Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration.

The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.

Radiomics-Based Risk Assessment Correlates With Outcomes in Patients With Acute Type B Aortic Dissection Undergoing Thoracic Endovascular Repair.

OBJECTIVES: Our study aimed to investigate the correlations between radiomics-based assessment and outcomes, including positive aortic remodeling (PAR), reintervention for dissection at 1 year, and overall survival, in patients with Type B aortic dissection (TBAD) who underwent thoracic endovascular aortic repair (TEVAR). METHODS: This was a single-center, retrospective, cohort study. The cohort comprised 104 patients who had undergone TEVAR of TBAD in our institution between January 2010 and October 2022. We segmented preoperative computed tomography (CT) images of the patients' descending aorta regions, then extracted a comprehensive set of radiomic features, including first-order features, shape features (2D and 3D), gray-level co-occurrence matrix (GLCM), gray-level size zone matrix, gray-level run length matrix, gray-level dependence matrix, neighborhood gray-tone difference matrix, from the regions of interest. Next, we selected radiomics features associated with total descending aorta positive aortic remodeling (TDA-PAR) and reintervention by least absolute shrinkage and selection operator (LASSO) regression and features associated with survival by LASSO-Cox regression. This enabled us to calculate radiomics-based risk scores for each patient. We then allocated the patients to high and low radiomics-based risk groups, the cutoff being the median score. We used 3 different models to validate the radiomics-based risk scores. RESULTS: The patients' baseline characteristics did not differ between those who achieved TDA-PAR and those who did not. The radiomics-based risk scores were significantly and independently associated with all 3 outcomes. As to the impact of specific radiomics features, we found that GLSZM_SmallAreaLowGrayLevelEmphasis and shape_Maximum2DDiameterColumn had positive impacts on both reintervention and survival outcomes, whereas GLCM_Idmn positively affected survival but negatively affected reintervention. We found that radiomics-based risk for TDA-PAR correlated most significantly with zone 6 PAR. CONCLUSIONS: Radiomics-based risk scores were significantly associated with the outcomes of TDA-PAR, reintervention, and overall survival. Radiomics has the potential to make significant contributions to prediction of outcomes in patients with TBAD undergoing TEVAR. CLINICAL IMPACT: In this study of 104 patients with Type B aortic dissection, we demonstrated associations between radiomics-based risk and postoperative outcomes, including total descending aorta positive aortic remodeling, reintervention and survival. These findings highlight radiomics' potential as a tool for risk stratification and prognostication in acute Type B aortic dissection management.

Establishing a Classification System for Predicting Flow-Limiting Dissection After Balloon Angioplasty Using Explainable Machine-Learning Models: A Multicenter Retrospective Cohort Study.

OBJECTIVE: Percutaneous transluminal angioplasty (PTA) is the primary method for treatment in peripheral arterial disease. However, some patients experience flow-limiting dissection (FLD) after PTA. We utilized machine learning and SHapley Additive exPlanations to identify and optimize a classification system to predict FLD after PTA. METHODS: This was a multi-center, retrospective, cohort study. The cohort comprised 407 patients who underwent treatment of the femoropopliteal (FP) arteries in 3 institutions between January 2021 and June 2023. Preoperative computed tomography angiography images were evaluated to identify FP artery grading, chronic total occlusion (CTO), and vessel calcification (peripheral artery calcium scoring system [PACSS]). After PTA, FLD was identified by angiography. We trained and validated 6 machine-learning models to estimate FLD occurrence after PTA, and the best model was selected. Then, the sum of the Shapley values for each of CTO, FP, and PACSS was calculated for each patient to produce the CTO-FP-PACSS value. The CTO-FP-PACSS classification system was used to classify the patients into classes 1 to 4. Univariate and multivariate analyses were performed to validate the effectiveness of the CTO-FP-PACSS classification system for predicting FLD. RESULTS: Overall, 407 patients were analyzed, comprising 189 patients with FLD and 218 patients without FLD. Differences in sex (71% males vs 54% males, p<0.001), CTO (72% vs 43%, p<0.001), FP (3.26±0.94 vs 2.66±1.06, p<0.001), and PACSS (2.39±1.40 vs 1.74±1.35, p<0.001) were observed between patients with and without FLD, respectively. The random forest model demonstrated the best performance (validation set area under the curve: 0.82). SHapley Additive exPlanations revealed CTO, PACSS, and FP as the 3 most influential FLD predictors, and the univariate and multivariate analyses confirmed CTO-FP-PACSS classification as an independent FLD predictor (multivariate hazard ratio 4.13; p<0.001). CONCLUSION: The CTO-FP-PACSS classification system accurately predicted FLD after PTA. This user-friendly system may guide surgical decision-making, helping choose between PTA and additional devices to reduce FLD in FP artery treatment. CLINICAL IMPACT: We utilised machine-learning techniques in conjunction with SHapley Additive exPlanations to develop a clinical classification system that predicts the probability of flow-limiting dissection (FLD) after plain old balloon angioplasty. This classification system categorises lesions into Classes 1-4 based on three factors: chronic total occlusion, femoropopliteal grading, and peripheral artery calcium scoring. Each class demonstrated a different probability of developing FLD. This classification system may be valuable for surgeons in their clinical practice, as well as serving as a source of inspiration for other researchers.

