Plant diseases are a critical threat to the agricultural sector. Therefore, accurate plant disease classification is important. In recent years, some researchers have used synthetic images of GAN to enhance plant disease recognition accuracy. In this paper, we propose a generative adversarial classified network (GACN) to further improve plant disease recognition accuracy. The GACN comprises a generator, discriminator, and classifier. The proposed model can not only enhance convolutional neural network performance by generating synthetic images to balance plant disease datasets but the GACN classifier can also be directly applied to plant disease recognition tasks. Experimental results on the PlantVillage and AI Challenger 2018 datasets show that the contribution of the proposed method to improve the discriminability of the convolution neural network is greater than that of the label-conditional methods of CGAN, ACGAN, BAGAN, and MFC-GAN. The accuracy of the trained classifier for plant disease recognition is also better than that of the plant disease recognition models studied on public plant disease datasets. In addition, we conducted several experiments to observe the effects of different numbers and resolutions of synthetic images on the discriminability of convolutional neural network.

With the wide adoption of transcriptome sequencing an ever increasing amount of information is becoming available, together with spurious data originating from contamination. We show that sometimes errors and inaccuracy can turn beneficial, revealing insect and arthropod pests when analysing plant transcriptomes. We have found a large number of soluble olfactory proteins, odorant-binding proteins (OBPs) and chemosensory proteins (CSPs), in plant databases, likely due to contamination by guest insects. In fact, both classes of proteins are only expressed in insects, with few CSPs also present in other arthropods. In addition, we found many sequences of the Niemann-Pick (Npc2) family, proteins dedicated to cholesterol transport in vertebrates and hypothesised to be involved in chemical communication in insects, but absent in plants. In several cases we were able to trace down members of the three classes of proteins to the insect or arthopod species responsible for contamination. Our work suggests that genes found in plants and recognised as contaminants can be turned into useful information to investigate plant-insect relationships or to identify new sequences from insects species not yet investigated.

Plant diseases caused by necrotrophic fungal pathogens result in large economic losses in field crop production worldwide. Effectors are important players of plant-pathogen interaction and deployed by pathogens to facilitate plant colonization and nutrient acquisition. Compared to biotrophic and hemibiotrophic fungal pathogens, effector biology is poorly understood for necrotrophic fungal pathogens. Recent bioinformatics advances have accelerated the prediction and discovery of effectors from necrotrophic fungi, and their functional context is currently being clarified. In this review we examine effectors utilized by necrotrophic fungi and hemibiotrophic fungi in the latter stages of disease development, including plant cell death manipulation. We define "effectors" as secreted proteins and other molecules that affect plant physiology in ways that contribute to disease establishment and progression. Studying and understanding the mechanisms of necrotrophic effectors is critical for identifying avenues of genetic intervention that could lead to improved resistance to these pathogens in plants.

Differences between plant genomes range from single nucleotide polymorphisms to large-scale duplications, deletions and rearrangements. The large polymorphisms are termed structural variants (SVs). SVs have received significant attention in human genetics and were found to be responsible for various chronic diseases. However, little effort has been directed towards understanding the role of SVs in plants. Many recent advances in plant genetics have resulted from improvements in high-resolution technologies for measuring SVs, including microarray-based techniques, and more recently, high-throughput DNA sequencing. In this review we describe recent reports of SV in plants and describe the genomic technologies currently used to measure these SVs.

Complex diseases involve dynamic perturbations of pathophysiological processes during disease progression. Transcriptional programs underlying such perturbations are unknown in many diseases. Here, we present core transcriptional regulatory circuits underlying early and late perturbations in prion disease. We first identified cellular processes perturbed early and late using time-course gene expression data from three prion-infected mouse strains. We then built a transcriptional regulatory network (TRN) describing regulation of early and late processes. We found over-represented feed-forward loops (FFLs) comprising transcription factor (TF) pairs and target genes in the TRN. Using gene expression data of brain cell types, we further selected active FFLs where TF pairs and target genes were expressed in the same cell type and showed correlated temporal expression changes in the brain. We finally determined core transcriptional regulatory circuits by combining these active FFLs. These circuits provide insights into transcriptional programs for early and late pathophysiological processes in prion disease.

