Integrating pH into the metabolic theory of ecology to predict bacterial diversity in soil.

Microorganisms play essential roles in soil ecosystem functioning and maintenance, but methods are currently lacking for quantitative assessments of the mechanisms underlying microbial diversity patterns observed across disparate systems and scales. Here we established a quantitative model to incorporate pH into metabolic theory to capture and explain some of the unexplained variation in the relationship between temperature and soil bacterial diversity. We then tested and validated our newly developed models across multiple scales of ecological organization. At the species level, we modeled the diversification rate of the model bacterium Pseudomonas fluorescens evolving under laboratory media gradients varying in temperature and pH. At the community level, we modeled patterns of bacterial communities in paddy soils across a continental scale, which included natural gradients of pH and temperature. Last, we further extended our model at a global scale by integrating a meta-analysis comprising 870 soils collected worldwide from a wide range of ecosystems. Our results were robust in consistently predicting the distributional patterns of bacterial diversity across soil temperature and pH gradients-with model variation explaining from 7 to 66% of the variation in bacterial diversity, depending on the scale and system complexity. Together, our study represents a nexus point for the integration of soil bacterial diversity and quantitative models with the potential to be used at distinct spatiotemporal scales. By mechanistically representing pH into metabolic theory, our study enhances our capacity to explain and predict the patterns of bacterial diversity and functioning under current or future climate change scenarios.

Community assembly of organisms regulates soil microbial functional potential through dual mechanisms.

Unraveling the influence of community assembly processes on soil ecosystem functioning presents a major challenge in the field of theoretical ecology, as it has received limited attention. Here, we used a series of long-term experiments spanning over 25 years to explore the assembly processes of bacterial, fungal, protist, and nematode communities using high-throughput sequencing. We characterized the soil microbial functional potential by the abundance of microbial genes associated with carbon, nitrogen, phosphorus, and sulfur cycling using GeoChip-based functional gene profiling, and determined how the assembly processes of organism groups regulate soil microbial functional potential through community diversity and network stability. Our results indicated that balanced fertilization (NPK) treatment improved the stochastic assembly of bacterial, fungal, and protist communities compared to phosphorus-deficient fertilization (NK) treatment. However, there was a nonsignificant increase in the normalized stochasticity ratio of the nematode community in response to fertilization across sites. Our findings emphasized that soil environmental factors influenced the assembly processes of the biotic community, which regulated soil microbial functional potential through dual mechanisms. One mechanism indicated that the high phosphorus levels and low soil nutrient stoichiometry may increase the stochasticity of bacterial, fungal, and protist communities and the determinism of the nematode community under NPK treatment, ultimately enhancing soil microbial functional potential by reinforcing the network stability of the biotic community. The other mechanism indicated that the low phosphorus levels and high soil nutrient stoichiometry may increase the stochastic process of the bacterial community and the determinism of the fungal, protist, and nematode communities under NK treatment, thereby enhancing soil microbial functional potential by improving the ß-diversity of the biotic community. Taken together, these results provide valuable insights into the mechanisms underlying the assembly processes of the biotic community that regulate ecosystem functioning.

Organic amendments increased Chinese milk vetch symbiotic nitrogen fixation by enriching Mesorhizobium in rhizosphere.

