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The perennially unfrozen zones (taliks) in the Eruu area of central Yakutia have a complex stratigraphic structure, and the dynamic characteristics of groundwater in this region have been insufficiently studied. This study analyzed the results of the explorations and geophysical studies conducted by the Melnikov Permafrost Institute of the Siberian Branch of the Russian Academy of Science. In addition, we simulated and analyzed the dynamic characteristics of groundwater in the area based on hydro-meteorological data, snow data, and remote sensing data. During the process, the dynamic changes in the attributes of aquifers due to the seasonal freeze–thaw processes of soils, including the active layer, were also taken into account. The results showed the following: (1) According to the analysis of the measured data on water levels in hydrogeological observation well 14E/2014, the difference between the simulated and measured values of groundwater levels in monitoring wells for over 99% of the measurements was less than 0.1 m. The average difference between the measured (excluding missing values) and simulated values of groundwater level in the monitoring wells was 0.028 m/d. (2) The annual average water level in the study area declined. The simulated value dropped at a rate of 0.10 m/a, with only a gap of 0.01 m/a with the measured value. Meanwhile, the simulated water head was greatly influenced by the terrain, especially in the central area, where the head decreased rapidly from the perimeter toward the lakes (8.9 m/km on average). (3) From 1 September 2014 to 31 August 2015, the mean value of the simulated discharge in the study area was 3888.39 L/d, which was in line with the results of previous monitoring (the average flow was 4147.20 L/d and 3715.20 L/d in 2014 and 2015, respectively). This study can provide a reference for the reasonable exploitation and utilization of groundwater under the influence of the distribution of perennially unfrozen zones, or taliks, and provides an effective three-dimensional modeling method for quantifying the analysis of groundwater dynamics in permafrost regions.

Background Transient receptor potential vanilloid subtype 1 (TRPV1) plays a pivotal role in neurons and is closely related to pain transduction. However, the role of TRPV1 in pan-cancer remains unclear. Methods Data visualization was performed using TCGA, GETx, GEPIA2, TIMER, TISIDB, DiseaseMeth, GeneMANIA, GSEA, and Depmap Portal database and R language. Results We explored the pan-cancer expression patterns and prognostic value of TRPV1 across multiple databases and found that TRPV1 served as a tumor suppressor in most cancers. In particular, genetic alteration and DNA methylation analysis across 33 tumors revealed that gene deletion and DNA hypermethylation may contribute to its downregulation. We further constructed a transcription factors-TRPV1 regulatory network and revealed a series of key upstream transcription factors of TRPV1 in certain cancers. Additionally, we studied the relationship between TRPV1 levels and the tumor microenvironment, immune cells, immune checkpoints, and its sensitivity to small-molecule inhibitors. Conclusions Our study curated both the genetic and epigenetic status of TRPV1 and its regulatory networks in cancers and highlighted that TRPV1 could serve as a prognostic biomarker and is correlated with immunotherapy and chemotherapy.

Background Due to the latent onset of novel coronavirus disease 2019 (COVID-19), it is important to identify patients with increased probabilities for disease progression early in order to implement timely medical strategies. This study aimed to identify the factors associated with increased COVID-19 severity and evaluate the current antiviral drugs, especially in severe patients. Methods This was a retrospective observational study performed at the No. 7 Hospital of Wuhan (Wuhan, China) with hospitalized patients confirmed with COVID-19 from January 11 to March 13, 2020. Multivariable logistic regression analysis was used to identify the associated factors of severe COVID. Treatments of antivirus drugs were collected and evaluated. Results Of the 550 patients, 292 (53.1%) were female and 277 (50.4%) were > 60 years old. The most common symptom was fever (n = 372, 67.7%), followed by dry cough (n = 257, 46.7%), and dyspnea (n = 237, 43.1%), and fatigue (n = 224, 40.7%). Among the severe patients, 20.2% required invasive ventilator support and 18.0% required non-invasive ventilator. The identified risk factors for severe cases were: age ≥ 60 years (odds ratio (OR) =3.02, 95% confidence interval (CI): 1.13–8.08, P = 0.028), D-dimer > 0.243 μg/ml (OR = 2.734, 95%CI: 1.012–7.387, P = 0.047), and low oxygenation index (OR = 0.984, 95%CI: 0.980–0.989, P P = 0.029). Conclusions Age > 60 years, D-dimer > 0.243 μg/ml, and lower oxygenation index were associated with severe COVID-19. Arbidol might provide more clinical benefits in treating patients with severe COVID-19 compared with ribavirin.

