The field of object detection has made great progress in recent years. Most of these improvements are derived from using a more sophisticated convolutional neural network. However, in the case of ...humans, the attention mechanism, global structure information, and local details of objects all play an important role for detecting an object. In this paper, we propose a novel fully convolutional network, named as Attention CoupleNet, to incorporate the attention-related information and global and local information of objects to improve the detection performance. Specifically, we first design a cascade attention structure to perceive the global scene of the image and generate class-agnostic attention maps. Then the attention maps are encoded into the network to acquire object-aware features. Next, we propose a unique fully convolutional coupling structure to couple global structure and local parts of the object to further formulate a discriminative feature representation. To fully explore the global and local properties, we also design different coupling strategies and normalization ways to make full use of the complementary advantages between the global and local information. Extensive experiments demonstrate the effectiveness of our approach. We achieve state-of-the-art results on all three challenging data sets, i.e., a mAP of 85.7% on VOC07, 84.3% on VOC12, and 35.4% on COCO. Codes are publicly available at https://github.com/tshizys/CoupleNet.
The Salt Overly Sensitive (SOS) pathway regulates intracellular sodium ion homeostasis as a salt‐stress response in plants. This pathway involves three main genes designated as SOS1, SOS2 and SOS3, ...which are members of the Na+/H+ exchanger (NHX), CBL‐interacting protein kinase (CIPK) and Calcineurin B‐like (CBL) gene families, respectively. To identify and characterize SOS genes in spinach (Spinacia oleracea), a species of the Amaranthaceae family, we conducted genome‐wide identification and phylogenetic analyses of NHX, CIPK and CBL genes from four Amaranthaceae species, Arabidopsis and rice. Most Amaranthaceae genes exhibited orthologous relationships with Arabidopsis and/or rice, except a clade of Vac‐type Amaranthaceae NHX genes. Phylogenetic analyses also revealed gene gain/loss events in Amaranthaceae species and the intron‐less to intron‐rich evolution of CIPK genes. A bacterial protein‐rooted CIPK tree allowed naming most of the phylogenetic clades based on their evolutionary history. Single S. oleracea (So) SOS1, SOS2 and SOS3 proteins were identified. Direct protein–protein interaction was observed between SoSOS2 and SoSOS3 but not between SoSOS2 and SoSOS1 based on yeast two‐hybrid assay. This may suggest distinct modes of action of spinach SOS proteins compared to Arabidopsis SOS proteins. Unlike SoSOS1 and SoSOS2, which were expressed at similar or higher levels in leaves than roots, SoSOS3 expression was significantly higher in roots than leaves, suggesting its greater importance in roots. The expression of SoSOS3 was upregulated in both roots and leaves under salinity compared to the control; however, SoSOS1 was only upregulated in roots. Thus, this study demonstrated the conservation of SOS pathway genes in spinach and also highlighted the complexity of SOS signaling in Amaranthaceae species.
Gene transfer among reproductively isolated organisms can lead to novel phenotypes and increased fitness. Among the Sternorrhyncha, a suborder of plant sap-feeding hemipteran insects, both aphids and ...adelgids acquired carotenoid biosynthesis genes from a fungal donor that result in ecologically relevant pigmentation. Phylloxerids form another family that are closely related to aphids and adelgids and share similar pigmentation, but are largely uncharacterized for their presence and number of pigment genes that have duplicated among aphids. Here, we examined the transcriptomes of nine phylloxerid species, and performed PCR to amplify carotenoid genes from their genomic DNA. We identified carotenoid cyclase/synthase and desaturase genes in each species and demonstrated that they share the common fungal origin as those of aphids and adelgids based on their exon-intron gene structures and phylogenetic relationships. The phylogenetic analyses also indicated that carotenoid genes evolved following the differentiation of aphids, adelgids, and phylloxerids at the levels of family, genus, and species. Unlike aphids that duplicated these genes in their genomes, phylloxerids maintained only single copies, and some species may lack expression of certain genes. These results suggest that the phylloxerid lifestyle undergoes reduced selection pressure to expand carotenoid synthesis genes, and provides insight into these gene functions in insects.
