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Background Enterococcus raffinosus is one of the Enterococcus species that often cause nosocomial infections. To date, only one E. raffinosus genome has been completely assembled, and the genomic features have not been characterized. Here, we report the complete genome sequence of the strain CX012922, isolated from the feces of a Crohn's disease patient, and perform a comparative genome analysis to the relevant Enterococcus spp. strains in silico. Results De novo assembly of the sequencing reads of the strain CX012922 generated a circular genome of 2.83 Mb and a circular megaplasmid of 0.98 Mb. Phylogenomic analysis revealed that the strain CX012922 belonged to the E. raffinosus species. By comparative genome analysis, we found that some strains previously identified as E. raffinosus or E. gilvus should be reclassified as novel species. Genome islands (GIs), virulence factors, and antibiotic genes were found in both the genome and the megaplasmid, although pathogenic genes were mainly encoded in the genome. A large proportion of the genes encoded in the megaplasmid were involved in substrate utilization, such as raffinose metabolism. Giant megaplasmids (~1 Mb) equipped with toxin-antitoxin (TA) systems generally formed symbiosis relationships with the genome of E. raffinosus strains. Conclusions Enterococcus spp. have a higher species-level diversity than is currently appreciated. The pathogenicity of E. raffinosus is mainly determined by the genome-encoded virulence factors, while the megaplasmid broadens the gene function pool. The symbiosis between the genome and the megaplasmids endows E. raffinosus with large genomic sizes as well as versatile gene functions, especially for their colonization, adaptation, virulence, and pathogenesis in the human gut. Keywords: Enterococcus, Megaplasmid, Antibiotic resistance genes, Virulence factor, Toxin-antitoxin system, Author(s): Hailan Zhao[sup.1], Yao Peng[sup.2,3], Xunchao Cai[sup.3], Yongjian Zhou[sup.1,2], Youlian Zhou[sup.1,2], Hongli Huang[sup.1,2], Long Xu[sup.3] and Yuqiang Nie[sup.1,2] Background Enterococcus is a Gram-positive and lactic acid bacteria of the phylum [...]

Chinese Materia Medica Resources (CMMRs) are crucial for developing the tradition and industry of traditional Chinese medicine. Given the increasing demand for CMMRs, an accurate and effective understanding of CMMRs is urgently needed. Chinese medicinal plants (CMPs) are the most important sources of CMMRs. Traditional methods of investigating medicinal plant resources have limitations, including severe subjectivity and poor timeliness, which make it difficult to meet the demand for real-time monitoring of large-scale medicinal plant resources. In recent years, remote sensing technology has become an important means of obtaining information on medicinal plants, and the application of this technology has made up for the shortcomings of traditional methods. This paper first discusses the development of investigation methods of CMMRs; points out the importance of remote sensing technology in the application of spatial distribution and information identification and extraction of Chinese medicinal plant resources (CMPRs); analyzes the characteristics of CMPs in different planting patterns, different habitats, and different regions from the perspective of remote sensing information extraction; and explores the selection of suitable data sources, providing a reference for medicinal plant identification and information extraction. Secondly, according to the existing classification and identification methods, previous studies are summarized from the perspectives of classification scales, classification features, and classification accuracy, and the advantages and disadvantages of the commonly used remote sensing classification methods in the investigation of CMPRs are summarized and compared. Finally, the development trend of remote sensing technology in the identification and information extraction of CMPs is examined, and the key technical problems to be solved in the identification and classification of CMPs and the extraction of area information are summarized so as to provide technical support and experience references for the application of remote sensing in the investigation of CMPRs. [ABSTRACT FROM AUTHOR]

