Publications by authors named "Chaoyang Zhao"

28 Publications

  • Page 1 of 1

Tripartite parasitic and symbiotic interactions as a possible mechanism of horizontal gene transfer.

Ecol Evol 2021 Jun 6;11(11):7018-7028. Epub 2021 Apr 6.

Sino-American Biological Control Laboratory Institute of Plant Protection Chinese Academy of Agricultural Sciences Beijing China.

Herbivory is a highly sophisticated feeding behavior that requires abilities of plant defense suppression, phytochemical detoxification, and plant macromolecule digestion. For plant-sucking insects, salivary glands (SGs) play important roles in herbivory by secreting and injecting proteins into plant tissues to facilitate feeding. Little is known on how insects evolved secretory SG proteins for such specialized functions. Here, we investigated the composition and evolution of secretory SG proteins in the brown marmorated stink bug () and identified a group of secretory SG phospholipase C (PLC) genes with highest sequence similarity to the bacterial homologs. Further analyses demonstrated that they were most closely related to of , a genus of Gammaproteobacteria living in symbiosis with insect-parasitizing nematodes. These suggested that might acquire these from through the mechanism of horizontal gene transfer (HGT), likely mediated by a nematode during its parasitizing an insect host. We also showed that the original HGT event was followed by gene duplication and expansion, leading to functional diversification of the bacterial-origin PLC genes in . Thus, this study suggested that an herbivore might enhance adaptation through gaining genes from an endosymbiont of its parasite in the tripartite parasitic and symbiotic interactions.
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http://dx.doi.org/10.1002/ece3.7550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8207144PMC
June 2021

Ionic framework constructed with protic ionic liquid units for improving ammonia uptake.

Chem Commun (Camb) 2021 May;57(36):4384-4387

College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, P. R. China.

In this work, an ionic framework [Ph3ImH][Tf2N]2 constructed from protic imidazolium ionic liquid units through ionic and hydrogen bonding interactions was synthesized for selective ammonia uptake. Investigation of the NH3 uptake mechanism indicates that the acid sites in [Ph3ImH][Tf2N]2 would be frustrated when contacted with NH3, and the frustration of [Ph3ImH][Tf2N]2 precipitates NH3 capture by hydrogen bonding and physical interactions, and the NH3 could be released under mild conditions. There was no obvious decrease in capacity over 10 consecutive cycles of ammonia uptake and release.
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http://dx.doi.org/10.1039/d1cc00441gDOI Listing
May 2021

A new contrast-to-noise ratio for image quality characterization of a coded-aperture γ camera.

Appl Radiat Isot 2021 Apr 13;170:109592. Epub 2021 Jan 13.

College of Physics, Key Laboratory of Radiation Physics and Technology, Ministry of Education, Sichuan University, Chengdu, 610064, China.

The gamma-ray imaging technique was developed and is widely used in several nuclear engineering fields. Specifically, compared with the traditional point-by-point radiation detector, the coded-aperture gamma camera has advantages of a wide field of view, high angular resolution, and high efficiency. Several methods for characterizing image quality, including the figure of merit (FOM) method and the contrast-to-noise ratio (CNR) method, were assessed and developed. These methods have their respective drawbacks depending on the circumstances. The FOM lacks reliability in exhibiting the impact of background noise fluctuation on the purity of a real image. The CNR characterizes image quality with inconsistent sensitivity while the source moves along the X and Y directions. Therefore, a new CNR method was proposed to achieve better performance and greater consistency in real imaging. With our coded-aperture imaging system developed in the laboratory, we performed simulations within the MATLAB and Geant4 platforms and real imaging experiments to analyze and compare images and the results of these three characterization methods. The results show that the new CNR method is reliable and practical in regard to real imaging performance.
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http://dx.doi.org/10.1016/j.apradiso.2021.109592DOI Listing
April 2021

Real-time signal processing in field programmable gate array based digital gamma-ray spectrometer.

