SCREE: a comprehensive pipeline for single-cell multi-modal CRISPR screen data processing and analysis.

Single-cell CRISPR screens have been widely used to investigate gene regulatory circuits in diverse biological systems. The recent development of single-cell CRISPR screens has enabled multimodal profiling of perturbed cells with both gene expression, chromatin accessibility and protein levels. However, current methods cannot meet the analysis requirements of different types of data and have limited functions. Here, we introduce Single-cell CRISPR screens data analysEs and perturbation modEling (SCREE) as a comprehensive and flexible pipeline to facilitate the analyses of various types of single-cell CRISPR screens data. SCREE performs read alignment, sgRNA assignment, quality control, clustering and visualization, perturbation enrichment evaluation, perturbation efficiency modeling, gene regulatory score calculation and functional analyses of perturbations for single-cell CRISPR screens with both RNA, ATAC and multimodal readout. SCREE is available at https://github.com/wanglabtongji/SCREE.

Single-cell gene regulation network inference by large-scale data integration.

Single-cell ATAC-seq (scATAC-seq) has proven to be a state-of-art approach to investigating gene regulation at the single-cell level. However, existing methods cannot precisely uncover cell-type-specific binding of transcription regulators (TRs) and construct gene regulation networks (GRNs) in single-cell. ChIP-seq has been widely used to profile TR binding sites in the past decades. Here, we developed SCRIP, an integrative method to infer single-cell TR activity and targets based on the integration of scATAC-seq and a large-scale TR ChIP-seq reference. Our method showed improved performance in evaluating TR binding activity compared to the existing motif-based methods and reached a higher consistency with matched TR expressions. Besides, our method enables identifying TR target genes as well as building GRNs at the single-cell resolution based on a regulatory potential model. We demonstrate SCRIP's utility in accurate cell-type clustering, lineage tracing, and inferring cell-type-specific GRNs in multiple biological systems. SCRIP is freely available at https://github.com/wanglabtongji/SCRIP.

The therapeutic effect of Yinqiaosan decoction against influenza A virus infection by regulating T cell receptor signaling pathway.

Background: Yinqiaosan decoction (YQSD), a traditional Chinese medicinal recipe, has been employed to treat influenza in China for approximately 300 years. Objective: Our study aimed to explore the mechanisms of YQSD against influenza via in vivo and in vitro experimental studies. Study design: and methods UHPLC-Q-TOF-MS/MS was utilized to examine the substances of the YQSD. The chemical components of YQSD detected by UHPLC-Q-TOF-MS/MS were used for network pharmacology analysis. The antiviral effect of YQSD in vivo was investigated. The potential mechanisms of YQSD in combating influenza, which were predicted from network pharmacology analysis, were validated in vitro. Results: By use of UHPLC-Q-TOF-MS/MS, 97 compounds were identified from YQSD. Network pharmacology analysis revealed that the therapeutic effect of YQSD against influenza may be associated with the regulation of T cell receptors (TCR) and Phosphoinositide 3-Kinase (PI3K)- protein kinase B (Akt) signaling pathways. Treatment with YQSD significantly prolonged the mean survival time of the mice and reduced lung injury due to the influenza A virus in vivo. It was discovered that YQSD efficiently inhibited the expression of inflammation-related cytokines. Moreover, YQSD has been found to significantly reduce the expression levels of cluster of differentiation 3 (CD3), monocyte chemoattractant protein-1 (MCP-1), and H1N1 virus nucleoprotein (NP), and prevent the decrease of epithelial cadherin (E-cadherin) protein. In addition, YQSD can inhibit the phosphorylation of the zeta chain of T cell receptor-associated protein kinase 70 (ZAP70) and PI3K proteins in vitro. Conclusion: The capacity of YQSD to suppress viral multiplication and inflammatory response by modulating T cell immunity may explain its effect against influenza viral pneumonia, which may involve the regulation of TCR and PI3K signaling pathways.

Unlocking the potential of phenolated kraft lignin as a versatile feed additive.

Lignin, a renewable natural antioxidant and bacteriostat, holds promise as a versatile, cost-effective feed additive. However, traditional industrial lignin faces limitations, including low reactivity, poor uniformity, and unstable properties, necessitating chemical modification. Complex modification methods pose economic and toxicity challenges, so this study adopted a relatively simple alkali-catalyzed phenolization approach, using phenol, catechol, and pyrogallol to modify kraft lignin, and characterized the resulting products using various techniques. Subsequently, their antioxidant, antibacterial, adsorption properties for heavy metal ions and mycotoxins, growth-promoting properties, and antiviral abilities were assessed. The phenolation process led to lignin depolymerization and a notable increase in phenolic hydroxyl content, particularly in pyrogallol-phenolated lignin (Py-L), rising from 3.08 to 4.68 mmol/g. These modified lignins exhibited enhanced antioxidant activity, with over 99 % inhibition against E. coli and S. aureus, and remarkable adsorption capacities for heavy metal ions and mycotoxins. Importantly, Py-L improved the growth performance of mice and reduced influenza mortality. Furthermore, density functional theory calculations elucidated the mechanism behind the enhanced antioxidant properties. This study presents a promising avenue for developing versatile feed additives to address challenges related to animal feed antioxidant supplementation, bacterial control, and growth promotion.

