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A novel monoraphid diatom species, Cocconeis crisscrossis You, Yu, Kociolek & Wang, sp. nov. is examined and described from the Qingyi River and Maolan Nature Reserve of southern China. The morphological description is based on light microscopy and scanning electron microscopy observations and the new species is compared with similar taxa in this genus. The characteristics unique to Cocconeis crisscrossis sp. nov. include its central area extending irregularly to both sides, it having closed valvocopulae with heavily silicified fimbriate margins and poles of the valvocopulae have ‘sword-shaped’ siliceous extensions. These features differentiate this new species from others in the genus. This new species was found in alkaline waterbodies, including streams, waterfall and ponds. It was usually found as an epiphyte on the stones; however, it was present on other substrates such as mosses.

Diatom cell walls are diverse and unique, providing the basis for species identification and supporting the ecological and economic value of diatoms. However, these important structures sometimes change in response to environmental fluctuations, especially under salt adaptation. Although studies have shown that salinity induces morphological plasticity changes in diatom cell walls, most research has focused on physiological responses rather than molecular mechanisms. In this study, Skeletonema subsalsum was cultured under four salinity conditions (0, 3, 6, 12). Through morphological and physiological methods, we found that salinity increased the cell diameter, protrusion lengths, distance between adjacent cells (DBCs), and nanopore size, while reducing cell height and silicification degree. To further investigate the mechanism underlying morphological changes in S. subsalsum, complementary transcriptome analysis was performed. In total, 20,138 differentially expressed genes (DEGs) were identified among the four treatments. Among them, 231 DEGs were screened and found to be closely associated with morphological changes, of which 107 were downregulated and 124 were upregulated. The findings demonstrated that elevated salinity inhibited silicon transport and deposition via downregulating the expression of DEGs involved in functions including chitin metabolism, putrescine metabolism, and vesicle transport, resulting in reduced silicon content and cell height. Increased salinity promoted the expression of DEGs related to microtubules (MTs), actin, and ubiquitin, which synchronously induced morphological changes. These findings provide a more comprehensive understanding of the salt tolerance of algae and a foundation for future studies on cell wall morphogenesis.

Developing policies to optimize the planting structure is essential to ensure an adequate supply of agricultural products and guarantee food security. However, the rationality and comprehensiveness of China’s cropping structure optimization policies require scientific evaluation. Therefore, this research established an evaluation index system for China’s planting structure optimization policies using text mining and the PMC-Index model to evaluate eight agricultural cropping structure optimization policies in China since 2003. The results showed that: (1) The PMC-Index showed a general upward trend across the eight policies, with scores ranging from 4.88 to 6.61. (2) Seven of the eight policies were deemed acceptable, while one was classified as low. (3) The Chinese government has long focused on optimizing the structure of agricultural cultivation, and relevant policies have made significant progress in terms of logical connotation and long-term feasibility. However, there is still room for improvement in enhancing regulatory effectiveness and strengthening interdepartmental collaboration. It is recommended that the government develop more flexible and diverse incentive mechanisms, strengthen interdepartmental coordination, expand policy coverage, enhance the comprehensiveness of policy functions, and elevate support for agricultural technology.

Exploring the spatiotemporal dynamics, spatial mismatch, and complex influencing mechanism of grain production and cropland productivity in the black soil region of northeast China (BSRNC) is essential for the synergistic protection and utilization of black soil cropland and sustainable grain production. The BSRNC has realized cropland expansion and grain production increases in the past decades. This implied a substantial investment has been made in the region’s agriculture. However, at present, knowledge on the spatial mismatch and influencing factors of grain production and cropland productivity is still unclear. This study analyzed the spatial–temporal mismatch characteristics of grain production and cropland net primary productivity (CNPP) using the gravity center model, spatial autocorrelation analysis, and spatial mismatch index (SMI), and identified the spatial heterogeneity and prediction–response relationships of influencing factors based on a geographically and temporally weighted regression (GTWR) model and boosted regression tree (BRT) machine learning algorithm. The findings indicated that grain production and CNPP have been increasing, but the overall spatial pattern of cold hotspots has not changed obviously in the BSRNC from 2000 to 2020. The SMI has shown a decreasing trend, indicating that the synergistic development of grain production and CNPP has been obvious, which plays an important role in sustainable food supply capacity. Agricultural production and the natural environment have always been critical factors influencing the spatial mismatch. Specifically, the marginal impact of fertilizer application has undergone a shift. This study may provide new clues for the formulation of regional strategies for sustainable food supply and black soil cropland system protection.