Rev Sci Instrum 2020 Oct;91(10):104707

Institute of Electronic Engineering, China Academy of Engineering Physics, Mianyang 621999, China.

Field programmable gate arrays (FPGAs) are attractive for a digital spectrometer due to its advantages of digital signal processing. However, how to improve the versatility of the spectrometer and increase the operating frequency of the digital shaper has gradually become a limitation that needs to be resolved in the FPGA-based spectrometer. A solution to improve the universality of the FPGA-based digital spectroscopy system is presented in this work, and the implementation of the real-time digital signal processing unit is improved to obtain a higher operating frequency, and then the optimal parameters of the digital trapezoidal shaper and the processing unit are also discussed through a series of experiments; finally, a FPGA-based digital spectrometer is developed. With the HPGe detector, the spectrometer achieves excellent energy resolution performance of 0.35% at 662 keV, 0.25% at 1173.2 keV, and 0.23% at 1332.5 keV.
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http://dx.doi.org/10.1063/5.0005694DOI Listing
October 2020

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest.

BMC Biol 2020 07 23;18(1):90. Epub 2020 Jul 23.

INRAE, Institute of Ecology and Environmental Sciences, Versailles, France.

Background: Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture.

Results: Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world.

Conclusions: The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.
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http://dx.doi.org/10.1186/s12915-020-00820-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376646PMC
July 2020

BSA-Seq Discovery and Functional Analysis of Candidate Hessian Fly () Genes.

Front Plant Sci 2020 25;11:956. Epub 2020 Jun 25.

Department of Entomology, Purdue University, West Lafayette, IN, United States.

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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http://dx.doi.org/10.3389/fpls.2020.00956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7330099PMC
June 2020

Isolation and characterization of Salt Overly Sensitive family genes in spinach.

Physiol Plant 2021 Apr 16;171(4):520-532. Epub 2020 Jun 16.

USDA-ARS, US Salinity Lab, 450 W Big Springs Road, Riverside, California, 92507, USA.

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.
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http://dx.doi.org/10.1111/ppl.13125DOI Listing
April 2021

NPC1b as a novel target in controlling the cotton bollworm, Helicoverpa armigera.

Pest Manag Sci 2020 Jun 3;76(6):2233-2242. Epub 2020 Mar 3.

State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China.

Background: Insects cannot synthesize sterols and must acquire them from food. The mechanisms underlying how insects uptake dietary sterols are largely unknown except that NPC1b, an integral membrane protein, has been shown to be responsible for dietary cholesterol uptake in Drosophila melanogaster. However, whether NPC1b orthologs in other insect species, particularly the economically important pests, function similarly remains to be determined.

Results: In this study, we characterized the function of NPC1b in Helicoverpa armigera, a global pest that causes severe yield losses to many important crops. Limiting dietary cholesterol uptake to insects significantly inhibited food ingestion and weight gain. Compared to the wild-type H. armigera, the CRISPR/Cas9-edited NPC1b mutant larvae were incapable of getting adequate cholesterol and died in their early life stage. Gene expression profile and in situ hybridization analyses indicated that NPC1b was mainly expressed in the midgut where dietary cholesterol was absorbed. Expression of NPC1b was also correlated with the feeding life stages and was especially upregulated during early larval instars. Protein-ligand docking and sequence similarity analyses further demonstrated that NPC1b proteins of lepidopteran insects shared a relatively conserved cholesterol binding region, NPC1b_NTD, which, however, was highly divergent from bees-derived sequences.

Conclusion: NPC1b was crucial for dietary cholesterol uptake and growth of H. armigera, and therefore could serve as an insecticide target for the development of a novel pest-management approach to control this economically significant insect pest with little off-target effect on bees and sterol-autotrophic animals. © 2020 Society of Chemical Industry.
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http://dx.doi.org/10.1002/ps.5761DOI Listing
June 2020

Secretory RING finger proteins function as effectors in a grapevine galling insect.

