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Papers by James Carolan

Additional file 7: Table S6. Enriched Gene Ontology terms in genes coding for haemolymph-associat... more Additional file 7: Table S6. Enriched Gene Ontology terms in genes coding for haemolymph-associated differentially expressed proteins during the bumblebee queen life cycle stages.

Additional file 1: Table S1. ANOVA statistics (P- and q-values) for all proteins (Benjamini-Hochb... more Additional file 1: Table S1. ANOVA statistics (P- and q-values) for all proteins (Benjamini-Hochberg FDRâ

PLOS ONE

Entomopathogenic nematodes (EPN) of the genera Steinernema and Heterorhabditis are parasites whic... more Entomopathogenic nematodes (EPN) of the genera Steinernema and Heterorhabditis are parasites which kill and reproduce within insects. While both have life cycles centred around their developmentally arrested, nonfeeding and stress tolerant infective juvenile (IJ) stage, they are relatively distantly related. These IJs are promising biocontrol agents, and their shelf life and stress tolerance may be enhanced by storage at low temperatures. The purpose of this study was to investigate how the proteome of the IJs of two distantly related EPN species is affected by storage at 9°C (for up to 9 weeks) and 20°C (for up to 6 weeks), using label-free quantitative proteomics. Overall, more proteins were detected in S. carpocapsae (2422) than in H. megidis (1582). The S. carpocapsae proteome was strongly affected by temperature, while the H. megidis proteome was affected by both time and temperature. The proteins which increased in abundance to the greatest extent in S. carpocapsae IJs after c...

MOESM1 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

Additional file 1: Table S1. The 129 proteins identified from the haemolymph of unmated and mated... more Additional file 1: Table S1. The 129 proteins identified from the haemolymph of unmated and mated queens prior to, during and after diapause.

MOESM2 of The liver proteome in a mouse model for Ascaris suum resistance and susceptibility: evidence for an altered innate immune response

Additional file 2: Table S4. Proteins identified from the liver left lobes of C57BL/6J and CBA/Ca... more Additional file 2: Table S4. Proteins identified from the liver left lobes of C57BL/6J and CBA/Ca mice with and without Ascaris infection. Table S5. t-test (P

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Background: The shift from solitary to social behavior is one of the major evolutionary transitio... more Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Microorganisms, 2021

The immunocompromised airways are susceptible to infections caused by a range of pathogens which ... more The immunocompromised airways are susceptible to infections caused by a range of pathogens which increases the opportunity for polymicrobial interactions to occur. Pseudomonas aeruginosa and Staphylococcus aureus are the predominant causes of pulmonary infection for individuals with respiratory disorders such as cystic fibrosis (CF). The spore-forming fungus Aspergillus fumigatus, is most frequently isolated with P. aeruginosa, and co-infection results in poor outcomes for patients. It is therefore clinically important to understand how these pathogens interact with each other and how such interactions may contribute to disease progression so that appropriate therapeutic strategies may be developed. Despite its persistence in the airways throughout the life of a patient, A. fumigatus rarely becomes the dominant pathogen. In vitro interaction studies have revealed remarkable insights into the molecular mechanisms that drive agonistic and antagonistic interactions that occur between A...

Simultaneous determination of pesticides from soils: A comparison between QuEChERS extraction and Dutch Mini-Luke extraction methods

Analytical Methods, 2021

The expanding nature of the agricultural sector has fuelled the intensification of plant protecti... more The expanding nature of the agricultural sector has fuelled the intensification of plant protection products usage, including pesticides. These pesticides may persist in soils, necessitating their accurate determination in a...

Journal of Natural History, 2018

Bombus terrestris and Bombus pratorum were found for the first time in the Azores in 2005. Until ... more Bombus terrestris and Bombus pratorum were found for the first time in the Azores in 2005. Until then Bombus ruderatus was the only bumblebee species known from this group of nine mid-Atlantic islands. The identity of B. terrestris was confirmed by DNA barcoding.

Horticulturae, 2020

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of ... more Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognitio...