Background and Aim: Autophagy and gut microbiota correlates closely with the inflammatory bowel disease. Herein, we aimed to study the roles of rapamycin on the gut microbiota in inflammatory bowel disease. Methods: Acute colitis was induced with dextran sodium sulfate (DSS) and 2,4,6‐trinitrobenzenesulfonic acid solution in mice. Mice were administered with rapamycin or hydroxychloroquine. Weight loss, disease activity index scores, histopathological score, serum inflammatory cytokines, intestinal permeability, and colonic autophagy‐related proteins were detected. Cecal content was also preserved in liquid nitrogen and subsequently analyzed following the 16S DNA sequencing. The antibiotic cocktail‐induced microbiome depletion was performed to further investigate the relationship between autophagy activation and gut microbiota. Results: Compared with the control group, the colonic autophagy‐related proteins of P62, mTOR, and p‐mTOR increased significantly, while the levels of LC3B and ATG16L1 decreased (all P < 0.05) in the model group. After rapamycin intervention, the colonic pathology of mice improved, while the disease activity index score decreased substantially; the colon length increased, and the expression of IL‐6 and TNF‐α decreased. Following hydroxychloroquine treatment, some indicators suggested aggravation of colitis. Principal coordinates analysis showed that the DSS group was located on a separate branch from the rapamycin group but was closer to the hydroxychloroquine group. Compared with the DSS group, the rapamycin group was associated with higher abundances of f_Lactobacillaceae (P = 0.0151), f_Deferribacteraceae (P = 0.0290), g_Lactobacillus (P = 0.0151), g_Mucispirillum (P = 0.0137), s_Lactobacillus_reuteri (P = 0.0028), and s_Clostridium sp Culture_Jar‐13 (P = 0.0082) and a lower abundance of s_Bacteroides_sartorii (P = 0.0180). Linear discriminant analysis effect size showed that rapamycin increased the abundances of Lactobacillus‐reuteri, Prevotellaceae, Paraprevotella, Christensenella and Streptococcus and decreased those of Peptostreptococcaceae and Romboutsia Bacteroides‐sartorii. Besides, the improvement effect of autophagy activation on colitis disappears following gut microbiome depletion. Conclusion: The therapeutic effects of rapamycin on extenuating experimental colitis may be related to the gut microbiota. [ABSTRACT FROM AUTHOR]

Background and Aim: Mucosal healing has emerged as a desirable treatment goal for patients with ulcerative colitis (UC). Healing of mucosal wounds involves epithelial cell proliferation and differentiation, and Y‐box transcription factor ZONAB has recently been identified as the key modulator of intestinal epithelial restitution. Methods: We studied the characteristics of UXT‐V1 expression in UC patients using immunohistochemistry and qPCR. The functional role of UXT‐V1 in the colonic epithelium was investigated using lentivirus‐mediated shRNA in vitro and ex vivo. Through endogenous Co‐immunoprecipitation and LC–MS/MS, we identified ZONAB as a UXT‐V1‐interactive protein. Results: Herein, we report that UXT‐V1 promotes differentiation of intestinal epithelial cells by regulating the nuclear translocation of ZONAB. UXT‐V1 was upregulated in the intestinal epithelia of UC patients compared with that of healthy controls. Knocking down UXT‐V1 in NCM‐460 cells led to the enrichment of pathways associated with proliferation and differentiation. Furthermore, the absence of UXT‐V1 in cultured intestinal epithelial cells and colonic organoids inhibited differentiation to the goblet cell phenotype. Mechanistically, the loss of UXT‐V1 in the intestinal epithelial cells allowed nuclear translocation of ZONAB, wherein it regulated the transcription of differentiation‐related genes, including AML1 and KLF4. Conclusion: Taken together, our study reveals a potential role of UXT‐V1 in regulating epithelial cell differentiation, proving a molecular basis for mucosal healing in UC. [ABSTRACT FROM AUTHOR]

With the trend towards the precise and digital planting management of orchards, apple cultivation relies more heavily on the planting management supporting technologies of orchards. In recent years, continuous breakthroughs made in spatial resolution and revisiting frequency have made remote sensing technology a major supporting technology for the precise planting management of apple orchards. However, there is an absence of reviews of the application status and prospect of this technology in the planting management of orchards. Based on the analysis of primary applications of remote sensing technology in the precise planting management of apple orchards, this study classified the applications into three major categories, namely the surveys of basic orchard information, inversions of orchard parameters, and the planting management support of orchards. Furthermore, this study reviewed the methods and performance of the applications of remote sensing technology in various fields and explored the application potential. Finally, it identified three types of problems with current research and application of remote sensing technology, namely insufficient studies on mechanisms and in some application fields, low - degree integration of multiple technologies, and the lack of large - scale application models. In addition, this study proposed four hot research and application topics in the future, namely models used to simulate the growth mechanisms of apple trees, the integrated support system for the planting management of apple trees, the single - tree monitoring based on satellite data, and the diversified services of remote sensing - based monitoring products. [ABSTRACT FROM AUTHOR]