BMC Genomics 2019 Dec 3;20(1):923. Epub 2019 Dec 3.

Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.

Background: 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.

Results: 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.

Conclusions: 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.
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http://dx.doi.org/10.1186/s12864-019-6313-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892190PMC
December 2019

TERT rs10069690 polymorphism and cancers risk: A meta-analysis.

Mol Genet Genomic Med 2019 10 27;7(10):e00903. Epub 2019 Aug 27.

Department of Surgical Oncology, Second Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China.

Background: Studies have identified that the telomerase reverse transcriptase (TERT) gene polymorphism rs10069690 (C>T) is associated with cancer risk, but the results remain inconclusive.

Methods: To provide a more precise estimation of the relationship, we performed a meta-analysis of 45 published studies including 329,035 cases and 730,940 controls. We conducted a search in PubMed, Google Scholar and Web of Science to select studies on the association between rs10069690 and cancer risk. Stratification by ethnicity, cancer type, cancers' classification, source of control, sample size, and genotype method was used to explore the source of heterogeneity. The pooled odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were evaluated using random effects models. Sensitivity, publication bias, false-positive report probability (FPRP) and statistical power were also assessed.

Results: The result demonstrated that rs10069690 was significantly associated with an increased risk of cancer overall (OR = 1.09, 95% CI: 1.06-1.12, p < .001) under the allele model. Stratification analysis revealed an increased cancer risk in subgroups of breast cancer, ovarian cancer, lung cancer, thyroid cancer, and renal cell carcinoma (RCC). However, a significantly decreased association was observed in pancreatic cancer in the European population (OR = 0.93,95% CI: 0.87-0.99, p = .031). In the subgroup analysis based on cancer type, no significant association was found in prostate cancer, leukemia, colorectal cancer and glioma.

Conclusions: This meta-analysis suggested that the TERT rs10069690 polymorphism may be a risk factor for cancer, especially breast cancer, ovarian cancer, lung cancer, thyroid cancer, and RCC. Further functional studies are warranted to reveal the role of the polymorphism in carcinogenesis.
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http://dx.doi.org/10.1002/mgg3.903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6785442PMC
October 2019

Evaluation of GALNT16 polymorphisms to breast cancer risk in Chinese population.

Mol Genet Genomic Med 2019 08 8;7(8):e848. Epub 2019 Jul 8.

Surgical Oncology, The Second Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China.

Background: Polypeptide N-acetylgalactosaminyltransferase 16 (GALNT16) is an N-acetylgalactosaminyltransferase gene that alters protein O-glycosylation, which plays a role in tumor development. This study aims to explore the association of eight GALNT16 polymorphisms with susceptibility to breast cancer (BC).

Methods: This case-control study included 563 BC patients and 552 age-matched healthy controls from the Chinese Han population. The genotypes of GALNT16 polymorphisms were detected using the Agena MassARRAY. The relationship between GALNT16 polymorphisms and BC risk was evaluated using a chi-squared test with an odds ratio (OR) and 95% confidence intervals (CI) under five genetic models.

Results: We observed that rs2105269 and rs72625676 were associated with higher BC risk in younger patients with age ≤51 (rs2105269, codominant: p = .006; recessive: p = .005 additive: p = .018; and allele: p = .012; rs72625676, codominant: p = .038; recessive: p = .037). For rs1275678 polymorphism, there was a significantly decreased risk of BC among elder patients (codominant: p = .017; dominant: p = .019; additive: p = .030; and allele: p = .029). Further analysis by clinical characteristics showed rs2105269 was associated with tumor size and lymph node metastasis.

Conclusion: Our study suggests that GALNT16 polymorphisms are associated with BC susceptibility in Chinese population.
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http://dx.doi.org/10.1002/mgg3.848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687646PMC
August 2019

Analysis of MIR155HG variants and colorectal cancer susceptibility in Han Chinese population.