In this study, we investigated how Radix pseudostellariae polysaccharide (RPP) enhances the immune response of the inactivated porcine reproductive and respiratory syndrome virus (PRRSV) vaccine through interactions with the microbiome and metabolome. We pretreated sows with 10 mg/kg body weight of RPP via drinking water for 7 days prior to intramuscular injection of the PRRSV vaccine. This significantly increased the concentrations of PRRSV GP5 protein antibody, interleukin (IL)-2, IL-4, IL-10, and interferon (IFN)-γ. Oral administration of RPP also significantly improved the abundance of beneficial bacteria in the stool, such as Parabacteroides distasonis, Prevotella_copri, Eubacterium_sp., and Clostridium_sp._CAG:226, and decreased the levels of potentially pathogenic bacteria, such as Paraeggerthella and [Clostridium] innocuum, compared to the vaccine alone. These bacterial changes were confirmed using quantitative real-time polymerase chain reaction (Q-PCR). Moreover, RPP treatment significantly increased the blood concentrations of L-theanine, taurodeoxycholic acid (TDCA), and N-arachidonoyl proline, and decreased the levels of L-glutamine, oclacitinib, lipoxin C4, and leukotriene C5 in sows after immunization (p< 0.05). The concentrations of various blood metabolites were validated using sandwich enzyme-linked immunosorbent assay (ELISA), confirming the accuracy of the metabolomics data. Intriguingly, the integration of microbiome and metabolome analyses highlighted the significance of Prevotella_copri and TDCA. We consequently developed a mouse immunity model using GP5 protein and discovered that oral administration of RPP significantly enhanced the levels of GP5 protein antibodies, IL-2, IL-4, IL-10, and IFN-γ in mouse serum. It also increased the number of CD3+ and CD3+CD4+ cells in the spleen. Additionally, Prevotella_copri was administered into the large intestine via the anus for 7 days prior to the intramuscular injection of the PRRSV GP5 protein. The results demonstrated a significant increase in TDCA and GP5 antibody concentration in the mouse serum, indicating that RPP modulates Prevotella_copri to elevate its metabolite TDCA, thereby enhancing the GP5 antibody level. In conclusion, oral administration of 10 mg/kg RPP optimizes gut flora diversity and blood metabolites, particularly Prevotella_copri and TDCA, thereby improving the immune response to the inactivated PRRSV vaccine.

Identifying the interactions of land use functions (LUFs) is of great significance for alleviating the contradiction between human and land, and promoting sustainable use of land resources. However, few studies concerned the interactions of LUFs in urban agglomerations of ecologically fragile areas in China at a fine scale. In this study, we constructed a quantitative and visualized evaluation system of LUFs that conforms to three primary functions, ten sub-functions, and nineteen indicators of Lanzhou-Xining urban agglomeration (LXUA) in the upper reaches of the Yellow River basin based on the production-living- ecological functions. Then, the comprehensive evaluation method, hot spot analysis, and geographic weighted regression (GWR) model were used to identify the interactions among LUFs and influencing factors of LXUA from 2000 to 2020 at the county and grid scales. The results show that the LXUA is dominated by ecological function (EF), and EF and living function (LF) showing a “U” shaped change feature, while production function (PF) show an inverted “U” shaped change feature. Meanwhile, the cold spots and hot spots of PF and EF present the spatial characteristic of “overall dispersion and local aggregation”, while the LF has no cold spots, and the hot spots present the spatial characteristic of “point-axis”. Moreover, the PF and LF are in a synergistic relationship at two scales, with complementarity in space, while the EF and PF and the PF and LF are both in a trade-offs relationship, with overlap in space. Finally, socioeconomic development factors have remarkable impact on LUFs at the county scale, while LUFs at the grid scale is the comprehensive result of natural conditions, socioeconomic factors, accessibility and political factors. The results can provide references for the LXUA to differentiated design the land use policy, and provide empirical case for other ecologically fragile areas to alleviate the trade-offs of LUFs.

ABSTRACT: A comparative study was performed to investigate the differences in plasma pharmacokinetics (PKs) and tissue residues of trimethoprim (TMP) between silky fowls and 817 broilers. The 2 breeds of chickens received compound sulfadiazine suspension by gavage at 20 mg/kg (measured as TMP). Blood and tissue samples were collected at predetermined time points. The concentrations of TMP in plasma and tissue samples were determined by a validated high-performance liquid chromatography (HPLC) method. The plasma concentration-time data were subjected to noncompartment analysis by WinNonlin program (Pharsight Co., Mountain View, CA). The mean plasma concentrations of TMP in silky fowls were significantly lower than those in 817 broilers at all time-points. Significant differences were also observed between silky fowls and 817 broilers in maximum concentration (Cmax), area under the curve from time 0 to 24 h (AUC0 → 24 h), apparent volume of distribution (Vd), and total body clearance (ClB). Silky fowls had significantly higher muscle TMP concentrations and longer tissue residual time than 817 broilers. The tissue concentration of TMP followed the order of leg muscle > breast muscle > liver, which was obviously different from that of 817 broilers. The half-lives of TMP in the leg muscle, breast muscle, and liver of silky fowls were 31.42, 10.78, and 0.38 d, respectively. The current withdrawal time (WDT) was not sufficient to prevent violative residues of TMP in the edible tissues of silky fowls, and a WDT much longer than 8 d might be required.

A new freshwater diatom species, Achnanthidium kangdingnese Yu, You & Wang, sp. nov. from Sichuan Province, China, is described. The morphology of this species was analyzed with scanning electron microscopy (SEM) and light microscopy (LM). A. kangdingnese belongs to the A. initium-like subgroup, which has external distal raphe ends curved in opposite directions of the valve. The main characteristics of A. kangdingnese are its linear shape, rounded apices and transpically-elongated areolae on the both valves. The central area is well defined with one or two spaced striae of the raphe valve. And on the internal valve, areolae are occluded by hymens perforated by delicate slits, and each hymen is closely joined with the adjacent hymen. We compared the new species with other similar species of Achnanthidium, A. kangdingnese is considered to be sufficiently different from other similar species based on valve outline, shape of the axial and center areas, and striae density. The new species is known only from its type locality, a mountain lake in Kangding County.