The aim of this study was to assess the characteristics of mitral annular plane systolic excursion (MAPSE) in different longitudinal directions in normal fetuses using a new method, automatic cardiac motion quantification (aCMQ).A cross-sectional study was conducted in 164 fetuses with structurally normal hearts. The time-displacement curves of the septal mitral annulus (SMA) in three directions, including point A, B and C (MAPSE-SMA-A, MAPSE-SMA-B, MAPSE-SMA-C), were recorded by aCMQ. The time to peak (TTP) in three directions, including point A, B and C (TTP-SMA-A, TTP-SMA-B, TTP-SMA-C) were recorded. In the same way, various parameters of the lateral mitral annulus (LMA) were obtained including MAPSE-LMA-A, MAPSE-LMA-B, MAPSE-LMA-C, TTP-LMA-A, TTP-LMA-B and TTP-LMA-C. Free angle M-mode echocardiography (FAM) was used to obtain MAPSE of LMA (FAM-MAPSE). Finally, all the data were analyzed statistically.MAPSE was positively correlated with gestational age, and the difference between the second- and third-trimester groups was statistically significant. MAPSE-LMA in point B and C were greater than those of SMA. MAPSE-LMA-C and MAPSE-SMA-A were the largest in three directions.The difference between point B and C were statistically significant (The longitudinal movement of the fetal mitral annulus is comprehensive, with multiple directions and different displacements. Perpendicular to the mitral annulus is the maximum displacement. It is positively related to the gestational age. From the second trimester, the longitudinal contraction of the left ventricle wall has good synchronization. It possesses clinical value in selecting different methods and parameters during evaluating left ventricular function.

Herbaceous peony is a promising oilseed crop. ‘Hangshao’ and ‘Fenghuang Niepan’ are two cultivars with high yield and oil content. In this study, seed reserved nutrient of these two genotypes were investigated during seed development process. Results showed that ‘Hangshao’ and ‘Fenghuang Niepan’ matured approximately 85 ​d after flowering (DAF). The development process could be divided into four stages: seed formation and enlargement stage (S1), seed inclusion and enrichment stage (S2), crude fat rapid accumulation stage (S3) and dehydration and color transition stage (S4). During this process, 100-seed fresh weight (HFW) and 100-seed dry weight (HDW) increased, whereas water content (WC) decreased. HFW, HDW and WC for ‘Hangshao’ seed at 85 DAF were 28.56 g, 20.78 ​g and 37.50% respectively, whereas those for ‘Fenghuang Niepan’ seed were 27.2 ​g, 19.78 ​g, and 30.85% respectively. In terms of the primary metabolites measuring, soluble protein content was consistently low (only 2.24%–3.15%), while starch content was relatively high (5.60%–24.81%). They displayed a trend of gradual increasing in early stage, followed by rapid decline. Crude fat tended to accumulate continuously with a linear upward trend starting at 40 DAF, and its maximum level was reached at 85 DAF (27.57% for ‘Hangshao’ and 29.57% for ‘Fenghuang Niepan’). For the secondary metabolites determination, total phenols content was relatively steady, maintaining at 107.7–129.9 ​mg/g for both cultivars, while total flavonoids content varied within 25.33–65.33 ​mg/g for ‘Hangshao’ and 24.33–52.37 ​mg/g for ‘Fenghuang Niepan’. The maximum level for both cultivars occurred at 55 DAF. Furthermore, crude fat content was found to be highly correlated with WC by correlation analysis and linear regression model definition (P ​≤ ​0.01 and r ​= ​0.954). Thus, WC was recommended for evaluating crude fat in peony seed. These findings could provide scientific reference for high-yielding production practice for oleaginous peony plant.

The WRKY family is a specific super gene family in plants that plays a significant regulatory role in abiotic stress in plants. In this paper, the PlWRKY70 gene was cloned by RT-PCR from Paeonia lactiflora ‘Da Fugui’ buds (GenBank accession no. KU891819). The open reading frame of the gene was 936 bp in length, encoding 311 amino acids. The PlWRKY70 gene contained a WRKY domain in its coding region that belonged to the group III WRKY family and was evolutionarily the closest to Paeonia suffruticosa. PlWRKY70 was widely expressed and found at an extremely high level in buds. Moreover, the PlWRKY70 protein was mostly detected in the nucleus. The expression of PlWRKY70 was remarkably influenced by different abiotic stresses with completely different patterns. It could be significantly induced by low-temperature and salt stress, rapidly reaching peak levels after the initial 4 or 8 h of the stress treatment, whereas under waterlogging stress, it was considerably suppressed, dramatically dropping to minimum levels after 2 h of treatment. These profiles suggested that PlWRKY70 was sensitive to low-temperature, salt, and waterlogging stresses in P. lactiflora.