Cinnamon (Cinnamomum zeylanicum, and Cinnamon cassia), the eternal tree of tropical medicine, belongs to the Lauraceae family. Cinnamon is one of the most important spices used daily by people all over the world. Cinnamon primarily contains vital oils and other derivatives, such as cinnamaldehyde, cinnamic acid, and cinnamate. In addition to being an antioxidant, anti-inflammatory, antidiabetic, antimicrobial, anticancer, lipid-lowering, and cardiovascular-disease-lowering compound, cinnamon has also been reported to have activities against neurological disorders, such as Parkinson's and Alzheimer's diseases. This review illustrates the pharmacological prospective of cinnamon and its use in daily life.

Pathogenesis of complex diseases involves the integration of genetic and environmental factors over time, making it particularly difficult to tease apart relationships between phenotype, genotype, and environmental factors using traditional experimental approaches.

Drug delivery across the skin is used for several millennia to ease gastrointestinal (GI) ailments in Traditional Persian Medicine (TPM). TPM topical remedies are generally being applied on the stomach, lower abdomen, lower back and liver to alleviate GI illnesses such as dyspepsia, gastritis, GI ulcers, inflammatory bowel disease, intestinal worms and infections. The aim of the present study is to survey the topical GI remedies and plant species used as ingredients for these remedies in TPM. In addition, pharmacological activities of the mentioned plants have been discussed. For this, we searched major TPM textbooks to find plants used to cure GI problems in topical use. Additionally, scientific databases were searched to obtain pharmacological data supporting the use of TPM plants in GI diseases. Rosa × damascena, Pistacia lentiscus, Malus domestica, Olea europaea and Artemisia absinthium are among the most frequently mentioned ingredients of TPM remedies. β-asarone, amygdalin, boswellic acids, guggulsterone, crocin, crocetin, isomasticadienolic acid, and cyclotides are the most important phytochemicals present in TPM plants with GI-protective activities. Pharmacological studies demonstrated GI activities for TPM plants supporting their extensive traditional use. These plants play pivotal role in alleviating GI disorders through exhibiting numerous activities including antispasmodic, anti-ulcer, anti-secretory, anti-colitis, anti-diarrheal, antibacterial and anthelmintic properties. Several mechanisms underlie these activities including the alleviation of oxidative stress, exhibiting cytoprotective activity, down-regulation of the inflammatory cytokines, suppression of the cellular signaling pathways of inflammatory responses, improving re-epithelialization and angiogenesis, down-regulation of anti-angiogenic factors, blocking activity of acetylcholine, etc.

ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. In ppdb, the promoter structures are determined by sets of promoter elements identified by a position-sensitive extraction method called local distribution of short sequences (LDSS). By using this database, the core promoter structure, the presence of regulatory elements and the distribution of TSS clusters can be identified. Although no differentiation of promoter architecture among plant species has been reported, there is some divergence of utilized sequences for promoter elements. Therefore, ppdb is based on species-specific sets of promoter elements, rather than on general motifs for multiple species. Each regulatory sequence is hyperlinked to literary information, a PLACE entry served by a plant cis-element database, and a list of promoters containing the regulatory sequence.

