scholarly journals Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics

2020 ◽  
Vol 10 (7) ◽  
pp. 2275-2296 ◽  
Author(s):  
Ian Will ◽  
Biplabendu Das ◽  
Thienthanh Trinh ◽  
Andreas Brachmann ◽  
Robin A. Ohm ◽  
...  
Keyword(s):  
Species Interactions ◽  
Expression Patterns ◽  
Fungal Growth ◽  
Host Manipulation ◽  
Feeding Behaviors ◽  
Camponotus Floridanus ◽  
Rnaseq Data ◽  
A Site ◽  
Globally Distributed ◽  
Identify Gene Expression

Ant-infecting Ophiocordyceps fungi are globally distributed, host manipulating, specialist parasites that drive aberrant behaviors in infected ants, at a lethal cost to the host. An apparent increase in activity and wandering behaviors precedes a final summiting and biting behavior onto vegetation, which positions the manipulated ant in a site beneficial for fungal growth and transmission. We investigated the genetic underpinnings of host manipulation by: (i) producing a high-quality hybrid assembly and annotation of the Ophiocordyceps camponoti-floridani genome, (ii) conducting laboratory infections coupled with RNAseq of O. camponoti-floridani and its host, Camponotus floridanus, and (iii) comparing these data to RNAseq data of Ophiocordyceps kimflemingiae and Camponotus castaneus as a powerful method to identify gene expression patterns that suggest shared behavioral manipulation mechanisms across Ophiocordyceps-ant species interactions. We propose differentially expressed genes tied to ant neurobiology, odor response, circadian rhythms, and foraging behavior may result by activity of putative fungal effectors such as enterotoxins, aflatrem, and mechanisms disrupting feeding behaviors in the ant.

scholarly journals Genetic underpinnings of host manipulation by Ophiocordyceps as revealed by comparative transcriptomics

2020 ◽  
Author(s):  
Ian Will ◽  
Biplabendu Das ◽  
Thienthanh Trinh ◽  
Andreas Brachmann ◽  
Robin Ohm ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Fungal Growth ◽  
Behavioral Changes ◽  
Host Manipulation ◽  
Hybrid Assembly ◽  
Apparent Increase ◽  
Similar Work ◽  
A Site ◽  
Globally Distributed ◽  
Biting Behavior

AbstractThe ant-infecting Ophiocordyceps fungi are globally distributed, host manipulating, specialist parasites that drive aberrant behaviors in infected ants, at a lethal cost to the host. An apparent increase in activity and wandering behaviors precedes a final summiting and biting behavior on to vegetation, positioning the manipulated ant in a site beneficial for fungal growth and transmission. Notably, across Ophiocordyceps species and other known host manipulators, the molecular mechanisms underlying behavioral changes remain largely unclear. We explored possible genetic underpinnings of host manipulation by: (i) producing a hybrid assembly of the Ophiocordyceps camponoti-floridani genome, (ii) conducting laboratory infections coupled with RNAseq of both O. camponoti-floridani and its host, Campontous floridanus, and (iii) using these data for a comparative analysis to similar work performed in Ophiocordyceps kimflemingiae and Camponotus castaneus. We propose differentially expressed genes tied to ant neurobiology, odor response, circadian rhythms, and foraging behavior may be the result of putative fungal effectors such as enterotoxins, aflatrem, and mechanisms disrupting nutrition-sensing or caste-identity pathways.

scholarly journals The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages

2016 ◽  
Vol 283 (1829) ◽  
pp. 20160354 ◽  
Author(s):  
Kimberly A. Selkoe ◽  
Oscar E. Gaggiotti ◽  
Eric A. Treml ◽  
Johanna L. K. Wren ◽  
Mary K. Donovan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Species Interactions ◽  
Allelic Richness ◽  
Coral Cover ◽  
Species Turnover ◽  
Depth Range ◽  
Ecological Communities ◽  
Effective Population ◽  
A Site ◽  
New Strategies

Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here, we use seascape genetic analysis of a diversity metric, allelic richness (AR), for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover harbour the greatest genetic diversity on average. We found that a species's life history (e.g. depth range and herbivory) mediates response of genetic diversity to seascape drivers in logical ways. Furthermore, a metric of combined multi-species AR showed strong coupling to species richness and habitat area, quality and stability that few species showed individually. We hypothesize that macro-ecological forces and species interactions, by mediating species turnover and occupancy (and thus a site's mean effective population size), influence the aggregate genetic diversity of a site, potentially allowing it to behave as an apparent emergent trait that is shaped by the dominant seascape drivers. The results highlight inherent feedbacks between ecology and genetics, raise concern that genetic resilience of entire reef communities is compromised by factors that reduce coral cover or available habitat, including thermal stress, and provide a foundation for new strategies for monitoring and preserving biodiversity of entire reef ecosystems.

scholarly journals Ethanol-driven building fungus colonisation: “Whisky Black” in urban built environments

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Nigel Craig ◽  
Nick Pilcher ◽  
Alan M. Forster ◽  
Craig Kennedy
Keyword(s):  
Building Materials ◽  
Fungal Growth ◽  
Built Environments ◽  
Content Type ◽  
Significant Release ◽  
Carbon Nutrition ◽  
Surrounding Areas ◽  
A Site ◽  
Production Areas ◽  
Corporate Social

PurposeThe spirits industry is a major economic contributor worldwide, often requiring years of maturation in barrels that is associated with significant release of ethanol into the surrounding environment. This provides carbon nutrition for colonisation of black fungal growths, one type being Baudoinia compniacensis, or Whisky Black. Although growth is localised in production areas, numerous sites exist globally, and this paper's purpose is to investigate the extent and implications of colonisation.Design/methodology/approachThe paper presents and discusses the results of a visual survey of the area surrounding a site where whisky is maturing in nearby bonded warehouses. The evaluation considers radial zoning distance from the ethanol source and material substrate types and surface textures. Classical key stages of Building Pathology, namely manifestation, diagnosis, prognosis and therapy, are considered.FindingsKey findings are that the colonisation of the fungus is non-uniform and dependent on the substrate building material. Additionally, rougher-textured building materials displayed heavier levels of fungal manifestation than smooth materials. Aspects such as distance, wind direction and moisture are considered relative to the extent and level of fungal growth.Originality/valueThis investigation provides the first assessment of the extent and nature of the fungal growth in properties built in surrounding areas to bonded warehouses. Such information can facilitate open dialogue between stakeholders that recognise the aspirations of values of corporate social responsibility, whilst balancing the economic importance of distilling with recognition of the fungus's impact on property values and appropriate recurring remedial treatments.

scholarly journals DPAC: a tool for Differential Poly(A) Site usage from poly(A)–targeted RNAseq data

2019 ◽  
Author(s):  
Andrew Routh
Keyword(s):  
Gene Expression ◽  
Alternative Polyadenylation ◽  
Data Mapping ◽  
Library Synthesis ◽  
Sequencing Data ◽  
Synthesis Strategy ◽  
Rnaseq Data ◽  
Differential Gene ◽  
A Site

AbstractPoly(A)-tail targeted RNAseq approaches, such as 3’READS, PAS-seq and Poly(A)-ClickSeq, are becoming popular alternatives to random-primed RNAseq for simplified gene expression analyses as well as to measure changes in poly(A) site usage. We and others have recently demonstrated that these approaches perform similarly to other RNAseq strategies, while saving on the volume of sequencing data required and providing a simpler library synthesis strategy. Here, we present DPAC; a streamlined pipeline for the preprocessing of poly(A)-tail targeted RNAseq data, mapping of poly(A)-sites and poly(A) clustering, and determination of differential poly(A) site usage using DESeq2. Changes in poly(A) site usage is simultaneously used to report differential gene expression, differential terminal exon usage and alternative polyadenylation (APA).

scholarly journals The vernalisation regulator FLOWERING LOCUS C is differentially expressed in biennial and annual Brassica napus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sarah V. Schiessl ◽  
Daniela Quezada-Martinez ◽  
Ellen Tebartz ◽  
Rod J. Snowdon ◽  
Lunwen Qian
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Differentially Expressed ◽  
Growth Type ◽  
Flowering Locus C ◽  
Vernalisation Requirement ◽  
Rnaseq Data ◽  
Spring Type ◽  
Flowering Locus