Efficacy Analysis of Drug-Coated Balloons in the Treatment of Ultra-Long Segment Lesions of Femoral Popliteal Artery.

BACKGROUND: To evaluate the midterm clinical efficacy of paclitaxel drug-coated balloons (DCBs) in the treatment of femoral artery TransAtlantic Inter-Society Consensus (TASC) grades C/D lesions. METHODS: The clinical data of 73 cases with TASC grades C/D lesions of femoral artery treated with paclitaxel DCBs at the Department of Vascular Surgery, the First Hospital of Fujian Medical University from August 2016 to January 2020 were retrospectively analyzed. The primary endpoint was the primary patency rate. The secondary endpoints were freedom from reintervention, Rutherford classification, ankle-brachial index (ABI), amputation events, and all-cause death. RESULTS: A total of 73 cases of limb lesions received endoluminal treatment. The mean age of the patients including 49 males and 24 females was (72.66 ± 11.1) years, with an initial Rutherford classification of 2-5 and an ABI of 0.4 ± 0.1. The mean Rutherford classification was 3.70 ± 0.95. The mean lesion length was (25.75 ± 9.67) cm, including 61.64% chronic occlusive lesions and 27.39% stenotic lesions, the remaining 10.97% were mixed lesions, containing multiple segments of stenosis and chronic total occlusion lesions. 43.8% of the lesions were associated with severe calcification. Stent implantation rate was 8%. Overall mortality at follow-up was 4% at 1 year and 8% at 2 years, and no amputations seen. The ABI was 0.83 ± 0.07 at 1-year follow-up and 0.78 ± 0.05 at 2-year follow-up. The Kaplan-Meier survival curve predicted the 1-year phase I patency rate was 75.3% ± 5% and the 2-year patency rate was 63.3% ± 5.7%. Freedom from target lesion revascularization was 78.4 ± 4.9% at 1 year and 69.2% ± 3.6% at 2 years. Logistic regression analysis showed that diabetes mellitus, severe calcification, chronic renal insufficiency, and restenosis were the significant factors affecting the patency of target lesions. CONCLUSIONS: Paclitaxel DCBs in the treatment of femoral artery with TASC grades C/D lesions can achieve relatively satisfactory midterm clinical safety and efficacy results, provided there is an acceptable result on completion angiogram.

Syringe-assisted test-aspiration with mechanical aspiration thrombectomy results in good safety and short-term outcomes in the treatment of patients with deep venous thrombosis.

OBJECTIVE: To evaluate the short-term outcomes and safety of syringe-assisted test-aspiration with mechanical aspiration thrombectomy in the treatment of deep venous thrombosis. METHODS: This was a single-center, retrospective study of hospitalized patients with iliofemoral and/or inferior vena caval deep venous thrombosis, excluding those with pulmonary embolism. We collected the following patient data from the electronic medical records: age, sex, provoked/unprovoked deep venous thrombosis, symptom duration, thrombosed segments, and the presence of a tumor, thrombophilia, diabetes, and/or iliac vein compression syndrome. Venography and computed tomographic venography were performed in all patients before the procedure. All patients underwent syringe-assisted test-aspiration with mechanical aspiration thrombectomy under local anesthesia and sedation, and all received low-molecular-weight heparin peri-operatively. All patients underwent implantation of an inferior vena caval filter. Rivaroxaban was administered post-procedure, instead of heparin, for 3-6 months, with lower extremity compression. RESULTS: Overall, 29 patients with deep venous thrombosis underwent syringe-assisted test-aspiration with mechanical aspiration thrombectomy from January 2022 to October 2022 in our institution. Technical success (>70% thrombus resolution) was achieved in all patients, and using a single procedure in 25/29 patients (86%). Concomitant stenting was performed in 18/29 (62%) of the patients, and 21/29 (69%) underwent angioplasty. The median (interquartile range) procedure time was 110 min (100-122), the median intra-operative bleeding volume was 150 mL (120-180), and the median decrease in the hemoglobin concentration from pre- to post-operative was 7 g/L (4-14). The median follow-up duration was 7 months (5-9). All patients obtained symptomatic relief, and 27/29 achieved near-remission or full remission (combined total). No patients experienced peri-operative bleeding complications, or symptom recurrence or post-thrombectomy syndrome during follow-up. CONCLUSION: The short-term outcomes following syringe-assisted test-aspiration with mechanical aspiration thrombectomy in the treatment of deep venous thrombosis were excellent, and the procedure was safe.

