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Li Q, Button-Simons KA, Sievert MAC, Chahoud E, Foster GF, Meis K, Ferdig MT, Milenković T. Enhancing Gene Co-Expression Network Inference for the Malaria Parasite Plasmodium falciparum. Genes (Basel) 2024; 15:685. [PMID: 38927622 PMCID: PMC11202799 DOI: 10.3390/genes15060685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Malaria results in more than 550,000 deaths each year due to drug resistance in the most lethal Plasmodium (P.) species P. falciparum. A full P. falciparum genome was published in 2002, yet 44.6% of its genes have unknown functions. Improving the functional annotation of genes is important for identifying drug targets and understanding the evolution of drug resistance. RESULTS Genes function by interacting with one another. So, analyzing gene co-expression networks can enhance functional annotations and prioritize genes for wet lab validation. Earlier efforts to build gene co-expression networks in P. falciparum have been limited to a single network inference method or gaining biological understanding for only a single gene and its interacting partners. Here, we explore multiple inference methods and aim to systematically predict functional annotations for all P. falciparum genes. We evaluate each inferred network based on how well it predicts existing gene-Gene Ontology (GO) term annotations using network clustering and leave-one-out crossvalidation. We assess overlaps of the different networks' edges (gene co-expression relationships), as well as predicted functional knowledge. The networks' edges are overall complementary: 47-85% of all edges are unique to each network. In terms of the accuracy of predicting gene functional annotations, all networks yielded relatively high precision (as high as 87% for the network inferred using mutual information), but the highest recall reached was below 15%. All networks having low recall means that none of them capture a large amount of all existing gene-GO term annotations. In fact, their annotation predictions are highly complementary, with the largest pairwise overlap of only 27%. We provide ranked lists of inferred gene-gene interactions and predicted gene-GO term annotations for future use and wet lab validation by the malaria community. CONCLUSIONS The different networks seem to capture different aspects of the P. falciparum biology in terms of both inferred interactions and predicted gene functional annotations. Thus, relying on a single network inference method should be avoided when possible. SUPPLEMENTARY DATA Attached.
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Affiliation(s)
- Qi Li
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
| | - Katrina A. Button-Simons
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mackenzie A. C. Sievert
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Elias Chahoud
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Preprofessional Studies, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gabriel F. Foster
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Kaitlynn Meis
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael T. Ferdig
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Tijana Milenković
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
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2
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Shetty V, Adelman ZN, Slotman MA. Effects of circadian clock disruption on gene expression and biological processes in Aedes aegypti. BMC Genomics 2024; 25:170. [PMID: 38347446 PMCID: PMC10863115 DOI: 10.1186/s12864-024-10078-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/01/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND This study explores the impact of disrupting the circadian clock through a Cycle gene knockout (KO) on the transcriptome of Aedes aegypti mosquitoes. The investigation aims to uncover the resulting alterations in gene expression patterns and physiological processes. RESULTS Transcriptome analysis was conducted on Cyc knockout (AeCyc-/-) and wild-type mosquitoes at four time points in a light-dark cycle. The study identified system-driven genes that exhibit rhythmic expression independently of the core clock machinery. Cyc disruption led to altered expression of essential clock genes, affecting metabolic processes, signaling pathways, stimulus responses and immune responses. Notably, gene ontology enrichment of odorant binding proteins, indicating the clock's role in sensory perception. The absence of Cyc also impacted various regulation of metabolic and cell cycle processes was observed in all time points. CONCLUSIONS The intricate circadian regulation in Ae. aegypti encompasses both core clock-driven and system-driven genes. The KO of Cyc gene instigated extensive gene expression changes, impacting various processes, thereby potentially affecting cellular and metabolic functions, immune responses, and sensory perception. The circadian clock's multifaceted involvement in diverse biological processes, along with its role in the mosquito's daily rhythms, forms a nexus that influences the vector's capacity to transmit diseases. These insights shed light on the circadian clock's role in shaping mosquito biology and behavior, opening new avenues for innovative disease control strategies.
