Shanxi Agricultural University

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Deep learning is a branch of artificial intelligence. In recent years, with the advantages of automatic learning and feature extraction, it has been widely concerned by academic and industrial circles. It has been widely used in image and video processing, voice processing, and natural language processing. At the same time, it has also become a research hotspot in the field of agricultural plant protection, such as plant disease recognition and pest range assessment, etc. The application of deep learning in plant disease recognition can avoid the disadvantages caused by artificial selection of disease spot features, make plant disease feature extraction more objective, and improve the research efficiency and technology transformation speed. This review provides the research progress of deep learning technology in the field of crop leaf disease identification in recent years. In this paper, we present the current trends and challenges for the detection of plant leaf disease using deep learning and advanced imaging techniques. We hope that this work will be a valuable resource for researchers who study the detection of plant diseases and insect pests. At the same time, we also discussed some of the current challenges and problems that need to be resolved.

Tartary buckwheat (Fagopyrum tataricum) is an important pseudocereal crop that is strongly adapted to growth in adverse environments. Its gluten-free grain contains complete proteins with a well-balanced composition of essential amino acids and is a rich source of beneficial phytochemicals that provide significant health benefits. Here, we report a high-quality, chromosome-scale Tartary buckwheat genome sequence of 489.3 Mb that is assembled by combining whole-genome shotgun sequencing of both Illumina short reads and single-molecule real-time long reads, sequence tags of a large DNA insert fosmid library, Hi-C sequencing data, and BioNano genome maps. We annotated 33 366 high-confidence protein-coding genes based on expression evidence. Comparisons of the intra-genome with the sugar beet genome revealed an independent whole-genome duplication that occurred in the buckwheat lineage after they diverged from the common ancestor, which was not shared with rosids or asterids. The reference genome facilitated the identification of many new genes predicted to be involved in rutin biosynthesis and regulation, aluminum stress resistance, and in drought and cold stress responses. Our data suggest that Tartary buckwheat's ability to tolerate high levels of abiotic stress is attributed to the expansion of several gene families involved in signal transduction, gene regulation, and membrane transport. The availability of these genomic resources will facilitate the discovery of agronomically and nutritionally important genes and genetic improvement of Tartary buckwheat.

Tubulointerstitial fibrosis is a common consequence of various kidney diseases that lead to end-stage renal failure, and lymphocyte infiltration plays an important role in renal fibrosis. We previously found that depletion of cluster of differentiation 8+ (CD8+) T cells increases renal fibrosis following ureteric obstruction, and interferon-γ (IFN-γ)-expressing CD8+ T cells contribute to this process. CD8+ T cells are cytotoxic T cells; however, whether their cytotoxic effect reduces fibrosis remains unknown. This study showed that CD8+ T cells isolated from obstructed kidney showed mRNA expression of the cytotoxicity-related genes perforin 1, granzyme A, granzyme B, and FAS ligand; additionally, CD8 knockout significantly reduced the expression levels of these genes in obstructed kidney. Infiltrated CD8+ T cells were distributed around fibroblasts, and they are associated with fibroblast apoptosis in obstructed kidney. Moreover, CD11c+ CD8+ T cells expressed higher levels of the cytotoxicity-related genes than CD11c− CD8+ T cells, and infiltrated CD11c+ CD8+ T cells in obstructed kidney could induce fibroblast death in vitro. Results indicated that induction of fibroblast apoptosis partly contributed to the effect of CD8+ T cells on reduction of renal fibrosis. Given that inflammatory cells are involved in fibrosis, our results suggest that kidney fibrosis is a multifactorial process involving different arms of the immune system.