Symbiotic nitrogen fixation of Chinese milk vetch (Astragalus sinicus L.) can fix nitrogen from the atmosphere and serve as an organic nitrogen source in agricultural ecosystems. Exogenous organic material application is a common practice of affecting symbiotic nitrogen fixation; however, the results of the regulation activities remain under discussion. Studies on the impact of organic amendments on symbiotic nitrogen fixation have focused on dissolved organic carbon content changes, whereas the impact on dissolved organic carbon composition and the underlying mechanism remain unclear. In situ pot experiments were carried out using soils from a 40-year-old field experiment platform to investigate symbiotic nitrogen fixation rate trends, dissolved organic carbon concentration and component, and diazotroph community structure in roots and in rhizosphere soils following long-term application of different exogenous organic substrates, i.e., green manure, green manure and pig manure, and green manure and rice straw. Remarkable increases in rate were observed in and when compared with that in green manure treatment, with the greatest enhancement observed in the treatment. Moreover, organic amendments, particularly pig manure application, altered diazotroph community composition in rhizosphere soils, therefore increasing the abundance of the host-specific genus Mesorhizobium. Furthermore, organic amendments influence the diazotroph communities through two primary mechanisms. Firstly, the components of dissolved organic carbon promote an increase in available iron, facilitated by the presence of humus substrates. Secondly, the elevated content of dissolved organic carbon and available iron expands the niche breadth of Mesorhizobium within the rhizosphere. Consequently, these alterations result in a modified diazotroph community within the rhizosphere, which in turn influences Mesorhizobium nodulation in the root and symbiotic nitrogen fixation rate. The results of the present study enhance our understanding of the impact of organic amendments on symbiotic nitrogen fixation and the underlying mechanism, highlighting the key role of dissolved organic carbon composition on diazotroph community composition in the rhizosphere.

Comprehensive investigations of 2-phenylethanol production by the filamentous fungus Annulohypoxylon stygium.

2-Phenylethanol (2-PE) is an aromatic compound with a rose-like fragrance that is widely used in food and other industries. Yeasts have been implicated in the biosynthesis of 2-PE; however, few studies have reported the involvement of filamentous fungi. In this study, 2-PE was detected in Annulohypoxylon stygium mycelia grown in both potato dextrose broth (PDB) and sawdust medium. Among the 27 A. stygium strains investigated in this study, the strain "Jinjiling" (strain S20) showed the highest production of 2-PE. Under optimal culture conditions, the concentration of 2-PE was 2.33 g/L. Each of the key genes in Saccharomyces cerevisiae shikimate and Ehrlich pathways was found to have homologous genes in A. stygium. Upon the addition of L-phenylalanine to the medium, there was an upregulation of all key genes in the Ehrlich pathway of A. stygium, which was consistent with that of S. cerevisiae. A. stygium as an associated fungus provides nutrition for the growth of Tremella fuciformis and most spent composts of T. fuciformis contain pure A. stygium mycelium. Our study on the high-efficiency biosynthesis of 2-PE in A. stygium offers a sustainable solution by utilizing the spent compost of T. fuciformis and provides an alternative option for the production of natural 2-PE. KEY POINTS: • Annulohypoxylon stygium can produce high concentration of 2-phenylethanol. • The pathways of 2-PE biosynthesis in Annulohypoxylon stygium were analyzed. • Spent compost of Tremella fuciformis is a potential source for 2-phenylethanol.

Biogeographical patterns of abundant and rare bacterial biospheres in paddy soils across East Asia.

Soil bacterial communities play fundamental roles in ecosystem functioning and often display a skewed distribution of abundant and rare taxa. So far, relatively little is known about the biogeographical patterns and mechanisms structuring the assembly of abundant and rare biospheres of soil bacterial communities. Here, we studied the geographical distribution of different bacterial sub-communities by examining the relative influence of environmental selection and dispersal limitation on taxa distributions in paddy soils across East Asia. Our results indicated that the geographical patterns of four different bacterial sub-communities consistently displayed significant distance-decay relationships (DDRs). In addition, we found niche breadth and dispersal rates to significantly explain differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs. While conditionally rare and abundant taxa displayed the strongest DDR due to higher environmental filtering and dispersal limitation, moderate taxa sub-communities had the weakest DDR due to greater environmental tolerance and dispersal rate. Random forest models indicated that soil pH (9.13%-49.78%) and average annual air temperature (16.59%-46.49%) were the most important predictors of the variation in the bacterial community. This study advances our understanding of the intrinsic links between fundamental ecological processes and microbial biogeographical patterns in paddy soils.