Glycyrrhiza uralensis Fisch is a medicinal plant widely used to treat multiple diseases in Europe and Asia, and its efficacy largely depends on liquiritin and glycyrrhizic acid. The regulatory pattern responsible for the difference in efficacy between wild and cultivated G. uralensis remains largely undetermined. Here, we collected roots and rhizosphere soils from wild (WT) G. uralensis as well as those farmed for 1 year (C1) and 3 years (C3), generated metabolite and transcript data for roots, microbiota data for rhizospheres and conducted comprehensive multi-omics analyses. We updated gene structures for all 40 091 genes in G. uralensis, and based on 52 differentially expressed genes, we charted the route-map of both liquiritin and glycyrrhizic acid biosynthesis, with genes BAS, CYP72A154 and CYP88D6 critical for glycyrrhizic acid biosynthesis being significantly expressed higher in wild G. uralensis than in cultivated G. uralensis. Additionally, multi-omics network analysis identified that Lysobacter was strongly associated with CYP72A154, which was required for glycyrrhizic acid biosynthesis. Finally, we developed a holistic multi-omics regulation model that confirmed the importance of rhizosphere microbial community structure in liquiritin accumulation. This study thoroughly decoded the key regulatory mechanisms of liquiritin and glycyrrhizic acid, and provided new insights into the interactions of the plant's key metabolites with its transcriptome, rhizosphere microbes and environment, which would guide future cultivation of G. uralensis.

Plant pathogenic fungi cause important yield losses in crops. In order to develop efficient and environmental friendly crop protection strategies, molecular studies of the fungal biological cycle, virulence factors, and interaction with its host are necessary. For that reason, several approaches have been performed using both classical genetic, cell biology, and biochemistry and the modern, holistic, and high-throughput, omic techniques. This work briefly overviews the tools available for studying Plant Pathogenic Fungi and is amply focused on MS-based Proteomics analysis, based on original papers published up to December 2009. At a methodological level, different steps in a proteomic workflow experiment are discussed. Separate sections are devoted to fungal descriptive (intracellular, subcellular, extracellular) and differential expression proteomics and interactomics. From the work published we can conclude that Proteomics, in combination with other techniques, constitutes a powerful tool for providing important information about pathogenicity and virulence factors, thus opening up new possibilities for crop disease diagnosis and crop protection.

There is an urgency to supplant the heavy reliance on chemical control of Fusarium diseases in different economically important, staple food crops due to development of resistance in the pathogen population, the high cost of production to the risk-averse grower, and the concomitant environmental impacts. Pathogenomics has enabled (i) the creation of genetic inventories which identify those putative genes, regulators, and effectors that are associated with virulence, pathogenicity, and primary and secondary metabolism; (ii) comparison of such genes among related pathogens; (iii) identification of potential genetic targets for chemical control; and (iv) better characterization of the complex dynamics of host-microbe interactions that lead to disease. This type of genomic data serves to inform host-induced gene silencing (HIGS) technology for targeted disruption of transcription of select genes for the control of Fusarium diseases. This review discusses the various repositories and browser access points for comparison of genomic data, the strategies for identification and selection of pathogenicity- and virulence-associated genes and effectors in different Fusarium species, HIGS and successful Fusarium disease control trials with a consideration of loss of RNAi, off-target effects, and future challenges in applying HIGS for management of Fusarium diseases.

Plant trichomes often function as physical barriers in preventing arthropod feeding and oviposition. Even though insects are frequently reported being entrapped and killed by trichome traps, the actual trapping behavior has not yet been described in detail. Capture experiments showed that capture efficiency during the plant's vegetative stage was considerably higher than in the fruiting and cotyledon stages. The ventral surface of the leaf was more effective in trapping flies than other parts of the plant. Capture-events monitoring showed that the mouthparts, legs, and ovipositor of Liriomyza trifolii adults are the body parts involved in entrapment by surface trichomes on Phaseolus vulgaris plants, and subsequently, deter their ability to feed, walk, and oviposit. Of the three main body parts normally affected, mouthparts was found to be the body part most susceptible to the trichomes. Entrapments were most often caused by landing, followed by puncturing or feeding, and occasionally by walking or fighting. Using scanning electron microscopy (SEM) and optical microscopy, we determined the susceptible positions of each body part and found that the flies were all trapped by hooked trichomes. This study revealed the process by which leafminer flies are entrapped by surface trichomes of the host plant and evaluated the capture efficiency. The results will contribute to our understanding of physical defenses against herbivores.