Clinical efficacy of Fufang Yinhua Jiedu (FFYH) granules in mild COVID-19 and its anti-SARS-CoV-2 mechanism by blocking autophagy through inhibiting the AKT/mTOR signaling pathway.

Background: Fufang Yinhua Jiedu (FFYH) granules are recommended for treating coronavirus pneumonia (COVID-19) in China. However, its anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity and clinical efficacy against COVID-19 remain to be confirmed. Aims: Our study aimed to investigate the anti-SARS-CoV-2 effect and potential mechanism of FFYH. Materials and Methods: The activity of FFYH against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was evaluated via cell pathogenic effects, immunoblotting, immunofluorescence staining, and qRT-PCR. The potential mechanism of FFYH against SARS-CoV-2 was investigated by immunoblotting. One head-to-head randomized controlled trial was designed to evaluate the clinical efficacy of FFYH in mild COVID-19. Two hundred patients were randomly recruited to receive either FFYH or LHQW (Lianhua Qingwen) granules. Results: The in vitro results indicated that FFYH effectively inhibited SARS-CoV-2 replication by suppressing CPE and decreasing viral RNA and protein expression. A time-of-drug-addition assay confirmed that FFYH mainly targeted the binding and replication stages of the SARS-CoV-2 life cycle. Mechanistic studies revealed that blocking SARS-CoV-2-triggered autophagy may be the primary mechanism by which FFYH protects against SARS-CoV-2 infection by regulating the phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling pathway. Clinical results confirmed that FFYH effectively shortened the recovery time of clinical symptoms and viral nucleic acid negativity, improved abnormal hematology parameters, and controlled excessive cytokine responses in mild COVID-19 patients. Subgroup analysis revealed that FFYH improved the recovery time of clinical symptoms, improved hematological parameters, and controlled excessive cytokine storms to a greater extent in the mild COVID-19 male subgroup, abnormal hematology subgroup, and 32-42-year-old subgroup than in the corresponding LHQW subgroup (P < 0.05). No patients progressed to severe or critical cases. Conclusion: Our results indicate that FFYH not only has good anti-viral activity against SARS-CoV-2 but also has significant efficacy against COVID-19, indicating that FFYH may be a novel complementary option for treating COVID-19.

Application of an Ovate Leaf Shape Model to Evaluate Leaf Bilateral Asymmetry and Calculate Lamina Centroid Location.

Leaf shape is an important leaf trait, with ovate leaves common in many floras. Recently, a new leaf shape model (referred to as the MLRF equation) derived from temperature-dependent bacterial growth was proposed and demonstrated to be valid in describing leaf boundaries of many species with ovate leaf shape. The MLRF model's parameters can provide valuable information of leaf shape, including the ratio of lamina width to length and the lamina centroid location on the lamina length axis. However, the model wasn't tested on a large sample of a single species, thereby limiting its overall evaluation for describing leaf boundaries, for evaluating lamina bilateral asymmetry and for calculating lamina centroid location. In this study, we further test the model using data from two Lauraceae species, Cinnamomum camphora and Machilus leptophylla, with >290 leaves for each species. The equation was found to be credible for describing those shapes, with all adjusted root-mean-square errors (RMSE) smaller than 0.05, indicating that the mean absolute deviation is smaller than 5% of the radius of an assumed circle whose area equals lamina area. It was also found that the larger the extent of lamina asymmetry, the larger the adjusted RMSE, with approximately 50% of unexplained variation by the model accounted for by the lamina asymmetry, implying that this model can help to quantify the leaf bilateral asymmetry in future studies. In addition, there was a significant difference between the two species in their centroid ratio, i.e., the distance from leaf petiole to the point on the lamina length axis associated with leaf maximum width to the leaf maximum length. It was found that a higher centroid ratio does not necessarily lead to a greater investment of mass to leaf petiole relative to lamina, which might depend on the petiole pattern.

A technique system for the measurement, reconstruction and character extraction of rice plant architecture.

