Northeast Agricultural University

Abiotic stresses are one of the major constraints to crop production and food security worldwide. The situation has aggravated due to the drastic and rapid changes in global climate. Heat and drought are undoubtedly the two most important stresses having huge impact on growth and productivity of the crops. It is very important to understand the physiological, biochemical, and ecological interventions related to these stresses for better management. A wide range of plant responses to these stresses could be generalized into morphological, physiological, and biochemical responses. Interestingly, this review provides a detailed account of plant responses to heat and drought stresses with special focus on highlighting the commonalities and differences. Crop growth and yields are negatively affected by sub-optimal water supply and abnormal temperatures due to physical damages, physiological disruptions, and biochemical changes. Both these stresses have multi-lateral impacts and therefore, complex in mechanistic action. A better understanding of plant responses to these stresses has pragmatic implication for remedies and management. A comprehensive account of conventional as well as modern approaches to deal with heat and drought stresses have also been presented here. A side-by-side critical discussion on salient responses and management strategies for these two important abiotic stresses provides a unique insight into the phenomena. A holistic approach taking into account the different management options to deal with heat and drought stress simultaneously could be a win-win approach in future.

. We show that CQ mainly inhibits autophagy by impairing autophagosome fusion with lysosomes rather than by affecting the acidity and/or degradative activity of this organelle. Furthermore, CQ induces an autophagy-independent severe disorganization of the Golgi and endo-lysosomal systems, which might contribute to the fusion impairment. Strikingly, HCQ-treated mice also show a Golgi disorganization in kidney and intestinal tissues. Altogether, our data reveal that CQ and HCQ are not bona fide surrogates for other types of late stage lysosomal inhibitors for in vivo experiments. Moreover, the multiple cellular alterations caused by CQ and HCQ call for caution when interpreting results obtained by blocking autophagy with this drug.

In vitro and some animal models have shown that quercetin, a polyphenol derived from plants, has a wide range of biological actions including anti-carcinogenic, anti-inflammatory and antiviral activities; as well as attenuating lipid peroxidation, platelet aggregation and capillary permeability. This review focuses on the physicochemical properties, dietary sources, absorption, bioavailability and metabolism of quercetin, especially main effects of quercetin on inflammation and immune function. According to the results obtained both in vitro and in vivo, good perspectives have been opened for quercetin. Nevertheless, further studies are needed to better characterize the mechanisms of action underlying the beneficial effects of quercetin on inflammation and immunity.

False positives in a Genome-Wide Association Study (GWAS) can be effectively controlled by a fixed effect and random effect Mixed Linear Model (MLM) that incorporates population structure and kinship among individuals to adjust association tests on markers; however, the adjustment also compromises true positives. The modified MLM method, Multiple Loci Linear Mixed Model (MLMM), incorporates multiple markers simultaneously as covariates in a stepwise MLM to partially remove the confounding between testing markers and kinship. To completely eliminate the confounding, we divided MLMM into two parts: Fixed Effect Model (FEM) and a Random Effect Model (REM) and use them iteratively. FEM contains testing markers, one at a time, and multiple associated markers as covariates to control false positives. To avoid model over-fitting problem in FEM, the associated markers are estimated in REM by using them to define kinship. The P values of testing markers and the associated markers are unified at each iteration. We named the new method as Fixed and random model Circulating Probability Unification (FarmCPU). Both real and simulated data analyses demonstrated that FarmCPU improves statistical power compared to current methods. Additional benefits include an efficient computing time that is linear to both number of individuals and number of markers. Now, a dataset with half million individuals and half million markers can be analyzed within three days.