Mol Genet Genomic Med 2019 08 22;7(8):e778. Epub 2019 Jun 22.

Surgical Oncology, The Second Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China.

Background: MIR155HG plays an important role in malignant tumors, but it is rarely reported in the occurrence and development of colorectal cancer (CRC). This study investigated the effects of MIR155HG polymorphisms on CRC susceptibility from the perspective of molecular genetics.

Methods: Eight SNPs in MIR155HG were selected and genotyped among 514 CRC cases and 510 healthy controls using the Agena MassARRAY platform. The associations between these SNPs and the CRC risk were evaluated under genetic models using conditional logistic regression analysis. The HaploReg v4.1 database was used for SNPs functional prediction.

Results: The allele "C" of rs12482371 (p = 0.047), allele "C" of rs1893650 (p = 0.025), and the allele "A" of rs928883 (p = 0.037) in MIR155HG were significantly associated with CRC risk. Genetic model analysis revealed that rs12482371 and rs1893650 increased CRC risk; whereas rs928883 was associated with reduced CRC risk. Stratification analysis showed that rs9383938 was a protective factor in CRC patients under 60 years old. Rs12482371 and rs1893650 were associated with the CRC risk in females. Rs11911469 and rs34904192 may affect the clinical stage and lymph node metastasis. Moreover, the haplotypes CTT and GTC of LD block rs4143370|rs77218221|rs12482371, and the haplotypes CATGA and CACGG of LD block rs77699734|rs11911469|rs1893650|rs34904192|rs928883 were significantly associated with CRC risk.

Conclusion: This study revealed that MIR155HG SNPs were associated with CRC susceptibility and could be predictive biomarkers for CRC risk.
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http://dx.doi.org/10.1002/mgg3.778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687631PMC
August 2019

Real-Time Multi-Scale Face Detector on Embedded Devices.

Sensors (Basel) 2019 May 9;19(9). Epub 2019 May 9.

National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.

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.
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http://dx.doi.org/10.3390/s19092158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6539187PMC
May 2019

Attention CoupleNet: Fully Convolutional Attention Coupling Network for Object Detection.

IEEE Trans Image Process 2019 Jan 13;28(1):113-126. Epub 2018 Aug 13.

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.
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http://dx.doi.org/10.1109/TIP.2018.2865280DOI Listing
January 2019

Unified equivalent circuit model for carbon nanotube-based nanocomposites.

Nanotechnology 2018 Jul 9;29(30):305503. Epub 2018 May 9.

School of Manufacturing Science and Engineering, Key Laboratory of Testing for Manufacturing Process, Ministry of Education, Southwest University of Science and Technology, Mianyang 621010, People's Republic of China.

Carbon nanotubes form a complex network in nanocomposites. In the network, the configuration of the nanotubes is various. A carbon nanotube may be curled or straight, and it may be parallel or crossed to another. As a result, carbon nanotube-based composites exhibit integrated characteristics of inductor, capacitor and resistor. In this work, it is hypothesised that carbon nanotube-based composites all adhere to a RLC interior circuit. To verify the hypothesis, three different composites, viz multi-walled carbon nanotube/polyvinylidene fluoride (MWCNT/PVDF), multi-walled carbon nanotube/epoxy (MWCNT/EP), multi-walled carbon nanotube/polydimethylsiloxane (MWCNT/PDMS) were fabricated and tested. The resistances and the dielectric loss tangent (tanδ) of the materials were measured in direct and alternating currents. The measurement shows that the value of tanδ is highly affected by the volume fraction of MWCNT in the composites. The experimental results prove that the proposed RLC equivalent circuit model can fully describe the electrical properties of the MWCNT network in nanocomposites. The RLC model provides a new route to detect the inductance and capacitance of carbon nanotubes. Moreover, the model also indicates that the carbon nanotube-based composite films may be used to develop wireless strain sensors.
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http://dx.doi.org/10.1088/1361-6528/aac36dDOI Listing
July 2018

Phylloxerids share ancestral carotenoid biosynthesis genes of fungal origin with aphids and adelgids.