Face detection is the basic step in video face analysis and has been studied for many years. However, achieving real-time performance on computation-resource-limited embedded devices still remains an ...open challenge. To address this problem, in this paper we propose a face detector, EagleEye, which shows a good trade-off between high accuracy and fast speed on the popular embedded device with low computation power (e.g., the Raspberry Pi 3b+). The EagleEye is designed to have low floating-point operations per second (FLOPS) as well as enough capacity, and its accuracy is further improved without adding too much FLOPS. Specifically, we design five strategies for building efficient face detectors with a good balance of accuracy and running speed. The first two strategies help to build a detector with low computation complexity and enough capacity. We use convolution factorization to change traditional convolutions into more sparse depth-wise convolutions to save computation costs and we use successive downsampling convolutions at the beginning of the face detection network. The latter three strategies significantly improve the accuracy of the light-weight detector without adding too much computation costs. We design an efficient context module to utilize context information to benefit the face detection. We also adopt information preserving activation function to increase the network capacity. Finally, we use focal loss to further improve the accuracy by handling the class imbalance problem better. Experiments show that the EagleEye outperforms the other face detectors with the same order of computation costs, on both runtime efficiency and accuracy.
All eukaryotes share a conserved network of processes regulated by the proteasome and fundamental to growth, development, or perception of the environment, leading to complex but often predictable ...responses to stress. As a specialized component of the ubiquitin-proteasome system (UPS), the RING finger domain mediates protein-protein interactions and displays considerable versatility in regulating many physiological processes in plants. Many pathogenic organisms co-opt the UPS through RING-type E3 ligases, but little is known about how insects modify these integral networks to generate novel plant phenotypes.
Using a combination of transcriptome sequencing and genome annotation of a grapevine galling species, Daktulosphaira vitifoliae, we identified 138 putatively secretory protein RING-type (SPRINGs) E3 ligases that showed structure and evolutionary signatures of genes under rapid evolution. Moreover, the majority of the SPRINGs were more expressed in the feeding stage than the non-feeding egg stage, in contrast to the non-secretory RING genes. Phylogenetic analyses indicated that the SPRINGs formed clusters, likely resulting from species-specific gene duplication and conforming to features of arthropod host-manipulating (effector) genes. To test the hypothesis that these SPRINGs evolved to manipulate cellular processes within the plant host, we examined SPRING interactions with grapevine proteins using the yeast two-hybrid assay. An insect SPRING interacted with two plant proteins, a cellulose synthase, CSLD5, and a ribosomal protein, RPS4B suggesting secretion reprograms host immune signaling, cell division, and stress response in favor of the insect. Plant UPS gene expression during gall development linked numerous processes to novel organogenesis.
Taken together, D. vitifoliae SPRINGs represent a novel gene expansion that evolved to interact with Vitis hosts. Thus, a pattern is emerging for gall forming insects to manipulate plant development through UPS targeting.
