An Overview of High-Throughput Crop Phenotyping: Platform, Image Analysis, Data Mining, and Data Management.

In this chapter, we explore the application of high-throughput crop phenotyping facilities for phenotype data acquisition and the extraction of significant information from the collected data through image processing and data mining methods. Additionally, the construction and outlook of crop phenotype databases are introduced and the need for global cooperation and data sharing is emphasized. High-throughput crop phenotyping significantly improves accuracy and efficiency compared to traditional measurements, making significant contributions to overcoming bottlenecks in the phenotyping field and advancing crop genetics.

Maturity Classification of Rapeseed Using Hyperspectral Image Combined with Machine Learning.

Oilseed rape is an important oilseed crop planted worldwide. Maturity classification plays a crucial role in enhancing yield and expediting breeding research. Conventional methods of maturity classification are laborious and destructive in nature. In this study, a nondestructive classification model was established on the basis of hyperspectral imaging combined with machine learning algorithms. Initially, hyperspectral images were captured for 3 distinct ripeness stages of rapeseed, and raw spectral data were extracted from the hyperspectral images. The raw spectral data underwent preprocessing using 5 pretreatment methods, namely, Savitzky-Golay, first derivative, second derivative (D2nd), standard normal variate, and detrend, as well as various combinations of these methods. Subsequently, the feature wavelengths were extracted from the processed spectra using competitive adaptive reweighted sampling, successive projection algorithm (SPA), iterative spatial shrinkage of interval variables (IVISSA), and their combination algorithms, respectively. The classification models were constructed using the following algorithms: extreme learning machine, k-nearest neighbor, random forest, partial least-squares discriminant analysis, and support vector machine (SVM) algorithms, applied separately to the full wavelength and the feature wavelengths. A comparative analysis was conducted to evaluate the performance of diverse preprocessing methods, feature wavelength selection algorithms, and classification models, and the results showed that the model based on preprocessing-feature wavelength selection-machine learning could effectively predict the maturity of rapeseed. The D2nd-IVISSA-SPA-SVM model exhibited the highest modeling performance, attaining an accuracy rate of 97.86%. The findings suggest that rapeseed maturity can be rapidly and nondestructively ascertained through hyperspectral imaging.

Association between baseline office blood pressure level and the incidence and development of long-term frailty in the community-dwelling very elderly with hypertension.

Frailty is the most important risk factor causing disability in the elderly. Hypertension is one of the most common chronic diseases in the elderly and is closely related to frailty, but there is still controversy about the association between blood pressure and frailty. To explore the association between baseline blood pressure level and the incident and development of long-term frailty in the community-dwelling very elderly (i.e., over 80 years old [1]) with hypertension, in order to provide a basis for scientific blood pressure management of very elderly hypertension. In this study, very elderly hypertensive patients who received comprehensive geriatric assessment from January to June 2019 and with complete data were included, and follow-up was conducted from January 1 to February 14, 2023. A total of 330 very elderly individuals with hypertension were enrolled in this study. FRAIL scale was used to evaluate frailty. Binomial logistic regression analysis was used to calculate the OR and 95%CI between baseline systolic blood pressure (SBP), diastolic blood pressure (DBP), pulse pressure (PP) levels and long-term incident and development of frailty. The dose-response relationship between baseline office SBP, DBP or PP levels and incident frailty and its development was analyzed by Generalized Additive Model (GAM) using smooth curve fitting and threshold effect analysis. Smooth curve fitting and threshold effect analysis showed that the relationship between baseline office SBP level and incident frailty was U-shaped, with the nadir of the U-shaped curve at 135 mmHg after adjustment. Baseline office SBP, PP level and development frailty was U-shaped and the nadir was 140 mmHg and 77 mmHg. In the community-dwelling very elderly with hypertension, baseline office SBP level had a relationship with long-term incident frailty and its development and PP level had a relationship with long-term development of frailty.

Inhalation of diesel exhaust particulate matter accelerates weight gain via regulation of hypothalamic appetite-related genes and gut microbiota metabolism.