PLoS One 2017 11;12(10):e0185484. Epub 2017 Oct 11.

Department of Botany and Plant Science, University of California, Riverside, California, United States of America.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185484PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5636080PMC
October 2017

Plant manipulation through gall formation constrains amino acid transporter evolution in sap-feeding insects.

BMC Evol Biol 2017 06 27;17(1):153. Epub 2017 Jun 27.

Department of Botany and Plant Sciences, University of California, Riverside, 900 University Avenue, Batchelor Hall room 2140, Riverside, CA, 92521, USA.

Background: The herbivore lifestyle leads to encounters with plant toxins and requires mechanisms to overcome suboptimal nutrient availability in plant tissues. Although the evolution of bacterial endosymbiosis alleviated many of these challenges, the ability to manipulate plant nutrient status has evolved in lineages with and without nutritional symbionts. Whether and how these alternative nutrient acquisition strategies interact or constrain insect evolution is unknown. We studied the transcriptomes of galling and free-living aphidomorphs to characterize how amino acid transporter evolution is influenced by the ability to manipulate plant resource availability.

Results: Using a comparative approach we found phylloxerids retain nearly all amino acid transporters as other aphidomorphs, despite loss of nutritional endosymbiosis. Free living species show more transporters than galling species within the same genus, family, or infraorder, indicating plant hosts influence the maintenance and evolution of nutrient transport within herbivores. Transcript profiles also show lineage specificity and suggest some genes may facilitate life without endosymbionts or the galling lifestyle.

Conclusions: The transcript abundance profiles we document across fluid feeding herbivores support plant host constraint on insect amino acid transporter evolution. Given amino acid uptake, transport, and catabolism underlie the success of herbivory as a life history strategy, this suggests that plant host nutrient quality, whether constitutive or induced, alters the selective environment surrounding the evolution and maintenance of endosymbiosis.
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http://dx.doi.org/10.1186/s12862-017-1000-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5488444PMC
June 2017

Quantitative RT-PCR Gene Evaluation and RNA Interference in the Brown Marmorated Stink Bug.

PLoS One 2016 4;11(5):e0152730. Epub 2016 May 4.

Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, 44691, United States of America.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152730PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856283PMC
April 2017

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

Nat Commun 2016 Feb 2;7:10165. Epub 2016 Feb 2.

Pest Control Biology and Research Technologies, Bayer CropScience AG, Monheim 40789, Germany.

The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
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http://dx.doi.org/10.1038/ncomms10165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740739PMC
February 2016

Avirulence gene mapping in the Hessian fly (Mayetiola destructor) reveals a protein phosphatase 2C effector gene family.

J Insect Physiol 2016 Jan 9;84:22-31. Epub 2015 Oct 9.

Department of Entomology, Purdue University, West Lafayette, IN 47907, United States. Electronic address:

The genetic tractability of the Hessian fly (HF, Mayetiola destructor) provides an opportunity to investigate the mechanisms insects use to induce plant gall formation. Here we demonstrate that capacity using the newly sequenced HF genome by identifying the gene (vH24) that elicits effector-triggered immunity in wheat (Triticum spp.) seedlings carrying HF resistance gene H24. vH24 was mapped within a 230-kb genomic fragment near the telomere of HF chromosome X1. That fragment contains only 21 putative genes. The best candidate vH24 gene in this region encodes a protein containing a secretion signal and a type-2 serine/threonine protein phosphatase (PP2C) domain. This gene has an H24-virulence associated insertion in its promoter that appears to silence transcription of the gene in H24-virulent larvae. Candidate vH24 is a member of a small family of genes that encode secretion signals and PP2C domains. It belongs to the fraction of genes in the HF genome previously predicted to encode effector proteins. Because PP2C proteins are not normally secreted, our results suggest that these are PP2C effectors that HF larvae inject into wheat cells to redirect, or interfere, with wheat signal transduction pathways.
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http://dx.doi.org/10.1016/j.jinsphys.2015.10.001DOI Listing
January 2016

Weighted Part Context Learning for Visual Tracking.

