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Deep homology in the age of next-generation sequencing

Patrick Tschopp, Clifford J. Tabin
2016 Philosophical Transactions of the Royal Society of London. Biological Sciences  
The principle of homology is central to conceptualizing the comparative aspects of morphological evolution.  ...  One contribution of 17 to a theme issue 'Evodevo in the genomics era, and the origins of morphological diversity'.  ...  Moreover, cell culture-based assays for large-scale comparative studies of epigenomic states and enhancer activities can function as invaluable proxies to delineate regulatory logic across species boundaries  ... 
doi:10.1098/rstb.2015.0475 pmid:27994118 pmcid:PMC5182409 fatcat:gzjyazw5obhqbj4uo4ylryerhi

Open Frontiers in Neural Cell Type Investigations; Lessons From Caenorhabditis elegans and Beyond, Toward a Multimodal Integration

Georgia Rapti
2022 Frontiers in Neuroscience  
It highlights underlying principles, emerging themes, and open frontiers in the study of nervous system development, regulatory logic and evolution.  ...  Nervous system cells, the building blocks of circuits, have been studied with ever-progressing resolution, yet neural circuits appear still resistant to schemes of reductionist classification.  ...  I thank Scott Emmons, David Hall, Stephen Larson, and Mei Zhen for permitting use of images from open-source websites.  ... 
doi:10.3389/fnins.2021.787753 pmid:35321480 pmcid:PMC8934944 fatcat:ynbsuctaqjbnxph2nul25ijnt4

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

Dawn Thompson, Aviv Regev, Sushmita Roy
2015 Annual Review of Cell and Developmental Biology  
Comparative approaches that examine the conservation and divergence of circuits and their components across strains and species can help reconstruct circuits as well as provide insights into the evolution  ...  Finally, we discuss the promise and open challenges in linking regulatory divergence to phenotypic divergence and adaptation. 6.1  ...  ACKNOWLEDGMENTS We thank Leslie Gaffney for help with preparation of figures. D.T. is supported by the NIH (R01CA119176-01).  ... 
doi:10.1146/annurev-cellbio-100913-012908 pmid:26355593 fatcat:sryxj3e2gvapnnnkmnzdhnyzr4

Multiplex transcriptional characterizations across diverse bacterial species using cell‐free systems

Sung Sun Yim, Nathan I Johns, Jimin Park, Antonio LC Gomes, Ross M McBee, Miles Richardson, Carlotta Ronda, Sway P Chen, David Garenne, Vincent Noireaux, Harris H Wang
2019 Molecular Systems Biology  
Here, we describe DNA Regulatory element Analysis by cell-Free Transcription and Sequencing (DRAFTS), a rapid and robust in vitro approach for multiplexed measurement of transcriptional activities from  ...  thousands of regulatory sequences in a single reaction.  ...  Acknowledgements We thank members of the Wang Lab for advice and comments on the manu-  ... 
doi:10.15252/msb.20198875 pmid:31464371 pmcid:PMC6692573 fatcat:y52yill7n5elnp2ns7hodpnckm

The Same but Different: Worms Reveal the Pervasiveness of Developmental System Drift

Eric S. Haag, Artyom Kopp
2014 PLoS Genetics  
To give an unbiased estimate of the extent of DSD, Verster et al. [10] performed what may be the largest comparative analysis of gene function ever.  ...  For example, a survey of over 100 transcription factor knockouts in Candida albicans, a distant relative of Saccharomyces cerevisiae, allowed the phenotypes of orthologs to be compared [5] .  ... 
doi:10.1371/journal.pgen.1004150 pmid:24516407 pmcid:PMC3916242 fatcat:qhd64mxbjbdatkv3mmhosxnu6a

Ancestral regulatory mechanisms specify conserved midbrain circuitry in arthropods and vertebrates

Jessika C. Bridi, Zoe N. Ludlow, Benjamin Kottler, Beate Hartmann, Lies Vanden Broeck, Jonah Dearlove, Markus Göker, Nicholas J. Strausfeld, Patrick Callaerts, Frank Hirth
2020 Proceedings of the National Academy of Sciences of the United States of America  
Genetic tracing reveals that the embryonic DTB gives rise to adult midbrain circuits that in flies control auditory and vestibular information processing and motor coordination, as do MHB-derived circuits  ...  We show that cis-regulatory elements and the gene networks they regulate direct the formation and function of midbrain circuits for balance and motor coordination in insects and mammals.  ...  Accordingly, it is the comparative analysis of ground patterns across phylogenetic lineages that allows the identification of correspondences among cell types, tissue, and organs and that informs about  ... 
doi:10.1073/pnas.1918797117 pmid:32747566 fatcat:ysevmhmnbba35ikezdhmwf4dlm

Fibration symmetries uncover the building blocks of biological networks

Flaviano Morone, Ian Leifer, Hernán A. Makse
2020 Proceedings of the National Academy of Sciences of the United States of America  
We exemplify the symmetry fibrations in gene regulatory networks and then show that they universally apply across species and domains from biology to social and infrastructure networks.  ...  The building blocks are classified into topological classes of input trees characterized by integer branching ratios and fractal golden ratios of Fibonacci sequences representing cycles of information.  ...  We show selected examples of circuits and input trees and bases. The full list of fibers appears in SI Appendix, Fig. 4 . 4 Fibration landscape across domains and species.  ... 
doi:10.1073/pnas.1914628117 pmid:32234788 fatcat:eime7ybw7nemppqf3e46vd255e

