Agriculture and Forestry University

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.

1,2,3,5-Tetrakis(carbazol-9-yl)-4,6-dicyanobenzene (4CzIPN) is a typical donor-acceptor fluorophore, with carbazolyl as an electron donor and dicyanobenzene as an electron acceptor. It has emerged as a powerful organophotocatalyst since 2016. Excellent redox window, good chemical stability and broad applicability make 4CzIPN an attractive metal-free photocatalyst. In this review, the recent advances of the application of 4CzIPN as a photoredox catalyst in the past three years (2016-2018) for various organic reactions are summarized.

Carbon dots have attracted a great deal of attention because of their high performance, cheap and facile preparation, and potential applications in a wide area. In order to broaden their applications, especially to meet specific requirements, surface engineering, including tailoring surface functional group coating and subsequent chemical modification as required, is an effective strategy for further functionalization of carbon dots. In this article, representative approaches to coating the surface with various functional groups, and strategies for conjugating specific materials onto the surface of carbon dots for functional modification via covalent bonds, electrostatic interactions and hydrogen bonds are highlighted, as well as the results from explorations of their various applications in target modulated sensing, accurate drug delivery and bioimaging at high resolution.

Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici, afflicts bread wheat (Triticum aestivum). New virulent races collectively referred to as "Ug99" have emerged, which threaten global wheat production. The wheat gene Sr33, introgressed from the wild relative Aegilops tauschii into bread wheat, confers resistance to diverse stem rust races, including the Ug99 race group. We cloned Sr33, which encodes a coiled-coil, nucleotide-binding, leucine-rich repeat protein. Sr33 is orthologous to the barley (Hordeum vulgare) Mla mildew resistance genes that confer resistance to Blumeria graminis f. sp. hordei. The wheat Sr33 gene functions independently of RAR1, SGT1, and HSP90 chaperones. Haplotype analysis from diverse collections of Ae. tauschii placed the origin of Sr33 resistance near the southern coast of the Caspian Sea.

Bamboo is widely distributed in Southeast Asia, Africa, and Latin America. As a major non-wood forest product and wood substitute, bamboo is of increasing interest to ecologists owing to its rapid growth and correspondingly high potential for mitigating climate change. With a long history of production and utilization of bamboo, China is one of the countries with the richest bamboo resources and largest area of bamboo forest, and has paid unprecedented attention in recent decades to management of its bamboo forests. This review summarizes the versatility of bamboo in terms of its ecological benefits including carbon sequestration, water and soil conservation, its benefits for socioeconomic development, and its potential to mitigate climate change. Current problems, and the future potential of and challenges to rapidly expanding bamboo forests under both wider use of intensive management and the effects of global warming, are also discussed.

Meeting global demand of safe and healthy food for the ever-increasing population now and into the future is currently a crucial challenge. Increasing crop production by preserving environment and mitigating climate change should thus be the main goal of today’s agriculture. Conventional farming is characterized by use of high-yielding varieties, irrigation water, chemical fertilizers and synthetic pesticides to increase yields. However, due to either over- or misuse of chemical fertilizers or pesticides in many agro-ecosystems, such farming is often blamed for land degradation and environmental pollution and for adversely affecting the health of humans, plants, animals and aquatic ecosystems. Of all inputs required for increased agricultural production, nutrients are considered to be the most important ones. Organic farming, with use of organic sources of nutrients, is proposed as a sustainable strategy for producing safe, healthy and cheaper food and for restoring soil fertility and mitigating climate change. However, there are several myths and controversies surrounding the use of organic versus inorganic sources of nutrients. The objectives of this paper are: (i) to clarify some of the myths or misconceptions about organic versus inorganic sources of nutrients and (ii) to propose alternative solutions to increase on-farm biomass production for use as organic inputs for improving soil fertility and increasing crop yields. Common myths identified by this review include that organic materials/fertilizers can: (i) supply all required macro- and micro-nutrients for plants; (ii) improve physical, chemical and microbiological properties of soils; (iii) be applied universally on all soils; (iv) always produce quality products; (v) be cheaper and affordable; and (vi) build-up of large amount of soil organic matter. Other related myths are: “legumes can use entire amount of N2 fixed from atmosphere” and “bio-fertilizers increase nutrient content of soil.” Common myths regarding chemical fertilizers are that they: (i) are not easily available and affordable, (ii) degrade land, (iii) pollute environment and (iv) adversely affect health of humans, animals and agro-ecosystems. The review reveals that, except in some cases where higher yields (and higher profits) can be found from organic farming, their yields are generally 20–50% lower than that from conventional farming. The paper demonstrates that considering the current organic sources of nutrients in the developing countries, organic nutrients alone are not enough to increase crop yields to meet global food demand and that nutrients from inorganic and organic sources should preferably be applied at 75:25 ratio. The review identifies a new and alternative concept of Evergreen Agriculture (an extension of Agroforestry System), which has potential to supply organic nutrients in much higher amounts, improve on-farm soil fertility and meet nutrient demand of high-yielding crops, sequester carbon and mitigate greenhouse gas emissions, provide fodder for livestock and fuelwood for farmers and has potential to meet global food demand. Evergreen Agriculture has been widely adapted by tens of millions of farmers in several African countries and the review proposes for evaluation and scaling-up of such technology in Asian and Latin American countries too.