Establishment and validation of lncRNA-related prognostic signatures in cholangiocarcinoma.

BACKGROUND: The prognosis of CCA is extremely poor, making it one of the most lethal cancers. Therefore, there is a need to elucidate the pathogenic mechanisms of CCA. In this study, we aimed at identifying lncRNA-related prognostic signatures for CCA through bioinformatics analysis and further validated their functions in CCA tumorigenesis and progression. METHODS: The RNA-seq data of CCA were downloaded from public databases. Differentially expressed lncRNAs (DElncRNAs) were screened. Then, candidate OS- and DFS-related DElncRNAs were selected through Kaplan-Meier survival analysis. Furthermore, LASSO regression was performed to establish the OS and DFS signatures, respectively. Multivariate COX models and nomograms for overall survival (OS) and disease-free survival (DFS) were established based on OS/DFS signature and clinical data. Hub lncRNAs were identified and enrichment analyses were performed to explore their potential functions. Finally, in vitro and in vivo models were used to validate the effects of the hub lncRNAs in CCA tumorigenesis and progression. RESULTS: A total of 925 DElncRNAs were selected, of which six candidate OS-related lncRNAs and 15 candidate DFS-related lncRNAs were identified. The OS and DFS signatures were then established using four lncRNAs, respectively. We found that the OS signature and vascular invasion were independent risk factors for the OS of CCA, while the DFS signature, vascular invasion, and CA19-9 were independent risk factors for the DFS of CCA. Then, nomograms were established to achieve personalized CCA recurrence and death prediction. Furthermore, our study uncovered that MIR4435-2HG and GAPLINC might play crucial roles in CCA progression and be selected as hub lncRNAs. GO and KEGG enrichment analyses revealed that the two hub lncRNAs were closely related to CCA tumorigenesis. Finally, we demonstrated that MIR4435-2HG and GAPLINC can stimulate CCA proliferation and migration in vitro and in vivo. CONCLUSIONS: The established OS and DFS signatures are independent risk factors for OS and DFS of CCA patients, respectively. MIR4435-2HG and GAPLINC were identified as hub lncRNAs. In vitro and in vivo models revealed that MIR4435-2HG and GAPLINC can prompt CCA progression, which might be novel prognostic biomarkers and therapeutic targets for CCA.

Microbial inoculants using spent mushroom substrates as carriers improve soil multifunctionality and plant growth by changing soil microbial community structure.

Peat is typically used as a carrier for microbial inoculants; however, due to its non-renewable nature alternatives need to be identified as reliable and renewable carriers for mineral-solubilizing inoculants. In pot experiments, solid microbial inoculants were comprised of peat (P), biochar (BC), and spent mushroom substrates (SMS) using Medicago sativa L. as experimental materials, and the purpose of this study is to assess the effect of solid microbial inoculants on soil multifunctionality and plant growth. The results revealed that the SMS microbial inoculant had the greatest positive impact on plant biomass and significantly stimulated soil multifunctionality which is typically managed or assessed based on various soil functions or processes that are crucial for sustaining productivity, in contrast to the peat microbial inoculant, particularly at a supply level of 100 g/pot. There was no significant correlation between soil multifunctionality and bacterial/fungal microbial diversity. However, according to the co-occurrence network of bacteria and fungi, soil multifunctionality was intimately correlated with the biodiversity of the main ecological clusters (modules) of bacteria and fungi, rather than to the entire soil microbial community structure. The keystone species of module hubs and connectors play critical roles in maintaining the stability of ecological clusters of microbial co-occurrence networks and linkages between ecological clusters. Soil pH is a major predictor of changes in plant biomass, and leads to changes therein by affecting the major ecological clusters of bacterial and fungal co-occurrence networks. These results suggested that SMS may serve as a good alternative to peat as a carrier of mineral-solubilizing microorganisms to maintain soil multifunctionality and promote plant growth.

