Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes.

Background: Compatibility between plant parasites and their hosts is genetically determined {Citation}both interacting organisms. For example, plants may carry resistance (R) genes or deploy chemical defences. Aphid saliva contains many proteins that are secreted into host tissues.

Correction: Proteomic profiling of cereal aphid saliva reveals both ubiquitous and adaptive secreted proteins.

[This corrects the article DOI: 10.1371/journal.pone.

Establishing the extent of pesticide contamination in Irish agricultural soils.

To establish meaningful and sustainable policy directives for sustainable pesticide use in agriculture, baseline knowledge of pesticide levels in soils is required. To address this, five pesticides and one metabolite widely used in Irish agriculture and five neonicotinoid compounds pesticides were screened from soils from 25 fields. These sites represented a diversity of soil and land use types.

The boundary of life and death: changes in mitochondrial and cytosolic proteomes associated with programmed cell death of suspension culture cells.

Introduction: Despite the critical role of programmed cell death (PCD) in plant development and defense responses, its regulation is not fully understood. It has been proposed that mitochondria may be important in the control of the early stages of plant PCD, but the details of this regulation are currently unknown.

Methods: We used cell suspension culture, a model system that enables induction and precise monitoring of PCD rates, as well as chemical manipulation of this process to generate a quantitative profile of the alterations in mitochondrial and cytosolic proteomes associated with early stages of plant PCD induced by heat stress.

Signatures of Adaptation, Constraints, and Potential Redundancy in the Canonical Immune Genes of a Key Pollinator.

All organisms require an immune system to recognize, differentiate, and defend against pathogens. From an evolutionary perspective, immune systems evolve under strong selective pressures exerted by fast-evolving pathogens. However, the functional diversity of the immune system means that different immune components and their associated genes may evolve under varying forms of selection.

Investigating the effects of glyphosate on the bumblebee proteome and microbiota.

Glyphosate is one of the most widely used herbicides globally. It acts by inhibiting an enzyme in an aromatic amino acid synthesis pathway specific to plants and microbes, leading to the view that it poses no risk to other organisms. However, there is growing concern that glyphosate is associated with health effects in humans and an ever-increasing body of evidence that suggests potential deleterious effects on other animals including pollinating insects such as bees.

Low-temperature exposure has immediate and lasting effects on the stress tolerance, chemotaxis and proteome of entomopathogenic nematodes.

Temperature is one of the most important factors affecting soil organisms, including the infective stages of parasites and entomopathogenic nematodes, which are important biological control agents. We investigated the response of 2 species of entomopathogenic nematodes to different storage regimes: cold (9°C), culture temperature (20°C) and temperature swapped from 9 to 20°C. For , cold storage had profound effects on chemotaxis, stress tolerance and protein expression that were retained in temperature-swapped individuals.

Assessing availability of European plant protection product data: an example evaluating basic area treated.

Besides the benefits of plant protection products (PPPs) for agricultural production, there is an increasing acknowledgement of the associated potential environmental risks. Here, we examine the feasibility of summarizing the extent of PPP usage at the country level, using Ireland as a case study, as well as at the European level. We used the area over which PPPs are applied (basic area) as an example variable that is relevant to initially assess the geographic extent of environmental risk.

The effect of temperature conditioning (9°C and 20°C) on the proteome of entomopathogenic nematode infective juveniles.

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.

Exposure to the secretome alters the proteome and secondary metabolite production of .

The fungal pathogen is frequently cultured from the sputum of cystic fibrosis (CF) patients along with the bacterium secretes a range of secondary metabolites, and one of these, gliotoxin, has inhibitory effects on the host immune response. The effect of culture filtrate (CuF) on fungal growth and gliotoxin production was investigated. Exposure of hyphae to cells induced increased production of gliotoxin and a decrease in fungal growth.

Global protein responses of multidrug resistance plasmid-containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin.

Objectives: This study compared the proteomics of Escherichia coli containing the multidrug resistance plasmid pEK499 under antimicrobial stress and with no antimicrobial.

Methods: We utilised mass spectrometry-based proteomics to compare the proteomes of the bacteria and plasmid under antimicrobial stress and no antimicrobial.

Results: Our analysis identified statistically significant differentially abundant (SSDA) proteins common to groups exposed to the β-lactam antimicrobials but not ciprofloxacin, indicating a β-lactam stress response to exposure from this class of drugs, irrespective of β-lactam resistance or susceptibility.

Simultaneous determination of pesticides from soils: a comparison between QuEChERS extraction and Dutch mini-Luke extraction methods.

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 variety of soil types. However, due to their complex nature, the effective extraction of pesticide residues from soil matrices can present challenges to pesticide detection and quantification.

Patient Experience and Satisfaction With Immediate Sequential and Delayed Sequential Bilateral Cataract Surgery.

Purpose: In bilaterally pseudophakic patients who received immediate or delayed sequential bilateral cataract surgery (ISBCS or DSBCS), we sought to determine patient experience, particularly related to the loss of opportunity to modify the surgical plan for the second eye.

Design: Cross-sectional.

Methods: Patients who received ISBCS (n = 1818) and DSBCS (n = 1818) in the Kaiser Permanente Northern California system between 2017 and 2019 who actively used the electronic patient portal were randomly selected and sent a survey link.