Intercropping, which grows at least two crop species on the same pieces of land at the same time, can increase grain yields greatly. Legume-grass intercrops are known to overyield because of legume nitrogen fixation. However, many agricultural soils are deficient in phosphorus. Here we show that a new mechanism of overyielding, in which phosphorus mobilized by one crop species increases the growth of a second crop species grown in alternate rows, led to large yield increases on phosphorus-deficient soils. In 4 years of field experiments, maize (Zea mays L.) overyielded by 43% and faba bean (Vicia faba L.) overyielded by 26% when intercropped on a low-phosphorus but high-nitrogen soil. We found that overyielding of maize was attributable to below-ground interactions between faba bean and maize in another field experiment. Intercropping with faba bean improved maize grain yield significantly and above-ground biomass marginally significantly, compared with maize grown with wheat, at lower rates of P fertilizer application (<75 kg of P(2)O(5) per hectare), and not significantly at high rate of P application (>112.5 kg of P(2)O(5) per hectare). By using permeable and impermeable root barriers, we found that maize overyielding resulted from its uptake of phosphorus mobilized by the acidification of the rhizosphere via faba bean root release of organic acids and protons. Faba bean overyielded because its growth season and rooting depth differed from maize. The large increase in yields from intercropping on low-phosphorus soils is likely to be especially important on heavily weathered soils.

Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq). SLAF-seq technology has several distinguishing characteristics: i) deep sequencing to ensure genotyping accuracy; ii) reduced representation strategy to reduce sequencing costs; iii) pre-designed reduced representation scheme to optimize marker efficiency; and iv) double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations.

The reaction between ferrous iron (Fe(II)) with peroxymonosulfate (PMS) generates reactive oxidants capable of degrading refractory organic contaminants. However, the slow transformation from ferric iron (Fe(III)) back to Fe(II) limits its widespread application. Here, we added hydroxylamine (HA), a common reducing agent, into Fe(II)/PMS process to accelerate the transformation from Fe(III) to Fe(II). With benzoic acid (BA) as probe compound, the addition of HA into Fe(II)/PMS process accelerated the degradation of BA rapidly in the pH range of 2.0-6.0 by accelerating the key reactions, including the redox cycle of Fe(III)/Fe(II) and the generation of reactive oxidants. Both sulfate radicals and hydroxyl radicals were considered as the primary reactive oxidants for the degradation of BA in HA/Fe(II)/PMS process with the experiments of electron spin resonance and alcohols quenching. Moreover, HA was gradually degraded to N2, N2O, NO2 (−), and NO3 (−), while the environmentally friendly gas of N2 was considered as its major end product in the process. The present study might provide a promising idea based on Fe(II)/PMS process for the rapid degradation of refractory organic contaminants in water treatment.

Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.

In the field of agricultural information, the automatic identification and diagnosis of maize leaf diseases is highly desired. To improve the identification accuracy of maize leaf diseases and reduce the number of network parameters, the improved GoogLeNet and Cifar10 models based on deep learning are proposed for leaf disease recognition in this paper. Two improved models that are used to train and test nine kinds of maize leaf images are obtained by adjusting the parameters, changing the pooling combinations, adding dropout operations and rectified linear unit functions, and reducing the number of classifiers. In addition, the number of parameters of the improved models is significantly smaller than that of the VGG and AlexNet structures. During the recognition of eight kinds of maize leaf diseases, the GoogLeNet model achieves a top - 1 average identification accuracy of 98.9%, and the Cifar10 model achieves an average accuracy of 98.8%. The improved methods are possibly improved the accuracy of maize leaf disease, and reduced the convergence iterations, which can effectively improve the model training and recognition efficiency.

Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.

Antimicrobial peptides (AMPs), critical components of the innate immune system, are widely distributed throughout the animal and plant kingdoms. They can protect against a broad array of infection-causing agents, such as bacteria, fungi, parasites, viruses, and tumor cells, and also exhibit immunomodulatory activity. AMPs exert antimicrobial activities primarily through mechanisms involving membrane disruption, so they have a lower likelihood of inducing drug resistance. Extensive studies on the structure-activity relationship have revealed that net charge, hydrophobicity, and amphipathicity are the most important physicochemical and structural determinants endowing AMPs with antimicrobial potency and cell selectivity. This review summarizes the recent advances in AMPs development with respect to characteristics, structure-activity relationships, functions, antimicrobial mechanisms, expression regulation, and applications in food, medicine, and animals.