Cadmium tolerance in Elodea canadensis Michx: Subcellular distribution and metabolomic analysis.

The aquatic plant Elodea canadensis is considered a good candidate for ecotoxicological investigations. Cadmium (Cd) is a widespread contaminant in aquatic systems. In this study, to better elucidate the underlying tolerance mechanism and molecular impact of environmentally relevant Cd concentration in aquatic plants, subcellular distribution, chemical forms, and gas chromatography-mass spectrometry-based non-targeted metabolomics profiles were comprehensively analyzed in E. canadensis subjected to 0 and 10 µM Cd treatment for 5 d. Subcellular fractionation analysis of Cd-containing leaves showed that 67% of Cd was compartmentalized in cell wall followed by the soluble fraction (24 %) and organelles (9 %). The majority of Cd (90 %) was found in the extraction using 1 M NaCl. Metabolomic analysis using unsupervised principal component analyses and a supervised partial least squares discriminant analysis revealed clear differences in metabolic profiles between the two groups, demonstrating the metabolic effects of Cd. The 155 identified compounds altered by Cd were mainly from primary metabolism, including sugars, amino acids, organic acids, and their derivatives. Secondary metabolites such as polyphenols and phenolamides were also detected. The massive up-regulation of metabolites, including trehalose, proline, sarcosine, nicotianamine, putrescine, α-ketoglutaric acid, citric acid, and phytol might represent a detoxification mechanism. These findings highlighted the mechanistic strategies that E. canadensis employs to defend against Cd toxicity.

A Novel Cochlioquinone Derivative, CoB1, Regulates Autophagy in Pseudomonas aeruginosa Infection through the PAK1/Akt1/mTOR Signaling Pathway.

Owing to multiple antibiotic resistance, Pseudomonas aeruginosa causes the most intractable infections to human beings worldwide, thus exploring novel drugs to defend against this bacterium remains of great importance. In this study, we purified a novel cochlioquinone B derivative (CoB1) from Salvia miltiorrhiza endophytic Bipolaris sorokiniana and reveal its role in host defense against P. aeruginosa infection by activating cytoprotective autophagy in alveolar macrophages (AMs) both in vivo and in vitro. Using a P. aeruginosa infection model, we observed that CoB1-treated mice manifest weakened lung injury, reduced bacterial systemic dissemination, decreased mortality, and dampened inflammatory responses, compared with the wild type littermates. We demonstrate that CoB1-induced autophagy in mouse AMs is associated with decreased PAK1 expression via the ubiquitination-mediated degradation pathway. The inhibition of PAK1 decreases the phosphorylation level of Akt, blocks the Akt/mTOR signaling pathway, and promotes the release of ULK1/2-Atg13-FIP200 complex from mTOR to initiate autophagosome formation, resulting in increased bacterial clearance capacity. Together, our results provide a molecular basis for the use of CoB1 to regulate host immune responses against P. aeruginosa infection and indicate that CoB1 is a potential option for the treatment of infection diseases.

A network physiology approach to oxygen saturation variability during normobaric hypoxia.

NEW FINDINGS: What is the central question of this study? What is the physiological interpretation of SpO2 fluctuations observed during normobaric hypoxia in healthy individuals? What is the main finding and its importance? There is a significant flow of information between SpO2 and other cardio-respiratory time series during graded hypoxia. Analysis of the pattern of SpO2 variations has potential for non-invasive assessment of the engagement of respiratory control system in health and disease. ABSTRACT: Peripheral capillary oxygen saturation ( SpO2 ) exhibits a complex pattern of fluctuations during hypoxia. The physiological interpretation of SpO2 variability is not well understood. In this study, we tested the hypothesis that SpO2 fluctuation carries information about integrated cardio-respiratory control in healthy individuals using a network physiology approach. We explored the use of transfer entropy in order to compute the flow of information between cardio-respiratory signals during hypoxia. Twelve healthy males (mean (SD) age 22 (4) years) were exposed to four simulated environments (fraction of inspired oxygen ( FIO2 ): 0.12, 0.145, 0.17, and 0.2093) for 45 min, in a single blind randomized controlled design. The flow of information between different physiological parameters ( SpO2 , respiratory frequency, tidal volume, minute ventilation, heart rate, end-tidal pressure of O2 and CO2 ) were analysed using transfer entropy. Normobaric hypoxia was associated with a significant increase in entropy of the SpO2 time series. The transfer entropy analysis showed that, particularly at FIO2 0.145 and 0.12, the flow of information between SpO2 and other physiological variables exhibits a bidirectional relationship. While reciprocal interactions were observed between different cardio-respiratory parameters during hypoxia, SpO2 remained the main hub of this network. SpO2 fluctuations during graded hypoxia exposure carry information about cardio-respiratory control. Therefore, SpO2 entropy analysis has the potential for non-invasive assessment of the functional connectivity of respiratory control system in various healthcare settings.