STOP-Bang Questionnaire Is Associated With Aortic Remodeling in Patients With Acute Type B Aortic Dissection Undergoing Standard Thoracic Endovascular Aortic Repair.

PURPOSE: To determine whether the STOP-Bang questionnaire, which is a tool for evaluating obstructive sleep apnea, is associated with aortic remodeling after thoracic endovascular aortic repair (TEVAR) in patients with type B aortic dissection (TBAD). METHODS: Patients with TBAD who underwent standard TEVAR at our center from January 2015 to December 2020 were enrolled. For the included patients, we recorded baseline characteristics, comorbidities, preoperative computed tomographic angiography findings, procedure details, and complications. The STOP-Bang questionnaire was administered to each patient. Total scores comprised points for 4 yes/no questions and 4 clinical measurements. STOP-Bang ≥5 and STOP-Bang <5 groups were then created using the STOP-Bang total scores. We evaluated aortic remodeling 1 year after discharge and the reintervention rate, as well as false lumen complete thrombosis (FLCT) and non-FLCT length. RESULTS: Fifty-five patients were enrolled in the study; STOP-Bang <5, n=36, and STOP-Bang ≥5, n=19. Compared with the STOP-Bang ≥5 group, the STOP-Bang <5 group achieved statistically significantly higher descending aorta positive aortic remodeling (PAR) rates in zones 3 to 5 (zone 3: p=0.002; zone 4: p=0.039; zone 5: p=0.023), higher total descending aorta-PAR rate (66.7% vs 36.8%, respectively; p=0.004), and lower reintervention rate (8.1% vs 38.9%, respectively; p=0.005). In the logistic regression analysis, STOP-Bang ≥5 had an odds ratio of 0.12 (95% confidence interval: 0.03-0.58; p=0.008). There was no significant difference in overall survival between the groups. CONCLUSION: STOP-Bang questionnaire scores were associated with aortic remodeling after TEVAR in patients with TBAD. Increasing the frequency of surveillance after TEVAR might be beneficial in these patients. CLINICAL IMPACT: We analysed aortic remodelling 1 year after thoracic endovascular aortic repair (TEVAR) in acute type B aortic dissection (TBAD) patients with STOP-Bang < 5 and STOP-Bang ≥ 5. Aortic remodelling was better, and the reintervention rate was higher in patients with STOP-Bang < 5 compared with patients with STOP-Bang ≥ 5. In patients with STOP-Bang ≥ 5, aortic remodelling was worse in zones 3-5 compared with zones 6-9. This study suggests that the STOP-Bang questionnaire results is associated with aortic remodelling after TEVAR in patients with TBAD.

Angiosome Oriented or Least Diseased Vessel, Which Is the Optimal Target Arterial Path for Endovascular Revascularisation in Patients With Diabetic Foot Ulcers?

OBJECTIVE: The aims were to determine whether, when treating diabetic foot ulcers (1), selecting an angiosome directed (AD) vessel as the target arterial path (TAP) when candidate vessels have comparably severe disease impacts outcomes and (2) whether a more severely affected AD vessel or a less severely affected non-angiosome directed (NAD) vessel should be chosen. METHODS: This was a retrospective observational study. Patients with diabetic foot ulcers who had undergone endovascular revascularisation in the institution between January 2016 and May 2020 and had been followed up for two years were included. Eligible patients were identified retrospectively and relevant data were collected from the institution's electronic medical records. The severity of the lesions was classified using the Global Limb Anatomic Staging System (GLASS). Outcomes between various subgroups were compared according to the severity of the lesions to determine the optimal TAP choice in each case. RESULTS: The study cohort comprised 215 patients (216 limbs). The affected limbs were classified as follows: 93 (43.1%) as GLASS 1 - 2 AD; 27 (12.5%) as GLASS 1 - 2 NAD, 62 (28.7%) as GLASS 3 AD, and 34 (15.7%) as GLASS 3 NAD groups. In the GLASS 1 - 2 group, rates of ulcer healing, survival, and amputation free survival were higher and time to healing shorter in the AD than NAD group. In the GLASS 3 group, there were no significant differences between the AD and NAD groups for any studied outcome measures, including ulcer healing and overall survival. Using a more severely diseased AD as the TAP did not achieve significantly better outcomes than using a less severely affected NAD vessel. CONCLUSION: Selecting the AD vessel may achieve better outcomes when two candidate TAPs belong to GLASS 1 - 2, whereas selecting the least diseased vessel as the TAP regardless of AD or NAD status may be preferable in other situations.