Characterizing the photosynthetic capacity of grassland is essential for exploring the carbon cycle under climate change. However, little research has been conducted to date on photosynthetic accumulation per leaf area (NPP/LAI) in spatial and temporal terms, especially on how they respond to climate change. Hence, this study analyzed the spatiotemporal patterns of NPP/LAI based on MODIS products, explored the partial correlation of NPP/LAI with climatic factors for the annual and growing season, and quantified the time lag effects of climatic factors on NPP/LAI for seasonal in alpine grassland ecosystems at the source of the Yellow River Basin. The results indicated that NPP, LAI, and NPP/LAI of growing season increased in the study area between 2000 and 2021 whiles annual NPP/LAI decreased. At the same time, the spatial distribution of the multiannual mean values of precipitation and temperature approximately reversed and gradually increased on the time scale. The annual NPP/LAI for each grassland type gradually decreased between 2000 and 2021, with the mean of the growing season in NPP/LAI ranging from montane meadows (12.595 g C·m–2) > swamps (11.859 g C·m–2) > alpine meadows (11.718 g C·m–2) > temperate steppes (10.994 g C·m–2). It is also interesting to note that the mean values for montane meadows and alpine meadows were slightly higher in summer than in autumn, while the opposite was true for temperate steppes and swamps. Regarding the effects of climate, the response of NPP/LAI to temperature and precipitation varied among grassland types on an annual and seasonal basis. In addition, the seasonal lag effect of climate factors showed that the overall degree of effect of winter temperature on NPP/LAI in subsequent seasons increased as the seasonal interval progressed, while the opposite was true for precipitation, meaning that temperature affected NPP/LAI over a longer period compared to precipitation. Moreover, the seasonal time lag effects of climatic factors in different grassland types had varying degrees of influence on NPP/LAI, with the NPP/LAI of montane meadows and alpine grasslands being more closely related to climatic factors than those of temperate steppes and swamps. This study provides a basis for effective monitoring of photosynthetic capacity dynamics and helps develop policies to cope with climate change in alpine grasslands.

Abstract Background Fowl Adenovirus serotype 4 (FAdV-4) infection causes severe inflammatory response leading to hepatitis-hydropericardium syndrome (HHS) in poultry. As an essential functional amino acid of poultry, arginine plays a critical role in anti-inflammatory and anti-oxidative stress. Results In this study, the differential expression genes (DEGs) were screened by transcriptomic techniques, and the DEGs in gene networks of inflammatory response-induced by FAdV-4 in broiler’s liver were analyzed by Kyoto encyclopedia of genes and genomes (KEGG) enrichment. The results showed that the cytokines pathway and JAK/STAT pathway were significantly enriched, in which the DEGs levels of IL-6, IL-1β, IFN-α, JAK and STAT were significantly up-regulated after FAdV-4 infection. It was further verified with real-time fluorescence quantitative polymerase chain reaction (Real-time qPCR) and Western blotting (WB) in vitro and in vivo. The findings demonstrated that FAdV-4 induced inflammatory response and activated JAK2/STAT3 pathway. Furthermore, we investigated whether arginine could alleviate the liver inflammation induced by FAdV-4. After treatment with 1.92% arginine level diet to broilers or 300 μg/mL arginine culture medium to LMH cell line with FAdV-4 infection at the same time, we found that the mRNA levels of IL-6, IL-1β, IFN-α and the protein levels of p-JAK2, p-STAT3 were down-regulated, compared with FAdV-4 infection group. Furthermore, we confirmed that the inflammation induced by FAdV-4 was ameliorated by pre-treatment with JAK inhibitor AG490 in LMH cells, and it was further alleviated in LMH cells treatment with AG490 and ARG. Conclusions These above results provide new insight that arginine protects hepatocytes against inflammation induced by FAdV-4 through JAK2/STAT3 signaling pathway.

We describe two new Achnanthidium species, A. anhuense sp. nov. and A. qingxiense sp. nov., from Qingxi River, Anhui Province, China, based on light and scanning electron microscopy. Both species belong to the “A. pyrenaicum complex” of the Achnanthidium genus, based on their possession of transapically-elongated areolae and deflected external distal raphe fissures. A. anhuense sp. nov. has a slightly irregular linear-lanceolate valve with rounded or weakly protracted apices and a transapically rectangular or bow tie central area on the raphe valve. A. qingxiense sp. nov. has a linear-lanceolate valve with rounded apices and the axial area distinct expanded apices on the rapheless valve. Both species differ sufficiently from other similar species, based on valve outline, shape of the axial and central areas and striae density. These new species were all collected from stone substratum.

Parrots have undergone substantial karyotype evolution compared to most other birds. Here, Huang et al. analyze chromosome-level genome assemblies for four parrot species and elucidate the complex evolutionary history of parrot chromosomes.