As in other eukaryotes, protein kinases play major regulatory roles in filamentous fungi. Although the genomes of many plant pathogenic fungi have been sequenced, systematic characterization of their kinomes has not been reported. The wheat scab fungus Fusarium graminearum has 116 protein kinases (PK) genes. Although twenty of them appeared to be essential, we generated deletion mutants for the other 96 PK genes, including 12 orthologs of essential genes in yeast. All of the PK mutants were assayed for changes in 17 phenotypes, including growth, conidiation, pathogenesis, stress responses, and sexual reproduction. Overall, deletion of 64 PK genes resulted in at least one of the phenotypes examined, including three mutants blocked in conidiation and five mutants with increased tolerance to hyperosmotic stress. In total, 42 PK mutants were significantly reduced in virulence or non-pathogenic, including mutants deleted of key components of the cAMP signaling and three MAPK pathways. A number of these PK genes, including Fg03146 and Fg04770 that are unique to filamentous fungi, are dispensable for hyphal growth and likely encode novel fungal virulence factors. Ascospores play a critical role in the initiation of wheat scab. Twenty-six PK mutants were blocked in perithecia formation or aborted in ascosporogenesis. Additional 19 mutants were defective in ascospore release or morphology. Interestingly, F. graminearum contains two aurora kinase genes with distinct functions, which has not been reported in fungi. In addition, we used the interlog approach to predict the PK-PK and PK-protein interaction networks of F. graminearum. Several predicted interactions were verified with yeast two-hybrid or co-immunoprecipitation assays. To our knowledge, this is the first functional characterization of the kinome in plant pathogenic fungi. Protein kinase genes important for various aspects of growth, developmental, and infection processes in F. graminearum were identified in this study.

Paratuberculosis, a chronic disease affecting ruminant livestock, is caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has direct and indirect economic costs, impacts animal welfare and arouses public health concerns. In a survey of 48 countries we found paratuberculosis to be very common in livestock. In about half the countries more than 20% of herds and flocks were infected with MAP. Most countries had large ruminant populations (millions), several types of farmed ruminants, multiple husbandry systems and tens of thousands of individual farms, creating challenges for disease control. In addition, numerous species of free-living wildlife were infected. Paratuberculosis was notifiable in most countries, but formal control programs were present in only 22 countries. Generally, these were the more highly developed countries with advanced veterinary services. Of the countries without a formal control program for paratuberculosis, 76% were in South and Central America, Asia and Africa while 20% were in Europe. Control programs were justified most commonly on animal health grounds, but protecting market access and public health were other factors. Prevalence reduction was the major objective in most countries, but Norway and Sweden aimed to eradicate the disease, so surveillance and response were their major objectives. Government funding was involved in about two thirds of countries, but operations tended to be funded by farmers and their organizations and not by government alone. The majority of countries (60%) had voluntary control programs. Generally, programs were supported by incentives for joining, financial compensation and/or penalties for non-participation. Performance indicators, structure, leadership, practices and tools used in control programs are also presented. Securing funding for long-term control activities was a widespread problem. Control programs were reported to be successful in 16 (73%) of the 22 countries. Recommendations are made for future control programs, including a primary goal of establishing an international code for paratuberculosis, leading to universal acknowledgment of the principles and methods of control in relation to endemic and transboundary disease. An holistic approach across all ruminant livestock industries and long-term commitment is required for control of paratuberculosis.