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Affiliation(s)
- Vinaya Shetty
- Department of Entomology, Texas A&M University, College station, TX, 77843, USA.
| | - Zach N Adelman
- Department of Entomology, Texas A&M University, College station, TX, 77843, USA
| | - Michel A Slotman
- Department of Entomology, Texas A&M University, College station, TX, 77843, USA
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3
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Raghavan V, Eichele G, Larink O, Karin EL, Söding J. RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton. NAR Genom Bioinform 2023; 5:lqad007. [PMID: 36814456 PMCID: PMC9939569 DOI: 10.1093/nargab/lqad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/19/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
Zooplankton are important eukaryotic constituents of marine ecosystems characterized by limited motility in the water. These metazoans predominantly occupy intermediate trophic levels and energetically link primary producers to higher trophic levels. Through processes including diel vertical migration (DVM) and production of sinking pellets they also contribute to the biological carbon pump which regulates atmospheric CO2 levels. Despite their prominent role in marine ecosystems, and perhaps, because of their staggering diversity, much remains to be discovered about zooplankton biology. In particular, the circadian clock, which is known to affect important processes such as DVM has been characterized only in a handful of zooplankton species. We present annotated de novo assembled transcriptomes from a diverse, representative cohort of 17 marine zooplankton representing six phyla and eight classes. These transcriptomes represent the first sequencing data for a number of these species. Subsequently, using translated proteomes derived from this data, we demonstrate in silico the presence of orthologs to most core circadian clock proteins from model metazoans in all sequenced species. Our findings, bolstered by sequence searches against publicly available data, indicate that the molecular machinery underpinning endogenous circadian clocks is widespread and potentially well conserved across marine zooplankton taxa.
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Affiliation(s)
| | | | - Otto Larink
- Evolutionary Biology, Zoological Institute, Technical University Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Eli Levy Karin
- Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
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4
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Stanton D, Justin HS, Reitzel AM. Step in Time: Conservation of Circadian Clock Genes in Animal Evolution. Integr Comp Biol 2022; 62:1503-1518. [PMID: 36073444 DOI: 10.1093/icb/icac140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 01/05/2023] Open
Abstract
Over the past few decades, the molecular mechanisms responsible for circadian phenotypes of animals have been studied in increasing detail in mammals, some insects, and other invertebrates. Particular circadian proteins and their interactions are shared across evolutionary distant animals, resulting in a hypothesis for the canonical circadian clock of animals. As the number of species for which the circadian clockwork has been described increases, the circadian clock in animals driving cyclical phenotypes becomes less similar. Our focus in this review is to develop and synthesize the current literature to better understand the antiquity and evolution of the animal circadian clockwork. Here, we provide an updated understanding of circadian clock evolution in animals, largely through the lens of conserved genes characterized in the circadian clock identified in bilaterian species. These comparisons reveal extensive variation within the likely composition of the core clock mechanism, including losses of many genes, and that the ancestral clock of animals does not equate to the bilaterian clock. Despite the loss of these core genes, these species retain circadian behaviors and physiology, suggesting novel clocks have evolved repeatedly. Additionally, we highlight highly conserved cellular processes (e.g., cell division, nutrition) that intersect with the circadian clock of some animals. The conservation of these processes throughout the animal tree remains essentially unknown, but understanding their role in the evolution and maintenance of the circadian clock will provide important areas for future study.
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Affiliation(s)
- Daniel Stanton
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
| | - Hannah S Justin
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte NC 28223, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte NC 28223, USA
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5
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Wang P, Wang D. Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2829-2841. [PMID: 34383649 DOI: 10.1109/tcbb.2021.3103280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Gene co-expression network (GCN) becomes an increasingly important tool in omics data analysis. A great challenge for GCN construction is that the sample size is far lower than the number of genes. Traditional methods rely on considerable samples. Moreover, association signals are likely weak, nonlinear and stochastic, which are difficult to be identified among thousands of candidates. In this paper, the gray correlation coefficient (GCC) is introduced, and a novel method to construct gene differential co-expression networks (GDCNs) is proposed. Based on the GDCNs, three measures are proposed to explore informative genes. The proposed method can make full use of the information provided by a handful of samples and overcome the shortages of GCNs, which can evaluate the changes of co-expression relationships that are possibly triggered by treatments. Based on RNA-seq data of Brassica napus, GDCNs under multiple experimental conditions are constructed and investigated. It is found that the GCC-based method is very robust to data processing. The GDCNs facilitate the inference of gene functions and the identification of informative genes that are responsible for stress responsiveness. The GDCN-based approaches integrate the 'guilt by association' and the 'guilt by rewiring' rules, which provide alternative tools for omics data analysis.