Spinach is a nutritious leafy vegetable growing worldwide. Here, the authors report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 accessions, and provide insights into spinach domestication and the genetic basis of agronomic traits.

Harmful cyanobacterial blooms damage aquatic ecosystems and pose a threat to human health. To identify key factors causing cyanobacterial blooms in eutrophic shallow lakes, we analyzed cyanobacterial and physicochemical water samples of 12 sites collected monthly from December 2012 to December 2019 in Dianshan Lake. We found that the rapid growth of cyanobacteria was limited by a temperature threshold. When the air temperature was below 18 °C, the sampled physicochemical factors could not make difference in cyanobacterial abundance regardless the values of these parameters. However, when the air temperature was above 18 °C, the measured physicochemical factors played important roles in influencing cyanobacterial abundance. We developed a data-driven predictive model for cyanobacterial blooms based on seven-year data from Dianshan Lake using multiple logistic regression. Such a model could be easily used to predict cyanobacterial blooms. Our weight analysis of model parameters indicated that dissolved substances other than TN and TP are the key factor determining cyanobacterial blooms in nitrogen and phosphorus rich shallow freshwater lakes once air temperature is above 18 °C. Eutrophic shallow lakes are prone to cyanobacterial blooms, and unwashed data analysis may mask key factors determining cyanobacterial blooms, which obscures the prediction of cyanobacteria blooms. Our results are helpful to uncover the real causes of the blooms of eutrophic shallow lakes in China and elsewhere, and hence improve the understanding and management in controlling cyanobacterial blooms.

Soil water–salt variations at different spatiotemporal scales and their influencing factors are essential for regional vegetation restoration and management. However, the study of soil water–salt of the alpine area has not taken into account the effect of topography, especially in the long time series. This work investigated the spatiotemporal characteristics of water and salt in topsoil from 2000 to 2021, using regression analysis of on-site data and MODIS products. The heterogeneity and trends of soil water–salt in various topographic factors (elevation, slope, and aspect) were also explored by selecting the maximum area of each gradient factor as the constrained condition with the help of ArcGIS software. The results revealed that 1) the models applied to SWC (soil water content), EC (electrical conductivity), and pH utilizing vegetation indices were suitable for estimating the spatiotemporal variations of soil water–salt. 2) Soil water–salt exhibited local aggregation characteristics with an upward trend in SWC and a downward trend in EC and pH as a whole. 3) Mean annual SWC peaked at 3,400–3,800 m with increasing elevation and trended downward with increasing slope. The aspect of mean annual SWC was characterized by lower values in the southwest and south and higher values in the north, while the results for pH were reversed. The slope had a greater influence on EC than on SWC and pH. 4) The trend change of SWC, EC, and pH fluctuated at 2000–2,400 m and >4,600 m with a clear inflection point at 4°–8° and 20°–24°, respectively. In summary, the effects of topography responded to the distribution and trends of soil water–salt. The results have significant implications for implementing ecological improvements in regions with complicated topography and can serve as a reference for formulating future ecological policies.

Cyanobacterial blooms are global threats to freshwater ecosystem functioning, human health, and ecoservices. We assessed impacts of cyanobacterial bloom intensity on plankton ecosystem functioning using eukaryotic phytoplankton and zooplankton indicators and associated key physicochemical data collected from four seasons of two years at 24 evenly distributed sites in Lake Taihu that has year-around cyanobacterial blooms. Our analyses involved comparison of four site-groups with different bloom intensities and analyzing all sampling sites together using comparison, hierarchical partitioning analysis, generalized additive mixed model, and structural equation model. We found that cyanobacterial abundance positively associated with TP and temperature (negatively with TN:TP), while phytoplankton positively associated with TN. There was an inverse relation trend between relative abundances of phytoplankton and cyanobacteria, but there was no clear trend between absolute abundances of phytoplankton and cyanobacteria. Rotifers were most dominant when cyanobacteria were unabundant, while cladocerans presented higher abundance when cyanobacteria were in high abundance. Phytoplankton functional richness and species richness negatively and zooplankton functional richness and species richness positively associated with cyanobacterial bloom intensity. Cyanobacterial bloom intensity negatively associated with resource use efficiencies (RUEs) of phytoplankton and rotifers, and positively associated with RUE of cladocerans. Our analytical approach of integrating comparison of site-groups and analyzing all sites together uncovered how cyanobacterial bloom intensity shifted and altered physicochemical and biological conditions and plankton ecosystem functioning, and identified the mechanism and strength of the interactive linkages among physicochemical and biological indicators. Although our results may be different from oligotrophic lakes or reservoirs, our findings provide new insights in understanding the impacts of cyanobacterial bloom intensity on the dynamics of plankton communities and ecosystem functioning for polymictic eutrophic lakes, which may have broad application in enhancing the knowledge of this subject and provides the science base for managing polymictic eutrophic lake water quality and ecosystem functioning.

