| 1. |
- Ahearn, Thomas U., et al.
(author)
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Common variants in breast cancer risk loci predispose to distinct tumor subtypes
- 2022
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In: Breast Cancer Research. - : Springer Nature. - 1465-5411 .- 1465-542X. ; 24:1
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Journal article (peer-reviewed)abstract
- BackgroundGenome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear.MethodsAmong 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes.ResultsEighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions.ConclusionThis report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
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| 2. |
- Kapoor, Pooja Middha, et al.
(author)
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Combined associations of a polygenic risk score and classical risk factors with breast cancer risk
- 2021
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 113:3, s. 329-337
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Journal article (peer-reviewed)abstract
- We evaluated the joint associations between a new 313-variant PRS (PRS313) and questionnaire-based breast cancer risk factors for women of European ancestry, using 72 284 cases and 80 354 controls from the Breast Cancer Association Consortium. Interactions were evaluated using standard logistic regression and a newly developed case-only method for breast cancer risk overall and by estrogen receptor status. After accounting for multiple testing, we did not find evidence that per-standard deviation PRS313 odds ratio differed across strata defined by individual risk factors. Goodness-of-fit tests did not reject the assumption of a multiplicative model between PRS313 and each risk factor. Variation in projected absolute lifetime risk of breast cancer associated with classical risk factors was greater for women with higher genetic risk (PRS313 and family history) and, on average, 17.5% higher in the highest vs lowest deciles of genetic risk. These findings have implications for risk prevention for women at increased risk of breast cancer.
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| 3. |
- Middha, Pooja K., et al.
(author)
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A genome-wide gene-environment interaction study of breast cancer risk for women of European ancestry
- 2023
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In: Breast Cancer Research. - : BioMed Central (BMC). - 1465-5411 .- 1465-542X. ; 25:1
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Journal article (peer-reviewed)abstract
- Background Genome-wide studies of gene-environment interactions (GxE) may identify variants associated with disease risk in conjunction with lifestyle/environmental exposures. We conducted a genome-wide GxE analysis of similar to 7.6 million common variants and seven lifestyle/environmental risk factors for breast cancer risk overall and for estrogen receptor positive (ER +) breast cancer. Methods Analyses were conducted using 72,285 breast cancer cases and 80,354 controls of European ancestry from the Breast Cancer Association Consortium. Gene-environment interactions were evaluated using standard unconditional logistic regression models and likelihood ratio tests for breast cancer risk overall and for ER + breast cancer. Bayesian False Discovery Probability was employed to assess the noteworthiness of each SNP-risk factor pairs. Results Assuming a 1 x 10(-5) prior probability of a true association for each SNP-risk factor pairs and a Bayesian False Discovery Probability < 15%, we identified two independent SNP-risk factor pairs: rs80018847(9p13)-LINGO2 and adult height in association with overall breast cancer risk (ORint = 0.94, 95% CI 0.92-0.96), and rs4770552(13q12)-SPATA13 and age at menarche for ER + breast cancer risk (ORint = 0.91, 95% CI 0.88-0.94). Conclusions Overall, the contribution of GxE interactions to the heritability of breast cancer is very small. At the population level, multiplicative GxE interactions do not make an important contribution to risk prediction in breast cancer.
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| 4. |
- Stenberg, Johan A, et al.