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6
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Pfenning-Butterworth AC, Nguyen DT, Hite JL, Cressler CE. Circadian rhythms mediate infection risk in Daphnia dentifera. Ecol Evol 2022; 12:e9264. [PMID: 36177139 PMCID: PMC9463024 DOI: 10.1002/ece3.9264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
Biological rhythms mediate important within-host processes such as metabolism, immunity, and behavior which are often linked to combating disease exposure. For many hosts, exposure to pathogens occurs while feeding. However, the link between feeding rhythms and infection risk is unclear because feeding behavior is tightly coupled with immune and metabolic processes which may decrease susceptibility to infection. Here, we use the Daphnia dentifera-Metschnikowia bicuspidata host-pathogen system to determine how rhythms in feeding rate and immune function mediate infection risk. The host is known to have a nocturnal circadian rhythm in feeding rate, yet we found that they do not exhibit a circadian rhythm in phenoloxidase activity. We found that the time of day when individuals are exposed to pathogens affects the probability of infection with higher infection prevalence at night, indicating that infection risk is driven by a host's circadian rhythm in feeding behavior. These results suggest that the natural circadian rhythm of the host should be considered when addressing epidemiological dynamics.
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Affiliation(s)
| | - David T Nguyen
- School of Biological Sciences University of Nebraska-Lincoln Lincoln Nebraska USA
| | - Jessica L Hite
- School of Biological Sciences University of Nebraska-Lincoln Lincoln Nebraska USA.,Department of Pathobiological Sciences University of Wisconsin-Madison Madison Wisconsin USA
| | - Clayton E Cressler
- School of Biological Sciences University of Nebraska-Lincoln Lincoln Nebraska USA
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7
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Cremer R, Wacker A, Schwarzenberger A. More Light Please: Daphnia Benefit From Light Pollution by Increased Tolerance Toward Cyanobacterial Chymotrypsin Inhibitors. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.834422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Cryptochromes are evolutionary ancient blue-light photoreceptors that are part of the circadian clock in the nervous system of many organisms. Cryptochromes transfer information of the predominant light regime to the clock which results in the fast adjustment to photoperiod. Therefore, the clock is sensitive to light changes and can be affected by anthropogenic Artificial Light At Night (ALAN). This in turn has consequences for clock associated behavioral processes, e.g., diel vertical migration (DVM) of zooplankton. In freshwater ecosystems, the zooplankton genus Daphnia performs DVM in order to escape optically hunting predators and to avoid UV light. Concomitantly, Daphnia experience circadian changes in food-supply during DVM. Daphnia play the keystone role in the carbon-transfer to the next trophic level. Therefore, the whole ecosystem is affected during the occurrence of cyanobacteria blooms as cyanobacteria reduce food quality due to their production of digestive inhibitors (e.g., protease inhibitors). In other organisms, digestion is linked to the circadian clock. If this is also the case for Daphnia, the expression of protease genes should show a rhythmic expression following circadian expression of clock genes (e.g., cryptochrome 2). We tested this hypothesis and demonstrated that gene expression of the clock and of proteases was affected by ALAN. Contrary to our expectations, the activity of one type of proteases (chymotrypsins) was increased by ALAN. This indicates that higher protease activity might improve the diet utilization. Therefore, we treated D. magna with a chymotrypsin-inhibitor producing cyanobacterium and found that ALAN actually led to an increase in Daphnia’s growth rate in comparison to growth on the same cyanobacterium in control light conditions. We conclude that this increased tolerance to protease inhibitors putatively enables Daphnia populations to better control cyanobacterial blooms that produce chymotrypsin inhibitors in the Anthropocene, which is defined by light pollution and by an increase of cyanobacterial blooms due to eutrophication.
