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Editorial: Adaptation and Phenotypic Plasticity to Climate Change

Lisa N. S. Shama, Jennifer M. Donelson, Jose M. Eirin-Lopez, Timothy Ravasi, Timothy Ravasi
2022 Frontiers in Marine Science  
Editorial on the Research Topic Adaptation and Phenotypic Plasticity to Climate Change Anthropogenic activities are driving rapid changes in aquatic environments. Numerous studies suggest that climatic shifts and anomalies will convey severe consequences for ecosystems worldwide, leading to disruptions in key processes within populations including larval development, individual growth, and reproductive success. This is further exacerbated by the negative impacts on between-species interactions,
more » ... and changes to biodiversity and ecosystem services (Munday et al., 2013) . Understanding the responses of organisms to environmental shifts is imperative to help predict their fate on a changing planet. Particularly, the capacity of individuals and populations to cope through phenotypic plasticity and adaptation is of critical interest, with advances in genomics and epigenomics techniques helping to unveil the underlying molecular mechanisms (Eirin-Lopez and Putnam, 2019). However, major knowledge gaps remain about the adaptive potential of marine organisms to respond to future ocean conditions. The aim of this Research Topic was to bring together novel research approaches that examine acclimation and adaptation processes in marine organisms, their role in population resilience, and implications for geographical distributions and range shifts under rapid climate change. Contributions to the topic span a broad range of taxa, and investigate a diverse array of response mechanisms such as thermal safety margins (Bennett et al.), thermotolerance via endosymbionts and gene expression (Naugle et al.), tolerance via changes in allele frequencies (Knöbel et al.), local adaptation and maternal effects (Richards et al.), transgenerational plasticity (TGP; Chang et al.), environment-dependent reproductive success (Wanzenböck et al.), and phenological shifts to long-term seasonal changes (Xia et al.). Furthermore, the importance of environmental variability (not only mean changes) at different time scales, the role of developmental or life history stage in phenotypic responses, as well as future challenges for plasticity research (both within and across generations) are outlined in Bautista and Crespel.
doi:10.3389/fmars.2022.893117 doaj:d505bff3599d4256bfff2d5307c9c460 fatcat:6ln2arkveragpg7krzlweyxayq

Modeling Skewness in Human Transcriptomes

Joaquim Casellas, Luis Varona, Timothy Ravasi
2012 PLoS ONE  
Gene expression data are influenced by multiple biological and technological factors leading to a wide range of dispersion scenarios, although skewed patterns are not commonly addressed in microarray analyses. In this study, the distribution pattern of several human transcriptomes has been studied on free-access microarray gene expression data. Our results showed that, even in previously normalized gene expression data, probe and differential expression within probe effects suffer from
more » ... al departures from the commonly assumed symmetric Gaussian distribution. We developed a flexible mixed model for non-competitive microarray data analysis that accounted for asymmetric and heavy-tailed (Student's t distribution) dispersion processes. Random effects for gene expression data were modeled under asymmetric Student's t distributions where the asymmetry parameter (l) took values from perfect symmetry (l = 0) to right-(l.0) or left-side (l.0) over-expression patterns. This approach was applied to four free-access human data sets and revealed clearly better model performance when comparing with standard approaches accounting for traditional symmetric Gaussian distribution patterns. Our analyses on human gene expression data revealed a substantial degree of right-hand asymmetry for probe effects, whereas differential gene expression addressed both symmetric and left-hand asymmetric patterns. Although these results cannot be extrapolated to all microarray experiments, they highlighted the incidence of skew dispersion patterns in human transcriptome; moreover, we provided a new analytical approach to appropriately address this biological phenomenon. The source code of the program accommodating these analytical developments and additional information about practical aspects on running the program are freely available by request to the corresponding author of this article.
doi:10.1371/journal.pone.0038919 pmid:22701729 pmcid:PMC3372486 fatcat:kp6pdhygsbhjhjjdojilfal44y

Selective phosphorylation during early macrophage differentiation

Huoming Zhang, Pei-Yuan Qian, Timothy Ravasi
2015 Proteomics  
This work was supported by a grant from The King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia, to Timothy Ravasi. www.proteomics-journal.com Page 20 Proteomics This  ... 
doi:10.1002/pmic.201400511 pmid:26307563 fatcat:dxadklsr25ar7nqmei7hqt7w2i

Neuro-molecular characterization of fish cleaning interactions [article]

Sandra Ramirez-Calero, Jose Ricardo Paula, Eve Otjacques, Rui Rosa, Timothy Ravasi, Celia Schunter
2021 bioRxiv   pre-print
Coral reef fish exhibit a large variety of behaviours crucial for fitness and survival. The cleaner wrasse Labroides dimidiatus displays cognitive abilities during interspecific interactions by providing services of ectoparasite cleaning, thus serving as a good model to understand the processes of complex social behaviour. However, little is known about the molecular underpinnings of cooperative behaviour between L. dimidiatus and a potential client fish (Acanthurus leucosternon). Therefore, we
more » ... investigated the molecular mechanisms in three regions of the brain (fore-, mid-, and hindbrain) during the interaction of these fishes. Here we show, using transcriptomics, that most of the transcriptional response in both species was regulated in the hindbrain and forebrain regions and that the interacting behaviour responses of L. dimidiatus involved immediate early gene alteration, dopaminergic and glutamatergic pathways, the expression of neurohormones (such as isotocin) and steroids (e.g. progesterone and estrogen), as well as social decision-making genes. In contrast, in the client, fewer molecular alterations were found, mostly involving pituitary hormone responses. The particular pathways found suggested learning and memory processes in the cleaner wrasse, while the client indicated stress relief and a reduction in aggression.
doi:10.1101/2021.06.22.449532 fatcat:7xjm3rs2xzamlofnxtbf2w6wbi

