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Abstract Background Mushroom poisoning is a significant food safety issue in Guizhou Province, China. Studies on this topic are essential for its prevention and control. We aimed to analyze the epidemiological characteristics of mushroom poisoning and study the correlation between its cases and meteorological factors in Guizhou Province. Methods We collected data on mushroom poisoning and meteorological factors in Guizhou Province in 2023. A descriptive analysis was conducted on the epidemiological features of mushroom poisoning and meteorological factors. We used Spearman correlation analysis and the generalized additive model to examine the relationship between meteorological factors and the number of mushroom poisoning cases. Results In 2023, mushroom poisoning cases in Guizhou Province were concentrated among individuals aged 20–59. Clinical symptoms were primarily gastrointestinal symptoms and occurrences peaked from June to October, mainly in the northeastern region of the province. Most incidents occurred in households. In 72 mushroom poisoning incidents where species were identified, 33 poisonous mushrooms were found. The number of mushroom poisoning cases in Guizhou Province was positively correlated with each meteorological factor(P

Abstract Background Mushroom poisoning is a major public health issue in China. The integration of medical resources from different institutes of different levels is crucial in reducing the harm of mushroom poisoning. However, few studies have provided comprehensive implementation procedures and postimplementation effectiveness evaluations. To reduce the harm caused by mushroom poisoning, a network system for the prevention and treatment of mushroom poisoning (NSPTMP) was established in Chuxiong, Yunnan Province, a high-risk area for mushroom poisoning. Methods The NSPTMP consists of three types of institutions, namely, centers for disease prevention, hospitals, and health administration departments, with each kind of institution comprising prefecture, county/city, town, and village levels. After three years of implementation, the network was evaluated by comparing the indices before and after network implementation using data from the “Foodborne Disease Outbreak Surveillance System” and 17 hospitals in Chuxiong. The indices included the fatalities caused by mushroom poisoning, the composition ratios of different types of mushrooms for both outpatients and inpatients and the hospitalization rates. Results Compared to the average fatality rate of mushroom poisoning from 2015 to 2017, the average fatality rate from 2018 to 2020 significantly decreased from 0.57 to 0.06% (P

A comprehensive analytical method based on liquid chromatography–tandem mass spectrometry (LC-MS/MS) was developed for the simultaneous detection of 12 mushroom toxins (ibotenic acid, muscimol, muscarine, β-amanitin, α-amanitin, desoxoviroidin, γ-amanitin, phallisacin, illudin S, phallacidin, phalloidin and illudin M) in mushrooms, serum, urine and simulated gastric fluid. The samples were extracted with water or acetonitrile solution, and the serum sample was further purified with PSA sorbent. Chromatographic separation was performed on an ACQUITY UPLC HSS T3 column with gradient elution using methanol and water containing 1 mM ammonia fluoride as a mobile phase. Mass spectrometric acquisition was performed in electrospray positive ionization mode. Good linearities (R2 > 0.994) were obtained for 12 toxins over the range of 0.05~200 µg/L. Matrix-matched calibration curves were used for quantification. The method limits of quantification were 0.01~0.2 mg/kg for mushrooms and 0.15~2.0 µg/L for three biological liquid samples. The mean recoveries of 12 target toxins (spiked at three concentration levels) ranged from 73.0% to 110.3%, with relative standard deviations not exceeding 19.4%, which meets the requirements for the determination of trace compounds in a biological matrix. This method was applied to the analysis of mushroom samples from Yunnan Province. As a result, 11 toxins, not including illudin M, were detected with a concentration range of 0.61~2143 mg/kg.

Tumor-associated macrophages (TAMs)-based immunotherapy is a promising strategy. Since TAMs are mainly composed of M2-type macrophages, they have a promoting effect on tumor growth, invasion, and metastasis. M2-type macrophages contain a specific receptor CD163 on their surface, providing a prerequisite for active targeting to TAMs. In this study, we prepared CD163 monoclonal antibody modified doxorubicin-polymer prodrug nanoparticles (abbreviated as mAb-CD163-PDNPs) with pH responsiveness and targeted delivery. First, DOX was bonded with the aldehyde group of a copolymer by Schiff base reaction to form an amphiphilic polymer prodrug, which could self-assemble into nanoparticles in the aqueous solution. Then, mAb-CD163-PDNPs were generated through a “Click” reaction between the azide group on the surface of the prodrug nanoparticles and dibenzocyclocytyl-coupled CD163 monoclonal antibody (mAb-CD163-DBCO). The structure and assembly morphology of the prodrug and nanoparticles were characterized by 1H NMR, MALDI-TOF MS, FT-IR UV-vis spectroscopy, and dynamic light scattering (DLS). In vitro drug release behavior, cytotoxicity, and cell uptake were also investigated. The results show that the prodrug nanoparticles have regular morphology and stable structure, especially mAb-CD163-PDNPs, which can actively target TAMs at tumor sites, respond to the acidic environment in tumor cells, and release drugs. While depleting TAMs, mAb-CD163-PDNPs can actively enrich drugs at the tumor site and have a strong inhibitory effect on TAMs and tumor cells. The result of the in vivo test also shows a good therapeutic effect, with a tumor inhibition rate of 81%. This strategy of delivering anticancer drugs in TAMs provides a new way to develop targeted drugs for immunotherapy of malignant tumors.