Bacterial Interactions with in the Immunocompromised Lung.

The immunocompromised airways are susceptible to infections caused by a range of pathogens which increases the opportunity for polymicrobial interactions to occur. and are the predominant causes of pulmonary infection for individuals with respiratory disorders such as cystic fibrosis (CF). The spore-forming fungus , is most frequently isolated with , and co-infection results in poor outcomes for patients.

Development and Validation of Machine Learning Models: Electronic Health Record Data To Predict Visual Acuity After Cataract Surgery.

Background: To develop predictive models of final corrected distance visual acuity (CDVA) following cataract surgery using machine learning algorithms and electronic health record data.

Methods: In this predictive modeling study we used decision tree, random forest, and gradient boosting. We included the first surgical eye of 64,768 members of Kaiser Permanente Northern California who underwent cataract surgery from June 1, 2010 through May 31, 2015.

Endophthalmitis Prophylaxis Failures in Patients Injected With Intracameral Antibiotic During Cataract Surgery.

Purpose: To estimate the association of cefuroxime and moxifloxacin in relation to the occurrence of endophthalmitis following phacoemulsification cataract surgery.

Design: Retrospective clinical cohort study.

Methods: We studied patients with noncomplex phacoemulsification cataract surgery in Kaiser Permanente Northern California during 2014-2019.

Visual outcomes after cataract surgery: topical nonsteroidal anti-inflammatory drug prophylaxis compared with prednisolone.

Purpose: To compare visual outcomes in patients without a history of macular edema after phacoemulsification using combination topical nonsteroidal anti-inflammatory drug plus prednisolone with prednisolone alone.

Setting: Kaiser Permanente Northern California, USA.

Design: Retrospective cohort study.

Intraocular Pressure Reduction after Phacoemulsification: A Matched Cohort Study.

Purpose: Phacoemulsification has been linked to lowered intraocular pressure (IOP) in patients with glaucoma, ocular hypertension, anatomic narrow angles, and in glaucoma suspects, but the magnitude of change has varied.

Design: Retrospective cohort study.

Participants: Patients with glaucoma treated from June 2010 through May 2015 who underwent phacoemulsification (surgical group) were matched to patients who did not (nonsurgical group) for age, gender, type of glaucoma, baseline IOP, and number and type of glaucoma medications.

The Secretome Alters the Proteome of to Stimulate Bacterial Growth: Implications for Co-infection.

Individuals with cystic fibrosis are susceptible to co-infection by and Despite the persistence of in the cystic fibrosis lung eventually predominates as the primary pathogen. Several factors are likely to facilitate colonization in the airways, including alterations to the microbial environment. The cystic fibrosis airways are hypoxic, nitrate-rich environments, and the sputum has higher amino acid concentrations than normal.

Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2).

Development of small molecule inhibitors of protein-protein interactions (PPIs) is hampered by our poor understanding of the druggability of PPI target sites. Here, we describe the combined application of alanine-scanning mutagenesis, fragment screening, and FTMap computational hot spot mapping to evaluate the energetics and druggability of the highly charged PPI interface between Kelch-like ECH-associated protein 1 (KEAP1) and nuclear factor erythroid 2 like 2 (Nrf2), an important drug target. FTMap identifies four binding energy hot spots at the active site.

The salivary gland proteome of root-galling grape phylloxera (Daktulosphaira vitifoliae Fitch) feeding on Vitis spp.

The successful parasitisation of a plant by a phytophagous insect is dependent on the delivery of effector molecules into the host. Sedentary gall forming insects, such as grape phylloxera (Daktulosphaira vitifoliae Fitch, Phylloxeridae), secrete multiple effectors into host plant tissues that alter or modulate the cellular and molecular environment to the benefit of the insect. The identification and characterisation of effector proteins will provide insight into the host-phylloxera interaction specifically the gall-induction processes and potential mechanisms of plant resistance.

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

Background: Understanding the mechanisms by which organisms adapt to unfavourable conditions is a fundamental question in ecology and evolutionary biology. One such mechanism is diapause, a period of dormancy typically found in nematodes, fish, crustaceans and insects. This state is a key life-history event characterised by arrested development, suppressed metabolism and increased stress tolerance and allows an organism to avoid prolonged periods of harsh and inhospitable environmental conditions.

Fungicides, herbicides and bees: A systematic review of existing research and methods.

Bees and the pollination services they deliver are beneficial to both food crop production, and for reproduction of many wild plant species. Bee decline has stimulated widespread interest in assessing hazards and risks to bees from the environment in which they live. While there is increasing knowledge on how the use of broad-spectrum insecticides in agricultural systems may impact bees, little is known about effects of other pesticides (or plant protection products; PPPs) such as herbicides and fungicides, which are used more widely than insecticides at a global scale.

The role of the liver in the migration of parasites of global significance.

Many parasites migrate through different tissues during their life-cycle, possibly with the aim to enhance their fitness. This is true for species of three parasite genera of global importance, Ascaris, Schistosoma and Plasmodium, which cause significant global morbidity and mortality. Interestingly, these parasites all incorporate the liver in their life-cycle.