Labeling Nodes Using Three Degrees of Propagation

Sara Mostafavi, Anna Goldenberg, Quaid Morris, Timothy Ravasi
2012 PLoS ONE  
The properties (or labels) of nodes in networks can often be predicted based on their proximity and their connections to other labeled nodes. So-called "label propagation algorithms" predict the labels of unlabeled nodes by propagating information about local label density iteratively through the network. These algorithms are fast, simple and scale to large networks but nonetheless regularly perform better than slower and much more complex algorithms on benchmark problems. We show here,
more » ... that these algorithms have an intrinsic limitation that prevents them from adapting to some common patterns of network node labeling; we introduce a new algorithm, 3Prop, that retains all their advantages but is much more adaptive. As we show, 3Prop performs very well on node labeling problems ill-suited to label propagation, including predicting gene function in protein and genetic interaction networks and gender in friendship networks, and also performs slightly better on problems already well-suited to label propagation such as labeling blogs and patents based on their citation networks. 3Prop gains its adaptability by assigning separate weights to label information from different steps of the propagation. Surprisingly, we found that for many networks, the third iteration of label propagation receives a negative weight.
doi:10.1371/journal.pone.0051947 pmid:23284828 pmcid:PMC3532359 fatcat:275vqosxtrbezbqitazoiigri4

Systems biology of innate immunity

Jesper Tegnér, Roland Nilsson, Vladimir B. Bajic, Johan Björkegren, Timothy Ravasi
2006 Cellular Immunology  
Systems Biology has emerged as an exciting research approach in molecular biology and functional genomics that involves a systematic use of genomic, proteomic, and metabolomic technologies for the construction of network-based models of biological processes. These endeavors, collectively referred to as systems biology establish a paradigm by which to systematically interrogate, model, and iteratively refine our knowledge of the regulatory events within a cell. Here, we present a new systems
more » ... oach, integrating DNA and transcript expression information, specifically designed to identify transcriptional networks governing the macrophage immune response to lipopolysaccharide (LPS). Using this approach, we are not only able to infer a global macrophage transcriptional network, but also timespecific sub-networks that are dynamically active across the LPS response. We believe that our system biological approach could be useful for identifying other complex networks mediating immunological responses.
doi:10.1016/j.cellimm.2007.01.010 pmid:17433274 pmcid:PMC1947944 fatcat:m4hq3rthfjcrjaefak7ns5uncq

Spatial Intuition in Elementary Arithmetic: A Neurocomputational Account

Qi Chen, Tom Verguts, Timothy Ravasi
2012 PLoS ONE  
Elementary arithmetic (e.g., addition, subtraction) in humans has been shown to exhibit spatial properties. Its exact nature has remained elusive, however. To address this issue, we combine two earlier models for parietal cortex: A model we recently proposed on number-space interactions and a modeling framework of parietal cortex that implements radial basis functions for performing spatial transformations. Together, they provide us with a framework in which elementary arithmetic is based on
more » ... lutionarily more basic spatial transformations, thus providing the first implemented instance of Dehaene and Cohen's recycling hypothesis.
doi:10.1371/journal.pone.0031180 pmid:22348052 pmcid:PMC3278421 fatcat:tl2n6pqtuzh6pf5pssekdt2udu

A Conserved Mammalian Protein Interaction Network

Åsa Pérez-Bercoff, Corey M. Hudson, Gavin C. Conant, Timothy Ravasi
2013 PLoS ONE  
Physical interactions between proteins mediate a variety of biological functions, including signal transduction, physical structuring of the cell and regulation. While extensive catalogs of such interactions are known from model organisms, their evolutionary histories are difficult to study given the lack of interaction data from phylogenetic outgroups. Using phylogenomic approaches, we infer a upper bound on the time of origin for a large set of human protein-protein interactions, showing that
more » ... most such interactions appear relatively ancient, dating no later than the radiation of placental mammals. By analyzing paired alignments of orthologous and putatively interacting protein-coding genes from eight mammals, we find evidence for weak but significant co-evolution, as measured by relative selective constraint, between pairs of genes with interacting proteins. However, we find no strong evidence for shared instances of directional selection within an interacting pair. Finally, we use a network approach to show that the distribution of selective constraint across the protein interaction network is non-random, with a clear tendency for interacting proteins to share similar selective constraints. Collectively, the results suggest that, on the whole, protein interactions in mammals are under selective constraint, presumably due to their functional roles.
doi:10.1371/journal.pone.0052581 pmid:23320073 pmcid:PMC3539715 fatcat:2ynh5gsqnnf75br3md545in2mm