Abstract Phytoplankton functional traits can represent particular environmental conditions in complex aquatic ecosystems. Categorizing phytoplankton species into functional groups is challenging and time‐consuming, and requires high‐level expertise in species autecology. In this study, we introduced an affinity analysis to aid the identification of candidate associations of phytoplankton from two data sets comprised of phytoplankton and environmental information. In the Huaihe River Basin with a drainage area of 270,000 km2 in China, samples were collected from 217 selected sites during the low‐water period in May 2013; monthly samples were collected during 2006–2011 in a man‐made pond, Dishui Lake. Our results indicated that the affinity analysis can be used to define some meaningful functional groups. The identified phytoplankton associations reflect the ecological preferences of phytoplankton in terms of light and nutrient acquisition. Advantages and disadvantages of applying the affinity analysis to identify phytoplankton associations are discussed with perspectives on their utility in ecological assessment.

In this paper we inventory the continental diatom taxa described from inland waters in China, from the first species descriptions dating back to 1848 through 2019. China’s geography and hydrography are complex, including the world’s highest mountains, many large rivers, salty lakes, and large karst regions. From this area, a total of 1128 taxa have been described from China over this time period. We examine the number of taxa described in ca. 20-year intervals and note the periods of time of no to few descriptions, versus time intervals with many taxon descriptions. Early on, taxon descriptions of freshwater diatoms from China were done by mostly by Europeans working alone, and the time frame of 1948 to 1967 had few descriptions, as a devasting famine and the cultural revolution impacted scientific work and productivity. B.V. Skvortzov produced a large number of taxon descriptions, during his time in residence in Harbin, later while in Sao Paulo, Brazil, and even posthumously. More recently, a wide range of labs and collaborations across China, and with a diverse array of international partners, is ushering in a new, robust era of research on the biodiversity of continental diatoms. A few areas of research and work for the future are discussed.

Previous studies focused on the status and driving factors of non-grain cultivated land (NGCL), but lacked research on the impact mechanism of NGCL on sustainable agricultural development from the perspective of farmers’ household livelihoods and agricultural production factor allocation. Therefore, the concept of resilience was introduced. According to official statistics of China from 2010 to 2021, such as the local statistical yearbooks, the impact of NGCL on agricultural development resilience (ADR) in the main grain-producing area of Northeast China was explored based on the threshold effect model and the spatial lag model. The results indicate that: (1) the overall level of NGCI in the study area from 2011 to 2020 show an upward followed by a downward trend; (2) the size of agricultural labor force and average area per labor constrain the impact of NGCI on ADR, and the change can be characterized by negative to positive, increasing and then decreasing respectively, and the former is more constrained than the latter; (3) a negative effect of the NGCI trend on ADR exists without spatial spillover effect. The expansion of food production exacerbates the risk of factor mismatch, which is accentuated by the governance environment that pursues food production excessively. Establishing the NFP governance standards should consider the transformation of farmers’ livelihoods and the optimization of production factor allocation. Constructing a resilient risk management mechanism, promoting moderate scale operation and optimizing agricultural labor scale are specific paths for improving the governance mechanisms of NGCI. This study provides a theoretical reference for the development of policies and governance strategies for NGCI in underdeveloped areas.

Woodwardia japonica is a kind of great potential edible and medicinal fern. In a previous study, it was found that flavonoid and antioxidant activity of W. japonica from different sites were different. However, the cause of the differences has still been unclear, which has restricted the utilization of W. japonica. In this paper, flavonoid and antioxidant activity of W. japonica from nine different regions were determined with the method of a colorimetric assay with UV-VIS spectrophotometry and HPLC-ESI-TOF-MS, and the effects of climate factors on flavonoids and antioxidant activities were evaluated by mathematical modeling and statistical methods. The results showed: (1) total flavonoid content (TFC) of W. japonica from Wuyi Mountain (Jiangxi) was the highest, which might be related to the low temperature; (2) the differences of antioxidant activities of W. japonica might be related to precipitation; (3) five flavonols, two flavones and one isoflavone were tentatively identified in W. japonica; (4) flavonol and isoflavone might be affected by sunshine duration, and flavones were probably related to temperature. In conclusion, the effects of climate factors on flavonoids and antioxidants are significant, which would provide an important basis for further exploring the mechanism of climate affecting secondary metabolites.

The classification of Trachelomonas and Strombomonas is based on the morphology of loricae, which may not reflect phylogenetic relationships. There are different views on the relationship between the two genera. It is thus important for researchers to classify the two genera based on more characteristics besides loricae, such as protoplast and molecular data, and to establish a natural classification system. In this study, 29 strains (13 species) of Trachelomonas and 12 strains (eight species) of Strombomonas were collected from various locations in China. The morphological characteristics of Trachelomonas and Strombomonas were observed in the field and culture conditions, and the sequences of nuclear SSU rDNA, nuclear LSU rDNA, plastid-encoded LSU rDNA and plastid-encoded LSU rDNA of strains were obtained. We constructed a phylogenetic tree by combining four gene sequences with maximum likelihood and Bayesian methods. Based on the development of the loricae, it was found that the shape of the loricae and the presence or absence of the collar were relatively stable in culture, while the length of the collar presence or absence of spines and the color of the loricae changed. The phylogenetic tree showed that Trachelomonas and Strombomonas were sister branches, which supported Trachelomonas and Strombomonas as independent genera. Taxa in the genus Strombomonas sorted into two clades and Trachelomonas sorted into five strongly supported clades. Key morphological features could be attributed to each of the clades.

