scholarly journals Protein interaction networks at the host–microbe interface in Diaphorina citri , the insect vector of the citrus greening pathogen

2017 ◽  
Vol 4 (2) ◽  
pp. 160545 ◽  
Author(s):  
J. S. Ramsey ◽  
J. D. Chavez ◽  
R. Johnson ◽  
S. Hosseinzadeh ◽  
J. E. Mahoney ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Bacterial Pathogen ◽  
Pathogen Transmission ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Differentially Expressed ◽  
Citrus Greening ◽  
Insect Vector ◽  
Diaphorina Citri ◽  
Citrus Greening Disease

The Asian citrus psyllid ( Diaphorina citri) is the insect vector responsible for the worldwide spread of ‘ Candidatus Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that D. citri transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the D. citri immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host–microbe relationships. Using protein interaction reporter technology, a D. citri haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a D. citri myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with D. citri proteins. These co-evolved protein interaction networks at the host–microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.

scholarly journals Infection Density Dynamics of the Citrus Greening Bacterium “Candidatus Liberibacter asiaticus” in Field Populations of the Psyllid Diaphorina citri and Its Relevance to the Efficiency of Pathogen Transmission to Citrus Plants

2015 ◽  
Vol 81 (11) ◽  
pp. 3728-3736 ◽  
Author(s):  
Rie Ukuda-Hosokawa ◽  
Yasutsune Sadoyama ◽  
Misaki Kishaba ◽  
Takashi Kuriwada ◽  
Hisashi Anbutsu ◽  
...  
Keyword(s):  
Bacterial Pathogen ◽  
Threshold Level ◽  
Pathogen Transmission ◽  
Citrus Greening ◽  
Diaphorina Citri ◽  
Infection Level ◽  
Content Type ◽  
Liberibacter Asiaticus ◽  
Density Dynamics ◽  
Infection Density

ABSTRACTHuanglongbing, or citrus greening, is a devastating disease of citrus plants recently spreading worldwide, which is caused by an uncultivable bacterial pathogen, “CandidatusLiberibacter asiaticus,” and vectored by a phloem-sucking insect,Diaphorina citri. We investigated the infection density dynamics of “Ca. Liberibacter asiaticus” in field populations ofD. citriwith experiments using field-collected insects to address how “Ca. Liberibacter asiaticus” infection density in the vector insect is relevant to pathogen transmission to citrus plants. Of 500 insects continuously collected from “Ca. Liberibacter asiaticus”-infected citrus trees with pathological symptoms in the spring and autumn of 2009, 497 (99.4%) were “Ca. Liberibacter asiaticus” positive. The infections were systemic across head-thorax and abdomen, ranging from 103to 107bacteria per insect. In spring, the infection densities were low in March, at ∼103bacteria per insect, increasing up to 106to 107bacteria per insect in April and May, and decreasing to 105to 106bacteria per insect in late May, whereas the infection densities were constantly ∼106to 107bacteria per insect in autumn. Statistical analysis suggested that several factors, such as insect sex, host trees, and collection dates, may be correlated with “Ca. Liberibacter asiaticus” infection densities in fieldD. citripopulations. Inoculation experiments with citrus seedlings using field-collected “Ca. Liberibacter asiaticus”-infected insects suggested that (i) “Ca. Liberibacter asiaticus”-transmitting insects tend to exhibit higher infection densities than do nontransmitting insects, (ii) a threshold level (∼106bacteria per insect) of “Ca. Liberibacter asiaticus” density inD. citriis required for successful transmission to citrus plants, and (iii)D. citriattaining the threshold infection level transmits “Ca. Liberibacter asiaticus” to citrus plants in a stochastic manner. These findings provide valuable insights into understanding, predicting, and controlling this notorious citrus pathogen.

scholarly journals Functional module detection through integration of single-cell RNA sequencing data with protein–protein interaction networks

2019 ◽  
Author(s):  
Florian Klimm ◽  
Enrique M. Toledo ◽  
Thomas Monfeuga ◽  
Fang Zhang ◽  
Charlotte M. Deane ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Protein Protein Interaction ◽  
Single Cell Rna Sequencing ◽  
Protein Protein Interaction Networks

AbstractRecent advances in single-cell RNA sequencing (scRNA-seq) have allowed researchers to explore transcriptional function at a cellular level. In this study, we present scPPIN, a method for integrating single-cell RNA sequencing data with protein–protein interaction networks (PPINs) that detects active modules in cells of different transcriptional states. We achieve this by clustering RNA-sequencing data, identifying differentially expressed genes, constructing node-weighted PPINs, and finding the maximum-weight connected subgraphs with an exact Steiner-tree approach. As a case study, we investigate RNA-sequencing data from human liver spheroids but the techniques described here are applicable to other organisms and tissues. scPPIN allows us to expand the output of differential expressed genes analysis with information from protein interactions. We find that different transcriptional states have different subnetworks of the PPIN significantly enriched which represent biological pathways. In these pathways, scPPIN also identifies proteins that are not differentially expressed but have a crucial biological function (e.g., as receptors) and therefore reveals biology beyond a standard differentially expressed gene analysis.