Mice exposed to diesel exhaust particulate matter (DEPM) exhibited accelerated weight gain. Several hypothalamic genes, hormones (serum Hypothalamic-Pituitary-Adrenal (HPA) axis hormones and gastrointestinal peptide tyrosine tyrosine (PYY)), metabolites (intrahepatic triglyceride (IHTG) and fecal short-chain fatty acids (SCFAs)), and gut microbiota structure, which may influence obesity and appetite regulation, were examined. The result suggested that DEPM-induced accelerated weight gain may be associated with increased expression of hypothalamic Gamma-aminobutyric acid (GABA) type B receptor, tight junction protein, and orexin receptors, in addition with decreased IHTG and repressed HPA axis. Moreover, changes in the structure of intestinal microbiota are also related to weight changes, especially for phylum Firmicutes, genus Lactobacillus, and the ratio of relative abundance of Firmicutes and Bacteroidetes (F/B). DEPM exposure also caused widespread increase in the levels of intestinal SCFAs, the concentrations of propionic acid and isobutyric acid were associated with weight gain rate and the abundance of some bacteria. Although DEPM exposure caused changes in expression of hypothalamic serotonin, NPY, and melanocortin receptors, they were not associated with weight changes. Furthermore, no significant difference in gastrointestinal PYY and expression of hypothalamic receptors for leptin, insulin, and glucagon-like peptide 1 receptors was observed between DEPM-exposed and control mice.

Inhalation of diesel exhaust particulate matter induces locomotor hyperactivity and its relationship with brain and gut metabolism.

Diesel exhaust particulate matter (DEPM) are important components of urban air pollution worldwide. Recent studies proved that airborne DEPM can enter the human brain, which was associated with brain and mental diseases. In this study, we investigated the effects of DEPM exposure on behavior, and explored potential mechanisms from the perspective of metabolism in specific brain regions and short chain fatty acids (SCFAs) in the gut using mice. The results showed that inhalation of DEPM induced locomotor hyperactivity and a tendency for memory decline in mice. Exposure to DEPM disrupted motor behavior generation related cerebellar Purkinje cells, induced widespread reduction of neurotransmitters in the frontal cortex, and downregulated expression of genes encoding Brain-derived neurotrophic factor (BDNF) and involved in the Brain-blood-barrier (BBB) in the hippocampus. Moreover, there was a DEPM dose-dependent increase in fecal SCFA levels. Correlation analysis showed that DEPM-induced locomotor hyperactivity was mainly associated with decreased neurotransmission in the frontal cortex and increased gut SCFAs, and those associations were discussed. This study provides new insights into the mechanisms underpinning behavioral changes caused by air pollution, and extends our knowledge on the toxicity and health effects of airborne pollutants.

Culturable and inhalable airborne bacteria in a semiunderground municipal wastewater treatment plant: Distribution, transmission, and health risk assessment.

Airborne pathogens constitute a growing threat to global public health. Wastewater treatment plants (WWTPs) are important sources of airborne bacteria, which pose great health risks to the employee and nearby residents. In this study, the distribution, transmission and health risk of the airborne culturable and inhalable bacteria carried by PM2.5 in a semiunderground WWTP were evaluated. The concentrations of culturable bacteria in the air were 21.2-1431.1 CFU/m3, with the main contributions of primary and biological treatments. The relative abundances of culturable and total inhalable bacterial taxa were positively correlated (p < 0.05). However, certain bacteria, including Bacillus, Acinetobacter and Enterococcus, exhibited high reproductive capacity despite their low concentration in the air, suggesting that they can survive and regrow in suitable environments. Transmission modeling revealed that the concentrations of airborne bacteria exponentially decreased with distance from 18.67 to 24.12 copies /m3 at the source to 0.06-0.14 copies /m3 at 1000 m downwind. The risks of 8-h exposure in this WWTP except the outlet exceeded the reference value recommended by WHO, which were primarily dependent on P. aeruginosa, Salmonella, and E. coli. Management practices should consider improved controls for bioaerosols in order to reduce the risk of disease transmission.

Single-cell whole-genome sequencing, haplotype analysis in prenatal diagnosis of monogenic diseases.

Monogenic inherited diseases are common causes of congenital disabilities, leading to severe economic and mental burdens on affected families. In our previous study, we demonstrated the validity of cell-based noninvasive prenatal testing (cbNIPT) in prenatal diagnosis by single-cell targeted sequencing. The present research further explored the feasibility of single-cell whole-genome sequencing (WGS) and haplotype analysis of various monogenic diseases with cbNIPT. Four families were recruited: one with inherited deafness, one with hemophilia, one with large vestibular aqueduct syndrome (LVAS), and one with no disease. Circulating trophoblast cells (cTBs) were obtained from maternal blood and analyzed by single-cell 15X WGS. Haplotype analysis showed that CFC178 (deafness family), CFC616 (hemophilia family), and CFC111 (LVAS family) inherited haplotypes from paternal and/or maternal pathogenic loci. Amniotic fluid or fetal villi samples from the deafness and hemophilia families confirmed these results. WGS performed better than targeted sequencing in genome coverage, allele dropout (ADO), and false-positive (FP) ratios. Our findings suggest that cbNIPT by WGS and haplotype analysis have great potential for use in prenatally diagnosing various monogenic diseases.

