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No relative expansion of the number of prefrontal neurons in primate and human evolution.
Gabi M, Neves K, Masseron C, Ribeiro PF, Ventura-Antunes L, Torres L, Mota B, Kaas JH, Herculano-Houzel S
(2016) Proc Natl Acad Sci U S A 113: 9617-22
MeSH Terms: Animals, Biological Evolution, Cell Count, Female, Gray Matter, Humans, Male, Microtomy, Neurons, Prefrontal Cortex, Primates, Species Specificity, White Matter
Show Abstract · Added March 30, 2020
Human evolution is widely thought to have involved a particular expansion of prefrontal cortex. This popular notion has recently been challenged, although controversies remain. Here we show that the prefrontal region of both human and nonhuman primates holds about 8% of cortical neurons, with no clear difference across humans and other primates in the distribution of cortical neurons or white matter cells along the anteroposterior axis. Further, we find that the volumes of human prefrontal gray and white matter match the expected volumes for the number of neurons in the gray matter and for the number of other cells in the white matter compared with other primate species. These results indicate that prefrontal cortical expansion in human evolution happened along the same allometric trajectory as for other primate species, without modification of the distribution of neurons across its surface or of the volume of the underlying white matter. We thus propose that the most distinctive feature of the human prefrontal cortex is its absolute number of neurons, not its relative volume.
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A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1.
Nnamani MC, Ganguly S, Erkenbrack EM, Lynch VJ, Mizoue LS, Tong Y, Darling HL, Fuxreiter M, Meiler J, Wagner GP
(2016) Cell Rep 15: 2097-2108
MeSH Terms: Allosteric Regulation, Amino Acid Sequence, Amino Acid Substitution, Animals, Biological Evolution, CREB-Binding Protein, DNA-Activated Protein Kinase, Forkhead Box Protein O1, HeLa Cells, Homeodomain Proteins, Humans, Intrinsically Disordered Proteins, Mice, Models, Biological, Models, Molecular, Phosphorylation, Protein Binding, Protein Domains, Protein Structure, Secondary, Transcriptional Activation
Show Abstract · Added April 8, 2017
Transcription factors (TFs) play multiple roles in development. Given this multifunctionality, it has been assumed that TFs are evolutionarily highly constrained. Here, we investigate the molecular mechanisms for the origin of a derived functional interaction between two TFs, HOXA11 and FOXO1. We have previously shown that the regulatory role of HOXA11 in mammalian endometrial stromal cells requires interaction with FOXO1, and that the physical interaction between these proteins evolved before their functional cooperativity. Here, we demonstrate that the derived functional cooperativity between HOXA11 and FOXO1 is due to derived allosteric regulation of HOXA11 by FOXO1. This study shows that TF function can evolve through changes affecting the functional output of a pre-existing protein complex.
Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.
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20 MeSH Terms
Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes.
Wisecaver JH, Alexander WG, King SB, Hittinger CT, Rokas A
(2016) Mol Biol Evol 33: 1979-87
MeSH Terms: Adaptation, Biological, Amino Acid Sequence, Bacteria, Bacterial Proteins, Biological Evolution, Computational Biology, Databases, Nucleic Acid, Dihydropteridine Reductase, Escherichia coli Proteins, Eukaryota, Evolution, Molecular, Fungi, Gene Duplication, Gene Transfer, Horizontal, Hemeproteins, NADH, NADPH Oxidoreductases, Nitric Oxide, Phylogeny
Show Abstract · Added April 6, 2017
Due to their functional independence, proteins that comprise standalone metabolic units, which we name single-protein metabolic modules, may be particularly prone to gene duplication (GD) and horizontal gene transfer (HGT). Flavohemoglobins (flavoHbs) are prime examples of single-protein metabolic modules, detoxifying nitric oxide (NO), a ubiquitous toxin whose antimicrobial properties many life forms exploit, to nitrate, a common source of nitrogen for organisms. FlavoHbs appear widespread in bacteria and have been identified in a handful of microbial eukaryotes, but how the distribution of this ecologically and biomedically important protein family evolved remains unknown. Reconstruction of the evolutionary history of 3,318 flavoHb protein sequences covering the family's known diversity showed evidence of recurrent HGT at multiple evolutionary scales including intrabacterial HGT, as well as HGT from bacteria to eukaryotes. One of the most striking examples of HGT is the acquisition of a flavoHb by the dandruff- and eczema-causing fungus Malassezia from Corynebacterium Actinobacteria, a transfer that growth experiments show is capable of mediating NO resistance in fungi. Other flavoHbs arose via GD; for example, many filamentous fungi possess two flavoHbs that are differentially targeted to the cytosol and mitochondria, likely conferring protection against external and internal sources of NO, respectively. Because single-protein metabolic modules such as flavoHb function independently, readily undergo GD and HGT, and are frequently involved in organismal defense and competition, we suggest that they represent "plug-and-play" proteins for ecological arms races.
© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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18 MeSH Terms
Editorial overview: Genomes and evolution: "Seq-ing" answers in life's genomes.
Rokas A, Soltis PS
(2015) Curr Opin Genet Dev 35: iv-vi
MeSH Terms: Animals, Bacteria, Biodiversity, Biological Evolution, Chromosome Mapping, Genetic Variation, Genome, High-Throughput Nucleotide Sequencing, Humans, Plants
Added February 22, 2016
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10 MeSH Terms
The evolution of the human genome.
Simonti CN, Capra JA
(2015) Curr Opin Genet Dev 35: 9-15
MeSH Terms: Biological Evolution, Evolution, Molecular, Gene Expression Regulation, Genetic Variation, Genetics, Population, Genome, Human, Humans, Regulatory Sequences, Nucleic Acid, Selection, Genetic
Show Abstract · Added April 29, 2016
Human genomes hold a record of the evolutionary forces that have shaped our species. Advances in DNA sequencing, functional genomics, and population genetic modeling have deepened our understanding of human demographic history, natural selection, and many other long-studied topics. These advances have also revealed many previously underappreciated factors that influence the evolution of the human genome, including functional modifications to DNA and histones, conserved 3D topological chromatin domains, structural variation, and heterogeneous mutation patterns along the genome. Using evolutionary theory as a lens to study these phenomena will lead to significant breakthroughs in understanding what makes us human and why we get sick.
Copyright © 2015 Elsevier Ltd. All rights reserved.
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9 MeSH Terms
Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes.
Bordenstein SR, Theis KR
(2015) PLoS Biol 13: e1002226
MeSH Terms: Animals, Biological Evolution, Humans, Metagenome, Microbiota, Mutation, Plants, Selection, Genetic, Symbiosis
Show Abstract · Added October 8, 2015
Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.
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9 MeSH Terms
Integrated Immune and Cardiovascular Function in Pancrustacea: Lessons from the Insects.
Hillyer JF
(2015) Integr Comp Biol 55: 843-55
MeSH Terms: Animals, Biological Evolution, Cardiovascular Physiological Phenomena, Crustacea, Insecta
Show Abstract · Added February 5, 2016
When pathogens invade the insect hemocoel (body cavity) they immediately confront two major forces: immune-responses and circulatory currents. The immune response is mediated by circulating and sessile hemocytes, the fat body, the midgut, and the salivary glands. These tissues drive cellular and humoral immune processes that kill pathogens via phagocytosis, melanization, lysis, encapsulation, and nodulation. Moreover, immune-responses take place within a three-dimensional and dynamic space that is governed by the forces of the circulatory system. The circulation of hemolymph (insect blood) is primarily controlled by the wave-like contraction of a dorsal vessel, which is a muscular tube that extends the length of the insect and is divided into a thoracic aorta and an abdominal heart. Distributed along the heart are valves, called ostia, that allow hemolymph to enter the vessel. Once inside the heart, hemolymph is sequentially propelled to the anterior and to the posterior of the body. During an infection, circulatory currents sweep small pathogens to all regions of the body. As they circulate, pathogens encounter immune factors of the insect that range from soluble cytotoxic peptides to phagocytic hemocytes. A prominent location for these encounters is the surface of the heart. Specifically, periostial hemocytes aggregate in the extracardiac regions that flank the heart's ostia (the periostial regions) and phagocytoze pathogens in areas of high flow of hemolymph. This review summarizes the biology of the immune and circulatory systems of insects, including how these two systems have co-adapted to fight infection. This review also compares the immune and circulatory systems of insects to that of crustaceans, and details how attachment of hemocytes to cardiac tissues and the biology of the lymphoid organ demonstrate that dynamic interactions between the immune and circulatory systems also occur in lineages of crustaceans.