Objective Analyzing on-site disposal process of a mushroom poisoning in Wuhan. Identifying the toxin in the mushrooms and providing references for similar poisoning incidents. Methods Epidemiological investigation, clinical treatment data and suspicious poisonous mushroom sample were collected. Mushroom sample was identified by molecular analysis. Results All patients ate different quantity of fried mushroom. The early clinical symptom were mainly gastrointestinal symptoms, and the liver, kidney and coagulopathy were damaged in the later stage. The mushroom samples were identified as Amanita rimosa. Conclusion According to epidemiological, clinical, morphological and molecular biological evidence, this incident was confirmed to be a mushroom poisoning incident caused by Amanita rimosa.

Objective: This study evaluated iron overload after intracerebral hemorrhage (ICH) using ESWAN sequences.Methods: This single-center prospective observational cohort study enrolled supratentorial ICH patients. MRI was obtained with a 3.0-T scanner at day 1, day 14, day 30, and follow-up (300 days or later). R2* mapping was generated based on the ESWAN. R2* value of the ipsilateral side represented iron deposition, and the R2* value of the contralateral side served as control. R2* value was adjusted by volume and used to assess total iron overload. Brain edema was measured on T2 FLAIR-weighted images. Brain atrophy was calculated as the contralateral hemisphere volume minus the injured hemisphere volume.Results: Twnety-seven patients with a spontaneous supratentorial ICH were included in this analysis. The ipsilateral R2* value was 40.27 ± 11.62, 41.92 ± 13.56, and 60.89 ± 14.09 at days 1, 14, and 30, respectively. The R2* value was significantly higher in the ICH side than the contralateral side (p < 0.01). Increased R2* value was seen on day 30 compared to day 14 (p < 0.01). The R2* value showed logistic decay with the distance to the hematoma margin (p < 0.01). Brain edema at day 14 and brain atrophy at follow-up correlated with R2* value adjusted by volume at day 14 (p < 0.01).Conclusions: After ICH, the iron deposition in the perihematomal region was progressively increased during the first month. R2* value adjusted by volume predicted acute brain edema and chronic brain atrophy.

Two new Russula species, R. subbrevipes and R. callainomarginis, from China are described based on morphological and molecular characteristics. Russula subbrevipes has thus far only been found in southwestern China at altitudes of higher than 3400 m and is characterized by a yellow ochre pileal surface, glabrous or tomentose stipe, fruity odor, subglobose to ellipsoid basidiospores, isolated or partially connected warts and pleurocystidia with a cap appendage. Russula callainomarginis is characterized by a cream to white pileus, light turquoise lamellae margin, spongy stipe, light turquoise zone on the top of the stipe, pungent odor, globose to ellipsoid basidiospores and dominant isolated warts. The phylogenetic tree of Russula was constructed with multi-gene sequences, including the internal transcribed spacer regions (ITS), the ribosomal large subunit (nrLSU), the small subunit of the mitochondrial rRNA gene (mtSSU) and the second largest subunit of RNA polymerase II (RPB2). The results show that both R. subbrevipes and R. callainomarginis represent new lineages in Russula subg. Brevipes. Description and illustration of the two new species are presented.

Background: Long non-coding RNAs (lncRNAs) show great potential as diagnostic tools in many diseases. We aimed to develop sensitive and noninvasive biomarkers in saliva for detecting early hepatocellular carcinoma (HCC). Methods: Candidate lncRNA biomarkers identified by Agilent microarray were subjected to validation using qPCR for the quantification of their expression levels in independent tissue, plasma and saliva sample sets, including healthy controls, HBsAg carriers, patients with chronic Hepatitis B, liver cirrhosis, early HCC, and advanced HCC. Levels of candidate biomarkers were also measured in totally 108 saliva samples from patients with any one of other nine leading causes of cancer death in men and women. Findings: Lnc-PCDH9-13:1 was significantly elevated in HCC tissues, plasma and saliva of HCC patients compared with healthy controls and groups of several benign liver diseases and other leading cancers. Its level was significantly reduced after curative hepatectomy but significantly elevated again if HCC recurrence occurred. Salivary lnc-PCDH9-13:1 showed reasonable specificities and sensitivities for detecting HCC compared with several control groups. Furthermore, the overexpression of lnc-PCDH9-13:1 promotes cell proliferation and migration in vitro. Interpretation: Salivary lnc-PCDH9-13:1 is a desirable biomarker for early HCC. It may help warrant prospective validation with larger sample sizes in multi-centers. Keywords: Long non-coding RNA, Saliva, Biomarker, Early diagnosis, Hepatocellular carcinoma

