J Exp Bot , IF:6.992 , 2021 Dec , V72 (22) : P7927-7941 doi: 10.1093/jxb/erab373
Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors.
The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.; Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, The Netherlands.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.; Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK.; John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.; Institute of Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany.
Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.
PMID: 34387350
iScience , IF:5.458 , 2021 Dec , V24 (12) : P103462 doi: 10.1016/j.isci.2021.103462
Biomolecular mechanisms for signal differentiation.
Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK.; Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK.; Department of Computer Science, University of Oxford, Oxford OX1 3QD, UK.
Cells can sense temporal changes of molecular signals, allowing them to predict environmental variations and modulate their behavior. This paper elucidates biomolecular mechanisms of time derivative computation, facilitating the design of reliable synthetic differentiator devices for a variety of applications, ultimately expanding our understanding of cell behavior. In particular, we describe and analyze three alternative biomolecular topologies that are able to work as signal differentiators to input signals around their nominal operation. We propose strategies to preserve their performance even in the presence of high-frequency input signal components which are detrimental to the performance of most differentiators. We find that the core of the proposed topologies appears in natural regulatory networks and we further discuss their biological relevance. The simple structure of our designs makes them promising tools for realizing derivative control action in synthetic biology.
PMID: 34927021
Phytopathology , IF:4.025 , 2021 Dec : PPHYTO09200383R doi: 10.1094/PHYTO-09-20-0383-R
Untargeted Metabolomic Investigation of Wheat Infected with Stinking Smut Tilletia caries.
Institute of Biological Chemistry, Washington State University, Pullman, WA 99164.; Department of Biological Sciences, Butler University, Indianapolis, IN 46208.; Department of Plant Pathology, Washington State University, Pullman, WA 99164.
Tilletia caries infection of wheat (Triticum aestivum) has become an increasing problem in organic wheat agriculture throughout the world. Little is known about how this pathogen alters host metabolism to ensure a successful infection. We investigated how T. caries allocates resources from wheat for its growth over the life cycle of the pathogen. An untargeted metabolomics approach that combined gas chromatography time-of-flight mass spectrometry and ultraperformance liquid chromatography tandem mass spectrometry platforms was used to determine which primary or specialized metabolite pathways are targeted and altered during T. caries infection. We found that T. caries does not dramatically alter the global metabolome of wheat but instead alters key metabolites for its own nutrient uptake and to antagonize host defenses by reducing wheat's sweet immunity response and other related pathways. Our results highlight metabolic characteristics needed for selecting wheat varieties that are resistant to T. caries infection for organic agriculture. In addition, several wheat metabolites were identified that could be used in developing a diagnostic tool for early detection of T. caries infection.
PMID: 34865506
Prev Vet Med , IF:2.67 , 2021 Dec , V199 : P105556 doi: 10.1016/j.prevetmed.2021.105556
Preventive effect of on-farm biosecurity practices against highly pathogenic avian influenza (HPAI) H5N6 infection on commercial layer farms in the Republic of Korea during the 2016-17 epidemic: A case-control study.
Veterinary Epidemiology Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea; Department of Public Health, Graduate School, Korea University, Seoul, 02841, Republic of Korea. Electronic address: shanuar@korea.kr.; Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.; Department of Public Health, Graduate School, Korea University, Seoul, 02841, Republic of Korea.; Veterinary Epidemiology Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.; Farm Animal Clinical Training and Research Center, Seoul National University, Pyeongchang, 25354, Republic of Korea.; Department of Computer and Information Science, Korea University, Seojong, 30019, Republic of Korea.