Since 2015, Fowl adenovirus serotype 4 (FAdV-4) infection has caused serious economic losses to the poultry industry worldwide. We isolated and identified the FAdV-4 strain NP, from infected chickens on a layer farm, using chicken embryo allantoic cavity inoculation, electron microscopy, viral genome sequencing, and regression analysis. To explore the pathogenesis of FAdV-4 infection, we conducted transcriptome sequencing analysis of the liver in chickens infected with FAdV-4, using the Illumina® HiSeq 2000 system. Two days after infection with the FAdV-4 NP strain, 13,576 differentially expressed genes (DEGs) were screened in the liver, among which, 7,480 were up-regulated and 6,096 were down-regulated. Gene ontology (GO) analysis indicated that these genes were involved in 52 biological functions. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that those DEGs were involved in 33 pathways. We then focused on the KEGG pathway of phagosome and found that mRNA levels of the 25 DEGs in that pathway were up-regulated, and seven DEGs were down-regulated. Real-time quantitative polymerase chain reaction (qPCR) confirmed the accuracy and reliability of these findings. Moreover, 24 h after LMH cells were infected with FAdV-4, the mRNA levels of F-actin, Rab7, TUBA, and DVnein were significantly increased. These four genes were all subsequently silenced by RNA interference, and viral replication of FAdV-4 was then significantly down-regulated. These findings demonstrate the isolation and identification of the FAdV-4 NP strain, and the DEGs in KEGG pathway of phagosome were utilized by FAdV-4 to benefit its infection.

Spinach is an economically important vegetable crop but previous genomic resources were of limited use for comparative and functional analyses. Here, Xuet al. present a high quality draft spinach genome and transcriptome data for multiple Spinaciaaccessions providing insight into Caryophyllales genome evolution.

Dihydroflavonol 4-reductase (DFR), a key enzyme involved in the biosynthesis of anthocyanins, has been cloned from various species. However, little research has been conducted on this enzyme in ferns, which occupy a unique evolutionary position. In this study, we isolated two novel DFR genes from the fern Dryopteris erythrosora. In vitro enzymatic analysis revealed that DeDFR1 and DeDFR2 enzymes can catalyze dihydrokaempferol and dihydroquercetin but cannot catalyze dihydromyricetin. Amino acid sequence analysis showed that DeDFR1 and DeDFR2 have an arginine at the same substrate-specificity-determining site as that in the ferns Salvinia cucullata and Azolla filiculoides. Thus, we speculate that the Arg-type DFR is a new DFR functional type. To further verify the substrate preferences of the Arg-type DFR, an amino acid substitution assay was conducted. When N133 was mutated to R133, Arabidopsis DFR protein completely lost its catalytic activity for dihydromyricetin, as observed for DeDFR1 and DeDFR2. Additionally, heterologous expression of DeDFR2 in the Arabidopsis tt3-1 mutant resulted in increasing anthocyanin accumulation. In summary, DeDFR1 and DeDFR2 are considered to be a new type of DFR with unique structures and functions. The discovery of the Arg-type DFR provides new insights into the anthocyanin biosynthesis pathway in ferns.

Isoetes sinensis Palmer is a critically endangered, first-class protected plant in China. Until now, researchers have primarily focused on the ultrastructure, phylogeny, and transcriptomes of the plant. However, flavonoid profiles and bioactivity of I. sinensis have not been extensively investigated. To develop the endangered I. sinensis for edible and medicinal purposes, flavonoid content, chemical constitution, and antioxidant activities were investigated in this study. Results revealed the following. 1) The total flavonoid content was determined as 10.74 ± 0.25 mg/g., 2) Antioxidant activities were stronger than most ferns, especially ABTS free radical scavenging activities. 3) Four flavones, containing apigenin, apigenin-7-glucuronide, acacetin-7-O-glcopyranoside, and homoplantageninisoetin; four flavonols, namely, isoetin, kaempferol-3-O-glucoside, quercetin-3-O-[6"-O-(3-hydroxy-3-methylglutaryl)-β-D-glucopyranoside], and limocitrin-Neo; one prodelphinidin (procyanidins;) and one nothofagin (dihydrochalcone) were tentatively identified in the mass spectrometry-DAD (254nm) chromatograms. This study was the first to report on flavonoid content and antioxidant activities of I. sinensis. Stronger antioxidant activity and flavonoid content suggests that the endangered I. sinensis is an important and potentially edible and medicinal plant.

This article summarizes the current knowledge regarding omics approaches, which include genomics, transcriptomics, proteomics and metabolomics, in the context of bio-hydrogen production in Chlamydomonas reinhardtii. In this paper, critical genes (HydA1, Hyd A2, Sulp, Tla1, Sta7, PFL1) involved in H2 metabolism were identified and analyzed for their function in H2 accumulation. Furthermore, the advantages of gene microarrays and RNA-seq were compared, as well as their applications in transcriptomic analysis of H2 production. Moreover, as a useful tool, proteomic analysis could identify different proteins that participate in H2 metabolism. This review provides fundamental theory and an experimental basis for H2 production, and further research effort is needed in this field.