This article concerns the SIRC epidemiological model for influenza A, which efficiently describes the mechanism of disease spreading, including the susceptible (S), the infected (I) and the recovered (R), along with a cross-immune class (C) that recovers after being inflected by different strains of the same viral subtype. The dynamics of the model is completely determined by the basic reproduction number $R_0$. If $R_0\leq 1$, the disease-free equilibrium of the SIRC model is globally asymptotically stable, which means influenza A will die out. Otherwise, the SIRC model may have exactly one endemic equilibrium which is globally asymptotically stable under certain parametric conditions. Also, numerical simulations are given to support our analytical results.

With the development of e-commerce, delivery time is regarded as a key competitive advantage in an oligopoly market, as shortening the delivery time can stimulate demand for products. Many firms adopt a variety of strategies to shorten delivery time, and holding sufficient inventory is reported as an effective way. This study integrates a market share attraction model based on delivery time competition with the traditional inventory model to determine the optimal delivery time and order quantity. With the use of supermodular game method, we investigate the effect of changes in marketing and operations factors on the equilibrium delivery time and order quantity in non-dominated and dominated oligopolistic markets. The results reveal that the equilibrium delivery time and order quantity exhibit a directional response to changes in marketing and operations factors, and the response differs between the non-dominated oligopoly and the dominated oligopoly. Furthermore, under a cooperative oligopolistic market with asymmetry, it is beneficial for the firms with high competitive strength to adopt the delivery time strategy, but it fails to do so for the firm with the low competitive strength. Lastly, numerical analysis suggests that marketing factors play a more important role in affecting equilibrium measures than operations factors.

Amatoxins and phallotoxins are toxic cyclopeptides found in the genus Amanita and are among the predominant causes of fatal food poisoning in China. In the treatment of Amanita mushroom poisoning, an early and definite diagnosis is necessary for a successful outcome, which has prompted the development of protocols for the fast and confirmatory determination of amatoxins and phallotoxins in human biological fluids. For this purpose, a simple, rapid and sensitive multiresidue UPLC-MS/MS method for the simultaneous determination of α-amanitin, β-amanitin, γ-amanitin, phalloidin (PHD) and phallacidin (PCD) in human plasma, serum and urine was developed and validated. The diluted plasma, serum and urine samples were directly purified with a novel PRiME technique on a 96-well μElution plate platform, which allowed high-throughput sample processing and low reagent consumption. After purification, a UPLC-MS/MS analysis was performed using positive electrospray ionization (ESI+) in multiple reaction monitoring (MRM) mode. This method fulfilled the requirements of a validation test, with good results for the limit of detection (LOD), lower limit of quantification (LLOQ), accuracy, intra- and inter-assay precision, recovery and matrix effects. All of the analytes were confirmed and quantified in authentic plasma, serum and urine samples obtained from cases of poisoning using this method. Using the PRiME μElution technique for quantification reduces labor and time costs and represents a suitable method for routine toxicological and clinical emergency analysis.

With the development of e-commerce and the rapid updating of products, multi-period pricing has been widely attempted in dual-channel supply chains. In this paper, we develop a two-period game-theoretical model to investigate the problem of two-period pricing and strategy choice for a dual-channel supply chain in which a manufacturer sells a product through its direct channel and an independent retailer. The two common pricing strategies, i.e., dynamic pricing and preannounced pricing, are considered. Through analyzing and comparing, we derive a unique Stackelberg equilibrium under the two pricing strategies and find that dynamic pricing dominates preannounced pricing and achieves a win-win result for the retailer and the manufacturer. Moreover, under this strategy, the manufacturer charges a higher or lower direct price in the second period than in the first period depending on channel competition, whereas the retailer always set a lower retail price in the second period. Finally, we extend our models to consider a unique wholesale pricing strategy, the profit discount factor, and different decision sequences for the selling prices of the two channels. We show that our main results are robust, except that the decision sequence changes the optimal pricing strategy choice of the retailer. [ABSTRACT FROM AUTHOR]