Abstract Plants in temperate areas evolved vernalisation requirement to avoid pre-winter flowering. In Brassicaceae, a period of extended cold reduces the expression of the flowering inhibitor FLOWERING LOCUS C (FLC) and paves the way for the expression of downstream flowering regulators. As with all polyploid species of the Brassicaceae, the model allotetraploid Brassica napus (rapeseed, canola) is highly duplicated and carries 9 annotated copies of Bna.FLC. To investigate whether these multiple homeologs and paralogs have retained their original function in vernalisation or undergone subfunctionalisation, we compared the expression patterns of all 9 copies between vernalisation-dependent (biennial, winter type) and vernalisation-independent (annual, spring type) accessions, using RT-qPCR with copy-specific primers and RNAseq data from a diversity set. Our results show that only 3 copies – Bna.FLC.A03b, Bna.FLC.A10 and to some extent Bna.FLC.C02 – are differentially expressed between the two growth types, showing that expression of the other 6 copies does not correlate with growth type. One of those 6 copies, Bna.FLC.C03b, was not expressed at all, indicating a pseudogene, while three further copies, Bna.FLC.C03a and Bna.FLC.C09ab, did not respond to cold treatment. Sequence variation at the COOLAIR binding site of Bna.FLC.A10 was found to explain most of the variation in gene expression. However, we also found that Bna.FLC.A10 expression is not fully predictive of growth type.

Dietary zinc status reversibly alters both the feeding behaviors of the rats and gene expression patterns in diencephalon

BioFactors ◽  
2012 ◽  
Vol 38 (3) ◽  
pp. 203-218 ◽  
Author(s):  
Shinji Okada ◽  
Moe Abuyama ◽  
Ryo Yamamoto ◽  
Takashi Kondo ◽  
Masataka Narukawa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Zinc Status ◽  
Dietary Zinc ◽  
Feeding Behaviors

scholarly journals Different combinations of serotonin receptors regulate predatory and bacterial feeding behaviors in the nematode Pristionchus pacificus

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Yuuki Ishita ◽  
Takahiro Chihara ◽  
Misako Okumura
Keyword(s):  
Feeding Behavior ◽  
Serotonin Receptors ◽  
Double Mutant ◽  
Tooth Movement ◽  
Expression Patterns ◽  
Neural Pathways ◽  
Feeding Behaviors ◽  
Pristionchus Pacificus ◽  
Knockout Mutants ◽  
Insight Into

Abstract Feeding behavior is one of the most fundamental behaviors in animals, and regulation of this behavior is critical for proper food intake. The nematode Pristionchus pacificus exhibits dimorphism in feeding behavior, bacterial feeding and predatory feeding on other nematodes, and the latter behavior is assumed to be an evolutionarily novel behavior. Both types of feeding behavior are modulated by serotonin; however, the downstream mechanism that modulates these behaviors is still to be clarified. Here, we focused on serotonin receptors and examined their expression patterns in P. pacificus. We also generated knockout mutants of the serotonin receptors using the CRISPR/Cas9 system and examined feeding behaviors. We found that Ppa-ser-5 mutants and the Ppa-ser-1; Ppa-ser-7 double mutant decreased predation. Detailed observation of the pharyngeal movement revealed that the Ppa-ser-1; Ppa-ser-7 double mutant reduces tooth movement, which is required for efficient predatory feeding. Conversely, Ppa-ser-7 and Ppa-mod-1 mutants decreased bacterial feeding. This study revealed that specific combinations of serotonin receptors are essential for the modulation of these distinct feeding behaviors, providing insight into the evolution of neural pathways to regulate novel feeding behavior.

scholarly journals Probing the Honey Bee Diet-Microbiota-Host Axis Using Pollen Restriction and Organic Acid Feeding

Insects ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 291
Author(s):  
Vincent A. Ricigliano ◽  
Kirk E. Anderson
Keyword(s):  
Organic Acid ◽  
Honey Bee ◽  
Expression Patterns ◽  
Feeding Behaviors ◽  
Fermentation Products ◽  
Bacterial Fermentation ◽  
Bee Health ◽  
Gene Transcripts ◽  
The Impact

