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IntroductionObservational studies have discovered a contradictory phenomenon between Helicobacter pylori (H. pylori) infection and inflammatory bowel disease (IBD). The study aimed to confirm the causal association between H. pylori and IBD, including ulcerative colitis (UC) and Crohn's disease (CD).MethodsWe conducted a Mendelian randomization (MR) study with two sample Genome-Wide Association Studies (GWAS) to determine whether there is a causal relationship between H. pylori infection and IBD, as well as the possible pathogenic factors that may be involved. The reliability of the main MR assumptions was examined through a series of sensitivity analyses.ResultsTwo genetic variants (SNPs) previously identified were employed as instrumental variables (IVs) for H. pylori infection. GWAS data for IBD, UC, and CD were obtained from the recent DF10 release10 of the FinnGen study. Our findings indicated a significant association between H. pylori seropositivity and an increased risk of IBD and UC (IBD: OR: 1.16, 95% CI, 1.03–1.31, P < 0.05; UC: OR: 1.22, 95% CI, 1.08–1.37, P < 0.001) while no causal relationship with CD (P > 0.05). Analysis of the main virulence pathogenic factors revealed a causal relationship between cytotoxin-associated protein A (CagA) and IBD and UC (IBD: OR: 1. 06, 95% CI, 1.001–1.11, P < 0.05; UC: OR: 1.07, 95% CI, 1.004–1.14, P < 0.05), while no correlation was found for vacuolar cytotoxin A (VacA) (P > 0.05). After applying the False Discovery Rate (FDR) correction, the causal relationship between CagA and the risk of IBD or UC was no longer statistically significant.ConclusionThis study suggests a potential causal relationship between H. pylori infection and IBD, particularly UC. The effect may be more pronounced in individuals with previous H. pylori infections.

IntroductionChrysanthemum morifolium Ramat. is a perennial herb in the Compositae family, often employed in traditional Chinese medicine due to its medicinal value. The planting of C. morifolium faces the challenges of continuous cropping, and intercropping is able to somewhat overcome the obstacles of continuous cropping.MethodsIn our study, we designed two different C. morifolium-maize intercropping patterns, including C. morifolium-maize narrow-wide row planting (IS) and C. morifolium-maize middle row planting (IM). Compared with monoculture, the agronomic traits, yield, active ingredients, soil physicochemical properties, soil enzyme activities, and rhizosphere soil microbial communities of C. morifolium and maize were measured under the two C. morifolium-maize intercropping patterns.ResultsThe findings indicated that (1) Intercropping elevated the agronomic traits, yield, and active ingredients of C. morifolium, especially in C. morifolium-maize narrow-wide row planting pattern, which indicating that interspecific distance played an important role in intercropping system; (2) Intercropping enhanced soil physicochemical properties and enzyme activities of C. morifolium and maize; (3) Intercropping altered rhizosphere soil microbial communities of C. morifolium and maize, making microbial interrelationships more complex. (4) Intercropping could recruit a large number of beneficial microorganisms enrich in the soil, including Bacillus, Sphingomonas, Burkholderia-Caballeronia-Paraburkholderia, Chaetomium, and Ceratorhiza, which may increase the content of AN, NN, AvK, ExCa, AvCu, AvZn and other nutrients in soil and promoted the growth and quality of C. morifolium.DiscussionIn summary, intercropping with maize could promote the accumulation of beneficial microorganisms in the soil, thus improving the overall growing environment, and finally realizing the growth and improvement of C. morifolium.

IntroductionDuck circovirus (DuCV) infection is currently recognized as an important immunosuppressive disease in commercial duck flocks in China. Specific antibodies against DuCV viral proteins are required to improve diagnostic assays and understand the pathogenesis of DuCV infection.Methods and resultsTo generate DuCV-specific monoclonal antibodies (mAbs), a recombinant DuCV capsid protein without the first 36 N-terminal amino acids was produced in Escherichia coli. Using the recombinant protein as an immunogen, a mAb was developed that reacted specifically with the DuCV capsid protein, expressed in E. coli and baculovirus systems. Using homology modeling and recombinant truncated capsid proteins, the antibody-binding epitope was mapped within the region of 144IDKDGQIV151, which is exposed to solvent in the virion capsid model structure. To assess the applicability of the mAb to probe the native virus antigen, the murine macrophage cell line RAW267.4 was tested for DuCV replicative permissiveness. Immunofluorescence and Western blot analysis revealed that the mAb recognized the virus in infected cells and the viral antigen in tissue samples collected from clinically infected ducks.DiscussionThis mAb, combined with the in vitro culturing method, would have widespread applications in diagnosing and investigating DuCV pathogenesis.

Recently, a novel poplar mosaic disease caused by bean common mosaic virus (BCMV) was investigated in Populus alba var. pyramidalis in China. Symptom characteristics, physiological performance of the host, histopathology, genome sequences and vectors, and gene regulation at the transcriptional and posttranscriptional levels were analyzed and RT−qPCR (quantitative reverse transcription PCR) validation of expression was performed in our experiments. In this work, the mechanisms by which the BCMV pathogen impacts physiological performance and the molecular mechanisms of the poplar response to viral infection were reported. The results showed that BCMV infection decreased the chlorophyll content, inhibited the net photosynthesis rate (Pn) and stomatal conductance (Gs), and significantly changed chlorophyll fluorescence parameters in diseased leaves. Transcriptome analysis revealed that the expression of the majority of DEGs (differentially expressed genes) involved in the flavonoid biosynthesis pathway was promoted, but the expression of all or almost all DEGs associated with photosynthesis-antenna proteins and the photosynthesis pathway was inhibited in poplar leaves, suggesting that BCMV infection increased the accumulation of flavonoids but decreased photosynthesis in hosts. Gene set enrichment analysis (GSEA) illustrated that viral infection promoted the expression of genes involved in the defense response or plant-pathogen interaction. MicroRNA-seq analysis illustrated that 10 miRNA families were upregulated while 6 families were downregulated in diseased poplar leaves; moreover, miR156, the largest family with the most miRNA members and target genes, was only differentially upregulated in long-period disease (LD) poplar leaves. Integrated transcriptome and miRNA-seq analyses revealed 29 and 145 candidate miRNA−target gene pairs; however, only 17 and 76 pairs, accounting for 2.2% and 3.2% of all DEGs, were authentically negatively regulated in short-period disease (SD) and LD leaves, respectively. Interestingly, 4 miR156/SPL (squamosa promoter-binding-like protein) miRNA−target gene pairs were identified in LD leaves: the miR156 molecules were upregulated, but SPL genes were downregulated. In conclusion, BCMV infection significantly changed transcriptional and posttranscriptional gene expression in poplar leaves, inhibited photosynthesis, increased the accumulation of flavonoids, induced systematic mosaic symptoms, and decreased physiological performance in diseased poplar leaves. This study elucidated the fine-tuned regulation of poplar gene expression by BCMV; moreover, the results also suggested that miR156/SPL modules played important roles in the virus response and development of viral systematic symptoms in plant virus disease.