Introduction Viral diseases have become a vital factor limiting the development of the alfalfa ( Medicago sativa ) industry. Six viruses infecting alfalfa with a high incidence rate are Alfalfa ...mosaic virus (AMV), Medicago sativa alphapartitivirus 1 (MsAPV1), Medicago sativa alphapartitivirus 2 (MsAPV2), Medicago sativa deltapartitivirus 1 (MsDPV1), Medicago sativa amalgavirus 1 (MsAV1), and Cnidium vein yellowing virus 1 (CnVYV1). The purpose of this study was to develop preventive measures against these viruses by investigating their transmission through alfalfa seeds. Methods In this study, we investigated the transmission rate of alfalfa viruses from seed to seedling by PCR, determined the location of viruses in seed by dissecting seed embryos and seed coat, tracked the changes of viruses in seedlings, and finally discover effective elimination measures for alfalfa viruses from 16 measures. Results and discussion Our results demonstrated that all these six viruses could be transmitted from alfalfa seeds to seedlings with the transmission rate ranging from 44.44% to 88.89%. For AMV, MsAPV2, and MsAV1, the viral load was significantly higher in the seed coats than in the seed embryos; however, it did not show significant differences between these two parts of the seeds for MsAPV1, MsDPV1, and CnVYV1. Dynamic accumulation analysis of AMV and MsAPV2 indicated that the viral load in plants increased continuously in the early growth stage, making it important to inactivate these viruses prior to their seed-to-seedling transmission. Sixteen treatments including physical, chemical, and combinations of physical and chemical measures were compared in terms of their elimination efficiency on AMV and MsAPV2 and impacts on seed germination. The results showed that soaking alfalfa seeds in sterile distilled water for 2h + 2% NaClO for 1h or 2% NaClO for 1h were more promisingly applicable because it could significantly reduce AMV and MsAPV2 particles in both seeds and seedlings. Our data revealed a route of virus transmission in alfalfa and shed light on the discovery of a highly efficient method for the management of alfalfa viral diseases.
The brown marmorated stink bug (Halyomorpha halys) has emerged as one of the most important invasive insect pests in the United States. Functional genomics in H. halys remains unexplored as molecular ...resources in this insect have recently been developed. To facilitate functional genomics research, we evaluated ten common insect housekeeping genes (RPS26, EF1A, FAU, UBE4A, ARL2, ARP8, GUS, TBP, TIF6 and RPL9) for their stability across various treatments in H. halys. Our treatments included two biotic factors (tissues and developmental stages) and two stress treatments (RNAi injection and starvation). Reference gene stability was determined using three software algorithms (geNorm, NormFinder, BestKeeper) and a web-based tool (RefFinder). The qRT-PCR results indicated ARP8 and UBE4A exhibit the most stable expression across tissues and developmental stages, ARL2 and FAU for dsRNA treatment and TBP and UBE4A for starvation treatment. Following the dsRNA treatment, all genes except GUS showed relatively stable expression. To demonstrate the utility of validated reference genes in accurate gene expression analysis and to explore gene silencing in H. halys, we performed RNAi by administering dsRNA of target gene (catalase) through microinjection. A successful RNAi response with over 90% reduction in expression of target gene was observed.
The Hessian fly (HF,
) is a plant-galling parasite of wheat (
spp.). Seven percent of its genome is composed of highly diversified signal-peptide-encoding genes that are transcribed in HF larval ...salivary glands. These observations suggest that they encode effector proteins that are injected into wheat cells to suppress basal wheat immunity and redirect wheat development towards gall formation. Genetic mapping has determined that mutations in four of these genes are associated with HF larval survival (virulence) on plants carrying four different resistance (
) genes. Here, this line of investigation was pursued further using bulked-segregant analysis combined with whole genome resequencing (BSA-seq). Virulence to wheat
genes
,
and
was examined. Mutations associated with
virulence had been mapped previously. Therefore, we used
to test the capacity of BSA-seq to map virulence using a field-derived HF population. This was the first time a non-structured HF population had been used to map HF virulence.
virulence had not been mapped previously. Using a structured laboratory population, BSA-seq associated
virulence with mutations in two candidate effector-encoding genes. Using a laboratory population,
virulence was previously positioned in a region spanning the centromere of HF autosome 2. BSA-seq resolved
virulence to a 1.3 Mb fragment on the same chromosome but failed to identify candidate mutations. Map-based candidate effectors were then delivered to
plant cells
the type III secretion system of
bacteria. These experiments demonstrated that the genes associated with virulence to wheat
genes
and
are capable of suppressing plant immunity. Results are consistent with the hypothesis that effector proteins underlie the ability of HFs to survive on wheat.
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