The Relationship Between the Global Limb Anatomic Staging System Inframalleolar Modifier and the Outcomes of Diabetic Foot Ulcer with Peripheral Artery Disease.

BACKGROUND: We aimed to investigate the relationship between the condition of the inframalleolar (IM) arteries, as assessed by the Global Limb Anatomic Staging System Inframalleolar (GLASS IM) modifier, and the outcomes of patients with diabetic foot ulcers. METHODS: The data of 215 patients, who underwent endovascular therapy from January 2016 to May 2020 at our center, were retrospectively reviewed. Patients were divided into the P0, P1, and P2 groups according to the angiography results. The rates of ulcer healing, limb salvage, survival, and amputation-free survival were compared during the 2-year period after discharge. RESULTS: Of the 216 affected limbs, 35 (16%) were classed as P0, 122 (57%) as P1, and 59 (27%) as P2. Compared with the P2 group, the P0 + P1 group had a higher ulcer healing rate (P = 0.001), a shorter ulcer healing time (P = 0.004), and a higher survival rate (P = 0.044). GLASS IM Modifier classification P2 was an independent predictor of nonhealing ulcers. No significant difference was observed between the P0 versus P1 groups. CONCLUSIONS: GLASS IM modifier classification P2 is an independent risk factor for a poor outcome. GLASS IM modifier classification P0 versus P1 demonstrates similar outcomes to each other.

Mineral-solubilizing microbial inoculant positively affects the multifunctionality of anthropogenic soils in abandoned mining areas.

The mining industry has a significant negative impact on ecosystems, and the remediation of abandoned mining sites requires effective strategies. One promising approach is the incorporation of mineral-solubilizing microorganisms into current external soil spray seeding technologies. These microorganisms possess the ability to decrease mineral particle sizes, promote plant growth, and enhance the release of vital soil nutrients. However, most previous studies on mineral-solubilizing microorganisms have been conducted in controlled greenhouse environments, and their practical application in field settings remains uncertain. To address this knowledge gap, we conducted a four-year field experiment at an abandoned mining site to investigate the efficacy of mineral-solubilizing microbial inoculants in restoring derelict mine ecosystems. We assessed soil nutrients, enzyme activities, functional genes, and soil multifunctionality. We also examined microbial compositions, co-occurrence networks, and community assembly processes. Our results demonstrated that the application of mineral-solubilizing microbial inoculants significantly enhanced soil multifunctionality. Interestingly, certain bacterial phyla or class taxa with low relative abundances were found to be key drivers of multifunctionality. Surprisingly, we observed no significant correlation between microbial alpha diversity and soil multifunctionality, but we did identify positive associations between the relative abundance and biodiversity of keystone ecological clusters (Module #1 and #2) and soil multifunctionality. Co-occurrence network analysis revealed that microbial inoculants reduced network complexity while increasing stability. Additionally, we found that stochastic processes played a predominant role in shaping bacterial and fungal communities, and the inoculants increased the stochastic ratio of microbial communities, particularly bacteria. Moreover, microbial inoculants significantly decreased the relative importance of dispersal limitations and increased the relative importance of drift. High relative abundances of certain bacterial and fungal phyla were identified as major drivers of the microbial community assembly process. In conclusion, our findings highlight the crucial role of mineral-solubilizing microorganisms in soil restoration at abandoned mining sites, shedding light on their significance in future research endeavors focused on optimizing the effectiveness of external soil spray seeding techniques.

Contrasting plant responses to multivariate environmental variations among species with divergent elevation shifts.