Forest aboveground biomass (AGB) plays an important role in the study of the carbon cycle and climate change in the global terrestrial ecosystem. AGB estimation based on remote sensing is an effective method for regional scale. In this study, Landsat 8 Operational Land Imager and Sentinel-1A data and China's National Forest Continuous Inventory data in combination with three algorithms, either the linear regression (LR), random forest (RF), or the extreme gradient boosting (XGBoost), were used to estimate biomass of the subtropical forests in Hunan Province, China. XGBoost is a scalable tree boosting system that is widely used by data scientists and provides state-of-the-art results for many problems. It can process an entire dataset with billions of examples using a minimal amount of computational resources through the particular way of cache access patterns, data compression, and data fragmentation. The results include: (1) The combination of Landsat 8 and Sentinel-1A images as predictor variables in the XGBoost model provided the best AGB estimation. (2) In contrast to the LR method, the F-test results indicated that a significant improvement in AGB estimation was achieved with the RF and XGBoost algorithms. (3) The effect of parameter optimization was found to be more significant on XGBoost than on RF. (4) The XGBoost model is an effective method for AGB estimation and can reduce the problems of overestimation and underestimation. This research provides a new way of estimating AGB for the subtropical forest based on remote sensing through the synergy of different sensors datasets and modeling algorithms.

We previously showed that the N6-methyladenosine (m(6)A) mRNA methylase is essential during Arabidopsis thaliana embryonic development. We also demonstrated that this modification is present at varying levels in all mature tissues. However, the requirement for the m(6)A in the mature plant was not tested. Here we show that a 90% reduction in m(6)A levels during later growth stages gives rise to plants with altered growth patterns and reduced apical dominance. The flowers of these plants commonly show defects in their floral organ number, size, and identity. The global analysis of gene expression from reduced m(6)A plants show that a significant number of down-regulated genes are involved in transport, or targeted transport, and most of the up-regulated genes are involved in stress and stimulus response processes. An analysis of m(6)A distribution in fragmented mRNA suggests that the m(6)A is predominantly positioned toward the 3' end of transcripts in a region 100-150 bp before the poly(A) tail. In addition to the analysis of the phenotypic changes in the low methylation Arabidopsis plants we will review the latest advances in the field of mRNA internal methylation.

Fruit detection forms a vital part of the robotic harvesting platform. However, uneven environment conditions, such as branch and leaf occlusion, illumination variation, clusters of tomatoes, shading, and so on, have made fruit detection very challenging. In order to solve these problems, a modified YOLOv3 model called YOLO-Tomato models were adopted to detect tomatoes in complex environmental conditions. With the application of label what you see approach, densely architecture incorporation, spatial pyramid pooling and Mish function activation to the modified YOLOv3 model, the YOLO-Tomato models: YOLO-Tomato-A at AP 98.3% with detection time 48 ms, YOLO-Tomato-B at AP 99.3% with detection time 44 ms, and YOLO-Tomato-C at AP 99.5% with detection time 52 ms, performed better than other state-of-the-art methods.

Silicon (Si) can improve drought tolerance in plants, but the mechanism is still not fully understood. Previous research has been concentrating on Si's role in leaf water maintenance in Si accumulators, while little information is available on its role in water uptake and in less Si-accumulating plants. Here, we investigated the effects of Si on root water uptake and its role in decreasing oxidative damage in relation to root hydraulic conductance in tomato (Solanum lycopersicum 'Zhongza No.9') under water stress. Tomato seedlings were subjected to water stress induced by 10% (w/v) polyethylene glycol-6000 in the absence or presence of 2.5 mM added silicate. The results showed that Si addition ameliorated the inhibition in tomato growth and photosynthesis, and improved water status under water stress. The root hydraulic conductance of tomato plants was decreased under water stress, and it was significantly increased by added Si. There was no significant contribution of osmotic adjustment in Si-enhanced root water uptake under water stress. The transcriptions of plasma membrane aquaporin genes were not obviously changed by Si under water stress. Water stress increased the production of reactive oxygen species and induced oxidative damage, while added Si reversed these. In addition, Si addition increased the activities of superoxide dismutase and catalase and the levels of ascorbic acid and glutathione in the roots under stress. It is concluded that Si enhances the water stress tolerance via enhancing root hydraulic conductance and water uptake in tomato plants. Si-mediated decrease in membrane oxidative damage may have contributed to the enhanced root hydraulic conductance.