Pteroceltis tatarinowii Maxim, the only species of the genus Pteroceltis (family Ulmaceae), is an endemic rare tree species in China. This study was performed to explore vegetative propagation techniques for P. tatarinowii using stem cuttings. First, the effects of exogenous indole-3-butyric acid (IBA) and cutting positions on rooting performance were investigated to screen the appropriate exogenous auxin treatment and to determine the proper cuttings type. The results showed that the control cuttings pretreated with no exogenous IBA, irrespective of whether the stem cuttings were terminal, middle, or basal, rooted in a manner significantly inferior to that of cuttings pretreated with IBA. Their rooting percentage was less than 50%. Among the IBA-treated cuttings, the middle cuttings pretreated with 1000 mg·L−1 IBA rooted best, with the shortest number of days until rooting emergence (20 days), the highest rooting percentage (84.0%), the lowest mortality rate (4.0%), the greatest root number (average of 6.7 per cutting), and the longest roots per cutting (44.4 cm per cutting). Terminal cuttings pretreated with 1000 mg·L−1 IBA acquired satisfactory rooting traits and had the same shortest rooting duration (20 days) and the following parameters: rooting, 70.7%; mortality, 10.7%; average roots per cutting, 5.2; and longest root, 29.1 cm. To further determine the optimum cutting propagation time for this plant, a second experiment was performed and the cuttings were collected beginning in early June, when the growth of the current season was feasible for harvesting cuttings. Stem cuttings collected in late June and middle July had significantly higher rooting percentages (≥80%) compared with those collected in early June (66.7%). The other three rooting parameters were not significantly affected by the collection date. However, according to the overall rooting traits, the cuttings collected in both late June and middle July remarkably outperformed those collected in early June regarding the number of roots and the total root length per cutting. The initial nutrient reserves in the cuttings were also determined. A significant difference in the soluble carbohydrate level was found among collection times, but the nitrogen level in the cuttings was similar. The study revealed that stem cutting propagation of P. tatarinowii was achievable, and it was best achieved with cuttings collected from the terminal and middle positions of the branches of the current season from late June to middle July and treated with 1000 mg·L−1 IBA using the quick dip method.

Background: Due to the latent onset of novel coronavirus disease 2019 (COVID-19), it is important to identify patients with increased probabilities for disease progression early in order to implement timely medical strategies. This study aimed to identify the factors associated with increased COVID-19 severity and evaluate the current antiviral drugs, especially in severe patients. Methods: This was a retrospective observational study performed at the No. 7 Hospital of Wuhan (Wuhan, China) with hospitalized patients confirmed with COVID-19 from January 11 to March 13, 2020. Multivariable logistic regression analysis was used to identify the associated factors of severe COVID. Treatments of antivirus drugs were collected and evaluated.Results: Of the 550 patients, 292 (53.1%) were female and 277 (50.4%) were >60 years old. The most common symptom was fever (n=372, 67.7%), followed by dry cough (n=257, 46.7%), and dyspnea (n=237, 43.1%), and fatigue (n=224, 40.7%). Among the severe patients, 20.2% required invasive ventilator support and 18.0% required non-invasive ventilator. The identified risk factors for severe cases were: age ≥60 years (odds ratio (OR) =3.02, 95% confidence interval (CI): 1.13-8.08, P=0.028), D-dimer >0.243 μg/ml (OR=2.734, 95%CI: 1.012-7.387, P=0.047), and low oxygenation index (OR=0.984, 95%CI: 0.980-0.989, PConclusions: Age >60 years, D-dimer >0.243 µg/ml, and lower oxygenation index were associated with severe COVID-19. Arbidol might provide more clinical benefits in treating patients with severe COVID-19 compared with ribavirin.