Equity in the inheritance culture of family property is an important component of humanistic health in modern living environments. The inheritance of property under Chinese traditional family culture is the material basis for the continuation of family and clan. This study demonstrates the equity component embedded in traditional family inheritance culture and further studies of the healthy human settlements environment. Based on the theory of “equal share for all sons” in ancient China and the “equity” and “justice” that are of modern significance, this paper analyzes the family division culture of individual traditional housing and the corresponding impact indices of family division equity. Taking Renhe Village, a typical local residential building of the middle and late Qing Dynasty as the research object, this study built a spatial syntax data model and 3D simulation technology for the simulation analysis of space and climate. The results show that Renhe Village meets the requirements of the equity evaluation system of housing property rights distribution in terms of the natural unit indicator (quantity, lighting, ventilation) and the overall spatial indicator (privacy, centrality, convenience). In other words, equity does not mean an absolute average share, but an equity culture formed after six evaluation indices under the subdivision of two indicators are balanced. Based on the above, an equity system model of housing property rights distribution was established, and the weight of the ancients' attention to the housing distribution standard was explored. It is further found that the ancients attached more importance to light among the natural unit indicators, and attached the most importance to centrality in the overall spatial indicators. These findings provide new ideas for understanding the equity of property inheritance under Chinese traditional family culture. They also provide quantifiable criteria for the distribution of modern rural housing and social security housing, and ultimately provide a reference for the humanistic public health of the modern living environment.

Psoriasis is an immune-mediated, persistent inflammatory disease with a genetic predisposition, and the involvement of multiple organs in psoriasis remains indicative of systemic disease. Atherosclerosis (AS) is a common complication of patients with severe or prolonged psoriasis. The specific pathogenesis of psoriasis is still unclear. Current studies suggest that psoriasis is a polygenic genetic disease with the interaction of multiple factors such as heredity and environment. Keratinocytes are proliferated through immune-mediated inflammatory pathway, which leads to cell activation, infiltration of dermis cells and release of inflammatory factors. Activation of inflammatory cells and pro-inflammatory factors play an important role in the progression of psoriasis and atherosclerosis. Studies have found that there is a close relationship between psoriasis and atherosclerosis, and systemic inflammation may be the common feature of psoriasis and AS. This paper attempts to explore the possibility of the relationship between psoriasis and atherosclerotic comorbidities from the aspects of potential epidemiology and immune mechanism, in order to provide some reference for the subsequent scientific research.

Fungal pathogens can induce canker lesions, wilting, and even dieback in many species. Trees can suffer serious physiological effects from stem cankers. In this study, we investigated the effects of Botryosphaeria dothidea (B. dothidea) on Populus bolleana (P. bolleana) leaves photosynthesis and stomatal responses, when stems were inoculated with the pathogen. To provide experimental and theoretical basis for preventing poplar canker early. One-year-old poplar stems were inoculated with B. dothidea using an epidermal scraping method. In the early stage of B. dothidea inoculation (2–14 days post inoculation, dpi), the gas exchange, stomatal dynamics, hormone content, photosynthetic pigments content, chlorophyll fluorescence parameters, and non-structural carbohydrate (NSC) were evaluated to elucidate the pathophysiological mechanism of B. dothidea inhibiting photosynthesis. Compared with the control groups, B. dothidea noteworthily inhibited the net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO2 concentration (Ci), transpiration rate (Tr), and other photosynthetic parameters of poplar leaves, but stomatal limit value (Ls) increased. Consistent with the above results, B. dothidea also reduced stomatal aperture and stomatal opening rate. In addition, B. dothidea not only remarkably reduced the content of photosynthetic pigments, but also decreased the maximum photochemical efficiency (Fv/Fm), actual photochemical efficiency (ΦPSII), electron transfer efficiency (ETR), and photochemical quenching coefficient (qP). Furthermore, both chlorophyll and ΦPSII were positively correlated with Pn. In summary, the main reason for the abated Pn under stem canker pathogen was that B. dothidea not merely inhibited the stomatal opening, but hindered the conversion of light energy, electron transfer and light energy utilization of poplar leaves. In general, the lessened CO2 and Pn would reduce the synthesis of photosynthetic products. Whereas, sucrose and starch accumulated in poplar leaves, which may be due to the local damage caused by B. dothidea inoculation in phloem, hindering downward transport of these products.

Artemisia argyi Levl. et Van is an important Asteraceae species with a high medicinal value. There are abundant A. argyi germplasm resources in Asia, especially in China, but the evolutionary relationships of these varieties and the systematic localization of A. argyi in the family Asteraceae are still unclear. In this study, the chloroplast (cp) genomes of 72 A. argyi varieties were systematically analyzed. The 72 varieties originated from 47 regions in China at different longitudes, latitudes and altitudes, and included both wild and cultivated varieties. The A. argyi cp genome was found to be ∼151 kb in size and to contain 114 genes, including 82 protein-coding, 28 tRNA, and 4 rRNA genes. The number of short sequence repeats (SSRs) in A. argyi cp genomes ranged from 35 to 42, and most of them were mononucleotide A/T repeats. A total of 196 polymorphic sites were detected in the cp genomes of the 72 varieties. Phylogenetic analysis demonstrated that the genetic relationship between A. argyi varieties had a weak relationship with their geographical distribution. Furthermore, inverted repeat (IR) boundaries of 10 Artemisia species were found to be significantly different. A sequence divergence analysis of Asteraceae cp genomes showed that the variable regions were mostly located in single-copy (SC) regions and that the coding regions were more conserved than the non-coding regions. A phylogenetic tree was constructed using 43 protein-coding genes common to 67 Asteraceae species. The resulting tree was consistent with the traditional classification system; Artemisia species were clustered into one group, and A. argyi was shown to be closely related to Artemisia lactiflora and Artemisia montana. In summary, this study systematically analyzed the cp genome characteristics of A. argyi and compared cp genomes of Asteraceae species. The results provide valuable information for the definitive identification of A. argyi varieties and for the understanding of the evolutionary relationships between Asteraceae species.

Artemisia argyi is widely distributed in Asia, and it often becomes the dominant population in the field because of its strong ecological niche competitiveness. Allelochemicals secreted by plants are generally considered an important reason for their dominance in ecological competition. In this study, the allelochemicals in A. argyi were screened by a series of experiments and their mechanisms were explored via transcriptomics. First, the inhibitory effects of A. argyi on Echinochloa crusgalli, Setaria viridis, Portulaca oleracea and Amaranthus retroflexus were evaluated. Then, we carried out a qualitative and quantitative analysis of the chemical composition of the aqueous extract of A. argyi to screen for potential allelochemicals that can inhibit weed growth. Four potential allelochemicals were quantified: neochlorogenic acid (5-CQA), chlorogenic acid (3-CQA), cryptochlorogenic acid (4-CQA), and caffeic acid (CA). Coincidentally, their allelopathic effects on weeds seemed to be identical to their content, in the order CA>4−CQA>5−CQA>3-CQA. These findings suggested that CA might be the main allelopathic compound in the aqueous extract of A. argyi. Subsequently, the allelopathic effect and molecular mechanism of CA on S. viridis leaves were investigated. The physiological results showed that CA significantly induced reactive oxygen species (ROS) production, led to malondialdehyde (MDA) accumulation, and disrupted enzyme activities (POD, SOD, CAT) in S. viridis leaves. Moreover, transcriptome results revealed that CA inhibited S. viridis growth by downregulating multiple genes involved in gibberellin (GA) and phytoalexin biosynthesis and Mitogen-activated protein kinase (MAPK) signaling pathways. In addition, differentially expressed genes (DEGs) related to the biosynthesis and signaling pathways of phytohormones were verified by Quantitative Real-Time PCR (RT-qPCR). Taken together, this study may be the first to identify allelochemicals and explore their molecular mechanism about A. argyi. Importantly, the ecological advantages of A. argyi could be applied to ecological regulation and the development of botanical herbicides.