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

Nitrate is an essential nutrient and signaling molecule for plant growth. Plants sense intracellular nitrate to adjust their metabolic and growth responses. Here we identify the primary nitrate sensor in plants. We found that mutation of all seven Arabidopsis NIN-like protein (NLP) transcription factors abolished plants’ primary nitrate responses and developmental programs. Analyses of NIN-NLP7 chimeras and nitrate binding revealed that NLP7 is derepressed upon nitrate perception via its amino terminus. A genetically encoded fluorescent split biosensor, mCitrine-NLP7, enabled visualization of single-cell nitrate dynamics in planta. The nitrate sensor domain of NLP7 resembles the bacterial nitrate sensor NreA. Substitutions of conserved residues in the ligand-binding pocket impaired the ability of nitrate-triggered NLP7 to control transcription, transport, metabolism, development, and biomass. We propose that NLP7 represents a nitrate sensor in land plants.

The use of carbon based materials on the removal of antibiotics with high concentrations has been well studied, however the effect of this removal method is not clear on the actual concentration of environments, such as the hospital wastewater, sewage treatment plants and aquaculture wastewater. In this study, experimental studies on the adsorption of 7 antibiotics in environmental concentration of aqueous solutions by carbon based materials have been observed. Three kinds of carbon materials have shown very fast adsorption to antibiotics by liquid chromatography-tandem mass spectrometry (LC-MS-MS) detection, and the highest removal efficiency of antibiotics could reach to 100% within the range of detection limit. Surprisedly, the adsorption rate of graphene with small specific surface area was stronger than other two biochar, and adsorption rate of the two biochar which have approximate specific surface and different carbonization degree, was significantly different. The key point to the present observation were the π-π interactions between aromatic rings on adsorbed substance and carbon based materials by confocal laser scanning microscope observation. Moreover, adsorption energy markedly increased with increasing number of the π rings by using the density functional theory (DFT), showing the particular importance of π-π interactions in the adsorption process.

ABSTRACT Knowledge of changes associated with advances in crop productivity is essential for understanding yield limiting factors and developing strategies for future genetic improvement. The objectives of this study are to understand genetic gain for grain yield and associated traits in the Northern China Winter Wheat Region (NCWWR). Four trials, comprised of 47 leading common wheat ( Triticum aestivum L.) cultivars from the NCWWR from 1960 to 2000, were conducted during 2001 to 2003 using a completely randomized block design of three replicates under controlled field environments. Molecular markers were used to detect the presence of dwarfing genes and the 1B/1R translocation. Results showed that average annual genetic gain in grain yield ranged from 32.07 to 72.11 kg ha −1 yr −1 or from 0.48 to 1.23% annually in different provinces. The most significant increase in grain yield occurred in the early 1980s, largely because of the successful utilization of dwarfing genes and the 1B/1R translocation. There was no common trend across trials in terms of changes in spikes m −2 , kernels per spike, 1000‐kernel weight (TKW), or biomass. The genetic improvement in grain yield was primarily attributed to increased grain weight per spike, reduced plant height, and increased harvest index (HI). The dwarfing allele Rht‐D1b was the most frequent (68.0%) among the cultivars, followed by Rht 8 (42.0%) and Rht‐B1b (16.0%). The frequency of 1B/1R translocation cultivars was 42.6%. The future challenge of wheat breeding in this region is to maintain the genetic gain in grain yield and to improve grain quality, without increasing inputs for the wheat‐maize double cropping system.

The demand for agricultural goods is currently higher than it has ever been before due to the expansion of the world population. This has resulted in the conversion of grassland into agricultural areas, the development of high-energy-intensive agriculture production systems, and the use of additional chemical and organic inputs in agricultural production systems. The output of greenhouse gases (GHGs) has also increased in the same way. Carbon dioxide (CO2), Nitrous Oxide (N2O), and Methane (CH4) is the most significant greenhouse gases (GHGS) that are producing a variety of disastrous consequences due to climate change. Despite the fact that CH4 and N2O are released in smaller amounts than CO2, they have a larger Global Warming Potential than CO2. This analysis begins with an examination of the variables that contribute to greenhouse gas emissions, which covers both inorganic factors (such as nitrogen, phosphorus, and potassium fertilizers) and organic factors (Animal manure, composted manure, bio-solids, crop species). This study underlines the need for more research into the intricate interactions of physical, chemical, and biological elements in the near future. Field crops other than cereals, such as legumes, oilseeds, vegetables, and fruits, account for a significant amount of greenhouse gas (GHG) emissions. Precision agriculture may be a viable option for increasing agricultural efficiency. Optimal management practices should be implemented in farm and field settings through methodical, site-specific approaches.