© The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.
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5 MeSH Terms
Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus.
Lind AL, Wisecaver JH, Smith TD, Feng X, Calvo AM, Rokas A
(2015) PLoS Genet 11: e1005096
MeSH Terms: Aspergillus, Biological Evolution, Evolution, Molecular, Genome, Fungal, Metabolic Networks and Pathways
Show Abstract · Added February 22, 2016
Filamentous fungi produce diverse secondary metabolites (SMs) essential to their ecology and adaptation. Although each SM is typically produced by only a handful of species, global SM production is governed by widely conserved transcriptional regulators in conjunction with other cellular processes, such as development. We examined the interplay between the taxonomic narrowness of SM distribution and the broad conservation of global regulation of SM and development in Aspergillus, a diverse fungal genus whose members produce well-known SMs such as penicillin and gliotoxin. Evolutionary analysis of the 2,124 genes comprising the 262 SM pathways in four Aspergillus species showed that most SM pathways were species-specific, that the number of SM gene orthologs was significantly lower than that of orthologs in primary metabolism, and that the few conserved SM orthologs typically belonged to non-homologous SM pathways. RNA sequencing of two master transcriptional regulators of SM and development, veA and mtfA, showed that the effects of deletion of each gene, especially veA, on SM pathway regulation were similar in A. fumigatus and A. nidulans, even though the underlying genes and pathways regulated in each species differed. In contrast, examination of the role of these two regulators in development, where 94% of the underlying genes are conserved in both species showed that whereas the role of veA is conserved, mtfA regulates development in the homothallic A. nidulans but not in the heterothallic A. fumigatus. Thus, the regulation of these highly conserved developmental genes is divergent, whereas-despite minimal conservation of target genes and pathways-the global regulation of SM production is largely conserved. We suggest that the evolution of the transcriptional regulation of secondary metabolism in Aspergillus represents a novel type of regulatory circuit rewiring and hypothesize that it has been largely driven by the dramatic turnover of the target genes involved in the process.
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5 MeSH Terms
Friends with social benefits: host-microbe interactions as a driver of brain evolution and development?
Stilling RM, Bordenstein SR, Dinan TG, Cryan JF
(2014) Front Cell Infect Microbiol 4: 147
MeSH Terms: Adaptation, Biological, Animals, Behavior, Biological Evolution, Brain, Epigenesis, Genetic, Gene-Environment Interaction, Host-Pathogen Interactions, Humans, Microbiota, Symbiosis
Show Abstract · Added October 8, 2015
The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behavior. In this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a "social triangle" that drives human social behavior and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective.
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11 MeSH Terms
Nuclear and chloroplast DNA phylogeny reveals complex evolutionary history of Elymus pendulinus.
Yan C, Hu Q, Sun G
(2014) Genome 57: 97-109
MeSH Terms: Base Sequence, Biological Evolution, Cell Nucleus, Chloroplasts, DNA, Chloroplast, Elymus, Evolution, Molecular, Genome, Chloroplast, Genome, Plant, Hordeum, Polyploidy, RNA Polymerase II, Ribosomal Proteins, Sequence Analysis, DNA, Serine Endopeptidases
Show Abstract · Added May 15, 2018
Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo complex reticulate evolution. In this study, 13 accessions of tetraploid Elymus pendulinus were analyzed using two low-copy nuclear genes (RPB2 and PepC) and two regions of chloroplast genome (Rps16 and trnD-trnT). Previous studies suggested that Pseudoroegneria (St) and an unknown diploid (Y) were genome donors to E. pendulinus, and that Pseudoroegneria was the maternal donor. Our results revealed an extreme reticulate pattern, with at least four distinct gene lineages coexisting within this species that might be acquired through a possible combination of allotetraploidization and introgression from both within and outside the tribe Hordeeae. Chloroplast DNA data identified two potential maternal genome donors (Pseudoroegneria and an unknown species outside Hordeeae) to E. pendulinus. Nuclear gene data indicated that both Pseudoroegneria and an unknown Y diploid have contributed to the nuclear genome of E. pendulinus, in agreement with cytogenetic data. However, unexpected contributions from Hordeum and unknown aliens from within or outside Hordeeae to E. pendulinus without genome duplication were observed. Elymus pendulinus provides a remarkable instance of the previously unsuspected chimerical nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events.
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