Objective: To explore the cerebral hemodynamic changes after revascularization in patients with hemorrhagic moyamoya disease (MMD).Materials and Methods: We retrospectively included 57 hemorrhagic MMD patients in a high-volume stroke center from January 2016 to December 2018. All subjects were evaluated with whole-brain CT perfusion (CTP) before and after surgical revascularization. Absolute and relative CTP values in the regions of cortical middle cerebral artery territory (CMT) and deep brain area (DBA) of hemorrhagic hemispheres were measured. Differences between pre- and post-operative CTP values were assessed comprehensively. The patients were categorized into subgroups based on revascularization subtypes and postoperative CTP intervals.Results: The relative cerebral blood volume (rCBV) in DBA and CMT significantly reduced in postoperative CTP (P < 0.05). The median and interquartile range of the proportion of rCBV decrease (rCBVc%) were 7.2% (2.3–13.2%). The rCBV reduction retained statistical significant in patients who received subtypes of revascularization, and in patients with variable intervals of follow-up (P < 0.05). There was no significant difference of rCBVc% between patients who received different revascularization and among patients with different postoperative CTP intervals (P > 0.05). The relative mean transit time (rMTT) and relative time to peak (rTTP) also showed downward trends, but without retainable statistical significance in stratified analysis. There was no significant change in relative cerebral blood flow (rCBF) (P > 0.05).Conclusion: In patients with hemorrhagic MMD, the CBV appeared to decrease and be relatively stable in the chronic phase after revascularization, with varying degrees of MTT and TTP shortening. However, there was no significant change in CBF.

Meaning in life, which has two possible sources: self-acceptance and social support, is essential to the mental health and development of college students. The current study aims to further clarify the symptom-level relations between meaning in life, self-acceptance, and social support, finding possible ways to improve meaning in the life of college students. Thousand three hundred and forty-eight Chinese college students completed the online questionnaire, including Self-acceptance Questionnaire, Social Support Rating Scale, and Meaning in Life Questionnaire and the data from 1,263 participants was used. Cross-sectional network analysis was used to examine the relation between self-acceptance and social support. We also explored the relation between dimensions of self-acceptance and social support and meaning in life using the flow network. The results show symptom “SlA” (self-acceptance) is the bridge symptom linking self-acceptance and social support. In the flow diagrams, “SlA” is directly and positively associated with the presence of meaning. Objective Support shares the strongest positive association with the search for meaning. The symptom “SIA” may be an important targeting symptom when trying to improve the meaning in life of college students. Additionally, social support is essential for college students to develop meaning in life.

Accurate identification the species composition in mixtures poses a significant challenge, especially in processed mixtures comprising multiple species, such as those found in food and pharmaceuticals. Therefore, we have attempted to utilize shotgun metabarcoding technology to tackle this issue. In this study, the method was initially established using two mock samples of the Mongolian compound preparation Gurigumu-7 (G-7), which was then applied to three pharmaceutical products and 12 hospital-made preparations. A total of 119.72 Gb of raw data sets were obtained through shotgun metagenomic sequencing. By combining ITS2, matK, and rbcL, all the labeled bio-ingredients specified in the G-7 prescription can be detected, although some species may not be detectable in all samples. The prevalent substitution of Akebia quinata can be found in all the pharmaceutical and hospital samples, except for YN02 and YN12. The toxic alternative to Akebia quinata, Aristolochia manshuriensis, was exclusively identified in the YN02 sample. To further confirm this result, we validated it in YN02 using HPLC and real-time PCR with TaqMan probes. The results showed that aristolochic acid A (AAA) was detected in YN02 using HPLC, and the ITS2 sequence of Aristolochia manshuriensis has been validated in YN02 through qPCR and the use of a TaqMan probe. This study confirms that shotgun metabarcoding can effectively identify the biological components in Mongolian medicine compound preparation G-7. It also demonstrates the method’s potential to be utilized as a general identification technique for mixtures containing a variety of plants.

Rhodiola L. is a genus exhibiting rapid radiation and represents a typical case for studying plastid gene adaptation in species that spread from high altitudes to low altitudes. In this study, 23 samples of 18 Rhodiola species were collected from the Qinghai-Tibetan Plateau and five scattered alpine areas, and the plastid genomes (plastomes) of these species were sequenced, annotated, and compared between high-altitude and widely distributed groups. The plastomes of Rhodiola were found to be highly conserved in terms of gene size, content, and order but highly variable in several lineage-specific features, such as codon usage bias, IR boundary shifting, and distinct repeat sequence structures binding to SSRs. Codon usage in the genes of photosystem II exhibited an obvious preference, reflecting significant environmental adaptation pressures. In this study, three repeat regions compounded with trinucleotide and mononucleotide repeats were found for the first time in R. forrestii, R. himalensis, and R. yunnanensis. High-variability regions such as ndhF, ycf1, trnH-psbA, and rpoC1-rpoB were screened, laying the foundation for the precise identification of these species. The phylogenetic analysis revealed the occurrence of cyto-nuclear discordance, likely originating from the frequent interspecific hybridization events observed within Rhodiola species during rapid radiation. Dioecious and hermaphrodite species can be broadly categorized into two subclades, probably they have different environmental adaptation strategies in response to climate change. In addition, the phylogenetic tree supported the monophyly of R. forrestii and R. yunnanensis, which compose R. Sect. Pseudorhodiola. In conclusion, plastome data enrich the genetic information available for the Rhodiola genus and may provide insight into species migration events during climate change.

Bacterial infection is a major challenge that could threaten the patient’s life in repairing bone defects with implant materials. Developing functional scaffolds with an intelligent antibacterial function that can be used for bone repair is very important. We constructed a drug delivery (HA@TA-CS/SA) scaffold with curcumin-loaded dendritic mesoporous organic silica nanoparticles (DMON@Cur) via 3D printing for antibacterial bone repair. Inspired by the adhesion mechanism of mussels, the HA@TA-CS/SA scaffold of hydroxyapatite (HA) and chitosan (CS) is bridged by tannic acid (TA), which in turn binds sodium alginate (SA) using electrostatic interactions. The results showed that the HA@TA-CS/SA composite scaffold had better mechanical properties compared with recent literature data, reaching 68.09 MPa. It displayed excellent degradation and mineralization capabilities with strong biocompatibility in vitro. Furthermore, the antibacterial test results indicated that the curcumin-loaded scaffold inhibited S.aureus and E.coli with 99.99% and 96.56% effectiveness, respectively. These findings show that 3D printed curcumin-loaded HA@TA-CS/SA scaffold has considerable promise for bone tissue engineering.