20(S)-Protopanaxatriol ameliorates MAFLD by inhibiting NLRP3 inflammasome.

Metabolic associated fatty liver disease (MAFLD) is one of the most common chronic liver diseases and may develop into non-alcoholic steatohepatitis (NASH), fibrosis, cirrhosis, and even hepatocellular carcinoma, which has threatened human health. Although NLRP3 inflammasome is widely recognized in the pathogenesis of MAFLD, there are currently no drugs targeting NLRP3 inflammasome approved by regulatory agencies. Panax ginseng and its main saponin components have been used to regulate inflammatory and metabolic disorders. Notably, 20(S)-protopanaxatriol (PPT) is an active metabolite of protopanaxatriol saponins with prominent anti-inflammatory activity. However, the mechanism by which PPT ameliorates MAFLD has not been fully elucidated. Therefore, this study explored the efficacy and mechanism of PPT in treating MAFLD based on the inhibition of NLRP3 inflammasome activation. First, we screened potential NLRP3 inflammasome blockers from protopanaxadiol saponins in mouse primary bone marrow-derived macrophages (BMDMs) stimulated by LPS and different inflammasome inducers. Second, LPS-primed mouse BMDMs, mouse primary hepatocytes, mouse primary Kupffer cells and human peripheral blood mononuclear cells (PBMCs) stimulated by cholesterol and ATP were used to evaluate the effect of PPT in inhibiting NLRP3 inflammasome. Finally, MCD-induced mouse MAFLD were established to verify the therapeutic effect of PPT by inhibiting NLRP3 inflammasome. Our results showed that PPT of ginseng saponins significantly inhibited NLRP3 inflammasome activation in multiple primary cells, suppressed systemic inflammation, restored liver function, and attenuated liver inflammation as well as fibrosis in MCD--induced mouse MAFLD. Collectively, protopanaxatriol saponins metabolite PPT, may serve as a potent therapeutic agent for MAFLD by inhibiting NLRP3 inflammasome activation.

Endometrial transcriptome profiling of patients with recurrent implantation failure during hormone replacement therapy cycles.

Background: The molecular mechanisms underlying window of implantation (WOI) displacement in patients with recurrent implantation failure (RIF) remain unclear. This study aims to explore the transcriptomic signatures of endometrium with normal and displaced WOIs and to identify the causes of endometrial receptivity (ER) abnormalities and WOI displacement in RIF patients. Methods: In this study, 40 RIF patients were recruited and underwent personalized embryo transfer (pET) guided by the predicted results of endometrial receptivity diagnosis (ERD) model. Transcriptome analysis of endometrium from patients with clinical pregnancies after pET was performed to identify differentially expressed genes (DEGs) associated with WOI displacement. Gene expression data from HRT and natural cycle endometrium were compared to identify specific gene expression patterns of ER-related genes during WOI. Results: The ERD results indicated that 67.5% of RIF patients (27/40) were non-receptive in the conventional WOI (P+5) of the HRT cycle. The clinical pregnancy rate in RIF patients improved to 65% (26/40) after ERD-guided pET, indicating the effectiveness of transcriptome-based WOI prediction. Among the 26 patients with clinical pregnancy, the gene expression profiles of P+5 endometrium from advanced (n=6), normal (n=10) and delayed (n=10) WOI groups were significantly different from each other. Furthermore, 10 DEGs identified among P+5 endometrium of 3 groups were involved in immunomodulation, transmembrane transport and tissue regeneration, which could accurately classify the endometrium with different WOIs. Additionally, a large number of ER-related genes showed significant correlation and similar gene expression patterns in P+3, P+5, and P+7 endometrium from HRT cycles and LH+5, LH+7, and LH+9 endometrium from natural cycles. Conclusion: Our study shows that ER-related genes share similar gene expression patterns during WOI in both natural and HRT cycles, and their aberrant expression is associated with WOI displacements. The improvement of pregnancy outcomes in RIF patients by adjusting ET timing according to ERD results demonstrates the importance of transcriptome-based endometrial receptivity assessment and the clinical efficiency of ERD model.