IEEE Trans Image Process 2015 Dec 16;24(12):5140-51. Epub 2015 Sep 16.

Context information is widely used in computer vision for tracking arbitrary objects. Most of the existing studies focus on how to distinguish the object of interest from background or how to use keypoint-based supporters as their auxiliary information to assist them in tracking. However, in most cases, how to discover and represent both the intrinsic properties inside the object and the surrounding context is still an open problem. In this paper, we propose a unified context learning framework that can effectively capture spatiotemporal relations, prior knowledge, and motion consistency to enhance tracker's performance. The proposed weighted part context tracker (WPCT) consists of an appearance model, an internal relation model, and a context relation model. The appearance model represents the appearances of the object and the parts. The internal relation model utilizes the parts inside the object to directly describe the spatiotemporal structure property, while the context relation model takes advantage of the latent intersection between the object and background regions. Then, the three models are embedded in a max-margin structured learning framework. Furthermore, prior label distribution is added, which can effectively exploit the spatial prior knowledge for learning the classifier and inferring the object state in the tracking process. Meanwhile, we define online update functions to decide when to update WPCT, as well as how to reweight the parts. Extensive experiments and comparisons with the state of the arts demonstrate the effectiveness of the proposed method.
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http://dx.doi.org/10.1109/TIP.2015.2479460DOI Listing
December 2015

A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor.

Curr Biol 2015 Mar 5;25(5):613-20. Epub 2015 Feb 5.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms that these arthropods use to induce plant galls are poorly understood. We sequenced the genome of the Hessian fly (Mayetiola destructor; Diptera: Cecidomyiidae), a plant parasitic gall midge and a pest of wheat (Triticum spp.), with the aim of identifying genic modifications that contribute to its plant-parasitic lifestyle. Among several adaptive modifications, we discovered an expansive reservoir of potential effector proteins. Nearly 5% of the 20,163 predicted gene models matched putative effector gene transcripts present in the M. destructor larval salivary gland. Another 466 putative effectors were discovered among the genes that have no sequence similarities in other organisms. The largest known arthropod gene family (family SSGP-71) was also discovered within the effector reservoir. SSGP-71 proteins lack sequence homologies to other proteins, but their structures resemble both ubiquitin E3 ligases in plants and E3-ligase-mimicking effectors in plant pathogenic bacteria. SSGP-71 proteins and wheat Skp proteins interact in vivo. Mutations in different SSGP-71 genes avoid the effector-triggered immunity that is directed by the wheat resistance genes H6 and H9. Results point to effectors as the agents responsible for arthropod-induced plant gall formation.
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http://dx.doi.org/10.1016/j.cub.2014.12.057DOI Listing
March 2015

Core RNAi machinery and gene knockdown in the emerald ash borer (Agrilus planipennis).

J Insect Physiol 2015 Jan 23;72:70-78. Epub 2014 Dec 23.