IntroductionGaleola lindleyana is a mycoheterotrophic orchid belonging to the tribe Vanilleae within the subfamily Vanilloideae.MethodsIn this study, the G. lindleyana plastome was assembled and annotated, and compared with other Vanilleae orchids, revealing the evolutionary variations between the photoautotrophic and mycoheterotrophic plastomes.ResultsThe G. lindleyana plastome was found to include 32 protein-coding genes, 16 tRNA genes and four ribosomal RNA genes, including 11 pseudogenes. Almost all of the genes encoding photosynthesis have been lost physically or functionally, with the exception of six genes encoding ATP synthase and psaJ in photosystem I. The length of the G. lindleyana plastome has decreased to 100,749 bp, while still retaining its typical quadripartite structure. Compared with the photoautotrophic Vanilloideae plastomes, the inverted repeat (IR) regions and the large single copy (LSC) region of the mycoheterotrophic orchid’s plastome have contracted, while the small single copy (SSC) region has expanded significantly. Moreover, the difference in length between the two ndhB genes was found to be 682 bp, with one of them spanning the IRb/SSC boundary. The Vanilloideae plastomes were varied in their structural organization, gene arrangement, and gene content. Even the Cyrtosia septentrionalis plastome which was found to be closest in length to the G. lindleyana plastome, differed in terms of its gene arrangement and gene content. In the LSC region, the psbA, psbK, atpA and psaB retained in the G. lindleyana plastome were missing in the C. septentrionalis plastome, while, the matK, rps16, and atpF were incomplete in the C. septentrionalis plastome, yet still complete in that of the G. lindleyana. Lastly, compared with the G. lindleyana plastome, a 15 kb region located in the SSC area between ndhB-rrn16S was found to be inverted in the C. septentrionalis plastome. These changes in gene content, gene arrangment and gene structure shed light on the polyphyletic evolution of photoautotrophic orchid plastomes to mycoheterotrophic orchid plastomes.DiscussionThus, this study’s decoding of the mycoheterotrophic G. lindleyana plastome provides valuable resource data for future research and conservation of endangered orchids.

In recent years, natural polysaccharides have attracted more and more attention and research because of their value in the medicine, beauty and food fields. Salvia miltiorrhiza is a traditional Chinese herb that has been used for thousands of years and has antidiabetic, antifibrotic, neuroprotective, antioxidation, anti-inflammatory and other effects. It mainly includes rosmarinic acid, tanshinone I, tanshinone IIA, tanshinone IIB, procatechualdehyde, polysaccharide and salvianolic acids. Salvia miltiorrhiza polysaccharide is a polysaccharide extracted and isolated from Salvia miltiorrhiza and has diverse biological functions, including antioxidation, anti-tumor, hepatoprotective, anti-inflammatory, immune regulatory and cardioprotective effect. In this review, the extraction, purification, structural characterization and biological activity of SMPs are summarized and new perspectives for the future work of SMPs were also proposed, we hope our research can provide a reference for further research on SMPs.

The intestinal microbiota and fecal metabolome have been shown to play a vital role in human health, and can be affected by genetic and environmental factors. We found that individuals with Down syndrome (DS) had abnormal serum cytokine levels indicative of a pro-inflammatory environment. We investigated whether these individuals also had alterations in the intestinal microbiome. High-throughput sequencing of bacterial 16S rRNA gene in fecal samples from 17 individuals with DS and 23 non-DS volunteers revealed a significantly higher abundance of Prevotella, Escherichia/Shigella, Catenibacterium, and Allisonella in individuals with DS, which was positively associated with the levels of pro-inflammatory cytokines. GC-TOF-MS-based fecal metabolomics identified 35 biomarkers (21 up-regulated metabolites and 14 down-regulated metabolites) that were altered in the microbiome of individuals with DS. Metabolic pathway enrichment analyses of these biomarkers showed a characteristic pattern in DS that included changes in valine, leucine, and isoleucine biosynthesis and degradation; synthesis and degradation of ketone bodies; glyoxylate and dicarboxylate metabolism; tyrosine metabolism; lysine degradation; and the citrate cycle. Treatment of mice with fecal bacteria from individuals with DS or Prevotella copri significantly altered behaviors often seen in individuals with DS, such as depression-associated behavior and impairment of motor function. These studies suggest that changes in intestinal microbiota and the fecal metabolome are correlated with chronic inflammation and behavior disorders associated with DS.

Atractylodes species are widely distributed across East Asia and are cultivated as medicinal herbs in China, Japan, and Korea. Their unclear morphological characteristics and low levels of genetic divergence obscure the taxonomic relationships among these species. In this study, 24 plant samples were collected representing five species of Atractylodes located in China; of these, 23 belonged to members of the A. lancea complex. High-throughput sequencing was used to obtain the concatenated nrDNA sequences (18S-ITS1-5.8S-ITS2-28S) and plastid genomes. The concatenated nrDNA sequence lengths for all the Atractylodes species were 5,849 bp, and the GC content was 55%. The lengths of the whole plastid genome sequences ranged from 152,138 bp (A. chinensis) to 153,268 bp (A. lancea), while their insertion/deletion sites were mainly distributed in the intergenic regions. Furthermore, 33, 34, 36, 31, and 32 tandem repeat sequences, as well as 30, 30, 29, 30, and 30 SSR loci, were detected in A. chinensis, A. koreana, A. lancea, A. japonica, and A. macrocephala, respectively. In addition to these findings, a considerable number of heteroplasmic variations were detected in the plastid genomes, implying a complicated phylogenetic history for Atractylodes. The results of the phylogenetic analysis involving concatenated nrDNA sequences showed that A. lancea and A. japonica formed two separate clades, with A. chinensis and A. koreana constituting their sister clade, while A. lancea, A. koreana, A. chinensis, and A. japonica were found based on plastid datasets to represent a mixed clade on the phylogenetic tree. Phylogenetic network analysis suggested that A. lancea may have hybridized with the common ancestor of A. chinensis and A. japonica, while ABBA–BABA tests of SNPs in the plastid genomes showed that A. chinensis was more closely related to A. japonica than to A. lancea. This study reveals the extensive discordance and complexity of the relationships across the members of the A. lancea complex (A. lancea, A. chinensis, A. koreana, and A. japonica) according to cytonuclear genomic data; this may be caused by interspecific hybridization or gene introgression.