[Concentrations and Community Structures of Culturable Bacteria in Aerosols of Household Garbage Stations in Shanghai].

The airborne microorganism has attracted increasing attention, and household garbage carries various pathogenic bacteria that affect the surrounding environment and public health. In this study, the culturable bacteria in the air were collected by using a six-level Anderson sampler, and the temperature, relative humidity, PM2.5, and PM10 in the garbage stations and their surrounding environment were recorded. The relationships between environmental factors and culturable bacterial pollution in the air were also analyzed. The results showed that the culturable bacterial concentrations in five sampling sites (the garbage station of a villa and the area downwind, the garbage station of a campus, the roof of an office building, and the garbage station of a residential area) were (1254±92), (280±123), (172±47), (84±18), and (175±174) CFU·m-3, respectively. The concentrations of the culturable bacteria in the garbage station of the villa were significantly higher than those of other sampling sites, mainly because there were biochemical treatment facilities for the on-site treatment of wet garbage in the garbage house. The sizes of the culturable bacteria in the garbage station of the villa mainly ranged from 1.1-4.7 µm, and the bacterial sizes at the other four sampling sites were primarily larger than 7 µm, with a few bacteria ranging from 1.1-2.1 µm. In this study, Proteobacteria and Firmicutes were the dominant phyla, and Corynebacterium and Bacillus were the dominant genera. More importantly, some opportunistic pathogens such as Corynebacterium, Staphylococcus, and Acinetobacter were also detected. The concentrations of the culturable bacteria in the garbage station of the villa were highly correlated with temperature, relative humidity, PM2.5, and PM10. Exiguobacterium in the air was highly correlated with PM10, temperature, and relative humidity. The health hazard quotient (HQ) values of the five sampling sites were all less than 1; however, the results of microbial quantitative risk assessment showed that the health risks of the male and female staff in the three garbage houses were all higher than the corresponding reference values. This study revealed the influence of garbage stations on the bioaerosol in the surrounding environment and provided references for the evaluation of air quality in and around garbage stations.

Public health events emergency management supervision strategy considering citizens' and new media's different ways of participation.

Public health events have done great harm. Emergency management requires the joint participation of multiple parties including government department, pharmaceutical enterprises, citizens and new media. Then, what are the effects of different strategy choices in participation of citizens and new media on emergency management? To answer the question, we construct a four-party evolutionary game model, considering the citizens' two participation ways consisted of true evaluation and false evaluation, and the new media's two participation ways consisted of report after verification and report without verification. This is of more practical significance than simply studying whether citizens and new media participate in emergency management or not because citizen and new media participation does not represent the completely positive behavior. Then, we conduct the evolutionary stability analysis, solve the stable equilibrium points using the Lyapunov first method and conduct the simulation analysis with MATLAB 2020b. The results show that, firstly, the greater the probability of citizens making true evaluation, the more inclined the government department is to strictly implement the emergency management system; secondly, when the probability of citizens making true evaluation decreases, new media are more inclined to report after verification, and when new media lose more pageview value or should be punished more for reporting without verification, the probability that they report without verification is smaller; thirdly, the greater the probability of citizens making false evaluation, the less enthusiasm of pharmaceutical enterprises to participate in emergency management, which indicates that false evaluation is detrimental to prompt pharmaceutical enterprises to participate; what's more, the greater the probability of new media reporting after verification, the greater the probability of pharmaceutical enterprises actively participating, which shows that new media's verification to citizens' evaluation is beneficial to emergency management.

Rhubarb free anthraquinones improved mice nonalcoholic fatty liver disease by inhibiting NLRP3 inflammasome.

BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases and has become a huge public health issue worldwide. Inhibition of nucleotide oligomerization domain-like receptors containing pyrin domain 3 (NLRP3) inflammasome is a potential therapeutic strategy for NAFLD. Currently, there are no drugs targeting NLRP3 inflammasome for clinical treatment of NAFLD. In this study, we explored the efficacy and mechanism of rhubarb free anthraquinones (RFAs) in treating NAFLD by inhibiting NLRP3 inflammasome. METHODS: First, NLRP3 inflammasome was established in mouse bone marrow-derived macrophages (BMDMs), Kuffer cells and primary hepatocytes stimulated by lipopolysaccharide (LPS) and inflammasome inducers to evaluate the effect of RFAs on inhibiting NLRP3 inflammasome and explore the possible mechanism. Further, Mice NAFLD were established by methionine and choline deficiency diet (MCD) to verify the effect of RFAs on ameliorating NAFLD by inhibiting NLRP3 inflammasome. RESULTS: Our results demonstrated that RFAs including rhein/diacerein, emodin, aloe emodin and 1,8-dihydroxyanthraquinone inhibited interleukin-1 beta (IL-1ß) but had no effect on tumor necrosis factor-alpha (TNF-α). Similar results were also showed in mouse primary hepatocytes and Kuffer cells. RFAs inhibited cleavage of caspase-1, formation of apoptosis-associated speck-like protein containing a CARD (ASC) speck, and the combination between NLRP3 and ASC. Moreover, RFAs improved liver function, serum inflammation, histopathological inflammation score and liver fibrosis. CONCLUSIONS: RFAs including rhein/diacerein, emodin, aloe emodin and 1,8-dihydroxyanthraquinone ameliorated NAFLD by inhibiting NLRP3 inflammasome. RFAs might be a potential therapeutic agent for NAFLD.

A correlational study of Weifuchun and its clinical effect on intestinal flora in precancerous lesions of gastric cancer.

BACKGROUND: Weifuchun (WFC), a Chinese herbal prescription consisting of Red Ginseng, Isodon amethystoides and Fructus Aurantii, is commonly used in China to treat a variety of chronic stomach disorders. The aim of the paper was to determine the effect of WFC on intestinal microbiota changes in precancerous lesions of gastric cancer (PLGC) patients. METHODS: PLGC patients of H. pylori negative were randomly divided into two groups and received either WFC tablets for a dose of 1.44 g three times a day or vitacoenzyme (Vit) tablets for a dose of 0.8 g three times a day. All patients were treated for 6 months consecutively. Gastroscopy and histopathology were used to assess the histopathological changes in gastric tissues before and after treatment. 16S rRNA gene sequencing was carried out to assess the effects WFC on intestinal microbiota changes in PLGC patients. Receiver Operating Characteristics (ROC) analysis was used to assess the sensitivity and specificity of different intestinal microbiota in distinguishing between PLGC patients and healthy control group. RESULTS: Gastroscopy and histopathological results indicated that WFC could improve the pathological condition of PLGC patients, especially in the case of atrophy or intestinal metaplasia. The results of 16S rRNA gene sequencing indicated that WFC could regulate microbial diversity, microbial composition, and abundance of the intestinal microbiota of PLGC patients. Following WFC treatment, the relative abundance of Parabacteroides decreased in WFC group when compared with the Vit group. ROC analysis found that the Parabacteroides could effectively distinguish PLGC patients from healthy individuals with sensitivity of 0.79 and specificity of 0.8. CONCLUSIONS: WFC could slow down the progression of PLGC by regulating intestinal microbiota abundance. Trial registration NCT03814629. Name of registry: Randomized Clinical Trial: Weifuchun Treatment on Precancerous Lesions of Gastric Cancer. Registered 3 August 2018-Retrospectively registered, https://register.clinicaltrials.gov/ NCT03814629.

Babao Dan improves neurocognitive function by inhibiting inflammation in clinical minimal hepatic encephalopathy.