In silico Characterization of a Candidate Protein from Aphid Gelling Saliva with Potential for Aphid Control in Plants

Protein & Peptide Letters, 2019

Background: Sheath or gelling saliva, secreted during feeding by aphids, is a hard material that ... more Background: Sheath or gelling saliva, secreted during feeding by aphids, is a hard material that supports the piercing mouthparts and remains in the plant after feeding. Solidification or gelling of the saliva might be due to the composition of amino acids in the constituent proteins, many of which probably interact with plant defenses. Objective : The complete complement of proteins in the gelling saliva are still unknown, although one sheath protein (SHP) has previously been identified as a potential candidate protein to control aphid feeding, but its structure and its physiochemical role remains obscure. The current study provides structural information and biochemical properties of the aphid sheath protein. Methods: Sheath protein encoding gene was amplified from cDNA of the pea aphid (Acyrthosiphon pisum) through PCR using specific gene primers. Sequence was in silico characterized by using EXPASY, Berkeley Drosophila Genome Project (BDGP) Neural Network Promoter Prediction, Bi...

Parasites & Vectors, 2019

Background: Ascariasis is a neglected tropical disease that affects 800 million people worldwide.... more Background: Ascariasis is a neglected tropical disease that affects 800 million people worldwide. Whereas most people only experience light worm burden, some people experience heavy worm burdens even after several rounds of chemotherapy, a phenomenon known as predisposition. Such heavy infections are associated with more severe symptoms and increased chronic morbidity. In order to investigate potential mechanisms that may explain the observed predisposition, we infected mice with the porcine ascarid Ascaris suum using an established mouse model with two different mouse strains, where the C57BL/6J strain is more susceptible to infection and therefore a model for heavy infection and the CBA/Ca strain is more resistant and thus a model for light infection. At day 7 post-infection we investigated the liver proteome, using shotgun mass spectrometry, of both infected and control mice of each strain. We identified intrinsic differences, between the two mouse strains, in both oxidative phosphorylation proteins and proteins involved in retinol metabolism. Additionally, we found differences between the two mouse strains in activation of the complement system, where the CBA/Ca strain has higher protein abundances for lectin pathway proteins and the C57BL/6J strain has higher protein abundances for complement inhibiting proteins. The CBA/Ca strain had a higher abundance of proteins involved in the activation of the complement cascade via the lectin pathway. In contrast, the C57BL/6J strain demonstrated a higher abundance of proteins involved in arresting the complement pathway. We observed clear differences between the two mouse strains both intrinsically and under infection.

Genome biology and evolution, Jun 1, 2018

Effector proteins play crucial roles in plant-parasite interactions by suppressing plant defenses... more Effector proteins play crucial roles in plant-parasite interactions by suppressing plant defenses and hijacking plant physiological responses to facilitate parasite invasion and propagation. Although effector proteins have been characterized in many microbial plant pathogens, their nature and role in adaptation to host plants are largely unknown in insect herbivores. Aphids rely on salivary effector proteins injected into the host plants to promote phloem sap uptake. Therefore, gaining insight into the repertoire and evolution of aphid effectors is key to unveiling the mechanisms responsible for aphid virulence and host plant specialization. With this aim in mind, we assembled catalogues of putative effectors in the legume specialist aphid, Acyrthosiphon pisum, using transcriptomics and proteomics approaches. We identified 3,603 candidate effector genes predicted to be expressed in A. pisum salivary glands (SGs), and 740 of which displayed up-regulated expression in SGs in compariso...

Journal of insect physiology, Jan 19, 2017

Varroa destructor is a haemophagous ectoparasite of honeybees and is considered a major causal ag... more Varroa destructor is a haemophagous ectoparasite of honeybees and is considered a major causal agent of colony losses in Europe and North America. Although originating in Eastern Asia where it parasitizes Apis cerana, it has shifted hosts to the western honeybee Apis mellifera on which it has a greater deleterious effect on the individual and colony level. To investigate this important host-parasite interaction and to determine whether Varroa causes different effects on different castes we conducted a label free quantitative proteomic analysis of Varroa-parasitized and non-parasitized drone and worker Apis mellifera pupae. 1195 proteins were identified in total, of which 202 and 250 were differentially abundant in parasitized drone and worker pupae, respectively. Both parasitized drone and worker pupae displayed reduced abundance in proteins associated with the cuticle, lipid transport and innate immunity. Proteins involved in metabolic processes were more abundant in both parasitiz...