Crop-distribution information constitutes the premise of precise management for crop cultivation. Euclidean distance and spectral angle mapper algorithms (ED and SAM) mostly use the spectral similarity and difference metric (SSDM) to determine the spectral variance associated with the spatial location for crop distribution acquisition. These methods are relatively insensitive to spectral shape or amplitude variation and must reconstruct a reference curve representing the entire class, possibly resulting in notable indeterminacy in the ultimate results. Few studies utilize these methods to compute the spectral variance associated with time and to define a new index for crop identification—namely, the spectral variance at key stages (SVKS)—even though this temporal spectral characteristic could be helpful for crop identification. To integrate the advantages of sensibility and avoid reconstructing the reference curve, an object self-reference combined algorithm comprising ED and SAM (CES) was proposed to compute SVKS. To objectively validate the crop-identification capability of SVKS-CES (SVKS computed via CES), SVKS-ED (SVKS computed via ED), SVKS-SAM (SVKS computed via SAM), and five spectral index (SI) types were selected for comparison in an example of maize identification. The results indicated that SVKS-CES ranges can characterize greater interclass spectral separability and attained better identification accuracy compared to other identification indexes. In particular, SVKS-CES2 provided the greatest interclass spectral separability and the best PA (92.73%), UA (100.00%), and OA (98.30%) in maize identification. Compared to the performance of the SI, SVKS attained greater interclass spectral separability, but more non-maize fields were incorrectly identified as maize fields via SVKS usage. Owning to the accuracy-improvement capability of SVKS-CES, the omission and commission errors were obviously reduced via the combined utilization of SVKS-CES and SI. The findings suggest that SVKS-CES application is expected to further spread in crop identification. [ABSTRACT FROM AUTHOR]

As the core component of wearable electronic devices, flexible energy storage materials play an irreplaceable role. At present, it is still a challenge to prepare flexible electrode materials with high energy density. In this paper, a polyaniline‐based composite flexible conductive hydrogel (PPG‐P) with a two‐level conductive network is successfully prepared by a secondary induced assembly in situ polymerization method. The special conductive structure greatly promotes the efficiency of charge transfer and the utilization of electroactive substances, so that PPG‐P exhibits excellent electrochemical performance. In a three‐electrode system, PPG‐P has a mass‐specific capacitance as high as 989 F g−1 (0.5 A g−1). After 1000 charge and discharge cycles, the capacitance retention is 87%. Symmetrical flexible supercapacitors based on PPG‐P have high specific capacitance (176 F g−1/0.5 A g−1) and high energy density (15.6 Wh kg−1). After 1000 cycles of constant current charge and discharge, the capacitance maintains 78.1%. The preparation of PPG‐P with a hierarchical structure demonstrates the possibility of achieving high energy density in flexible electrode materials, which has great application potential in the development of energy storage elements in wearable devices. [ABSTRACT FROM AUTHOR]

Background: Pancreatic cancer (PC) is a devasting disease of which mortality almost parallels its incidence. PC tissue may express aberrantly methylated neuronal pentraxin II (NPTX2), but it is unclear what the consequences of this are. Methods: We systematically searched PubMed, Web of Science, the Chinese National Knowledge Infrastructure (CNKI), from inception to July 15, 2020, to identify if the detection of methylated NPTX2 have sufficient sensitivity and specificity to identify PC from other benign pancreatic diseases. Results: Majority of the studies obtained samples from pancreatic juice by endoscopy or surgery and composed of population with chronic pancreatitis, benign cystic lesion, intraductal papillary mucinous neoplasm, and healthy controls. Our results demonstrated that the diagnostic value of methylated NPTX2 is of widely various sensitivity and specificity and it shown higher specificity in differentiate PC from benign diseases. The lab method of quantitative real‐time methylation‐specific PCR (QMSP) has higher specificity than real‐time methylation‐specific PCR (MSP) in detecting the indicator. Conclusions: NPTX2 methylation could serve as a promising molecular biomarker for pancreatic cancer diagnosis, for its high diagnostic value in differentiating pancreatic cancer from benign pancreatic disease with the lab method. The variable sensitivity of methylated NPTX2 was multifactorial, and it must be promoted before applied as screening test in clinical practice. Furthermore, experiments on methylated NPTX2 were needed to expanded for lower the heterogeneity. [ABSTRACT FROM AUTHOR]