BACKGROUND AND PURPOSE: Inflammation has been considered a precipitating event that contributes to neurocognitive dysfunction in minimal hepatic encephalopathy (MHE). Inhibition TLR-4 related inflammation can effectively improve neurocognitive dysfunction of MHE. Our previous study showed that Babao Dan (BBD) effectively inhibited inflammation and ameliorated neurocognitive function in rats with acute hepatic encephalopathy (HE) and chronic HE. The mechanism may lie in the regulation of TLR4 signaling pathway. Therefore, this study aimed to evaluate the role of BBD in the treatment of MHE patients with cirrhosis and to elucidate the underlying mechanism by which BBD regulated TLR4 pathway to alleviate inflammation. METHODS: A randomized controlled trial (n = 62) was conducted to evaluate the clinical efficacy between BBD plus lactulose (n = 31) and lactulose alone (n = 31) in MHE patients by testing neurocognitive function (NCT-A and DST), blood ammonia, liver function (ALT, AST and TBIL) and blood inflammation (IL-1ß, IL-6 and TNF-α). Afterward, we detected NO, inflammatory cytokines (IL-1ß, IL-6 and TNF-α) and the phosphorylation of P65, JNK, ERK as well as P38 in LPS-activated rat primary bone marrow-derived macrophages (BMDMs), peritoneal macrophages (PMs), and mouse primary BMDMs/PMs/microglia/astrocytes, to investigate the underlying mechanism of BBD inhibiting inflammation through TLR4 pathway. Also, the survival rate of mice, liver function (ALT, AST), blood inflammation (IL-1ß, IL-6 and TNF-α), inflammatory cytokines (IL-1ß, IL-6 and TNF-α) and histopathological changes in the liver, brain and lung were measured to assess the anti-inflammatory effect of BBD on neurocognitive function in endotoxin shock/endotoxemia mice. RESULTS: BBD combined with lactulose significantly ameliorated neurocognitive function by decreasing NCT-A (p＜0.001) and increasing DST (p＜0.001); inhibited systemic inflammation by decreasing IL-1ß (p＜0.001), IL-6(p＜0.001) and TNF-α (p＜0.001); reduced ammonia level (p = 0.005), and improved liver function by decreasing ALT(p = 0.043), AST(p = 0.003) and TBIL (p = 0.026) in MHE patients. Furthermore, BBD inhibited gene and protein expression of IL-1ß, IL-6 and TNF-α as well as NO in rat primary BMDMs/PMs, and mouse primary BMDMs/PMs/microglia/astrocytes in a dose-dependent manner. BBD inhibited the activation of mouse primary BMDMs/PMs/microglia/astrocytes by regulating TLR4 pathway involving the phosphorylation of P65, JNK, ERK and P38. Also, BBD reduced the mortality of mice with endotoxin shock/endotoxemia; serum levels of ALT, AST, IL-1ß, IL-6 and TNF-α; gene expression of IL-1ß, IL-6 and TNF-α in the liver, brain and lung, and tissue damage in the liver and lung. CONCLUSION: Our study provided for the first time clinical and experimental evidence supporting the use of BBD in MHE, and revealed that BBD could play a crucial role in targeting and regulating TLR4 inflammatory pathway to improve neurocognitive function in MHE patients.

An Allele-Specific Functional SNP Associated with Two Systemic Autoimmune Diseases Modulates IRF5 Expression by Long-Range Chromatin Loop Formation.

Both systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are autoimmune diseases sharing similar genetic backgrounds. Genome-wide association studies have constantly disclosed numerous genetic variants conferring to both disease risks at 7q32.1, but the functional mechanisms underlying them are still largely unknown. Through a series of bioinformatics and functional analyses, we prioritized a potential independent functional single-nucleotide polymorphism (rs13239597) within TNPO3 promoter region, residing in a putative enhancer element and validated that IRF5 is the distal target gene (∼118 kb) of rs13239597, which is a key regulator involved in pathogenic autoantibody dysregulation, increasing risk of both SLE and SSc. We experimentally validated the long-range chromatin interactions between rs13239597 and IRF5 using chromosome conformation capture assay. We further demonstrated that rs13239597-A acted as an allele-specific enhancer regulating IRF5 expression, independently of TNPO3 by using dual-luciferase reporter assays and CRISPR-Cas9. Particularly, the transcription factor EVI1 could preferentially bind to rs13239597-A allele and increase the enhancer activity to regulate IRF5 expression. Taken together, our results uncovered a mechanistic insight of a noncoding functional variant acting as an allele-specific distal enhancer to directly modulate IRF5 expression, which might obligate in understanding of complex genetic architectures of SLE and SSc pathogenesis.

BabaoDan cures hepatic encephalopathy by decreasing ammonia levels and alleviating inflammation in rats.