We developed a strategy for coupling hollow Fe3O4-Fe nanoparticles with graphene sheets for high-performance electromagnetic wave absorbing material. The hollow Fe3O4-Fe nanoparticles with average diameter and shell thickness of 20 and 8 nm, respectively, were uniformly anchored on the graphene sheets without obvious aggregation. The minimal reflection loss RL values of the composite could reach -30 dB at the absorber thickness ranging from 2.0 to 5.0 mm, greatly superior to the solid Fe3O4-Fe/G composite and most magnetic EM wave absorbing materials recently reported. Moreover, the addition amount of the composite into paraffin matrix was only 18 wt %.

Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.

Most human diseases and agriculturally important traits are complex. Dissecting their genetic architecture requires continued development of innovative and powerful statistical methods. Corresponding advances in computing tools are critical to efficiently use these statistical innovations and to enhance and accelerate biomedical and agricultural research and applications. The genome association and prediction integrated tool (GAPIT) was first released in 2012 and became widely used for genome-wide association studies (GWAS) and genomic prediction. The GAPIT implemented computationally efficient statistical methods, including the compressed mixed linear model (CMLM) and genomic prediction by using genomic best linear unbiased prediction (gBLUP). New state-of-the-art statistical methods have now been implemented in a new, enhanced version of GAPIT. These methods include factored spectrally transformed linear mixed models (FaST-LMM), enriched CMLM (ECMLM), FaST-LMM-Select, and settlement of mixed linear models under progressively exclusive relationship (SUPER). The genomic prediction methods implemented in this new release of the GAPIT include gBLUP based on CMLM, ECMLM, and SUPER. Additionally, the GAPIT was updated to improve its existing output display features and to add new data display and evaluation functions, including new graphing options and capabilities, phenotype simulation, power analysis, and cross-validation. These enhancements make the GAPIT a valuable resource for determining appropriate experimental designs and performing GWAS and genomic prediction. The enhanced R-based GAPIT software package uses state-of-the-art methods to conduct GWAS and genomic prediction. The GAPIT also provides new functions for developing experimental designs and creating publication-ready tabular summaries and graphs to improve the efficiency and application of genomic research.

The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.

Maize zein was hydrolyzed for 0.5-5 h by alcalase or papain. Protein solubility increased (P < 0.05) with the degree of hydrolysis (DH) and was higher for alcalase-hydrolyzed zein than for papain-hydrolyzed zein. The zein hydrolysates with both enzymes consisted mostly of small peptides or amino acids nondetectable by 15% acrylamide gel electrophoresis. Alcalase-hydrolyzed zein exhibited a stronger (P < 0.05) antioxidant activity than papain-hydrolyzed zein, as indicated by peroxide and thiobarbituric acid-reactive substance values in a liposome-oxidizing system. Zein hydrolysates possessed strong Cu(2+) chelation ability and marked reducing power, both of which were accentuated with hydrolysis time. The protein hydrolysates also showed strong radical-scavenging ability, which was not influenced by hydrolysis time. The antioxidant activity of alcalase-hydrolyzed zein at some specific low concentrations was close or comparable to those of butylated hydroxyanisole, alpha-tocopherol, and ascorbate. Although intact zein displayed an antioxidative effect, it was far less potent than hydrolyzed zein. The results demonstrated that enzyme-hydrolyzed zein can act as a metal ion chelator or a hydrogen donor, as well as a radical stabilizer to inhibit lipid oxidation. The effectiveness of the protein hydrolysates appeared to depend on both the concentration and the peptide/amino acid composition of the soluble protein fraction.