It is well known that crop classification is essential for genetic resources and phenotype development. Compared with traditional methods, convolutional neural networks can be utilized to identify features automatically. Nevertheless, crops and scenarios are quite complex, which makes it challenging to develop a universal classification method. Furthermore, manual design demands professional knowledge and is time-consuming and labor-intensive. In contrast, auto-search can create network architectures when faced with new species. Using rapeseed images for experiments, we collected eight types to build datasets (rapeseed dataset (RSDS)). In addition, we proposed a novel target-dependent search method based on VGGNet (target-dependent neural architecture search (TD-NAS)). The result shows that test accuracy does not differ significantly between small and large samples. Therefore, the influence of the dataset size on generalization is limited. Moreover, we used two additional open datasets (Pl@ntNet and ICL-Leaf) to test and prove the effectiveness of our method due to three notable features: (a) small sample sizes, (b) stable generalization, and (c) free of unpromising detections.

ObjectiveCerebral aneurysms are classified as severe cerebrovascular diseases due to hidden and critical onset, which seriously threaten life and health. An effective strategy to control intracranial aneurysms is the regular diagnosis and timely treatment by CT angiography (CTA) imaging technology. However, unpredictable patient movements make it challenging to capture sub-millimeter-level ultra-high resolution images in a CTA scan. In order to improve the doctor's judgment, it is necessary to improve the clarity of the cerebral aneurysm medical image algorithm.MethodsThis paper mainly focuses on researching a three-dimensional medical image super-resolution algorithm applied to cerebral aneurysms. Although some scholars have proposed super-resolution reconstruction methods, there are problems such as poor effect and too much reconstruction time. Therefore, this paper designs a lightweight super-resolution network based on a residual neural network. The residual block structure removes the B.N. layer, which can effectively solve the gradient problem. Considering the high-resolution reconstruction needs to take the complete image as the research object and the fidelity of information, this paper selects the channel domain attention mechanism to improve the performance of the residual neural network.ResultsThe new data set of cerebral aneurysms in this paper was obtained by CTA imaging technology of patients in the Department of neurosurgery, the second affiliated of Guizhou Medical University Hospital. The proposed model was evaluated from objective evaluation, model effect, model performance, and detection comparison. On the brain aneurysm data set, we tested the PSNR and SSIM values of 2 and 4 magnification factors, and the scores of our method were 33.01, 28.39, 33.06, and 28.41, respectively, which were better than those of the traditional SRCNN, ESPCN and FSRCNN. Subsequently, the model is applied to practice in this paper, and the effect, performance index and diagnosis of auxiliary doctors are obtained. The experimental results show that the high-resolution image reconstruction model based on the residual neural network designed in this paper plays a more influential role than other image classification methods. This method has higher robustness, accuracy and intuition.ConclusionWith the wide application of CTA images in the clinical diagnosis of cerebral aneurysms and the increasing number of application samples, this method is expected to become an additional diagnostic tool that can effectively improve the diagnostic accuracy of cerebral aneurysms.

Mycoplasma gallisepticum (M. gallisepticum) is a primary respiratory pathogen of poultry and causes significant economic losses to the poultry industry. There were no reported articles concerning the Pharmacokinetics/Pharmacodynamics (PK/PD) interactions of tilmicosin against M. gallisepticum in vivo. In the current study, we established an in vivo M. gallisepticum infection model and tilmicosin was administered orally to the M. gallisepticum-infected chickens by different dosage regimens. The concentration of tilmicosin in lung tissue was determined by high-pressure liquid chromatography/tandem mass spectrometry (HPLC–MS/MS), besides the counting of the viable colony of M. gallisepticum in lung tissue was also monitored dynamically to appraise the PK/PD interactions of tilmicosin against M. gallisepticum. We found that anti-mycoplasmal activity was concentration-dependent and mycoplasmacidal activity was observed at tilmicosin dosage >7.5 mg/kg. The PK/PD parameter of AUC/MIC (The area under the concentration–time curve divided by the minimal inhibitory concentration) correlated well with anti-mycoplasmal efficacy (R2 = 0.92). The ratios of AUC/MIC for 1 log10 and 3 log10 colony-forming units [CFU]/lung reductions were 300.02 and 6,950.15 h, respectively. These findings indicated that tilmicosin may be therapeutically effective in chickens to treat M. gallisepticum lung infections if administered at a dose of 9.12 mg/kg.

IntroductionTeratomas are rare neoplasms that arise from pluripotent germ cells. Sacrococcygeal teratomas are often diagnosed in infants but are rare in adults; a mature teratoma can contain hair, teeth, bony tissue, and other mature tissue types. Herein, we report for the first time a patient with a teratoma containing intact bones that formed a pseudoarthrosis.Case reportA 49-year-old woman was admitted to hospital after a massive life-long sciatic tumor had begun to grow larger over the past year. A 16 cm × 25 cm solid mass with a clear boundary was palpable in the sacrococcygeal region. Radiography, computed tomography, and magnetic resonance imaging indicated a sacrococcygeal teratoma, although blood alpha-fetoprotein levels were normal. The teratoma was completely excised using 3-dimensional reconstruction mixed reality (MR) technology with no notable complications. Postoperative pathological examination of the excised lesion confirmed a mature teratoma. Interestingly, two intact irregular bones that formed a pseudoarthrosis were isolated; one was 11 cm and the other 6 cm. The patient is currently healthy and has experienced no recurrences.ConclusionSacrococcygeal teratomas are rare, especially in adults, and often comprised lots of components, such as fat, bony tissue. However, it's first reported that formation of pseudoarthrosis in this case so far. It is difficult for surgeons to achieve complete excision without complications owing to the complex anatomic structure of the sacrum. The 3-dimensional reconstruction and mixed reality (MR) technology based on computed tomography can provide spatial visualization, which allows surgeons to examine the teratoma at different angles preoperatively. Combining 3-dimensional reconstruction and mixed reality (MR) technology in this case facilitated complete resection and prevented recurrence.

To realize efficient remote human-computer interaction of robots, a robot remote operating system based on virtual reality and digital twin is proposed. The system builds a digital twin model based on the Unity 3D engine to establish a connection with the robot entity, assisting the online remote programming and real-time manipulation of the robot unit. The system uses HTC VIVE to build a virtual reality framework. To actualize the mutual drive between the real space and the virtual space, a mathematical model of the robot is constructed through the forward and inverse kinematics of the robot. Through the combination of eye-tracking-based eye movement interaction and the unique controller interaction of virtual reality system, a multi-sensory multi-input collaborative interaction method is accomplished. The method realizes the robot joints driving of users using multiple interaction methods simultaneously, simplifies the robot programming and control procedure, and optimizes the operation experience. Tests demonstrate that the system is capable of effectively providing monitoring, teleoperation and programming services for remote interaction of robots.

To solve the motion planning of the live working manipulator, this research proposes a hybrid data-model–driven algorithm called the P-SAC algorithm. In the model-driven part, to avoid obstacles and make the trajectory as smooth as possible, we designed the trajectory model of the sextic polynomial and used the PSO algorithm to optimize the parameters of the trajectory model. The data generated by the model-driven part are then passed into the replay buffer to pre-train the agent. Meanwhile, to guide the manipulator in reaching the target point, we propose a reward function design based on region guidance. The experimental results show that the P-SAC algorithm can reduce unnecessary exploration of reinforcement learning and can improve the learning ability of the model-driven algorithm for the environment.