Background and Aim: We comprehensively carry out a systematic review and meta‐analysis of previous studies to determine the association between intestinal Faecalibacterium prausnitzii (F. prausnitzii) and inflammatory bowel disease (IBD) in human studies. Methods: A systematic literature search of PubMed, Embase, and the Cochrane Library database was conducted until April 1, 2020. Inclusion criteria were studies involving patients with Crohn's disease (CD) or ulcerative colitis (UC) with abundance of F. prausnitzii. The quality of the studies was assessed by the modified Newcastle–Ottawa scale. Results: A total of 1669 subjects (427 CD patients, 560 UC patients, and 682 healthy controls) were enrolled from 16 studies. Both CD (standardized mean difference [SMD]: −1.36; 95% CI, −1.74 to −0.98; P < 0.00001) and UC patients (SMD: −0.81; 95% CI, −1.21 to −0.42; P < 0.0001) had a lower abundance of F. prausnitzii than the healthy controls. Compared with the IBD remission patients, the IBD active patients had lower levels of F. prausnitzii (SMD: ‐0.56; 95% CI, −0.91 to −0.21; P = 0.002). In the subgroup analyses, the abundance of F. prausnitzii was reduced in both active CD patients (SMD: −0.78; 95% CI, −1.51 to −0.04; P = 0.04) and active UC patients (SMD:−0.44; 95%CI, −0.81 to −0.07; P = 0.02) when compared with the patients with CD or UC in remission, respectively. Conclusion: A negative association between abundance of F. prausnitzii and IBD activity is observed, but a cut‐off level of F. prausnitzii to diagnose and/or to start treating IBD is not determined. [ABSTRACT FROM AUTHOR]

Acquired immune deficiency syndrome, caused by the human immunodeficiency virus (HIV), has been associated with intestinal dysbiosis, which includes an increase in the number of mucosa-associated pathobionts. In the present study, the intestinal mucosal microbiota patterns of HIV-infected patients were compared with those of healthy individuals in a population from Guangzhou, China. The gut microbiota of intestinal mucosal samples from 12 patients with HIV (transmission routes included sex and intravenous drug abuse) was compared with that of 12 healthy age- and sex-matched controls. Gut microbial communities were profiled via sequencing of the bacterial 16S ribosomal RNA genes. Dysbiosis in HIV-infected individuals was characterized by decreased α-diversity, decreased levels of Firmicutes and increased levels of Proteobacteria. Furthermore, low mean counts of Lachnoclostridium, Roseburia, Thauera, Dorea and Roseburia inulinivorans, and high mean counts of Halomonas and Shewanella bacteria, were indicated to be HIV-associated mucosal bacterial alterations. The relative abundance of Fusobacterium and Lachnoclostridium was significantly decreased, while that of Halomonas and Shewanella was significantly increased in patients with sexually transmitted HIV-infection compared with healthy controls. Alterations of the gut microbiota during HIV infection were also indicated to be associated with the route of HIV transmission. Certain bacteria may be potential biomarkers for HIV infection in patients from Guangzhou, China. [ABSTRACT FROM AUTHOR]

Purpose: The aim of this study was to investigate the underlying mechanisms of diabetic retinopathy (DR) development. Methods: Real-Time qPCR was used to detect Casein kinase 2 interacting protein-1 (CKIP-1) and Nuclear factor E2-related factor 2 (Nrf2) mRNA levels. Western Blot was employed to detect protein levels. Malondialdehyde (MDA) assay kit, superoxide dismutase (SOD) kit and glutathione peroxidase (GSH-Px) kit were used to evaluate oxidative stress in high-glucose treated human retinal endothelial cells (HRECs). Calcein-AM/propidium iodide (PI) double stain kit was employed to detect cell apoptosis. Enzyme-linked ImmunoSorbent Assay (ELISA) was used to detect inflammation associated cytokines secretion. Co-immunoprecipitation (CO-IP) was performed to investigate the interactions between CKIP-1 and Nrf2. Luciferase reporter gene system was used to detect the transcriptional activity of Nrf2. Results: CKIP-1 was significantly downregulated in either DR tissues or high-glucose treated HRECs comparing to the Control groups. Besides, high-glucose (25 mM) inhibited HRECs viability and induced oxidative stress, inflammation associated cytokines (TNF-α, IL-6 and IL-1β) secretion and cell apoptosis, which were all reversed by synergistically overexpressing CKIP-1 and aggravated by knocking down CKIP-1. Of note, we found that overexpressed CKIP-1 activated Nrf2/ARE signaling pathway and increased its downstream targets including HO-1, NQO-1, γGCS and SOD in high-glucose treated HRECs. Further results also showed that CKIP-1 regulated cell viability, oxidative stress, inflammation and apoptosis in high-glucose treated HRECs by activating Nrf2/ARE signaling pathway. Conclusion: We concluded that overexpressed CKIP-1 alleviated DR progression by activating Nrf2/ARE signaling pathway. [ABSTRACT FROM AUTHOR]