Air pollutants from residential solid fuel combustion are attracting growing public concern. Field measured emission factors (EFs) of various air pollutants for solid fuels are close to the reality and urgently needed for better emission estimations. In this study, emission factors of particulate matter (PM), organic carbon (OC), elemental carbon (EC), and various polycyclic aromatic hydrocarbons (PAHs) from residential combustions of coal briquette, coal cake, and wood were measured in rural Heshun County, China. The measured EFs of PM, OC, and EC were 8.1-8.5, 2.2-3.6, 0.91-1.6 g/kg for the wood burnt in a simple metal stove, 0.54-0.64, 0.13-0.14, 0.040-0.0041 g/kg for the briquette burned in an improved stove with a chimney, and 3.2-8.5, 0.38-0.58, 0.022-0.052 g/kg for the homemade coal cake combusted in a brick stove with a flue, respectively. EFs of 28 parent PAHs, 4 oxygenated PAHs, and 9 nitro-PAHs were 182-297, 7.8-10, 0.14-0.55 mg/kg for the wood, 14-16, 1.7-2.6, 0.64-0.83 mg/kg for the briquette, and 168-223, 4.7-9.5, 0.16-2.4 mg/kg for the coal cake, respectively. Emissions from the wood and coal cake combustions were much higher than those for the coal briquette, especially true for high molecular weight PAHs. Most EFs measured in the field were higher than those measured in stove combustions under laboratory conditions.

Structural degradation of silt clay loam soils in Delta, British Columbia, has resulted from intensive cultivation of vegetable crops. A field experiment and a laboratory incubation study were conducted to assess the ability of nonleguminous winter cover crops, spring barley ( Hordeum vulgare L.), fall rye ( Secale cereale L.), and annual ryegrass ( Lolium multiflorum Lam.), to affect soil organic C, total and dilute acid extractable polysaccharides, and aggregate stability, expressed as mean weight diameter (MWD). The field experiment included four treatments: three cover crops (spring barley, fall rye, and annual ryegrass) and control (bare soil) arranged in a randomized complete block design. Annual ryegrass and fall rye increased MWD, and all of the cover crops increased soil dilute acid extractable polysaccharides. In the incubation experiment, starch (2.68 g C kg −1 soil) or chopped shoots and coarse roots of fall rye (single‐ [4.14 g C kg −1 soil] and double‐dose [8.28 g C kg −1 soil]) and annual ryegrass (4.62 g C kg −1 soil) were added to a soil from the cover‐crop site and incubated for 2, 4, and 8 wk. Cover crop and starch amendments increased soil organic C, dilute acid–extractable polysaccharides, and soil MWD. After 2‐wk incubation, the starch amendment had the greatest MWD in all the treatments, increasing by 25, 44, and 45%, compared with the annual ryegrass, double‐dose fall rye, and fall rye amendments, respectively ( P < 0.05). After 8‐wk incubation, however, the MWD in the starch amendment containers decreased by 18% compared with that in the double‐dose fall rye amendment treatments ( P < 0.05). All the cover crop amendments increased MWD and percentages of water stable 2‐ to 6‐mm aggregates at all incubation periods ( P < 0.05). Soil aggregate stability highly correlated with dilute acid‐extractable polysaccharides in the field and in incubation experiments. This study suggests that the dilute acid‐extractable polysaccharide fraction represents active binding agents under short‐term cover crops. It has been shown that soil aggregate stability can be increased under 8‐mo nonleguminous cover crops in the intensively cultivated soils.

infection is largely tolerated without any obvious ill effects. However, primary infection in immunosuppressed patients can result in acute cerebral or systemic disease, and reactivation of latent tissue cysts can lead to a deadly outcome. It is imperative that treatment of life-threatening toxoplasmic encephalitis is timely and effective. Several therapeutic and prophylactic regimens have been used in clinical practice. Current approaches can control infection caused by the invasive and highly proliferative tachyzoites but cannot eliminate the dormant tissue cysts. Adverse events and other limitations are associated with the standard pyrimethamine-based therapy, and effective vaccines are unavailable. In this review, the epidemiology, economic impact, pathophysiology, diagnosis, and management of cerebral toxoplasmosis are discussed, and critical areas for future research are highlighted.