(author)
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When is it biological control? A framework of definitions, mechanisms, and classifications
- 2021
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In: Journal of Pest Science. - : Springer Science and Business Media LLC. - 1612-4758 .- 1612-4766. ; 94, s. 665-676
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Research review (peer-reviewed)abstract
- Biological control, or biocontrol, is the exploitation of living agents (incl. viruses) to combat pestilential organisms (incl. pathogens, pests, and weeds) for diverse purposes to provide human benefits. Thus, during the last century the practices and concepts involved have evolved in separate streams associated with distinct scientific and taxonomic disciplines. In parallel developments, there have been increasing references to biological control in industrial contexts and legislation, resulting in conceptual and terminological disintegration. The aim of this paper is to provide a global conceptual and terminological platform that facilitates future development of the field. We review use of previously suggested terms in key fields (e.g., phytopathology, entomology, and weed science), eliminate redundant terminology, identify three principles that should underpin the concept, and then present a new framework for biological control, rooted in seminal publications. The three principles establish that (1) only living agents can mediate biological control, (2) biological control always targets a pest, directly or indirectly, and (3) all biocontrol methods can be classified in four main categories depending on whether resident agents are utilized, with or without targeted human intervention (conservation biological control and natural biological control, respectively) or agents are added for permanent or temporary establishment (classical biological control and augmentative biological control, respectively). Correct identification of what is, and is not, biological control can help efforts to understand and optimize biological pest control for human and environmental benefits. The new conceptual framework may contribute to more uniform and appropriate regulatory approaches to biological control, and more efficient authorization and application of biocontrol products.
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| 5. |
- Alsanius, Beatrix, et al.
(author)
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The power of light from a non-phototrophic perspective: a phyllosphere dilemma
- 2024
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In: Frontiers in Photobiology. - 2813-8228. ; 2
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Journal article (peer-reviewed)abstract
- Plants and crop stands are considered holobionts, colonized by both autotrophic and by non-phototrophic heterotrophic microbiota. The dilemma in the exisiting body of studies is that the focus is primarily directed towards environmental specificties relevant for phototrophic organisms (predominantly plants), but does not take into account non-phototrophs. By definition, non-phototrophic heterotrophic bacteria do not use light as an energy source. Light energy and wavelength are rather used as a signal that can provoke shifts in both their metabolism and microbial lifestyle. Reaction and recovery time can vary between organisms and is dependent on the organism’s physiological stage. The length of the lighting event affects the energy an organism is exposed to. We argue that to obtain a deeper and more distinct understanding of light exposure (irradiance, exposure length), quantity (light intensity), and quality (wavelength/spectral distribution, bandwidth at full-width half-maximum) related mechanisms on non-phototrophic bacteria in the phyllosphere, the light environment needs to be further strictly characterized. This includes information on the actual energy hitting planktonic or sessile non-phototrophic bacteria resident on and inside plants aboveground. Mapping the light environment in ecosystems aids in unraveling light-phyllosphere interactions and strengthens their transdisciplinary character. This issue is fundamental in order to revisit and repeat others’ experimental approaches and findings but also to be able to translate findings into further action.
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| 6. |
- Andreadis, Stefanos, et al.
(author)
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Survey of arthropod assemblages responding to live yeasts in an organic apple orchard
- 2015
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In: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 3
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Journal article (peer-reviewed)abstract
- Associations between yeasts and insect herbivores are widespread, and these interkingdom interactions play a crucial role in yeast and insect ecology and evolution. We report a survey of insect attraction to live yeast from a community ecology perspective. In the summer of 2013 we screened live yeast cultures of Metschnikowia pulcherrima, M. andauensis, M. hawaiiensis, M. lopburiensis, and Cryptococcus tephrensis in an organic apple orchard. More than 3000 arthropods from 3 classes, 15 orders, and 93 species were trapped; ca. 79% of the trapped specimens were dipterans, of which 43% were hoverflies (Syrphidae), followed by Sarcophagidae, Phoridae, Lauxaniidae, Cecidomyidae, Drosophilidae, and Chironomidae. Traps baited with M. pulcherrima, M. andauensis, and C. tephrensis captured typically 2.4 times more specimens than control traps; traps baited with M. pulcherrima, M. hawaiiensis, M. andauensis, M. lopburiensis, and C. tephrensis were more species-rich than unbaited control traps. We conclude that traps baited with live yeasts of the genera Metschnikowia and Cryprococcus are effective attractants and therefore of potential value for pest control. Yeast-based monitoring or attract-and-kill techniques could target pest insects or enhance the assemblage of beneficial insects. Manipulation of insect behavior through live yeast cultures should be further explored for the development of novel plant protection techniques.