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8
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Pfenning-Butterworth A, Cooper RO, Cressler CE. Daily feeding rhythm linked to microbiome composition in two zooplankton species. PLoS One 2022; 17:e0263538. [PMID: 35113950 PMCID: PMC8812976 DOI: 10.1371/journal.pone.0263538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/20/2022] [Indexed: 01/04/2023] Open
Abstract
Host-associated microbial communities are impacted by external and within-host factors, i.e., diet and feeding behavior. For organisms known to have a circadian rhythm in feeding behavior, microbiome composition is likely impacted by the different rates of microbe introduction and removal across a daily cycle, in addition to any diet-induced changes in microbial interactions. Here, we measured feeding behavior and used 16S rRNA sequencing to compare the microbial community across a diel cycle in two distantly related species of Daphnia, that differ in their life history traits, to assess how daily feeding patterns impact microbiome composition. We find that Daphnia species reared under similar laboratory conditions have significantly different microbial communities. Additionally, we reveal that Daphnia have daily differences in their microbial composition that correspond with feeding behavior, such that there is greater microbiome diversity at night during the host’s active feeding phase. These results highlight that zooplankton microbiomes are relatively distinct and are likely influenced by host phylogeny.
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Affiliation(s)
- Alaina Pfenning-Butterworth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
| | - Reilly O. Cooper
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Clayton E. Cressler
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
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9
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Li D, Huang J, Zhou Q, Gu L, Sun Y, Zhang L, Yang Z. Artificial Light Pollution with Different Wavelengths at Night Interferes with Development, Reproduction, and Antipredator Defenses of Daphnia magna. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1702-1712. [PMID: 35014268 DOI: 10.1021/acs.est.1c06286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Artificial light at night (ALAN) dramatically alters the natural daily cycle of light and may cause a suite of physiological and behavioral responses of freshwater crustacean Daphnia. Here, we conducted a life table experiment to investigate the effect of different wavelengths [white (L-L, 400-800 nm), red (R, 614 nm), green (G, 527 nm), and blue (B, 447 nm)] and flashing modes [three colors flash alternately (3-Flash), seven colors strobe alternately (7-Strobe)] of ALAN on the development, reproduction, and predator-induced defenses of Daphnia magna. The results showed that G inhibited the development of the body and tail spine of Daphnia at sexual maturity and decreased their reproduction. The 7-Strobe promoted Daphnia to develop a larger eye. There was an interaction between fish kairomones and ALAN, which intensified over time. ALAN enhanced the response of the relative tail spine length to fish kairomone at sexual maturity. In addition, L-L and R inhibited the body length of 10th instar D. magna in response to fish kairomone. Through the hierarchical cluster method, the 3-Flash and B are recommended as friendly artificial lighting to Daphnia. Our results highlight the interference effects of ALAN on Daphnia, which are helpful to assess the potential impact of light pollution on zooplankton.
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Affiliation(s)
- Da Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, China
| | - Jing Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, China
| | - Qiming Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, China
| | - Lei Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, China
| | - Yunfei Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, China
| | - Lu Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, China
| | - Zhou Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, China
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10
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Rawlinson KA, Reid AJ, Lu Z, Driguez P, Wawer A, Coghlan A, Sankaranarayanan G, Buddenborg SK, Soria CD, McCarthy C, Holroyd N, Sanders M, Hoffmann KF, Wilcockson D, Rinaldi G, Berriman M. Daily rhythms in gene expression of the human parasite Schistosoma mansoni. BMC Biol 2021; 19:255. [PMID: 34852797 PMCID: PMC8638415 DOI: 10.1186/s12915-021-01189-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background The consequences of the earth’s daily rotation have led to 24-h biological rhythms in most organisms. Even some parasites are known to have daily rhythms, which, when in synchrony with host rhythms, can optimise their fitness. Understanding these rhythms may enable the development of control strategies that take advantage of rhythmic vulnerabilities. Recent work on protozoan parasites has revealed 24-h rhythms in gene expression, drug sensitivity and the presence of an intrinsic circadian clock; however, similar studies on metazoan parasites are lacking. To address this, we investigated if a metazoan parasite has daily molecular oscillations, whether they reveal how these longer-lived organisms can survive host daily cycles over a lifespan of many years and if animal circadian clock genes are present and rhythmic. We addressed these questions using the human blood fluke Schistosoma mansoni that lives in the vasculature for decades and causes the tropical disease schistosomiasis. Results Using round-the-clock transcriptomics of male and female adult worms collected from experimentally infected mice, we discovered that ~ 2% of its genes followed a daily pattern of expression. Rhythmic processes included a stress response during the host’s active phase and a ‘peak in metabolic activity’ during the host’s resting phase. Transcriptional profiles in the female reproductive system were mirrored by daily patterns in egg laying (eggs are the main drivers of the host pathology). Genes cycling with the highest amplitudes include predicted drug targets and a vaccine candidate. These 24-h rhythms may be driven by host rhythms and/or generated by a circadian clock; however, orthologs of core clock genes are missing and secondary clock genes show no 24-h rhythmicity. Conclusions There are daily rhythms in the transcriptomes of adult S. mansoni, but they appear less pronounced than in other organisms. The rhythms reveal temporally compartmentalised internal processes and host interactions relevant to within-host survival and between-host transmission. Our findings suggest that if these daily rhythms are generated by an intrinsic circadian clock then the oscillatory mechanism must be distinct from that in other animals. We have shown which transcripts oscillate at this temporal scale and this will benefit the development and delivery of treatments against schistosomiasis. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01189-9.