The data saturation problem in Landsat imagery is well recognized and is regarded as an important factor resulting in inaccurate forest aboveground biomass (AGB) estimation. However, no study has examined the saturation values for different vegetation types such as coniferous and broadleaf forests. The objective of this study is to estimate the saturation values in Landsat imagery for different vegetation types in a subtropical region and to explore approaches to improving forest AGB estimation. Landsat Thematic Mapper imagery, digital elevation model data, and field measurements in Zhejiang province of Eastern China were used. Correlation analysis and scatterplots were first used to examine specific spectral bands and their relationships with AGB. A spherical model was then used to quantitatively estimate the saturation value of AGB for each vegetation type. A stratification of vegetation types and/or slope aspects was used to determine the potential to improve AGB estimation performance by developing a specific AGB estimation model for each category. Stepwise regression analysis based on Landsat spectral signatures and textures using grey-level co-occurrence matrix (GLCM) was used to develop AGB estimation models for different scenarios: non-stratification, stratification based on either vegetation types, slope aspects, or the combination of vegetation types and slope aspects. The results indicate that pine forest and mixed forest have the highest AGB saturation values (159 and 152 Mg/ha, respectively), Chinese fir and broadleaf forest have lower saturation values (143 and 123 Mg/ha, respectively), and bamboo forest and shrub have the lowest saturation values (75 and 55 Mg/ha, respectively). The stratification based on either vegetation types or slope aspects provided smaller root mean squared errors (RMSEs) than non-stratification. The AGB estimation models based on stratification of both vegetation types and slope aspects provided the most accurate estimation with the smallest RMSE of 24.5 Mg/ha. Relatively low AGB (e.g., less than 40 Mg/ha) sites resulted in overestimation and higher AGB (e.g., greater than 140 Mg/ha) sites resulted in underestimation. The smallest RMSE was obtained when AGB was 80–120 Mg/ha. This research indicates the importance of stratification in mitigating the data saturation problem, thus improving AGB estimation.

Soil is a fundamental part of successful agriculture, and its quality has to be improved to maximize crop yield and soil fertility. To increase crop productivity and soil fertility, biochar can be applied to the soil. Biochar is a solid carbon-rich product produced from biomass of agricultural crop residues, wastes, and wood, through pyrolysis in an oxygen-deficient condition. Carbon sequestration through biochar is important because of its potential applications in recycling wastes, retaining nutrients in the soil and lowering greenhouse gas emissions. In this review, we explore the various applications of biochar to ensure the safe and sustainable improvement of soil fertility. This review provides an overview of biochar properties, production technology, and its employment in the agriculture. This review would be a useful resource for researchers, farmers, and academics who are interested in the utilization of biochar.

Systems pharmacology is an emerging field that integrates systems biology and pharmacology to advance the process of drug discovery, development and the understanding of therapeutic mechanisms. The aim of the present work is to highlight the role that the systems pharmacology plays across the traditional herbal medicines discipline, which is exemplified by a case study of botanical drugs applied in the treatment of depression. First, based on critically examined pharmacology and clinical knowledge, we propose a large-scale statistical analysis to evaluate the efficiency of herbs used in traditional medicines. Second, we focus on the exploration of the active ingredients and targets by carrying out complex structure-, omics- and network-based systematic investigations. Third, specific informatics methods are developed to infer drug-disease connections, with purpose to understand how drugs work on the specific targets and pathways. Finally, we propose a new systems pharmacology method, which is further applied to an integrated platform (Herbal medicine Systems Pharmacology) of blended herbal medicine and omics data sets, allowing for the systematization of current and traditional knowledge of herbal medicines and, importantly, for the application of this emerging body of knowledge to the development of new drugs for complex human diseases.