L-Carnitine protects against tacrolimus-induced renal injury by attenuating programmed cell death via PI3K/AKT/PTEN signaling.

Reducing immunosuppressant-related complications using conventional drugs is an efficient therapeutic strategy. L-carnitine (LC) has been shown to protect against various types of renal injury. In this study, we investigated the renoprotective effects of LC in a rat model of chronic tacrolimus (TAC) nephropathy. SD rats were injected with TAC (1.5 mg · kg-1 · d-1, sc) for 4 weeks. Renoprotective effects of LC were assessed in terms of renal function, histopathology, oxidative stress, expression of inflammatory and fibrotic cytokines, programmed cell death (pyroptosis, apoptosis, and autophagy), mitochondrial function, and PI3K/AKT/PTEN signaling. Chronic TAC nephropathy was characterized by severe renal dysfunction and typical histological features of chronic nephropathy. At a molecular level, TAC markedly increased the expression of inflammatory and fibrotic cytokines in the kidney, induced oxidative stress, and led to mitochondrial dysfunction and programmed cell death through activation of PI3K/AKT and inhibition of PTEN. Coadministration of LC (200 mg · kg-1 · d-1, ip) caused a prominent improvement in renal function and ameliorated histological changes of kidneys in TAC-treated rats. Furthermore, LC exerted anti-inflammatory and antioxidant effects, prevented mitochondrial dysfunction, and modulated the expression of a series of apoptosis- and autophagy-controlling genes to promote cell survival. Human kidney proximal tubular epithelial cells (HK-2 cells) were treated with TAC (50 µg/mL) in vitro, which induced production of intracellular reactive oxygen species and expression of an array of genes controlling programmed cell death (pyroptosis, apoptosis, and autophagy) through interfering with PI3K/AKT/PTEN signaling. The harmful responses of HK-2 cells to TAC were significantly attenuated by cotreatment with LC and the PI3K inhibitor LY294002 (25 µM). In conclusion, LC treatment protects against chronic TAC nephropathy through interfering the PI3K/AKT/PTEN signaling.

Derivation and validation of thresholds of cadmium, chromium, lead, mercury and arsenic for safe rice production in paddy soil.

Cadmium (Cd), chromium (Cr), lead (Pb), mercury (Hg) and arsenic (As) are potent toxicants to human health via dietary intake. It is imperative to establish accurate soil thresholds based on soil-plant transfer models and food safety standards for safe agricultural production. This study takes rice genotypes and soil properties into account to derive soil thresholds for five heavy metal(loid)s using the bioconcentration factors (BCF) and species sensitivity distribution (SSD) based on the food safety standard. The BCF generated from two paddy soils was calculated to investigate the sensitivity of heavy metal accumulation in nine rice cultivars in a greenhouse pot experiment. Then, empirical soil-plant transfer models were developed from a middle-sensitivity rice cultivar (Denong 2000, one selected from nine rice) grown in nineteen paddy soils with various soil properties under a proper exogenously metal(loid)s concentration gradient. After normalization, hazardous concentrations from the fifth percentile (HC5) were calculated from the SSD curves, and the derived soil thresholds were obtained from HC5 prediction models that based on the combination of pH and organic carbon (OC) or cation exchange capacity (CEC). The soil Cd threshold derived based on pH and organic carbon (pH < 7.5, OC ≥ 20 g kg-1) was 1.3-fold of those only considering pH, whereas the Pb threshold (pH > 6, CEC ≥ 20 cmolc kg-1) was 3.1 times lower than the current threshold. The derived thresholds for five elements were validated to be reliable through literature data and field experiments. The results suggested that deriving soil heavy metal(loid)s threshold using SSD method and local food safety standards is feasible and also applicable to other crops as well as other regions with potential health risks of toxic elements contamination in agricultural production.