Department of Entomology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA. Electronic address:

The RNA interference (RNAi) technology has been widely used in insect functional genomics research and provides an alternative approach for insect pest management. To understand whether the emerald ash borer (Agrilus planipennis), an invasive and destructive coleopteran insect pest of ash tree (Fraxinus spp.), possesses a strong RNAi machinery that is capable of degrading target mRNA as a response to exogenous double-stranded RNA (dsRNA) induction, we identified three RNAi pathway core component genes, Dicer-2, Argonaute-2 and R2D2, from the A. planipennis genome sequence. Characterization of these core components revealed that they contain conserved domains essential for the proteins to function in the RNAi pathway. Phylogenetic analyses showed that they are closely related to homologs derived from other coleopteran species. We also delivered the dsRNA fragment of AplaScrB-2, a β-fructofuranosidase-encoding gene horizontally acquired by A. planipennis as we reported previously, into A. planipennis adults through microinjection. Quantitative real-time PCR analysis on the dsRNA-treated beetles demonstrated a significantly decreased gene expression level of AplaScrB-2 appearing on day 2 and lasting until at least day 6. This study is the first record of RNAi applied in A. planipennis.
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http://dx.doi.org/10.1016/j.jinsphys.2014.12.002DOI Listing
January 2015

Avirulence effector discovery in a plant galling and plant parasitic arthropod, the Hessian fly (Mayetiola destructor).

PLoS One 2014 25;9(6):e100958. Epub 2014 Jun 25.

Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America.

Highly specialized obligate plant-parasites exist within several groups of arthropods (insects and mites). Many of these are important pests, but the molecular basis of their parasitism and its evolution are poorly understood. One hypothesis is that plant parasitic arthropods use effector proteins to defeat basal plant immunity and modulate plant growth. Because avirulence (Avr) gene discovery is a reliable method of effector identification, we tested this hypothesis using high-resolution molecular genetic mapping of an Avr gene (vH13) in the Hessian fly (HF, Mayetiola destructor), an important gall midge pest of wheat (Triticum spp.). Chromosome walking resolved the position of vH13, and revealed alleles that determine whether HF larvae are virulent (survive) or avirulent (die) on wheat seedlings carrying the wheat H13 resistance gene. Association mapping found three independent insertions in vH13 that appear to be responsible for H13-virulence in field populations. We observed vH13 transcription in H13-avirulent larvae and the salivary glands of H13-avirulent larvae, but not in H13-virulent larvae. RNA-interference-knockdown of vH13 transcripts allowed some H13-avirulent larvae to escape H13-directed resistance. vH13 is the first Avr gene identified in an arthropod. It encodes a small modular protein with no sequence similarities to other proteins in GenBank. These data clearly support the hypothesis that an effector-based strategy has evolved in multiple lineages of plant parasites, including arthropods.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100958PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071006PMC
November 2015

A neo-sex chromosome that drives postzygotic sex determination in the hessian fly (Mayetiola destructor).

Genetics 2010 Mar 21;184(3):769-77. Epub 2009 Dec 21.

Department of Entomology, Purdue University, West Lafayette, Indiana 47907-2089, USA.

Two nonoverlapping autosomal inversions defined unusual neo-sex chromosomes in the Hessian fly (Mayetiola destructor). Like other neo-sex chromosomes, these were normally heterozygous, present only in one sex, and suppressed recombination around a sex-determining master switch. Their unusual properties originated from the anomalous Hessian fly sex determination system in which postzygotic chromosome elimination is used to establish the sex-determining karyotypes. This system permitted the evolution of a master switch (Chromosome maintenance, Cm) that acts maternally. All of the offspring of females that carry Cm-associated neo-sex chromosomes attain a female-determining somatic karyotype and develop as females. Thus, the chromosomes act as maternal effect neo-W's, or W-prime (W') chromosomes, where ZW' females mate with ZZ males to engender female-producing (ZW') and male-producing (ZZ) females in equal numbers. Genetic mapping and physical mapping identified the inversions. Their distribution was determined in nine populations. Experimental matings established the association of the inversions with Cm and measured their recombination suppression. The inversions are the functional equivalent of the sciarid X-prime chromosomes. We speculate that W' chromosomes exist in a variety of species that produce unisexual broods.
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http://dx.doi.org/10.1534/genetics.109.108589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845344PMC
March 2010

A BAC-based physical map of the Hessian fly genome anchored to polytene chromosomes.