Background Due to the latent onset of novel coronavirus disease 2019 (COVID-19), it is important to identify patients with increased probabilities for disease progression early in order to implement timely medical strategies. This study aimed to identify the factors associated with severe COVID-19 and evaluate the current antiviral drugs, especially in severe patients. Methods This was a retrospective observational study performed at the No. 7 Hospital of Wuhan (Wuhan, China) with hospitalized patients confirmed with COVID-19 from January 11 to March 13, 2020. Multivariable logistic regression analysis was used to identify the associated factors of severe COVID. Treatment of antivirus drugs were collected and evaluated. Results Of the 550 patients, 292 (53.1%) were female and 277 (50.4%) were ≥ 60 years old. The most common symptom was fever (n = 372, 67.7%), followed by dry cough (n = 257, 46.7%), and dyspnea (n = 237, 43.1%), and fatigue (n = 224, 40.7%). Among the severe patients, 20.2% required invasive ventilator support and 18.0% required non-invasive ventilator. The identified risk factors for severe cases were: age ≥ 60 years (odds ratio (OR) = 3.02, 95% confidence interval (CI): 1.13–8.08, P = 0.028), D-dimer > 0.243 µg/ml (OR = 2.734, 95%CI: 1.012–7.387, P = 0.047), and low oxygenation index (OR = 0.984, 95%CI: 0.980–0.989, P 0.243 µg/ml, and lower oxygenation index were associated with severe cases. Arbidol might provide more clinical benefits in treating patients with severe COVID-19 compared with other antiviral drugs.

In this study, the disease resistance gene PlWRKY65 was isolated from the leaves of Paeonia lactiflora and analyzed by bioinformatics methods, and the localization of the encoded protein was explored. Quantitative real-time PCR (qRT-PCR) was also used to explore the response of this gene to Alternaria tenuissima. The results showed that the gene sequence contained multiple cis-acting elements involved in the response to hormone signaling molecules belonging to the IIe subgroup of the WRKY family, and the encoded proteins were located in the nucleus. The PlWRKY65 gene has a positive regulatory effect on A. tenuissima infection. After silencing the PlWRKY65 gene via virus-induced gene silencing (VIGS), it was found that the gene-silenced plants were more sensitive to A. tenuissima infection than the wild plants, exhibiting more severe infection symptoms and different degrees of changes in the expression of the pathogenesis-related (PR) genes. In addition, we showed that the endogenous jasmonic acid (JA) content of P. lactiflora was increased in response to A. tenuissima infection, whereas the salicylic acid (SA) content decreased. After PlWRKY65 gene silencing, the levels of the two hormones changed accordingly, indicating that PlWRKY65, acting as a disease resistance-related transcriptional activator, exerts a regulatory effect on JA and SA signals. This study lays the foundation for functional research on WRKY genes in P. lactiflora and for the discovery of candidate disease resistance genes.

Many members of the WRKY family regulate plant growth and development. Recent studies have shown that members of the WRKY family, specifically WRKY13, play various roles in the regulation of plant stress resistance. To study the function of WRKY family members in peony, the PlWRKY13 gene (KY271095) was cloned from peony leaves. Sequence analysis and subcellular localization results revealed that PlWRKY13 has no introns, belongs to the type IIc subgroup of the WRKY family, and functions in the nucleus. The expression pattern of PlWRKY13 was analysed via real-time quantitative RT-PCR (qRT-PCR), which showed that the expression of PlWRKY13 was induced by four types of abiotic stress, low-temperature, high-temperature, waterlogging and salt stress, and was positively upregulated in response to these stresses. In addition, the expression of PlWRKY13 tended to first decrease and then increase after infection with Alternaria tenuissima. Virus-induced gene silencing (VIGS) technology was used to explore the function of PlWRKY13 in the resistance of Paeonia lactiflora to fungal infection further, and the results showed that PlWRKY13-silenced plants displayed increased sensitivity to A. tenuissima. The infection was more severe and the disease index (DI) significantly greater in the PlWRKY13-silenced plants than in the control plants, and the expression of pathogenesis-related (PR) genes was also significantly altered in the PlWRKY13-silenced plants compared with the control plants. The contents of the endogenous hormones jasmonic acid (JA) and salicylic acid (SA) were measured, and the results showed that the JA content increased gradually after infection with A. tenuissima and that JA may play an active role in the resistance of P. lactiflora to pathogen infection, while the SA content decreased after PlWRKY13 silencing. The contents of the two hormones decreased overall, suggesting that they are related to the transcription of PlWRKY13 and that PlWRKY13 may be involved in the disease-resistance pathway mediated by JA and SA. In summary, the results of our study showed that PlWRKY13 expression was induced by stress and had a positive effect on the resistance of P. lactiflora to fungal infection.