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Affiliation(s)
| | - Adam J Reid
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Zhigang Lu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patrick Driguez
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia
| | - Anna Wawer
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Avril Coghlan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | | | | | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Mandy Sanders
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Karl F Hoffmann
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - David Wilcockson
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Gabriel Rinaldi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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11
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Pfenning-Butterworth AC, Amato K, Cressler CE. Circadian Rhythm in Feeding Behavior of Daphnia dentifera. J Biol Rhythms 2021; 36:589-594. [PMID: 34753340 DOI: 10.1177/07487304211054404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circadian rhythms enable organisms to mediate their molecular and physiological processes with changes in their environment. Although feeding behavior directly affects within-organism processes, there are few examples of a circadian rhythm in this key behavior. Here, we show that Daphnia have a nocturnal circadian rhythm in feeding behavior that corresponds with their diel vertical migration (DVM), an important life history strategy for predator and UV avoidance. In addition, this feeding rhythm appears to be temperature compensated, which suggests that feeding behavior is robust to seasonal changes in water temperature. A circadian rhythm in feeding behavior can impact energetically demanding processes like metabolism and immunity, which may have drastic effects on susceptibility to disease, starvation risk, and ultimately, fitness.
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Affiliation(s)
| | - Kristina Amato
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Clayton E Cressler
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska
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12
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Schwarzenberger A, Handke NH, Romer T, Wacker A. Geographic clines in Daphnia magna's circadian clock gene expression: Local adaptation to photoperiod. ZOOLOGY 2020; 144:125856. [PMID: 33202364 DOI: 10.1016/j.zool.2020.125856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 11/28/2022]
Abstract
Nearly all organisms show daily and seasonal physiological and behavioural responses that are necessary for their survival. Often these responses are controlled by the rhythmic activity of an endogenous clock that perceives day length. Day length differs not only between seasons but also along latitudes, with different seasonal day lengths between the north and the south. Both seasonal and latitudinal differences in day length are discussed to be perceived/processed by the endogenous clock. Some species are distributed over a wide range of latitudes; it should be highly adaptive for these species to be able to time physiological responses (e.g. migration behaviour and diapause) according to the organisms' respective photoperiod, i.e. their respective seasonal and latitudinal day length. The mediator of day length is the indoleamine hormone melatonin which is synthesized by melatonin-producing enzymes (AANAT and HIOMT). These enzymes are in turn controlled by an endogenous clock. The ubiquitous aquatic keystone organism Daphnia possess clock and melatonin synthesis genes that are rhythmically expressed over 24hours. We were able to show that the 24-h rhythm of D. magna's clock persists in constant darkness and is thus truly circadian. In one particular photoperiod, all D. magna clones produced a similar melatonin concentration due to a fixed AANAT activity. However, we have demonstrated that clones originating from different latitudes are adapted to their respective photoperiod by showing a geographic cline in clock and downstream melatonin synthesis gene expression. These findings hint at the problem locally adapted organisms face when they are forced to leave their respective photoperiod, e.g. because of climate change-driven range-expansion. If such a species is incapable of adjusting its endogenous clock to an unknown photoperiod, it will likely become extinct.