Exogenous pancreatic kininogenase protects against renal fibrosis in rat model of unilateral ureteral obstruction.

Tissue kallikrein has protective function against various types of injury. In this study, we investigated whether exogenous pancreatic kininogenase (PK) conferred renoprotection in a rat model of unilateral ureteral obstruction (UUO) and H2O2-treated HK-2 cells in vitro. SD rats were subjected to UUO surgery, then PK (7.2 U/g per day, ip) was administered for 7 or 14 days. After the treatment, rats were euthanized; the obstructed kidneys were harvested for further examination. We found that PK administration significantly attenuated interstitial inflammation and fibrosis, and downregulated the expression of proinflammatory (MCP-1, TLR-2, and OPN) and profibrotic (TGF-ß1 and CTGF) cytokines in obstructed kidney. UUO-induced oxidative stress, closely associated with excessive apoptotic cell death and autophagy via PI3K/AKT/FoxO1a signaling, which were abolished by PK administration. We further showed that PK administration increased the expression of bradykinin receptors 1 and 2 (B1R and B2R) mRNA and the production of NO and cAMP in kidney tissues. Coadministration with either B1R antagonist (des-Arg9-[Leu8]-bradykinin) or B2R antagonist (icatibant) abrogated the renoprotective effects of PK, and reduced the levels of NO and cAMP in obstructed kidney. In H2O2-treated HK-2 cells, addition of PK (6 pg/mL) significantly decreased ROS production, regulated the expression of oxidant and antioxidant enzymes, suppressed the expression of TGF-ß1 and MCP-1, and inhibited cell apoptosis. Our data demonstrate that PK treatment protects against the progression of renal fibrosis in obstructed kidneys.

Responses of duckweed (Lemna minor L.) to aluminum stress: Physiological and proteomics analyses.

Aluminum (Al) is commonly considered an abiotic stress factor under acidic conditions. Duckweed (Lemna minor L.) has wide application in ecotoxicological research as a model organism and, in this study, its response to Al bioaccumulation was evaluated at morphological, physiological and proteomic levels. The Al accumulation in L. minor was accompanied by chlorosis and growth inhibition. Overproduction of superoxide and hydrogen peroxide, and decreased chlorophyll and protein contents, suggested that Al exposure induced oxidative stress. Inhibition of photosynthesis was evident in a significant decrease in maximum photosystem II quantum yield. There were 261 proteins, with significant changes in expression, successfully identified and quantified through isobaric tags for relative and absolute quantification (iTRAQ) analysis. Among the KEGG pathway enrichment proteins, those related to the citrate cycle and amino acid metabolism were predominantly up-regulated, whereas those associated with energy metabolism and glyoxylate and dicarboxylate metabolism were predominantly down-regulated. In addition, antioxidant enzyme related proteins played an important role in the response of L. minor to Al. The western blot analysis further validated the changes in photosynthetic related proteins. These results provide comprehensive insights into the physiological and molecular mechanisms of Al toxicity and tolerance in L. minor.

Comparison of Four Quantitative Techniques for Monitoring Microalgae Disruption by Low-Frequency Ultrasound and Acoustic Energy Efficiency.