This study developed a technique system for the measurement, reconstruction, and trait extraction of rice canopy architectures, which have challenged functional-structural plant modeling for decades and have become the foundation of the design of ideo-plant architectures. The system uses the location-separation-measurement method (LSMM) for the collection of data on the canopy architecture and the analytic geometry method for the reconstruction and visualization of the three-dimensional (3D) digital architecture of the rice plant. It also uses the virtual clipping method for extracting the key traits of the canopy architecture such as the leaf area, inclination, and azimuth distribution in spatial coordinates. To establish the technique system, we developed (i) simple tools to measure the spatial position of the stem axis and azimuth of the leaf midrib and to capture images of tillers and leaves; (ii) computer software programs for extracting data on stem diameter, leaf nodes, and leaf midrib curves from the tiller images and data on leaf length, width, and shape from the leaf images; (iii) a database of digital architectures that stores the measured data and facilitates the reconstruction of the 3D visual architecture and the extraction of architectural traits; and (iv) computation algorithms for virtual clipping to stratify the rice canopy, to extend the stratified surface from the horizontal plane to a general curved surface (including a cylindrical surface), and to implement in silico. Each component of the technique system was quantitatively validated and visually compared to images, and the sensitivity of the virtual clipping algorithms was analyzed. This technique is inexpensive and accurate and provides high throughput for the measurement, reconstruction, and trait extraction of rice canopy architectures. The technique provides a more practical method of data collection to serve functional-structural plant models of rice and for the optimization of rice canopy types. Moreover, the technique can be easily adapted for other cereal crops such as wheat, which has numerous stems and leaves sheltering each other.

Quantitative descriptions of rice plant architecture and their application.

Plant architecture is an important agronomic trait, and improving plant architecture has attracted the attention of scientists for decades, particularly studies to create desirable plant architecture for high grain yields through breeding and culture practices. However, many important structural phenotypic traits still lack quantitative description and modeling on structural-functional relativity. This study defined new architecture indices (AIs) derived from the digitalized plant architecture using the virtual blade method. The influences of varieties and crop management on these indices and the influences of these indices on biomass accumulation were analyzed using field experiment data at two crop growth stages: early and late panicle initiation. The results indicated that the vertical architecture indices (LAI, PH, 90%-DRI, MDI, 90%-LI) were significantly influenced by variety, water, nitrogen management and the interaction of water and nitrogen, and compact architecture indices (H-CI, Q-CI, 90%-LI, 50%-LI) were significantly influenced by nitrogen management and the interaction of variety and water. Furthermore, there were certain trends in the influence of variety, water, and nitrogen management on AIs. Biomass accumulation has a positive linear correlation with vertical architecture indices and has a quadratic correlation with compact architecture indices, respectively. Furthermore, the combination of vertical and compact architecture indices is the indicator for evaluating the effects of plant architecture on biomass accumulation.

Prevalence and seroepidemiology of Haemophilus parasuis in Sichuan province, China.

Haemophilus parasuis, the causative agent of Glässer's disease, has been reported as widespread, but little is known about its epidemiology in the Sichuan province of China. The goal of our research is to reveal the prevalence and distribution of H. parasuis in this area. Sampling and isolation were performed across Sichuan; isolates were processed using serotyping multiplex PCR (serotyping-mPCR) and agar gel diffusion (AGD) for confirmation of serovar identity. This study was carried out from January 2014 to May 2016 and 254 H. parasuis field strains were isolated from 576 clinical samples collected from pigs displaying clinical symptoms. The isolation frequency was 44.10%. Statistically very significant differences of infection incidence were found in three age groups (P < 0.01) and different seasons (P < 0.01). Serovars 5 (25.98%) and 4 (23.62%) were the most prevalent, however, non-typeable isolates accounted for nearly 7.87%. In terms of geographical distribution, serovars 5 and 4 were mostly prevalent in west and east Sichuan. The results confirmed that the combined approach was dependable and revealed the diversity and distribution of serovars in Sichuan province, which is vital for efforts aimed at developing vaccine candidates allowing for the prevention or control of H. parasuis outbreaks.

[HLA-DRB and -DQB allele contribution to narcolepsy susceptibility in Chinese patients with narcolepsy].