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Affiliation(s)
- Anke Schwarzenberger
- University of Konstanz, Limnological Institute, Mainaustr. 252, 78464 Konstanz, Germany.
| | - Natascha H Handke
- University of Konstanz, Limnological Institute, Mainaustr. 252, 78464 Konstanz, Germany
| | - Tina Romer
- University of Konstanz, Limnological Institute, Mainaustr. 252, 78464 Konstanz, Germany
| | - Alexander Wacker
- University of Greifswald, Zoological Institute and Museum, Department of Animal Ecology, Loitzer Str. 26, 17489 Greifswald, Germany
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13
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Newaz K, Ghalehnovi M, Rahnama A, Antsaklis PJ, Milenković T. Network-based protein structural classification. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191461. [PMID: 32742675 PMCID: PMC7353965 DOI: 10.1098/rsos.191461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Experimental determination of protein function is resource-consuming. As an alternative, computational prediction of protein function has received attention. In this context, protein structural classification (PSC) can help, by allowing for determining structural classes of currently unclassified proteins based on their features, and then relying on the fact that proteins with similar structures have similar functions. Existing PSC approaches rely on sequence-based or direct three-dimensional (3D) structure-based protein features. By contrast, we first model 3D structures of proteins as protein structure networks (PSNs). Then, we use network-based features for PSC. We propose the use of graphlets, state-of-the-art features in many research areas of network science, in the task of PSC. Moreover, because graphlets can deal only with unweighted PSNs, and because accounting for edge weights when constructing PSNs could improve PSC accuracy, we also propose a deep learning framework that automatically learns network features from weighted PSNs. When evaluated on a large set of approximately 9400 CATH and approximately 12 800 SCOP protein domains (spanning 36 PSN sets), the best of our proposed approaches are superior to existing PSC approaches in terms of accuracy, with comparable running times. Our data and code are available at https://doi.org/10.5281/zenodo.3787922.
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Affiliation(s)
- Khalique Newaz
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Center for Network and Data Science, University of Notre Dame, Notre Dame, IN 46556, USA
- Eck institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mahboobeh Ghalehnovi
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Arash Rahnama
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Panos J. Antsaklis
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Tijana Milenković
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Center for Network and Data Science, University of Notre Dame, Notre Dame, IN 46556, USA
- Eck institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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14
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Krylov VV, Papchenkova GA, Osipova EA. The Influence of Changes in Magnetic Variations and Light-Dark Cycle on Life-History Traits of Daphnia magna. Bioelectromagnetics 2020; 41:338-347. [PMID: 32297359 DOI: 10.1002/bem.22264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/12/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Abstract
Day-night cycle is the main zeitgeber (time giver) for biological circadian rhythms. Recently, it was suggested that natural diurnal geomagnetic variation may also be utilized by organisms for the synchronization of these rhythms. In this study, life-history traits in Daphnia magna were evaluated after short-term and multigenerational exposure to 16 h day/8 h night cycle, 32 h day/16 h night cycle, diurnal geomagnetic variation of 24 h, simulated magnetic variation of 48 h, and combinations of these conditions. With short-term exposure, the lighting mode substantially influenced the brood to brood period and the lifespan in daphnids. The brood to brood period, brood size, and body length of crustaceans similarly depended on the lighting mode during the multigenerational exposure. At the same time, an interaction of lighting mode and magnetic variations affected to a lesser extent brood to brood period, brood size, and newborn's body length. The influence of simulated diurnal variation on life-history traits in daphnids appeared distinctly as effects of synchronization between periods of lighting mode and magnetic variations during the multigenerational exposure. Newborn's body length significantly depended on the lighting regime when the periods of both studied zeitgebers were unsynchronized, or on the interaction of light regime with magnetic variations when the periods were synchronized. These results confirm the hypothesis that diurnal geomagnetic variation is an additional zeitgeber for biological circadian rhythms. Possible mechanisms for these observed effects are discussed. Bioelectromagnetics. © 2020 Bioelectromagnetics Society.