Plastic polymers are widely used in agriculture, industry, and our daily life because of their convenient and economic properties. However, pollution caused by plastic polymers, especially polyethylene (PE), affects both animal and human health when they aggregate in the environment, as they are not easily degraded under natural conditions. In this study, Enterobacter sp. D1 was isolated from the guts of wax moth (Galleria mellonella). Microbial colonies formed around a PE film after 14 days of cultivation with D1. Roughness, depressions, and cracks were detected on the surface of the PE film by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Fourier transform infrared spectroscopy (FTIR) showed the presence of carbonyl functional groups and ether groups on the PE film that was treated with D1. Liquid chromatography-tandem mass spectrometry (LC-MS) also revealed that the contents of certain alcohols, esters, and acids were increased as a result of the D1 treatment, indicating that oxidation reaction occurred on the surface of the PE film treated with D1 bacteria. These observations confirmed that D1 bacteria has an ability to degrade PE.

The psyllid Cacopsylla chinensis (Yang & Li) (Hemiptera: Psyllidae) is a serious pest of pears in China. To determine and contrast the fitness of the psyllid on two endemic cultivars of Pyrus bretschneideri (i.e., BHXS and BSL) and two introduced cultivars of Pyrus communis (i.e., CB and CRB), we analyzed data on the development, survival, and fecundity from C. chinensis individuals reared on the four cultivars. The age-stage, two-sex life table theory was used in order to enable the inclusion of males in the analysis as well as a means of identifying the variation in developmental durations among individuals. Results indicated that C. chinensis can successfully develop and reproduce on all four pear cultivars. However, based on the lower preadult survival rate, longer preadult duration, longer total preoviposition period (TPOP), and lower fecundity that occurred on both cultivars of P. communis, these two cultivars are less favorable hosts for C. chinensis than the P. bretschneideri cultivars. The lower intrinsic rate of increase (r), finite rate of increase (λ), and net reproduction rate (R0) on CB and CRB pears showed these two introduced cultivars are more resistant to C. chinensis than the endemic BHXS and BSL pears. These resistant cultivars would be appropriate candidates for managing C. chinensis. We used the bootstrap technique to estimate the uncertainty of the population parameters (r, λ, R0, etc.), while also demonstrating that it can be used for estimating the 0.025 and 0.975 percentile confidence intervals of the age of survival rate.

Climate change significantly influences changes in ecological phenomena and processes, such as species distribution and phenology, thus accelerating the rate of species extinction or prosperity. Climate change is considered to be one of the most important threats to global biodiversity in the 21st century and will pose significant challenges to biodiversity conservation in the future. The use of niche modelling to predict changes in the suitable distribution of species under climate change scenarios is becoming a hot topic of biological conservation. In this study, we use data from China’s National Forest Continuous Inventory as well as specimen collection data of Cunninghamia lanceolata (Lamb.) Hook to run optimized Maxent models to predict potential suitable distribution of the species in the present day, 2050s, and 2070s under different climate change scenarios in China. In the modeling process, the most important uncorrelated variables were chosen, and the sample-size-adjusted Akaike information criterion (AICc) was used to select the optimal combination of feature type and regularization multiplier. Variable selection reduced the number of variables used and the complexity of the model, and the use of the AICc reduced overfitting. Variables relating to precipitation were more important than temperature variables in predicting C. lanceolata distribution in the optimal model. The predicted suitable distribution areas of C. lanceolata were different for the different periods under different climate change scenarios, with the centroids showing a degree of northward movement. The suitable distribution area is predicted to become more fragmented in the future. Our results reveal the climate conditions required for the suitable distribution of C. lanceolata in China and the likely changes to its distribution pattern in the future, providing a scientific basis for the sustainable management, protection, and restoration of the suitable habitat of this economically important tree species in the context of climate change.

Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.

Abstract Climate change has the potential to change the distribution of pests globally and their resistance to pesticides, thereby threatening global food security in the 21st century. However, predicting where these changes occur and how they will influence current pest control efforts is a challenge. Using experimentally parameterised and field-tested models, we show that climate change over the past 50 years increased the overwintering range of a global agricultural insect pest, the diamondback moth ( Plutella xylostella ), by ~2.4 million km 2 worldwide. Our analysis of global data sets revealed that pesticide resistance levels are linked to the species’ overwintering range: mean pesticide resistance was 158 times higher in overwintering sites compared to sites with only seasonal occurrence. By facilitating local persistence all year round, climate change can promote and expand pesticide resistance of this destructive species globally. These ecological and evolutionary changes would severely impede effectiveness of current pest control efforts and potentially cause large economic losses.

Our previous study showed that miR-29 attenuates muscle wasting in chronic kidney disease. Other studies found that miR-29 has anti-fibrosis activity. We hypothesized that intramuscular injection of exosome-encapsulated miR-29 would counteract unilateral ureteral obstruction (UUO)-induced muscle wasting and renal fibrosis. We used an engineered exosome vector, which contains an exosomal membrane protein gene Lamp2b that was fused with the targeting peptide RVG (rabies viral glycoprotein peptide). RVG directs exosomes to organs that express the acetylcholine receptor, such as kidney. The intervention of Exo/miR29 increased muscle cross-sectional area and decreased UUO-induced upregulation of TRIM63/MuRF1 and FBXO32/atrogin-1. Interestingly, renal fibrosis was partially depressed in the UUO mice with intramuscular injection of Exo/miR29. This was confirmed by decreased TGF-β, alpha-smooth muscle actin, fibronectin, and collagen 1A1 in the kidney of UUO mice. When we used fluorescently labeled Exo/miR29 to trace the Exo/miR route in vivo and found that fluorescence was visible in un-injected muscle and in kidneys. We found that miR-29 directly inhibits YY1 and TGF-β3, which provided a possible mechanism for inhibition of muscle atrophy and renal fibrosis by Exo/miR29. We conclude that Exo/miR29 ameliorates skeletal muscle atrophy and attenuates kidney fibrosis by downregulating YY1 and TGF-β pathway proteins. Our previous study showed that miR-29 attenuates muscle wasting in chronic kidney disease. Other studies found that miR-29 has anti-fibrosis activity. We hypothesized that intramuscular injection of exosome-encapsulated miR-29 would counteract unilateral ureteral obstruction (UUO)-induced muscle wasting and renal fibrosis. We used an engineered exosome vector, which contains an exosomal membrane protein gene Lamp2b that was fused with the targeting peptide RVG (rabies viral glycoprotein peptide). RVG directs exosomes to organs that express the acetylcholine receptor, such as kidney. The intervention of Exo/miR29 increased muscle cross-sectional area and decreased UUO-induced upregulation of TRIM63/MuRF1 and FBXO32/atrogin-1. Interestingly, renal fibrosis was partially depressed in the UUO mice with intramuscular injection of Exo/miR29. This was confirmed by decreased TGF-β, alpha-smooth muscle actin, fibronectin, and collagen 1A1 in the kidney of UUO mice. When we used fluorescently labeled Exo/miR29 to trace the Exo/miR route in vivo and found that fluorescence was visible in un-injected muscle and in kidneys. We found that miR-29 directly inhibits YY1 and TGF-β3, which provided a possible mechanism for inhibition of muscle atrophy and renal fibrosis by Exo/miR29. We conclude that Exo/miR29 ameliorates skeletal muscle atrophy and attenuates kidney fibrosis by downregulating YY1 and TGF-β pathway proteins.