Journal of insect physiology, Jul 1, 2017

Galleria mellonella is a well-established model species regularly employed in the study of the in... more Galleria mellonella is a well-established model species regularly employed in the study of the insect immune response at cellular and humoral levels to investigate fungal pathogenesis and biocontrol agents. A cellular and proteomic analysis of the effect of culture filtrate of three entomopathogenic fungi (EPF) species on the immune system of G. mellonella was performed. Treatment with Beauveria caledonica and Metarhizium anisopliae 96h culture filtrate facilitated a significantly increased yeast cell density in larvae (3-fold and 3.8-fold, respectively). Larvae co-injected with either M. anisopliae or B. caledonica culture filtrate and Candida albicans showed significantly increased mortality. The same was not seen for larvae injected with Beauveria bassiana filtrate. Together these results suggest that B. caledonica and M. anisopliae filtrate are modulating the insect immune system allowing a subsequent pathogen to proliferate. B. caledonica and M. anisopliae culture filtrates imp...

PLoS neglected tropical diseases, Aug 1, 2016

The helminth Ascaris causes ascariasis in both humans and pigs. Humans, especially children, expe... more The helminth Ascaris causes ascariasis in both humans and pigs. Humans, especially children, experience significant morbidity including respiratory complications, growth deficits and intestinal obstruction. Given that 800 million people worldwide are infected by Ascaris, this represents a significant global public health concern. The severity of the symptoms and associated morbidity are related to the parasite burden and not all hosts are infected equally. While the pathology of the disease has been extensively examined, our understanding of the molecular mechanisms underlying resistance and susceptibility to this nematode infection is poor. In order to investigate host differences associated with heavy and light parasite burden, an experimental murine model was developed utilising Ascaris-susceptible and -resistant mice strains, C57BL/6J and CBA/Ca, respectively, which experience differential burdens of migratory Ascaris larvae in the host lungs. Previous studies identified the liv...

Management of Insect Pests to Agriculture, 2016

The physical interface between a phloem-feeding insect and its host plant is a single cell buried... more The physical interface between a phloem-feeding insect and its host plant is a single cell buried deep within the plant tissue. As such, the molecular interactions between these notorious agricultural pests and the crop plants upon which they feed are diffi cult to study. 'Omic' technologies have proved crucial in revealing some of the fascinating detail of the molecular interplay between these partners. Here we review the role of proteomics in identifying putative components of the secreted saliva of phloem-feeding insects, particularly aphids, and discuss the limited knowledge concerning the function of these proteins.

Genome Biology, 2015

Supplementary information, statistics and verification of Bombus terrestris genome 2-3 Statistics... more Supplementary information, statistics and verification of Bombus terrestris genome 2-3 Statistics of repetitive elements in the bumblebee genomes 4 Details of gene model predictions for B. terrestris and B. impatiens 5-7 Protein domain information, including unique, expanded/contracted domains and arrangements 8-10 Bumblebee Juvenile hormone binding proteins, a phylogenetic tree of these proteins, and a map of these proteins in B. terrestris 11 Biogenic amine receptors 12-18 Bumblebee neuropeptide sequences, with immature neuropeptide, cleavage site, and signal peptide predictions 19 Differences in corazonin between B. terrestris and B. impatiens 20 Neuropeptide gene suites across various arthropods 21-22 Halloween gene (p450) table and phylogenetic tree 23-29 Table of B. terrestris Odorant Receptors 30-61 B. terrestris Odorant Receptor predicted proteins 62-65 Odorant receptor phylogenetic tree 66 Table of B. terrestris Gustatory Receptors 67-71 B. terrestris Gustatory Receptor predicted proteins 72-73 Gustatory receptor phylogenetic tree 74 Table of B. terrestris Ionotrophic Receptors 75-85 B. terrestris Ionotrophic Receptor predicted proteins 86-87 Ionotrophic receptor phylogenetic tree 88 Table of B. terrestris Odorant Binding Proteins 88-90 B. terrestris Odorant Binding Proteins predicted proteins 91 Odorant Binding Proteins phylogenetic tree 92-93 Hypothetical proteins identified within B. terrestris queen hemolymph 94 RNAi overview and phylogenetic tree of insect SID proteins 95-97 DNA methylation genes, functional characterization of methylated genes, genome wide distribution of methylation, and genomic methylation levels 98-99 Sample data and analyses of B. impatiens SNPs mapped to the genome

Current biology : CB, Jan 4, 2015

Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, ... more 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...

PLoS Biology, 2010

Aphids are important agricultural pests and also biological models for studies of insect-plant in... more Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.