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| 7. |
- Becher, Paul, et al.
(author)
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A Conserved Dedicated Olfactory Circuit for Detecting Harmful Microbes in Drosophila
- 2012
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In: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 151, s. 1345-1357
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Journal article (peer-reviewed)abstract
- Flies, like all animals, need to find suitable and safe food. Because the principal food source for Drosophila melanogaster is yeast growing on fermenting fruit, flies need to distinguish fruit with safe yeast from yeast covered with toxic microbes. We identify a functionally segregated olfactory circuit in flies that is activated exclusively by geosmin. This microbial odorant constitutes an ecologically relevant stimulus that alerts flies to the presence of harmful microbes. Geosmin activates only a single class of sensory neurons expressing the olfactory receptor Or56a. These neurons target the DA2 glomerulus and connect to projection neurons that respond exclusively to geosmin. Activation of DA2 is sufficient and necessary for aversion, overrides input from other olfactory pathways, and inhibits positive chemotaxis, oviposition, and feeding. The geosmin detection system is a conserved feature in the genus Drosophila that provides flies with a sensitive, specific means of identifying unsuitable feeding and breeding sites.
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| 8. |
- Becher, Paul
(author)
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Current knowledge of interactions between Drosophila suzukii and microbes, and their potential utility for pest management
- 2016
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In: Journal of Pest Science. - : Springer Science and Business Media LLC. - 1612-4758 .- 1612-4766. ; 89, s. 621-630
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Research review (peer-reviewed)abstract
- Insects exhibit complex symbiotic interactions with microorganisms, which provide an opportunity for developing novel pest management strategies. Closely related to Drosophila melanogaster, which is commonly used as a model to explore insect-microbe interactions, Drosophila suzukii is an important invasive insect pest of fruit crops in the Americas and Europe. We provide an overview of Drosophila-microbe interactions and review current research with D. suzukii. Recent studies revealed yeast and bacterial species associated with D. suzukii flies, fly guts and infested fruit. The ecological importance of these insect-microbe interactions is under investigation. Microbes have a strong impact on insect physiology and D. suzukii responds both positively and aversively to microbial volatiles. We highlight potential pest management strategies that take advantage of D. suzukii-microbe ecology, including improved monitoring as well as management using behavioural manipulation, phagostimulants and biotechnology.
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| 9. |
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| 10. |
- Becher, Paul
(author)
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Functional transcriptome analyses of Drosophila suzukii antennae reveal mating-dependent olfaction plasticity in females
- 2019
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In: Insect Biochemistry and Molecular Biology. - : Elsevier BV. - 0965-1748 .- 1879-0240. ; 105, s. 51-59
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Journal article (peer-reviewed)abstract
- Insect olfaction modulates basal behaviors and it is often influenced by the physiological condition of each individual such as the reproductive state. Olfactory plasticity can be achieved by modifications at both peripheral and central nervous system levels. Here we performed a genome-wide transcriptomic analysis of the main olfactory organ, the antenna, to investigate how gene expression varies with female mating status in Drosophila suzukii, a destructive and invasive soft fruit pest. We observed a wide mating-induced up-regulation of chemosensory-related genes in females, especially odorant receptor (Or) genes. We then used a candidate gene approach to define the comprehensive dataset of antenna-expressed chemosensory receptors and binding proteins, which showed many similarities with Drosophila melanogaster. Candidate gene approach was also used to finely quantify differential expression at Or isoform level, suggesting post-mating transcriptional modulation of genes involved in the peripheral olfactory system. We identified 27 up-regulated Or transcripts encoded by 25 genes, seven of them were duplications specific to D. suzukii lineage. Post-mating olfactory modulation was further supported by electroantennogram recordings that showed a differential response according to mating status to one out of eight odors tested (isoamyl-acetate). Our study characterizes the transcriptional mechanisms driven by mating in D. suzukii female antennae. Understanding the role of genes differentially expressed in virgin or mated females will be crucial to better understand host finding and the crop-damaging oviposition behavior of this species.
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