Ultrasound has been regarded as an environmental friendly technology to utilize microalgae biomass and control algal blooms. In this study, four quantitative techniques, including cell counting, optical density of algal suspension, pigments release, and protein release, were performed on three species of microalgae ( M. aeruginosa, C. pyrenoidosa, and C. reinhardtii) to develop effective techniques for rapid monitoring of cell disruption and to optimize the acoustic energy efficiency. Results showed optical density of algal suspensions was not an optimal indicator to monitor cell disruption, although it is a common technique for determining cell concentration in microbial cultures. Instead, an accurate and reliable technique was to determine the release of intracellular pigments (absorbance peaks of supernatant) for indicating cell rupture. The protein released during sonication could also be a useful indicator if it is the component of interest. A fitted power functional model showed a strong relationship between cell disruption and energy consumption ( R2 > 0.87). This model could provide an effective approach to directly compare the energy efficiency of ultrasound in different systems or with varying microalgae species. This study provides valuable information for microalgae utilization and the treatment of algal blooms by ultrasound, so as to achieve energy conservation and environmental safety.

Response of Spirodela polyrhiza to cerium: subcellular distribution, growth and biochemical changes.

Rare earth elements are new and emerging contaminants in freshwater systems. Greater duckweed (Spirodela polyrhiza L.) is a common aquatic plant widely used in phytotoxicity tests for xenobiotic substances. In this study, the cerium (Ce) accumulation potential, the distribution of Ce in bio-molecules, and ensuing biochemical responses were investigated in greater duckweed fronds when they were exposed to Ce (0, 10, 20, 40, and 60µM). There was a concentration dependent increase in Ce accumulation, which reached a maximum of 67mgg-1 of dry weight (DW) at 60µM Ce after 14 d. The Ce concentrations in bio-macromolecules followed the order: cellulose and pectin > proteins > polysaccharides > lipids. In response to Ce exposure, significant chlorosis; declines in growth, photosynthetic pigment and protein contents; and cell death were noted at the highest Ce concentration. Photosystem II inhibition, degradation of the reaction center protein D1, and damage to chloroplast ultrastructure were observed in Ce treated S. polyrhiza fronds, as revealed by chlorophyll a fluorescence transients, immunoblotting, and transmission electron microscopy (TEM). O2.- accumulation and malondialdehyde (MDA) content in the treated fronds increased in a concentration dependent manner, which indicated that oxidative stress and unsaturated fatty acids (C18:3) were specifically affected by Ce exposure. These results suggest Ce exerts its toxic effects on photosynthesis, with a primary effect on PS II, through oxidative stress.

Streptomyces tremellae sp. nov., isolated from a culture of the mushroom Tremella fuciformis.

A novel actinomycete strain, designated Js-1T, was isolated from Tremella fuciformis collected from Gutian, Fujian Province, in southeastern China. The taxonomic status of this strain was determined by a polyphasic approach, which demonstrated that the novel strain was a member of the genus Streptomyces. The cell walls of this strain were found to contain ll-diaminopimelic acid, muramic acid and glycine. An analysis of whole-cell hydrolysates revealed that no characteristic sugar was present. The key identified menaquinones were MK-9 (H6) and MK-9 (H8), while the diagnostic polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmethylethanolamine and phosphatidylglycerol. The main cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0. An analysis of an almost complete 16S rRNA gene sequence showed that the strain shared the highest levels of sequence similarity with Streptomyces sannanensisKC-7038T (97.87 %), Streptomyces hebeiensis YIM 001T (97.84 %), Streptomyces pathocidini NBRC 13812T (97.80 %), Streptomyces cocklensis BK168T (97.25 %), Streptomyces coerulescens NBRC 12758T (97.12 %), Streptomyces aurantiogriseus NBRC 12842T (97.06 %) and Streptomyces rimosussubsp. rimosus ATCC 10970T (97.04 %). The DNA G+C content of the genomic DNA of strain Js-1T was 70.1 mol%. Furthermore, DNA-DNA hybridization tests revealed that the relatedness values between strain Js-1T and the most closely related species ranged from 15.10 to 47.20 %. Based on its phenotypic and genotypic characteristics, strain Js-1T (=CCTCC M 2011365T=JCM 30846T) is considered to represent a novel species within the genus Streptomyces, which we classified as Streptomycestremellae sp. nov.