Introduction: POLD2 is an indispensable subunit of DNA polymerase δ, which is responsible for the synthesis of the backward accompanying strand in eukaryotic organisms. Current studies have found an association between POLD2 and the development of a variety of cancers. However, its value in cancer immunotherapy has not been fully established.Methods: POLD2 expression was analyzed using RNA expression and clinical data from TCGA and GTEx databases. The prognostic impact of POLD2 on tumor patients was analyzed using clinical survival data from TCGA. Gene enrichment analysis was performed using the R package “cluster analyzer” to explore the role of POLD2. We used the TIMER2 database to analyze the relationship between immune cell infiltration and POLD2 expression in TCGA. We downloaded relevant data from TCGA and analyzed the relationship between POLD2 and immune checkpoints, immunosuppressive genes, immune activating genes, chemokines and chemokine receptors.Results: POLD2 was significantly overexpressed in most tumors compared to normal tissue. High POLD2 expression was significantly associated with advanced tumor stage, significantly shorter overall survival and progression-free survival. Also, we found that POLD2 expression correlated strongly with immunomodulatory genes, and significantly negatively with most immune checkpoints (PD-L1, CTLA4, TIM3, and CD28). Pathway enrichment analysis suggests that low expression of POLD2 promotes immune regulation-related pathways and high expression promotes metabolic and DNA repair-related pathways. Furthermore, tumor microenvironment analysis suggests that high POLD2 expression inhibits infiltration of CD8+ T cells and CD4+ memory T cells.Discussion: In conclusion, POLD2 may be a molecular biomarker for pan-cancer prognosis and immunotherapy. It may serve as a potential target for new insights in human tumor prognosis prediction and immunotherapy assessment.

Osteosarcoma is one of the bone malignancies in children and adolescents. Long noncoding RNAs (lncRNAs) have been demonstrated to participate in osteosarcoma development and progression. Linc00265 has been shown to involve in osteosarcoma oncogenesis; however, the underlying mechanism is largely unclear. In this study, we investigated the function of linc00265 in osteosarcoma cells, including cell viability, migration and invasion. Moreover, we elucidated mechanistically the involvement of linc00265 in osteosarcoma. We found that linc00265 overexpression promoted viability, migration and invasion of osteosarcoma cells. Notably, linc00265 sponged miR-485-5p and increased the expression of USP22, one target of miR-485-5p, in osteosarcoma cells. Strikingly, linc00265 exerted its oncogenic function via regulating miR-485-5p and USP22 in osteosarcoma. Taken together, targeting linc00265 is a promising approach for treating osteosarcoma patients.

Alfalfa long-term continuous cropping (CC) can pose a serious threat to alfalfa production. However, the mechanism of alfalfa CC obstacle is unclear as of today. Our preliminary study showed that the main factors of CC obstacle were not the lack of nutrients or water in alfalfa rhizosphere soils. Further, we evaluated physic-chemical property, microbial population structure, and metabolite differences of alfalfa rhizosphere soils with CC for 1, 7, and 14 years based on analysis of metabolomics and microbiomics. Four phenolic acid metabolites, including p-coumaric acid, ferulic acid, vanillic acid, and p-hydroxybenzoic acid, were found to have significant differences among different CC years, which may be the key factors of CC obstacle. Among them, p-coumaric acid and ferulic acid could significantly decrease the germination rate of alfalfa seeds by 21.11 and 16.67% at the concentration of 100 μg/mL and the height (root length) of alfalfa seedlings by 21% (32.9%) and 13.72% (16.45%). Moreover, these metabolites could effectively promote the growth of some pathogenic fungi, causing alfalfa root rot. Among them, p-coumaric acid obviously and significantly aggravated the occurrence of alfalfa root rot. With the increase of CC years, soil microbial community changed from fungi to bacteria; fungi decreased by 10.83%, fungi increased by 8.08%, and beneficial microorganisms decreased with the increase of CC years. Field analysis and experimental verification showed that the above results were consistent with that of CC obstacle in the field. Among the key metabolites, the autotoxicity of p-coumaric acid was the strongest. This study fully proved that the continuous accumulation of autotoxic substances in alfalfa rhizosphere was the key factor causing alfalfa CC obstacles.

Osteosarcoma (OS) is the common bone tumor in children and adolescents. Because of chemotherapy resistance, the OS patients have a poor prognosis. The one reason of chemotherapeutic resistance is the development of cancer stem cells (CSCs). CSCs represent a small portion of tumor cells with the capacity of self-renewal and multipotency, which are associated with tumor initiation, metastasis, recurrence and drug resistance. Recently, noncoding RNAs (ncRNAs) have been reported to critically regulate CSCs. Therefore, in this review article, we described the role of ncRNAs, especially miRNAs, lncRNAs and circRNAs, in regulating CSCs development and potential mechanisms. Specifically, we discussed the role of multiple miRNAs in targeting CSCs, including miR-26a, miR-29b, miR-34a, miR-133a, miR-143, miR-335, miR-382, miR-499a, miR-1247, and let-7days. Moreover, we highlighted the functions of lncRNAs in regulating CSCs in OS, such as B4GALT1-AS1, DANCR, DLX6-AS1, FER1L4, HIF2PUT, LINK-A, MALAT1, SOX2-OT, and THOR. Due to the critical roles of ncRNAs in regulation of OS CSCs, targeting ncRNAs might be a novel strategy for eliminating CSCs for OS therapy.

CO2 miscible flooding is an important technology for enhancing oil recovery and greenhouse gas storage in the world. As a tertiary recovery technology, it is usually applied after water flooding. Therefore, the actual reservoirs usually contain a lot of injected water in addition to connate water. The salinity of these formation waters varies from place to place. CO2 is an acid gas. After it is injected into the reservoir, it easily reacts with formation water and rock and affects the physical properties of the reservoir. However, no research results have been reported whether this reaction affects the minimum miscibility pressure (MMP) of CO2-crude oil, a key parameter determining miscible flooding in formation water. Based on CO2-formation water–rock interaction experiments, this paper uses the core flooding method to measure the CO2-crude oil MMP under different salinity in formation water. Results show that CO2 causes a formation water pH decrease from 7.4 to 6.5 due to its dissolution in formation water. At the same time, CO2 reacts with formation water, albite, potassium feldspar, and carbonate minerals in the cores to generate silicate and carbonate precipitates, which could migrate to the pore throat together with the released clay particles. Overall, CO2 increased core porosity by 5.63% and reduced core permeability by 7.43%. In addition, when the salinity of formation water in cores was 0, 4,767, and 6,778 mg/L, the MMP of CO2-crude oil was 20.58, 19.85, and 19.32 MPa, respectively. In other words, the MMP of CO2-crude oil decreased with the increase of salinity of formation water.