Over 100 years after trypanosomatids were first discovered in plant tissues, Phytomonas parasites have now been isolated across the globe from members of 24 different plant families. Most identified species have not been associated with any plant pathology and to date only two species are definitively known to cause plant disease. These diseases (wilt of palm and coffee phloem necrosis) are problematic in areas of South America where they threaten the economies of developing countries. In contrast to their mammalian infective relatives, our knowledge of the biology of Phytomonas parasites and how they interact with their plant hosts is limited. This review draws together a century of research into plant trypanosomatids, from the first isolations and experimental infections to the recent publication of the first Phytomonas genomes. The availability of genomic data for these plant parasites opens a new avenue for comparative investigations into trypanosomatid biology and provides fresh insight into how this important group of parasites have adapted to survive in a spectrum of hosts from crocodiles to coconuts.

To facilitate rapid, unbiased, differential diagnosis of infectious diseases, we designed GreeneChipPm, a panmicrobial microarray comprising 29,455 sixty-mer oligonucleotide probes for vertebrate viruses, bacteria, fungi, and parasites. Methods for nucleic acid preparation, random primed PCR amplification, and labeling were optimized to allow the sensitivity required for application with nucleic acid extracted from clinical materials and cultured isolates. Analysis of nasopharyngeal aspirates, blood, urine, and tissue from persons with various infectious diseases confirmed the presence of viruses and bacteria identified by other methods, and implicated Plasmodium falciparum in an unexplained fatal case of hemorrhagic feverlike disease during the Marburg hemorrhagic fever outbreak in Angola in 2004-2005.

Current clinical agents for autoimmunity disorders treatment often cause substantial adverse effects and safety concerns, owing to non-specific immune modulation. Due to the prominent contribution of effector T cells in pathogenesis of rheumatoid arthritis (RA) and inflammatory bowel disease (IBD), and preferential location of co-stimulatory receptor-ligand pair OX40-OX40L at the inflamed sites, selectively targeting autoaggressive T cells by blockade OX40-OX40L, might represent an alternative strategy. Herein, we developed a new strategy to antagonize OX40-OX40L interaction by engineering a cell membrane derived nanovesicles (NVs) expressing OX40 receptors (OX40 NVs), and explored their potential for autoimmune disorders therapy. OX40 NVs showed specific binding capability to inflamed HUVECs in vitro, it also possessed distinct arthritic-targeting capacity in RA inflamed joints, and preferential accumulation in IBD inflamed colon. OX40 NVs efficiently suppressed the progression of both RA and IBD diseases through reducing CD4+OX40+ T cells population, and proinflammatory cytokines (i.e., TNF-α and IL-1β), while reinforcing Tregs immune-suppressive effect, with superior therapeutic efficacy than anti-OX40L. Additionally, dexamethasone (DEX) loading can further enhance the potential of OX40 NVs for RA treatment. Owing to their preferential localization to inflamed sites, and potent immune-suppression ability, targeting OX40-OX40L blockade by OX40 NVs for autoimmune therapy is highly promising.