Both genetic and environmental factors affect the morphology of oysters. Molecular identification is currently the primary means of species identification, but it is inconvenient and costly. In this research, we evaluated the effectiveness of geometric morphometric (GM) techniques in distinguishing between two oyster species, Crassostrea gigas and C. ariakensis. We used traditional morphometric and GM methods, including principal component analysis (PCA), thin-plate spline analysis (TPS) and canonical variable analysis (CVA), to identify specific features that distinguish the two species. We found that differences in shape can be visualised using GM methods. The Procrustes analysis revealed significant differences in shell morphology between C. gigas and C. ariakensis. The shells of C. ariakensis are more prominent at the widest point and are more scattered and have a greater variety of shapes. The shells of C. gigas are more oval in shape. PCA results indicated that PC1 explained 45.22%, PC2 explained 22.09% and PC3 explained 10.98% of the variation between the two species, which suggests that the main morphological differences are concentrated in these three principal components. Combining the TPS analysis function plots showed that the shell shape of C. ariakensis is mainly elongated and spindle-shaped, whereas the shell shape of C. gigas is more oval. The CVA results showed that the classification rate for the two species reached 100% which means that C. ariakensis and C. gigas have distinct differences in shell morphology and can be completely separated, based on morphological characteristics. Through these methods, a more comprehensive understanding of the morphological characteristics of different oyster populations can be obtained, providing a reference for oyster classification and identification.

ObjectiveAfter fully lifting coronavirus disease 2019 (COVID-19) pandemic control measures in mainland China in 12/2022, the incidence of COVID-19 has increased markedly, making it difficult to meet the general time-in-range (TIR) requirement. We investigated a more clinically practical TIR threshold and examined its association with the prognosis of COVID-19 patients with type 2 diabetes(T2D).Research design and methods63 T2D patients complicated with COVID-19 were evaluated. Patients were divided into favorable outcome group and adverse outcome group according to whether achieving composite endpoint (a >20-day length of stay, intensive care unit admission, mechanical ventilation use, or death). TIR, the time-below-range (TBR) and the time-above-range (TAR) were calculated from intermittently scanned continuous glucose monitoring. Logistic regression analysis and other statistical methods were used to analyze the correlation between glucose variability and prognosis to establish the appropriate reference range of TIR.ResultsTIR with thresholds of 80 to 190 mg/dL was significantly associated with favorable outcomes. An increase of 1% in TIR is connected with a reduction of 3.70% in the risk of adverse outcomes. The Youden index was highest when the TIR was 54.73%, and the sensitivity and specificity were 58.30% and 77.80%, respectively. After accounting for confounding variables, our analysis revealed that threshold target ranges (TARs) ranging from 200 mg/dL to 230 mg/dL significantly augmented the likelihood of adverse outcomes.ConclusionThe TIR threshold of 80 to 190 mg/dL has a comparatively high predictive value of the prognosis of COVID-19. TIR >54.73% was associated with a decreased risk of adverse outcomes. These findings provide clinically critical insights into possible avenues to improve outcomes for COVID-19 patients with T2D.

The influence of different environmental factors on the infectivity of H1N1 influenza virus was measured. We found less than 1-log reduction when viruses were exposed to NaCl solutions up to 5 M or solutions with pH = 4 through 11 for one hour. The infectivity of the virus was sensitive to the solution temperature. A log reduction ranging from 2 to more than 6 was observed starting at 50 °C and spanning just 3 or 5 for 10- or 30 min exposures, respectively. Drying the virus in media on aluminum or polymer coupons for 48 h resulted in a log reduction of 4 when kept at room temperature, but less than one when kept at 4 °C or -20 °C. Log reduction greater than 6 occurred at room temperature after 3 days, but only 1-log reduction occurred at 4 and -20 °C after 6 days. Drying on different coinage achieved similar results, except for pennies, where more than 6-log reduction was observed after 24 h. HOCl was used to fog the aluminum and polymer surfaces, placed vertically, for 5 and 7.5 min to achieve a log reduction of 4 and for 6.5 respectively. Storage of opened solution containers for 9 months at ambient resulted in a decrease in chlorine concentration from 550 ppm to 240 ppm. Fogging with the old solution was still able to achieve a log reduction of 6.5 after 7.5 min fogging. The study indicates that exposure to common environmental conditions such as a wide pH range, high salinity, and low temperatures has only a minor effect on infectivity. which can persist for more than 5 days when dried on commonly encountered surfaces, allowing accumulation of infectious viral titre. Fogging with HOCl is an effective method of delivering disinfectants to large areas, achieving complete reduction of the viral titer on both horizontal and vertical surfaces.

River conditions are complex and affected by human activities. Various hydraulic structures change the longitudinal slope and cross-sectional shape of the riverbed, which has a significant impact on the simulation of water-head evolution. With continuous population growth, the hydrological characteristics of the Yongding River Basin have undergone significant changes. Too little or too much water discharge may be insufficient to meet downstream ecological needs or lead to the wastage of water resources, respectively. It is necessary to consider whether the total flow in each key section can achieve the expected value under different discharge flows. Therefore, a reliable computer model is needed to simulate the evolution of the water head and changes in the water level and flow under different flow rates to achieve efficient water resource allocation. A one-dimensional hydrodynamic coupling model based on the Saint-Venant equations was established for the Yongding River Basin. Different coupling methods were employed to calibrate the coupling model parameters, using centralised water replenishment data for the autumn of 2022, and the simulation results were verified using centralised water replenishment data for the spring of 2023. The maximum error of the water-head arrival time between different river sections was 4 h, and the maximum error of the water-head arrival time from the Guanting Reservoir to each key cross-section was 6 h. The maximum flow error was less than 5 m3/s, and the changing trend of the flow over time was consistent with the measured data. The model effectively solved the problem of low accuracy of the water level and flow calculation results when using the traditional one-dimensional hydrodynamic model to simulate the flow movement of complex river channels in the Yongding River. The output results of the model include the time when the water head arrives at the key section, the change process of the water level and flow of each section, the change process of the water storage of lakes and gravel pits, and the change process of the total flow and water surface area of the key section. This paper reports data that support the development of an ecological water compensation scheme for the Yongding River.