The general predictions of climate impacts on species shifts (e.g., upward shift) cannot directly inform local species conservation, because local-scale studies find divergent patterns instead of a general one. For example, our previous study found three shift patterns with elevation (strong down-, moderate down-, and up-slope shifts) in temperate mountain forests. The divergent shifts are hypothesized to arise from both multivariate environmental variations with elevation and corresponding species-specific responses. To test this hypothesis, we sampled soils and leaves to measure elevation variations in soil conditions and determined plant responses using discriminations against heavier isotopes, carbon (13 C) and nitrogen (15 N). Functional traits of the species studied were also extracted from a public trait dataset. We found that: (1) With low soil water contents at low elevations, only the leaves of up-shifters had lower 13 C discriminations at low vs. high elevations; (2) With low soil P contents at high elevations, only the leaves of moderate down-shifters had higher 15 N discriminations at high vs. low elevations; (3) The leaves of strong down-shifters did not show significant elevation patterns of the discriminations; (4) The contrasting responses among the three types of shifters agree with their functional dissimilarity, suggested by their separate locations in a multitrait space. Taken together, the divergent shifts are associated with the elevation variations in environmental conditions and contrasting plant responses. The contrasting responses could result from the functional dissimilarity among species. Therefore, a detailed understanding of both local environmental variations and species-specific responses can facilitate accurate predictions of species shifts to inform local species conservation.

Angiosome-Guided Endovascular Revascularization for Treatment of Diabetic Foot Ulcers with Peripheral Artery Disease.

BACKGROUND: Because diabetic foot ulcers (DFUs) are difficult to heal and cause huge economic losses to the society, accelerating their healing has become extremely important. The purpose of this study was to evaluate the effect of revascularization based on the angiosome concept on DFU. METHODS: Between January 2018 and July 2020, 112 consecutive legs with DFUs, in 111 patients who were discharged from the vascular surgery department of our hospital were retrospectively evaluated. The legs were assigned to two groups depending on whether direct arterial flow to the foot ulcer based on the angiosome concept was achieved. Comparisons of the ulcer healing rate, mean time to ulcer healing, major amputation rate, survival rate, and major amputation-free survival rate between the angiosome direct revascularization (DR) and angiosome indirect revascularization (IR) groups were performed. RESULTS: DR was achieved in 71 legs (63%) compared with IR in 41 legs. The ulcer healing rate (70.4% in the DR group versus 34.1% in the IR group, P < 0.01), the mean time to ulcer healing (7.01 ± 4.26 months versus 10.09 ± 3.24 months, P < 0.01), the survival rate (90.1 vs. 53.7%, P < 0.01), and the major amputation-free survival rate (81.7 vs. 48.8%, P < 0.01) were significantly higher in the DR group than in the IR group. Undergoing DR did not significantly reduce the major amputations rate compared to IR (13.4 and 34.1%, respectively, P = 0.15), but there might be a trend. In multivariate models, DR remained a significant predictor for ulcer healing (HR, 7.07; 95% confidence interval (CI), 6.54-7.60, P < 0.01). Opening multiple infrapopliteal arteries in the DR group compared with restoring only one infrapopliteal artery did not significantly improve the ulcer healing rate (P = 0.59), the mean time to ulcer healing (P = 0.70), major amputation rate (P = 0.83), the survival rate (P = 0.31), and the major amputation-free survival rate (P = 0.40). CONCLUSIONS: Attaining a direct arterial flow based on the angiosome concept may be important for ulcer healing, survival, and amputation-free survival in diabetic foot patients. Opening multiple infrapopliteal arteries in DR patients may not improve the ulcer healing, survival, major amputation or amputation-free survival compared with single DR vessel patency.

Tissue-specific transcriptome for Dendrobium officinale reveals genes involved in flavonoid biosynthesis.

Dendrobium officinale is a kind of crop and precious herbal that is widely distributed in China. We applied transcriptomics to investigate the flavonoids and their biosynthesis-related genes from different tissues. Total flavonoid was determined in three different tissues. In this study, nine cDNA libraries were generated from Dendrobium officinale. A total of 530 million (70.73%) of the high-quality reads were successfully mapped to the reference genome of Dendrobium officinale and nine libraries were combined and assembled into 24,927 non-redundant genes. We mapped all of these genes to reference pathways in the KEGG database to identify polysaccharide and secondary metabolites pathways in which the genes may be involved. We outlined the biosynthetic pathway of flavonoids and identified putative genes, which provide understanding of the biosynthesis and regulation of Dendrobium officinale flavonoids at the molecular level. We identified five CHS genes from Dendrobium officinale and characterized the CHS gene family. The flavonoid-related key enzyme genes were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR. These data on flavonoid genes obtained in this work will be useful in understanding the molecular mechanisms of different tissues in Dendrobium officinale.