A Jacalin-Related Lectin Regulated the Formation of Aerial Mycelium and Fruiting Body in Flammulina velutipes.

Flammulina velutipes, one of the most popular mushroom species in the world, has been recognized as a useful model system to study the biochemical and physiological aspects of the formation and elongation of fruit body. However, few reports have been published on the regulation of fruiting body formation in F. velutipes at the molecular level. In this study, a jacalin-related lectin gene from F. velutipes was characterized. The phylogenetic tree revealed that Fv-JRL1 clustered with other basidiomycete jacalin-like lectins. Moreover, the transcriptional pattern of the Fv-JRL1 gene in different developmental stages of F. velutipes implied that Fv-JRL1 could be important for formation of fruit body. Additionally, RNA interference (RNAi) and overexpression analyses provided powerful evidence that the lectin gene Fv-JRL1 from F. velutipes plays important roles in fruiting body formation.

Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map.

Molecular markers and genetic maps are useful tools in genetic studies. Novel molecular markers and their applications have been developed in recent years. With the recent advancements in sequencing technology, the genomic sequences of an increasingly great number of fungi have become available. A novel type of molecular marker was developed to construct the first reported linkage map of the edible and economically important basidiomycete Volvariella volvacea by using 104 structural variation (SV) markers that are based on the genomic sequences. Because of the special and simple life cycle in basidiomycete, SV markers can be effectively developed by genomic comparison and tested in single spore isolates (SSIs). This stable, convenient and rapidly developed marker may assist in the construction of genetic maps and facilitate genomic research for other species of fungi.

Optimal codons in Tremella fuciformis end in C/G, a strong difference with known Tremella species.

Tremella fuciformis is a popular edible fungus with fruiting bodies that can be produced in large quantities at low costs, while it is easy to transform and cultivate as yeast. This makes it an attractive potential bioreactor. Enhanced heterologous gene expression through codon optimization would be useful, but until now codon usage preferences in T. fuciformis remain unknown. To precisely determine the preferred codon usage of T. fuciformis we sequenced the genome of strain Tr26 resulting in a 24.2 Mb draft genome with 10,040 predicted genes. 3288 of the derived predicted proteins matched the UniProtKB/Swiss-Prot databases with 40% or more similarity. Corresponding gene models of this subset were subsequently optimized through repetitive comparison of alternative start codons and selection of best length matching gene models. For experimental confirmation of gene models, 96 random clones from an existing T. fuciformis cDNA library were sequenced, generating 80 complete CDSs. Calculated optimal codons for the 3288 predicted and the 80 cloned CDSs were highly similar, indicating sufficient accuracy of predicted gene models for codon usage analysis. T. fuciformis showed a strong preference for C and then G at the third base pair position of used codons, while average GC content of predicted genes was slightly higher than the total genome sequence average. Most optimal codons ended in C or G except for one, and an increased frequency of C ending codons was observed in genes with higher expression levels. Surprisingly, the preferred codon usage in T. fuciformis strongly differed from T. mesenterica and C. neoformans. Instead, optimal codon usage was similar to more distant related species such as Ustilago maydis and Neurospora crassa. Despite much higher overall sequence homology between T. fuciformis and T. mesenterica, only 7 out of 21 optimal codons were equal, whereas T. fuciformis shared up to 20 out of 21 optimal codons with other species. Clearly, codon usage in Tremella can differ largely and should be estimated for individual species. The precise identification of optimal and high expression related codons is therefore an important step in the development of T. fuciformis as a bioreactor system.