Community Structure in Social Networks: Applications for Epidemiological Modelling

Stephan Kitchovitch, Pietro Liò, Timothy Ravasi
2011 PLoS ONE  
During an infectious disease outbreak people will often change their behaviour to reduce their risk of infection. Furthermore, in a given population, the level of perceived risk of infection will vary greatly amongst individuals. The difference in perception could be due to a variety of factors including varying levels of information regarding the pathogen, quality of local healthcare, availability of preventative measures, etc. In this work we argue that we can split a social network,
more » ... ing a population, into interacting communities with varying levels of awareness of the disease. We construct a theoretical population and study which such communities suffer most of the burden of the disease and how their awareness affects the spread of infection. We aim to gain a better understanding of the effects that communitystructured networks and variations in awareness, or risk perception, have on the disease dynamics and to promote more community-resolved modelling in epidemiology.
doi:10.1371/journal.pone.0022220 pmid:21789238 pmcid:PMC3138783 fatcat:d2653tmpj5f7lkjvdd3icr43dm

Dynamic Epigenetic Control of Highly Conserved Noncoding Elements

Loqmane Seridi, Taewoo Ryu, Timothy Ravasi, Christophe Antoniewski
2014 PLoS ONE  
Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown. Results: To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such
more » ... ts during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains. Conclusion: HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.
doi:10.1371/journal.pone.0109326 pmid:25289637 pmcid:PMC4188601 fatcat:h5bdoucybfaypbu4gixsihklpq

The evolution of ultraconserved elements with different phylogenetic origins

Taewoo Ryu, Loqmane Seridi, Timothy Ravasi
2012 BMC Evolutionary Biology  
Authors' contributions TR1 (Taewoo Ryu) and TR2 (Timothy Ravasi) conceived the overall study; TR1 and LS performed the data analysis; TR1, LS, and TR2 drafted the manuscript; all authors read and approved  ... 
doi:10.1186/1471-2148-12-236 pmid:23217155 pmcid:PMC3556307 fatcat:fwu7dalpbfhsjpeu6f5sga25oy

Highlighting nonlinear patterns in population genetics datasets

Gregorio Alanis-Lobato, Carlo Vittorio Cannistraci, Anders Eriksson, Andrea Manica, Timothy Ravasi
2015 Scientific Reports  
Detecting structure in population genetics and case-control studies is important, as it exposes phenomena such as ecoclines, admixture and stratification. Principal Component Analysis (PCA) is a linear dimension-reduction technique commonly used for this purpose, but it struggles to reveal complex, nonlinear data patterns. In this paper we introduce non-centred Minimum Curvilinear Embedding (ncMCE), a nonlinear method to overcome this problem. Our analyses show that ncMCE can separate
more » ... s into ethnic groups in cases in which PCA fails to reveal any clear structure. This increased discrimination power arises from ncMCE's ability to better capture the phylogenetic signal in the samples, whereas PCA better reflects their geographic relation. We also demonstrate how ncMCE can discover interesting patterns, even when the data has been poorly pre-processed. The juxtaposition of PCA and ncMCE visualisations provides a new standard of analysis with utility for discovering and validating significant linear/nonlinear complementary patterns in genetic data.
doi:10.1038/srep08140 pmid:25633916 pmcid:PMC4311249 fatcat:5q4wwa5ltrfq5ofy2uufujcwny

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Kai Tan, Jesper Tegner, Timothy Ravasi
2008 Genomics  
Integrative systems biology has emerged as an exciting research approach in molecular biology and functional genomics that involves the integration of genomics, proteomics, and metabolomics datasets. These endeavors establish a systematic paradigm by which to interrogate, model, and iteratively refine our knowledge of the regulatory events within a cell. Here we review the latest technologies available to collect highthroughput measurements of a cellular state as well as the most successful
more » ... ods for the integration and interrogation of these measurements. In particular we will focus on methods available to infer transcription regulatory networks in mammals. Published by Elsevier Inc.
doi:10.1016/j.ygeno.2007.11.005 pmid:18191937 fatcat:mzq7hk63tjh2faiskciqj3yk2q

Microbial Bebop: Creating Music from Complex Dynamics in Microbial Ecology

Peter Larsen, Jack Gilbert, Timothy Ravasi
2013 PLoS ONE  
In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop
more » ... tion, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.
doi:10.1371/journal.pone.0058119 pmid:23483981 pmcid:PMC3590156 fatcat:cjom5rfq5rfk7iqztuf6ktqdmy

Viral ecogenomics across the Porifera

Cecília Pascelli, Patrick W. Laffy, Emmanuelle Botté, Marija Kupresanin, Thomas Rattei, Miguel Lurgi, Timothy Ravasi, Nicole S. Webster
2020 Microbiome  
Background Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and
more » ... ven from the Red Sea. Results Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts. Conclusions Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts.
doi:10.1186/s40168-020-00919-5 pmid:33008461 fatcat:wqj7dwbnxnfabfdsmgp5cb4ekq
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