ETHNOPHARMACOLOGICAL RELEVANCE: BabaoDan (BBD) is a famous traditional Chinese formula frequently used in TCM clinics to eliminate jaundice and treat infectious viral hepatitis. This paper assesses BBD's preventive and therapeutic effects on hepatic encephalopathy after liver cirrhosis (CHE) and acute liver failure (AHE) in rats and explains its possible mechanism of action. METHODS: CHE rat model was established by injection of carbon tetrachloride (CCl4) twice a week for a total of 9 weeks and then by injection of thioacetamide (TAA) to induce hepatic encephalopathy. AHE rat model was established by injection of TAA once a day for a total of 3 days. In CHE rat model, BBD was gavaged once a day at the end of the 6th week until the experiment ended. In AHE rat model,BBD was gavaged once a day 3 days before TAA injection until the experiment ended. The preventive and therapeutic effects of BBD on brain dysfunction, as well as liver injury, pathology and fibrosis were evaluated in vivo. The role of BBD in the regulation of inflammatory factors and myeloid differentiation factor 88/Toll-like receptor 4/nuclear factor kappa-B (TLR4/MyD88/NK-κ B) pathway was detected in both liver and brain in vivo. The rat bone marrow derived macrophages (BMDMs) were activated by Lipopolysaccharide (LPS), and the role of BBD in the regulation of inflammatory factors and NK-κ B pathway were detected in vitro. RESULTS: In CHE rat model: BBD significantly improved the total distance as well as the activity rate of rats. BBD also improved the learning and memory abilities of rats compared with the control group. In addition, BBD effectively decreased ammonia levels and significantly decreased the levels of alanine aminotransferase (ALT), aspartate transaminase (AST), total bilirubin (TBil) and total bile acid (TBA), as well as improved the levels of total protein (TP) and albumin (Alb). In the liver, BBD not only inhibited the gene expressions of tumor necrosis factor alpha (TNF-α), interleukini-6 (IL-6), TLR4, MyD88, and NF-κ B but also inhibited the protein expressions of TLR4, MyD88, NK-κ B and TNF-α. In the brain, BBD inhibited the gene expressions of iNOS, IL-6, TNF-α, TLR-4, MyD88, and NF-κ B, as well as inhibited the protein expressions of TLR4, MyD88, P65 TNF-α and ionized calcium binding adapter molecule 1 (Iba-1). BBD also decreased NO and TNF-α in the blood. IN AHE RAT MODEL: BBD improved neurological scores, blood ammonia levels and the brain inflammatory gene expressions of iNOS, TNF-α and IL-1ß. BBD also improved liver function biomarkers such as ALT, TBil, TBA, TP, ALB and inflammatory and apoptotic gene expressions of TNF-α, IL-1ß, IL-6, Bax, Bcl-2, caspase-9, caspase-3 and NF-κ B. In LPS-activated rat BMDMs, BBD decreased NO and TNF-α production in BMDM culture supernatant. In addition, BBD inhibited the gene expressions of TNF-α, IL-1 ß and IL-6 as well as the phosphorylation of P65. CONCLUSION: BBD can prevent and cure hepatic encephalopathy (HE) derived from both chronic and acute liver diseases. BBD can reduce hyperammonemia as well as the systematic and neurological inflammation. Inflammation is likely an important target of BBD to treat HE. The anti-inflammatory role of BBD may lie in its regulation of the TLR4/MyD88/NF-κ B pathways.

Concomitant adenosquamous carcinoma and cystadenocarcinoma of the extrahepatic bile duct: A case report.

BACKGROUND: Infiltrative adenosquamous carcinoma (ASC) of the extrahepatic bile duct is reported infrequently, which is an unusual variant of the ordinary adenocarcinoma. The simultaneous development of ASC and cystadenocarcinoma in the extrahepatic biliary tree is rare. In addition, the accurate preoperative diagnosis of concomitant carcinoma in the multiple biliary trees at an early stage is often difficult. Thus, awareness of the risk of the multiplicity of biliary tumors is perhaps the most important factor in identifying these cases. CASE SUMMARY: Here, we report a case of a 63-year-old female with jaundice, who was referred to Shuguang Hospital because of abdominal pain for 1 mo. An abdominal contrast-enhanced computed tomography revealed a type I choledochal cyst and intraluminal masses suggestive of adenoma of the common bile duct. In addition, a preoperative diagnosis of a concomitant Klatskin tumor and type I choledochal cyst was made. The patient underwent anti-inflammatory therapy, followed by radical surgery due to hilar cholangiocarcinoma and resection of the choledochal cyst. Examination of the surgical specimen revealed a papillary tumor of the common bile duct, which arose from the malignant transformation of a pre-existing cystadenoma. Histologic examination confirmed a special type of cholangiocarcinoma; the tumor in the hilar bile duct was an ASC, whereas the tumor in the common bile duct was a moderately differentiated cystadenocarcinoma. The patient showed rapid deterioration 8 mo after surgery. CONCLUSION: Although concomitant ASC and cystadenocarcinoma of the extrahepatic bile duct is difficult to diagnose before surgery, and the prognosis is poor after surgery, surgical resection is still the preferred treatment.