Comparative physiological mechanisms of arbuscular mycorrhizal fungi in mitigating salt-induced adverse effects on leaves and roots of Zelkova serrata.

Arbuscular mycorrhizal (AM) fungi enhance plant salt tolerance. However, physiological mechanisms of enhanced salt tolerance in leaves and roots of trees rarely have been compared. To reveal the different mechanisms, our study utilized comprehensive analyses of leaves and roots to examine the effects of Funneliformis mosseae on the salinity tolerance of Zelkova serrata. Seedlings of Z. serrata were exposed to four salt levels in a greenhouse with and without F. mosseae inoculation. Treatment comparisons revealed that following F. mosseae inoculation, (1) nutrient deficiency caused by osmotic stress was mitigated by the fungus enhancing nutrient contents (K, Ca, and Mg) in roots and (N, P, K, Ca, and Mg) in leaves, with Ca and K contents being higher in both leaves and roots; (2) mycorrhizas alleviated ion toxicity by maintaining a favorable ion balance (e.g., K+/Na+), and this regulatory effect was higher in leaves than that in roots; and (3) oxidative damage was reduced by an increase in the activities of antioxidant enzymes and accumulation of antioxidant compounds in mycorrhizal plants although the increase differed in leaves and roots. In particular, AM fungus-enhanced catalase activity and reduced glutathione content only occurred in leaves, whereas an enhanced content of reduced ascorbic acid was only noted in roots. Growth, root vitality, leaf photosynthetic pigments, net photosynthetic rate, and dry weight were higher in seedlings with AM fungus inoculation. These results suggest that AM fungus inoculation improved salinity tolerance of Z. serrata, but the physiological mechanisms differed between leaves and roots.

Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways.

Dendrobium is widely used in traditional Chinese medicine, which contains many kinds of active ingredients. In recent years, many Dendrobium transcriptomes have been sequenced. Hence, weighted gene co-expression network analysis (WGCNA) was used with the gene expression profiles of active ingredients to identify the modules and genes that may associate with particular species and tissues. Three kinds of Dendrobium species and three tissues were sampled for RNA-seq to generate a high-quality, full-length transcriptome database. Based on significant changes in gene expression, we constructed co-expression networks and revealed 19 gene modules. Among them, four modules with properties correlating to active ingredients regulation and biosynthesis, and several hub genes were selected for further functional investigation. This is the first time the WGCNA method has been used to analyze Dendrobium transcriptome data. Further excavation of the gene module information will help us to further study the role and significance of key genes, key signaling pathways, and regulatory mechanisms between genes on the occurrence and development of medicinal components of Dendrobium.

Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues.

BACKGROUND: Dendrobium moniliforme (Linnaeus) Swartz is a well-known plant used in traditional Chinese medicine due to bioactive constituents. Polysaccharides are the main medicinal ingredients, yet no studies have been published on polysaccharide biosynthesis in D. moniliforme. To comprehensively investigate the polysaccharide at the transcription level, we performed de novo transcriptome sequencing for the first time to produce a comprehensive transcriptome of D. moniliforme. RESULTS: In our study, a database of 562,580 unigenes (average length = 1115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, we identified 1204 carbohydrate-active related unigenes against CAZy database, including 417 glycosyltransferase genes (GTs), 780 glycoside hydrolases (GHs), 19 carbohydrate esterases (CEs), 75 carbohydrate-binding modules (CBMs), and 44 polysaccharide lyases (PLs). In the cellulose synthase family, 21 differential expression genes (DEGs) related to polysaccharide were identified. Subsequently, the tissue-specific expression patterns of the genes involved in polysaccharide pathway were investigated, which provide understanding of the biosynthesis and regulation of DMP at the molecular level. The two key enzyme genes (Susy and SPS) involved in the polysaccharide pathway were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR. CONCLUSIONS: We determined the content of polysaccharides from Dendrobium moniliforme under different tissues, and we obtained a large number of differential genes by transcriptome sequencing. This database provides a pool of candidate genes involved in biosynthesis of polysaccharides in D. moniliforme. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb.

Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis.