BMC Genomics 2009 Jul 2;10:293. Epub 2009 Jul 2.

Department of Entomology, Purdue University, West Lafayette, IN 47907, USA.

Background: The Hessian fly (Mayetiola destructor) is an important insect pest of wheat. It has tractable genetics, polytene chromosomes, and a small genome (158 Mb). Investigation of the Hessian fly presents excellent opportunities to study plant-insect interactions and the molecular mechanisms underlying genome imprinting and chromosome elimination. A physical map is needed to improve the ability to perform both positional cloning and comparative genomic analyses with the fully sequenced genomes of other dipteran species.

Results: An FPC-based genome wide physical map of the Hessian fly was constructed and anchored to the insect's polytene chromosomes. Bacterial artificial chromosome (BAC) clones corresponding to 12-fold coverage of the Hessian fly genome were fingerprinted, using high information content fingerprinting (HIFC) methodology, and end-sequenced. Fluorescence in situ hybridization (FISH) co-localized two BAC clones from each of the 196 longest contigs on the polytene chromosomes. An additional 70 contigs were positioned using a single FISH probe. The 266 FISH mapped contigs were evenly distributed and covered 60% of the genome (95,668 kb). The ends of the fingerprinted BACs were then sequenced to develop the capacity to create sequenced tagged site (STS) markers on the BACs in the map. Only 3.64% of the BAC-end sequence was composed of transposable elements, helicases, ribosomal repeats, simple sequence repeats, and sequences of low complexity. A relatively large fraction (14.27%) of the BES was comprised of multi-copy gene sequences. Nearly 1% of the end sequence was composed of simple sequence repeats (SSRs).

Conclusion: This physical map provides the foundation for high-resolution genetic mapping, map-based cloning, and assembly of complete genome sequencing data. The results indicate that restriction fragment length heterogeneity in BAC libraries used to construct physical maps lower the length and the depth of the contigs, but is not an absolute barrier to the successful application of the technology. This map will serve as a genomic resource for accelerating gene discovery, genome sequencing, and the assembly of BAC sequences. The Hessian fly BAC-clone assembly, and the names and positions of the BAC clones used in the FISH experiments are publically available at (http://genome.purdue.edu/WebAGCoL/Hfly/WebFPC/).
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http://dx.doi.org/10.1186/1471-2164-10-293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709663PMC
July 2009

Folate receptor-targeted quantum dot liposomes as fluorescence probes.

J Drug Target 2009 Aug;17(7):502-11

School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

In this study, the preparation of the novel imaging agents, folate receptor (FR)-targeted liposomes encapsulating hydrophilic CdTe quantum dots (QDs), and their use as luminescence probes for live cell imaging are reported. Hydrophilic CdTe QDs were directly synthesized in the water phase, and FR-targeted QD liposomes were prepared by hydrating the lipid thin film with CdTe suspension. Formulations were characterized by UV-visible and fluorescent measurements, liposomal particle size, and zeta potential. The targeting and imaging ability of FR-targeted liposomes were investigated against the human uterine cervix cancer cell line (HeLa). Furthermore, the cytotoxicity of QD liposomes was evaluated by HeLa cells incubated with FR-targeted QD liposomes, nontargeted QD liposomes, and free QDs. The results showed that FR-targeted QD liposomes were spherically shaped with high fluorescence yield, excellent photochemical stability, good cancer targeting, and minimal cytotoxicity. The average size of FR-targeted fluorescence liposomes was ~105 nm, and their size distribution was rather narrow. After storage at 4 degrees C for 11 months, QD liposomes maintained similar size and did not show any leakage of QDs. FR-targeted CdTe QD liposomes, which can target tumor cells via FR-mediated endocytosis, would become an attractive probe for tumor cell or tissue imaging for a long-time monitoring.
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http://dx.doi.org/10.1080/10611860903013248DOI Listing
August 2009
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