ABSTRACT: The major histocompatibility complex (MHC) is a highly polymorphic cluster of genes which contribute to immune response. Located on chromosome 16, the chicken MHC has great influence over disease resistance and susceptibility. Through the use of a high-density SNP panel which encompasses the MHC-B region, haplotypes can be easily identified. This study aims to use an MHC-B SNP panel to evaluate the MHC-B variability in the Chantecler breed. This breed is native to Quebec, Canada, and is a dual-purpose breed known for its strong resistance to extreme cold temperatures. The Chantecler breed faced a near extinction event in the 1970s, which most likely resulted in a genetic bottleneck and loss of diversity. Despite this, SNP haplotype diversity was observed among 4 Chantecler populations. A total of 8 haplotypes were observed. Of these haplotypes, 6 were previously defined in other breeds, and the other 2 were unique to the Chantecler. Within the populations, the number of haplotypes ranged from 4 to 7, with 3 haplotypes, including the novel BSNP-Chant01, being present in all the groups. This study shows existence of reasonable diversity in the MHC-B region of the Chantecler breed and our results further contribute to understanding the variability of this region in chickens.

Panax notoginseng saponins (PNSs) are used as industrial raw materials to produce many drugs to treat cardio-cerebrovascular diseases. However, it is a heat-sensitive plant, and its large-scale artificial cultivation is impeded by high temperature stress, leading to decreases in productivity and PNSs yield. Here, we examined exogenous foliar leucine to alleviate heat stress and explored the underlying mechanism using metabolomics. The results indicated that 3 and 5 mM exogenous foliar leucine significantly alleviated heat stress in one-year- and two-year-old P. notoginseng in pots and field trials. Exogenous foliar leucine enhanced the antioxidant capacity by increasing the activities of antioxidant enzymes (POD, SOD) and the contents of antioxidant metabolites (amino acids). Moreover, exogenous foliar leucine enhanced carbohydrate metabolism, including sugars (sucrose, maltose) and TCA cycle metabolites (citric acid, aconitic acid, succinic acid and fumaric acid), in P. notoginseng leaves, stems, and fibrous roots to improve the energy supply of plants and further alleviate heat stress. Field experiments further verified that exogenous foliar leucine increased the productivity and PNSs accumulation in P. notoginseng. These results suggest that leucine application is beneficial for improving the growth and quality of P. notoginseng under heat stress. It is therefore possible to develop plant growth regulators based on leucine to improve the heat resistance of P. notoginseng and other crops.

Green agriculture can minimize the negative impact of agriculture on the environment. As countries around the world strongly advocate green production and green life style, not only is consumers' awareness about green consumption rising, but the demand for green agricultural products at home and abroad is gradually increasing as well. Brand image has been a crucial factor for consumers to make their final purchasing decisions, thus playing a critical role in influencing the purchasing decisions of consumers. Based on the theory of the brand image, this paper undergoes a comprehensive theoretical and positive analysis and explores the influence mechanism of brand image of green agricultural products on consumers' purchasing intention. A hypothetical model with perceived value as mediators is constructed by us to examine the influence of brand image of green agricultural products on consumers' purchasing intention. A quantitative study was conducted for a random sample of 341 consumers who purchased green agricultural products in China according to a questionnaire-based survey using a cluster random sampling technique. The study showed that the overall image of agribusiness, the image of agricultural products, the social image of agribusiness, and the image of consumers are all positively related to consumption intention. The overall image of agribusiness, the image of agricultural products, the social image of agribusiness, and the image of consumers have a positive influence on perceived value. Moreover, perceived value plays a part in the mediating role in the influence of the overall image of agribusiness, the image of agricultural products, the social image of agribusiness, and the image of consumers on consumption intention. These findings shed lights on enterprises in establishing a scientific and effective brand strategy and building an excellent brand image. The research conclusion can provide new insight into how to enhance the consumption willingness for green agricultural products and promote sustainable development.