Saccharomyces genome database informs human biology

Marek S Skrzypek, Robert S Nash, Edith D Wong, Kevin A MacPherson, Sage T Hellerstedt, Stacia R Engel, Kalpana Karra, Shuai Weng, Travis K Sheppard, Gail Binkley, Matt Simison, Stuart R Miyasato (+1 others)
2017 Nucleic Acids Research  
distant as humans.  ...  These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health.  ... 
doi:10.1093/nar/gkx1112 pmid:29140510 pmcid:PMC5753351 fatcat:bzd2jvlocnbqpbczmgoofs3tmi

Behavioral Evolution of Drosophila: Unraveling the Circuit Basis

Sato, Tanaka, Ishikawa, Yamamoto
2020 Genes  
the fru-circuit or the motor pathways downstream of the fru-circuit are susceptible to changes associated with behavioral species differences.  ...  Therefore, any difference in behavior among different species is, in theory, an outcome of interspecies diversification in the structure and/or function of the nervous system.  ...  Conflicts of Interest: The authors declare no competing or financial interests.  ... 
doi:10.3390/genes11020157 pmid:32024133 pmcid:PMC7074016 fatcat:a6gyzihc3vd6dctv4d7pxeqqsu

Bacterial regulatory networks are extremely flexible in evolution

I. Lozada-Chavez
2006 Nucleic Acids Research  
From our comparative analysis, it is possible to infer that transcriptional regulation is more flexible than the genetic component of the organisms and its complexity and structure plays an important role  ...  Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche on  ...  ACKNOWLEDGEMENTS We would like to thank Heladia Salgado Osorio for supplying the interaction data from RegulonDB and to Kenta Nakai and Yuko Makita for providing us the data of transcriptional regulation  ... 
doi:10.1093/nar/gkl423 pmid:16840530 pmcid:PMC1524901 fatcat:y2dbkzrtzjdu7c43ve4cl4p52e

Morphology and behaviour: functional links in development and evolution

Rinaldo C. Bertossa
2011 Philosophical Transactions of the Royal Society of London. Biological Sciences  
of analysis.  ...  A possible framework to accommodate and compare form and function at different levels of the biological hierarchy is outlined. At the end, some methodological issues are discussed.  ...  For the same reason, it will be difficult to infer function from the evolutionary conservation of the DNA sequence [115] , both regulatory and coding, unless the compared species are closely related and  ... 
doi:10.1098/rstb.2011.0035 pmid:21690124 pmcid:PMC3130372 fatcat:nl6e4gj5a5ge5jt3h3wcebtwiu

Multiplex transcriptional characterizations across diverse and hybrid bacterial cell-free expression systems [article]

Sung Sun Yim, Nathan I. Johns, Jimin Park, Antonio L.C. Gomes, Ross M. McBee, Miles Richardson, Carlotta Ronda, Sway P. Chen, David Garenne, Vincent Noireaux, Harris H. Wang
2018 bioRxiv   pre-print
Here, we describe DNA Regulatory element Analysis by cell-Free Transcription and Sequencing (DRAFTS), a rapid and robust in vitro approach for multiplexed measurement of transcriptional activities from  ...  Finally, we constructed and examined the transcriptional capacities of dual-species "hybrid" cell lysates that can simultaneously harness gene expression properties of multiple organisms.  ...  Figure 3 . 3 Comparative functional analysis of regulatory sequences across 10 bacterial species through DRAFTS.  ... 
doi:10.1101/427559 fatcat:ht5lkustpvalzlnopvxadfpwye

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

Joseph R. Ecker, Daniel H. Geschwind, Arnold R. Kriegstein, John Ngai, Pavel Osten, Damon Polioudakis, Aviv Regev, Nenad Sestan, Ian R. Wickersham, Hongkui Zeng
2017 Neuron  
A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors  ...  species and during development.  ...  We gratefully acknowledge the generous and enabling support of the NIH BRAIN Initiative. A.K. is a founder, shareholder and Board member of Neurona Therapeutics.  ... 
doi:10.1016/j.neuron.2017.10.007 pmid:29096072 pmcid:PMC5689454 fatcat:mk5lxcbpvfdabb4ky533va24lm

The evolution of distributed association networks in the human brain

Randy L. Buckner, Fenna M. Krienen
2013 Trends in Cognitive Sciences  
Canonical circuit (canonical macrocircuit): a network of brain areas characterized by dense local connectivity between areas and a serial, hierarchical flow of information across areas.  ...  Across species, most variation in brain size is predicted by body mass. The ratio of actual brain size versus the predicted brain size from body mass is known as the encephalization quotient.  ...  Acknowledgments The authors thank Felix Warneken, Dan Lieberman, Chet Sherwood, Jim Rilling, and two anonymous reviewers for comments, discussion, and pointers to relevant literature, Dan Lieberman for  ... 
doi:10.1016/j.tics.2013.09.017 pmid:24210963 fatcat:qhorja6njveodcfz4pfvfayliq

Evolution of affiliation: patterns of convergence from genomes to behaviour

Eva K. Fischer, Jessica P. Nowicki, Lauren A. O'Connell
2019 Philosophical Transactions of the Royal Society of London. Biological Sciences  
In particular, additional comparative studies within and across major vertebrate lineages will be essential in resolving when and why shared neural substrates are repeatedly targeted in the independent  ...  evolution of affiliation, and how similar mechanisms are evolutionarily tuned to give rise to species-specific variations in behaviour.  ...  However, a more comparative analysis of the avpr1a microsatellite across 21 Microtus species and eight Peromyscus species found no role for microsatellite involvement in the evolution of pair bonding in  ... 
doi:10.1098/rstb.2018.0242 pmid:31154971 pmcid:PMC6560274 fatcat:n6sgfopy5bfphgs7whnwntmrjy
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