Abstract Salt stress activates defence responses in plants, including changes in leaf surface structure. Here, we showed that the transcriptional activation of cutin deposition and antioxidant defence by the R2R3‐type MYB transcription factor AtMYB49 contributed to salt tolerance in Arabidopsis thaliana . Characterization of loss‐of‐function myb49 mutants, and chimeric AtMYB49‐SRDX‐ overexpressing SRDX49 transcriptional repressor and AtMYB49 ‐overexpressing ( OX49 ) overexpressor plants demonstrated a positive role of AtMYB49 in salt tolerance. Transcriptome analysis revealed that many genes belonging to the category “cutin, suberin and wax biosyntheses” were markedly up‐regulated and down‐regulated in OX49 and SRDX49 plants, respectively, under normal and/or salt stress conditions. Some of these differentially expressed genes, including MYB41 , ASFT , FACT and CYP86B1 , were also shown to be the direct targets of AtMYB49 and activated by AtMYB49. Biochemical analysis indicated that AtMYB49 modulated cutin deposition in the leaves. Importantly, cuticular transpiration, chlorophyll leaching and toluidine blue‐staining assays revealed a link between increased AtMYB49‐mediated cutin deposition in leaves and enhanced salt tolerance. Additionally, increased AtMYB49 expression elevated Ca 2+ level in leaves and improved antioxidant capacity by up‐regulating genes encoding peroxidases and late embryogenesis abundant proteins. These results suggest that genetic manipulation of AtMYB49 may provide a novel way to improve salt tolerance in plants.

This study presents a novel method to apply the RGB-D (Red Green Blue-Depth) sensors and fuse aligned RGB and NIR images with deep convolutional neural networks (CNN) for fruit detection. It aims to build a more accurate, faster, and more reliable fruit detection system, which is a vital element for fruit yield estimation and automated harvesting. Recent work in deep neural networks has led to the development of a state-of-the-art object detector termed Faster Region-based CNN (Faster R-CNN). A common Faster R-CNN network VGG16 was adopted through transfer learning, for the task of kiwifruit detection using imagery obtained from two modalities: RGB (red, green, blue) and Near-Infrared (NIR) images. Kinect v2 was used to take a bottom view of the kiwifruit canopy's NIR and RGB images. The NIR (1 channel) and RGB images (3 channels) were aligned and arranged side by side into a 6-channel image. The input layer of the VGG16 was modified to receive the 6-channel image. Two different fusion methods were used to extract features: Image-Fusion (fusion of the RGB and NIR images on input layer) and Feature-Fusion (fusion of feature maps of two VGG16 networks where the RGB and NIR images were input respectively). The improved networks were trained end-to-end using back-propagation and stochastic gradient descent techniques and compared to original VGG16 networks with RGB and NIR image input only. Results showed that the average precision (APs) of the original VGG16 with RGB and NIR image input only were 88.4% and 89.2% respectively, the 6-channel VGG16 using the Feature-Fusion method reached 90.5%, while that using the Image-Fusion method reached the highest AP of 90.7% and the fastest detection speed of 0.134 s/image. The results indicated that the proposed kiwifruit detection approach shows a potential for better fruit detection.

Abstract Nitrogen (N) and carbon (C) are essential elements for plant growth and crop yield. Thus, improved N and C utilisation contributes to agricultural productivity and reduces the need for fertilisation. In the present study, we find that overexpression of a single rice gene, Oryza sativa plasma membrane (PM) H + -ATPase 1 ( OSA1 ), facilitates ammonium absorption and assimilation in roots and enhanced light-induced stomatal opening with higher photosynthesis rate in leaves. As a result, OSA1 overexpression in rice plants causes a 33% increase in grain yield and a 46% increase in N use efficiency overall. As PM H + -ATPase is highly conserved in plants, these findings indicate that the manipulation of PM H + -ATPase could cooperatively improve N and C utilisation, potentially providing a vital tool for food security and sustainable agriculture.