BACKGROUND: Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a traditional Chinese herbal medicine with high medicinal value in China. Polysaccharides and alkaloids are its main active ingredients. To understand the difference of main active ingredients in different tissues, we determined the contents of polysaccharides and alkaloids in the roots, stems and leaves of D. huoshanense. In order to explore the reasons for the differences of active ingredients at the level of transcription, we selected roots, stems and leaves of D. huoshanenese for transcriptome sequencing and pathway mining. RESULTS: The contents of polysaccharides and alkaloids of D. huoshanense were determined and it was found that there were significant differences in different tissues. A total of 716,634,006 clean reads were obtained and 478,361 unigenes were assembled by the Illumina platform sequencing. We identified 1407 carbohydrate-active related unigenes against CAZy database including 447 glycosyltransferase genes (GTs), 818 glycoside hydrolases (GHs), 60 carbohydrate esterases (CEs), 62 carbohydrate-binding modules (CBMs), and 20 polysaccharide lyases (PLs). In the glycosyltransferases (GTs) family, 315 differential expression genes (DEGs) were identified. In total, 124 and 58 DEGs were associated with the biosynthesis of alkaloids in Dh_L vs. Dh_S and Dh_R vs. Dh_L, respectively. A total of 62 DEGs associated with the terpenoid pathway were identified between Dh_R and Dh_S. Five key enzyme genes involved in the terpenoids pathway were identified, and their expression patterns in different tissues was validated using quantitative real-time PCR. CONCLUSIONS: In summary, our study presents a transcriptome profile of D. huoshanense. These data contribute to our deeper relevant researches on active ingredients and provide useful insights into the molecular mechanisms regulating polysaccharides and alkaloids in Dendrobium.

Effects of sulfuric, nitric, and mixed acid rain on Chinese fir sapling growth in Southern China.

The influence of acid rain on plant growth includes direct effects on foliage as well as indirect soil-mediated effects that cause a reduction in root growth. In addition, the concentration of NO3- in acid rain increases along with the rapid growth of nitrogen deposition. In this study, we investigated the impact of simulated acid rain with different SO42-/NO3- (S/N) ratios, which were 1:0, 5:1, 1:1, 1:5 and 0:1, on Chinese fir sapling growth from March 2015 to April 2016. Results showed that Chinese fir sapling height growth rate (HGR) and basal diameter growth rate (DGR) decreased as acid rain pH decreased, and also decreased as the percentage of NO3- increased in acid rain. Acid rain pH significantly decreased the Chlorophyll a (Chla) and Chlorophyll b (Chlb) content, and Chla and Chlb contents with acid rain S/N 1:5 were significantly lower than those with S/N 1:0 at pH 2.5. The chlorophyll fluorescence parameters, maximal efficiency of Photosystem II photochemistry (Fv/Fm) and non-photochemical quenching coefficient (NPQ), with most acid rain treatments were significantly lower than those with CK treatments. Root activities first increased and then decreased as acid rain pH decreased, when acid rain S/N ratios were 1:1, 1:5 and 0:1. Redundancy discriminant analysis (RDA) showed that the Chinese fir DGR and HGR had positive correlations with Chla, Chlb, Fv/Fm ratio, root activity, catalase and superoxide dismutase activities in roots under the stress of acid rain with different pH and S/N ratios. The structural equation modelling (SEM) results showed that acid rain NO3- concentration and pH had stronger direct effects on Chinese fir sapling HGR and DGR, and the direct effects of acid rain NO3- concentration and pH on HGR were lower than those on DGR. Our results suggest that the ratio of SO42- to NO3- in acid rain is an important factor which could affect the sustainable development of monoculture Chinese fir plantations in southern China.

Immobilized Silver Nanoparticles on Chitosan with Special Surface State-Enhanced Antimicrobial Efficacy and Reduced Cytotoxicity.

Immobilized chitosan-Ag nanoparticles (CTS-Ag NPs) with special surface state have been synthesized successfully through immobilizing Ag NPs on the amino-enriched surface of CTS by reducing Ag (I) in situ. The antimicrobial efficiency and potency of CTS-Ag NPs against Escherichia coli and Staphylococcus aureus were studied. Our results reveal that surface-immobilized CTS-Ag NPs show better antimicrobial efficacy than several other reported monodisperse colloidal Ag NPs, because the unique surface state of our CTS-Ag NPs leads to both "contact killing" and "ion mediated killing" functions. Due to the synergetic effect of CTS and Ag NPs, the immobilized CTS-Ag NPs present a broader antimicrobial spectrum and a more effective antifungal activity against Monilia albican. In addition, CTS as an environment friendly dispersant can help to reduce the cytotoxicity of Ag NPs on higher organisms. The immobilized CTS-Ag NPs are stable and can maintain good disinfection potential after 6 months' shelf-time.