[Prevention and Treatment of Atherosclerosis by Three Different Chinese Medical Compounds: a Mechanism Study].

OBJECTIVE: To study the effect of Buyang Huanwu Decoction (BHD), Xuefu Zhuyu Decoction (XZD), and Sijunzi Decoction (SD) contained serums on expressions of Toll-like receptor 4 (TLR4)/nuclear factor (NF)-κB signals, lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1), tumor necrosis factor-α (TNF-α), vascular cell adhesion molecule-1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), and to explore possible anti-atherosclerotic mechanisms. METHODS: Twenty New Zealand rabbits were divided into 4 groups at random, i.e., the normal control group, the BHD group (6.7 g/kg), the XZD group (3.6 g/kg), and the SD group (1.6 g/kg), 5 in each group. All medication lasted for 7 successive days. Two h after the final medication, about 50 mL blood was withdrawn from rabbit heart for preparing serums. Human umbilical vein endothelial cell ECV304 were cultured in vitro for 18 h and randomly divided into the blank control group, the model group, the Western medicine (WM) control group, the BHD group, the XZD group, and the SD group at random. ECV304, except in the blank control group, were stimulated with lipopolysaccharide (LPS) for 2 h. Those in the WM control group and CM groups were treated respectively with corresponding CM contained serum for 24 h. Finally gene and protein expressions of TLR4, myeloid differentiation factor 88 (MyD88), tumor necrosis factor receptor-associated factor-6 (TRAF-6), NF-κB, LOX-1, TNF-α, ICAM-1, and VCAM-1 were detected by fluorescent quantitative PCR and Western blot. RESULTS: Compared with the blank control group, mRNA expressions of TLR4, MyD88, TRAF-6, NF-KB, LOX-1 , TNF-cx, ICAM-1, and VCAM-1 increased significantly; protein expressions of TLR4, NF-κB, LOX-1, TNF-α, ICAM-1, and VCAM-1 also increased significantly in the model group (P < 0.01). Compared with the model group, mRNA and protein expressions of each index could be significantly inhibited in the BHD group, the XZD group, and the WM control group (P < 0.05). Besides, mRNA and protein expressions of each index could be significantly elevated more in the BHD group and the XZD group than in the WM control group (P < 0.05). No statistical difference existed in each index between the SD group and the rest groups (P > 0.05). CONCLUSIONS: The mechanism of BHD and XZD for fighting against atherosclerosis might be associated with inhibiting TLR4/NF-κB signal transduction pathway and expressions of its downstream inflammatory factors such as LOX-1, TNF-α, ICAM-1, and VCAM-1. But SD showed no associated effect on atherosclerosis.

Soil aggregate stratification of nematodes and ammonia oxidizers affects nitrification in an acid soil.

Nitrification plays a central role in global nitrogen cycle, which is affected by interaction between soil microfauna and microorganisms. The impact of synchronized changes in nematodes and ammonia oxidizers within aggregate fractions on nitrification was investigated in an acid soil under 10-year manure application. Nematodes, ammonia oxidizers and potential nitrification activity (PNA) were examined in three soil aggregate fractions under four fertilization regimes. Pyrosequencing data revealed that the dominant bacterial amoA operational taxonomic units (OTUs) were related to Nitrosospira species, while archaeal OTUs were affiliated with Nitrososphaera and Nitrosotalea species. PNA was more strongly correlated with ammonia-oxidizing bacteria (AOB) abundance than ammonia-oxidizing archaea (AOA) abundance, although AOA were dominant in the acid soil. Plant parasites had a negative effect on AOB abundance; however, bacterivores stimulated AOB abundance and contributed more to PNA than plant parasites. Aggregate fractions exerted significant impacts on AOA abundance and AOB community composition. Total carbon content strongly affected the abundance and composition of AOA community, while soil pH primarily affected that of AOB community. Soil variables explained 62.7% and 58.1% variations, and nematode variables explained 11.7% and 19.5% variations in the AOA and AOB community composition respectively.