Dehydrins (DHNs) proteins play a protective role in plants under different abiotic stress conditions. In this study, a stress-responsive dehydrin gene PlDHN1 (GenBank accession number: KX524516) wa...

Mitogen-activated protein kinases (MAPKs) are important components in signal transduction modules which play crucial roles in regulation of many biological processes in plants. Although genome-wide analysis of MAPK and MAPKK family has been carried out in poplar species, few data about the biological function analysis of this gene family are available to date. In this study, a group C MAPK gene 84KMPK14 was cloned from hybrid poplar (Populus alba × P. glandulosa cv. “84K”). It contained a typical protein kinase domain, a conserved TEY-motif and an atypical conserved common docking (CD) domain. Sequence alignment revealed that 84KMPK14 was the most homologous to Populus trichocarpa PtMPK14. Expression analysis indicated that the transcript of 84KMPK14 in roots and young leaves was higher than that in other tissues. The expression of 84KMPK14 was down-regulated by low or high temperature and was induced by H2O2 significantly. It was suppressed by drought and salinity stresses slightly one hour after treatment and then increased quickly three hours after treatment. These results indicated that 84KMPK14 may be involved in environmental stresses, which provides basis for further characterization of the physiological analysis on this gene.

Phascolarctobacterium can produce short-chain fatty acids, including acetate and propionate, and can be associated with the metabolic state and mood of the host. The present study investigated the colonization characteristics of Phascolarctobacterium faecium in healthy individuals 1 year old). The permillage of Phascolarctobacterium faecium in total bacteria ranged between 0.004–1.479. There was presence of Phascolarctobacterium faecium-like bacteria in younger individuals with a gradual increase in the number of bacteria maintained at a high level with increasing ages (between 1 and 60 years old), but with a decrease in elderly individuals (>60 years old). The results of the present study demonstrated that Phascolarctobacterium faecium is abundantly colonized in the human gastrointestinal tract.

GA20-oxidase (GA20ox) gene encodes a key enzyme in gibberellins (GAs) biosynthesis pathway. Previously, we have cloned a PlGA20ox gene (GeneBank accession number: KU886552) from Paeonia lactiflora. To further reveal its function, we constructed an expression vector in the present study and then transformed it into Arabidopsis thaliana plants by floral dip method. The transgenic plants exhibited an early bolting, increased height and improved vegetative growth. These results provided efficient vector tool and functional information of PlGA20ox for future gene engineering in peony.

In this study, the disease resistance gene PlWRKY65 was isolated from the leaves of Paeonia lactiflora and analyzed by bioinformatics methods, and the localization of the encoded protein was explored. Quantitative real-time PCR (qRT-PCR) was also used to explore the response of this gene to Alternaria tenuissima. The results showed that the gene sequence contained multiple cis-acting elements involved in the response to hormone signaling molecules belonging to the IIe subgroup of the WRKY family, and the encoded proteins were located in the nucleus. The PlWRKY65 gene has a positive regulatory effect on A. tenuissima infection. After silencing the PlWRKY65 gene via virus-induced gene silencing (VIGS), it was found that the gene-silenced plants were more sensitive to A. tenuissima infection than the wild plants, exhibiting more severe infection symptoms and different degrees of changes in the expression of the pathogenesis-related (PR) genes. In addition, we showed that the endogenous jasmonic acid (JA) content of P. lactiflora was increased in response to A. tenuissima infection, whereas the salicylic acid (SA) content decreased. After PlWRKY65 gene silencing, the levels of the two hormones changed accordingly, indicating that PlWRKY65, acting as a disease resistance-related transcriptional activator, exerts a regulatory effect on JA and SA signals. This study lays the foundation for functional research on WRKY genes in P. lactiflora and for the discovery of candidate disease resistance genes.