The hypoxic environment imposes severe selective pressure on species living at high altitude. To understand the genetic bases of adaptation to high altitude in dogs, we performed whole-genome sequencing of 60 dogs including five breeds living at continuous altitudes along the Tibetan Plateau from 800 to 5100 m as well as one European breed. More than 150× sequencing coverage for each breed provides us with a comprehensive assessment of the genetic polymorphisms of the dogs, including Tibetan Mastiffs. Comparison of the breeds from different altitudes reveals strong signals of population differentiation at the locus of hypoxia-related genes including endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1) and beta hemoglobin cluster. Notably, four novel nonsynonymous mutations specific to high-altitude dogs are identified at EPAS1, one of which occurred at a quite conserved site in the PAS domain. The association testing between EPAS1 genotypes and blood-related phenotypes on additional high-altitude dogs reveals that the homozygous mutation is associated with decreased blood flow resistance, which may help to improve hemorheologic fitness. Interestingly, EPAS1 was also identified as a selective target in Tibetan highlanders, though no amino acid changes were found. Thus, our results not only indicate parallel evolution of humans and dogs in adaptation to high-altitude hypoxia, but also provide a new opportunity to study the role of EPAS1 in the adaptive processes.

Information on the distribution of vernalization genes and their association with growth habit is crucial to understanding the adaptability of wheat ( Triticum aestivum L.) cultivars to different environments. In this study, 278 Chinese wheat cultivars were characterized with molecular markers for the vernalization genes Vrn‐A1 , ‐B1 , ‐D1 , and ‐B3 Heading time was evaluated in a greenhouse under long days without vernalizaton. The dominant Vrn‐D1 allele showed the highest frequency in the Chinese wheat cultivars (37.8%), followed by the dominant Vrn‐A1 , ‐B1 , and ‐B3 alleles. Ninety‐two winter cultivars carried recessive alleles of all four vernalization loci, whereas 172 spring genotypes contained at least one dominant Vrn allele. All cultivars released in the North China Plain Winter Wheat Zone were winter type. Winter (53.0%), spring (36.1%), and early‐heading (10.9%) cultivars were grown in the Yellow and Huai River Valley Winter Zone. Most of the spring genotypes from this zone carried only the dominant Vrn‐D1 allele, which was also predominant (64.1%) in the Middle and Lower Yangtze Valley Winter Zone and Southwestern Winter Wheat Zone. In three spring‐sown wheat zones, all cultivars were early‐heading spring types that frequently possessed the strongest dominant Vrn‐A1a allele and combinations with other dominant Vrn gene(s). The Vrn‐D1 allele is associated with the latest heading time, Vrn‐A1 the earliest, and Vrn‐B1 intermediate values. The information is important for breeding programs in countries interested in using Chinese wheats.

Abstract Aberrant RNA splicing is recognized to contribute to cancer pathogenesis, but the underlying mechanisms remain mainly obscure. Here, we report that the splicing factor SRSF2 is upregulated frequently in human hepatocellular carcinoma (HCC), where this event is associated with poor prognosis in patients. RNA-seq and other molecular analyses were used to identify SRSF2-regulated alternative splicing events. SRSF2 binding within an alternative exon was associated with its inclusion in the RNA, whereas SRSF2 binding in a flanking constitutive exon was associated with exclusion of the alternative exon. Notably, cancer-associated splice variants upregulated by SRSF2 in clinical specimens of HCC were found to be crucial for pathogenesis and progression in hepatoma cells, where SRSF2 expression increased cell proliferation and tumorigenic potential by controlling expression of these variants. Our findings identify SRSF2 as a key regulator of RNA splicing dysregulation in cancer, with possible clinical implications as a candidate prognostic factor in patients with HCC. Cancer Res; 77(5); 1168–78. ©2017 AACR.

Biochar shows great promise for use in adsorbing pollutants. However, a process for enhancing its adsorption capacity and re-collection efficiency is yet to be further developed. Hence, in this study, we developed a type of biochar coated with magnetic Fe3O4 nanoparticles (i.e., magnetic biochar (MBC)) and assessed its use for crystal violet (CV) adsorption as well as its recycling potential. The coating of Fe3O4 nanoparticles, which was not only on the surface, but also in the interior of biochar, performed two functions. Firstly, it produced a saturation magnetization of 61.48 emu/g, which enabled the biochar being efficiently re-collected using a magnet. Secondly, it significantly enhanced the adsorption capacity of the biochar (from 80.36 to 99.19 mg/g). The adsorption capacity of the MBC was determined to be the largest by so far (349.40 mg/g) for an initial CV concentration of 400 mg/L, pH of 6.0, and temperature of 40 °C, and the adsorption capacity of re-collected MBC was 73.31 mg/g. The adsorption of CV by the MBC was found to be a spontaneous and endothermic physical process in which the intraparticle diffusion was the limiting step. These findings inspire us to use other similar materials to tackle the menace of pollutions.