Ceratopteris thalictroides, a model fern, has two kinds of gametophytes with different sex expression: male and hermaphrodite. Hermaphroditic gametophytes have one or several archegonia beneath the growing point and a few antheridia at the base or margin. Male gametophytes show a spoon-like shape with much longer than the width and produce many antheridia at the margin and surface. The results of chlorophyll fluorescence detection showed that the photochemical efficiency of hermaphrodites was higher than that of males. By using two-dimensional electrophoresis and mass spectrometry, the differentially abundant proteins in hermaphroditic and male gametophytes were identified. A total of 1136 ± 55 protein spots were detected in Coomassie-stained gels of proteins from hermaphroditic gametophytes, and 1130 ± 65 spots were detected in gels of proteins from male gametophytes. After annotation, 33 spots representing differentially abundant proteins were identified. Among these, proteins involved in photosynthesis and chaperone proteins were over-represented in hermaphrodites, whereas several proteins involved in metabolism were increased in male gametophytes in order to maintain their development under relatively nutritionally deficient conditions. Furthermore, the differentially abundant cytoskeletal proteins detected in this study, such as centrin and actin, may be involved in the formation of sexual organs and are directly related to sex expression. These differentially abundant proteins are important for maintaining the development of gametophytes of different sexes in C. thalictroides.

Flavonoids are secondary metabolites of plants that often have medical applications. The influences of different sample drying pretreatments on flavonoids and antioxidant activity of ferns have not studies. Dryopteris erythrosora leaves used to analyze flavonoid alterations resulting from drying pretreatments. The total flavonoid content of D. erythrosora leaves exposed to different pretreatments was significantly different. The total flavonoid content of samples initially air-dried in shade and then oven-dried at 75°C were the highest (7.6%), while samples initially dried at 75°C had the lowest content (2.17%). Antioxidant activities of D. erythrosora leaves with different pretreatments varied. Group B first air-dried in the shade and then oven-dried at 75°C and group C first air-dried in the sun and then oven-dried at 75°C, both showed relatively stronger antioxidant activity. The best pretreatment for preserving the flavonoids was to first dry the plant material in the shade and then complete the drying process in an oven at 75°C. It was tentatively identified 22 flavonoids among the four different pretreatments by HPLC-ESI-TOF-MS.

The green algae, Chlamydomonas reinhardtii, is one of the model species used to study lipid production, although research has focused on nitrogen-deficient cultures, that inhibit the development of biomass by C. reinhardtii and limit lipid production. In this study, Azotobacter chroococcum was added to the algal culture to improve lipid accumulation and productivity of C. reinhardtii. The maximum lipid content and production of C. reinhardtii in the co-culture were 65.85% and 387.76 mg/L, respectively, which were 2.3 and 5.9 times the control's levels of 29.11% and 65.99 mg/L, respectively. The maximum lipid productivity of C. reinhardtii in the co-culture was 141.86 mg/(L·day), which was 19.4 times the control's levels of 7.33 mg/(L·day). These increases were attributed to the enhanced growth and biomass and the change in the activity of enzymes related to lipid regulation (ACCase, DGAT, and PDAT). Compared to the conventional strategy of nitrogen deprivation, A. chroococcum added to the culture of C. reinhardtii resulted in higher lipid accumulation and activity, greater efficiency in the conversion of proteins to lipids, higher biomass, and increased growth of C. reinhardtii. Therefore, using A. chroococcum to improve the growth and biomass of C. reinhardtii is an efficient, rapid, and economically viable strategy for enhancing lipid production in C. reinhardtii.

In this study, the mechanism of Muscovy duck reovirus (MDRV) p10.8 protein-induced pathogenesis was investigated, with a focus on endoplasmic reticulum (ER) stress. In chicken embryo fibroblasts cell lines (DF1), pCI-neo-flg-p10.8 protein transfection increased the phosphorylation (p-) levels of PERK and eIF2α as shown by Western blotting analysis and led to the dissociation of BiP from PERK as shown by co-immunoprecipitation (Co-IP) analysis. Results of treatment with both ER stress activator and inhibitor further confirmed that p10.8 protein induced ER stress. Subsequently, using flow cytometry analysis, it was also found that p10.8 protein induced cell cycle arrest during the G0/G1 phase. Furthermore, p10.8 transfection increased the phosphorylation levels of PERK and eIF2α, and reduced the expression levels of CDK2, CDK4, and Cyclin E according to Western blotting analysis. Treatment with ER stress activator and ER stress inhibitor after p10.8 protein transfection in DF1 cells further indicated that p10.8 protein induced ER stress, which resulted in cell cycle arrest. The results of knockdown of either PERK or eIF2α genes further confirmed that p10.8 protein-induced ER stress led to cell cycle arrest through the PERK/eIF2α pathway. Further results showed that p10.8 protein induced ER stress and apoptosis in DF1 cells. The expression levels of p-PERK, p-eIF2α, CHOP, cleaved-Caspase12, and cleaved-Caspase3 were increased by p10.8 protein. Test results of treatment with each of Tunicamycin, TUDCA and knockdown of PERK, and eIF2α, confirmed that p10.8 protein induced ER stress involving apoptosis via the PERK/eIF2α pathway. In conclusion, MDRV p10.8 protein induced ER stress that caused cell cycle arrest and apoptosis through the PERK/eIF2α pathway.