According to the World Health Organization (WHO) newly updated situation report on March 18th, 2020, the coronavirus disease 2019 (COVID-19) pandemic has confirmed 191,127 cases and claimed 7807 deaths worldwide. 1 6] Currently, there are no approved prophylactic vaccines or therapeutic drugs that are specific to COVID-19. Blocking monoclonal antibodies (mAbs), due to their extraordinary antigen specificity, are one of the best candidates for neutralizing virus infection. Therefore, identifying and cloning blocking mAbs that can specifically target surface viral proteins to block the viral entry to host cells is a very attractive approach for preventing and treating COVID-19, in particular when effective vaccines and therapeutics are unavailable in the outbreak of the COVID-19 pandemic. We then sought to identify and clone blocking mAbs from the memory B cell repertoire of recently recovered COVID-19 patients to prevent the entry of COVID-19 virus to the host cells.

Abstract Northeast China is the leading grain production region in China where one-fifth of the national grain is produced; however, consistent and reliable crop maps are still unavailable, impeding crop management decisions for regional and national food security. Here, we produced annual 10-m crop maps of the major crops (maize, soybean, and rice) in Northeast China from 2017 to 2019, by using (1) a hierarchical mapping strategy (cropland mapping followed by crop classification), (2) agro-climate zone-specific random forest classifiers, (3) interpolated and smoothed 10-day Sentinel-2 time series data, and (4) optimized features from spectral, temporal, and texture characteristics of the land surface. The resultant maps have high overall accuracies (OA) spanning from 0.81 to 0.86 based on abundant ground truth data. The satellite estimates agreed well with the statistical data for most of the municipalities (R 2 ≥ 0.83, p &lt; 0.01). This is the first effort on regional annual crop mapping in China at the 10-m resolution, which permits assessing the performance of the soybean rejuvenation plan and crop rotation practice in China.

The chemistry of humic substances (HSs) occurs hidden from our sight, but is of key importance to agriculture and the environment, and nowadays even to medicine and technology. HSs are nowadays not only natural, but extracted and engineered, and in the past 20 years such products have been widely used in soil improvement and environment governance. In this review, we collate and summarize the applications and working principles of such HSs in agriculture and environmental ecology, mainly to elaborate the multiple roles of this functional polymer along with physical chemical quantification. Then several of the latest synthesis technologies, including hydrothermal humification technology (HTH), hydrothermal carbonization technology (HTC) and hydrogen peroxide oxidation technology (HOT) are presented, which were introduced to prepare artificial humic substances (A-HSs). The availability of reproducible and tunable synthetic A-HSs is a new chemical tool, and effects such as solubilization of insoluble phosphorus minerals, recovery of phosphorus, improvement of soil fertility for crop growth and reduction of toxicity of typical pollutants, can now be analyzed in detail and quantified. As a result, we can provide an effective chemical technology for utilizing biomass side products ("biowaste") to generate A-HSs of different types, thus realizing improvement in agricultural production and control of environmental pollution by the macro-synthesis of A-HSs-.

Auxin binding protein 1 (ABP1) has been studied for decades. It has been suggested that ABP1 functions as an auxin receptor and has an essential role in many developmental processes. Here we present our unexpected findings that ABP1 is neither required for auxin signaling nor necessary for plant development under normal growth conditions. We used our ribozyme-based CRISPR technology to generate an Arabidopsis abp1 mutant that contains a 5-bp deletion in the first exon of ABP1, which resulted in a frameshift and introduction of early stop codons. We also identified a T-DNA insertion abp1 allele that harbors a T-DNA insertion located 27 bp downstream of the ATG start codon in the first exon. We show that the two new abp1 mutants are null alleles. Surprisingly, our new abp1 mutant plants do not display any obvious developmental defects. In fact, the mutant plants are indistinguishable from wild-type plants at every developmental stage analyzed. Furthermore, the abp1 plants are not resistant to exogenous auxin. At the molecular level, we find that the induction of known auxin-regulated genes is similar in both wild-type and abp1 plants in response to auxin treatments. We conclude that ABP1 is not a key component in auxin signaling or Arabidopsis development.