An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation.

Genome-wide association studies (GWASs) have reproducibly associated variants within intergenic regions of 1p36.12 locus with osteoporosis, but the functional roles underlying these noncoding variants are unknown. Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339) (∼360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.

Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer.

RANKL is a key regulator involved in bone metabolism, and a drug target for osteoporosis. The clinical diagnosis and assessment of osteoporosis are mainly based on bone mineral density (BMD). Previous powerful genomewide association studies (GWASs) have identified multiple intergenic single-nucleotide polymorphisms (SNPs) located over 100 kb upstream of RANKL and 65 kb downstream of AKAP11 at 13q14.11 for osteoporosis. Whether these SNPs exert their roles on osteoporosis through RANKL is unknown. In this study, we conducted integrative analyses combining expression quantitative trait locus (eQTL), genomic chromatin interaction (high-throughput chromosome conformation capture [Hi-C]), epigenetic annotation, and a series of functional assays. The eQTL analysis identified six potential functional SNPs (rs9533090, rs9594738, r8001611, rs9533094, rs9533095, and rs9594759) exclusively correlated with RANKL gene expression (p < 0.001) at 13q14.11. Co-localization analyses suggested that eQTL signal for RANKL and BMD-GWAS signal shared the same causal variants. Hi-C analysis and functional annotation further validated that the first five osteoporosis SNPs are located in a super-enhancer region to regulate the expression of RANKL via long-range chromosomal interaction. Particularly, dual-luciferase assay showed that the region harboring rs9533090 in the super-enhancer has the strongest enhancer activity, and rs9533090 is an allele-specific regulatory SNP. Furthermore, deletion of the region harboring rs9533090 using CRISPR/Cas9 genome editing significantly reduced RANKL expression in both mRNA level and protein level. Finally, we found that the rs9533090-C robustly recruits transcription factor NFIC, which efficiently elevates the enhancer activity and increases the RANKL expression. In summary, we provided a feasible method to identify regulatory noncoding SNPs to distally regulate their target gene underlying the pathogenesis of osteoporosis by using bioinformatics data analyses and experimental validation. Our findings would be a potential and promising therapeutic target for precision medicine in osteoporosis. © 2018 American Society for Bone and Mineral Research.

Genetics association study and functional analysis on osteoporosis susceptibility gene BDNF.

To explore the relationship between brain-derived neurotrophic factor (BDNF) gene and bone mineral density (BMD) in Chinese Han population, we performed association analysis of 14 tag SNPs on BDNF gene with hip/spine BMD in 1300 Han Chinese samples from Shaanxi Province. We found that 8 of the 14 SNPs were significantly associated with hip or spine BMD (P < 0.05). Moreover, the SNP rs16917237 was significantly associated with both hip and spine BMD, with significant Bonferroni correlation (P value 0.05/14 = 0.0036) in hip BMD. To further explore the regulatory mechanism of BDNF gene in osteoporosis, we further performed a set of data analyses, including linkage disequilibrium and haplotype analysis, epigenetic annotation, expression quantitative trait locus (eQTL) analysis and metabolic pathway analysis. Further, we have established a mouse pre-osteoblasts differentiation cell model (MC3T3-E1) by recombination human bone morphogenetic protein (rh-BMP2) induction. siRNA- mediated knock down of BDNF in this cell model showed that all 14 SNPs are in the same haplotype block. Strong signals of active histone H3K4me1, H3K4me3, H3K27ac modifications and P300 binding were observed in osteoblasts, in the region surrounding the most significant SNP rs16917237, suggesting that this SNP might have a regulatory function in osteoblasts. Furthermore, analysis of genotype data of rs16917237 and BDNF expression in multiple tissues from GTEx showed that rs16917237 SNP could significantly affect the expression of BDNF in 11 tissues. Through analysis of the various BDNF pathways, we showed that BDNF participates in the MAPK pathway, which is a vital and well-established pathway affecting osteoblasts proliferation and differentiation. siRNA knock down of BDNF significantly decreased the mRNA and protein levels of CREB, which is important in the MAPK pathway in osteoblast differentiation. These findings suggest that BDNF might affect osteoblast differentiation via regulation of CREB expression. In conclusion, our results from combined genetic association and functional analyses show that BDNF is a vital osteoporosis susceptibility gene, which can affect BMD not only in Chinese Han but also likely in other populations.