The Bay of Bengal (BoB) is conventionally believed to be a low productive, oligotrophic marine ecosystem, where the diazotroph communities presumed to play a vital role in adding “new” nitrogen through the nitrogen fixation process. However, the diazotroph communities in the oceanic region of the BoB are still poorly understood though it represents most of the seawater volume. The present study investigated a detailed account of the bacterioplankton community structure and distribution in the oceanic BoB during the winter monsoon using high throughput sequencing targeting the 16S rRNA and nifH genes. Our study observed diverse groups of bacterioplankton communities in the BoB including both cyanobacterial and non-cyanobacterial phylotypes. Cyanobacteria (Prochlorococcus spp. and Synechococcus spp.) and Proteobacteria (mainly α-, γ-, and δ-Proteobacteria) were the most abundant groups within the bacterial communities, possessing differential vertical distribution patterns. Cyanobacteria were more abundant in the surface waters, whereas Proteobacteria dominated the deeper layers (75 m). However, within the diazotroph communities, Proteobacteria (mainly γ-Proteobacteria) were the most dominant groups than Cyanobacteria. Function prediction based on PICRUSt revealed that nitrogen fixation might more active to add fixed nitrogen in the surface waters, while nitrogen removal pathways (denitrification and anammox) might stronger in deeper layers. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and silicate were major environmental factors driving the distribution of bacterial communities. Additionally, phosphate was also an important factor in regulating the diazotroph communities in the surface water. Overall, this study provided detailed information on bacterial communities and their vital role in the nitrogen cycles in oligotrophic ecosystems.

Marine picocyanobacteria Synechococcus exhibit highly diverse pigment types (PTs) and hence possess great advantage to utilize different spectrum of light effectively and to occupy a wide range of light niches. In this study, we explored the diversity of Synechococcus PTs in the eastern Indian Ocean (EIO), surface water of Strait of Malacca (SSM), and coastal waters of Sri Lanka (SSL). All the detected PTs were phycourobilin (PUB) containing PT 3 and showed distinct distribution patterns. Low PUB PT 3a and partial chromatic acclimater PT 3eA dominated in coastal and shallow waters (SSM and SSL). In contrast, high PUB and chromatic acclimaters PT 3dA and PT 3c/3dB were mainly distributed in open ocean (EIO). PT 3dA and PT 3c/3dB occurred at similar depths of the lower euphotic layers but showed distinct distribution pattern that are partially exclusive, indicating that they compete with each other for the same light niche. Interestingly, the newly described PT 3f was detected with high relative abundances at all stations and particularly dominated in the upper euphotic layer in EIO, which was confirmed with PT-specific quantitative polymerase chain reaction (qPCR). The relative abundance of PT 3f was negatively correlated with nutrient level, implying that PT 3f is adapted to oligotrophic waters. Pronounced niche partition of different PTs was observed in the upper and lower layers of euphotic zone in EIO and SSM/SSL. Light, nutrients, and strong stratification may play important roles in the niche partition of different PTs. Further analysis about ecologically significant taxonomic units revealed high diversity within each PT at different locations, which provided insights for understanding specific PT with wide range of niches.

Na+ is the most abundant ion in living organisms and plays essential roles in regulating nutrient uptake, muscle contraction, and neurotransmission. The identification of Na+ in protein structures is crucial for gaining a deeper understanding of protein function in a physiological context. LeuT, a bacterial homolog of the neurotransmitter:sodium symporter family, uses the Na+ gradient to power the uptake of amino acids into cells and has been used as a paradigm for the study of Na+-dependent transport systems. We have devised a low-energy multi-crystal approach for characterizing low-Z (Z ≤ 20) anomalous scattering ions such as Na+, Mg2+, K+, and Ca2+ by combining Bijvoet-difference Fourier syntheses for ion detection and f” refinements for ion speciation. Using the approach, we experimentally identify two Na+ bound near the central leucine binding site in LeuT. Using LeuT microcrystals, we also demonstrate that Na+ may be depleted to study conformational changes in the LeuT transport cycle.