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Affiliation(s)
- Viacheslav V Krylov
- I.D. Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Borok, Russia
| | - Galina A Papchenkova
- I.D. Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Borok, Russia
| | - Elena A Osipova
- I.D. Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Borok, Russia
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15
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Tartarotti B, Sommaruga R, Saul N. Contrasting diurnal patterns in antioxidant capacities, but not in expression of stress protein genes among copepod populations from clear versus glacially fed alpine and subalpine lakes. JOURNAL OF PLANKTON RESEARCH 2019; 41:897-908. [PMID: 31920209 PMCID: PMC6946086 DOI: 10.1093/plankt/fbz061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
Short-term changes in environmental conditions largely influence planktonic organisms, but their responses will depend on the habitat characteristics. Here we studied diurnal patterns in antioxidative metabolites (lipophilic and hydrophilic antioxidant capacities) and in the expression of stress protein genes (heat shock proteins, hsp) of copepods to identify short-term stress responses in clear and turbid alpine lakes, as well as in less transparent subalpine ones. Cyclops abyssorum tatricus showed diurnal variation in antioxidant capacities with maxima around noon in clear, but not in glacially fed, turbid lakes. Low fluctuations of these metabolites were also observed in another copepod, Acanthodiaptomus denticornis. Although levels of hsp genes differed between populations living in clear or glacially fed lakes, there was no diurnal rhythmicity in gene expression. Our data show that when planktonic organisms may be at greatest risk of oxidative damage, such as during the daytime in high UV radiation environments, they activate antioxidant responses. Conversely, in less transparent lakes, the physiological response seems to be unnecessary. The difference in gene expression levels suggests an ecological, albeit not acute, role of these genes in copepods experiencing daily environmental fluctuations.
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Affiliation(s)
- Barbara Tartarotti
- Lake and Glacier Research Group, Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Ruben Sommaruga
- Lake and Glacier Research Group, Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Nadine Saul
- Molecular Genetics Group, Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany
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16
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Coldsnow KD, Relyea RA, Hurley JM. Evolution to environmental contamination ablates the circadian clock of an aquatic sentinel species. Ecol Evol 2017; 7:10339-10349. [PMID: 29238559 PMCID: PMC5723614 DOI: 10.1002/ece3.3490] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/03/2017] [Accepted: 09/14/2017] [Indexed: 01/17/2023] Open
Abstract
Environmental contamination is a common cause of rapid evolution. Recent work has shown that Daphnia pulex, an important freshwater species, can rapidly evolve increased tolerance to a common contaminant, sodium chloride (NaCl) road salt. While such rapid evolution can benefit organisms, allowing them to adapt to new environmental conditions, it can also be associated with unforeseen tradeoffs. Given that exposure to environmental contaminants can cause circadian disruption, we investigated whether the circadian clock was affected by evolving a tolerance to high levels of road salt. By tracking the oscillations of a putative clock gene, period, we demonstrated that D. pulex express per mRNA with approximately 20-hr oscillations under control conditions. This putative circadian rhythm was ablated in response to high levels of salinity; populations adapted to high NaCl concentrations exhibited an ablation of period oscillation. Moreover, we showed that while gene expression is increased in several other genes, including clock, actin, and Na+/K+-ATPase, upon the adaptation to high levels of salinity, per expression is unique among the genes we tracked in that it is the only gene repressed in response to salt adaptation. These results suggest that rapid evolution of salt tolerance occurs with the tradeoff of suppressed circadian function. The resultant circadian disruption may have profound consequences to individuals, populations, and aquatic food webs by affecting species interactions. In addition, our research suggests that circadian clocks may also be disrupted by the adaptation to other environmental contaminants.
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Affiliation(s)
- Kayla D Coldsnow
- Department of Biological Sciences Rensselaer Polytechnic Institute Troy NY USA.,Darrin Fresh Water Institute Rensselaer Polytechnic Institute Troy NY USA.,Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute Troy NY USA
| | - Rick A Relyea
- Department of Biological Sciences Rensselaer Polytechnic Institute Troy NY USA.,Darrin Fresh Water Institute Rensselaer Polytechnic Institute Troy NY USA.,Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute Troy NY USA
| | - Jennifer M Hurley
- Department of Biological Sciences Rensselaer Polytechnic Institute Troy NY USA.,Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute Troy NY USA
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