scholarly journals Functional module detection through integration of single-cell RNA sequencing data with protein–protein interaction networks

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Florian Klimm ◽  
Enrique M. Toledo ◽  
Thomas Monfeuga ◽  
Fang Zhang ◽  
Charlotte M. Deane ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Protein Protein Interaction ◽  
Single Cell Rna Sequencing ◽  
Protein Protein Interaction Networks

Abstract Background Recent advances in single-cell RNA sequencing have allowed researchers to explore transcriptional function at a cellular level. In particular, single-cell RNA sequencing reveals that there exist clusters of cells with similar gene expression profiles, representing different transcriptional states. Results In this study, we present scPPIN, a method for integrating single-cell RNA sequencing data with protein–protein interaction networks that detects active modules in cells of different transcriptional states. We achieve this by clustering RNA-sequencing data, identifying differentially expressed genes, constructing node-weighted protein–protein interaction networks, and finding the maximum-weight connected subgraphs with an exact Steiner-tree approach. As case studies, we investigate two RNA-sequencing data sets from human liver spheroids and human adipose tissue, respectively. With scPPIN we expand the output of differential expressed genes analysis with information from protein interactions. We find that different transcriptional states have different subnetworks of the protein–protein interaction networks significantly enriched which represent biological pathways. In these pathways, scPPIN identifies proteins that are not differentially expressed but have a crucial biological function (e.g., as receptors) and therefore reveals biology beyond a standard differential expressed gene analysis. Conclusions The introduced scPPIN method can be used to systematically analyse differentially expressed genes in single-cell RNA sequencing data by integrating it with protein interaction data. The detected modules that characterise each cluster help to identify and hypothesise a biological function associated to those cells. Our analysis suggests the participation of unexpected proteins in these pathways that are undetectable from the single-cell RNA sequencing data alone. The techniques described here are applicable to other organisms and tissues.

Proteomic Polyphenism in Color Morphotypes of Diaphorina citri, Insect Vector of Citrus Greening Disease

2021 ◽  
Author(s):  
Saeed Hosseinzadeh ◽  
Steven A. Higgins ◽  
John Ramsey ◽  
Kevin Howe ◽  
Michael Griggs ◽  
...  
Keyword(s):  
Citrus Greening ◽  
Insect Vector ◽  
Diaphorina Citri ◽  
Citrus Greening Disease ◽  
Greening Disease

scholarly journals Prenatal testosterone triggers long-term behavioral changes in male zebra finches: unravelling the neurogenomic mechanisms

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alexandra B. Bentz ◽  
Chad E. Niederhuth ◽  
Laura L. Carruth ◽  
Kristen J. Navara
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Differentially Expressed ◽  
Zebra Finches ◽  
Hub Genes ◽  
Prenatal Testosterone ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

Abstract Background Maternal hormones, like testosterone, can strongly influence developing offspring, even generating long-term organizational effects on adult behavior; yet, the mechanisms facilitating these effects are still unclear. Here, we experimentally elevated prenatal testosterone in the eggs of zebra finches (Taeniopygia guttata) and measured male aggression in adulthood along with patterns of neural gene expression (RNA-seq) and DNA methylation (MethylC-Seq) in two socially relevant brain regions (hypothalamus and nucleus taenia of the amygdala). We used enrichment analyses and protein-protein interaction networks to find candidate processes and hub genes potentially affected by the treatment. We additionally identified differentially expressed genes that contained differentially methylated regions. Results We found that males from testosterone-injected eggs displayed more aggressive behaviors compared to males from control eggs. Hundreds of genes were differentially expressed, particularly in the hypothalamus, including potential aggression-related hub genes (e.g., brain derived neurotrophic factor). There were also enriched processes with well-established links to aggressive phenotypes (e.g., somatostatin and glutamate signaling). Furthermore, several highly connected genes identified in protein-protein interaction networks also showed differential methylation, including adenylate cyclase 2 and proprotein convertase 2. Conclusions These results highlight genes and processes that may play an important role in mediating the effects of prenatal testosterone on long-term phenotypic outcomes, thereby providing insights into the molecular mechanisms that facilitate hormone-mediated maternal effects.

scholarly journals Biology and Management of the Asian Citrus Psyllid, Diaphorina citri Kuwayama, in Florida Citrus

EDIS ◽  
2007 ◽  
Vol 2007 (11) ◽  
Author(s):  
Michael E. Rogers ◽  
Philip A. Stansly
Keyword(s):  
Integrated Pest Management ◽  
Pest Management ◽  
Pathogen Transmission ◽  
Citrus Greening ◽  
Asian Citrus Psyllid ◽  
Diaphorina Citri ◽  
Feeding Damage ◽  
Citrus Greening Disease ◽  
Greening Disease ◽  
Florida Citrus

ENY-739, a 7-page illustrated fact sheet by Michael E. Rogers and Philip A. Stansly, provides information about the biology of this vector of citrus greening disease to aid growers in implementing integrated pest management (IPM) practices for suppressing the population in citrus-growing areas of Florida. It includes sections on identification and biology, psyllid feeding damage, pathogen transmission, management, and selected references. Published by the UF Department of Entomology and Nematology, June 2006.

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