The prevalence of obesity and diabetes, and their complicating mental disorders, severely affect public health. This study aimed to investigate the long-term effects of an Akkermansia muciniphila subtype (A. muciniphilasub) on high-fat diet-induced obesity and diabetes, and to evaluate whether this subtype can alleviate their complicated mental disorders. Whole genome sequencing and short chain fatty acid production analysis in supernatant of pure culture were performed. Female adult C57BL/6 mice were fed a high-fat diet or a normal chow diet and were gavaged with A. muciniphilasub or phosphate-buffered saline daily for 10 months. Body weight, food consumption and blood glucose were measured. At the end of the treatment period, all mice were subjected to the Y-maze test, sucrose preference test, analyses of serum, fecal microbiota analysis and histological examination. This A. muciniphilasub had 278 unique genes compared to the type strain (A. muciniphila ATCC BAA-835) and produced short chain fatty acids both. A. muciniphilasub administration significantly reduced body weight gain and improved the spatial memory of high-fat diet-fed mice. A. muciniphilasub increased Nissl bodies in neurons of the hippocampus, and restored the high-fat diet-inhibited tryptophan metabolism. The high-fat diet led to decreased serum 5-hydroxytryptamine and induced depression, which were not alleviated by A. muciniphilasub. A. muciniphilasub increased the relative fecal abundance of Bifidobacterium, and was negatively correlated with the fecal abundance of Bacteroides. The present study demonstrated the beneficial effects of this A. muciniphilasub on body weight, blood glucose control and the alleviation of the memory decay caused by a high-fat diet in mice.

Herbaceous peony (Paeonia lactiflora Pall.) is a prospective oilseed crop and is widely cultivated in temperate regions. In the present study, eleven fertility characteristics of sixteen peony genotypes were systematically investigated through two consecutive years of observation, and correlation analysis between the parameter seed yield per stem and other ten parameters was performed. Then the fatty acid composition in the seed oil was further determined with six peony cultivars selected from the investigation. The results showed that the examined sixteen genotypes exhibited a wide range of significant differences in fertility traits. A significant positive correlation was observed between seed yield and other seven parameters (P

DELLA protein plays a significant role in plant growth and development. In this study, PlDELLA with the open reading frame of 1866 bp in length was isolated from Paeonia lactiflora. Overexpression of PlDELLA in Arabidopsis thaliana showed that seed germination was significantly repressed as it took 144∼192 h for the OEs to reach 100 % germination and it required only 60 h for the WT. The OEs were also inhibited in bolting time and in plant vegetative growth. When PlDELLA was silenced in peony by virus-induced gene silencing method, peony budbreak occurred earlier by 8∼10 d and the vegetative growth was significantly accelerated compared with the control group. These results collectively indicated that PlDELLA negatively regulated dormancy release and plant growth. During chilling process to release peony endodormancy, PlDELLA expression down-regulated, and the content of both endogenous active GAs and ABA decreased, indicating decreasing of PlDELLA expression under chilling was not caused by the known gibberellin signal transduction pathway. Besides, PlDELLA had no interaction with the four screened PlWRKYs, PlWRKY13, PlWRKY18, PlWRKY40 or PlWRKY50. These findings not only enrich the knowledge of DELLA protein family, but also provide insights into understanding the function of PlDELLA protein in endodormancy release in peony.

Background Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content. Results Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins. Phylogenetic analysis identified three species-level A. muciniphila phylogroups exhibiting distinct metabolic and functional features. Based on the comprehensive genome catalogue, we reconstructed 106 newly A. muciniphila metagenome assembled genomes (MAGs) from available metagenomic datasets of human, mouse and pig gut microbiomes, revealing a transcontinental distribution of A. muciniphila phylogroups across mammalian gut microbiotas. Accurate quantitative analysis of A. muciniphila phylogroups in human subjects further demonstrated its strong correlation with body mass index and anti-diabetic drug usage. Furthermore, we found that, during their mammalian gut evolution history, A. muciniphila acquired extra genes, especially antibiotic resistance genes, from symbiotic microbes via recent lateral gene transfer. Conclusions The genome repertoire of A. muciniphila provided insights into population structure, evolutionary and functional specificity of this significant bacterium. Electronic supplementary material The online version of this article (10.1186/s12864-017-4195-3) contains supplementary material, which is available to authorized users.