With the widespread use of traditional medicine around the world, the safety and efficacy of traditional herbal patent medicine have become an increasing concern to the public. However, it is difficult to supervise the authenticity of herbal materials in mixed herbal products according to the current quality standards, especially for traditional herbal patent medicine, with a distinct variance in the dosage of herbal materials. This study utilized the shotgun metabarcoding approach to analyze the biological ingredients of Fuke Desheng Wan (FKDSW), which is an effective traditional herbal product for the treatment of dysmenorrhea. Six herbal materials were collected, and a lab-made mock FKDSW sample was produced to establish a method for the authentication assessment of biological ingredients in traditional herbal patent medicine based on shotgun metabarcoding. Furthermore, four commercial FKDSW samples were collected to verify the practicality of the shotgun metabarcoding approach. Then, a total of 52.16 Gb raw data for 174 million paired-end reads was generated using the Illumina NovaSeq sequencing platform. Meanwhile, 228, 23, and 14 operational taxonomic units (OTUs) were obtained for the ITS2, matK, and rbcL regions, respectively, after bioinformatic analysis. Moreover, no differences were evident between the assembly sequences obtained via shotgun metabarcoding and their corresponding reference sequences of the same species obtained via Sanger sequencing, except for part of the ITS2 and matK assembly sequences of Paeonia lactiflora Pall., Saussurea costus (Falc.) Lipsch. and Bupleurum chinense DC. with 1–6 different bases. The identification results showed that all six prescribed ingredients were successfully detected and that the non-authentic ingredient of Bupleuri Radix (Chaihu, Bupleurum chinense DC. or Bupleurum scorzonerifolium Willd.) was found in all the commercial samples, namely Bupleurum falcatum L. Here, 25 weed species representing 16 genera of ten families were detected. Moreover, 26 fungal genera belonging to 17 families were found in both lab-made and commercial FKDSW samples. This study demonstrated that the shotgun metabarcoding approach could overcome the biased PCR amplification and authenticate the biological ingredients of traditional herbal patent medicine with a distinct variance in the dosage of the herbal materials. Therefore, this provides an appropriate evaluation method for improving the safety and efficacy of traditional herbal patent medicine.

Long-term placement of non-degradable silicone rubber pancreatic duct stents in the body is likely to cause inflammation and injury. Therefore, it is necessary to develop degradable and biocompatible stents to replace silicone rubber tubes as pancreatic duct stents. The purpose of our research was to verify the feasibility and biological safety of extrusion-based 3D printed radiopaque chitosan (CS) ducts for pancreaticojejunostomy. Chitosan-barium sulfate (CS-Ba) ducts with different molecular weights (low-, medium-, and high-molecular weight CS-Ba: LCS-Ba, MCS-Ba, and HCS-Ba, respectively) were soaked in vitro in simulated pancreatic juice (SPJ) (pH 8.0) with or without pancreatin for 16 weeks. Changes in their weight, water absorption rate and mechanical properties were tested regularly. The biocompatibility, degradation and radiopaque performance were verified by in vivo and in vitro experiments. The results showed that CS-Ba ducts prepared by this method had regular compact structures and good molding effects. In addition, the lower the molecular weight of the CS-Ba ducts was, the faster the degradation rate was. Extrusion-based 3D-printed CS-Ba ducts have mechanical properties that match those of soft tissue, good biocompatibility and radioopacity. In vitro studies have also shown that CS-Ba ducts can promote the growth of fibroblasts. These stents have great potential for use in pancreatic duct stent applications in the future.

As one of the high-incidence diseases in the world, pharyngitis seriously affects the lives of those with the condition. Qingguo Wan is a herbal medicine used for treating pharyngitis, and its quality evaluation is currently only accomplished via traditional identification. However, precise identification becomes challenging with fake products on the market or fungal contamination during the production process. This study used the Illumina NovaSeq platform for targeting the ITS2, psbA-trnH, matK, and rbcL sequences to survey the species composition of lab-made and commercial samples. The results showed that a total of 34.56 Gb of raw data that was obtained represented more than 0.23 billion reads. After assembly, annotation, and operational taxonomic unit clustering, 103, 12, 10, and 12 OTUs were obtained, which belonged to the ITS2, psbA-trnH, matK, and rbcL sequences of the mock lab-made and commercial samples. The analytical results indicated that the sequences of all the prescription ingredients were successfully obtained in the two lab-made samples. The positive control medicinal Panax quinquefolius L. sequence was obtained in HSZY175, while Scutellaria baicalensis Georgi, Lonicera japonica Thunb. Menispermum dauricum DC. and Paeonia lactiflora Pall. were detected in the three commercial samples. The detection results of the other four herbs in different fragments were not all the same. In addition, a total of 28 fungi OTUs, representing 19 families and 20 genera, were obtained from both the commercial and mock lab-made samples. Aspergillus, Cladosporium, and Penicillium dominated among the 20 genera. This study demonstrated that the shotgun metabarcoding method is a powerful tool for the molecular identification of the biological ingredients in Qingguo Wan. It can be used to effectively supplement traditional methods while providing a new technique for the quality evaluation of Qingguo Wan.

Traditional herbal patent medicine typically consists of multiple ingredients, making it challenging to supervise contamination by impurities and the improper use of raw materials. This study employed shotgun metabarcoding for the species identification of biological ingredients in traditional herbal patent medicine, Wuhu San. The five prescribed herbal materials found in Wuhu San were collected, and their reference sequences were obtained by traditional DNA barcoding using Sanger sequencing. Two lab-made and three commercial Wuhu San samples were collected, and a total of 37.14 Gb of shotgun sequencing data was obtained for these five samples using the Illumina sequencing platform. A total of 1,421,013 paired-end reads were enriched for the Internal Transcribed Spacer 2 (ITS2), psbA and trnH intergenic spacer region (psbA-trnH), maturase k (matK), and ribulose-1, 5-bisphosphate carboxylase (rbcL) regions. Furthermore, 80, 11, 9, and 8 operational taxonomic units were obtained for the ITS2, psbA-trnH, matK, and rbcL regions, respectively, after metagenomic assembly, annotation, and chimeric detection. In the two lab-made mock samples, all labeled ingredients in the Wuhu San prescription were successfully detected, and the positive control, Panax quinquefolius L., was detected in the HSZY172 mock sample. Three species, namely Angelica sinensis (Oliv.) Diels, Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., and Carthamus tinctorius L., belonging to three labeled ingredients, Angelicae Sinensis Radix (Danggui), Saposhnikoviae Radix (Fangfeng), and Carthami Flos (Honghua), were detected in the three commercial samples. Angelica dahurica (Hoffm.) Benth. & Hook. f. ex Franch. & Sav., the original Angelicae Dahuricae Radix (Baizhi) species, was only detected in WHS003. Arisaema erubescens (Wall.) Schott, Arisaema heterophyllum Blume, or Arisaema amurense Maxim., the original Arisaematis Rhizoma (Tiannanxing) species, were not detected in any of the commercial samples, which could be attributed to the fact that this medicinal material underwent extensive processing. In addition, the Saposhnikovia divaricata adulterant was detected in all the commercial samples, while 24 fungal genera, including Aspergillus, were identified in both the lab-made and commercial samples. This study showed that shotgun metabarcoding provided alternative strategy and technical means for identifying prescribed ingredients in traditional herbal patent medicine and displayed the potential to effectively complement traditional methods.

