-α] levels in the ileum. Furthermore, we also found that SC06 enhanced the intestinal epithelial intercellular integrity (tight junction and adhesion belt) in the ileum. Microbial analysis showed that SC06 mainly increased the alpha diversity indices in the jejunum, ileum, and cecum. SC06 treatment also significantly (P < 0.05) increased the abundances of Bacteroidetes, Bacteroidales, Bacteroides, Fusobacteria, Clostridiaceae, and Veillonellaceae in the cecum and simultaneously decreased the abundances of Planococcaceae in the duodenum, Microbacteriaceae in the jejunum, and Lachnospiraceae, [Ruminococcus] and Ruminococcus in cecum. In conclusion, these results suggested that B. amyloliquefaciens instead of antibiotics showed a potential beneficial effect on the intestinal health of broilers.

Saccharomyces boulardii attenuates inflammatory response induced by Clostridium perfringens via TLR4/TLR15-MyD8 pathway in HD11 avian macrophages.

Macrophages are professional phagocytic cells that play a critical role in initiating immune responses by presenting antigen and phagocytic clearance. The macrophages can be targeted for immunomodulation by beneficial microbes, such as probiotics. The aim of this study is to investigate the protective effect of Saccharomyces boulardii against Clostridium perfringens infection in avian macrophage cell line HD11. In this study, HD11 macrophages were prestimulated with S. boulardii for 6 h and then infected with C. perfringens for 3 h. Results showed that S. boulardii enhanced phagocytosis and bactericidal capacity against C. perfringens by HD11 cells. The S. boulardii effectively promoted the mRNA expression of CD80, CD83, and CD197 cell-surface molecules in C. perfringens-infected HD11 cells. Moreover, we found that prestimulation with S. boulardii reduced the mRNA expression of CD40, toll-like receptor [TLR] 4, and TLR15 induced by C. perfringens and thereby downregulated the mRNA expression of myeloid differentiation primary response 88, TNF receptor associated factor 6, nuclear factor kappa-B p65 subunit, and c-Jun N-terminal kinase genes in HD11 cells. The upregulation of cytokines (interleukin [IL]-6, tumor necrosis factor alpha, and IL-10) and inducible nitric oxide synthase mRNA expression in C. perfringens-infected HD11 cells were noticeably inhibited by S. boulardii pretreatment. Conclusively, these results might provide a new insight into the role of S. boulardii in regulating avian immune defense against C. perfringens invasion and immune escape.

Stereo and region-selective biosynthesis of two new dihydroartemisinic acid glycosides by suspension-cultured cells of Artemisia annua.

BACKGROUND: The system of plant-cultured cells is one of the optimal systems to investigate biosynthesis pathway and their bioactive intermediates. OBJECTIVE: To study the biosynthesis of dihydroartemisinic acid (1) by suspension-cultured cells of Artemisia annua. MATERIALS AND METHODS: Substrate (compound 1) was administered into the suspension-cultured cells of A. annua and co-cultured for 2 days. The methanol extract was separated on various column chromatography methods and the structures of two biosynthesis products were elucidated based on the analysis of (1)H NMR, (13)C NMR, 2D NMR, and ESI-MS. Time-course curve was also established. Furthermore, in vitro antitumor activities of compounds 1-3 against HepG2, K562, and A549 cell lines were evaluated by MTT assay. RESULTS: Two new compounds were obtained, namely 3α-hydroxy-dihydroartemisinic acid-α-D-glucopyranosyl ester (2) and 15-hydroxy-cadin-4-en-12-oic acid-ß-d-glucopyranosyl ester (3). The results demonstrated that the cultured cells of A. annua possessed the abilities to stereo-selective hydroxylate and region-selective glycosylate sesquiterpene compounds in a highly efficient manner. Inhibitory effects of compounds 1-3 on proliferation of HepG2, K562, and A549 cell lines in vitro were also investigated. CONCLUSION: Two new dihydroartemisinic acid glycosides were obtained by stereo- and region-selective biosynthesis with cultured cells of A. annua.