Highly pathogenic avian influenza virus (HPAIv) H5N6 has destructive consequences on the global poultry production system. Recently, a growing number of layer farms have been heavily damaged from the HPAIv epidemic due to the increased virulence of the virus and the intensification of the production system. Therefore, stakeholders should implement effective preventive practices at the farm level that are aligned with contingency measures at the national level to minimize poultry losses. However, numerous biosecurity protocols for layer farm workers to follow have been developed, impeding efficient prevention and control. Furthermore, the effectiveness of biosecurity practices varies with the geographical condition and inter-farm contact structures. Hence, the objective of our study was to examine the preventive effect of five biosecurity actions commonly practiced at layer farms in the Republic of Korea against HPAIv H5N6: (i) fence installation around a farm, ii) rodent control inside a farm; iii) disinfection booth for visitors for disinfection protocols, iv) an anterior room in the sheds before entering the bird area and v) boots changes when moving between sheds in the same farm. We conducted a case-control study on 114 layer case farms and 129 layer control farms during the 2016-17 HPAI epidemic. The odds ratios for five on-farm biosecurity practices implemented in those study groups were estimated as a preventive effect on the HPAI infection with covariates, including seven geographical conditions and three network metrics using Bayesian hierarchical logistic regression and geographical location weighted logistic regression. The results showed that the use of a disinfection booth for personnel reduced the odds of HPAIv H5N6 infection (adjusted odds ratio [AOR] = 0.002, 95 % credible interval [CrI] = 0.00007 - 0.025) with relatively small spatial variation (minimum AOR - maximum AOR: 0.084-0.263). Changing boots between sheds on the same farm reduced the odds of HPAIv H5N6 infection (AOR = 0.160, 95 % CrI = 0.024-0.852) with relatively wide spatial variation (minimum AOR - maximum AOR = 0.270-0.688). Therefore, enhanced personnel biosecurity protocols at the farm of entry for layer farms is recommended to effectively prevent and respond to HPAIv H5N6 infection under different local condition. Our study provides an important message for layer farmers to effectively implement on-farm biosecurity actions against HPAIv H5N6 infection at their farms by setting priorities based on their spatial condition and network position.
PMID: 34896940
Eat Behav , 2021 Dec , V44 : P101590 doi: 10.1016/j.eatbeh.2021.101590
Evaluation of the cognitive behavioural theory of eating disorders: A network analysis investigation.
Department of Eating Disorders (Amarum), GGNet Mental Health, Warnsveld, the Netherlands. Electronic address: s.mares@ggnet.nl.; University of Groningen, University Medical Center Groningen, University Center Psychiatry (UCP) Interdisciplinary Center Psychopathology and Emotion Regulation (ICPE), Groningen, the Netherlands.; Department of Clinical Psychological Science, Maastricht University, Maastricht, the Netherlands.; Department of Eating Disorders (Amarum), GGNet Mental Health, Warnsveld, the Netherlands; Altrecht Eating Disorders Rintveld, Zeist, the Netherlands; Department of Clinical Psychology, Utrecht University, Utrecht, the Netherlands.; Department of Eating Disorders (Amarum), GGNet Mental Health, Warnsveld, the Netherlands; Radboud University Nijmegen, Behavioural Science Institute, NijCa2re, the Netherlands.
OBJECTIVE: One of the prevailing theories of eating disorders (ED) is the transdiagnostic cognitive behavioural theory of eating disorders, which suggests that certain ED symptoms, such as over-valuation of eating, shape, and weight, may be more central than others. In the present study, network analyses were used to evaluate these assumptions in a patient sample. METHODS: Participants were 336 individuals receiving treatment at an expert center for ED in the Netherlands. Eating disorder symptoms were used to create transdiagnostic and diagnosis-specific networks and assess symptom centrality and density of the networks. RESULTS: Networks for patients with bulimia nervosa and binge eating disorder confirmed that over-valuation of shape, weight, and eating is the most central symptom in the network. A transdiagnostic network of ED symptoms and separate networks for patients with anorexia nervosa and bulimia nervosa showed that strict dieting was an additional central ED symptom. An exploratory analysis revealed that, although eating disorder symptoms decreased, there were no differences in density of the eating disorder networks before and after treatment with cognitive behavioural therapy. DISCUSSION: In conclusion, the current study confirmed that over-valuation of shape, weight, and eating is a central symptom across eating disorders, in agreement with the transdiagnostic cognitive behavioural model of eating disorders. Specifically targeting this symptom in treatment could lead to other symptoms improving as a result.
PMID: 34896868