Growing on rooting media other than soils in situ -i.e., substrate-based growing- allows for higher yields than soil-based growing as transport rates of water, nutrients, and oxygen in substrate surpass those in soil. Possibly water-based growing allows for even higher yields as transport rates of water and nutrients in water surpass those in substrate, even though the transport of oxygen may be more complex. Transport rates can only limit growth when they are below a rate corresponding to maximum plant uptake. Our first objective was to compare Chrysanthemum growth performance for three water-based growing systems with different irrigation. We compared; multi-point irrigation into a pond (DeepFlow); one-point irrigation resulting in a thin film of running water (NutrientFlow) and multi-point irrigation as droplets through air (Aeroponic). Second objective was to compare press pots as propagation medium with nutrient solution as propagation medium. The comparison included DeepFlow water-rooted cuttings with either the stem 1 cm into the nutrient solution or with the stem 1 cm above the nutrient solution. Measurements included fresh weight, dry weight, length, water supply, nutrient supply, and oxygen levels. To account for differences in radiation sum received, crop performance was evaluated with Radiation Use Efficiency (RUE) expressed as dry weight over sum of Photosynthetically Active Radiation. The reference, DeepFlow with substrate-based propagation, showed the highest RUE, even while the oxygen supply provided by irrigation was potentially growth limiting. DeepFlow with water-based propagation showed 15–17% lower RUEs than the reference. NutrientFlow showed 8% lower RUE than the reference, in combination with potentially limiting irrigation supply of nutrients and oxygen. Aeroponic showed RUE levels similar to the reference and Aeroponic had non-limiting irrigation supply of water, nutrients, and oxygen. Water-based propagation affected the subsequent cultivation in the DeepFlow negatively compared to substrate-based propagation. Water-based propagation resulted in frequent transient discolorations after transplanting in all cultivation systems, indicating a factor, other than irrigation supply of water, nutrients, and oxygen, influencing plant uptake. Plant uptake rates for water, nutrients, and oxygen are offered as a more fundamental way to compare and improve growing systems.

Isolation, sequencing, assembly and gene prediction information of 39 A. muciniphila isolates and strain ATCC BAA-835. (XLSX 16 kb)

The rapid urbanization development has helped China's economy to rise sharply, and it has also plunged the countryside into a development dilemma. Based on a questionnaire survey of 25 industry experts, this paper uses SWOT-AHP analysis to study the advantages, disadvantages, opportunities and threats of rural development, and finally determines the development strategy of rural China. Put forward three suggestions on rural development in China, that is, grasp the national strategic opportunity to develop modern agriculture, upgrade the level of rural human capital and cultivate the concept of ecological civilization.

To construct a universal, highly attenuated orf virus expression vector for exogenous genes using green fluorescent protein (GFP) as the reporter gene.The flanking regions of the ORFV132 of orf virus DNA were amplified by PCR to construct the shuttle plasmid pSPV-132LF-EGFP-132RF. The shuttle plasmid was transfected into OFTu cells and GFP was incorporated into orf virus IA82Delta 121 by homologous recombination. The recombinant IA82Delta121-V was selected by green fluorescent signal. The deletion gene was identified by PCR and sequencing. The effects of ORFV132 knockout were evaluated by virus titration and by observing the proliferation of the infected vascular endothelial cells in vitro.The recombinant orf virus IA82Delta121-V was obtained successfully and quickly, and the deletion of ORFV132 did not affect the replication of the virus in vitro but reduced its virulence.Green fluorescent protein is a selectable marker for rapid, convenient and stable selection of the recombinant viruses. Highly attenuated recombinant orf virus IA82Delta121-V can serve as a new expression vector for exogenous genes.

Aim This study investigates the colonization rate of Akkermansia muciniphila in the gastrointestinal tracts of people living in southern China and applies a modified method for the isolation and subtyping of A. muciniphila strains from faecal samples. Methods and Results Fresh faecal samples were collected and bacterial DNA was extracted from these samples for real-time PCR analysis. Strains were separated using a culture-dependent sPCR-directed method and classified using an enterobacterial repetitive intergenic consensus (ERIC-PCR) DNA fingerprinting method. The colonization rate for the sample population from southern China was 51·74%. We isolated 22 strains from human faeces. The results revealed that all strains were identifiable as A. muciniphila with 99–100% identity to the type-strain ATCC BAA-835. ERIC-PCR resulted in grouping of the DNA fingerprints showed that 12 distinct clusters were distinguished with a delineation level of 100%. Conclusions Southern China has a high rate of A. muciniphila colonization and over 12 different subtype strains reside in faecal samples. Significance and Impact of the Study Akkermansia muciniphila has a beneficial role in human gastrointestinal tract. These studies provide a better understanding of A. muciniphila and details of its colonization in the human gastrointestinal tract.