[This corrects the article DOI: 10.1371/journal.pone.0173003.].

The flavonoids in bryophytes may have great significance in phylogeny and metabolism research. However, to date there has been little research on bryophyte metabolites, especially flavonoids. To redress this somewhat, we determined flavonoid concentrations of bryophytes from Tianmu Mountain through a colorimetric assay and considered the factors influencing the results. This is the first time that the flavonoid contents of bryophytes have been examined in detail. The results revealed a range of total flavonoid concentrations in 90 samples collected from Tianmu Mountain from 1.8 to 22.3 mg/g (w/w). The total flavonoid contents of liverworts were generally higher than those of mosses; acrocarpous mosses had generally higher values than that of pleurocarpous mosses. The total flavonoid contents of bryophytes growing at lower light levels were general higher than those growing in full-sun. The total flavonoid contents of epiphytic bryophytes were highest, while those of aquatic bryophytes were the lowest. Total flavonoid contents of species growing at low-latitudes were much higher than those at high-latitude individuals. In conclusion, total flavonoid contents of bryophytes have some connection with plant phylogeny; more flavonoids might be contained in relatively primitive bryophytes. Meanwhile, the effects of ecological factors on total flavonoid contents of bryophytes exist; light and habitat (especially tree habitat and river habitat) might be representative factor.

This study investigates multispectral characteristics of an unmanned aerial vehicle (UAV) at different observation angles by experiment. The UAV and its engine are tested on the ground in the cruise state. Spectral radiation intensities at different observation angles are obtained in the infrared band of 0.9–15 μm by a spectral radiometer. Meanwhile, infrared images are captured separately by long-wavelength infrared (LWIR), mid-wavelength infrared (MWIR), and short-wavelength infrared (SWIR) cameras. Additionally, orientation maps of the radiation area and radiance are obtained. The results suggest that the spectral radiation intensity of the UAV is determined by its exhaust plume and that the main infrared emission bands occur at 2.7 μm and 4.3 μm. At observation angles in the range of 0°–90°, the radiation area of the UAV in MWIR band is greatest; however, at angles greater than 90°, the radiation area in the SWIR band is greatest. In addition, the radiance of the UAV at an angle of 0° is strongest. These conclusions can guide IR stealth technique development for UAVs.

Plantago virginica L. has invaded many lawn ecosystems in the Eastern part of China. The invasion has incurred an economic cost to remove them. In order to prevent the invasion, it is critical to understand the invasive mechanisms of this species. However, few studies have been conducted on the allelopathic mechanisms of its invasion. In this study, we examined allelopathic effects of P. virginica on germination of seeds and growth of seedlings of four widely used lawn species. We found extensive allelopathic potential of P. virginica on other lawn species, which varied with species and developmental stage. While most effects of the extracts of P. virginica were inhibitory, some variables in some species were promoted by the addition of the extracts. The extracts of P. virginica significantly inhibited seed germination of Agrostis matsumurae. While the overall differences in seed germination rate of Poa annua were significant among treatments, difference between control and any of the treatments was not significant. The height of seedlings of A. matsumurae and Cynodon dactylon was significantly lower under the treatments of adding extracts of P. virginica. In contrast, growth of seedlings of Festuca elata and P. annua did not show significant differences among treatments. The root length of A. matsumurae, C. dactylon and P. annua was suppressed by the extracts of P. virginica whereas root length of F. elata was not affected. Aboveground biomass of A. matsumurae and F. elata was significantly higher than control, except for F. elata at the concentration of 50mg/mL, whereas aboveground biomass of C. dactylon and P. annua was reduced at higher concentrations of the extracts. Except for A. matsumurae, root biomass of the other three lawn species declined under the treatments with the extracts of P. virginica. Our results revealed that P. virginica had allelopathic potential on four lawn species and supported the theory of "novel weapons hypothesis". Invasion by P. virginica in lawn can be moderated by selecting those species that are not affected or promotionally affected by it.

Marchantia polymorpha L. is a representative bryophyte used as a traditional Chinese medicinal herb for scald and pneumonia. The phytochemicals in M. polymorpha L. are terpenoids and flavonoids, among which especially the flavonoids show significant human health benefits. Many researches on the gametophyte of M. polymorpha L. have been reported. However, as the reproductive organ of M. polymorpha L., the bioactivity and flavonoids profile of the archegoniophore have not been reported, so in this work the flavonoid profiles, antioxidant and acetylcholinesterase inhibition activities of the extracts from the archegoniophore and gametophyte of M. polymorpha L. were compared by radical scavenging assay methods (DPPH, ABTS, O2−), reducing power assay, acetylcholinesterase inhibition assay and LC-MS analysis. The results showed that the total flavonoids content in the archegoniophore was about 10-time higher than that of the gametophyte. Differences between the archegoniophore and gametophyte of M. polymorpha L. were observed by LC-MS analysis. The archegoniophore extracts showed stronger bio-activities than those of the gametophyte. The archegoniophore extract showed a significant acetylcholinesterase inhibition, while the gametophyte extract hardly inhibited it.