Background and Aims: Currently, there is a continuing upward trend for plant-based lifestyles in Germany and Europe. The implementation of vegetarian and vegan lifestyles is characterized by omitting defined food groups such as fish, meat, sausage (vegetarians), or dairy products and honey (vegans). This carries the risk of an undersupply of valuable nutrients. The NuEva study is designed to examine this hypothesis and to evaluate the impact of plant-based diets on health status and disease risk. Methods: The NuEva study is a parallel-designed trial with at least 55 participants for each diet (vegetarian, vegan, flexitarian [rare meat/sausage consumption, once or twice per week]), and participants who consume a traditional Western diet as the control group. In the screening period critical nutrients are identified for the studied diets by analysis of a broad spectrum of nutrients in the human samples (fatty acids, vitamins, minerals, trace elements, nutrient metabolites). Results: Based on the data from the screening period, defined menu plans, ensuring an adequate nutrient intake in accordance with the nutritional guidelines are prepared for each group. The plans are adapted and personalized to individual energy requirements based on the basal metabolic rate and physical activity level. The compliance with the NuEva concept and their impact on nutrient status and cardiovascular risk factors are validated during the intervention period of the NuEva study over 1 year. To investigate the impact of the studied diets on the microbiome, feces samples are collected at the beginning and after the 12 months intervention period (follow up: 12 months). Conclusion: The NuEva study is designed to investigate the impact of common diets on health and disease status, with focus on prevention of cardiovascular diseases. In addition, the effectiveness of the prepared nutritional coaching strategy, ensuring optimal nutrient intake in accordance with the guidelines, is validated during the intervention period of the NuEva study. Clinical Trial Registration: Registered under ClinicalTrials.gov Identifier no. NCT03582020.

Parasite-driven declines in wildlife have become increasingly common and can pose significant risks to natural populations. We used the IUCN Red List of Threatened and Endangered Species and compiled data on hosts threatened by infectious disease and their parasites to better understand the role of infectious disease in contemporary host extinctions. The majority of mammal species considered threatened by parasites were either carnivores or artiodactyls, two clades that include the majority of domesticated animals. Parasites affecting host threat status were predominantly viruses and bacteria that infect a wide range of host species, including domesticated animals. Counter to our predictions, parasites transmitted by close contact were more likely to cause extinction risk than those transmitted by other routes. Mammal species threatened by parasites were not better studied for infectious diseases than other threatened mammals and did not have more parasites or differ in four key traits demonstrated to affect parasite species richness in other comparative studies. Our findings underscore the need for better information concerning the distribution and impacts of infectious diseases in populations of endangered mammals. In addition, our results suggest that evolutionary similarity to domesticated animals may be a key factor associated with parasite-mediated declines; thus, efforts to limit contact between domesticated hosts and wildlife could reduce extinction risk.

Berberine (BBR) is an isoquinoline alkaloid that is widely distributed in the plant kingdom and is commonly found in Coptis chinensis Franch. It has low bioavailability, but it can interact with gut microbiota and affect a variety of diseases. The effects of BBR in diabetes, hyperlipidemia, atherosclerosis, liver diseases, intestinal diseases, mental disorders, autoimmune diseases, and other diseases are all thought to be related to gut microbiota. This review systematically and comprehensively summarize these interactions and their effects, and describes the changes of gut microbiota after the intervention of different doses of berberine and its potential clinical consequences, in order to provide a basis for the rational application of BBR in the future clinical treatment.

Rice disease has serious negative effects on crop yield, and the correct diagnosis of rice diseases is the key to avoid these effects. However, the existing disease diagnosis methods for rice are neither accurate nor efficient, and special equipment is often required. In this study, an automatic diagnosis method was developed and implemented in a smartphone app. The method was developed using deep learning based on a large dataset that contained 33,026 images of six types of rice diseases: leaf blast, false smut, neck blast, sheath blight, bacterial stripe disease, and brown spot. The core of the method was the Ensemble Model in which submodels were integrated. Finally, the Ensemble Model was validated using a separate set of images. Results showed that the three best submodels were DenseNet-121, SE-ResNet-50, and ResNeSt-50, in terms of several attributes, such as, learning rate, precision, recall, and disease recognition accuracy. Therefore, these three submodels were selected and integrated in the Ensemble Model. The Ensemble Model minimized confusion among the different types of disease, reducing misdiagnosis of the disease. Using the Ensemble Model to diagnose six types of rice diseases, an overall accuracy of 91% was achieved, which is considered to be reasonably good, considering the appearance similarities in some types of rice disease. The smartphone app allowed the client to use the Ensemble Model on the web server through a network, which was convenient and efficient for the field diagnosis of rice leaf blast, false smut, neck blast, sheath blight, bacterial stripe disease, and brown spot.