Microbial metabolites are considered important drivers of diet-based microbiota influence on the host, however, mechanistic models are confounded by interactions between diet, microbiota function, and host physiology. The honey bee harbors a simple microbiota that produces organic acids as fermentation products of dietary nectar and pollen, making it a model for gut microbiota research. Herein, we demonstrate that bacterial abundance in the honey bee gut is partially associated with the anterior rectum epithelium. We used dietary pollen restriction and organic acid feeding treatments to obtain information about the role of undigested pollen as a microbiota growth substrate and the impact of bacterial fermentation products on honey bee enteroendocrine signaling. Pollen restriction markedly reduced total and specific bacterial 16S rRNA abundance in the anterior rectum but not in the ileum. Anterior rectum expression levels of bacterial fermentative enzyme gene transcripts (acetate kinase, lactate dehydrogenase, and hydroxybutyryl-CoA dehydrogenase) were reduced in association with diet-induced microbiota shifts. To evaluate the effects of fermentative metabolites on host enteroendocrine function, pollen-restricted bees were fed an equimolar mixture of organic acid sodium salts (acetate, lactate, butyrate, formate, and succinate). Organic acid feeding significantly impacted hindgut enteroendocrine signaling gene expression, rescuing some effects of pollen restriction. This was specifically manifested by tissue-dependent expression patterns of neuropeptide F and allatostatin pathways, which are implicated in energy metabolism and feeding behaviors. Our findings provide new insights into the diet-microbiota-host axis in honey bees and may inform future efforts to improve bee health through diet-based microbiota manipulations.

scholarly journals Predicting bacterial growth conditions from mRNA and protein abundances

2018 ◽  
Author(s):  
Mehmet U. Caglar ◽  
Adam J. Hockenberry ◽  
Claus O. Wilke
Keyword(s):  
Gene Expression ◽  
Species Interactions ◽  
Low Cost ◽  
Expression Patterns ◽  
Single Species ◽  
Growth Conditions ◽  
Environmental Variable ◽  
Training Data ◽  
Specific Gene ◽  
Natural Environments

AbstractCells respond to changing nutrient availability and external stresses by altering the expression of individual genes. Condition-specific gene expression patterns may provide a promising and low-cost route to quantifying the presence of various small molecules, toxins, or species-interactions in natural environments. However, whether gene expression signatures alone can predict individual environmental growth conditions remains an open question. Here, we used machine learning to predict 16 closely-related growth conditions using 155 datasets of E. coli transcript and protein abundances. We show that models are able to discriminate between different environmental features with a relatively high degree of accuracy. We observed a small but significant increase in model accuracy by combining transcriptome and proteome-level data, and we show that stationary phase conditions are typically more difficult to distinguish from one another than conditions under exponential growth. Nevertheless, with sufficient training data, gene expression measurements from a single species are capable of distinguishing between environmental conditions that are separated by a single environmental variable.

scholarly journals Multiple modes of regulation control dynamic transcription patterns during the mitosis-G1 transition

2021 ◽  
Author(s):  
Luke A Wojenski ◽  
Lauren M Wainman ◽  
Geno J Villafano ◽  
Chris Kuhlberg ◽  
Pariksheet Nanda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Polymerase Activity ◽  
Gene Expression Patterns ◽  
Regulation Of Transcription ◽  
Dynamic Regulation ◽  
Gene Reactivation ◽  
Rna Polymerase Activity ◽  
Control Dynamic ◽  
A Site

Following cell division, genomes must reactivate gene expression patterns that reflect the identity of the cell. Here, we use PRO-seq to examine the mechanisms that reestablish transcription patterns after mitosis. We uncover regulation of the transcription cycle at multiple steps including initiation, promoter-proximal pause positioning and escape, poly-A site cleavage and termination during the mitotic-G1 transition. During mitosis, RNA polymerase activity is retained at initiation sites, albeit shifted in position relative to non-mitotic cells. This activity is strongly linked to maintenance of local chromatin architecture during mitosis and is more predictive of rapid gene reactivation than histone modifications previously associated with bookmarking. These molecular bookmarks, combined with sequence-specific transcription factors, direct expression of select cell growth and cell specific genes during mitosis followed by reactivation of functional gene groups with distinct kinetics after mitosis. This study details how dynamic regulation of transcription at multiple steps contributes to gene expression during the cell cycle.

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