Abstract Background Tetraploid Thinopyrum elongatum (2n = 4x = 28) is a promising source of useful genes, including those related to adaptability and resistance to diverse biotic (Fusarium head blight, rust, powdery mildew, and yellow dwarf virus) and abiotic (cold, drought, and salt) stresses. However, gene transfer rates are low for this species and relatively few species-specific molecular markers are available. Results The wheat-tetraploid Th. elongatum line K17–841-1 derived from a cross between a hexaploid Trititrigia and Sichuan wheat cultivars was characterized based on sequential genomic and fluorescence in situ hybridizations and simple sequence repeat markers. We revealed that K17–841-1 is a 1E (1D) chromosomal substitution line that is highly resistant to stripe rust pathogen strains prevalent in China. By comparing the sequences generated during genotyping-by-sequencing (GBS), we obtained 597 specific fragments on the 1E chromosome of tetraploid Th. elongatum. A total of 235 primers were designed and 165 new Th. elongatum-specific markers were developed, with an efficiency of up to 70%. Marker validation analyses indicated that 25 specific markers can discriminate between the tetraploid Th. elongatum chromosomes and the chromosomes of other wheat-related species. An evaluation of the utility of these markers in a F2 breeding population suggested these markers are linked to the stripe rust resistance gene on chromosome 1E. Furthermore, 28 markers are unique to diploid Th. elongatum, tetraploid Th. elongatum, or decaploid Thinopyrum ponticum, which carry the E genome. Finally, 48 and 74 markers revealed polymorphisms between Thinopyrum E-genome- containing species and Thinopyrum bessarabicum (Eb) and Pseudoroegneria libanotica (St), respectively. Conclusions This new substitution line provide appropriate bridge–breeding–materials for alien gene introgression to improve wheat stripe rust resistance. The markers developed using GBS technology in this study may be useful for the high-throughput and accurate detection of tetraploid Th. elongatum DNA in diverse materials. They may also be relevant for investigating the genetic differences and phylogenetic relationships among E, Eb, St, and other closely-related genomes and for further characterizing these complex species.

To examine the spatial pattern and controlling factors of the primary productivity (PP) of phytoplankton in the eastern Indian Ocean (EIO), deck-incubation carbon fixation (a 14C tracer technique) and the related hydrographic properties were measured at 15 locations during the pre-summer monsoon season (February–April 2017). There are knowledge gaps in the field observations of PP in the EIO. The estimated daily carbon production rates integrated over the photic zone ranged from 113 to 817 mgC m–2 d–1, with a mean of 522 mgC m–2 d–1. The mixed-layer integrated primary production (MLD-PP) ranged from 29.0 to 303.7 mgC m–2 d–1 (mean: 177.2 mgC m–2 d–1). The contribution of MLD-PP to the photic zone-integrated PP (PZI-PP) varied between 19 and 51% (mean: 36%). Strong spatial variability in the carbon fixation rates was found in the study region. Specifically, the surface primary production rates were relatively higher in the Bay of Bengal domain affected by riverine flux and lower in the equatorial domain owing to the presence of intermonsoonal Wyrtki jets, which were characterized by a depression of thermocline and nitracline. The PZI-PP exhibited a linear (positive) relationship with nutrient values, but with no significance, indicating a partial control of macronutrients and a light limitation of carbon fixation. As evident from the vertical profiles, the primary production process mainly occurred above the nitracline depth and at high photosynthetic efficiency. Phytoplankton (>5 μm), including dinoflagellates, Trichodesmium, coccolithophores, and dissolved nutrients, are thought to have been correlated with primary production during the study period. The measured on-deck biological data of our study allow for a general understanding of the trends in PP in the survey area of the EIO and can be incorporated into global primary production models.

ABSTRACT Management of crop root rot disease is one of the key factors in ensuring sustainable development in agricultural production. The accumulation of autotoxins and pathogens in soil has been reported as a primary driver of root rot diseases; however, less is known about the correlation of plants, their associated pathogens and microbiome mediated by autotoxins as well as the contributions autotoxins make to the occurrence of root rot disease. Here, we integrated metabolomic, transcriptomic, and rhizosphere microbiome analyses to identify the root cell wall degradants cellobiose and d-galacturonic acid as being induced by the autotoxic ginsenoside Rg1 of Panax notoginseng, and we found that exogenous cellobiose and d-galacturonic acid in addition to Rg1 could aggravate root rot disease by modifying the rhizosphere microbiome. Microorganisms that correlated positively with root rot disease were enriched and those that correlated negatively were suppressed by exogenous cellobiose, d-galacturonic acid, and Rg1. In particular, they promoted the growth and infection of the soilborne pathogen Ilyonectria destructans by upregulating pathogenicity-related genes. Cellobiose showed the highest ability to modify the microbiome and enhance pathogenicity, followed by Rg1 and then d-galacturonic acid. Collectively, autotoxins damaged root systems to release a series of cell wall degradants, some of which modified the rhizosphere microbiome so that the host plant became more susceptible to root rot disease. IMPORTANCE The accumulation of autotoxins and pathogens in soil has been reported as a primary driver of root rot disease and one of the key factors limiting sustainable development in agricultural production. However, less is known about the correlation of plants, their associated pathogens, and the microbiome mediated by autotoxins, as well as the contributions autotoxins make to the occurrence of root rot disease. In our study, we found that autotoxins can damage root systems, thus releasing a series of cell wall degradants, and both autotoxins and the cell wall degradants they induce could aggravate root rot disease by reassembling the rhizosphere microbiome, resulting in the enrichment of pathogens and microorganisms positively related to the disease but the suppression of beneficial microorganisms. Deciphering this mechanism among plants, their associated pathogens, and the microbiome mediated by autotoxins will advance our fundamental knowledge of and ability to degrade autotoxins or employ microbiome to alleviate root rot disease in agricultural systems.