Increased public awareness of nutritional and health issues has resulted in the increasing consumption of food and herbal products made from the root of Pueraria montana var. lobata (Willd.) Maesen & S. M. Almeida ex Sanjappa & Predeep (kudzu vine) and P. montana var. thomsonii (Benth.) M. R. Almeida. The famous herbal medicine Yufeng Ningxin, which is used to treat cardiovascular diseases, can be legally produced only using P. montana var. lobata. However, precise identification at the subspecies level is usually challenging when these products’ ingredients lose their morphological characteristics after deep processing. Here, six herbarium specimens, 21 expert-identified original plant samples, 30 raw material samples, 10 food products and 12 herbal products were collected to test the subspecies-level authentication abilities of ITS2 sequences. The results showed that ITS2 sequences can distinguish P. montana var. lobata from P. montana var. thomsonii with stable single nucleotide polymorphism (SNP) sites. A total of 93.3% of raw material samples were consistent with the markings on their labels, but only 50% of Gegen Powder samples were made from P. montana var. lobata. High-quality ITS2 sequences were successfully obtained from nine of the 12 herbal products using Sanger sequencing. Substitution and fungal contamination were detected in 3 herbal products by further DNA metabarcoding, even though thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) tests verified that the products met existing quality standards. This study demonstrated that DNA barcoding is a powerful tool for the identification of P. montana var. lobata and P. montana var. thomsonii at the subspecies level, and we conclude that DNA barcodes can be broadly applied to trace the raw materials of food and herbal products.

The Escherichia coli quorum sensing (QS) signal molecule, autoinducer-2 (AI-2), reaches its maximum concentration during mid-to-late growth phase after which it quickly degrades during stationary phase. This pattern of AI-2 concentration coincides with the up- then down-regulation of a recently described microcin PDI (mccPDI) effector protein (McpM). To determine if there is a functional relationship between these systems, a prototypical mccPDI-expressing strain of E. coli 25 was used to generate ΔluxS, ΔlsrACDBFG (Δlsr), and ΔlsrR mutant strains that are deficient in AI-2 production, transportation, and AI-2 transport regulation, respectively. Trans-complementation, RT-qPCR, and western blot assays were used to detect changes of microcin expression and synthesis under co-culture and monoculture conditions. Compared to the wild-type strain, the AI-2-deficient strain (ΔluxS) and -uptake negative strain (Δlsr) were >1,000-fold less inhibitory to susceptible bacteria (P < 0.05). With in trans complementation of luxS, the AI-2 deficient mutant reduced the susceptible E. coli population by 4-log, which was within 1-log of the wild-type phenotype. RT-qPCR and western blot results for the AI-2 deficient E. coli 25 showed a 5-fold reduction in mcpM transcription with an average 2-h delay in McpM synthesis. Furthermore, overexpression of sRNA micC and micF (both involved in porin protein regulation) was correlated with mcpM regulation, consistent with a possible link between QS and mcpM regulation. This is the direct first evidence that microcin regulation can be linked to quorum sensing in a Gram-negative bacterium.

Herbal drug authentication is an important task in traditional medicine; however, it is challenged by the limitations of traditional authentication methods and the lack of trained experts. DNA barcoding is conspicuous in almost all areas of the biological sciences and has already been added to the British pharmacopeia and Chinese pharmacopeia for routine herbal drug authentication. However, DNA barcoding for the Korean pharmacopeia still requires significant improvements. Here, we present a DNA barcode reference library for herbal drugs in the Korean pharmacopeia and developed a species identification engine named KP-IDE to facilitate the adoption of this DNA reference library for the herbal drug authentication. Using taxonomy records, specimen records, sequence records, and reference records, KP-IDE can identify an unknown specimen. Currently, there are 6,777 taxonomy records, 1,054 specimen records, 30,744 sequence records (ITS2 and psbA-trnH) and 285 reference records. Moreover, 27 herbal drug materials were collected from the Seoul Yangnyeongsi herbal medicine market to give an example for real herbal drugs authentications. Our study demonstrates the prospects of the DNA barcode reference library for the Korean pharmacopeia and provides future directions for the use of DNA barcoding for authenticating herbal drugs listed in other modern pharmacopeias.

Vibrio spp. are the most common pathogens for animals reared in aquaculture. Vibrio campbellii, which is often involved in shrimp, fish and mollusks diseases, is widely distributed in the marine environment worldwide, but our knowledge about its pathogenesis and antimicrobial resistance is very limited. The existence of this knowledge gap is at least partially because that V. campbellii was originally classified as Vibrio harveyi, and the detailed information of its comparative genome analysis to other Vibrio spp. is currently lacking. In this study, the complete genome of a V. campbellii predominant strain, LMB29, was determined by MiSeq in conjunction with PacBio SMRT sequencing. This genome consists of two circular DNA chromosomes and four megaplasmids. Comparative genome analysis indicates that LMB29 shares a 96.66% similarity (average nucleotide identity) with the V. campbellii ATCC strain BAA-1116 based on a 75% AF (average fraction) calculations, and its functional profile is very similar to V. campbellii E1 and V. campbellii CAIM115. Both type III secretion system (T3SS) and type VI secretion system (T6SS), along with the tlh gene which encodes a thermolabile hemolysin, are present in LMB29 which may contribute to the bacterial pathogenesis. The virulence of this strain was experimental confirmed by performing a LDH assay on a fish cell infection model, and cell death was observed as early as within 3 h post infection. Thirty-seven antimicrobial resistance genes (>45% identity) were predicted in LMB29 which includes a novel rifampicin ADP ribosyltransferase, arr-9, in plasmid pLMB157. The gene arr-9 was predicted on a genomic island with horizontal transferable potentials which may facilitate the rifampicin resistance dissemination. Future researches are needed to explore the pathogenesis of V. campbellii LMB29, but the availability of this genome sequence will certainly aid as a basis for further analysis.

Type III secretion systems (T3SSs) contribute to microbial pathogenesis of Vibrio species, but the regulatory mechanisms are complex. We determined if the classic ExsACDE protein-protein regulatory model from Pseudomonas aeruginosa applies to Vibrio alginolyticus. Deletion mutants in V. alginolyticus demonstrated that, as expected, the T3SS is positively regulated by ExsA and ExsC and negatively regulated by ExsD and ExsE. Interestingly, deletion of exsE enhanced the ability of V. alginolyticus to induce host-cell death while cytotoxicity was inhibited by in trans complementation of this gene in a wild-type strain, a result that differs from a similar experiment with Vibrio parahaemolyticus ExsE. We further showed that ExsE is a secreted protein that does not contribute to adhesion to Fathead minnow epithelial cells. An in vitro co-immunoprecipitation assay confirmed that ExsE binds to ExsC to exert negative regulatory effect on T3SS genes. T3SS in V. alginolyticus can be activated in the absence of physical contact with host cells and a separate regulatory pathway appears to contribute to the regulation of ExsA. Consequently, like ExsE from P. aeruginosa, ExsE is a negative regulator for T3SS gene expression in V. alginolyticus. Unlike the V. parahaemolyticus orthologue, however, deletion of exsE from V. alginolyticus enhanced in vitro cytotoxicity.