OBJECTIVES: To study the association of narcolepsy with HLA class II alleles in Chinese narcoleptic patients. METHODS: 31 patients with narcolepsy underwent brain computed tomography (CT) scan and magnetic resonance imaging (MRI) testing. All patients received a MSLT test following a routine night's sleep, and serological HLA typing for HLA DR(2). 21 patients received PCR-SSP HLA DR and DQ typing. RESULTS: All patients had sleepiness and cataplexy. There was no evidence for other functional or structural diseases. Sleep paralysis was elicited in 45%; hypnagogic hallucinations, in 61%. Mean sleep latency on MSLT was 2.1 min +/- 1.3 min; sleep-onset rapid eye movement (SOREM) occurred during 2/5 naps in 30 of 31 patients. The average number and latency of SOREM episodes were 4.2 +/- 1.0 episodes and 4.0 min +/- 1.8 min, respectively. All patients but one were HLA DR(2) positive and 86% were HLADRB(1) * 1501-HLADQB(1)*0602 positive. CONCLUSIONS: HLA DR(2) and HLADQw6 are markers for narcolepsy-cataplexy in Chinese.

[Influence of different sleep stages on respiratory regulation in normal humans].

OBJECTIVE: To understand the influence of different sleep stages on respiratory regulation in normal people. METHODS: We measured ventilation (VE) and occlusion pressure (P0.1) responses to hyperoxia hypercapnia (deltaVE/deltaPaCO2, deltaP0.1/deltaPaCO2) and isocapnic hypoxia (deltaVE/deltaSaO2 and deltaP0.1/deltaSaO2) in eleven non-snoring healthy people during wakefulness and during non-rapid eye movement (NREM) I + II, NREM III+IV, and rapid eye movement (REM) sleep stages. RESULTS: During NREM I + II and NREM III+IV, the normal subjects showed no significant decrease in P0.1, deltaP0.1/deltaSaO2 and deltaP0.1/deltaPaCO2 (P > 0.05), but deltaVE/ deltaSaO2 and deltaVE/ deltaPaCO2 decreased significantly (P < 0.05). During REM sleep, P0.1 maintained the level during wakefulness, but both hypoxic and hypercapnic responses decreased significantly (P < 0.05). CONCLUSIONS: Sleep has significant influence on respiratory regulation in normal people. The respiratory drive (P0.1) in both NREM and REM sleep stages could maintain the awake level due to an effective compensation to the increase of upper airway resistance. The P0.1 responses to both hypoxia and hypercapnia decrease only in REM sleep stage, which is in consistent with the clinical phenomenon that sleep disordered breathing occurs in REM in normal people.

The compliance with nasal continuous positive airway pressure in patients with sleep apnea syndrome.

OBJECTIVE: To investigate the compliance with nasal continuous positive airway pressure (nCPAP) therapy in patients with sleep apnea syndrome (SAS) and to analyze the factors influencing the compliance. METHODS: A questionnaire about compliance was sent to 118 patients with SAS who accepted nCPAP home therapy from Feb, 1994 to Aug, 2000. The factors influencing compliance were analyzed. RESULTS: The compliance rate of nCPAP was 57%. The major factors influencing compliance were apnea-hypopnea index (AHI, P = 0.035), the lowest oxygen saturation (LSaO(2)) during sleep (P = 0.006), Epworth sleepiness scale (ESS) before and after treatment (P < 0.001) and the quality of nCPAP ventilators (P < 0.001). CONCLUSIONS: (1) The self-reported compliance with nCPAP treatment is good. (2) The factors influencing compliance are AHI, LSaO(2) during sleep before treatment, ESS before and after treatment, and the quality of nCPAP ventilators.

[Respiratory control during sleep and the development of nocturnal hypoxia in patients with obstructive sleep apnea hypopnea syndrome].

OBJECTIVE: It is assumed that the reduced ventilatory control during sleep may be related to the nocturnal hypoxia in patients with obstructive sleep apnea hypopnea syndrome (OSAHS) and daytime CO(2) retention. METHODS: Oxygen desaturation index (ODI(4)), sleep time spent when SaO(2) was below 90% (SIT(90)), the lowest SaO(2) (LSaO(2)) and the mean SaO(2) (MSaO(2)) during sleep were measured in 24 OSAHS patients with daytime PaCO(2) > or = 45 mm Hg and 39 with PaCO(2) < 45 mm Hg. Hypoxic (DeltaP(0.1)/DeltaSaO(2)) and hypercapnic (DeltaP(0.1)/DeltaPaCO(2)) responsiveness were measured in 11 eucapnic and 4 hypercapnic patients during wakefulness, NREM and REM sleep stages. RESULTS: Compared with the eucapnic patients, all the hypercapnic patients had more severe hypoxia during sleep (P < 0.05). Although both groups had similar chemical responsiveness during wakefulness, the hypercapnic patients had lower DeltaP(0.1)/DeltaSaO(2) and DeltaP(0.1)/DeltaPaCO(2) during both REM and NREM sleep (P < 0.05). CONCLUSION: The depressed chemical responsiveness during sleep plays an important role in the development of nocturnal hypoxia in OSAHS patients with daytime CO(2) retention.