The root of Panax notoginseng (Burk.), in which saponins are the major active components, is a famous traditional Chinese medicine used to stop bleeding and to decrease inflammation and heart disease. Inflorescence removal increases the yield and quality of P. notoginseng, but the underlying molecular mechanisms are unknown. Here, the differences between inflorescence-removal treatment and control groups of P. notoginseng were compared using transcriptomics and metabolomics analyses. Illumina sequencing of cDNA libraries prepared from the rhizomes, leaves and roots of the two groups independently identified 6,464, 4,584, and 7,220 differentially expressed genes (DEG), respectively. In total, 345 differentially expressed transcription factors (TFs), including MYB and WRKY family members, were induced by the inflorescence-removal treatment. Additionally, 215 DEGs involved in saponin terpenoid backbone biosynthetic pathways were identified. Most genes involved in the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways were activated by inflorescence removal. The co-expression analysis showed that the low expression levels of flavonoid biosynthesis-related genes (e.g., C4H and F3H) decreased the biosynthesis and accumulation of some flavonoids after inflorescence removal. The results not only provide new insights into the fundamental mechanisms underlying the poorly studied inflorescence-removal process in P. notoginseng and other rhizome crops, but they also represent an important resource for future research on gene functions during inflorescence-removal treatments and the reproductive stage.

Microbial communities are composed of many rare species and a few abundant species. Considering the disproportionate importance of rare species for ecosystem functioning, it is important to understand the mechanisms structuring the rare and abundant components of a diverse community in response to environmental changes. Here, we used a 16S ribosomal RNA gene sequencing approach to investigate the bacterial community diversity in the Eastern Indian Ocean (EIO) during the monsoon and intermonsoon. We employed a phylogenetic null model and network analysis to evaluate the assembly processes and co-occurrence pattern of the microbial community. We found that higher bacterial diversity was detected in the intermonsoon with high temperature and low Chlorophyll a concentrations and N/P ratios. The balance between ecological deterministic processes and stochastic processes varied with seasons in the EIO. Meanwhile, conditionally rare taxa (CRT) were more likely modulated by variable selection processes than always rare taxa (ART) and abundant taxa (AT) (CRT > ART > AT). By linking assembly process and species co-occurrence, we demonstrated that the microbial co-occurrence associations tended to be higher when deterministic processes (mainly variable selection) were weaker. This negative trend was observed in rare species rather than abundant species. The linkage could enhance our understanding of the underlying mechanisms underpinning the generation and maintenance of microbial community diversity.

Community detection in the network has become an invaluable tool to explore and reveal the internal organization of nodes. In particular, the target community detection focuses on discovering the “local” links within and connecting to the target community related to user's preference, which refers to a limited number of nodes in the whole network. A few works in the literature discuss the target community detection. In this paper, we propose a target community detection with user's preference and attribute subspace. Our method utilizes not only network structure but also node attributes within a certain subspace to quantify both internal consistency and external separability, which is able to capture a user preferred target community. First, the similarity between nodes is calculated via both attributes and structures, and the center node set of the target community can be obtained by extending the sample node given by the user with its neighbors. Second, an attribute subspace calculation method with entropy weights is established based on the center node set, and the attribute subspace of the target community can thus be deduced. Finally, the target community quality, which is the combination of internal connectivity and external separability, is defined, based on which the target community with a user's preference can be detected. The experimental results on both synthetic network and real-world network datasets demonstrated the efficiency and effectiveness of the proposed algorithm.

Adjusting planting density is a common agricultural practice used to achieve maximum yields. However, whether the quality of medicinal herbs can be improved by implementing appropriate planting densities is still uncertain. The medicinal crop Panax notoginseng was used to analyze the effects of planting density on growth and ginsenoside accumulation, and the possible mechanisms of these effects were revealed through metabonomics. The results showed that P. notoginseng achieved high ginsenoside accumulation at high planting densities (8 × 8 and 10 × 10 cm), while simultaneously achieved high biomass and ginsenoside accumulation at moderate planting density of 15 × 15 cm. At the moderate planting density, the primary metabolism (starch and sucrose metabolism) and secondary metabolism (the biosynthesis of phytohormone IAA and ginsenoside) of the plants were significantly enhanced. However, the strong intraspecific competition at the high planting densities resulted in stress as well as the accumulation of phytohormones (SA and JA), antioxidants (gentiobiose, oxalic acid, dehydroascorbic acid) and other stress resistance-related metabolites. Interestingly, the dry biomass and ginsenoside content were significantly lower at low densities (20 × 20 and 30 × 30 cm) with low intraspecific competition, which disturbed normal carbohydrate metabolism by upregulating galactose metabolism. In summary, an appropriate planting density was benefit for the growth and accumulation of ginsenosides in P. notoginseng by balancing primary metabolism and secondary metabolism.